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US20130333068A1 - Genes and uses for plant enhancement - Google Patents

Genes and uses for plant enhancement Download PDF

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US20130333068A1
US20130333068A1 US12/386,976 US38697609A US2013333068A1 US 20130333068 A1 US20130333068 A1 US 20130333068A1 US 38697609 A US38697609 A US 38697609A US 2013333068 A1 US2013333068 A1 US 2013333068A1
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sense
ppr
pkinase
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enhanced
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Marie Coffin
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Monsanto Technology LLC
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Monsanto Technology LLC
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Priority to US12/386,976 priority Critical patent/US20130333068A1/en
Assigned to MONSANTO TECHNOLOGY LLC reassignment MONSANTO TECHNOLOGY LLC ASSIGNMENT OF ASSIGNORS INTEREST (SEE DOCUMENT FOR DETAILS). Assignors: COFFIN, MARIE
Publication of US20130333068A1 publication Critical patent/US20130333068A1/en
Priority to US14/544,230 priority patent/US20160122783A1/en
Priority to US15/732,766 priority patent/US10696975B2/en
Priority to US16/873,608 priority patent/US11274312B2/en
Priority to US17/803,149 priority patent/US20230048751A1/en
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    • C12N15/09—Recombinant DNA-technology
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    • C12N15/8273—Phenotypically and genetically modified plants via recombinant DNA technology with agronomic (input) traits, e.g. crop yield for stress resistance, e.g. heavy metal resistance for drought, cold, salt resistance
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    • C12N15/82—Vectors or expression systems specially adapted for eukaryotic hosts for plant cells, e.g. plant artificial chromosomes (PACs)
    • C12N15/8241—Phenotypically and genetically modified plants via recombinant DNA technology
    • C12N15/8261—Phenotypically and genetically modified plants via recombinant DNA technology with agronomic (input) traits, e.g. crop yield
    • C12N15/8271—Phenotypically and genetically modified plants via recombinant DNA technology with agronomic (input) traits, e.g. crop yield for stress resistance, e.g. heavy metal resistance
    • C12N15/8274—Phenotypically and genetically modified plants via recombinant DNA technology with agronomic (input) traits, e.g. crop yield for stress resistance, e.g. heavy metal resistance for herbicide resistance
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    • C12N15/82—Vectors or expression systems specially adapted for eukaryotic hosts for plant cells, e.g. plant artificial chromosomes (PACs)
    • C12N15/8241—Phenotypically and genetically modified plants via recombinant DNA technology
    • C12N15/8261—Phenotypically and genetically modified plants via recombinant DNA technology with agronomic (input) traits, e.g. crop yield
    • C12N15/8271—Phenotypically and genetically modified plants via recombinant DNA technology with agronomic (input) traits, e.g. crop yield for stress resistance, e.g. heavy metal resistance
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    • C12N15/8275—Glyphosate
    • Y—GENERAL TAGGING OF NEW TECHNOLOGICAL DEVELOPMENTS; GENERAL TAGGING OF CROSS-SECTIONAL TECHNOLOGIES SPANNING OVER SEVERAL SECTIONS OF THE IPC; TECHNICAL SUBJECTS COVERED BY FORMER USPC CROSS-REFERENCE ART COLLECTIONS [XRACs] AND DIGESTS
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    • Y02A40/00—Adaptation technologies in agriculture, forestry, livestock or agroalimentary production
    • Y02A40/10—Adaptation technologies in agriculture, forestry, livestock or agroalimentary production in agriculture
    • Y02A40/146—Genetically Modified [GMO] plants, e.g. transgenic plants

Definitions

  • Folder hmmer-2.3.2 contains the source code and other associated file for implementing the HMMer software for Pfam analysis.
  • Folder 495pfamDir contains 495 profile Hidden Markov Models. Both folders were created on the disk on Apr. 24, 2009 having a total size of 39,755,623 bytes when measured in MS-WINDOWS® operating system. 00001
  • recombinant DNA for providing enhanced traits to transgenic plants, seeds, pollen, plant cells and plant nucleui of such transgenic plants, methods of making and using such recombinant DNA, plants, seeds, pollen, plant cells and plant nuclei. Also disclosed are methods of producing hybrid seed comprising such recombinant DNA.
  • This invention provides recombinant DNA comprising polynucleotides characterized by SEQ ID NO: 1-803 and the cognate amino acid sequences of SEQ ID NO: 804-1606.
  • the recombinant DNA is used for providing enhanced traits when stably integrated into the chromosomes and expressed in the nuclei of transgenic plants cells.
  • the recombinant DNA encodes a protein; in other aspects the recombinant DNA is transcribed to RNA that suppresses the expression of a native gene.
  • Such recombinant DNA in a plant cell nuclus of this invention is provided in as a construct comprising a promoter that is functional in plant cells and that is operably linked to DNA that encodes a protein or to DNA that results in gene suppression.
  • DNA in the construct is sometimes defined by protein domains of an encoded protein targeted for production or suppression e.g. a “Pfam domain module” (as defined herein below) from the group of Pfam domain modules identified in Table 20.
  • a Pfam domain module as defined herein below
  • such DNA in the construct is defined a consensus amino acid sequence of an encoded protein that is targeted for production e.g.
  • the recombinant DNA is characterized by its cognate amino acid sequence that has at least 70% identity to any of SEQ ID NO: 804-1606.
  • transgenic plant cell nuclei comprising the recombinant DNA of the invention, transgenic plant cells comprising such nuclei, transgenic plants comprising a plurality of such transgenic plant cells, and transgenic seeds and transgenic pollen of such plants.
  • Such transgenic plants are selected from a population of transgenic plants regenerated from plant cells transformed with recombinant DNA by screening transgenic plants for an enhanced trait as compared to control plants.
  • the enhanced trait is one or more of enhanced water use efficiency, enhanced cold tolerance, increased yield, enhanced nitrogen use efficiency, enhanced heat tolerance, enhanced shade tolerance, enhanced high salinity tolerance, enhanced seed protein and enhanced seed oil.
  • Such recombinant DNA in a plant cell nuclus of this invention is provided in as a construct comprising a promoter that is functional in plant cells and that is operably linked to DNA that encodes a protein or to DNA that results in gene suppression.
  • DNA in the construct is sometimes defined by protein domains of an encoded protein targeted for production or suppression, e.g. a “Pfam domain module” (as defined herein below) from the group of Pfam domain modules identified in Table 20.
  • a Pfam domain module is not available
  • such DNA in the construct is defined a consensus amino acid sequence of an encoded protein that is targeted for production e.g. a protein having amino acid sequence with at least 90% identity to a consensus amino acid sequence in the group of SEQ ID NO: 94617 through SEQ ID NO: 94734.
  • the plant cell nuclei, cells, plants, seeds, and pollen further comprise DNA expressing a protein that provides tolerance from exposure to an herbicide applied at levels that are lethal to a wild type plant cell.
  • This invention also provides methods for manufacturing non-natural, transgenic seed that can be used to produce a crop of transgenic plants with an enhanced trait resulting from expression of stably-integrated, recombinant DNA in the nucleus of the plant cells. More specifically the method comprises (a) screening a population of plants for an enhanced trait and recombinant DNA, where individual plants in the population can exhibit the trait at a level less than, essentially the same as or greater than the level that the trait is exhibited in control plants which do not express the recombinant DNA; (b) selecting from the population one or more plants that exhibit the trait at a level greater than the level that said trait is exhibited in control plants and (c) collecting seed from a selected plant.
  • Such method further comprises steps (a) verifying that the recombinant DNA is stably integrated in said selected plants; and (b) analyzing tissue of a selected plant to determine the production of a protein having the function of a protein encoded by a recombinant DNA with a sequence of one of SEQ ID NO: 1-803; in one aspect of the invention the plants in the population further comprise DNA expressing a protein that provides tolerance to exposure to an herbicide applied at levels that are lethal to wild type plant cells and where the selecting is effected by treating the population with the herbicide, e.g. a glyphosate, dicamba, or glufosinate compound. In another aspect of the invention the plants are selected by identifying plants with the enhanced trait. The methods are used for manufacturing corn, soybean, cotton, canola, alfalfa, wheat, rice seed or any combinations thererof selected as having one of the enhanced traits described above.
  • Another aspect of the invention provides a method of producing hybrid corn seed comprising acquiring hybrid corn seed from a herbicide tolerant corn plant which also has a nucleus of this invention with stably-integrated, recombinant DNA.
  • the method further comprises producing corn plants from said hybrid corn seed, where a fraction of the plants produced from said hybrid corn seed is homozygous for said recombinant DNA, a fraction of the plants produced from said hybrid corn seed is hemizygous for said recombinant DNA, and a fraction of the plants produced from said hybrid corn seed has none of said recombinant DNA; selecting corn plants which are homozygous and hemizygous for said recombinant DNA by treating with an herbicide; collecting seed from herbicide-treated-surviving corn plants and planting said seed to produce further progeny corn plants; repeating the selecting and collecting steps at least once to produce an inbred corn line; and crossing the inbred corn line with a second corn line to produce hybrid seed.
  • this invention provides methods of growing a corn, cotton, soybean, or canola crop without irrigation water comprising planting seed having plant cells of the invention which are selected for enhanced water use efficiency.
  • methods comprise applying reduced irrigation water, e.g. providing up to 300 millimeters of ground water during the production of a corn crop.
  • This invention also provides methods of growing a corn, cotton, soybean or canola crop without added nitrogen fertilizer comprising planting seed having plant cells of the invention which are selected for enhanced nitrogen use efficiency.
  • FIGS. 1 , 2 and 3 illustrate plasmid maps.
  • FIG. 4 illustrates a consensus amino acid sequence of SEQ ID NO: 1325 and its homologs.
  • SEQ ID NO: 1-803 are nucleotide sequences of the coding strand of DNA for “genes” used in the recombinant DNA imparting an enhanced trait in plant cells, where each represents a coding sequence for a protein;
  • SEQ ID NO: 804-1606 are amino acid sequences of the cognate protein of the “genes” with nucleotide coding sequence 1-803;
  • SEQ ID NO: 1607-94613 are amino acid sequences of homologous proteins
  • SEQ ID NO: 94614 is a nucleotide sequence of a plasmid base vector for corn transformation.
  • SEQ ID NO: 94615 is a DNA sequence of a plasmid base vector for soybean transformation.
  • SEQ ID NO: 94616 is a DNA sequence of a plasmid base vector for cotton transformation.
  • SEQ ID NO: 94617-94734 are consensus sequences.
  • Table 1 lists the protein SEQ ID NOs and their corresponding consensus SEQ ID NOs.
  • the nuclei of this invention are identified by screening transgenic plants for one or more traits including enhanced drought stress tolerance, enhanced heat stress tolerance, enhanced cold stress tolerance, enhanced high salinity stress tolerance, enhanced low nitrogen availability stress tolerance, enhanced shade stress tolerance, enhanced plant growth and development at the stages of seed imbibition through early vegetative phase, and enhanced plant growth and development at the stages of leaf development, flower production and seed maturity.
  • a “plant cell” means a plant cell that is transformed with stably-integrated, non-natural, recombinant DNA, e.g. by Agrobacterium -mediated transformation or by bombardment using microparticles coated with recombinant DNA or other means.
  • a plant cell of this invention can be an originally-transformed plant cell that exists as a microorganism or as a progeny plant cell that is regenerated into differentiated tissue, e.g. into a transgenic plant with stably-integrated, non-natural recombinant DNA, or seed or pollen derived from a progeny transgenic plant.
  • transgenic plant means a plant whose genome has been altered by the stable integration of recombinant DNA.
  • a transgenic plant includes a plant regenerated from an originally-transformed plant cell and progeny transgenic plants from later generations or crosses of a transformed plant.
  • recombinant DNA means DNA which has been a genetically engineered and constructed outside of a cell including DNA containing naturally occurring DNA or cDNA or synthetic DNA.
  • a “homolog” means a protein in a group of proteins that perform the same biological function, e.g. proteins that belong to the same Pfam protein family and that provide a common enhanced trait in transgenic plants of this invention.
  • Homologs are expressed by homologous genes.
  • Homologous genes include naturally occurring alleles and artificially-created variants. Degeneracy of the genetic code provides the possibility to substitute at least one base of the protein encoding sequence of a gene with a different base without causing the amino acid sequence of the polypeptide produced from the gene to be changed.
  • a polynucleotide in the present invention can have any base sequence that has been changed from SEQ ID NO:1 through SEQ ID NO: 803 through substitution in accordance with degeneracy of the genetic code.
  • Homologs are proteins that, when optimally aligned, have at least about 60% identity, about 70% or higher, at least about 80% and at least about 90% identity over the full length of a protein identified as being associated with imparting an enhanced trait when expressed in plant cells.
  • Homologs include proteins with an amino acid sequence that has at least about 90% identity to a consensus amino acid sequence of proteins and homologs disclosed herein.
  • Homologs are identified by comparison of amino acid sequence, e.g. manually or by use of a computer-based tool using known homology-based search algorithms such as those commonly known and referred to as BLAST, FASTA, and Smith-Waterman.
  • a local sequence alignment program e.g. BLAST
  • BLAST can be used to search a database of sequences to find similar sequences, and the summary Expectation value (E-value) used to measure the sequence base similarity.
  • E-value Expectation value
  • a reciprocal query is used in the present invention to filter hit sequences with significant E-values for ortholog identification.
  • the reciprocal query entails search of the significant hits against a database of amino acid sequences from the base organism that are similar to the sequence of the query protein.
  • a hit can be identified as an ortholog, when the reciprocal query's best hit is the query protein itself or a protein encoded by a duplicated gene after speciation.
  • a further aspect of the homologs encoded by DNA in the transgenic plants of the invention are those proteins that differ from a disclosed protein as the result of deletion or insertion of one or more amino acids in a native sequence.
  • Homologous genes are genes which encode proteins with the same or similar biological function to the protein encoded by the second gene. Homologous genes can be generated by the event of speciation (see ortholog) or by the event of genetic duplication (see paralog). “Orthologs” refer to a set of homologous genes in different species that evolved from a common ancestral gene by specification. Normally, orthologs retain the same function in the course of evolution; and “paralogs” refer to a set of homologous genes in the same species that have diverged from each other as a consequence of genetic duplication. Thus, homologous genes can be from the same or a different organism. As used herein, “homolog” means a protein that performs the same biological function as a second protein including those identified by sequence identity search.
  • percent identity means the extent to which two optimally aligned DNA or protein segments are invariant throughout a window of alignment of components, for example nucleotide sequence or amino acid sequence.
  • An “identity fraction” for aligned segments of a test sequence and a reference sequence is the number of identical components that are shared by sequences of the two aligned segments divided by the total number of sequence components in the reference segment over a window of alignment which is the smaller of the full test sequence or the full reference sequence.
  • Percent identity (“% identity”) is the identity fraction times 100. Such optimal alignment is understood to be deemed as local alignment of DNA sequences. For protein alignment, a local alignment of protein sequences should allow introduction of gaps to achieve optimal alignment. Percent identity is calculated over the aligned length not including the gaps introduced by the alignment per se.
  • promoter means regulatory DNA for initializing transcription.
  • a “plant promoter” is a promoter capable of initiating transcription in plant cells whether or not its origin is a plant cell, e.g. is it well known that Agrobacterium promoters are functional in plant cells.
  • plant promoters include promoter DNA obtained from plants, plant viruses and bacteria such as Agrobacterium and Bradyrhizobium bacteria.
  • Examples of promoters under developmental control include promoters that preferentially initiate transcription in certain tissues, such as leaves, roots, or seeds. Such promoters are referred to as “tissue preferred”. Promoters that initiate transcription only in certain tissues are referred to as “tissue specific”.
  • a “cell type” specific promoter primarily drives expression in certain cell types in one or more organs, for example, vascular cells in roots or leaves.
  • An “inducible” or “repressible” promoter is a promoter which is under environmental control. Examples of environmental conditions that can effect transcription by inducible promoters include anaerobic conditions, or certain chemicals, or the presence of light. Tissue specific, tissue preferred, cell type specific, and inducible promoters constitute the class of “non-constitutive” promoters.
  • a “constitutive” promoter is a promoter which is active under most conditions.
  • operably linked refers to the association of two or more nucleic acid elements in a recombinant DNA construct, e.g. as when a promoter is operably linked with DNA that is transcribed to RNA whether for expressing or suppressing a protein.
  • Recombinant DNA constructs can be designed to express a protein which can be an endogenous protein, an exogenous homologue of an endogenous protein or an exogenous protein with no native homologue.
  • recombinant DNA constructs can be designed to suppress the level of an endogenous protein, e.g. by suppression of the native gene.
  • RNAi RNA interference
  • Gene suppression can also be effected by recombinant DNA that comprises antisense oriented DNA matched to the gene targeted for suppression.
  • Gene suppression can also be effected by recombinant DNA that comprises DNA that is transcribed to a microRNA matched to the gene targeted for suppression.
  • recombinant DNA for effecting gene suppression that imparts is identified by the term “antisense”. It will be understood by a person of ordinary skill in the art that any of the ways of effecting gene suppression are contemplated and enabled by a showing of one approach to gene suppression.
  • expressed means produced, e.g. a protein is expressed in a plant cell when its cognate DNA is transcribed to mRNA that is translated to the protein.
  • “suppressed” means decreased, e.g. a protein is suppressed in a plant cell when there is a decrease in the amount and/or activity of the protein in the plant cell.
  • the presence or activity of the protein can be decreased by any amount up to and including a total loss of protein expression and/or activity.
  • control plant means a plant that does not contain the recombinant DNA that expressed a protein that imparts an enhanced trait.
  • a control plant is to identify and select a transgenic plant that has an enhance trait.
  • a suitable control plant can be a non-transgenic plant of the parental line used to generate a transgenic plant, e.g. devoid of recombinant DNA.
  • a suitable control plant can in some cases be a progeny of a hemizygous transgenic plant line that is does not contain the recombinant DNA, known as a negative segregant.
  • Trait enhancement means a detectable and desirable difference in a characteristic in a transgenic plant relative to a control plant or a reference.
  • the trait enhancement can be measured quantitatively.
  • the trait enhancement can entail at least about 2% difference in an observed trait, at least about 5% desirable difference, at least about 10% difference, at least about 20% difference, at least about 30% difference, at least about 40%, at least about 50% difference, at least about 60%, at least about 70% difference, at least about 80% difference, at least about 90% difference, or at least about a 100% difference, or an even greater difference.
  • the trait enhancement is only measured qualitatively. It is known that there can be a natural variation in a trait.
  • the trait enhancement observed entails a change of the normal distribution of the trait in the transgenic plant compared with the trait distribution observed in a control plant or a reference, which is evaluated by statistical methods provided herein.
  • Trait enhancement includes, but is not limited to, yield increase, including increased yield under non-stress conditions and increased yield under environmental stress conditions. Stress conditions can include, for example, drought, shade, fungal disease, viral disease, bacterial disease, insect infestation, nematode infestation, cold temperature exposure, heat exposure, osmotic stress, reduced nitrogen nutrient availability, reduced phosphorus nutrient availability, high plant density, or any combinations thereof.
  • Yield can be affected by many properties including without limitation, plant height, pod number, pod position on the plant, number of internodes, incidence of pod shatter, grain size, efficiency of nodulation and nitrogen fixation, efficiency of nutrient assimilation, resistance to biotic and abiotic stress, carbon assimilation, plant architecture, resistance to lodging, percent seed germination, seedling vigor, and juvenile traits. Yield can also be affected by efficiency of germination (including germination in stressed conditions), growth rate (including growth rate in stressed conditions), ear number, seed number per ear, seed size, composition of seed (starch, oil, protein) and characteristics of seed fill.
  • Increased yield of a transgenic plant of the present invention can be measured in a number of ways, including test weight, seed number per plant, seed weight, seed number per unit area (e.g. seeds, or weight of seeds, per acre), bushels per acre, tonnes per acre, tons per acre, kilo per hectare.
  • maize yield can be measured as production of shelled corn kernels per unit of production area, for example in bushels per acre or metric tons per hectare, often reported on a moisture adjusted basis, for example at 15.5 percent moisture.
  • Increased yield can result from improved utilization of key biochemical compounds, such as nitrogen, phosphorous and carbohydrate, or from improved responses to environmental stresses, such as cold, heat, drought, salt, and attack by pests or pathogens.
  • Recombinant DNA used in this invention can also be used to provide plants having improved growth and development, and ultimately increased yield, as the result of modified expression of plant growth regulators or modification of cell cycle or photosynthesis pathways. Also of interest is the generation of transgenic plants that demonstrate enhanced yield with respect to a seed component that could correspond to an increase in overall plant yield. Such properties include enhancements in seed oil, seed molecules such as tocopherol, protein and starch, or oil particular oil components as can be manifest by alterations in the ratios of seed components.
  • Stress condition means a condition unfavorable for a plant, which adversely affect plant metabolism, growth and/or development.
  • a plant under the stress condition typically shows reduced germination rate, retarded growth and development, reduced photosynthesis rate, and eventually leading to reduction in yield.
  • water deficit stress used herein refers to the sub-optimal conditions for water and humidity needed for normal growth of natural plants.
  • Relative water content (RWC) can be used as a physiological measure of plant water deficit. It measures the effect of osmotic adjustment in plant water status, when a plant is under stressed conditions. Conditions which can result in water deficit stress include, but are not limited to, heat, drought, high salinity and PEG induced osmotic stress.
  • Cold stress means the exposure of a plant to a temperatures below (two or more degrees Celsius below) those normal for a particular species or particular strain of plant.
  • Nonrogen nutrient means any one or any mix of the nitrate salts commonly used as plant nitrogen fertilizer, including, but not limited to, potassium nitrate, calcium nitrate, sodium nitrate, ammonium nitrate.
  • ammonium as used herein means any one or any mix of the ammonium salts commonly used as plant nitrogen fertilizer, e.g., ammonium nitrate, ammonium chloride, ammonium sulfate, etc.
  • Low nitrogen availability stress means a plant growth condition that does not contain sufficient nitrogen nutrient to maintain a healthy plant growth and/or for a plant to reach its typical yield under a sufficient nitrogen growth condition.
  • a limiting nitrogen condition can refers to a growth condition with 50% or less of the conventional nitrogen inputs.
  • “Sufficient nitrogen growth condition” means a growth condition where the soil or growth medium contains or receives optimal amounts of nitrogen nutrient to sustain a healthy plant growth and/or for a plant to reach its typical yield for a particular plant species or a particular strain.
  • One skilled in the art would recognize what constitute such soil, media and fertilizer inputs for most plant species.
  • Shade stress means a growth condition that has limited light availability that triggers the shade avoidance response in plant. Plants are subject to shade stress when localized at lower part of the canopy, or in close proximity of neighboring vegetation. Shade stress can become exacerbated when the planting density exceeds the average prevailing density for a particular plant species.
  • a constitutively active mutant is constructed to achieve the desired effect.
  • a dominant negative gene is constructed to adversely affect the normal, wild-type gene product within the same cell.
  • DNA constructs are assembled using methods well known to persons of ordinary skill in the art and typically comprise a promoter operably linked to DNA, the expression of which provides the enhanced agronomic trait.
  • Other construct components can include additional regulatory elements, such as 5′ leaders and introns for enhancing transcription, 3′ untranslated regions (such as polyadenylation signals and sites), DNA for transit or signal peptides.
  • promoters that are active in plant cells have been described in the literature. These include promoters present in plant genomes as well as promoters from other sources, including nopaline synthase (NOS) promoter and octopine synthase (OCS) promoters carried on tumor-inducing plasmids of Agrobacterium tumefaciens and the CaMV35S promoters from the cauliflower mosaic virus as disclosed in U.S. Pat. Nos. 5,164,316 and 5,322,938. Promoters derived from plant genes are found in U.S. Pat. No. 5,641,876, which discloses a rice actin promoter, U.S. Pat. No.
  • NOS nopaline synthase
  • OCS octopine synthase
  • Promoters of interest for such uses include those from genes such as Arabidopsis thaliana ribulose-1,5-bisphosphate carboxylase (Rubisco) small subunit (Fischhoff et al. (1992) Plant Mol Biol. 20:81-93), aldolase and pyruvate orthophosphate dikinase (PPDK) (Taniguchi et al. (2000) Plant Cell Physiol. 41(1):42-48).
  • Rubisco Arabidopsis thaliana ribulose-1,5-bisphosphate carboxylase
  • PPDK pyruvate orthophosphate dikinase
  • the promoters can be altered to contain multiple “enhancer sequences” to assist in elevating gene expression.
  • enhancers are known in the art.
  • the expression of the selected protein can be enhanced.
  • These enhancers often are found 5′ to the start of transcription in a promoter that functions in eukaryotic cells, but can often be inserted upstream (5′) or downstream (3′) to the coding sequence.
  • these 5′ enhancing elements are introns.
  • enhancers are the 5′ introns of the rice actin 1 (see U.S. Pat. No. 5,641,876) and rice actin 2 genes, the maize alcohol dehydrogenase gene intron, the maize heat shock protein 70 gene intron (U.S. Pat. No. 5,593,874) and the maize shrunken 1 gene.
  • promoters for use for seed composition modification include promoters from seed genes such as napin (U.S. Pat. No. 5,420,034), maize L3 oleosin (U.S. Pat. No. 6,433,252), zein Z27 (Russell et al. (1997) Transgenic Res. 6(2):157-166), globulin 1 (Belanger et al (1991) Genetics 129:863-872), glutelin 1 (Russell (1997) supra), and peroxiredoxin antioxidant (Per1) (Stacy et al. (1996) Plant Mol Biol. 31(6):1205-1216).
  • seed genes such as napin (U.S. Pat. No. 5,420,034), maize L3 oleosin (U.S. Pat. No. 6,433,252), zein Z27 (Russell et al. (1997) Transgenic Res. 6(2):157-166), globulin 1 (Belanger et al (1991) Genetics
  • Recombinant DNA constructs prepared in accordance with the invention will also generally include a 3′ element that typically contains a polyadenylation signal and site.
  • 3′ elements include those from Agrobacterium tumefaciens genes such as nos 3′, tml 3′, tmr 3′, tms 3′, ocs 3′, tr7 3′, for example disclosed in U.S. Pat. No.
  • 3′ elements from plant genes such as wheat ( Triticum aesevitum ) heat shock protein 17 (Hsp17 3′), a wheat ubiquitin gene, a wheat fructose-1,6-biphosphatase gene, a rice glutelin gene, a rice lactate dehydrogenase gene and a rice beta-tubulin gene, all of which are disclosed in U.S. published patent application 2002/0192813 A1, incorporated herein by reference; and the pea ( Pisum sativum ) ribulose biphosphate carboxylase gene (rbs 3′), and 3′ elements from the genes within the host plant.
  • wheat Triticum aesevitum
  • Hsp17 3′ heat shock protein 17
  • rbs 3′ the pea ribulose biphosphate carboxylase gene
  • Constructs and vectors can also include a transit peptide for targeting of a gene to a plant organelle, particularly to a chloroplast, leucoplast or other plastid organelle.
  • a transit peptide for targeting of a gene to a plant organelle particularly to a chloroplast, leucoplast or other plastid organelle.
  • chloroplast transit peptides see U.S. Pat. No. 5,188,642 and U.S. Pat. No. 5,728,925, incorporated herein by reference.
  • the transit peptide region of an Arabidopsis EPSPS gene can be in the present invention, see Klee, H. J. et al ( MGG (1987) 210:437-442).
  • Gene suppression includes any of the well-known methods for suppressing transcription of a gene or the accumulation of the mRNA corresponding to that gene thereby preventing translation of the transcript into protein.
  • Posttranscriptional gene suppression is mediated by transcription of RNA that forms double-stranded RNA (dsRNA) having homology to a gene targeted for suppression.
  • dsRNA double-stranded RNA
  • Suppression can also be achieved by insertion mutations created by transposable elements can also prevent gene function.
  • transformation with the T-DNA of Agrobacterium can be readily achieved and large numbers of transformants can be rapidly obtained.
  • some species have lines with active transposable elements that can efficiently be used for the generation of large numbers of insertion mutations, while some other species lack such options.
  • Mutant plants produced by Agrobacterium or transposon mutagenesis and having altered expression of a polypeptide of interest can be identified using the polynucleotides of the present invention. For example, a large population of mutated plants can be screened with polynucleotides encoding the polypeptide of interest to detect mutated plants having an insertion in the gene encoding the polypeptide of interest.
  • Transgenic plants comprising or derived from plant cells of this invention transformed with recombinant DNA can be further enhanced with stacked traits, e.g. a crop plant having an enhanced trait resulting from expression of DNA disclosed herein in combination with herbicide and/or pest resistance traits.
  • genes of the current invention can be stacked with other traits of agronomic interest, such as a trait providing herbicide resistance, or insect resistance, such as using a gene from Bacillus thuringensis to provide resistance against lepidopteran, coliopteran, homopteran, hemiopteran, and other insects.
  • Herbicides for which transgenic plant tolerance has been demonstrated and the method of the present invention can be applied include, but are not limited to, glyphosate, dicamba, glufosinate, sulfonylurea, bromoxynil and norflurazon herbicides.
  • Polynucleotide molecules encoding proteins involved in herbicide tolerance are well-known in the art and include, but are not limited to, a polynucleotide molecule encoding 5-enolpyruvylshikimate-3-phosphate synthase (EPSPS) disclosed in U.S. Pat. Nos.
  • EPSPS 5-enolpyruvylshikimate-3-phosphate synthase
  • Patent Application publication 2003/0135879 A1 for imparting dicamba tolerance a polynucleotide molecule encoding bromoxynil nitrilase (Bxn) disclosed in U.S. Pat. No. 4,810,648 for imparting bromoxynil tolerance; a polynucleotide molecule encoding phytoene desaturase (crtl) described in Misawa et al, (1993) Plant J. 4:833-840 and in Misawa et al, (1994) Plant J.
  • Bxn bromoxynil nitrilase
  • crtl phytoene desaturase
  • Patent Application Publication 2003/010609 A1 for imparting N-amino methyl phosphonic acid tolerance polynucleotide molecules disclosed in U.S. Pat. No. 6,107,549 for impartinig pyridine herbicide resistance; molecules and methods for imparting tolerance to multiple herbicides such as glyphosate, atrazine, ALS inhibitors, isoxoflutole and glufosinate herbicides are disclosed in U.S. Pat. No. 6,376,754 and U.S. Patent Application Publication 2002/0112260, all of said U.S. patents and patent application Publications are incorporated herein by reference. Molecules and methods for imparting insect/nematode/virus resistance are disclosed in U.S. Pat. Nos. 5,250,515; 5,880,275; 6,506,599; 5,986,175 and U.S. Patent Application Publication 2003/0150017 A1, all of which are incorporated herein by reference.
  • a “consensus amino acid sequence” means an artificial, amino acid sequence indicating conserved amino acids in the sequence of homologous proteins as determined by statistical analyis of an optimal alignment, e.g. CLUSTALW, of amino acid sequence of homolog proteins.
  • the consensus sequences listed in the sequence listing were created by identifying the most frequent amino acid at each position in a set of aligned protein sequences. When there was 100% identity in an alignment the amino acid is indicated by a capital letter. When the occurance of an amino acid is at least about 70% in an alignemnt, the amino acid is indicated by a lower case letter. When there is no amino acid occurance of at least about 70%, e.g. due to diversity or gaps, the amino acid is inidcated by an “x”.
  • a consensus amino acid sequence When used to defined embodiments of the invention, a consensus amino acid sequence will be aligned with a query protein amino acid sequence in an optimal alignment, e.g. CLUSTALW.
  • An embodiment of the invention will have identity to the conserved amino acids indicated in the consensus amino acid sequence.
  • Arabidopsis means plants of Arabidopsis thaliana.
  • Pfam database is a large collection of multiple sequence alignments and hidden Markov models covering many common protein families, e.g. Pfam version 19.0 (December 2005) contains alignments and models for 8183 protein families and is based on the Swissprot 47.0 and SP-TrEMBL 30.0 protein sequence databases. See S. R. Eddy, “Profile Hidden Markov Models”, Bioinformatics 14:755-763, 1998. The Pfam database is currently maintained and updated by the Pfam Consortium. The alignments represent some evolutionary conserved structure that has implications for the protein's function. Profile hidden Markov models (profile HMMs) built from the protein family alignments can be used for automatically recognizing that a new protein belongs to an existing protein family even if the homology by alignment appears to be low.
  • profile HMMs Profile hidden Markov models
  • a “Pfam domain module” is a representation of Pfam domains in a protein, in order from N terminus to C terminus. In a Pfam domain module individual Pfam domains are separated by double colons “::”. The order and copy number of the Pfam domains from N to C terminus are attributes of a Pfam domain module. Although the copy number of repetitive domains is important, varying copy number often enables a similar function. Thus, a Pfam domain module with multiple copies of a domain should define an equivalent Pfam domain module with variance in the number of multiple copies.
  • a Pfam domain module is not specific for distance between adjacent domains, but contemplates natural distances and variations in distance that provide equivalent function.
  • the Pfam database contains both narrowly- and broadly-defined domains, leading to identification of overlapping domains on some proteins.
  • a Pfam domain module is characterized by non-overlapping domains. Where there is overlap, the domain having a function that is more closely associated with the function of the protein (based on the E value of the Pfam match) is selected.
  • Pfam modules for use in this invention, as more specifically disclosed below, are Syntaxin::SNARE, Pro_isomerase, Pkinase, ATP-synt_G, Carboxyl_trans, CDC50, GATase::GMP_synt_C, F-box::WD40::WD40::WD40, dsrm::dsrm, Pyr_redox — 2::Pyr_redox_dim, WAK::Pkinase, Pkinase_Tyr, PTPA, Biotin_lipoyl::E3_binding::2-oxoacid_dh, AAA, LRRNT — 2::LRR — 1::LRR — 1::LRR — 1, PRA1, TIM, YTH, ThiF, Hep — 59, Pkinase, PALP::Thr_dehydrat_C::Thr_dehydrat_C, zf-T
  • Transformation of plant material is practiced in tissue culture on a nutrient media, e.g. a mixture of nutrients that will allow cells to grow in vitro.
  • Recipient cell targets include, but are not limited to, meristem cells, hypocotyls, calli, immature embryos and gametic cells such as microspores, pollen, sperm and egg cells.
  • Callus can be initiated from tissue sources including, but not limited to, immature embryos, hypocotyls, seedling apical meristems, microspores and the like. Cells containing a transgenic nucleus are grown into transgenic plants.
  • a transgenic plant cell nucleus can be prepared by crossing a first plant having cells with a transgenic nucleus with recombinant DNA with a second plant lacking the trangenci nucleus.
  • recombinant DNA can be introduced into a nucleus from a first plant line that is amenable to transformation to transgenic nucleus in cells that are grown into a transgenic plant which can be crossed with a second plant line to introgress the recombinant DNA into the second plant line.
  • a transgenic plant with recombinant DNA providing an enhanced trait, e.g.
  • transgenic plant line having other recombinant DNA that confers another trait for example herbicide resistance or pest resistance
  • progeny plants having recombinant DNA that confers both traits Typically, in such breeding for combining traits the transgenic plant donating the additional trait is a male line and the transgenic plant carrying the base traits is the female line.
  • the progeny of this cross will segregate such that some of the plants will carry the DNA for both parental traits and some will carry DNA for one parental trait; such plants can be identified by markers associated with parental recombinant DNA, e.g.
  • Progeny plants carrying DNA for both parental traits can be crossed back into the female parent line multiple times, for example usually 6 to 8 generations, to produce a progeny plant with substantially the same genotype as one original transgenic parental line but for the recombinant DNA of the other transgenic parental line
  • DNA is introduced into only a small percentage of target cell nuclei.
  • Marker genes are used to provide an efficient system for identification of those cells with nuclei that are stably transformed by receiving and integrating a recombinant DNA molecule into their genomes.
  • Some marker genes provide selective markers that confer resistance to a selective agent, such as an antibiotic or herbicide.
  • Potentially transformed cells with a nucleus of the invention are exposed to the selective agent. In the population of surviving cells will be those cells where, generally, the resistance-conferring gene has been integrated and expressed at sufficient levels to permit cell survival. Cells can be tested further to confirm stable integration of the exogenous DNA in the nucleus.
  • Explementary selective marker genes include those conferring resistance to antibiotics such as kanamycin (nptII), hygromycin B (aph IV), spectinomycin (aadA) and gentamycin (aac3 and aacC4) or resistance to herbicides such as glufosinate (bar or pat), dicamba (DMO) and glyphosate is (EPSPS). Examples of such selectable markers are illustrated in U.S. Pat. Nos. 5,550,318; 5,633,435; 5,780,708 and 6,118,047, all of which are incorporated herein by reference.
  • Screenable markers which provide an ability to visually identify transformants can also be employed, e.g., a gene expressing a colored or fluorescent protein such as a luciferase or green fluorescent protein (GFP) or a gene expressing a beta-glucuronidase or uidA gene (GUS) for which various chromogenic substrates are known. It is also contemplated that combinations of screenable and selectable markers can be used for identification of transformed cells. See PCT publication WO 99/61129 (herein incorporated by reference) which discloses use of a gene fusion between a selectable marker gene and a screenable marker gene, e.g., an NPTII gene and a GFP gene.
  • a gene fusion between a selectable marker gene and a screenable marker gene e.g., an NPTII gene and a GFP gene.
  • Plant cells that survive exposure to the selective agent, or plant cells that have been scored positive in a screening assay, can be cultured in regeneration media and allowed to mature into plants.
  • Developing plantlets regenerated from transformed plant cells can be transferred to plant growth mix, and hardened off, for example, in an environmentally controlled chamber at about 85% relative humidity, 600 ppm CO 2 , and 25-250 microeinsteins m ⁇ 2 S ⁇ 1 of light, prior to transfer to a greenhouse or growth chamber for maturation.
  • Plants are regenerated from about 6 weeks to 10 months after a transformant is identified, depending on the initial tissue, and plant species.
  • Plants can be pollinated using conventional plant breeding methods known to those of skill in the art and seed produced, for example self-pollination is commonly used with transgenic corn.
  • the regenerated transformed plant or its progeny seed or plants can be tested for expression of the recombinant DNA and selected for the presence of enhanced agronomic trait.
  • Transgenic plants derived from transgenic plant cells having a transgenic nucleus of this invention are grown to generate transgenic plants having an enhanced trait as compared to a control plant and produce transgenic seed and haploid pollen of this invention.
  • Such plants with enhanced traits are identified by selection of transformed plants or progeny seed for the enhanced trait.
  • a selection method is designed to evaluate multiple transgenic plants (events) comprising the recombinant DNA, for example multiple plants from 2 to 20 or more transgenic events.
  • Transgenic plants grown from transgenic seed provided herein demonstrate improved agronomic traits that contribute to increased yield or other trait that provides increased plant value, including, for example, improved seed quality.
  • plants having enhanced water use efficiency, enhanced cold tolerance, increased yield, enhanced nitrogen use efficiency, enhanced seed protein and enhanced seed oil are plants having enhanced water use efficiency, enhanced cold tolerance, increased yield, enhanced nitrogen use efficiency, enhanced seed protein and enhanced seed oil.
  • Arabidopsis thaliana was transformed with a candidate recombinant DNA construct and screened for an enhanced trait.
  • Arabidopsis thaliana is used a model for genetics and metabolism in plants.
  • a two-step screening process was employed which included two passes of trait characterization to ensure that the trait modification was dependent on expression of the recombinant DNA, but not due to the chromosomal location of the integration of the transgene. Twelve independent transgenic lines for each recombinant DNA construct were established and assayed for the transgene expression levels. Five transgenic lines with high transgene expression levels were used in the first pass screen to evaluate the transgene's function in T2 transgenic plants. Subsequently, three transgenic events, which had been shown to have one or more enhanced traits, were further evaluated in the second pass screen to confirm the transgene's ability to impart an enhanced trait.
  • Table 3 summarizes the enhanced traits that have been confirmed as provided by a recombinant DNA construct.
  • Table 2 provides a list of protein encoding DNA (“genes”) as recombinant DNA for production of transgenic plants with enhanced agronomic trait, the elements of Table 2 are described by reference to:
  • PEP SEQ ID NO′′ identifies an amino acid sequence from SEQ ID NO: 804 to 1606.
  • NUC SEQ ID NO identifies a DNA sequence from SEQ ID NO:1 to 803
  • construct_id refers to an arbitrary number used to identify a particular recombinant DNA construct comprising the particular DNA.
  • Gene ID refers to an arbitrary name used to identify the particular DNA.
  • orientation refers to the orientation of the particular DNA in a recombinant DNA construct relative to the promoter.
  • DNA for use in the present invention to improve traits in plants have a nucleotide sequence of SEQ ID NO:1 through SEQ ID NO:803, as well as the homologs of such DNA molecules.
  • a subset of the DNA for gene suppression aspects of the invention includes fragments of the disclosed full polynucleotides consisting of oligonucleotides of 21 or more consecutive nucleotides.
  • the nucleotides for gne suppression can be 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30 or more consecutive nucleotides.
  • Oligonucleotides having a sequence selected from the group consisting of SEQ ID NO: 1 through SEQ ID NO: 803 can be as probes and primers for detection of the polynucleotides used in the invention.
  • this invention are variants of the DNA.
  • Such variants can be naturally occurring, including DNA from homologous genes from the same or a different species, or can be non-natural variants, for example DNA synthesized using chemical synthesis methods, or generated using recombinant DNA techniques.
  • Degeneracy of the genetic code provides the possibility to substitute at least one base of the protein encoding sequence of a gene with a different base without causing the amino acid sequence of the polypeptide produced from the gene to be changed.
  • a DNA in the present invention can have any base sequence that has been changed from the sequences provided herein by substitution in accordance with degeneracy of the genetic code.
  • DNA is substantially identical to a reference DNA if, when the sequences of the polynucleotides are optimally aligned there is about 60% nucleotide equivalence; about 70% equivalence; about 80% equivalence; about 85% equivalence; about 90%; about 95%; about 98%, about 99% equivalence or about 99.5 equivalence over a comparison window.
  • a comparison window can be at least 50-100 nucleotides or the entire length of the polynucleotide provided herein.
  • Optimal alignment of sequences for aligning a comparison window can be conducted by algorithms; for example by computerized implementations of these algorithms (such as, the Wisconsin Genetics Software Package Release 7.0-10.0, Genetics Computer Group, 575 Science Dr., Madison, Wis.).
  • the reference polynucleotide can be a full-length molecule or a portion of a longer molecule.
  • the window of comparison for determining polynucleotide identity of protein encoding sequences is the entire coding region.
  • Proteins used for imparting enhanced traits are entire proteins or at least a sufficient portion of the entire protein to impart the relevant biological activity of the protein. Proteins used for generation of transgenic plants having enhanced traits include the proteins with an amino acid sequence provided herein as SEQ ID NO: 804 through SEQ ID NO: 1606, as well as homologs of such proteins.
  • Homologs of the proteins in the invention are identified by comparison of the amino acid sequence of the protein to amino acid sequences of proteins from the same or different plant sources, e.g., manually or by using known homology-based search algorithms such as those commonly known and referred to as BLAST, FASTA, and Smith-Waterman.
  • a homolog is a protein from the same or a different organism that performs the same biological function as the polypeptide to which it is compared.
  • An orthologous relation between two organisms is not necessarily manifest as a one-to-one correspondence between two genes, because a gene can be duplicated or deleted after organism phylogenetic separation, such as speciation. For a given protein, there can be no ortholog or more than one ortholog.
  • a local sequence alignment program e.g., BLAST
  • E-value the summary Expectation value
  • BLAST a local sequence alignment program
  • BLAST can be used to search a database of sequences to find similar sequences, and the summary Expectation value (E-value) used to measure the sequence base similarity.
  • E-value the summary Expectation value
  • a reciprocal BLAST search is used in the present invention to filter hit sequences with significant E-values for ortholog identification.
  • the reciprocal BLAST entails search of the significant hits against a database of amino acid sequences from the base organism that are similar to the sequence of the query protein.
  • a hit is a likely ortholog, when the reciprocal BLAST's best hit is the query protein itself or a protein encoded by a duplicated gene after speciation.
  • homolog is used herein to describe proteins that are assumed to have functional similarity by inference from sequence base similarity.
  • the relationship of homologs with amino acid sequences of SEQ ID NO: 1607 to SEQ ID NO: 94613 to the proteins with amino acid sequences of SEQ ID NO: 804 to SEQ ID NO: 1606 are found in the listing of Table 19.
  • Other functional homolog proteins differ in one or more amino acids from those of a trait-improving protein disclosed herein as the result of one or more of the well-known conservative amino acid substitutions, e.g., valine is a conservative substitute for alanine and threonine is a conservative substitute for serine.
  • Conservative substitutions for an amino acid within the native sequence can be selected from other members of a class to which the naturally occurring amino acid belongs.
  • amino acids within these various classes include, but are not limited to: (1) acidic (negatively charged) amino acids such as aspartic acid and glutamic acid; (2) basic (positively charged) amino acids such as arginine, histidine, and lysine; (3) neutral polar amino acids such as glycine, serine, threonine, cysteine, tyrosine, asparagine, and glutamine; and (4) neutral nonpolar (hydrophobic) amino acids such as alanine, leucine, isoleucine, valine, proline, phenylalanine, tryptophan, and methionine.
  • conserveed substitutes for an amino acid within a native amino acid sequence can be selected from other members of the group to which the naturally occurring amino acid belongs.
  • a group of amino acids having aliphatic side chains is glycine, alanine, valine, leucine, and isoleucine
  • a group of amino acids having aliphatic-hydroxyl side chains is serine and threonine
  • a group of amino acids having amide-containing side chains is asparagine and glutamine
  • a group of amino acids having aromatic side chains is phenylalanine, tyrosine, and tryptophan
  • a group of amino acids having basic side chains is lysine, arginine, and histidine
  • a group of amino acids having sulfur-containing side chains is cysteine and methionine.
  • Naturally conservative amino acids substitution groups are: valine-leucine, valine-isoleucine, phenylalanine-tyrosine, lysine-arginine, alanine-valine, aspartic acid-glutamic acid, and asparagine-glutamine.
  • a further aspect of the invention comprises proteins that differ in one or more amino acids from those of a described protein sequence as the result of deletion or insertion of one or more amino acids in a native sequence.
  • Homologs of the trait-improving proteins provided herein will generally demonstrate significant sequence identity.
  • proteins having at least about 50% sequence identity, at least about 70% sequence identity or higher, e.g., at least about 80% sequence identity with an amino acid sequence of SEQ ID NO: 804 to SEQ ID NO: 1606.
  • Additional embodiments also include those with higher identity, e.g., about 90%, about 92.5%, about 95%, about 98%, about 99%, or to about 99.5% identity.
  • Identity of protein homologs is determined by optimally aligning the amino acid sequence of a putative protein homolog with a defined amino acid sequence and by calculating the percentage of identical and conservatively substituted amino acids over the window of comparison.
  • the window of comparison for determining identity can be the entire amino acid sequence disclosed herein, e.g., the full sequence of any of SEQ ID NO: 804 to SEQ ID NO: 1606.
  • Protein homologs include proteins with an amino acid sequence that has at least 90% identity to such a consensus amino acid sequence sequences.
  • Arabidopsis thaliana was transformed with a candidate recombinant DNA construct and screened for an enhanced trait. Arabidopsis thaliana is used a model for genetics and metabolism in plants.
  • Arabidopsis has a small genome, and well-documented studies are available. It is easy to grow in large numbers and mutants defining important genetically controlled mechanisms are either available, or can readily be obtained. Various methods to introduce and express isolated homologous genes are available (see Koncz, et al., Methods in Arabidopsis Research et al., (1992), World Scientific, New Jersey, N.J., in “Preface”).
  • a two-step screening process was employed which comprised two passes of trait characterization to ensure that the trait modification was dependent on expression of the recombinant DNA, but not due to the chromosomal location of the integration of the transgene. Twelve independent transgenic lines for each recombinant DNA construct were established and assayed for the transgene expression levels. Five transgenic lines with high transgene expression levels were used in the first pass screen to evaluate the transgene's function in T2 transgenic plants. Subsequently, three transgenic events, which had been shown to have one or more enhanced traits, were further evaluated in the second pass screen to confirm the transgene's ability to impart an enhanced trait.
  • Table 3 summarizes the enhanced traits that have been confirmed as provided by a recombinant DNA construct.
  • PEP SEQ ID which is the amino acid sequence of the protein cognate to the DNA in the recombinant DNA construct corresponding to a protein sequence of a SEQ ID NO. in the Sequence Listing.
  • construct_id is an arbitrary name for the recombinant DNA describe more particularly in Table 1.
  • “annotation” refers to a description of the top hit protein obtained from an amino acid sequence query of each PEP SEQ ID NO to GenBank database of the National Center for Biotechnology Information (ncbi). More particularly, “gi” is the GenBank ID number for the top BLAST hit.
  • “description” refers to the description of the top BLAST hit.
  • e-value provides the expectation value for the BLAST hit.
  • % id refers to the percentage of identically matched amino acid residues along the length of the portion of the sequences which is aligned by BLAST between the sequence of interest provided herein and the hit sequence in GenBank.
  • “traits” identify by two letter codes the confirmed enhancement in a transgenic plant provided by the recombinant DNA.
  • the codes for enhanced traits are:
  • PEG which indicates osmotic stress tolerance enhancement identified by a PEG induced osmotic stress tolerance screen
  • PP which indicates enhanced growth and development at early stages identified by an early plant growth and development screen
  • SP which indicates enhanced growth and development at late stages identified by a late plant growth and development screen provided herein.
  • campestris str ATCC 33913] 931 70130 1.00E ⁇ 161 99 ref
  • subtilis str. 168 1179 73164 0 93 ref
  • tomato str. DC3000 1268 73432 0 94 ref
  • LL tomato str. DC3000 1279 73565 0 95 ref
  • PCC 6803 1293 74485 0 88 ref
  • PCC 6803 1365 74966 0 99 ref
  • PCC 6803 1367 74934 0 96 ref
  • PCC 6803 1469 75920 0 100 ref
  • DS-Enhancement of drought tolerance identified by a soil drought stress tolerance screen Drought or water deficit conditions impose mainly osmotic stress on plants. Plants are particularly vulnerable to drought during the flowering stage.
  • the drought condition in the screening process disclosed in Example 1B started from the flowering time and was sustained to the end of harvesting.
  • the present invention provides recombinant DNA that can improve the plant survival rate under such sustained drought condition.
  • Exemplary recombinant DNA for conferring such drought tolerance are identified as such in Table 3.
  • Such recombinant DNA can find particular use in generating transgenic plants that are tolerant to the drought condition imposed during flowering time and in other stages of the plant life cycle.
  • transgenic plants with trait-improving recombinant DNA grown under such sustained drought condition can also have increased total seed weight per plant in addition to the increased survival rate within a transgenic population, providing a higher yield potential as compared to control plants.
  • PEG-Enhancement of drought tolerance identified by PEG induced osmotic stress tolerance screen Various drought levels can be artificially induced by using various concentrations of polyethylene glycol (PEG) to produce different osmotic potentials (Pilon-Smits et al., (1995) Plant Physiol. 107:125-130).
  • PEG polyethylene glycol
  • a PEG-induced osmotic stress tolerance screen can be a surrogate for drought tolerance screen.
  • embodiments of transgenic plants with trait-improving recombinant DNA identified in the PEG-induced osmotic stress tolerance screen can survive better drought conditions providing a higher yield potential as compared to control plants.
  • SS-Enhancement of drought tolerance identified by high salinity stress tolerance screen Three different factors are responsible for salt damages: (1) osmotic effects, (2) disturbances in the mineralization process, and (3) toxic effects caused by the salt ions, e.g., inactivation of enzymes. While the first factor of salt stress results in the wilting of the plants that is similar to drought effect, the ionic aspect of salt stress is clearly distinct from drought.
  • the present invention provides genes that help plants maintain biomass, root growth, and/or plant development in high salinity conditions, which are identified as such in Table 3.
  • trait-improving recombinant DNA identified in a high salinity stress tolerance screen can also provide transgenic crops with enhanced drought tolerance. As demonstrated from the model plant screen, embodiments of transgenic plants with trait-improving recombinant DNA identified in a high salinity stress tolerance screen can survive better drought conditions and/or high salinity conditions providing a higher yield potential as compared to control plants.
  • HS-Enhancement of drought tolerance identified by heat stress tolerance screen Heat and drought stress often occur simultaneously, limiting plant growth. Heat stress can cause the reduction in photosynthesis rate, inhibition of leaf growth and osmotic potential in plants. Thus, genes identified by the present invention as heat stress tolerance conferring genes can also impart enhanced drought tolerance to plants. As demonstrated from the model plant screen, embodiments of transgenic plants with trait-improving recombinant DNA identified in a heat stress tolerance screen can survive better heat stress conditions and/or drought conditions providing a higher yield potential as compared to control plants.
  • CK and CS-Enhancement of tolerance to cold stress Low temperature can immediately result in mechanical constraints, changes in activities of macromolecules, and reduced osmotic potential.
  • two screening conditions e.g., cold shock tolerance screen (CK) and cold germination tolerance screen (CS)
  • CK cold shock tolerance screen
  • CS cold germination tolerance screen
  • the transgenic Arabidopsis plants were exposed to a constant temperature of 8° C. from planting until day 28 post plating.
  • the trait-improving recombinant DNA identified by such screen can be used for the production of transgenic plant that can germinate more robustly in a cold temperature as compared to the wild type plants.
  • transgenic plants were first grown under the normal growth temperature of 22° C. until day 8 post plating, and subsequently were placed under 8° C. until day 28 post plating.
  • embodiments of transgenic plants with trait-improving recombinant DNA identified in a cold shock stress tolerance screen and/or a cold germination stress tolerance screen can survive better cold conditions providing a higher yield potential as compared to control plants.
  • Enhancement of tolerance to multiple stresses Different kinds of stresses often lead to identical or similar reaction in the plants. Genes that are activated or inactivated as a reaction to stress can either act directly in a way the genetic product reduces a specific stress, or they can act indirectly by activating other specific stress genes. By manipulating the activity of such regulatory genes, e.g., multiple stress tolerance genes, the plant can be enabled to react to different kinds of stresses.
  • PEP SEQ ID NO: 1000 can be used to enhance both salt stress tolerance and heat stress tolerance in plants.
  • plants transformed with PEP SEQ ID NO: 1495 can resist salt and heat stress. Plants transformed with PEP SEQ ID NO: 1483 can also improve growth in early stage and under heat stress.
  • the stress tolerance conferring genes provided by the present invention can be used in combinations to generate transgenic plants that can resist multiple stress conditions.
  • PP-Enhancement of earl plant growth and development It has been known in the art that to minimize the impact of disease on crop profitability, it is important to start the season with healthy and vigorous plants. This means avoiding seed and seedling diseases, leading to increased nutrient uptake and increased yield potential.
  • early planting and applying fertilizer are the methods used for promoting early seedling vigor.
  • plant embryos establish only the basic root-shoot axis, a cotyledon storage organ(s), and stem cell populations, called the root and shoot apical meristems that continuously generate new organs throughout post-embryonic development. “Early growth and development” used herein encompasses the stages of seed imbibition through the early vegetative phase.
  • the present invention provides genes that can be used to produce transgenic plants that have advantages in one or more processes including, but not limited to, germination, seedling vigor, root growth and root morphology under non-stressed conditions.
  • the transgenic plants starting from a more robust seedling are less susceptible to the fungal and bacterial pathogens that attach germinating seeds and seedling.
  • seedlings with advantage in root growth are more resistant to drought stress due to extensive and deeper root architecture. Therefore, it can be recognized by those skilled in the art that genes conferring the growth advantage in early stages to plants can also be used to generate transgenic plants that are more resistant to various stress conditions due to enhanced early plant development.
  • the present invention provides such exemplary recombinant DNA that confer both the stress tolerance and growth advantages to plants, identified as such in Table 3, e.g., PEP SEQ ID NO: 1043 which can improve the plant early growth and development, and impart heat stress tolerance to plants.
  • PEP SEQ ID NO: 1043 which can improve the plant early growth and development, and impart heat stress tolerance to plants.
  • embodiments of transgenic plants with trait-improving recombinant DNA identified in the early plant development screen can grow better under non-stress conditions and/or stress conditions providing a higher yield potential as compared to control plants.
  • “Late growth and development” used herein encompasses the stages of leaf development, flower production, and seed maturity.
  • transgenic plants produced using genes that confer growth advantages to plants provided by the present invention, identified as such in Table 3 exhibit at least one phenotypic characteristics including, but not limited to, increased rosette radius, increased rosette dry weight, seed dry weight, silique dry weight, and silique length.
  • the rosette radius and rosette dry weight are used as the indexes of photosynthesis capacity, and thereby plant source strength and yield potential of a plant.
  • the seed dry weight, silique dry weight and silique length are used as the indexes for plant sink strength, which are considered as the direct determinants of yield.
  • embodiments of transgenic plants with trait-improving recombinant DNA identified in the late development screen can grow better and/or have enhanced development during leaf development and seed maturation providing a higher yield potential as compared to control plants.
  • LL-Enhancement of tolerance to shade stress identified in a low light screen The effects of light on plant development are especially prominent at the seedling stage. Under normal light conditions with unobstructed direct light, a plant seeding develops according to a characteristic photomorphogenic pattern, in which plants have open and expanded cotyledons and short hypocotyls. Then the plant's energy is devoted to cotyledon and leaf development while longitudinal extension growth is minimized. Under low light condition where light quality and intensity are reduced by shading, obstruction or high population density, a seedling displays a shade-avoidance pattern, in which the seedling displays a reduced cotyledon expansion, and hypocotyls extension is greatly increased.
  • the present invention provides recombinant DNA that enable plants to have an attenuated shade avoidance response so that the source of plant can be contributed to reproductive growth efficiently, resulting higher yield as compared to the wild type plants.
  • embodiments of transgenic plants with trait-improving recombinant DNA identified in a shade stress tolerance screen can have attenuated shade response under shade conditions providing a higher yield potential as compared to control plants.
  • the transgenic plants generated by the present invention can be suitable for a higher density planting, thereby resulting increased yield per unit area.
  • the metabolism, growth and development of plants are profoundly affected by their nitrogen supply. Restricted nitrogen supply alters shoot to root ratio, root development, activity of enzymes of primary metabolism and the rate of senescence (death) of older leaves.
  • All field crops have a fundamental dependence on inorganic nitrogenous fertilizer. Since fertilizer is rapidly depleted from most soil types, it must be supplied to growing crops two or three times during the growing season. Enhanced nitrogen use efficiency by plants should enable crops cultivated under low nitrogen availability stress condition resulted from low fertilizer input or poor soil quality.
  • the transgenic plants provided by the present invention with enhanced nitrogen use efficiency can also have altered amino acid or protein compositions, increased yield and/or better seed quality.
  • the transgenic plants of the present invention can be productively cultivated under low nitrogen growth conditions, e.g., nitrogen-poor soils and low nitrogen fertilizer inputs, which would cause the growth of wild type plants to cease or to be so diminished as to make the wild type plants practically useless.
  • the transgenic plants also can be advantageously used to achieve earlier maturing, faster growing, and/or higher yielding crops and/or produce more nutritious foods and animal feedstocks when cultivated using nitrogen non-limiting growth conditions.
  • the present invention also encompasses transgenic plants with stacked engineered traits, e.g., a crop having an enhanced phenotype resulting from expression of a trait-improving recombinant DNA, in combination with herbicide and/or pest resistance traits.
  • genes of the current invention can be stacked with other traits of agronomic interest, such as a trait providing herbicide resistance, for example a RoundUp Ready® trait, or insect resistance, such as using a gene from Bacillus thuringensis to provide resistance against lepidopteran, coliopteran, homopteran, hemiopteran, and other insects.
  • Explementary herbicides include glyphosate herbicides, phosphinothricin herbicides, oxynil herbicides, imidazolinone herbicides, dinitroaniline herbicides, pyridine herbicides, sulfonylurea herbicides, bialaphos herbicides, sulfonamide herbicides and gluphosinate herbicides.
  • glyphosate herbicides include glyphosate herbicides, phosphinothricin herbicides, oxynil herbicides, imidazolinone herbicides, dinitroaniline herbicides, pyridine herbicides, sulfonylurea herbicides, bialaphos herbicides, sulfonamide herbicides and gluphosinate herbicides.
  • the invention provides methods for identifying a homologous gene with a DNA sequence homologous to any of SEQ ID NO: 1 through SEQ ID NO: 803, or a homologous protein with an amino acid sequence homologous to any of SEQ ID NO: 804 to SEQ ID NO: 1606.
  • the present invention provides the protein sequences of identified homologs for a sequence listed as SEQ ID NO: 1607 through SEQ ID NO: 94613.
  • the present invention also includes linking or associating one or more desired traits, or gene function with a homolog sequence provided herein.
  • the trait-improving recombinant DNA and methods of using such trait-improving recombinant DNA for generating transgenic plants with enhanced traits provided by the present invention are not limited to any particular plant species.
  • the plants according to the present invention can be of any plant species, e.g., can be monocotyledonous or dicotyledonous.
  • they are agricultural plants, e.g., plants cultivated by man for purposes of food production or technical, particularly industrial applications.
  • Of particular interest in the present invention are corn and soybean plants.
  • the recombinant DNA constructs optimized for soybean transformation and recombinant DNA constructs optimized for corn transformation are provided by the present invention.
  • Other plants of interest in the present invention for production of transgenic plants having enhanced traits include, without limitation, cotton, canola, wheat, sunflower, sorghum, alfalfa, barley, millet, rice, tobacco, fruit and vegetable crops, and turfgrass.
  • the present invention contemplates to use an orthologous gene in generating the transgenic plants with similarly enhanced traits as the transgenic Arabidopsis counterpart.
  • Enhanced physiological properties in transgenic plants of the present invention can be confirmed in responses to stress conditions, for example in assays using imposed stress conditions to detect enhanced responses to drought stress, nitrogen deficiency, cold growing conditions, or alternatively, under naturally present stress conditions, for example under field conditions.
  • Biomass measures can be made on greenhouse or field grown plants and can include such measurements as plant height, stem diameter, root and shoot dry weights, and, for corn plants, ear length and diameter.
  • Trait data on morphological changes can be collected by visual observation during the process of plant regeneration as well as in regenerated plants transferred to soil.
  • Such trait data includes characteristics such as normal plants, bushy plants, taller plants, thicker stalks, narrow leaves, striped leaves, knotted phenotype, chlorosis, albino, anthocyanin production, or altered tassels, ears or roots.
  • Other enhanced traits can be identified by measurements taken under field conditions, such as days to pollen shed, days to silking, leaf extension rate, chlorophyll content, leaf temperature, stand, seedling vigor, internode length, plant height, leaf number, leaf area, tillering, brace roots, stay green, stalk lodging, root lodging, plant health, barreness/prolificacy, green snap, and pest resistance.
  • trait characteristics of harvested grain can be confirmed, including number of kernels per row on the ear, number of rows of kernels on the ear, kernel abortion, kernel weight, kernel size, kernel density and physical grain quality.
  • hybrid yield in transgenic corn plants expressing genes of the present invention it can be desirable to test hybrids over multiple years at multiple locations in a geographical location where maize is conventionally grown, e.g., in Iowa, Ill. or other locations in the midwestern United States, under “normal” field conditions as well as under stress conditions, e.g., under drought or population density stress.
  • Transgenic plants can be used to provide plant parts according to the invention for regeneration or tissue culture of cells or tissues containing the constructs described herein.
  • Plant parts for these purposes can include leaves, stems, roots, flowers, tissues, epicotyl, meristems, hypocotyls, cotyledons, pollen, ovaries, cells and protoplasts, or any other portion of the plant which can be used to regenerate additional transgenic plants, cells, protoplasts or tissue culture.
  • Seeds of transgenic plants are provided by this invention can be used to propagate more plants containing the trait-improving recombinant DNA constructs of this invention. These descendants are intended to be included in the scope of this invention if they contain a trait-improving recombinant DNA construct of this invention, whether or not these plants are selfed or crossed with different varieties of plants.
  • Transformation vectors were prepared to constitutively transcribe DNA in either sense orientation (for enhanced protein expression) or anti-sense orientation (for endogenous gene suppression) under the control of an enhanced Cauliflower Mosaic Virus 35S promoter (U.S. Pat. No. 5,359,142) directly or indirectly (Moore, et al., PNAS 95:376-381, 1998; Guyer, e.g., Genetics 149: 633-639, 1998; International patent application NO. PCT/EP98/07577).
  • the transformation vectors also contain a bar gene as a selectable marker for resistance to glufosinate herbicide.
  • This example describes a soil drought tolerance screen to identify Arabidopsis plants transformed with recombinant DNA that wilt less rapidly and/or produce higher seed yield when grown in soil under drought conditions
  • T2 seeds were sown in flats filled with Metro/Mix® 200 (The Scotts® Company, USA).
  • Humidity domes were added to each flat and flats were assigned locations and placed in climate-controlled growth chambers. Plants were grown under a temperature regime of 22° C. at day and 20° C. at night, with a photoperiod of 16 hours and average light intensity of 170 ⁇ mol/m 2 /s. After the first true leaves appeared, humidity domes were removed. The plants were sprayed with glufosinate herbicide and put back in the growth chamber for 3 additional days. Flats were watered for 1 hour the week following the herbicide treatment. Watering was continued every seven days until the flower bud primordia became apparent, at which time plants were watered for the last time.
  • plants were evaluated for wilting response and seed yield. Beginning ten days after the last watering, plants were examined daily until 4 plants/line had wilted. In the next six days, plants were monitored for wilting response. Five drought scores were assigned according to the visual inspection of the phenotypes: 1 for healthy, 2 for dark green, 3 for wilting, 4 severe wilting, and 5 for dead. A score of 3 or higher was considered as wilted.
  • seed yield measured as seed weight per plant under the drought condition was characterized for the transgenic plants and their controls and analyzed as a quantitative response according to example 1M.
  • This example sets forth the heat stress tolerance screen to identify Arabidopsis plants transformed with the gene of interest that are more resistant to heat stress based on primarily their seedling weight and root growth under high temperature.
  • T2 seeds were plated on 1 ⁇ 2 X MS salts, 1% phytagel, with 10 ⁇ g/ml BASTA (7 per plate with 2 control seeds; 9 seeds total per plate). Plates were placed at 4° C. for 3 days to stratify seeds. Plates were then incubated at room temperature for 3 hours and then held vertically for 11 additional days at temperature of 34° C. at day and 20° C. at night. Photoperiod was 16 h. Average light intensity was ⁇ 140 ⁇ mol/m 2 /s. After 14 days of growth, plants were scored for glufosinate resistance, root length, final growth stage, visual color, and seedling fresh weight. A photograph of the whole plate was taken on day 14.
  • the seedling weight and root length were analyzed as quantitative responses according to example 1M.
  • the final grow stage at day 14 was scored as success if 50% of the plants had reached 3 rosette leaves and size of leaves are greater than 1 mm (Boyes, et al., (2001) The Plant Cell 13, 1499-1510).
  • the growth stage data was analyzed as a qualitative response according to example 1L.
  • Transgenic plants comprising recombinant DNA expressing protein as set forth in SEQ ID NO: 823, 825, 873, 886, 912, 916, 919, 928, 937, 942, 972, 986, 995, 1074, 1107, 1134, 1136, 1145, 1157, 1173, 1220, 1228, 1242, 1243, 1285, 1377, 1469, 1486, 1489, 1524, 1538, 1546, 1556, 1568, 1571, 1574, 1592, or 1603 showed enhanced heat stress tolerance by the second criteria as illustrated in Example 1L and 1M.
  • This example sets forth the high salinity stress screen to identify Arabidopsis plants transformed with the gene of interest that are tolerant to high levels of salt based on their rate of development, root growth and chlorophyll accumulation under high salt conditions.
  • T2 seeds were plated on glufosinate selection plates containing 90 mM NaCl and grown under standard light and temperature conditions. All seedlings used in the experiment were grown at a temperature of 22° C. at day and 20° C. at night, a 16-hour photoperiod, an average light intensity of approximately 120 umol/m 2 . On day 11, plants were measured for primary root length. After 3 more days of growth (day 14), plants were scored for transgenic status, primary root length, growth stage, visual color, and the seedlings were pooled for fresh weight measurement. A photograph of the whole plate was also taken on day 14.
  • the seedling weight and root length were analyzed as quantitative responses according to example 1M.
  • the final growth stage at day 14 was scored as success if 50% of the plants reached 3 rosette leaves and size of leaves are greater than 1 mm (Boyes, D. C., et al., (2001), The Plant Cell 13, 1499/1510).
  • the growth stage data was analyzed as a qualitative response according to example 1L.
  • Transgenic plants comprising recombinant DNA expressing protein as set forth in SEQ ID NO: 821, 834, 890, 919, 946, 961, 997, 1013, 1080, 1101, 1147, 1160, 1181, 1197, 1200, 1220, 1237, 1248, 1264, 1300, 1313, 1355, 1393, 1397, 1406, 1467, 1496, 1514, 1530 or 1561 showed enhanced salt stress tolerance by the second criteria as illustrated in Example 1L and 1M.
  • T2 seeds were plated on BASTA selection plates containing 3% PEG and grown under standard light and temperature conditions. Seeds were plated on each plate containing 3% PEG, 1 ⁇ 2 X MS salts, 1% phytagel, and 10 ⁇ g/ml glufosinate. Plates were placed at 4° C. for 3 days to stratify seeds. On day 11, plants were measured for primary root length. After 3 more days of growth, e.g., at day 14, plants were scored for transgenic status, primary root length, growth stage, visual color, and the seedlings were pooled for fresh weight measurement. A photograph of the whole plate was taken on day14.
  • Seedling weight and root length were analyzed as quantitative responses according to example 1M.
  • the final growth stage at day 14 was scored as success or failure based on whether the plants reached 3 rosette leaves and size of leaves are greater than 1 mm.
  • the growth stage data was analyzed as a qualitative response according to example 1L.
  • Table 7 A list of recombinant DNA constructs that improve osmotic stress tolerance in transgenic plants illustrated in Table 7.
  • Transgenic plants comprising recombinant DNA expressing protein as set forth in SEQ ID NO: 832, 833, 871, 874, 931, 974, 985, 997, 1021, 1024, 1031, 1043, 1053, 1059, 1060, 1091, 1111, 1115, 1118, 1120, 1124, 1127, 1128, 1159, 1172, 1179, 1185, 1197, 1213, 1226, 1230, 1244, 1253, 1265, 1306, 1320, 1327, 1354, 1355, 1357, 1362, 1367, 1381, 1395, 1398, 1399, 1407, 1462, 1494, 1499, 1500, 1523, 1529, 1532, 1544, 1548, 1569, 1572, 1573, 1595, or 1598 showed enhanced PEG osmotic stress tolerance by the second criteria as illustrated in Example 1L and 1M.
  • This example set forth a screen to identify Arabidopsis plants transformed with the genes of interest that are more tolerant to cold stress subjected during day 8 to day 28 after seed planting. During these crucial early stages, seedling growth and leaf area increase were measured to assess tolerance when Arabidopsis seedlings were exposed to low temperatures. Using this screen, genetic alterations can be found that enable plants to germinate and grow better than wild type plants under sudden exposure to low temperatures.
  • This example sets forth a screen to identify Arabidopsis plants transformed with the genes of interests are resistant to cold stress based on their rate of development, root growth and chlorophyll accumulation under low temperature conditions.
  • T2 seeds were plated and all seedlings used in the experiment were grown at 8° C. Seeds were first surface disinfested using chlorine gas and then seeded on assay plates containing an aqueous solution of 1 ⁇ 2 X Gamborg's B/5 Basal Salt Mixture (Sigma/Aldrich Corp., St. Louis, Mo., USA G/5788), 1% PhytagelTM (Sigma-Aldrich, P-8169), and 10 ug/ml glufosinate with the final pH adjusted to 5.8 using KOH. Test plates were held vertically for 28 days at a constant temperature of 8° C., a photoperiod of 16 hr, and average light intensity of approximately 100 umol/m 2 /s. At 28 days post plating, root length was measured, growth stage was observed, the visual color was assessed, and a whole plate photograph was taken.
  • the root length at day 28 was analyzed as a quantitative response according to example 1M.
  • the growth stage at day 7 was analyzed as a qualitative response according to example 1L.
  • Transgenic plants comprising recombinant DNA expressing protein as set forth in 826, 863, 864, 941, 985, 1071, 1123, 1170, 1194, 1259, 1312, 1339, 1433, 1465, 1543, 1556 showed enhanced cold stress tolerance by the second criterial as illustrated in Example 1L and 1M.
  • This protocol describes a screen to look for Arabidopsis plants that show an attenuated shade avoidance response and/or grow better than control plants under low light intensity. Of particular interest, we were looking for plants that didn't extend their petiole length, had an increase in seedling weight relative to the reference and had leaves that were more close to parallel with the plate surface.
  • T2 seeds were plated on glufosinate selection plates with 1 ⁇ 2 MS medium. Seeds were sown on 1 ⁇ 2 X MS salts, 1% Phytagel, 10 ug/ml BASTA. Plants were grown on vertical plates at a temperature of 22° C. at day, 20° C. at night and under low light (approximately 30 uE/m 2 /s, far/red ratio (655/665/725/735)-0.35 using PLAQ lights with GAM color filter #680). Twenty-three days after seedlings were sown, measurements were recorded including seedling status, number of rosette leaves, status of flower bud, petiole leaf angle, petiole length, and pooled fresh weights. A digital image of the whole plate was taken on the measurement day. Seedling weight and petiole length were analyzed as quantitative responses according to example 1M. The number of rosette leaves, flowering bud formation and leaf angel were analyzed as qualitative responses according to example 1L.
  • seeding weight if p ⁇ 0.05 and delta or risk score mean >0, the transgenic plants showed statistically significant trait enhancement as compared to the reference. If p ⁇ 0.2 and delta or risk score mean >0, the transgenic plants showed a trend of trait enhancement as compared to the reference with p ⁇ 0.2.
  • transgenic plants For “petiole length”, if p ⁇ 0.05 and delta ⁇ 0, the transgenic plants showed statistically significant trait enhancement as compared to the reference. If p ⁇ 0.2 and delta ⁇ 0, the transgenic plants showed a trend of trait enhancement as compared to the reference.
  • Transgenic plants comprising recombinant DNA expressing protein as set forth in SEQ ID NO: 805, 828, 833, 870, 936, 937, 939, 965, 988, 1007, 1010, 1016, 1038, 1050, 1060, 1070, 1079, 1089, 1095, 1100, 1117, 1125, 1129, 1134, 1135, 1145, 1150, 1154, 1155, 1158, 1184, 1204, 1210, 1214, 1216, 1217, 1225, 1226, 1235, 1248, 1252, 1255, 1260, 1271, 1278, 1282, 1283, 1289, 1292, 1297, 1304, 1311, 1312, 1317, 1328, 1336, 1338, 1348, 1363, 1366, 1383, 1386, 1400, 1428, 1448, 1451, 1453, 1462, 1491, 1493, 1505, 1516, 1520, 1528, 1533, 1545, 1579, or 1588 showed
  • This example sets forth a plate based phenotypic analysis platform for the rapid detection of phenotypes that are evident during the first two weeks of growth.
  • the transgenic plants with advantages in seedling growth and development were determined by the seedling weight and root length at day14 after seed planting.
  • T2 seeds were plated on glufosinate selection plates and grown under standard conditions ( ⁇ 100 uE/m 2 /s, 16 h photoperiod, 22° C. at day, 20° C. at night). Seeds were stratified for 3 days at 4° C. Seedlings were grown vertically (at a temperature of 22° C. at day 20° C. at night). Observations were taken on day 10 and day 14. Both seedling weight and root length at day 14 were analyzed as quantitative responses according to example 1M.
  • Root length Root length Seedling weight PEP at day 10 at day 14 at day 14 NUC SEQ Delta Delta Delta SEQ ID ID ID Orientation mean P-value mean P-value 52 855 SENSE 0.091 0.027 0.071 0.018 0.037 0.744 102 905 SENSE 0.188 0.210 0.104 0.247 0.308 0.021 121 924 SENSE 0.242 0.015 0.128 0.063 0.203 0.078 153 956 SENSE 0.153 0.027 0.122 0.197 0.256 0.010 134 937 SENSE 0.329 0.048 0.250 0.085 0.712 0.020 144 947 SENSE 0.127 0.146 0.045 0.566 0.371 0.023 101 904 SENSE 0.537 0.026 0.356 0.004 0.634 0.021 178 981 SENSE 0.372 0.136 0.273 0.033 0.346 0.082 179 982 SENSE 0.404 0.001 0.222 0.051 0.288 0.111
  • Transgenic plants comprising recombinant DNA expressing a protein as set forth in 810, 831, 844, 857, 865, 884, 892, 917, 950, 954, 970, 983, 992, 998, 1004, 1005, 1029, 1033, 1043, 1072, 1101, 1109, 1115, 1133, 1181, 1200, 1284, 1310, 1340, 1384, 1391, 1443, 1449, 1471, 1480, 1483, 1498, 1506, 1508, 1510, 1529, 1548, 1553, 1555, 1556, 1558, 1559, 1564, 1576, or 1577 showed enhanced tolerance to shade or low light condition by the second criterial as illustrated in Example 1L and 1M.
  • This example sets forth a soil based phenotypic platform to identify genes that confer advantages in the processes of leaf development, flowering production and seed maturity to plants.
  • Arabidopsis plants were grown on a commercial potting mixture (Metro Mix 360, Scotts Co., Marysville, Ohio) consisting of 30-40% medium grade horticultural vermiculite, 35-55% sphagnum peat moss, 10-20% processed bark ash, 1-15% pine bark and a starter nutrient charge. Soil was supplemented with Osmocote time-release fertilizer at a rate of 30 mg/ft 3 . T2 seeds were imbibed in 1% agarose solution for 3 days at 4° C. and then sown at a density of ⁇ 5 per 21 ⁇ 2′′ pot. Thirty-two pots were ordered in a 4 by 8 grid in standard greenhouse flat.
  • Plants were grown in environmentally controlled rooms under a 16 h day length with an average light intensity of ⁇ 200 ⁇ moles/m 2 /s. Day and night temperature set points were 22° C. and 20° C., respectively. Humidity was maintained at 65%. Plants were watered by sub-irrigation every two days on average until mid-flowering, at which point the plants were watered daily until flowering was complete.
  • glufosinate was performed to select T2 individuals containing the target transgene. A single application of glufosinate was applied when the first true leaves were visible. Each pot was thinned to leave a single glufosinate-resistant seedling ⁇ 3 days after the selection was applied.
  • the rosette radius was measured at day 25.
  • the silique length was measured at day 40.
  • the plant parts were harvested at day 49 for dry weight measurements if flowering production was stopped. Otherwise, the dry weights of rosette and silique were carried out at day 53.
  • the seeds were harvested at day 58. All measurements were analyzed as quantitative responses according to example 1M.
  • Table 12 A list of recombinant DNA constructs that improve late plant growth and development illustrated in Table 12.
  • the transgenic plants showed statistically significant trait enhancement as compared to the reference. If p ⁇ 0.2 and delta or risk score mean >0, the transgenic plants showed a trend of trait enhancement as compared to the reference.
  • Arabidopsis seedlings become chlorotic and have less biomass.
  • This example sets forth the limited nitrogen tolerance screen to identify Arabidopsis plants transformed with the gene of interest that are altered in their ability to accumulate biomass and/or retain chlorophyll under low nitrogen condition.
  • T2 seeds were plated on glufosinate selection plates containing 0.5 ⁇ N-Free Hoagland's T 0.1 mM NH 4 NO 3 T 0.1% sucrose T 1% phytagel media and grown under standard light and temperature conditions. At 12 days of growth, plants were scored for seedling status (e.g., viable or non-viable) and root length. After 21 days of growth, plants were scored for BASTA resistance, visual color, seedling weight, number of green leaves, number of rosette leaves, root length and formation of flowering buds. A photograph of each plant was also taken at this time point.
  • seedling status e.g., viable or non-viable
  • the seedling weight and root length were analyzed as quantitative responses according to example 1M.
  • the number green leaves, the number of rosette leaves and the flowerbud formation were analyzed as qualitative responses according to example 1L.
  • the leaf color raw data were collected on each plant as the percentages of five color elements (Green, DarkGreen, LightGreen, RedPurple, YellowChlorotic) using a computer imaging system.
  • a statistical logistic regression model was developed to predict an overall value based on five colors for each plant.
  • the transgenic plants For rosette weight, if p ⁇ 0.05 and delta or risk score mean >0, the transgenic plants showed statistically significant trait enhancement as compared to the reference. If p ⁇ 0.2 and delta or risk score mean >0, the transgenic plants showed a trend of trait enhancement as compared to the reference with p ⁇ 0.2. For root length, if p ⁇ 0.05, the transgenic plants showed statistically significant trait enhancement as compared to the reference. If p ⁇ 0.2, the transgenic plants showed a trend of trait enhancement as compared to the reference.
  • Transgenic plants comprising recombinant DNA expressing a protein as set forth in 807, 808, 817, 820, 829, 839, 847, 848, 850, 854, 858, 859, 866, 872, 875, 878, 889, 902, 908, 911, 922, 938, 944, 953, 963, 974, 980, 993, 1001, 1009, 1035, 1042, 1048, 1049, 1054, 1058, 1068, 1076, 1088, 1094, 1096, 1098, 1103, 1104, 1107, 1112, 1113, 1114, 1121, 1152, 1166, 1175, 1192, 1204, 1207, 1215, 1218, 1240, 1246, 1251, 1256, 1266, 1269, 1281, 1283, 1290, 1296, 1298, 1344, 1345, 1356, 1389, 1396, 1400, 1404, 1409, 1425, 1428, 1438, 1441, 1442, 1454,
  • the risk scores from multiple events of the transgene of interest were evaluated for statistical significance by t-test using SAS statistical software (SAS 9, SAS/STAT User's Guide, SAS Institute Inc, Cary, N.C., USA).
  • SAS 9 SAS/STAT User's Guide, SAS Institute Inc, Cary, N.C., USA.
  • RS with a value greater than 0 indicates that the transgenic plants perform better than the reference.
  • RS with a value less than 0 indicates that the transgenic plants perform worse than the reference.
  • the RS with a value equal to 0 indicates that the performance of the transgenic plants and the reference don't show any difference. If p ⁇ 0.05 and risk score mean >0, the transgenic plants showed statistically significant trait enhacement as compared to the reference. If p ⁇ 0.2 and risk score mean >0, the transgenic plants showed a trend of trait enhancement as compared to the reference.
  • the RS from each event was evaluated for statistical significance by t-test using SAS statistical software (SAS 9, SAS/STAT User's Guide, SAS Institute Inc, Cary, N.C., USA).
  • SAS 9 SAS/STAT User's Guide, SAS Institute Inc, Cary, N.C., USA.
  • the RS with a value greater than 0 indicates that the transgenic plants from this event ⁇ perform better than the reference.
  • the RS with a value less than 0 indicates that the transgenic plants from this event perform worse than the reference.
  • the RS with a value equal to 0 indicates that the performance of the transgenic plants from this event and the reference don't show any difference.
  • p ⁇ 0.05 and risk score mean >0 the transgenic plants from this event showed statistically significant trait enhancement as compared to the reference.
  • p ⁇ 0.2 and risk score mean >0 the transgenic plants showed a trend of trait enhancement as compared to the reference. If two or more events of the transgene of interest showed improvement in the same response, the transgene was
  • the measurements (M) of each plant were transformed by log 2 calculation.
  • the Delta was calculated as log 2 M(transgenic) ⁇ log 2 M(reference).
  • Two criteria were used to determine trait enhancement. A transgene of interest could show trait enhancement according to either or both of the two criteria.
  • the measurements (M) of each plant were transformed by log 2 calculation.
  • the Delta was calculated as log 2 M(transgenic) ⁇ log 2 M(reference). If the measured response was Petiole Length for the Low Light assay, Delta was subsequently multiplied by ⁇ 1, to account for the fact that a shorter petiole length is considered an indication of trait enhancement.
  • the Deltas from multiple events of the transgene of interest were evaluated for statistical significance by t-test using SAS statistical software (SAS 9, SAS/STAT User's Guide, SAS Institute Inc, Cary, N.C., USA).
  • Delta with a value greater than 0 indicates that the transgenic plants perform better than the reference.
  • Delta with a value less than 0 indicates that the transgenic plants perform worse than the reference.
  • the Delta with a value equal to 0 indicates that the performance of the transgenic plants and the reference don't show any difference. If p ⁇ 0.05 and risk score mean >0, the transgenic plants showed statistically significant trait enhancement as compared to the reference. If p ⁇ 0.2 and risk score mean >0, the transgenic plants showed a trend of trait enhancement as compared to the reference.
  • the delta from each event was evaluated for statistical significance by t-test using SAS statistical software (SAS 9, SAS/STAT User's Guide, SAS Institute Inc, Cary, N.C., USA).
  • SAS 9 SAS/STAT User's Guide, SAS Institute Inc, Cary, N.C., USA.
  • the Delta with a value greater than 0 indicates that the transgenic plants from this event perform better than the reference.
  • the Delta with a value less than 0 indicates that the transgenic plants from this event perform worse than the reference.
  • the Delta with a value equal to 0 indicates that the performance of the transgenic plants from this event and the reference don't show any difference.
  • p ⁇ 0.05 and delta mean >0 the transgenic plants from this event showed statistically significant trait improvement as compared to the reference.
  • p ⁇ 0.2 and delta mean >0 the transgenic plants showed a trend of trait enhancement as compared to the reference. If two or more events of the transgene of interest showed enhancement in the same response, the transgene was deemed to show trait improvement.
  • This example illustrates the construction of plasmids for transferring recombinant DNA into a plant cell nucleus that can be regenerated into transgenic plants.
  • a base corn transformation vector pMON93039 as set forth in SEQ ID NO: 94614, illustrated in Table 16 and FIG. 1 , is made for use in preparing recombinant DNA for Agrobacterium -mediated transformation into corn tissue.
  • T-AGRtu.nos A 3′ non-translated region of 5849-6101 the nopaline synthase gene of Agrobacterium tumefaciens Ti plasmid which functions to direct polyadenylation of the mRNA.
  • Maintenance OR-Ec.oriV-RK2 The vegetative origin of 6696-7092 in E. coli replication from plasmid RK2.
  • OR-Ec.ori-ColE1 The minimal origin of 9220-9808 replication from the E. coli plasmid ColE1.
  • Primers for PCR amplification of protein coding nucleotides of recombinant DNA are designed at or near the start and stop codons of the coding sequence in order to eliminate most of the 5′ and 3′ untranslated regions.
  • Each recombinant DNA coding for or suppressing a protein identified in Table 2 is amplified by PCR prior to insertion into the insertion site within the gene of interest expression cassette of the base vector.
  • Vectors for use in transformation of soybean and canola can also be prepared. Elements of an exemplary common expression vector pMON82053 (SEQ ID NO: 94615) are shown in Table 17 below and FIG. 2 .
  • T-AGRtu.nos A 3′ non-translated region of the 9466-9718 nopaline synthase gene of Agrobacterium tumefaciens Ti plasmid which functions to direct polyadenylation of the mRNA.
  • Gene of interest P-CaMV.35S-enh Promoter for 35S RNA from CaMV 1-613 expression containing a duplication of the ⁇ 90 to cassette ⁇ 350 region.
  • T-Gb.E6-3b 3′ untranslated region from the fiber 688-1002 protein E6 gene of sea-island cotton.
  • OR-Ec.oriV-RK2 The vegetative origin of replication 5661-6057 E. coli from plasmid RK2.
  • OR-Ec.ori-ColE1 The minimal origin of replication 2945-3533 from the E. coli plasmid ColE1.
  • Primers for PCR amplification of protein coding nucleotides of recombinant DNA are designed at or near the start and stop codons of the coding sequence in order to eliminate most of the 5′ and 3′ untranslated regions.
  • Each recombinant DNA coding for or suppressing a protein identified in Table 2 is amplified by PCR prior to insertion into the insertion site within the gene of interest expression cassette of the base vector.
  • Plasmids for use in transformation of cotton tissue are prepared with elements of expression vector pMON99053 (SEQ ID NO: 94616) are shown in Table 18 below and FIG. 3 .
  • Primers for PCR amplification of protein coding nucleotides of recombinant DNA are designed at or near the start and stop codons of the coding sequence in order to eliminate most of the 5′ and 3′ untranslated regions.
  • Each recombinant DNA coding for or suppressing a protein identified in Table 2 is amplified by PCR prior to insertion into the insertion site within the gene of interest expression cassette of the base vector.
  • T-AGRtu.nos A 3′ non-translated region of 3011-3263 the nopaline synthase gene of Agrobacterium tumefaciens Ti plasmid which functions to direct polyadenylation of the mRNA.
  • Maintenance in OR-Ec.oriV-RK2 The vegetative origin of 3837-4233 E. coli replication from plasmid RK2.
  • OR-Ec.ori-ColE1 The minimal origin of 6363-6949 replication from the E. coli plasmid ColE1.
  • T-Ec.aadA-SPC/STR Promoter for Tn7 7480-7521 adenylyltransferase (AAD(3′′)) CR-Ec.aadA-SPC/STR Coding region for Tn7 7522-8310 adenylyltransferase (AAD(3′′)) conferring spectinomycin and streptomycin resistance.
  • This example illustrates transformation methods in producing a transgenic nucleus in a corn plant cell and the plants, seeds and pollen produced from a transgenic cell with such a nucleus having an enhanced trait, e.g. enhanced water use efficiency, enhanced cold tolerance, increased yield, enhanced nitrogen use efficiency, enhanced seed protein and enhanced seed oil.
  • Plasmid vectors are prepared by cloning DNA identified in Table 2 in the base vector for use in corn transformation of corn tissue.
  • corn plants of a readily transformable line are grown in the greenhouse and ears are harvested when the embryos are 1.5 to 2.0 mm in length. Ears are surface sterilized by spraying or soaking the ears in 80% ethanol, followed by air drying. Immature embryos are isolated from individual kernels on surface sterilized ears. Prior to inoculation of maize cells, Agrobacterium cells are grown overnight at room temperature. Immature maize embryo cells are inoculated with Agrobacterium shortly after excision, and incubated at room temperature with Agrobacterium for 5-20 minutes. Immature embryo plant cells are then co-cultured with Agrobacterium for 1 to 3 days at 23° C. in the dark.
  • Co-cultured embryos are transferred to selection media and cultured for approximately two weeks to allow embryogenic callus to develop.
  • Embryogenic callus is transferred to culture medium containing 100 mg/L paromomycin and subcultured at about two week intervals.
  • Transformed plant cells are recovered 6 to 8 weeks after initiation of selection.
  • immature embryos are cultured for approximately 8-21 days after excision to allow callus to develop. Callus is then incubated for about 30 minutes at room temperature with the Agrobacterium suspension, followed by removal of the liquid by aspiration. The callus and Agrobacterium are co-cultured without selection for 3-6 days followed by selection on paromomycin for approximately 6 weeks, with biweekly transfers to fresh media. Paromomycin resistant calli are identified about 6-8 weeks after initiation of selection.
  • transgenic corn plants To regenerate transgenic corn plants a callus of transgenic plant cells resulting from transformation and selection is placed on media to initiate shoot development into plantlets which are transferred to potting soil for initial growth in a growth chamber at 26° C. followed by a mist bench before transplanting to 5 inch pots where plants are grown to maturity.
  • the regenerated plants are self-fertilized and seed is harvested for use in one or more methods to select seeds, seedlings or progeny second generation transgenic plants (R2 plants) or hybrids, e.g. by selecting transgenic plants exhibiting an enhanced trait as compared to a control plant.
  • Transgenic corn plant cells are transformed with recombinant DNA from each of the genes identified in Table 2. Progeny transgenic plants and seed of the transformed plant cells are screened for enhanced water use efficiency, enhanced cold tolerance, increased yield, enhanced nitrogen use efficiency, enhanced seed protein and enhanced seed oil as obtained in Example 7.
  • This example illustrates plant transformation in producing the transgenic soybean plants of this invention and the production and identification of transgenic seed for transgenic soybean having enhanced water use efficiency, enhanced cold tolerance, increased yield, enhanced nitrogen use efficiency, enhanced seed protein and enhanced seed oil.
  • soybean seeds are imbided overnight and the meristem explants excised.
  • the explants are placed in a wounding vessel.
  • Soybean explants and induced Agrobacterium cells from a strain containing plasmid DNA with the gene of interest cassette and a plant selectable marker cassette are mixed no later than 14 hours from the time of initiation of seed imbibition, and wounded using sonication.
  • explants are placed in co-culture for 2-5 days at which point they are transferred to selection media for 6-8 weeks to allow selection and growth of transgenic shoots.
  • Resistant shoots are harvested approximately 6-8 weeks and placed into selective rooting media for 2-3 weeks. Shoots producing roots are transferred to the greenhouse and potted in soil.
  • a DNA construct can be transferred into the genome of a soybean cell by particle bombardment and the cell regenerated into a fertile soybean plant as described in U.S. Pat. No. 5,015,580, herein incorporated by reference.
  • Transgenic soybean plant cells are transformed with recombinant DNA from each of the genes identified in Table 2.
  • Transgenic progeny plants and seed of the transformed plant cells are screened for enhanced water use efficiency, enhanced cold tolerance, increased yield, enhanced nitrogen use efficiency, enhanced seed protein and enhanced seed oil as obtained in Example 10.
  • Cotton transformation is performed as generally described in WO0036911 and in U.S. Pat. No. 5,846,797.
  • Transgenic cotton plants containing each recombinant DNA having a sequence of SEQ ID NO: 1 through SEQ ID NO: 803 are obtained by transforming with recombinant DNA from each of the genes identified in Table 2.
  • Progeny transgenic plants are selected from a population of transgenic cotton events under specified growing conditions and are compared with control cotton plants.
  • Control cotton plants are substantially the same cotton genotype but without the recombinant DNA, for example, either a parental cotton plant of the same genotype that was not transformed with the identical recombinant DNA or a negative isoline of the transformed plant.
  • a commercial cotton cultivar adapted to the geographical region and cultivation conditions e.g. cotton variety ST474, cotton variety FM 958, and cotton variety Siokra L-23, are used to compare the relative performance of the transgenic cotton plants containing the recombinant DNA.
  • the specified culture conditions are growing a first set of transgenic and control plants under “wet” conditions, e.g. irrigated in the range of 85 to 100 percent of evapotranspiration to provide leaf water potential of ⁇ 14 to ⁇ 18 bars, and growing a second set of transgenic and control plants under “dry” conditions, e.g. irrigated in the range of 40 to 60 percent of evapotranspiration to provide a leaf water potential of ⁇ 21 to ⁇ 25 bars.
  • Pest control such as weed and insect control is applied equally to both wet and dry treatments as needed.
  • Data gathered during the trial includes weather records throughout the growing season including detailed records of rainfall; soil characterization information; any herbicide or insecticide applications; any gross agronomic differences observed such as leaf morphology, branching habit, leaf color, time to flowering, and fruiting pattern; plant height at various points during the trial; stand density; node and fruit number including node above white flower and node is above crack boll measurements; and visual wilt scoring.
  • Cotton boll samples are taken and analyzed for lint fraction and fiber quality. The cotton is harvested at the normal harvest timeframe for the trial area. Enhanced water use efficiency is indicated by increased yield, improved relative water content, enhanced leaf water potential, increased biomass, enhanced leaf extension rates, and improved fiber parameters.
  • transgenic cotton plants of this invention are identified from among the transgenic cotton plants by agronomic trait screening as having increased yield and enhanced water use efficiency.
  • This example illustrates plant transformation in producing the transgenic canola plants of this invention and the production and identification of transgenic seed for transgenic canola having enhanced water use efficiency, enhanced cold tolerance, increased yield, enhanced nitrogen use efficiency, enhanced seed protein and enhanced seed oil.
  • Tissues from in vitro grown canola seedlings are prepared and inoculated with overnight-grown Agrobacterium cells containing plasmid DNA with the gene of interest cassette and a plant selectable marker cassette. Following co-cultivation with Agrobacterium , the infected tissues are allowed to grow on selection to promote growth of transgenic shoots, followed by growth of roots from the transgenic shoots. The selected plantlets are then transferred to the greenhouse and potted in soil. Molecular characterization is performed to confirm the presence of the gene of interest, and its expression in transgenic plants and progenies. Progeny transgenic plants are selected from a population of transgenic canola events under specified growing conditions and are compared with control canola plants.
  • Control canola plants are substantially the same canola genotype but without the recombinant DNA, for example, either a parental canola plant of the same genotype that is not transformed with the identical recombinant DNA or a negative isoline of the transformed plant
  • Transgenic canola plant cells are transformed with recombinant DNA from each of the genes identified in Table 1.
  • Transgenic progeny plants and seed of the transformed plant cells are screened for enhanced water use efficiency, enhanced cold tolerance, increased yield, enhanced nitrogen use efficiency, enhanced seed protein and enhanced seed oil as obtained in Example 7.
  • This example illustrates the identification of homologs of proteins encoded by the DNA identified in Table 1 which is used to provide transgenic seed and plants having enhanced agronomic traits. From the sequence of the homologs, homologous DNA sequence can be identified for preparing additional transgenic seeds and plants of this invention with enhanced agronomic traits.
  • An “All Protein Database” is constructed of known protein sequences using a proprietary sequence database and the National Center for Biotechnology Information (NCBI) non-redundant amino acid database (nr.aa). For each organism from which a polynucleotide sequence provided herein was obtained, an “Organism Protein Database” is constructed of known protein sequences of the organism; it is a subset of the All Protein Database based on the NCBI taxonomy ID for the organism.
  • NCBI National Center for Biotechnology Information
  • the All Protein Database is queried using amino acid sequences provided herein as SEQ ID NO: 804 through SEQ ID NO: 1606 using NCBI “blastp” program with E-value cutoff of 1 e ⁇ 8. Up to 1000 top hits are kept, and separated by organism names. For each organism other than that of the query sequence, a list is kept for hits from the query organism itself with a more significant E-value than the best hit of the organism. The list contains likely duplicated genes of the polynucleotides provided herein, and is referred to as the Core List. Another list is kept for all the hits from each organism, sorted by E-value, and referred to as the Hit List.
  • the Organism Protein Database is queried using polypeptide sequences provided herein as SEQ ID NO: 804 through SEQ ID NO: 1606 using NCBI “blastp” program with E-value cutoff of 1 e ⁇ 4 . Up to 1000 top hits are kept. A BLAST searchable database is constructed based on these hits, and is referred to as “SubDB”. SubDB is queried with each sequence in the Hit List using NCBI “blastp” program with E-value cutoff of leg. The hit with the best E-value is compared with the Core List from the corresponding organism. The hit is deemed a likely ortholog if it belongs to the Core List, otherwise it is deemed not a likely ortholog and there is no further search of sequences in the Hit List for the same organism.
  • ClustalW program is selected for multiple sequence alignments of an amino acid sequence of SEQ ID NO: 804 and its homologs, through SEQ ID NO: 1606 and its homologs.
  • Three major factors affecting the sequence alignments dramatically are (1) protein weight matrices; (2) gap open penalty; (3) gap extension penalty.
  • Protein weight matrices available for ClustalW program include Blosum, Pam and Gonnet series. Those parameters with gap open penalty and gap extension penalty were extensively tested. On the basis of the test results, Blosum weight matrix, gap open penalty of 10 and gap extension penalty of 1 were chosen for multiple sequence alignment.
  • the consensus sequence of SEQ ID NO: 1325 and its 30 homologs were derived according to the procedure described above and is displayed in FIG. 4 .
  • This example illustrates the identification of domain and domain module by Pfam analysis.
  • the amino acid sequence of the expressed proteins that were shown to be associated with an enhanced trait were analyzed for Pfam protein family against the current Pfam collection of multiple sequence alignments and hidden Markov models using the HMMER software in the appended computer listing.
  • the Pfam domain modules and individual protein domain for the proteins of SEQ ID NO: 804 through 1606 are shown in Table 20 and Table 21 respectively.
  • the Hidden Markov model databases for the identified patent families are also in the appended computer listing allowing identification of other homologous proteins and their cognate encoding DNA to enable the full breadth of the invention for a person of ordinary skill in the art. Certain proteins are identified by a single Pfam domain and others by multiple Pfam domains.
  • the protein with amino acids of SEQ ID NO: 830 is characterized by two Pfam domains, e.g. “Lectin_legB” and “Pkinase”. See also the protein with amino acids of SEQ ID NO: 817 which is characterized by four copies of the Pfam domain “Arm”.
  • “score” is the gathering score for the Hidden Markov Model of the domain which exceeds the gathering cutoff reported in Table 22.
  • Transgenic seed and plants in corn, soybean, cotton or canola with recombinant DNA identified in Table 2 are prepared by plant cells transformed with DNA that is stably integrated into the genome of the corn cell.
  • Transgenic corn plant cells are transformed with recombinant DNA from each of the genes identified in Table 2.
  • Progeny transgenic plants and seed of the transformed plant cells are screened for enhanced water use efficiency, enhanced cold tolerance, increased yield, enhanced nitrogen use efficiency, enhanced seed protein and enhanced seed oil as compared to control plants
  • Transgenic corn seeds provided by the present invention are planted in fields with three levels of nitrogen (N) fertilizer being applied, e.g. low level (0 N), medium level (80 lb/ac) and high level (180 lb/ac). A variety of physiological traits are monitored. Plants with enhanced NUE provide higher yield as compared to control plants.
  • N nitrogen
  • Effective selection of enhanced yielding transgenic plants uses hybrid progeny of the transgenic plants for corn, cotton, and canola, or inbred progeny of transgenic plants for soybeanplants plant such as corn, cotton, canola, or inbred plant such as soy, canola and cottoncotton over multiple locations with plants grown under optimal production management practices, and maximum pest control.
  • a target for improved yield is about a 5% to 10% increase or more in yield as compared to yield produced by plants grown from seed for a control plant.
  • Selection methods can be applied in multiple and diverse geographic locations, for example up to 16 or more locations, over one or more planting seasons, for example at least two planting seasons, to statistically distinguish yield improvement from natural environmental effects.
  • the selection process imposes a water withholding period to induce stressdrought followed by watering.
  • a selection process imposes 3 drought/re-water cycles on plants over a total period of 15 days after an initial stress free growth period of 11 days. Each cycle consists of 5 days, with no water being applied for the first four days and a water quenching on the 5th day of the cycle.
  • the primary phenotypes analyzed by the selection method are the changes in plant growth rate as determined by height and biomass during a vegetative drought treatment.
  • Cold field efficacy trial A cold field efficacy trial is used to identify gene constructs that confer enhanced cold vigor at germination and early seedling growth under early spring planting field conditions in conventional-till and simulated no-till environments. Seeds are planted into the ground around two weeks before local farmers begin to plant corn so that a significant cold stress is exerted onto the crop, named as cold treatment. Seeds also are planted under local optimal planting conditions such that the crop has little or no exposure to cold condition, named as normal treatment. At each location, seeds are planted under both cold and normal conditions with 3 repetitions per treatment. Two temperature monitors are set up at each location to monitor both air and soil temperature daily.
  • This example sets forth a high-throughput selection for identifying plant seeds with improvement in seed composition using the Infratec 1200 series Grain Analyzer, which is a near-infrared transmittance spectrometer used to determine the composition of a bulk seed sample (Table 26).
  • Near infrared analysis is a non-destructive, high-throughput method that can analyze multiple traits in a single sample scan.
  • An NIR calibration for the analytes of interest is used to predict the values of an unknown sample.
  • the NIR spectrum is obtained for the sample and compared to the calibration using a complex chemometric software package that provides predicted values as well as information on how well the sample fits in the calibration.
  • Infratec Model 1221, 1225, or 1227 with transport module by Foss North America is used with cuvette, item #1000-4033, Foss North America or for small samples with small cell cuvette, Foss standard cuvette modified by Leon Girard Co. Corn and soy check samples of varying composition maintained in check cell cuvettes are supplied by Leon Girard Co. NIT collection software is provided by Maximum Consulting Inc. Software. Calculations are performed automatically by the software. Seed samples are received in packets or containers with barcode labels from the customer. The seed is poured into the cuvettes and analyzed as received.
  • Typical sample(s) Whole grain corn and soybean seeds
  • Analytical time to Less than 0.75 min per sample run method Total elapsed time per run: 1.5 minute per sample
  • Typical analytical range Determined in part by the specific calibration. Corn - moisture 5-15%, oil 5-20%, protein 5-30%, starch 50-75%, and density 1.0-1.3%. Soybean - moisture 5-15%, oil 15-25%, and protein 35-50%.
  • Cotton transformation is performed as generally described in WO0036911 and in U.S. Pat. No. 5,846,797.
  • Transgenic cotton plants containing each of the recombinant DNA having a sequence of SEQ ID NO: 1 through SEQ ID NO: 803 are obtained by transforming with recombinant DNA from each of the genes identified in Table 2.
  • Progeny transgenic plants are selected from a population of transgenic cotton events under specified growing conditions and are compared with control cotton plants.
  • Control cotton plants are substantially the same cotton genotype but without the recombinant DNA, for example, either a parental cotton plant of the same genotype that was not transformed with the identical recombinant DNA or a negative isoline of the transformed plant.
  • a commercial cotton cultivar adapted to the geographical region and cultivation conditions e.g. cotton variety ST474, cotton variety FM 958, and cotton variety Siokra L-23, are used to compare the relative performance of the transgenic cotton plants containing the recombinant DNA.
  • the specified culture conditions are growing a first set of transgenic and control plants under “wet” conditions, e.g. irrigated in the range of 85 to 100 percent of evapotranspiration to provide leaf water potential of ⁇ 14 to ⁇ 18 bars, and growing a second set of transgenic and control plants under “dry” conditions, e.g. irrigated in the range of 40 to 60 percent of evapotranspiration to provide a leaf water potential of ⁇ 21 to ⁇ 25 bars.
  • Pest control such as weed and insect control is applied equally to both wet and dry treatments as needed.
  • Data gathered during the trial includes weather records throughout the growing season including detailed records of rainfall; soil characterization information; any herbicide or insecticide applications; any gross agronomic differences observed such as leaf morphology, branching habit, leaf color, time to flowering, and fruiting pattern; plant height at various points during the trial; stand density; node and fruit number including node above white flower and node above crack boll measurements; and visual wilt scoring.
  • Cotton boll samples are taken and analyzed for lint fraction and fiber quality. The cotton is harvested at the normal harvest timeframe for the trial area. Enhanced water use efficiency is indicated by increased yield, improved relative water content, enhanced leaf water potential, increased biomass, enhanced leaf extension rates, and improved fiber parameters.
  • transgenic cotton plants of this invention are identified from among the transgenic cotton plants by agronomic trait screening as having increased yield and enhanced water use efficiency.
  • This example illustrates plant transformation in producing the transgenic canola plants of this invention and the production and identification of transgenic seed for transgenic canola having enhanced water use efficiency, enhanced cold tolerance, increased yield, enhanced nitrogen use efficiency, enhanced seed protein and enhanced seed oil.
  • Tissues from in vitro grown canola seedlings are prepared and inoculated with a suspension of overnight grown Agrobacterium containing plasmid DNA with the gene of interest cassette and a plant selectable marker cassette. Following co-cultivation with Agrobacterium , the infected tissues are allowed to grow on selection to promote growth of transgenic shoots, followed by growth of roots from the transgenic shoots. The selected plantlets are then transferred to the greenhouse and potted in soil. Molecular characterizations are performed to confirm the presence of the gene of interest, and its expression in transgenic plants and progenies. Progeny transgenic plants are selected from a population of transgenic canola events under specified growing conditions and are compared with control canola plants.
  • Control canola plants are substantially the same canola genotype but without the recombinant DNA, for example, either a parental canola plant of the same genotype that is not transformed with the identical recombinant DNA or a negative isoline of the transformed plant
  • Transgenic canola plant cells are transformed with recombinant DNA from each of the genes identified in Table 2.
  • Transgenic progeny plants and seed of the transformed plant cells are screened for enhanced water use efficiency, enhanced cold tolerance, increased yield, enhanced nitrogen use efficiency, enhanced seed protein and enhanced seed oil.
  • This example illustrates the preparation and identification by selection of transgenic seeds and plants derived from transgenic plant cells of this invention where the plants and seed are identified by screening for a transgenic plant having an enhanced agronomic trait imparted by expression or suppression of a protein selected from the group including the homologous proteins identified in Example 7.
  • Transgenic plant cells of corn, soybean, cotton, canola, alfalfa, wheat and rice are transformed with recombinant DNA for expressing or suppressing each of the homologs identified in Example 7.
  • Plants are regenerated from the transformed plant cells and used to produce progeny plants and seed that are screened for enhanced water use efficiency, enhanced cold tolerance, increased yield, enhanced nitrogen use efficiency, enhanced seed protein and enhanced seed oil. Plants are identified exhibiting enhanced traits imparted by expression or suppression of the homologous proteins.
  • This example illustrates monocot and dicot plant transformation to produce nuclei of this invention in cells of a transgenic plant by transformation where the recombinant DNA suppresses the expression of an endogenous protein identified in Table 24.
  • Corn, soybean, cotton, or canola tissue are transformed as described in Examples 2-5 using recombinant DNA in the nucleus with DNA that is transcribed into RNA that forms double-stranded RNA targeted to an endogenous gene with DNA encoding the protein.
  • the genes for which the double-stranded RNAs are targeted are the native gene in corn, soybean, cotton or canola that are homologs of the genes encoding the protein that has the function of the protein of Arabidopsis thaliana as identified in Table 24.
  • Pfam module ID Traits 115 AP2 10177 LN 116 zf-C2H2 12155 CS SS 118 F-box::Tub 11873 LN PEG 154 Pex2_Pex12::zf-C3HC4 11113 CS Myb_DNA-binding::Myb_DNA- 188 binding 12325 LN 200 bZIP_1 71228 CK

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Abstract

Transgenic seed for crops with enhanced agronomic traits are provided by trait-improving recombinant DNA in the nucleus of cells of the seed where plants grown from such transgenic seed exhibit one or more enhanced traits as compared to a control plant. Of particular interest are transgenic plants that have increased yield. The present invention also provides recombinant DNA molecules for expression of a protein, and recombinant DNA molecules for suppression of a protein.

Description

    CROSS REFERENCE TO RELATED APPLICATIONS
  • This application claims benefit under 35 U.S.C. §119(e) of U.S. provisional application Ser. No. 61/125,908 filed on Apr. 29, 2008 which is incorporated herein by reference in its entirety.
    • INCORPORATION OF SEQUENCE LISTING
  • Two copies of the sequence listing (Copy 1 and Copy 2) and a computer readable form (CRF) of the sequence listing, all on CD-Rs, each containing the file named 38-21—54976—0001_seqlisting.txt, which is 319,329,870 bytes (measured in MS-WINDOWS) and was created on Apr. 24, 2009, are incorporated herein by reference in their entirety.
    • INCORPORATION OF COMPUTER PROGRAM LISTING
  • A Computer Program Listing folder named 38-21—54976—0001_programListing containing folders “hmmer-2.3.2” and “495pfamDir” is contained on a CD-R and is incorporated herein by reference in their entirety. Folder hmmer-2.3.2 contains the source code and other associated file for implementing the HMMer software for Pfam analysis. Folder 495pfamDir contains 495 profile Hidden Markov Models. Both folders were created on the disk on Apr. 24, 2009 having a total size of 39,755,623 bytes when measured in MS-WINDOWS® operating system. 00001
  • LENGTHY TABLES
    The patent application contains a lengthy table section. A copy of the table is available in electronic form from the USPTO web site (http://seqdata.uspto.gov/?pageRequest=docDetail&DocID=US20130333068A1). An electronic copy of the table will also be available from the USPTO upon request and payment of the fee set forth in 37 CFR 1.19(b)(3).
    • INCORPORATION OF TABLES
  • Two copies of Table 19 (Copy 1 and Copy 2) and a computer readable form (CRF), all on CD-Rs, each containing the file named 38-21—54976—0001_table19.txt, which is 884,823 bytes (measured in MS-WINDOWS), were created on Apr. 24, 2009, and comprise 417 pages when viewed in MS Word, are herein incorporated by reference.
    • FIELD OF THE INVENTION
  • Disclosed herein are recombinant DNA for providing enhanced traits to transgenic plants, seeds, pollen, plant cells and plant nucleui of such transgenic plants, methods of making and using such recombinant DNA, plants, seeds, pollen, plant cells and plant nuclei. Also disclosed are methods of producing hybrid seed comprising such recombinant DNA.
    • SUMMARY OF THE INVENTION
  • This invention provides recombinant DNA comprising polynucleotides characterized by SEQ ID NO: 1-803 and the cognate amino acid sequences of SEQ ID NO: 804-1606. The recombinant DNA is used for providing enhanced traits when stably integrated into the chromosomes and expressed in the nuclei of transgenic plants cells. In some aspects the recombinant DNA encodes a protein; in other aspects the recombinant DNA is transcribed to RNA that suppresses the expression of a native gene.
  • Such recombinant DNA in a plant cell nuclus of this invention is provided in as a construct comprising a promoter that is functional in plant cells and that is operably linked to DNA that encodes a protein or to DNA that results in gene suppression. Such DNA in the construct is sometimes defined by protein domains of an encoded protein targeted for production or suppression e.g. a “Pfam domain module” (as defined herein below) from the group of Pfam domain modules identified in Table 20. Alternatively, e.g. where a Pfam domain module is not available, such DNA in the construct is defined a consensus amino acid sequence of an encoded protein that is targeted for production e.g. a protein having amino acid sequence with at least 90% identity to a consensus amino acid sequence in the group of SEQ ID NO: 94617 through SEQ ID NO: 94734. In a particular aspect of the invention the recombinant DNA is characterized by its cognate amino acid sequence that has at least 70% identity to any of SEQ ID NO: 804-1606.
  • This invention also provides transgenic plant cell nuclei comprising the recombinant DNA of the invention, transgenic plant cells comprising such nuclei, transgenic plants comprising a plurality of such transgenic plant cells, and transgenic seeds and transgenic pollen of such plants. Such transgenic plants are selected from a population of transgenic plants regenerated from plant cells transformed with recombinant DNA by screening transgenic plants for an enhanced trait as compared to control plants. The enhanced trait is one or more of enhanced water use efficiency, enhanced cold tolerance, increased yield, enhanced nitrogen use efficiency, enhanced heat tolerance, enhanced shade tolerance, enhanced high salinity tolerance, enhanced seed protein and enhanced seed oil. Such recombinant DNA in a plant cell nuclus of this invention is provided in as a construct comprising a promoter that is functional in plant cells and that is operably linked to DNA that encodes a protein or to DNA that results in gene suppression. Such DNA in the construct is sometimes defined by protein domains of an encoded protein targeted for production or suppression, e.g. a “Pfam domain module” (as defined herein below) from the group of Pfam domain modules identified in Table 20. Alternatively, e.g. where a Pfam domain module is not available, such DNA in the construct is defined a consensus amino acid sequence of an encoded protein that is targeted for production e.g. a protein having amino acid sequence with at least 90% identity to a consensus amino acid sequence in the group of SEQ ID NO: 94617 through SEQ ID NO: 94734.
  • In another aspect of the invention the plant cell nuclei, cells, plants, seeds, and pollen further comprise DNA expressing a protein that provides tolerance from exposure to an herbicide applied at levels that are lethal to a wild type plant cell.
  • This invention also provides methods for manufacturing non-natural, transgenic seed that can be used to produce a crop of transgenic plants with an enhanced trait resulting from expression of stably-integrated, recombinant DNA in the nucleus of the plant cells. More specifically the method comprises (a) screening a population of plants for an enhanced trait and recombinant DNA, where individual plants in the population can exhibit the trait at a level less than, essentially the same as or greater than the level that the trait is exhibited in control plants which do not express the recombinant DNA; (b) selecting from the population one or more plants that exhibit the trait at a level greater than the level that said trait is exhibited in control plants and (c) collecting seed from a selected plant. Such method further comprises steps (a) verifying that the recombinant DNA is stably integrated in said selected plants; and (b) analyzing tissue of a selected plant to determine the production of a protein having the function of a protein encoded by a recombinant DNA with a sequence of one of SEQ ID NO: 1-803; in one aspect of the invention the plants in the population further comprise DNA expressing a protein that provides tolerance to exposure to an herbicide applied at levels that are lethal to wild type plant cells and where the selecting is effected by treating the population with the herbicide, e.g. a glyphosate, dicamba, or glufosinate compound. In another aspect of the invention the plants are selected by identifying plants with the enhanced trait. The methods are used for manufacturing corn, soybean, cotton, canola, alfalfa, wheat, rice seed or any combinations thererof selected as having one of the enhanced traits described above.
  • Another aspect of the invention provides a method of producing hybrid corn seed comprising acquiring hybrid corn seed from a herbicide tolerant corn plant which also has a nucleus of this invention with stably-integrated, recombinant DNA. The method further comprises producing corn plants from said hybrid corn seed, where a fraction of the plants produced from said hybrid corn seed is homozygous for said recombinant DNA, a fraction of the plants produced from said hybrid corn seed is hemizygous for said recombinant DNA, and a fraction of the plants produced from said hybrid corn seed has none of said recombinant DNA; selecting corn plants which are homozygous and hemizygous for said recombinant DNA by treating with an herbicide; collecting seed from herbicide-treated-surviving corn plants and planting said seed to produce further progeny corn plants; repeating the selecting and collecting steps at least once to produce an inbred corn line; and crossing the inbred corn line with a second corn line to produce hybrid seed.
  • Still other aspects of this invention relate to transgenic plants with enhanced water use efficiency or enhanced nitrogen use efficiency. For instance, this invention provides methods of growing a corn, cotton, soybean, or canola crop without irrigation water comprising planting seed having plant cells of the invention which are selected for enhanced water use efficiency. Alternatively methods comprise applying reduced irrigation water, e.g. providing up to 300 millimeters of ground water during the production of a corn crop. This invention also provides methods of growing a corn, cotton, soybean or canola crop without added nitrogen fertilizer comprising planting seed having plant cells of the invention which are selected for enhanced nitrogen use efficiency.
    • BRIEF DESCRIPTION OF THE DRAWINGS
  • FIGS. 1, 2 and 3 illustrate plasmid maps.
  • FIG. 4 illustrates a consensus amino acid sequence of SEQ ID NO: 1325 and its homologs.
    •  DETAILED DESCRIPTION OF THE INVENTION
  • In the attached sequence listing:
  • SEQ ID NO: 1-803 are nucleotide sequences of the coding strand of DNA for “genes” used in the recombinant DNA imparting an enhanced trait in plant cells, where each represents a coding sequence for a protein;
  • SEQ ID NO: 804-1606 are amino acid sequences of the cognate protein of the “genes” with nucleotide coding sequence 1-803;
  • SEQ ID NO: 1607-94613 are amino acid sequences of homologous proteins;
  • SEQ ID NO: 94614 is a nucleotide sequence of a plasmid base vector for corn transformation; and
  • SEQ ID NO: 94615 is a DNA sequence of a plasmid base vector for soybean transformation.
  • SEQ ID NO: 94616 is a DNA sequence of a plasmid base vector for cotton transformation.
  • SEQ ID NO: 94617-94734 are consensus sequences.
  • Table 1 lists the protein SEQ ID NOs and their corresponding consensus SEQ ID NOs.
  • TABLE 1
    NUC SEQ PEP CONSENSUS
    ID NO SEQ ID NO GENE ID SEQ ID NO
    5 808 CGPG1067 94617
    6 809 CGPG1095 94618
    7 810 CGPG1101 94619
    8 811 CGPG1109 94620
    10 813 CGPG1155 94621
    12 815 CGPG1171 94622
    13 816 CGPG1177 94623
    19 822 CGPG1279 94624
    20 823 CGPG1304 94625
    22 825 CGPG1327 94626
    57 860 CGPG1723 94627
    78 881 CGPG1972 94628
    88 891 CGPG2041 94629
    90 893 CGPG2070 94630
    98 901 CGPG2126 94631
    99 902 CGPG213 94632
    106 909 CGPG2193 94633
    108 911 CGPG2224 94634
    118 921 CGPG2319 94635
    121 924 CGPG2359 94636
    130 933 CGPG2408 94637
    133 936 CGPG2414 94638
    156 959 CGPG2863 94639
    172 975 CGPG3183 94640
    180 983 CGPG3280 94641
    191 994 CGPG3405 94642
    200 1003 CGPG3598 94643
    202 1005 CGPG3606 94644
    203 1006 CGPG3610 94645
    204 1007 CGPG3620 94646
    222 1025 CGPG3820 94647
    226 1029 CGPG3958 94648
    227 1030 CGPG3981 94649
    236 1039 CGPG4083 94650
    256 1059 CGPG4347 94651
    257 1060 CGPG4354 94652
    273 1076 CGPG4559 94653
    294 1097 CGPG4802 94654
    295 1098 CGPG4822 94655
    296 1099 CGPG4826 94656
    297 1100 CGPG4833 94657
    298 1101 CGPG4841 94658
    332 1135 CGPG5208 94659
    393 1196 CGPG5750 94660
    394 1197 CGPG5751 94661
    413 1216 CGPG5922 94662
    415 1218 CGPG5964 94663
    432 1235 CGPG6137 94664
    456 1259 CGPG6358 94665
    501 1304 CGPG6803 94666
    504 1307 CGPG6812 94667
    506 1309 CGPG6827 94668
    509 1312 CGPG6859 94669
    514 1317 CGPG6886 94670
    518 1321 CGPG6903 94671
    520 1323 CGPG6933 94672
    522 1325 CGPG6944 94673
    523 1326 CGPG6949 94674
    525 1328 CGPG6989 94675
    527 1330 CGPG7003 94676
    528 1331 CGPG7009 94677
    531 1334 CGPG7062 94678
    532 1335 CGPG7064 94679
    534 1337 CGPG7109 94680
    535 1338 CGPG7123 94681
    538 1341 CGPG7159 94682
    541 1344 CGPG7224 94683
    569 1372 CGPG7505 94684
    576 1379 CGPG7540 94685
    582 1385 CGPG7568 94686
    583 1386 CGPG7571 94687
    584 1387 CGPG7587 94688
    585 1388 CGPG7591 94689
    588 1391 CGPG7633 94690
    601 1404 CGPG7774 94691
    602 1405 CGPG7777 94692
    606 1409 CGPG7792 94693
    613 1416 CGPG7851 94694
    616 1419 CGPG7865 94695
    622 1425 CGPG7934 94696
    623 1426 CGPG7949 94697
    624 1427 CGPG7954 94698
    627 1430 CGPG7969 94699
    641 1444 CGPG8072 94700
    642 1445 CGPG8075 94701
    644 1447 CGPG8100 94702
    645 1448 CGPG8101 94703
    646 1449 CGPG8104 94704
    647 1450 CGPG8108 94705
    648 1451 CGPG8116 94706
    651 1454 CGPG8138 94707
    654 1457 CGPG8163 94708
    659 1462 CGPG8204 94709
    662 1465 CGPG8234 94710
    671 1474 CGPG8345 94711
    686 1489 CGPG8515 94712
    688 1491 CGPG8518 94713
    690 1493 CGPG8523 94714
    691 1494 CGPG8528 94715
    693 1496 CGPG8553 94716
    694 1497 CGPG8562 94717
    697 1500 CGPG8589 94718
    699 1502 CGPG8592 94719
    703 1506 CGPG8648 94720
    706 1509 CGPG8678 94721
    707 1510 CGPG8694 94722
    709 1512 CGPG8737 94723
    710 1513 CGPG8745 94724
    712 1515 CGPG8749 94725
    715 1518 CGPG8781 94726
    760 1563 CGPG9075 94727
    762 1565 CGPG9094 94728
    769 1572 CGPG9136 94729
    770 1573 CGPG9156 94730
    773 1576 CGPG9173 94731
    781 1584 CGPG921 94732
    788 1591 CGPG9281 94733
    792 1595 CGPG9304 94734
  • The nuclei of this invention are identified by screening transgenic plants for one or more traits including enhanced drought stress tolerance, enhanced heat stress tolerance, enhanced cold stress tolerance, enhanced high salinity stress tolerance, enhanced low nitrogen availability stress tolerance, enhanced shade stress tolerance, enhanced plant growth and development at the stages of seed imbibition through early vegetative phase, and enhanced plant growth and development at the stages of leaf development, flower production and seed maturity.
  • “As used herein a “plant cell” means a plant cell that is transformed with stably-integrated, non-natural, recombinant DNA, e.g. by Agrobacterium-mediated transformation or by bombardment using microparticles coated with recombinant DNA or other means. A plant cell of this invention can be an originally-transformed plant cell that exists as a microorganism or as a progeny plant cell that is regenerated into differentiated tissue, e.g. into a transgenic plant with stably-integrated, non-natural recombinant DNA, or seed or pollen derived from a progeny transgenic plant.
  • As used herein a “transgenic plant” means a plant whose genome has been altered by the stable integration of recombinant DNA. A transgenic plant includes a plant regenerated from an originally-transformed plant cell and progeny transgenic plants from later generations or crosses of a transformed plant.
  • As used herein “recombinant DNA” means DNA which has been a genetically engineered and constructed outside of a cell including DNA containing naturally occurring DNA or cDNA or synthetic DNA.
  • As used herein a “homolog” means a protein in a group of proteins that perform the same biological function, e.g. proteins that belong to the same Pfam protein family and that provide a common enhanced trait in transgenic plants of this invention. Homologs are expressed by homologous genes. Homologous genes include naturally occurring alleles and artificially-created variants. Degeneracy of the genetic code provides the possibility to substitute at least one base of the protein encoding sequence of a gene with a different base without causing the amino acid sequence of the polypeptide produced from the gene to be changed. Hence, a polynucleotide in the present invention can have any base sequence that has been changed from SEQ ID NO:1 through SEQ ID NO: 803 through substitution in accordance with degeneracy of the genetic code. Homologs are proteins that, when optimally aligned, have at least about 60% identity, about 70% or higher, at least about 80% and at least about 90% identity over the full length of a protein identified as being associated with imparting an enhanced trait when expressed in plant cells. Homologs include proteins with an amino acid sequence that has at least about 90% identity to a consensus amino acid sequence of proteins and homologs disclosed herein.
  • Homologs are identified by comparison of amino acid sequence, e.g. manually or by use of a computer-based tool using known homology-based search algorithms such as those commonly known and referred to as BLAST, FASTA, and Smith-Waterman. A local sequence alignment program, e.g. BLAST, can be used to search a database of sequences to find similar sequences, and the summary Expectation value (E-value) used to measure the sequence base similarity. As a protein hit with the best E-value for a particular organism could be an ortholog or the only ortholog, a reciprocal query is used in the present invention to filter hit sequences with significant E-values for ortholog identification. The reciprocal query entails search of the significant hits against a database of amino acid sequences from the base organism that are similar to the sequence of the query protein. A hit can be identified as an ortholog, when the reciprocal query's best hit is the query protein itself or a protein encoded by a duplicated gene after speciation. A further aspect of the homologs encoded by DNA in the transgenic plants of the invention are those proteins that differ from a disclosed protein as the result of deletion or insertion of one or more amino acids in a native sequence.
  • Homologous genes are genes which encode proteins with the same or similar biological function to the protein encoded by the second gene. Homologous genes can be generated by the event of speciation (see ortholog) or by the event of genetic duplication (see paralog). “Orthologs” refer to a set of homologous genes in different species that evolved from a common ancestral gene by specification. Normally, orthologs retain the same function in the course of evolution; and “paralogs” refer to a set of homologous genes in the same species that have diverged from each other as a consequence of genetic duplication. Thus, homologous genes can be from the same or a different organism. As used herein, “homolog” means a protein that performs the same biological function as a second protein including those identified by sequence identity search.
  • As used herein, “percent identity” means the extent to which two optimally aligned DNA or protein segments are invariant throughout a window of alignment of components, for example nucleotide sequence or amino acid sequence. An “identity fraction” for aligned segments of a test sequence and a reference sequence is the number of identical components that are shared by sequences of the two aligned segments divided by the total number of sequence components in the reference segment over a window of alignment which is the smaller of the full test sequence or the full reference sequence. “Percent identity” (“% identity”) is the identity fraction times 100. Such optimal alignment is understood to be deemed as local alignment of DNA sequences. For protein alignment, a local alignment of protein sequences should allow introduction of gaps to achieve optimal alignment. Percent identity is calculated over the aligned length not including the gaps introduced by the alignment per se.
  • As used herein, “promoter” means regulatory DNA for initializing transcription. A “plant promoter” is a promoter capable of initiating transcription in plant cells whether or not its origin is a plant cell, e.g. is it well known that Agrobacterium promoters are functional in plant cells. Thus, plant promoters include promoter DNA obtained from plants, plant viruses and bacteria such as Agrobacterium and Bradyrhizobium bacteria. Examples of promoters under developmental control include promoters that preferentially initiate transcription in certain tissues, such as leaves, roots, or seeds. Such promoters are referred to as “tissue preferred”. Promoters that initiate transcription only in certain tissues are referred to as “tissue specific”. A “cell type” specific promoter primarily drives expression in certain cell types in one or more organs, for example, vascular cells in roots or leaves. An “inducible” or “repressible” promoter is a promoter which is under environmental control. Examples of environmental conditions that can effect transcription by inducible promoters include anaerobic conditions, or certain chemicals, or the presence of light. Tissue specific, tissue preferred, cell type specific, and inducible promoters constitute the class of “non-constitutive” promoters. A “constitutive” promoter is a promoter which is active under most conditions.
  • As used herein, “operably linked” refers to the association of two or more nucleic acid elements in a recombinant DNA construct, e.g. as when a promoter is operably linked with DNA that is transcribed to RNA whether for expressing or suppressing a protein. Recombinant DNA constructs can be designed to express a protein which can be an endogenous protein, an exogenous homologue of an endogenous protein or an exogenous protein with no native homologue. Alternatively, recombinant DNA constructs can be designed to suppress the level of an endogenous protein, e.g. by suppression of the native gene. Such gene suppression can be effectively employed through a native RNA interference (RNAi) mechanism in which recombinant DNA comprises both sense and antisense oriented DNA matched to the gene targeted for suppression where the recombinant DNA is transcribed into RNA that can form a double-strand to initiate an RNAi mechanism. Gene suppression can also be effected by recombinant DNA that comprises antisense oriented DNA matched to the gene targeted for suppression. Gene suppression can also be effected by recombinant DNA that comprises DNA that is transcribed to a microRNA matched to the gene targeted for suppression. In the examples illustrating the invention recombinant DNA for effecting gene suppression that imparts is identified by the term “antisense”. It will be understood by a person of ordinary skill in the art that any of the ways of effecting gene suppression are contemplated and enabled by a showing of one approach to gene suppression.
  • As used herein “expressed” means produced, e.g. a protein is expressed in a plant cell when its cognate DNA is transcribed to mRNA that is translated to the protein.
  • As used herein “suppressed” means decreased, e.g. a protein is suppressed in a plant cell when there is a decrease in the amount and/or activity of the protein in the plant cell. The presence or activity of the protein can be decreased by any amount up to and including a total loss of protein expression and/or activity.
  • As used herein a “control plant” means a plant that does not contain the recombinant DNA that expressed a protein that imparts an enhanced trait. A control plant is to identify and select a transgenic plant that has an enhance trait. A suitable control plant can be a non-transgenic plant of the parental line used to generate a transgenic plant, e.g. devoid of recombinant DNA. A suitable control plant can in some cases be a progeny of a hemizygous transgenic plant line that is does not contain the recombinant DNA, known as a negative segregant.
  • “Trait enhancement” means a detectable and desirable difference in a characteristic in a transgenic plant relative to a control plant or a reference. In some cases, the trait enhancement can be measured quantitatively. For example, the trait enhancement can entail at least about 2% difference in an observed trait, at least about 5% desirable difference, at least about 10% difference, at least about 20% difference, at least about 30% difference, at least about 40%, at least about 50% difference, at least about 60%, at least about 70% difference, at least about 80% difference, at least about 90% difference, or at least about a 100% difference, or an even greater difference. In other cases, the trait enhancement is only measured qualitatively. It is known that there can be a natural variation in a trait. Therefore, the trait enhancement observed entails a change of the normal distribution of the trait in the transgenic plant compared with the trait distribution observed in a control plant or a reference, which is evaluated by statistical methods provided herein. Trait enhancement includes, but is not limited to, yield increase, including increased yield under non-stress conditions and increased yield under environmental stress conditions. Stress conditions can include, for example, drought, shade, fungal disease, viral disease, bacterial disease, insect infestation, nematode infestation, cold temperature exposure, heat exposure, osmotic stress, reduced nitrogen nutrient availability, reduced phosphorus nutrient availability, high plant density, or any combinations thereof.
  • “Yield” can be affected by many properties including without limitation, plant height, pod number, pod position on the plant, number of internodes, incidence of pod shatter, grain size, efficiency of nodulation and nitrogen fixation, efficiency of nutrient assimilation, resistance to biotic and abiotic stress, carbon assimilation, plant architecture, resistance to lodging, percent seed germination, seedling vigor, and juvenile traits. Yield can also be affected by efficiency of germination (including germination in stressed conditions), growth rate (including growth rate in stressed conditions), ear number, seed number per ear, seed size, composition of seed (starch, oil, protein) and characteristics of seed fill.
  • Increased yield of a transgenic plant of the present invention can be measured in a number of ways, including test weight, seed number per plant, seed weight, seed number per unit area (e.g. seeds, or weight of seeds, per acre), bushels per acre, tonnes per acre, tons per acre, kilo per hectare. For example, maize yield can be measured as production of shelled corn kernels per unit of production area, for example in bushels per acre or metric tons per hectare, often reported on a moisture adjusted basis, for example at 15.5 percent moisture. Increased yield can result from improved utilization of key biochemical compounds, such as nitrogen, phosphorous and carbohydrate, or from improved responses to environmental stresses, such as cold, heat, drought, salt, and attack by pests or pathogens. Recombinant DNA used in this invention can also be used to provide plants having improved growth and development, and ultimately increased yield, as the result of modified expression of plant growth regulators or modification of cell cycle or photosynthesis pathways. Also of interest is the generation of transgenic plants that demonstrate enhanced yield with respect to a seed component that could correspond to an increase in overall plant yield. Such properties include enhancements in seed oil, seed molecules such as tocopherol, protein and starch, or oil particular oil components as can be manifest by alterations in the ratios of seed components.
  • “Stress condition” means a condition unfavorable for a plant, which adversely affect plant metabolism, growth and/or development. A plant under the stress condition typically shows reduced germination rate, retarded growth and development, reduced photosynthesis rate, and eventually leading to reduction in yield. Specifically, “water deficit stress” used herein refers to the sub-optimal conditions for water and humidity needed for normal growth of natural plants. Relative water content (RWC) can be used as a physiological measure of plant water deficit. It measures the effect of osmotic adjustment in plant water status, when a plant is under stressed conditions. Conditions which can result in water deficit stress include, but are not limited to, heat, drought, high salinity and PEG induced osmotic stress.
  • “Cold stress” means the exposure of a plant to a temperatures below (two or more degrees Celsius below) those normal for a particular species or particular strain of plant.
  • “Nitrogen nutrient” means any one or any mix of the nitrate salts commonly used as plant nitrogen fertilizer, including, but not limited to, potassium nitrate, calcium nitrate, sodium nitrate, ammonium nitrate. The term ammonium as used herein means any one or any mix of the ammonium salts commonly used as plant nitrogen fertilizer, e.g., ammonium nitrate, ammonium chloride, ammonium sulfate, etc.
  • “Low nitrogen availability stress” means a plant growth condition that does not contain sufficient nitrogen nutrient to maintain a healthy plant growth and/or for a plant to reach its typical yield under a sufficient nitrogen growth condition. For example, a limiting nitrogen condition can refers to a growth condition with 50% or less of the conventional nitrogen inputs. “Sufficient nitrogen growth condition” means a growth condition where the soil or growth medium contains or receives optimal amounts of nitrogen nutrient to sustain a healthy plant growth and/or for a plant to reach its typical yield for a particular plant species or a particular strain. One skilled in the art would recognize what constitute such soil, media and fertilizer inputs for most plant species.
  • “Shade stress” means a growth condition that has limited light availability that triggers the shade avoidance response in plant. Plants are subject to shade stress when localized at lower part of the canopy, or in close proximity of neighboring vegetation. Shade stress can become exacerbated when the planting density exceeds the average prevailing density for a particular plant species.
  • In some embodiments of the invention a constitutively active mutant, is constructed to achieve the desired effect. In other embodiments of the invention, a dominant negative gene is constructed to adversely affect the normal, wild-type gene product within the same cell.
  • DNA constructs are assembled using methods well known to persons of ordinary skill in the art and typically comprise a promoter operably linked to DNA, the expression of which provides the enhanced agronomic trait. Other construct components can include additional regulatory elements, such as 5′ leaders and introns for enhancing transcription, 3′ untranslated regions (such as polyadenylation signals and sites), DNA for transit or signal peptides.
  • Numerous promoters that are active in plant cells have been described in the literature. These include promoters present in plant genomes as well as promoters from other sources, including nopaline synthase (NOS) promoter and octopine synthase (OCS) promoters carried on tumor-inducing plasmids of Agrobacterium tumefaciens and the CaMV35S promoters from the cauliflower mosaic virus as disclosed in U.S. Pat. Nos. 5,164,316 and 5,322,938. Promoters derived from plant genes are found in U.S. Pat. No. 5,641,876, which discloses a rice actin promoter, U.S. Pat. No. 7,151,204, which discloses a maize chloroplast aldolase promoter and a maize aldolase (FDA) promoter, and U.S. Patent Application Publication 2003/0131377 A1, which discloses a maize nicotianamine synthase promoter, all of which are incorporated herein by reference. These and numerous other promoters that function in plant cells are known to those skilled in the art and available for use in recombinant polynucleotides of the present invention to provide for expression of desired genes in transgenic plant cells.
  • In other aspects of the invention, preferential expression in plant green tissues is desired. Promoters of interest for such uses include those from genes such as Arabidopsis thaliana ribulose-1,5-bisphosphate carboxylase (Rubisco) small subunit (Fischhoff et al. (1992) Plant Mol Biol. 20:81-93), aldolase and pyruvate orthophosphate dikinase (PPDK) (Taniguchi et al. (2000) Plant Cell Physiol. 41(1):42-48).
  • Furthermore, the promoters can be altered to contain multiple “enhancer sequences” to assist in elevating gene expression. Such enhancers are known in the art. By including an enhancer sequence with such constructs, the expression of the selected protein can be enhanced. These enhancers often are found 5′ to the start of transcription in a promoter that functions in eukaryotic cells, but can often be inserted upstream (5′) or downstream (3′) to the coding sequence. In some instances, these 5′ enhancing elements are introns. In one embodiment, enhancers are the 5′ introns of the rice actin 1 (see U.S. Pat. No. 5,641,876) and rice actin 2 genes, the maize alcohol dehydrogenase gene intron, the maize heat shock protein 70 gene intron (U.S. Pat. No. 5,593,874) and the maize shrunken 1 gene.
  • In other aspects of the invention, sufficient expression in plant seed tissues is desired to affect improvements in seed composition. Exemplary promoters for use for seed composition modification include promoters from seed genes such as napin (U.S. Pat. No. 5,420,034), maize L3 oleosin (U.S. Pat. No. 6,433,252), zein Z27 (Russell et al. (1997) Transgenic Res. 6(2):157-166), globulin 1 (Belanger et al (1991) Genetics 129:863-872), glutelin 1 (Russell (1997) supra), and peroxiredoxin antioxidant (Per1) (Stacy et al. (1996) Plant Mol Biol. 31(6):1205-1216).
  • Recombinant DNA constructs prepared in accordance with the invention will also generally include a 3′ element that typically contains a polyadenylation signal and site. Well-known 3′ elements include those from Agrobacterium tumefaciens genes such as nos 3′, tml 3′, tmr 3′, tms 3′, ocs 3′, tr7 3′, for example disclosed in U.S. Pat. No. 6,090,627, incorporated herein by reference; 3′ elements from plant genes such as wheat (Triticum aesevitum) heat shock protein 17 (Hsp17 3′), a wheat ubiquitin gene, a wheat fructose-1,6-biphosphatase gene, a rice glutelin gene, a rice lactate dehydrogenase gene and a rice beta-tubulin gene, all of which are disclosed in U.S. published patent application 2002/0192813 A1, incorporated herein by reference; and the pea (Pisum sativum) ribulose biphosphate carboxylase gene (rbs 3′), and 3′ elements from the genes within the host plant.
  • Constructs and vectors can also include a transit peptide for targeting of a gene to a plant organelle, particularly to a chloroplast, leucoplast or other plastid organelle. For descriptions of the use of chloroplast transit peptides see U.S. Pat. No. 5,188,642 and U.S. Pat. No. 5,728,925, incorporated herein by reference. For description of the transit peptide region of an Arabidopsis EPSPS gene can be in the present invention, see Klee, H. J. et al (MGG (1987) 210:437-442).
  • Gene suppression includes any of the well-known methods for suppressing transcription of a gene or the accumulation of the mRNA corresponding to that gene thereby preventing translation of the transcript into protein. Posttranscriptional gene suppression is mediated by transcription of RNA that forms double-stranded RNA (dsRNA) having homology to a gene targeted for suppression. Suppression can also be achieved by insertion mutations created by transposable elements can also prevent gene function. For example, in many dicot plants, transformation with the T-DNA of Agrobacterium can be readily achieved and large numbers of transformants can be rapidly obtained. Also, some species have lines with active transposable elements that can efficiently be used for the generation of large numbers of insertion mutations, while some other species lack such options. Mutant plants produced by Agrobacterium or transposon mutagenesis and having altered expression of a polypeptide of interest can be identified using the polynucleotides of the present invention. For example, a large population of mutated plants can be screened with polynucleotides encoding the polypeptide of interest to detect mutated plants having an insertion in the gene encoding the polypeptide of interest.
  • Transgenic plants comprising or derived from plant cells of this invention transformed with recombinant DNA can be further enhanced with stacked traits, e.g. a crop plant having an enhanced trait resulting from expression of DNA disclosed herein in combination with herbicide and/or pest resistance traits. For example, genes of the current invention can be stacked with other traits of agronomic interest, such as a trait providing herbicide resistance, or insect resistance, such as using a gene from Bacillus thuringensis to provide resistance against lepidopteran, coliopteran, homopteran, hemiopteran, and other insects. Herbicides for which transgenic plant tolerance has been demonstrated and the method of the present invention can be applied include, but are not limited to, glyphosate, dicamba, glufosinate, sulfonylurea, bromoxynil and norflurazon herbicides. Polynucleotide molecules encoding proteins involved in herbicide tolerance are well-known in the art and include, but are not limited to, a polynucleotide molecule encoding 5-enolpyruvylshikimate-3-phosphate synthase (EPSPS) disclosed in U.S. Pat. Nos. 5,094,945; 5,627,061; 5,633,435 and 6,040,497 for imparting glyphosate tolerance; polynucleotide molecules encoding a glyphosate oxidoreductase (GOX) disclosed in U.S. Pat. No. 5,463,175 and a glyphosate-N-acetyl transferase (GAT) disclosed in U.S. Patent Application publication 2003/0083480 A1 also for imparting glyphosate tolerance; dicamba monooxygenase disclosed in U.S. Patent Application publication 2003/0135879 A1 for imparting dicamba tolerance; a polynucleotide molecule encoding bromoxynil nitrilase (Bxn) disclosed in U.S. Pat. No. 4,810,648 for imparting bromoxynil tolerance; a polynucleotide molecule encoding phytoene desaturase (crtl) described in Misawa et al, (1993) Plant J. 4:833-840 and in Misawa et al, (1994) Plant J. 6:481-489 for norflurazon tolerance; a polynucleotide molecule encoding acetohydroxyacid synthase (AHAS, aka ALS) described in Sathasiivan et al. (1990) Nucl. Acids Res. 18:2188-2193 for imparting tolerance to sulfonylurea herbicides; polynucleotide molecules known as bar genes disclosed in DeBlock, et al. (1987) EMBO J. 6:2513-2519 for imparting glufosinate and bialaphos tolerance; polynucleotide molecules disclosed in U.S. Patent Application Publication 2003/010609 A1 for imparting N-amino methyl phosphonic acid tolerance; polynucleotide molecules disclosed in U.S. Pat. No. 6,107,549 for impartinig pyridine herbicide resistance; molecules and methods for imparting tolerance to multiple herbicides such as glyphosate, atrazine, ALS inhibitors, isoxoflutole and glufosinate herbicides are disclosed in U.S. Pat. No. 6,376,754 and U.S. Patent Application Publication 2002/0112260, all of said U.S. patents and patent application Publications are incorporated herein by reference. Molecules and methods for imparting insect/nematode/virus resistance are disclosed in U.S. Pat. Nos. 5,250,515; 5,880,275; 6,506,599; 5,986,175 and U.S. Patent Application Publication 2003/0150017 A1, all of which are incorporated herein by reference.
  • A “consensus amino acid sequence” means an artificial, amino acid sequence indicating conserved amino acids in the sequence of homologous proteins as determined by statistical analyis of an optimal alignment, e.g. CLUSTALW, of amino acid sequence of homolog proteins. The consensus sequences listed in the sequence listing were created by identifying the most frequent amino acid at each position in a set of aligned protein sequences. When there was 100% identity in an alignment the amino acid is indicated by a capital letter. When the occurance of an amino acid is at least about 70% in an alignemnt, the amino acid is indicated by a lower case letter. When there is no amino acid occurance of at least about 70%, e.g. due to diversity or gaps, the amino acid is inidcated by an “x”. When used to defined embodiments of the invention, a consensus amino acid sequence will be aligned with a query protein amino acid sequence in an optimal alignment, e.g. CLUSTALW. An embodiment of the invention will have identity to the conserved amino acids indicated in the consensus amino acid sequence.
  • “Arabidopsis” means plants of Arabidopsis thaliana.
  • “Pfam” database is a large collection of multiple sequence alignments and hidden Markov models covering many common protein families, e.g. Pfam version 19.0 (December 2005) contains alignments and models for 8183 protein families and is based on the Swissprot 47.0 and SP-TrEMBL 30.0 protein sequence databases. See S. R. Eddy, “Profile Hidden Markov Models”, Bioinformatics 14:755-763, 1998. The Pfam database is currently maintained and updated by the Pfam Consortium. The alignments represent some evolutionary conserved structure that has implications for the protein's function. Profile hidden Markov models (profile HMMs) built from the protein family alignments can be used for automatically recognizing that a new protein belongs to an existing protein family even if the homology by alignment appears to be low.
  • A “Pfam domain module” is a representation of Pfam domains in a protein, in order from N terminus to C terminus. In a Pfam domain module individual Pfam domains are separated by double colons “::”. The order and copy number of the Pfam domains from N to C terminus are attributes of a Pfam domain module. Although the copy number of repetitive domains is important, varying copy number often enables a similar function. Thus, a Pfam domain module with multiple copies of a domain should define an equivalent Pfam domain module with variance in the number of multiple copies. A Pfam domain module is not specific for distance between adjacent domains, but contemplates natural distances and variations in distance that provide equivalent function. The Pfam database contains both narrowly- and broadly-defined domains, leading to identification of overlapping domains on some proteins. A Pfam domain module is characterized by non-overlapping domains. Where there is overlap, the domain having a function that is more closely associated with the function of the protein (based on the E value of the Pfam match) is selected.
  • Once one DNA is identified as encoding a protein which imparts an enhanced trait when expressed in transgenic plants, other DNA encoding proteins with the same Pfam domain module are identified by querying the amino acid sequence of protein encoded by candidate DNA against the Hidden Markov Models which characterizes the Pfam domains using HMMER software, a current version of which is provided in the appended computer listing. Candidate proteins meeting the same Pfam domain module are in the protein family and have cognate DNA that is used in constructing recombinant DNA for the use in the plant cells of this invention. Hidden Markov Model databases for use with HMMER software in identifying DNA expressing protein with a common Pfam domain module for recombinant DNA in the plant cells of this invention are also included in the appended computer listing.
  • Version 19.0 of the HMMER software and Pfam databases were used to identify known domains in the proteins corresponding to amino acid sequence of SEQ ID NO: 804 through SEQ ID NO:1606. All DNA encoding proteins that have scores higher than the gathering cutoff disclosed in Table 19 by Pfam analysis disclosed herein can be used in recombinant DNA of the plant cells of this invention, e.g. for selecting transgenic plants having enhanced agronomic traits. The relevant Pfam modules for use in this invention, as more specifically disclosed below, are Syntaxin::SNARE, Pro_isomerase, Pkinase, ATP-synt_G, Carboxyl_trans, CDC50, GATase::GMP_synt_C, F-box::WD40::WD40::WD40, dsrm::dsrm, Pyr_redox—2::Pyr_redox_dim, WAK::Pkinase, Pkinase_Tyr, PTPA, Biotin_lipoyl::E3_binding::2-oxoacid_dh, AAA, LRRNT—2::LRR—1::LRR—1::LRR—1, PRA1, TIM, YTH, ThiF, Hep—59, Pkinase, PALP::Thr_dehydrat_C::Thr_dehydrat_C, zf-Tim10_DDP, CAF1, Pkinase, Pyr_redox—2::Pyr_redox_dim, Response_reg, YIF1, NPH3, LRRNT—2::LRR—1::LRR—1::LRR—1::LRR—1::Pkinase_Tyr, NOI, Fer2, AA_permease, Caleosin, IF4E, Pkinase, Ribul_P—3_epim, F-box::WD40::WD40::WD40::WD40::WD40::WD40, MIP, p450, Ribosomal_S5::Ribosomal_S5_C, Hpt, TBC, Acyltransferase, Epimerase, Pkinase, Dus, SelR, PH, Tyr-DNA_phospho, RRM—1, Pkinase, ECH, SRPRB, DUF599, Pkinase::efhand::efhand::efhand::efhand, ORC2, PMEI, p450, GLTP, Suc_Fer-like, CBS::CBS, ADH_N::ADH_zinc_N, LRRNT—2::LRR—1::LRR—1::LRR—1::Pkinase, F-box, adh_short, polyprenyl_synt, GHMP_kinases_N::GHMP_kinases_C, PsbW, Na_H_Exchanger:TrkA_C, Ribosomal_L12, CDC50, DCP1, Pyr_redox—2::Pyr_redox_dim, Steroid_dh, tRNA-synt—1c::tRNA-synt—1c_C, peroxidase, Sugar_tr, Pro_isomerase, Iso_dh, PTS—2-RNA, Aminotran—5, ENOD93, KH—1::KH—1::KH—1::KH—1::KH—1, Mito_carr::Mito_carr::Mito_carr, DUF569::DUF569, C1—2::C1—2::C1—3::C1—2::C1—3::C1—2, DnaJ::zf-C2H2, Aldedh, AAA::Rep_fac_C, DUF641, Aminotran—1—2, TB2_DP1_HVA22, zf-C3HC4, RRM—1::RRM—2, Pkinase, PPR::PPR::PPR::PPR::PPR::PPR::PPR::PPR::PPR::PPR::PPR, Pyr_redox—2, IQ::IQ, SMP::SMP::SMP, AWPM-19, CLP_protease, Pkinase::NAF, PRMT5, PPR::PPR::PPR::PPR::PPR::PPR, Aldedh, ATP-synt_C::ATP-synt_C, adh_short, RCC1::RCC1::RCC1::RCC1::FYVE::DZC, p450, PfkB, PB1, Hexapep::Hexapep::Hexapep::Hexapep, Aminotran—1—2, DUF862, Aldedh, ADH_N::ADH_zinc_N, CDC48_N::AAA::AAA, AA_permease, UQ_con, Mem_trans, GFA, OPT, DUF887, Di19, U-box::Arm::Arm, DAO, G-alpha, Aminotran—3, 20G-FeII_Oxy, Lectin_legB::Pkinase, NAC::UBA, efhand_like::PI-PLC-X::PI-PLC-Y::C2, TLC, ATP-grasp—2::Ligase_CoA, Pkinase, PRC::PRC, MFS—1::Sugar_tr, Copine::zf-C3HC4, RRM—1::RRM—1::RRM—1, Pribosyltran, AA_kinase, PhzC-PhzF, Gp_dh_N::Gp_dh_C, Sugar_tr, Pre-SET::SET, Alpha-amylase::Alpha-amyl_C2, Cyclin_N, FAE1_CUT1_RppA::ACP_syn_III_C, RPE65, efhand_like::PI-PLC-X::PI-PLC-Y::C2, Mito_carr::Mito_carr::Mito_carr, Invertase_neut, DSPc, LANC_like, Aminotran—5, Glutaminase, PPR::PPR::PPR::PPR::PPR::PPR::PPR::PPR, PGI, SSB, p450, La::RRM—1::RRM—3, Methyltransf—11, SBF, NTP_transferase::Hexapep::Hexapep::Hexapep, Mov34, Hydrolase, AAA, RRM—1::RRM—1, Pkinase::NAF, F-box::FBA—1, p450, F-box::LRR—2, zf-DHHC, TBP::TBP, DUF607, FMO-like, adh_short, ATP-synt_ab_N::ATP-synt_ab, RNase_PH, PP2C, UQ_con, Aminotran—1—2, p450, FMO-like, Gp_dh_N::Gp_dh_C, Mito_carr::Mito_carr::Mito_carr, zf-CCCH::zf-CCCH::zf-CCCH::zf-CCCH::zf-CCCH, GST_C, GH3, PAP_fibrillin, ThiF, Ribul_P—3_epim, DUF260, p450, MACPF, Steroid_dh, Response_reg, Carb_anhydrase, Aldedh, Pkinase, Methyltransf—11, PK::PK_C, Pkinase, DEK_C::SWIB::SWIB, TATA_RF, Tryp_alpha_amyl, Y_phosphatase2, TATA_RF, NifU_N, ENT, Pkinase, F-box::Kelch—2::Kelch—2, WD40::WD40, MtN3_slv::MtN3_slv, TB2_DP1_HVA22, Pkinase, Aldedh, AAA, Pyridoxal_deC, zf-CCHC::zf-CCHC::zf-CCHC::zf-CCHC, Peptidase_M24, LRRNT—2::LRR—1:LRR—1:LRR—1:LRR—1::Pkinase, Arf, DUF1279, UPF0185, Rhodanese, adh_short, Tryp_alpha_amyl, Pkinase, UPF0139, CBS, Glyco_transf 29, iPGM_N::Metalloenzyme, Proteasome, Pkinase, UBX, ELFV_dehydrog_N::ELFV_dehydrog, p450, ADH_N::ADH_zinc_N, zf-C3HC4, NDK, NAD_Gly3P_dh_N::NAD_Gly3P_dh_C, GlutR_N::Shikimate_DH::GlutR_dimer, p450, SNF5, p450, Pribosyltran, AIG1, Response_reg::CCT, mTERF, DUF220, Pkinase::NAF, zf-CCCH::zf-CCCH, Pkinase, Pkinase, MATH::MATH, Asparaginase, Pkinase, Gp_dh_N::Gp_dh_C, Pkinase, KH—1, Fcfl, PK::PK_C::PEP-utilizers, CRAL_TRIO_N::CRAL_TRIO, Raffinose_syn, DUF584, BT1, Aminotran—1—2, C1—2::C1—3::C1—3::C1—2::C1—3::C1—3::C1—2, FMO-like, PLACE, F-box::Kelch—2::Kelch—1::Kelch—2, XS::XH, STT3, ABC_tran::ABC_tran, Aldo_ket_red, NTF2::RRM—1, DUF594, Biotin_lipoyl::2-oxoacid_dh, RRM—1, FHA, Mov34, MT-A70, Brix, X8, Auxin_inducible, Peptidase_M18, Sec61_beta, F-box::Kelch—1::Kelch—1, Brix, TIM, CTP_transf 1, Tetraspannin, PALP, DUF822, Pkinase, B3::B3, MFS—1, SFT2, F-box::Kelch—1::Kelch—1, DUF588, Thioredoxin, Alba, Ion_trans—2::Ion_trans—2, Peptidase_C48, YDG_SRA::Pre-SET::SET, Aldedh, Abhydrolase—3, p450, U-box::Arm::Arm::Arm::Arm, AA_permease, LAG1, peroxidase, PAD_porph, Pkinase, F-box, AIG2, p450, AARP2CN::DUF663, UPF0153, NAD_binding—2::6 PGD, Pkinase, B_lectin::S_locus_glycop::PAN—1::Pkinase, EMP24_GP25L, DUF6::DUF6, DUF163, Sina, adh_short, Rho_GDI, zf-CCHC::zf-CCHC::zf-CCHC::zf-CCHC::zf-CCHC::zf-CCHC::zf-CCHC, VHS::GAT, Pyrophosphatase, DMRL_synthase, Cyclin_N::Cyclin_C, NDK, TPP_enzyme_N::TPP_enzyme_M::TPP_enzyme_C, SH3—1, UDPG_MGDP_dh_N::UDPG_MGDP_dh::UDPG_MGDP_dh_C, UIM::efhand, DUF579, Pkinase, DHBP_synthase::GTP_cyclohydro2, Peptidase_C14, Glycolytic, Pkinase, Lipase—3, LRRNT—2::LRR—1::LRR—1::LRR—1::LRR—1, Snf7, BT1, PPDK_N::PEP-utilizers::PEP-utilizers_C, V-ATPase_G, RNA_pol_I_A49, Zip, WD40::WD40::WD40, Branch, RCC1::RCC1::RCC1::RCC1, TFIID-18 kDa, Pkinase, Cullin, TFIID-31 kDa, Asp, Pkinase, Ubie_methyltran, PPR::PPR, PPR::PPR::PPR::PPR::PPR::PPR::PPR, Fructosamin_kin, PPR::PPR::PPR::PPR::PPR::PPR, Pkinase_Tyr, p450, AA_permease, Glycos_transf—1, ECH::3HCDH_N::3HCDH, MIP, ADH_N::ADH_zinc_N, Aa_trans, DUF1517, Redoxin, RRS1, Pribosyltran, Sulfate_transp::STAS, DUF167, MMR_HSR1::DUF933, Aminotran—1—2, AA_permease, DUF620, Aldedh, Aminotran—1—2, LRR—1, CDP-OH_P_transf, DHBP_synthase::GTP_cyclohydro2, NHL::NHL, WD40::U3_snoRNA_C, Na_sulph_symp, adh_short, Thioredoxin, Ribosomal_L7Ae, OTCace_N::OTCace, Mito_carr::Mito_carr::Mito_carr, Pescadillo_N::BRCT, PPR::PPR::PPR::PPR::PPR::PPR::PPR::PPR::PPR::PPR, mTERF, Chalcone, Per1, PPR::PPR, Na_H_Exchangen:TrkA_N, DEAD::Helicase_C, Cyclin_N::Cyclin_C, PP-binding, SRF-TF, SATase_N::Hexapep::Hexapep::Hexapep, PK::PK_C, adh_short, DUF6::DUF6, Pyr_redox—2, G-patch, WD40::WD40::WD40::WD40, G-alpha, VQ, WD40::WD40::WD40::WD40::WD40, Aminotran—3, Pribosyltran, LRRNT—2::LRR—1::LRR—1::LRR—1::LRR—1::LRR—1, eIF3_subunit, H_PPase, Nodulin-like, Whi5, Tryp_alpha_amyl, RRM—1::RRM—1, Band—7, Asp, MFS—1, F420_oxidored, Pkinase, PRK, Na_Ca_ex::Na_Ca_ex, Bombesin, Pkinase, Epimerase, Pkinase, Inositol_P, Arm::Arm::Arm::Arm, PB 1, Hin1, p450, RNA_pol_Rpb5_N::RNA_pol_Rpb5_C, Adap_comp_sub, Peptidase_M16::Peptidase_M16—C, Pkinase, PGK, Biotin_lipoyl::E3_binding::2-oxoacid_dh, Alg6_Alg8, F-box, MMR_HSR1, G6PD_N::G6PD_C, DAD, malic::Malic_M::PTA_PTB, ADH_N::ADH_zinc_N, LRR—1::LRR—1::LRR—1::LRR—1::LRR—1::LRR—1::LRR—1, PfkB, PA, Pyr_redox—2::Pyr_redox_dim, SIP1, PP2C, BT1, AhpC-TSA, GASA, Aminotran—3, Sad1_UNC, Pkinase, zf-MYND::PDCD2_C, Pkinase, PGK, ArfGap, GATase::GMP_synt_C, p450, DUF1637, 2OG-Fell_Oxy, Aldedh, DUF231, Glyco_transf 8, Sec1, DUF1475, Cellulose_synt, RRM—1::RRM—1::RRM—1, Usp, AA_permease, Acetyltransf—1::Bromodomain, Glyco_tran—28_C, RNA_pol_N, NTP_transferase, malic::Malic_M, Histone, Epimerase, UPF0061, ClpS, LEA—5, Auxin_inducible, PAP_fibrillin, Aldo_ket_red, Gln-synt_C, DREPP, p450, SFT2, eIF2A, Cenp-O, CPSase_sm_chain::GATase, WD40::WD40::WD40, Pkinase, Porin—3, Pkinase, Aminotran—1—2, GST_N::GST_C, F-box::Kelch—1::Kelch—1, IU_nuc_hydro, SYF2, PDT, Subtilisin_N::PA, Sugar_tr, WD40::WD40, p450, DUF829, Pyr_redox—2::Pyr_redox_dim, Aminotran—1—2, Cyclin_N::Cyclin_C, YgbB, Sugar_tr, SRF-TF, DUF231, DUF584, BT1, zf-C3HC4, Metallophos, FA_hydroxylase, p450, ACBP::Ank::Ank, LSM, SAM—1, LRR—1::LRR—1::Pkinase, Cullin, F-box::FBA—1, peroxidase, Rib—5-P_isom_A, zf-A20::zf-AN1, Dimerisation::Methyltransf—2, PGAM, PTR2, Copine, PALP, Exo_endo_phos, G6PD_N::G6PD_C, PLAC8, Aldo_ket_red, Ank::Ank, FBPase, zf-C3HC4, ACT::ACT, Suc_Fer-like, Pkinase_Tyr, G-alpha, RAMP4, Glutaredoxin, RRM—1::RRM—1, MT-A70, Response_reg::CCT, Arf, AP2, DUF177, 2OG-Fell_Oxy, LRRNT—2::LRR—1::LRR—1::LRR—1::LRR—1::LRR—1, LRR—1, Aldedh, DUF1350, FAE1_CUT1_RppA::ACP_syn_III_C, Sybindin, zf-C3HC4, Nfu_N::NifU, Rho_GDI, PK::PK_C, NOSIC::Nop, PK::PK_C, PRK::Pribosyltran, PfkB, p450, DUF231, TFIID—30 kDa, Aldedh, zf-AN1, GHMP_kinases_N::GHMP_kinases_C, DUF423, Pkinase, Cu-oxidase—3::Cu-oxidase::Cu-oxidase—2, PCI, RNase_PH::RNase_PH_C, DUF59, NTP_transferase, CH::EB1, Pkinase::Pkinase_C, DUF866, SMP::SMP::SMP, Aminotran—3, Transket_pyr::Transketolase_C, Copine, His_biosynth, Tbf5, DUF543, p450, C2, DUF616, Gp_dh_N::Gp_dh_C, Smg4_UPF3, DUF231, DUF89, WD40::WD40, Aldedh, ACT::ACT::ACT::ACT, Pkinase, Pyridoxal_deC, Skp1_POZ::Skp1, NAP, FolB, p450, Pentapeptide::Pentapeptide, NTP_transferase::MannoseP_isomer, SQS_PSY, Cyclase, GASA, Rick—17 kDa_Anti, FMO-like, B_lectin::S_locus_glycop::PAN—2, Peptidase_C12, Ribosomal_S6e, Glyoxalase, Response_reg::CCT, PHD::SET, Redoxin, G_glu_transpept, Synaptobrevin, p450, RALF, PALP, Branch, DUF579, Aminotran—3, Nramp, Enolase_N::Enolase_C, Str_synth, FAD_binding—3, MOSC_N::MOSC, Spc97_Spc98, Glycolytic, F-box::WD40::WD40::WD40::WD40, AA_kinase::ACT::ACT, RALF, and ATP_bind—1.
    • Plant Cell Transformation Methods
  • Numerous methods for transforming chromosomes in a plant cell nucleus with recombinant DNA are known in the art and are used in methods of preparing a transgenic plant cell nucleus cell, and plant. Two effective methods for such transformation are Agrobacterium-mediated transformation and microprojectile bombardment. Microprojectile bombardment methods are illustrated in U.S. Pat. Nos. 5,015,580 (soybean); 5,550,318 (corn); 5,538,880 (corn); 5,914,451 (soybean); 6,160,208 (corn); 6,399,861 (corn); 6,153,812 (wheat) and 6,365,807 (rice) and Agrobacterium-mediated transformation is described in U.S. Pat. Nos. 5,159,135 (cotton); 5,824,877 (soybean); 5,463,174 (canola, also known as rapeseed); 5,591,616 (corn); 6,384,301 (soybean), 7,026,528 (wheat) and 6,329,571 (rice), all of which are incorporated herein by reference for enabling the production of transgenic plants. Transformation of plant material is practiced in tissue culture on a nutrient media, e.g. a mixture of nutrients that will allow cells to grow in vitro. Recipient cell targets include, but are not limited to, meristem cells, hypocotyls, calli, immature embryos and gametic cells such as microspores, pollen, sperm and egg cells. Callus can be initiated from tissue sources including, but not limited to, immature embryos, hypocotyls, seedling apical meristems, microspores and the like. Cells containing a transgenic nucleus are grown into transgenic plants.
  • In addition to direct transformation of a plant material with a recombinant DNA, a transgenic plant cell nucleus can be prepared by crossing a first plant having cells with a transgenic nucleus with recombinant DNA with a second plant lacking the trangenci nucleus. For example, recombinant DNA can be introduced into a nucleus from a first plant line that is amenable to transformation to transgenic nucleus in cells that are grown into a transgenic plant which can be crossed with a second plant line to introgress the recombinant DNA into the second plant line. A transgenic plant with recombinant DNA providing an enhanced trait, e.g. enhanced yield, can be crossed with transgenic plant line having other recombinant DNA that confers another trait, for example herbicide resistance or pest resistance, to produce progeny plants having recombinant DNA that confers both traits. Typically, in such breeding for combining traits the transgenic plant donating the additional trait is a male line and the transgenic plant carrying the base traits is the female line. The progeny of this cross will segregate such that some of the plants will carry the DNA for both parental traits and some will carry DNA for one parental trait; such plants can be identified by markers associated with parental recombinant DNA, e.g. marker identification by analysis for recombinant DNA or, in the case where a selectable marker is linked to the recombinant, by application of the selecting agent such as a herbicide for use with a herbicide tolerance marker, or by selection for the enhanced trait. Progeny plants carrying DNA for both parental traits can be crossed back into the female parent line multiple times, for example usually 6 to 8 generations, to produce a progeny plant with substantially the same genotype as one original transgenic parental line but for the recombinant DNA of the other transgenic parental line
  • In practice, DNA is introduced into only a small percentage of target cell nuclei. Marker genes are used to provide an efficient system for identification of those cells with nuclei that are stably transformed by receiving and integrating a recombinant DNA molecule into their genomes. Some marker genes provide selective markers that confer resistance to a selective agent, such as an antibiotic or herbicide. Potentially transformed cells with a nucleus of the invention are exposed to the selective agent. In the population of surviving cells will be those cells where, generally, the resistance-conferring gene has been integrated and expressed at sufficient levels to permit cell survival. Cells can be tested further to confirm stable integration of the exogenous DNA in the nucleus. Explementary selective marker genes include those conferring resistance to antibiotics such as kanamycin (nptII), hygromycin B (aph IV), spectinomycin (aadA) and gentamycin (aac3 and aacC4) or resistance to herbicides such as glufosinate (bar or pat), dicamba (DMO) and glyphosate is (EPSPS). Examples of such selectable markers are illustrated in U.S. Pat. Nos. 5,550,318; 5,633,435; 5,780,708 and 6,118,047, all of which are incorporated herein by reference. Screenable markers which provide an ability to visually identify transformants can also be employed, e.g., a gene expressing a colored or fluorescent protein such as a luciferase or green fluorescent protein (GFP) or a gene expressing a beta-glucuronidase or uidA gene (GUS) for which various chromogenic substrates are known. It is also contemplated that combinations of screenable and selectable markers can be used for identification of transformed cells. See PCT publication WO 99/61129 (herein incorporated by reference) which discloses use of a gene fusion between a selectable marker gene and a screenable marker gene, e.g., an NPTII gene and a GFP gene.
  • Plant cells that survive exposure to the selective agent, or plant cells that have been scored positive in a screening assay, can be cultured in regeneration media and allowed to mature into plants. Developing plantlets regenerated from transformed plant cells can be transferred to plant growth mix, and hardened off, for example, in an environmentally controlled chamber at about 85% relative humidity, 600 ppm CO2, and 25-250 microeinsteins m−2S−1 of light, prior to transfer to a greenhouse or growth chamber for maturation. Plants are regenerated from about 6 weeks to 10 months after a transformant is identified, depending on the initial tissue, and plant species. Plants can be pollinated using conventional plant breeding methods known to those of skill in the art and seed produced, for example self-pollination is commonly used with transgenic corn. The regenerated transformed plant or its progeny seed or plants can be tested for expression of the recombinant DNA and selected for the presence of enhanced agronomic trait.
    • Transgenic Plants and Seeds
  • Transgenic plants derived from transgenic plant cells having a transgenic nucleus of this invention are grown to generate transgenic plants having an enhanced trait as compared to a control plant and produce transgenic seed and haploid pollen of this invention. Such plants with enhanced traits are identified by selection of transformed plants or progeny seed for the enhanced trait. For efficiency a selection method is designed to evaluate multiple transgenic plants (events) comprising the recombinant DNA, for example multiple plants from 2 to 20 or more transgenic events. Transgenic plants grown from transgenic seed provided herein demonstrate improved agronomic traits that contribute to increased yield or other trait that provides increased plant value, including, for example, improved seed quality. Of particular interest are plants having enhanced water use efficiency, enhanced cold tolerance, increased yield, enhanced nitrogen use efficiency, enhanced seed protein and enhanced seed oil.
  • To identify nuclei with recombinant DNA that confer enhanced traits to plants, Arabidopsis thaliana was transformed with a candidate recombinant DNA construct and screened for an enhanced trait.
  • Arabidopsis thaliana is used a model for genetics and metabolism in plants. A two-step screening process was employed which included two passes of trait characterization to ensure that the trait modification was dependent on expression of the recombinant DNA, but not due to the chromosomal location of the integration of the transgene. Twelve independent transgenic lines for each recombinant DNA construct were established and assayed for the transgene expression levels. Five transgenic lines with high transgene expression levels were used in the first pass screen to evaluate the transgene's function in T2 transgenic plants. Subsequently, three transgenic events, which had been shown to have one or more enhanced traits, were further evaluated in the second pass screen to confirm the transgene's ability to impart an enhanced trait. The following Table 3 summarizes the enhanced traits that have been confirmed as provided by a recombinant DNA construct.
  • Table 2 provides a list of protein encoding DNA (“genes”) as recombinant DNA for production of transgenic plants with enhanced agronomic trait, the elements of Table 2 are described by reference to:
  • PEP SEQ ID NO″ identifies an amino acid sequence from SEQ ID NO: 804 to 1606.
  • “NUC SEQ ID NO” identifies a DNA sequence from SEQ ID NO:1 to 803 “construct_id” refers to an arbitrary number used to identify a particular recombinant DNA construct comprising the particular DNA.
  • “Gene ID” refers to an arbitrary name used to identify the particular DNA. “orientation” refers to the orientation of the particular DNA in a recombinant DNA construct relative to the promoter.
  • TABLE 2
    NUC PEP
    SEQ SEQ
    ID ID Construct
    NO NO Gene ID ID Orientation
    1 804 CGPG10 70244 SENSE
    2 805 CGPG1008 71108 SENSE
    3 806 CGPG1023 12816 SENSE
    4 807 CGPG1038 12650 ANTI-
    SENSE
    5 808 CGPG1067 12031 SENSE
    6 809 CGPG1095 12217 SENSE
    7 810 CGPG1101 12043 SENSE
    8 811 CGPG1109 12147 ANTI-
    SENSE
    9 812 CGPG1113 13638 ANTI-
    SENSE
    10 813 CGPG1155 11860 ANTI-
    SENSE
    11 814 CGPG1163 72361 SENSE
    12 815 CGPG1171 12230 SENSE
    13 816 CGPG1177 71626 SENSE
    14 817 CGPG1205 13454 ANTI-
    SENSE
    15 818 CGPG1207 12173 ANTI-
    SENSE
    16 819 CGPG1215 17806 ANTI-
    SENSE
    17 820 CGPG1223 12011 ANTI-
    SENSE
    18 821 CGPG1250 72915 SENSE
    19 822 CGPG1279 13231 SENSE
    20 823 CGPG1304 13913 SENSE
    21 824 CGPG1319 12749 ANTI-
    SENSE
    22 825 CGPG1327 78901 SENSE
    23 826 CGPG1329 75969 SENSE
    24 827 CGPG133 15606 SENSE
    25 828 CGPG1332 75946 SENSE
    26 829 CGPG1343 13050 ANTI-
    SENSE
    27 830 CGPG1348 75958 SENSE
    28 831 CGPG1349 17333 SENSE
    29 832 CGPG1373 76002 SENSE
    30 833 CGPG1377 78735 SENSE
    31 834 CGPG1412 13914 SENSE
    32 835 CGPG1421 14405 SENSE
    33 836 CGPG1426 75983 SENSE
    34 837 CGPG1433 70721 ANTI-
    SENSE
    35 838 CGPG1453 13811 SENSE
    35 838 CGPG1453 13828 ANTI-
    SENSE
    36 839 CGPG1454 13614 SENSE
    37 840 CGPG1463 76050 SENSE
    38 841 CGPG1464 13038 ANTI-
    SENSE
    39 842 CGPG1471 13040 ANTI-
    SENSE
    40 843 CGPG1481 70716 ANTI-
    SENSE
    40 843 CGPG1481 76039 SENSE
    41 844 CGPG1499 71611 SENSE
    42 845 CGPG150 70253 SENSE
    43 846 CGPG1536 14415 SENSE
    44 847 CGPG1539 13718 ANTI-
    SENSE
    45 848 CGPG155 10706 ANTI-
    SENSE
    45 848 CGPG155 10709 ANTI-
    SENSE
    46 849 CGPG1583 14340 ANTI-
    SENSE
    47 850 CGPG1588 13471 ANTI-
    SENSE
    48 851 CGPG16 18304 SENSE
    49 852 CGPG1609 13623 SENSE
    50 853 CGPG1629 18302 SENSE
    51 854 CGPG1637 15053 ANTI-
    SENSE
    52 855 CGPG1653 15624 SENSE
    53 856 CGPG1658 70412 SENSE
    54 857 CGPG1663 17902 SENSE
    55 858 CGPG1682 14272 ANTI-
    SENSE
    56 859 CGPG1701 15122 SENSE
    56 859 CGPG1701 70723 ANTI-
    SENSE
    57 860 CGPG1723 14248 SENSE
    58 861 CGPG1724 13965 ANTI-
    SENSE
    59 862 CGPG1726 75912 SENSE
    60 863 CGPG1736 14344 ANTI-
    SENSE
    61 864 CGPG1741 14807 ANTI-
    SENSE
    62 865 CGPG1783 17307 SENSE
    63 866 CGPG1790 16431 ANTI-
    SENSE
    64 867 CGPG1797 73075 SENSE
    65 868 CGPG1845 16323 SENSE
    66 869 CGPG1855 14833 ANTI-
    SENSE
    67 870 CGPG1870 17030 ANTI-
    SENSE
    68 871 CGPG1879 76414 SENSE
    69 872 CGPG1886 16021 SENSE
    70 873 CGPG1903 78701 SENSE
    71 874 CGPG1905 78702 SENSE
    72 875 CGPG1914 15220 ANTI-
    SENSE
    73 876 CGPG193 15623 SENSE
    74 877 CGPG1939 19402 SENSE
    75 878 CGPG1949 70559 SENSE
    76 879 CGPG1959 15111 ANTI-
    SENSE
    77 880 CGPG197 70832 SENSE
    78 881 CGPG1972 15129 SENSE
    79 882 CGPG1981 76086 SENSE
    80 883 CGPG1999 15203 ANTI-
    SENSE
    81 884 CGPG2 70216 SENSE
    82 885 CGPG2006 14910 ANTI-
    SENSE
    83 886 CGPG2010 70318 SENSE
    84 887 CGPG2011 15207 ANTI-
    SENSE
    85 888 CGPG2014 14915 ANTI-
    SENSE
    86 889 CGPG2023 15132 SENSE
    87 890 CGPG2026 16229 SENSE
    88 891 CGPG2041 14932 ANTI-
    SENSE
    89 892 CGPG2064 76017 SENSE
    90 893 CGPG2070 15964 ANTI-
    SENSE
    91 894 CGPG2077 17227 SENSE
    92 895 CGPG2095 72952 SENSE
    93 896 CGPG2105 73706 SENSE
    94 897 CGPG2108 18203 SENSE
    95 898 CGPG2111 16309 SENSE
    96 899 CGPG2124 15986 ANTI-
    SENSE
    97 900 CGPG2125 15987 ANTI-
    SENSE
    98 901 CGPG2126 16204 SENSE
    99 902 CGPG213 11133 SENSE
    100 903 CGPG2134 73977 SENSE
    101 904 CGPG2139 15995 ANTI-
    SENSE
    101 904 CGPG2139 18201 SENSE
    102 905 CGPG2140 16887 SENSE
    103 906 CGPG2153 16213 SENSE
    104 907 CGPG2163 15507 ANTI-
    SENSE
    105 908 CGPG2165 15508 ANTI-
    SENSE
    106 909 CGPG2193 15959 ANTI-
    SENSE
    107 910 CGPG2218 72427 ANTI-
    SENSE
    108 911 CGPG2224 19041 ANTI-
    SENSE
    109 912 CGPG2225 17802 SENSE
    110 913 CGPG2229 19042 ANTI-
    SENSE
    111 914 CGPG2243 76053 SENSE
    112 915 CGPG2254 16120 SENSE
    113 916 CGPG2268 15424 ANTI-
    SENSE
    114 917 CGPG227 16401 SENSE
    115 918 CGPG2312 72417 SENSE
    116 919 CGPG2315 73702 SENSE
    117 920 CGPG2316 70706 ANTI-
    SENSE
    118 921 CGPG2319 71145 SENSE
    119 922 CGPG235 11609 ANTI-
    SENSE
    120 923 CGPG2358 71706 SENSE
    121 924 CGPG2359 17325 SENSE
    122 925 CGPG2361 70102 SENSE
    123 926 CGPG2365 70106 SENSE
    124 927 CGPG2372 70113 SENSE
    125 928 CGPG2374 70115 SENSE
    126 929 CGPG2377 70118 SENSE
    127 930 CGPG2387 70128 SENSE
    128 931 CGPG2389 70130 SENSE
    129 932 CGPG2395 17103 ANTI-
    SENSE
    130 933 CGPG2408 72748 SENSE
    131 934 CGPG2409 17502 SENSE
    132 935 CGPG2410 17503 SENSE
    133 936 CGPG2414 78708 SENSE
    134 937 CGPG2416 17504 SENSE
    135 938 CGPG2441 17132 ANTI-
    SENSE
    136 939 CGPG2450 72965 SENSE
    137 940 CGPG2451 72796 SENSE
    138 941 CGPG2492 16617 SENSE
    139 942 CGPG2495 16640 SENSE
    140 943 CGPG2506 16603 SENSE
    141 944 CGPG2515 16612 SENSE
    142 945 CGPG2531 16614 SENSE
    143 946 CGPG2581 78354 SENSE
    144 947 CGPG2584 17818 SENSE
    145 948 CGPG2592 78370 SENSE
    146 949 CGPG2612 70411 SENSE
    147 950 CGPG2660 19154 SENSE
    148 951 CGPG2663 19155 SENSE
    149 952 CGPG2679 18307 SENSE
    150 953 CGPG2696 72030 SENSE
    151 954 CGPG2772 17916 SENSE
    152 955 CGPG2773 17917 SENSE
    153 956 CGPG281 17334 SENSE
    154 957 CGPG2846 71531 SENSE
    155 958 CGPG2852 18441 SENSE
    156 959 CGPG2863 19162 SENSE
    157 960 CGPG2870 73205 SENSE
    158 961 CGPG2877 18306 SENSE
    159 962 CGPG289 70808 SENSE
    160 963 CGPG2924 17653 SENSE
    161 964 CGPG2947 19535 SENSE
    162 965 CGPG2963 71719 SENSE
    163 966 CGPG2987 18546 SENSE
    164 967 CGPG3033 19534 SENSE
    165 968 CGPG3045 18421 SENSE
    166 969 CGPG3046 18422 SENSE
    167 970 CGPG3060 19539 SENSE
    168 971 CGPG3075 19244 SENSE
    169 972 CGPG310 15803 SENSE
    170 973 CGPG3103 19545 SENSE
    171 974 CGPG315 10222 ANTI-
    SENSE
    171 974 CGPG315 72356 SENSE
    172 975 CGPG3183 70425 SENSE
    173 976 CGPG3189 19237 SENSE
    174 977 CGPG3204 71303 SENSE
    175 978 CGPG3208 19240 SENSE
    176 979 CGPG3219 18535 SENSE
    177 980 CGPG3233 19450 SENSE
    178 981 CGPG3263 18221 SENSE
    179 982 CGPG3276 18233 SENSE
    180 983 CGPG3280 18236 SENSE
    181 984 CGPG3282 18238 SENSE
    182 985 CGPG3300 18309 SENSE
    183 986 CGPG3318 70337 SENSE
    184 987 CGPG3319 18319 SENSE
    185 988 CGPG3326 70338 SENSE
    186 989 CGPG333 10471 SENSE
    187 990 CGPG3338 18331 SENSE
    188 991 CGPG334 10228 ANTI-
    SENSE
    188 991 CGPG334 10473 SENSE
    189 992 CGPG3374 18261 SENSE
    190 993 CGPG3402 18848 SENSE
    191 994 CGPG3405 18268 SENSE
    192 995 CGPG3413 18345 SENSE
    193 996 CGPG3422 73607 SENSE
    194 997 CGPG3436 18352 SENSE
    195 998 CGPG3539 18357 SENSE
    196 999 CGPG3550 19423 SENSE
    197 1000 CGPG3551 78373 SENSE
    198 1001 CGPG3552 70603 SENSE
    199 1002 CGPG3572 19616 SENSE
    200 1003 CGPG3598 19425 SENSE
    201 1004 CGPG3599 19426 SENSE
    202 1005 CGPG3606 18382 SENSE
    203 1006 CGPG3610 71536 SENSE
    204 1007 CGPG3620 70419 SENSE
    205 1008 CGPG364 70827 SENSE
    206 1009 CGPG3676 19311 SENSE
    207 1010 CGPG3679 19323 SENSE
    208 1011 CGPG3686 19320 SENSE
    209 1012 CGPG3694 73613 SENSE
    210 1013 CGPG3696 70432 SENSE
    211 1014 CGPG3698 70433 SENSE
    212 1015 CGPG3699 70434 SENSE
    213 1016 CGPG3702 72614 SENSE
    214 1017 CGPG3703 70436 SENSE
    215 1018 CGPG3707 74226 SENSE
    216 1019 CGPG3710 70439 SENSE
    217 1020 CGPG3730 70446 SENSE
    218 1021 CGPG3731 70613 SENSE
    219 1022 CGPG3734 70447 SENSE
    220 1023 CGPG3745 71725 SENSE
    221 1024 CGPG3764 70462 SENSE
    222 1025 CGPG3820 70545 SENSE
    223 1026 CGPG3851 70741 SENSE
    224 1027 CGPG3911 19702 SENSE
    225 1028 CGPG3948 19985 SENSE
    226 1029 CGPG3958 19775 SENSE
    227 1030 CGPG3981 19829 SENSE
    228 1031 CGPG3996 19982 SENSE
    229 1032 CGPG4006 19755 SENSE
    230 1033 CGPG4025 19732 SENSE
    231 1034 CGPG4028 70365 SENSE
    232 1035 CGPG403 10476 SENSE
    233 1036 CGPG4041 19987 SENSE
    234 1037 CGPG4078 19893 SENSE
    235 1038 CGPG4079 19983 SENSE
    236 1039 CGPG4083 19825 SENSE
    237 1040 CGPG4092 19919 SENSE
    238 1041 CGPG4104 19979 SENSE
    239 1042 CGPG4127 19786 SENSE
    240 1043 CGPG4135 70903 SENSE
    241 1044 CGPG4161 70970 SENSE
    242 1045 CGPG4180 70980 SENSE
    243 1046 CGPG4191 70936 SENSE
    244 1047 CGPG4199 71425 SENSE
    245 1048 CGPG4241 78666 SENSE
    246 1049 CGPG427 71202 SENSE
    247 1050 CGPG4273 78973 SENSE
    248 1051 CGPG4301 76411 SENSE
    249 1052 CGPG4303 70635 SENSE
    250 1053 CGPG4313 73715 SENSE
    251 1054 CGPG4314 70638 SENSE
    252 1055 CGPG4329 70642 SENSE
    253 1056 CGPG4330 70643 SENSE
    254 1057 CGPG4338 71564 SENSE
    255 1058 CGPG4341 75039 SENSE
    256 1059 CGPG4347 70653 SENSE
    257 1060 CGPG4354 70655 SENSE
    258 1061 CGPG4386 78321 SENSE
    259 1062 CGPG4394 78307 SENSE
    260 1063 CGPG4396 71808 SENSE
    261 1064 CGPG4400 71810 SENSE
    262 1065 CGPG4401 71313 SENSE
    263 1066 CGPG441 72349 SENSE
    264 1067 CGPG4413 71318 SENSE
    265 1068 CGPG4427 71812 SENSE
    266 1069 CGPG4446 74060 SENSE
    267 1070 CGPG4448 71816 SENSE
    268 1071 CGPG4474 71569 SENSE
    269 1072 CGPG4482 70672 SENSE
    270 1073 CGPG4511 71336 SENSE
    271 1074 CGPG4517 71337 SENSE
    272 1075 CGPG4551 71339 SENSE
    273 1076 CGPG4559 71825 SENSE
    274 1077 CGPG4567 73696 SENSE
    275 1078 CGPG4586 70682 SENSE
    276 1079 CGPG4600 70686 SENSE
    277 1080 CGPG4631 78316 SENSE
    278 1081 CGPG4642 71667 SENSE
    279 1082 CGPG4645 71695 SENSE
    280 1083 CGPG4646 71696 SENSE
    281 1084 CGPG4649 72475 SENSE
    282 1085 CGPG4653 71677 SENSE
    283 1086 CGPG4656 71691 SENSE
    284 1087 CGPG4668 72476 SENSE
    285 1088 CGPG469 70803 SENSE
    286 1089 CGPG4708 71612 SENSE
    287 1090 CGPG4712 71637 SENSE
    288 1091 CGPG4714 71629 SENSE
    289 1092 CGPG4719 71622 SENSE
    290 1093 CGPG473 70810 SENSE
    291 1094 CGPG4734 72452 SENSE
    292 1095 CGPG4736 74071 SENSE
    293 1096 CGPG474 11042 SENSE
    294 1097 CGPG4802 72510 SENSE
    295 1098 CGPG4822 72537 SENSE
    296 1099 CGPG4826 72541 SENSE
    297 1100 CGPG4833 72617 SENSE
    298 1101 CGPG4841 73755 SENSE
    299 1102 CGPG4850 72630 SENSE
    300 1103 CGPG4868 72645 SENSE
    301 1104 CGPG4871 72647 SENSE
    302 1105 CGPG488 14316 SENSE
    303 1106 CGPG4908 73689 SENSE
    304 1107 CGPG4913 73345 SENSE
    305 1108 CGPG4921 73347 SENSE
    306 1109 CGPG4954 73231 SENSE
    307 1110 CGPG4956 78325 SENSE
    308 1111 CGPG4959 72658 SENSE
    309 1112 CGPG4965 72660 SENSE
    310 1113 CGPG4970 72662 SENSE
    311 1114 CGPG4980 73352 SENSE
    312 1115 CGPG4982 72814 SENSE
    313 1116 CGPG4985 72816 SENSE
    314 1117 CGPG4990 72820 SENSE
    315 1118 CGPG4991 73353 SENSE
    316 1119 CGPG5007 75066 SENSE
    317 1120 CGPG5015 78337 SENSE
    318 1121 CGPG5026 73317 SENSE
    319 1122 CGPG5029 73318 SENSE
    320 1123 CGPG5046 73749 SENSE
    321 1124 CGPG508 18704 SENSE
    322 1125 CGPG5103 73221 SENSE
    323 1126 CGPG511 71125 SENSE
    324 1127 CGPG5121 76203 SENSE
    325 1128 CGPG5126 75067 SENSE
    326 1129 CGPG5136 73729 SENSE
    327 1130 CGPG5146 75206 SENSE
    328 1131 CGPG5149 73248 SENSE
    329 1132 CGPG5181 73738 SENSE
    330 1133 CGPG52 73332 SENSE
    331 1134 CGPG5206 78335 SENSE
    332 1135 CGPG5208 75821 SENSE
    333 1136 CGPG5232 72038 SENSE
    334 1137 CGPG5239 72027 SENSE
    335 1138 CGPG5246 72016 SENSE
    336 1139 CGPG525 70835 SENSE
    337 1140 CGPG5268 72044 SENSE
    338 1141 CGPG5272 72092 SENSE
    339 1142 CGPG5333 72124 SENSE
    340 1143 CGPG5338 72110 SENSE
    341 1144 CGPG5341 73916 SENSE
    342 1145 CGPG5369 74268 SENSE
    343 1146 CGPG5372 74269 SENSE
    344 1147 CGPG5380 77902 SENSE
    345 1148 CGPG5386 74273 SENSE
    346 1149 CGPG5396 74280 SENSE
    347 1150 CGPG5397 74281 SENSE
    348 1151 CGPG5421 74287 SENSE
    349 1152 CGPG5433 73767 SENSE
    350 1153 CGPG5439 77304 SENSE
    351 1154 CGPG5453 73761 SENSE
    352 1155 CGPG5456 74721 SENSE
    353 1156 CGPG5483 74719 SENSE
    354 1157 CGPG5492 74257 SENSE
    355 1158 CGPG5508 72749 SENSE
    356 1159 CGPG5520 72703 SENSE
    357 1160 CGPG5525 72763 SENSE
    358 1161 CGPG5526 72775 SENSE
    359 1162 CGPG5530 72728 SENSE
    360 1163 CGPG5534 72776 SENSE
    361 1164 CGPG5537 72717 SENSE
    362 1165 CGPG5545 72718 SENSE
    363 1166 CGPG555 11715 SENSE
    364 1167 CGPG5558 72779 SENSE
    365 1168 CGPG5559 72791 SENSE
    366 1169 CGPG5562 72732 SENSE
    367 1170 CGPG5592 73027 SENSE
    368 1171 CGPG5625 73058 SENSE
    369 1172 CGPG5631 73126 SENSE
    370 1173 CGPG5632 73138 SENSE
    371 1174 CGPG5636 73174 SENSE
    372 1175 CGPG5637 73186 SENSE
    373 1176 CGPG564 11141 SENSE
    374 1177 CGPG5641 73139 SENSE
    375 1178 CGPG5650 73128 SENSE
    376 1179 CGPG5653 73164 SENSE
    377 1180 CGPG5657 73117 SENSE
    378 1181 CGPG5671 73142 SENSE
    379 1182 CGPG5672 73990 SENSE
    380 1183 CGPG5677 73166 SENSE
    381 1184 CGPG5678 73178 SENSE
    382 1185 CGPG5679 73190 SENSE
    383 1186 CGPG5682 73131 SENSE
    384 1187 CGPG5691 73108 SENSE
    385 1188 CGPG5699 73074 SENSE
    386 1189 CGPG5705 73132 SENSE
    387 1190 CGPG5722 73146 SENSE
    388 1191 CGPG5734 73147 SENSE
    389 1192 CGPG5736 73080 SENSE
    390 1193 CGPG5744 73077 SENSE
    391 1194 CGPG5747 73183 SENSE
    392 1195 CGPG5748 73018 SENSE
    393 1196 CGPG5750 73112 SENSE
    394 1197 CGPG5751 73988 SENSE
    395 1198 CGPG577 10908 ANTI-
    SENSE
    395 1198 CGPG577 11147 SENSE
    396 1199 CGPG5780 72909 SENSE
    397 1200 CGPG5793 73987 SENSE
    398 1201 CGPG5795 72922 SENSE
    / / / / /
    399 1202 CGPG5796 73036 SENSE
    400 1203 CGPG5800 72958 SENSE
    401 1204 CGPG5812 77006 SENSE
    402 1205 CGPG5815 74732 SENSE
    403 1206 CGPG5838 74333 SENSE
    404 1207 CGPG5844 74735 SENSE
    405 1208 CGPG5846 74736 SENSE
    406 1209 CGPG5851 74737 SENSE
    407 1210 CGPG5857 76657 SENSE
    408 1211 CGPG5862 76113 SENSE
    409 1212 CGPG5863 74747 SENSE
    410 1213 CGPG5867 77309 SENSE
    411 1214 CGPG5872 74322 SENSE
    412 1215 CGPG5913 76212 SENSE
    413 1216 CGPG5922 76514 SENSE
    414 1217 CGPG5961 75242 SENSE
    415 1218 CGPG5964 77324 SENSE
    416 1219 CGPG5968 74350 SENSE
    417 1220 CGPG5984 77606 SENSE
    418 1221 CGPG5991 76530 SENSE
    419 1222 CGPG6006 76716 SENSE
    420 1223 CGPG6015 77328 SENSE
    421 1224 CGPG603 12204 SENSE
    422 1225 CGPG6046 77011 SENSE
    423 1226 CGPG6063 77607 SENSE
    424 1227 CGPG6083 74612 SENSE
    425 1228 CGPG6092 76126 SENSE
    426 1229 CGPG6104 74376 SENSE
    427 1230 CGPG6106 74377 SENSE
    428 1231 CGPG6111 74381 SENSE
    429 1232 CGPG6113 78364 SENSE
    430 1233 CGPG6125 74623 SENSE
    431 1234 CGPG6132 74668 SENSE
    432 1235 CGPG6137 74629 SENSE
    433 1236 CGPG6147 74635 SENSE
    434 1237 CGPG6152 74638 SENSE
    435 1238 CGPG6154 76721 SENSE
    436 1239 CGPG6170 78365 SENSE
    437 1240 CGPG6171 74655 SENSE
    438 1241 CGPG6177 74660 SENSE
    439 1242 CGPG6181 74661 SENSE
    440 1243 CGPG6188 75259 SENSE
    441 1244 CGPG6202 75282 SENSE
    442 1245 CGPG6217 76724 SENSE
    443 1246 CGPG623 12350 ANTI-
    SENSE
    444 1247 CGPG6239 76522 SENSE
    445 1248 CGPG6244 77903 SENSE
    446 1249 CGPG6254 76653 SENSE
    447 1250 CGPG6266 76524 SENSE
    448 1251 CGPG627 11356 SENSE
    449 1252 CGPG6271 75275 SENSE
    450 1253 CGPG6278 76225 SENSE
    451 1254 CGPG6288 75281 SENSE
    452 1255 CGPG6309 74384 SENSE
    453 1256 CGPG633 71238 SENSE
    454 1257 CGPG635 12354 ANTI-
    SENSE
    455 1258 CGPG6350 76236 SENSE
    456 1259 CGPG6358 74682 SENSE
    457 1260 CGPG6365 73425 SENSE
    458 1261 CGPG6374 73438 SENSE
    459 1262 CGPG6377 73474 SENSE
    460 1263 CGPG638 70850 SENSE
    461 1264 CGPG6397 73429 SENSE
    462 1265 CGPG6398 73441 SENSE
    463 1266 CGPG6408 73466 SENSE
    464 1267 CGPG6415 73455 SENSE
    465 1268 CGPG6421 73432 SENSE
    466 1269 CGPG6442 73435 SENSE
    467 1270 CGPG6443 77726 SENSE
    468 1271 CGPG6446 73483 SENSE
    469 1272 CGPG6453 73472 SENSE
    470 1273 CGPG6466 73526 SENSE
    471 1274 CGPG6467 73538 SENSE
    472 1275 CGPG6470 73574 SENSE
    473 1276 CGPG6475 73539 SENSE
    474 1277 CGPG6477 73563 SENSE
    475 1278 CGPG6478 73575 SENSE
    476 1279 CGPG6493 73565 SENSE
    477 1280 CGPG6506 73531 SENSE
    478 1281 CGPG6518 73592 SENSE
    479 1282 CGPG6546 74149 SENSE
    480 1283 CGPG6556 74174 SENSE
    481 1284 CGPG6562 74151 SENSE
    482 1285 CGPG6566 74104 SENSE
    483 1286 CGPG6571 74164 SENSE
    484 1287 CGPG6576 74129 SENSE
    485 1288 CGPG659 72340 SENSE
    486 1289 CGPG6594 74155 SENSE
    487 1290 CGPG6603 74168 SENSE
    488 1291 CGPG6608 74133 SENSE
    489 1292 CGPG6634 74160 SENSE
    490 1293 CGPG6662 74485 SENSE
    491 1294 CGPG6667 74450 SENSE
    492 1295 CGPG6678 74487 SENSE
    493 1296 CGPG6695 74406 SENSE
    494 1297 CGPG6699 74454 SENSE
    495 1298 CGPG670 11361 SENSE
    496 1299 CGPG6705 74431 SENSE
    497 1300 CGPG6735 74411 SENSE
    498 1301 CGPG6744 74424 SENSE
    499 1302 CGPG6753 74525 SENSE
    500 1303 CGPG6757 74573 SENSE
    501 1304 CGPG6803 75827 SENSE
    502 1305 CGPG6806 77329 SENSE
    503 1306 CGPG6811 77330 SENSE
    504 1307 CGPG6812 75830 SENSE
    505 1308 CGPG6815 75832 SENSE
    506 1309 CGPG6827 75836 SENSE
    507 1310 CGPG6830 77034 SENSE
    508 1311 CGPG6839 76255 SENSE
    509 1312 CGPG6859 76542 SENSE
    510 1313 CGPG6864 77511 SENSE
    511 1314 CGPG6877 76261 SENSE
    512 1315 CGPG6878 78456 SENSE
    513 1316 CGPG6880 77041 SENSE
    514 1317 CGPG6886 76546 SENSE
    515 1318 CGPG6887 75848 SENSE
    516 1319 CGPG6895 77515 SENSE
    517 1320 CGPG6896 76266 SENSE
    518 1321 CGPG6903 75852 SENSE
    519 1322 CGPG6912 76556 SENSE
    520 1323 CGPG6933 77523 SENSE
    521 1324 CGPG6942 75863 SENSE
    522 1325 CGPG6944 77052 SENSE
    523 1326 CGPG6949 75865 SENSE
    524 1327 CGPG6969 76551 SENSE
    525 1328 CGPG6989 76280 SENSE
    526 1329 CGPG6991 75874 SENSE
    527 1330 CGPG7003 75879 SENSE
    528 1331 CGPG7009 75880 SENSE
    529 1332 CGPG7037 77519 SENSE
    530 1333 CGPG7051 76745 SENSE
    531 1334 CGPG7062 76554 SENSE
    532 1335 CGPG7064 76746 SENSE
    533 1336 CGPG7086 76750 SENSE
    534 1337 CGPG7109 76621 SENSE
    535 1338 CGPG7123 76623 SENSE
    536 1339 CGPG7136 76461 SENSE
    537 1340 CGPG7147 76462 SENSE
    538 1341 CGPG7159 78987 SENSE
    539 1342 CGPG7186 76568 SENSE
    540 1343 CGPG7222 76176 SENSE
    541 1344 CGPG7224 76177 SENSE
    542 1345 CGPG7233 78380 SENSE
    543 1346 CGPG7238 76629 SENSE
    544 1347 CGPG7253 76189 SENSE
    545 1348 CGPG7255 76761 SENSE
    546 1349 CGPG7286 78608 SENSE
    547 1350 CGPG7292 78115 SENSE
    548 1351 CGPG7301 74873 SENSE
    549 1352 CGPG7305 74826 SENSE
    550 1353 CGPG7307 74850 SENSE
    551 1354 CGPG7318 74887 SENSE
    552 1355 CGPG7319 74804 SENSE
    553 1356 CGPG7345 74831 SENSE
    554 1357 CGPG7368 74822 SENSE
    555 1358 CGPG7385 74836 SENSE
    556 1359 CGPG7391 74901 SENSE
    557 1360 CGPG7405 74974 SENSE
    558 1361 CGPG7415 74904 SENSE
    559 1362 CGPG7416 74916 SENSE
    560 1363 CGPG7420 74964 SENSE
    561 1364 CGPG7432 74918 SENSE
    562 1365 CGPG7436 74966 SENSE
    563 1366 CGPG7445 74979 SENSE
    564 1367 CGPG7465 74934 SENSE
    565 1368 CGPG7473 77814 SENSE
    566 1369 CGPG7489 75387 SENSE
    567 1370 CGPG7492 75328 SENSE
    568 1371 CGPG7499 77808 SENSE
    569 1372 CGPG7505 75389 SENSE
    570 1373 CGPG7507 75318 SENSE
    571 1374 CGPG7508 75330 SENSE
    572 1375 CGPG7509 75342 SENSE
    573 1376 CGPG7511 75366 SENSE
    574 1377 CGPG7515 75319 SENSE
    575 1378 CGPG7521 75391 SENSE
    576 1379 CGPG7540 75334 SENSE
    577 1380 CGPG7547 75323 SENSE
    578 1381 CGPG7561 75396 SENSE
    579 1382 CGPG7562 75401 SENSE
    580 1383 CGPG7563 75413 SENSE
    581 1384 CGPG7567 75461 SENSE
    582 1385 CGPG7568 75473 SENSE
    583 1386 CGPG7571 77817 SENSE
    584 1387 CGPG7587 75416 SENSE
    585 1388 CGPG7591 75464 SENSE
    586 1389 CGPG7597 75441 SENSE
    587 1390 CGPG7606 75454 SENSE
    588 1391 CGPG7633 75493 SENSE
    589 1392 CGPG7637 75446 SENSE
    590 1393 CGPG7649 75495 SENSE
    591 1394 CGPG7658 75705 SENSE
    592 1395 CGPG7664 77818 SENSE
    593 1396 CGPG7666 75525 SENSE
    594 1397 CGPG7668 75549 SENSE
    595 1398 CGPG7742 75582 SENSE
    596 1399 CGPG7746 75535 SENSE
    597 1400 CGPG7747 75547 SENSE
    598 1401 CGPG7752 75512 SENSE
    599 1402 CGPG7766 75673 SENSE
    600 1403 CGPG7770 75626 SENSE
    601 1404 CGPG7774 75674 SENSE
    602 1405 CGPG7777 75615 SENSE
    603 1406 CGPG7778 75627 SENSE
    604 1407 CGPG7786 75628 SENSE
    605 1408 CGPG7788 75652 SENSE
    606 1409 CGPG7792 75605 SENSE
    607 1410 CGPG78 70228 SENSE
    608 1411 CGPG783 13302 ANTI-
    SENSE
    609 1412 CGPG7832 75610 SENSE
    610 1413 CGPG7841 75623 SENSE
    611 1414 CGPG7845 75671 SENSE
    612 1415 CGPG7847 75695 SENSE
    613 1416 CGPG7851 75648 SENSE
    614 1417 CGPG7853 75672 SENSE
    615 1418 CGPG7857 75713 SENSE
    616 1419 CGPG7865 75714 SENSE
    617 1420 CGPG7869 75762 SENSE
    618 1421 CGPG7891 77954 SENSE
    619 1422 CGPG7892 77955 SENSE
    620 1423 CGPG7906 77541 SENSE
    621 1424 CGPG7924 78131 SENSE
    622 1425 CGPG7934 78134 SENSE
    623 1426 CGPG7949 77554 SENSE
    624 1427 CGPG7954 78992 SENSE
    625 1428 CGPG7964 77557 SENSE
    626 1429 CGPG7968 78128 SENSE
    627 1430 CGPG7969 77560 SENSE
    628 1431 CGPG7972 77561 SENSE
    629 1432 CGPG7982 77958 SENSE
    630 1433 CGPG7985 77563 SENSE
    631 1434 CGPG7993 78994 SENSE
    632 1435 CGPG8 74508 SENSE
    633 1436 CGPG80 70229 SENSE
    634 1437 CGPG8001 77959 SENSE
    635 1438 CGPG8009 77567 SENSE
    636 1439 CGPG802 11749 ANTI-
    SENSE
    637 1440 CGPG8049 77578 SENSE
    638 1441 CGPG806 11751 ANTI-
    SENSE
    639 1442 CGPG8060 77963 SENSE
    640 1443 CGPG8068 77925 SENSE
    641 1444 CGPG8072 77927 SENSE
    642 1445 CGPG8075 77345 SENSE
    643 1446 CGPG81 70230 SENSE
    644 1447 CGPG8100 77353 SENSE
    645 1448 CGPG8101 77354 SENSE
    646 1449 CGPG8104 77355 SENSE
    647 1450 CGPG8108 77588 SENSE
    648 1451 CGPG8116 77591 SENSE
    649 1452 CGPG8125 77594 SENSE
    650 1453 CGPG8134 77595 SENSE
    651 1454 CGPG8138 77364 SENSE
    652 1455 CGPG8156 78904 SENSE
    653 1456 CGPG8159 77937 SENSE
    654 1457 CGPG8163 77369 SENSE
    655 1458 CGPG8179 77940 SENSE
    656 1459 CGPG8193 78746 SENSE
    657 1460 CGPG8197 77372 SENSE
    658 1461 CGPG8198 78126 SENSE
    659 1462 CGPG8204 77951 SENSE
    660 1463 CGPG8211 75901 SENSE
    661 1464 CGPG823 12123 ANTI-
    SENSE
    662 1465 CGPG8234 75987 SENSE
    663 1466 CGPG8238 75940 SENSE
    664 1467 CGPG8260 75919 SENSE
    665 1468 CGPG8267 75908 SENSE
    666 1469 CGPG8268 75920 SENSE
    667 1470 CGPG8274 75992 SENSE
    668 1471 CGPG8277 75933 SENSE
    669 1472 CGPG8279 77965 SENSE
    670 1473 CGPG8284 77966 SENSE
    671 1474 CGPG8345 77972 SENSE
    672 1475 CGPG8408 78522 SENSE
    673 1476 CGPG842 12194 ANTI-
    SENSE
    674 1477 CGPG8421 78525 SENSE
    675 1478 CGPG8435 78527 SENSE
    676 1479 CGPG8440 78917 SENSE
    677 1480 CGPG8453 78920 SENSE
    678 1481 CGPG8470 78535 SENSE
    679 1482 CGPG8479 78538 SENSE
    680 1483 CGPG8489 78922 SENSE
    681 1484 CGPG8498 77984 SENSE
    682 1485 CGPG85 73938 SENSE
    683 1486 CGPG8501 78621 SENSE
    684 1487 CGPG8507 77990 SENSE
    685 1488 CGPG8509 78386 SENSE
    686 1489 CGPG8515 78001 SENSE
    687 1490 CGPG8517 78543 SENSE
    688 1491 CGPG8518 78002 SENSE
    689 1492 CGPG852 12259 SENSE
    690 1493 CGPG8523 78005 SENSE
    691 1494 CGPG8528 78008 SENSE
    692 1495 CGPG8552 78019 SENSE
    693 1496 CGPG8553 78020 SENSE
    694 1497 CGPG8562 78023 SENSE
    695 1498 CGPG8567 78548 SENSE
    696 1499 CGPG8580 78161 SENSE
    697 1500 CGPG8589 78162 SENSE
    698 1501 CGPG8590 78033 SENSE
    699 1502 CGPG8592 78622 SENSE
    700 1503 CGPG8594 78036 SENSE
    701 1504 CGPG8606 78043 SENSE
    702 1505 CGPG8628 78165 SENSE
    703 1506 CGPG8648 78066 SENSE
    704 1507 CGPG8654 78069 SENSE
    705 1508 CGPG8668 78183 SENSE
    706 1509 CGPG8678 78170 SENSE
    707 1510 CGPG8694 78953 SENSE
    708 1511 CGPG8702 78929 SENSE
    709 1512 CGPG8737 78564 SENSE
    710 1513 CGPG8745 78566 SENSE
    711 1514 CGPG8748 78591 SENSE
    712 1515 CGPG8749 78181 SENSE
    713 1516 CGPG8770 78190 SENSE
    714 1517 CGPG8777 78571 SENSE
    715 1518 CGPG8781 78933 SENSE
    716 1519 CGPG8786 78573 SENSE
    717 1520 CGPG8792 78632 SENSE
    718 1521 CGPG8801 78959 SENSE
    719 1522 CGPG8809 78191 SENSE
    720 1523 CGPG8840 78595 SENSE
    721 1524 CGPG8850 78646 SENSE
    722 1525 CGPG8870 76325 SENSE
    723 1526 CGPG8871 76337 SENSE
    724 1527 CGPG8872 76349 SENSE
    725 1528 CGPG8876 76302 SENSE
    726 1529 CGPG8902 76329 SENSE
    727 1530 CGPG8904 76353 SENSE
    728 1531 CGPG8907 76389 SENSE
    729 1532 CGPG8914 76378 SENSE
    730 1533 CGPG8931 76392 SENSE
    731 1534 CGPG8933 76321 SENSE
    732 1535 CGPG8935 76345 SENSE
    733 1536 CGPG8938 76381 SENSE
    734 1537 CGPG8944 76358 SENSE
    735 1538 CGPG895 12629 SENSE
    736 1539 CGPG8950 76335 SENSE
    737 1540 CGPG8961 76372 SENSE
    738 1541 CGPG8963 76396 SENSE
    739 1542 CGPG898 72314 SENSE
    740 1543 CGPG8993 77840 SENSE
    741 1544 CGPG8994 76886 SENSE
    742 1545 CGPG8995 76803 SENSE
    743 1546 CGPG90 10302 ANTI-
    SENSE
    744 1547 CGPG900 71107 SENSE
    745 1548 CGPG9002 76887 SENSE
    746 1549 CGPG9009 77842 SENSE
    747 1550 CGPG9011 76805 SENSE
    748 1551 CGPG9012 76817 SENSE
    749 1552 CGPG9017 77843 SENSE
    750 1553 CGPG9025 77844 SENSE
    751 1554 CGPG9026 76890 SENSE
    752 1555 CGPG9032 77839 SENSE
    753 1556 CGPG9040 76868 SENSE
    754 1557 CGPG9044 76821 SENSE
    755 1558 CGPG9048 76869 SENSE
    756 1559 CGPG9049 76881 SENSE
    757 1560 CGPG9058 76894 SENSE
    758 1561 CGPG906 11930 ANTI-
    SENSE
    759 1562 CGPG9070 76848 SENSE
    760 1563 CGPG9075 76901 SENSE
    761 1564 CGPG9084 76914 SENSE
    762 1565 CGPG9094 76939 SENSE
    763 1566 CGPG9098 76987 SENSE
    764 1567 CGPG9099 76904 SENSE
    765 1568 CGPG9110 76941 SENSE
    766 1569 CGPG9119 77113 SENSE
    767 1570 CGPG9125 77185 SENSE
    768 1571 CGPG913 12911 SENSE
    769 1572 CGPG9136 77127 SENSE
    770 1573 CGPG9156 77177 SENSE
    771 1574 CGPG9164 77178 SENSE
    772 1575 CGPG9172 77179 SENSE
    773 1576 CGPG9173 77191 SENSE
    774 1577 CGPG9185 77145 SENSE
    775 1578 CGPG9187 77169 SENSE
    776 1579 CGPG9190 77110 SENSE
    777 1580 CGPG9193 77146 SENSE
    778 1581 CGPG9195 77170 SENSE
    779 1582 CGPG9203 77171 SENSE
    780 1583 CGPG9209 77148 SENSE
    781 1584 CGPG921 11933 ANTI-
    SENSE
    782 1585 CGPG9210 77160 SENSE
    783 1586 CGPG9211 77172 SENSE
    784 1587 CGPG9212 77184 SENSE
    785 1588 CGPG9216 77225 SENSE
    786 1589 CGPG9226 77250 SENSE
    787 1590 CGPG9252 77277 SENSE
    788 1591 CGPG9281 77245 SENSE
    789 1592 CGPG9289 77246 SENSE
    790 1593 CGPG9298 77462 SENSE
    791 1594 CGPG9299 77414 SENSE
    792 1595 CGPG9304 77439 SENSE
    793 1596 CGPG9310 77463 SENSE
    794 1597 CGPG9316 77488 SENSE
    795 1598 CGPG9317 77441 SENSE
    796 1599 CGPG9318 77464 SENSE
    797 1600 CGPG9324 77442 SENSE
    798 1601 CGPG9357 77419 SENSE
    799 1602 CGPG965 12444 SENSE
    800 1603 CGPG970 11791 ANTI-
    SENSE
    800 1603 CGPG970 12445 SENSE
    801 1604 CGPG982 71249 SENSE
    802 1605 CGPG994 71237 SENSE
    803 1606 CGPG996 12315 ANTI-
    SENSE
    803 1606 CGPG996 12366 SENSE
    • Recombinant DNA
  • DNA for use in the present invention to improve traits in plants have a nucleotide sequence of SEQ ID NO:1 through SEQ ID NO:803, as well as the homologs of such DNA molecules. A subset of the DNA for gene suppression aspects of the invention includes fragments of the disclosed full polynucleotides consisting of oligonucleotides of 21 or more consecutive nucleotides. In some embodiments, the nucleotides for gne suppression can be 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30 or more consecutive nucleotides. Oligonucleotides having a sequence selected from the group consisting of SEQ ID NO: 1 through SEQ ID NO: 803 can be as probes and primers for detection of the polynucleotides used in the invention. Other embodiments this invention are variants of the DNA. Such variants can be naturally occurring, including DNA from homologous genes from the same or a different species, or can be non-natural variants, for example DNA synthesized using chemical synthesis methods, or generated using recombinant DNA techniques. Degeneracy of the genetic code provides the possibility to substitute at least one base of the protein encoding sequence of a gene with a different base without causing the amino acid sequence of the polypeptide produced from the gene to be changed. Hence, a DNA in the present invention can have any base sequence that has been changed from the sequences provided herein by substitution in accordance with degeneracy of the genetic code.
  • Homologs of the genes providing DNA demonstrated uses in improving traits in model plants disclosed herein will generally have significant identity with the DNA disclosed herein. DNA is substantially identical to a reference DNA if, when the sequences of the polynucleotides are optimally aligned there is about 60% nucleotide equivalence; about 70% equivalence; about 80% equivalence; about 85% equivalence; about 90%; about 95%; about 98%, about 99% equivalence or about 99.5 equivalence over a comparison window. A comparison window can be at least 50-100 nucleotides or the entire length of the polynucleotide provided herein. Optimal alignment of sequences for aligning a comparison window can be conducted by algorithms; for example by computerized implementations of these algorithms (such as, the Wisconsin Genetics Software Package Release 7.0-10.0, Genetics Computer Group, 575 Science Dr., Madison, Wis.). The reference polynucleotide can be a full-length molecule or a portion of a longer molecule. In one embodiment, the window of comparison for determining polynucleotide identity of protein encoding sequences is the entire coding region.
  • Proteins used for imparting enhanced traits are entire proteins or at least a sufficient portion of the entire protein to impart the relevant biological activity of the protein. Proteins used for generation of transgenic plants having enhanced traits include the proteins with an amino acid sequence provided herein as SEQ ID NO: 804 through SEQ ID NO: 1606, as well as homologs of such proteins.
  • Homologs of the proteins in the invention are identified by comparison of the amino acid sequence of the protein to amino acid sequences of proteins from the same or different plant sources, e.g., manually or by using known homology-based search algorithms such as those commonly known and referred to as BLAST, FASTA, and Smith-Waterman. As used herein, a homolog is a protein from the same or a different organism that performs the same biological function as the polypeptide to which it is compared. An orthologous relation between two organisms is not necessarily manifest as a one-to-one correspondence between two genes, because a gene can be duplicated or deleted after organism phylogenetic separation, such as speciation. For a given protein, there can be no ortholog or more than one ortholog. Other complicating factors include alternatively spliced transcripts from the same gene, limited gene identification, redundant copies of the same gene with different sequence lengths or corrected sequence. A local sequence alignment program, e.g., BLAST, can be used to search a database of sequences to find similar sequences, and the summary Expectation value (E-value) used to measure the sequence base similarity. As a protein hit with the best E-value for a particular organism could be an ortholog or the only ortholog, a reciprocal BLAST search is used in the present invention to filter hit sequences with significant E-values for ortholog identification. The reciprocal BLAST entails search of the significant hits against a database of amino acid sequences from the base organism that are similar to the sequence of the query protein. A hit is a likely ortholog, when the reciprocal BLAST's best hit is the query protein itself or a protein encoded by a duplicated gene after speciation. Thus, homolog is used herein to describe proteins that are assumed to have functional similarity by inference from sequence base similarity. The relationship of homologs with amino acid sequences of SEQ ID NO: 1607 to SEQ ID NO: 94613 to the proteins with amino acid sequences of SEQ ID NO: 804 to SEQ ID NO: 1606 are found in the listing of Table 19.
  • Other functional homolog proteins differ in one or more amino acids from those of a trait-improving protein disclosed herein as the result of one or more of the well-known conservative amino acid substitutions, e.g., valine is a conservative substitute for alanine and threonine is a conservative substitute for serine. Conservative substitutions for an amino acid within the native sequence can be selected from other members of a class to which the naturally occurring amino acid belongs. Representative amino acids within these various classes include, but are not limited to: (1) acidic (negatively charged) amino acids such as aspartic acid and glutamic acid; (2) basic (positively charged) amino acids such as arginine, histidine, and lysine; (3) neutral polar amino acids such as glycine, serine, threonine, cysteine, tyrosine, asparagine, and glutamine; and (4) neutral nonpolar (hydrophobic) amino acids such as alanine, leucine, isoleucine, valine, proline, phenylalanine, tryptophan, and methionine. Conserved substitutes for an amino acid within a native amino acid sequence can be selected from other members of the group to which the naturally occurring amino acid belongs. For example, a group of amino acids having aliphatic side chains is glycine, alanine, valine, leucine, and isoleucine; a group of amino acids having aliphatic-hydroxyl side chains is serine and threonine; a group of amino acids having amide-containing side chains is asparagine and glutamine; a group of amino acids having aromatic side chains is phenylalanine, tyrosine, and tryptophan; a group of amino acids having basic side chains is lysine, arginine, and histidine; and a group of amino acids having sulfur-containing side chains is cysteine and methionine. Naturally conservative amino acids substitution groups are: valine-leucine, valine-isoleucine, phenylalanine-tyrosine, lysine-arginine, alanine-valine, aspartic acid-glutamic acid, and asparagine-glutamine. A further aspect of the invention comprises proteins that differ in one or more amino acids from those of a described protein sequence as the result of deletion or insertion of one or more amino acids in a native sequence.
  • Homologs of the trait-improving proteins provided herein will generally demonstrate significant sequence identity. Of particular interest are proteins having at least about 50% sequence identity, at least about 70% sequence identity or higher, e.g., at least about 80% sequence identity with an amino acid sequence of SEQ ID NO: 804 to SEQ ID NO: 1606. Additional embodiments also include those with higher identity, e.g., about 90%, about 92.5%, about 95%, about 98%, about 99%, or to about 99.5% identity. Identity of protein homologs is determined by optimally aligning the amino acid sequence of a putative protein homolog with a defined amino acid sequence and by calculating the percentage of identical and conservatively substituted amino acids over the window of comparison. The window of comparison for determining identity can be the entire amino acid sequence disclosed herein, e.g., the full sequence of any of SEQ ID NO: 804 to SEQ ID NO: 1606.
  • Genes that are homologous to each other can be grouped into families and included in multiple sequence alignments. Then a consensus sequence for each group can be derived. This analysis enables the derivation of conserved and class—(family) specific residues or motifs that are functionally important. These conserved residues and motifs can be further validated with 3D protein structure if available. The consensus sequence can be used to define the full scope of the invention, e.g., to identify proteins with a homolog relationship. Thus, the present invention contemplates that protein homologs include proteins with an amino acid sequence that has at least 90% identity to such a consensus amino acid sequence sequences.
    • Discovery of Trait-Improving Recombinant DNA
  • To identify nuclei with recombinant DNA that confer enhanced traits to plants, Arabidopsis thaliana was transformed with a candidate recombinant DNA construct and screened for an enhanced trait. Arabidopsis thaliana is used a model for genetics and metabolism in plants.
  • Arabidopsis has a small genome, and well-documented studies are available. It is easy to grow in large numbers and mutants defining important genetically controlled mechanisms are either available, or can readily be obtained. Various methods to introduce and express isolated homologous genes are available (see Koncz, et al., Methods in Arabidopsis Research et al., (1992), World Scientific, New Jersey, N.J., in “Preface”).
  • A two-step screening process was employed which comprised two passes of trait characterization to ensure that the trait modification was dependent on expression of the recombinant DNA, but not due to the chromosomal location of the integration of the transgene. Twelve independent transgenic lines for each recombinant DNA construct were established and assayed for the transgene expression levels. Five transgenic lines with high transgene expression levels were used in the first pass screen to evaluate the transgene's function in T2 transgenic plants. Subsequently, three transgenic events, which had been shown to have one or more enhanced traits, were further evaluated in the second pass screen to confirm the transgene's ability to impart an enhanced trait. The following Table 3 summarizes the enhanced traits that have been confirmed as provided by a recombinant DNA construct.
  • In particular, Table 3 reports:
  • “PEP SEQ ID” which is the amino acid sequence of the protein cognate to the DNA in the recombinant DNA construct corresponding to a protein sequence of a SEQ ID NO. in the Sequence Listing.
  • “construct_id” is an arbitrary name for the recombinant DNA describe more particularly in Table 1.
  • “annotation” refers to a description of the top hit protein obtained from an amino acid sequence query of each PEP SEQ ID NO to GenBank database of the National Center for Biotechnology Information (ncbi). More particularly, “gi” is the GenBank ID number for the top BLAST hit.
  • “description” refers to the description of the top BLAST hit.
  • “e-value” provides the expectation value for the BLAST hit.
  • “% id” refers to the percentage of identically matched amino acid residues along the length of the portion of the sequences which is aligned by BLAST between the sequence of interest provided herein and the hit sequence in GenBank.
  • “traits” identify by two letter codes the confirmed enhancement in a transgenic plant provided by the recombinant DNA. The codes for enhanced traits are:
  • “CK” which indicates cold tolerance enhancement identified under a cold shock tolerance screen;
  • “CS” which indicates cold tolerance enhancement identified by a cold germination tolerance screen;
  • “DS” which indicates drought tolerance enhancement identified by a soil drought stress tolerance screen;
  • “PEG” which indicates osmotic stress tolerance enhancement identified by a PEG induced osmotic stress tolerance screen;
  • “HS” which indicates heat stress tolerance enhancement identified by a heat stress tolerance screen;
  • “SS” which indicates high salinity stress tolerance enhancement identified by a salt stress tolerance screen;
  • “LN” which indicates nitrogen use efficiency enhancement identified by a limited nitrogen tolerance screen;
  • “LL” which indicates attenuated shade avoidance response identified by a shade tolerance screen under a low light condition;
  • “PP” which indicates enhanced growth and development at early stages identified by an early plant growth and development screen;
  • “SP” which indicates enhanced growth and development at late stages identified by a late plant growth and development screen provided herein.
  • TABLE 3
    PEP
    SEQ Annotation
    ID E- %
    NO Construct value Id Description traits
    804 70244 0 95 ref|NP_193113.1|CYP83A1 (CYTOCHROME P450 83A1); HS
    oxygen binding [Arabidopsis thaliana]
    805 71108 3.00E−54 100 gb|AAB61093.1|F20P5.4 gene product [Arabidopsis LL
    thaliana]
    806 12816 0 79 ref|NP_190754.2|CAX3 (cation exchanger 3); cation:cation LN
    antiporter [Arabidopsis thaliana]
    807 12650 1.00E−159 89 gb|AAC25513.1|AAC25513Strong similarity to hypothetical LN
    protein gb|Y09823 from A. thaliana.
    808 12031 1.00E−56 88 ref|NP_179413.1|unknown protein [Arabidopsis thaliana] LN
    809 12217 1.00E−168 88 ref|NP_194233.1|unknown protein [Arabidopsis thaliana] LN
    810 12043 2.00E−46 100 ref|NP_194730.1|unknown protein [Arabidopsis thaliana] PP
    811 12147 2.00E−33 68 ref|NP_190718.1|unknown protein [Arabidopsis thaliana] LN
    812 13638 0 100 ref|NP_189940.1|unknown protein [Arabidopsis thaliana] DS
    813 11860 2.00E−81 93 ref|NP_973419.1|unknown protein [Arabidopsis thaliana] LN
    814 72361 1.00E−139 93 ref|NP_178534.2|IBR5 (INDOLE-3-BUTYRIC ACID CK
    RESPONSE 5); protein tyrosine/serine/threonine
    phosphatase [Arabidopsis thaliana]
    815 12230 1.00E−23 100 ref|NP_564545.1|TOM6 (TRANSLOCASE OF THE LN
    OUTER MITOCHONDRIAL MEMBRANE 6) [Arabidopsis
    thaliana] sp|Q9XIA7|TOM6_ARATH Mitochondrial import
    receptor subunit TOM6 homolog (Translocase of outer
    membrane 6 kDa subunit homolog)
    816 71626 1.00E−47 93 ref|NP_177455.1|unknown protein [Arabidopsis thaliana] CK
    817 13454 0 96 ref|NP_566136.1|armadillo/beta-catenin repeat family LN
    protein [Arabidopsis thaliana]
    818 12173 4.00E−49 100 ref|NP_186751.1|ATISU2/ISU2 (IscU-like 2); structural CK
    molecule [Arabidopsis thaliana]
    819 17806 1.00E−35 54 ref|NP_188341.2|unknown protein [Arabidopsis thaliana ] LN
    820 12011 1.00E−144 99 ref|NP_567393.1|ATP-binding family protein [Arabidopsis LN
    thaliana]
    821 72915 1.00E−135 77 sp|Q94A43|BEH2_ARATHBES1/BZR1 homolog protein 2 SS
    822 13231 1.00E−161 96 ref|NP_178361.2|nucleic acid binding [Arabidopsis HS
    thaliana]
    823 13913 1.00E−147 88 ref|NP_028242.1|PDV2 (PLASTID DIVISION2) HS
    [Arabidopsis thaliana] gb|AAD26950.1|expressed protein
    [Arabidopsis thaliana]
    824 12749 1.00E−140 100 ref|NP_196620.1|unknown protein [Arabidopsis thaliana] LN
    825 78901 0 97 ref|NP_565919.1|COI1 (CORONATINE INSENSITIVE 1); HS PP
    ubiquitin-protein ligase [Arabidopsis thaliana]
    826 75969 0 100 ref|NP_174005.1|ATCUL3/ATCUL3A/CUL3/CUL3A (Cullin CS HS
    3A); protein binding/ubiquitin-protein ligase [Arabidopsis
    thaliana]
    827 15606 0 96 gb|AAA32781.1|cyclin emb|CAA44169.1|cyclin HS
    [Arabidopsis thaliana]
    828 75946 0 96 ref|NP_171797.2|CUL2 (cullin 2) [Arabidopsis thaliana] LL
    829 13050 0 97 ref|NP_175955.1|F-box family protein [Arabidopsis LN
    thaliana]
    830 75958 0 94 ref|NP_177170.1|lectin protein kinase, putative HS LN
    [Arabidopsis thaliana]
    831 17333 0 93 gb|AAF02796.1|AF195115_16Similar to receptor-like PP
    protein kinase precusor; F5I10.19 [Arabidopsis thaliana]
    832 76002 0 100 ref|NP_193038.1|MHK; kinase [Arabidopsis thaliana] HS PEG
    sp|P43294|MHK_ARATH Serine/threonine-protein kinase
    MHK
    833 78735 0 94 ref|NP_187132.1|protein kinase, putative [Arabidopsis LL PEG
    thaliana]
    834 13914 0 100 ref|NP_195033.1|pyruvate decarboxylase, putative HS SS
    [Arabidopsis thaliana]
    835 14405 0 92 ref|NP_187341.1|DIN3/LTA1 (DARK INDUCIBLE 3); LN SP
    alpha-ketoacid dehydrogenase [Arabidopsis thaliana]
    836 75983 0 100 ref|NP_171655.1|ACS2 (1-Amino-cyclopropane-1- CK
    carboxylate synthase 2) [Arabidopsis thaliana]
    837 70721 0 94 ref|NP_851005.1|LPD2 (LIPOAMIDE DEHYDROGENASE HS LN
    2); FAD binding/dihydrolipoyl dehydrogenase/disulfide
    oxidoreductase/oxidoreductase [Arabidopsis thaliana]
    838 13811 0 92 ref|NP_178093.1|ATNADP-ME4 (NADP-MALIC ENZYME DS
    4); malate dehydrogenase (oxaloacetate-decarboxylating)
    (NADP+)/malic enzyme/oxidoreductase, acting on NADH
    or NADPH, NAD or NADP as acceptor [Arabidopsis
    thaliana]
    838 13828 0 92 ref|NP_178093.1|ATNADP-ME4 (NADP-MALIC ENZYME LN
    4); malate dehydrogenase (oxaloacetate-decarboxylating)
    (NADP+)/malic enzyme/oxidoreductase, acting on NADH
    or NADPH, NAD or NADP as acceptor [Arabidopsis
    thaliana]
    839 13614 1.00E−122 96 ref|NP_176518.1|ribulose-phosphate 3-epimerase, LN
    cytosolic, putative/pentose-5-phosphate 3-epimerase,
    putative [Arabidopsis thaliana]
    840 76050 0 97 ref|NP_567714.1|AMY1 (ALPHA-AMYLASE-LIKE); alpha- CS
    amylase [Arabidopsis thaliana]
    841 13038 0 100 ref|NP_194382.1|fructose-bisphosphate aldolase, LN
    cytoplasmic [Arabidopsis thaliana]
    842 13040 1.00E−104 92 gb|AAB66906.1|eukaryotic initiation factor (iso)-4F p28 LN
    subunit [Arabidopsis thaliana]
    843 70716 1.00E−172 100 ref|NP_974170.1|serine/threonine protein kinase, putative HS
    [Arabidopsis thaliana]
    843 76039 0 99 ref|NP_001078396.1|PPDK (PYRUVATE HS
    ORTHOPHOSPHATE DIKINASE) [Arabidopsis thaliana]
    844 71611 0 99 ref|NP_001078396.1|PPDK (PYRUVATE CK PP
    ORTHOPHOSPHATE DIKINASE) [Arabidopsis thaliana]
    845 70253 0 100 ref|NP_200694.1|CYP86A1 (cytochrome P450, family 86, HS CK
    subfamily A, polypeptide 1); oxygen binding [Arabidopsis
    thaliana]
    846 14415 0 96 ref|NP_568054.1|SEC14 cytosolic factor, putative/ LN
    phosptoglyceride transfer protein, putative [Arabidopsis
    thaliana]
    847 13718 4.00E−56 100 ref|NP_196413.1|unknown protein [Arabidopsis thaliana] LN
    sp|Q9SD88|U139_ARATH UPF0139 protein At5g07960
    848 10706 0 88 gb|AAA19118.1|glutamyl-tRNA reductase CK HS
    848 10709 0 88 gb|AAA19118.1|glutamyl-tRNA reductase LN
    849 14340 1.00E−125 93 ref|NP_175332.1|unknown protein [Arabidopsis thaliana] LN
    850 13471 1.00E−136 95 ref|NP_565858.1|unknown protein [Arabidopsis thaliana] LN
    851 18304 1.00E−133 94 ref|NP_189283.1|TIP2 (TONOPLAST INTRINSIC HS
    PROTEIN 2); water channel [Arabidopsis thaliana]
    852 13623 0 96 ref|NP_176001.2|GTP-binding protein-related [Arabidopsis DS
    thaliana]
    853 18302 0 100 ref|NP_194702.2|NFC5 (NUCLEOSOME/CHROMATIN HS
    ASSEMBLY FACTOR GROUP C 5) [Arabidopsis thaliana]
    sp|Q9SU78|MSI5_ARATH WD-40 repeat-containing
    protein MSI5
    854 15053 0 97 ref|NP_001031261.1|unknown protein [Arabidopsis LN
    thaliana]
    855 15624 0 93 ref|NP_171975.2|RabGAP/TBC domain-containing protein LL PP
    [Arabidopsis thaliana]
    856 70412 0 81 ref|NP_179257.1|nodulin family protein [Arabidopsis HS
    thaliana]
    857 17902 0 91 ref|NP_564843.1|integral membrane transporter family PP
    protein [Arabidopsis thaliana]
    858 14272 0 90 ref|NP_566584.1|YSL5 (YELLOW STRIPE LIKE 5); LN
    oligopeptide transporter [Arabidopsis thaliana]
    859 15122 0 95 ref|NP_565817.2|glycogenin glucosyltransferase LN
    (glycogenin)-related [Arabidopsis thaliana]
    859 70723 0 95 ref|NP_565817.2|glycogenin glucosyltransferase HS
    (glycogenin)-related [Arabidopsis thaliana]
    860 14248 1.00E−154 79 ref|NP_176081.1|unknown protein [Arabidopsis thaliana] DS
    861 13965 0 100 ref|NP_173104.1|Per1-like family protein [Arabidopsis CK
    thaliana]
    862 75912 1.00E−169 100 ref|NP_199075.1|unknown protein [Arabidopsis thaliana] CS LL
    863 14344 1.00E−81 100 ref|NP_566785.1|universal stress protein (USP) family CS
    protein [Arabidopsis thaliana]
    864 14807 0 89 gb|AAD20391.1|hypothetical protein [Arabidopsis thaliana] CS
    865 17307 0 89 dbj|BAE98505.1|hypothetical protein [Arabidopsis thaliana] PP
    866 16431 0 73 ref|NP_201248.1|octicosapeptide/Phox/Bem1p (PB1) LN
    domain-containing protein [Arabidopsis thaliana]
    867 73075 0 96 ref|NP_187459.2|protein binding/zinc ion binding CS
    [Arabidopsis thaliana]
    868 16323 9.00E−57 89 ref|NP_171768.2|transcription initiation factor IID (TFIID) LN
    18 kDa subunit (TAFII-18) family protein [Arabidopsis
    thaliana]
    869 14833 1.00E−141 90 ref|NP_176341|CCR4-NOT transcription complex SP
    protein, putative [Arabidopsis thaliana]
    870 17030 0 95 gb|AAG28899.1|AC008113_15F12A21.29 [Arabidopsis LL
    thaliana]
    871 76414 0 99 ref|NP_180595.1|CIPK11 (SNF1-RELATED PROTEIN PEG
    KINASE 3.22, SOS3-INTERACTING PROTEIN 4); kinase
    [Arabidopsis thaliana]
    872 16021 0 82 ref|NP_201301.1|CDKC;2 (CYCLIN-DEPENDENT KINASE LN
    C; 2); kinase [Arabidopsis thaliana]
    873 78701 0 93 ref|NP_564203.1|F-box family protein [Arabidopsis HS
    thaliana]
    874 78702 0 93 ref|NP_565142.1|F-box family protein (FBX3) [Arabidopsis PEG
    thaliana]
    875 15220 0 89 ref|NP_173623.1|kelch repeat-containing F-box family LN
    protein [Arabidopsis thaliana] sp|Q9LM55|FBK8_ARATH
    F-box/Kelch-repeat protein
    876 15623 0 88 ref|NP_179623.1|transducin family protein/WD-40 repeat HS
    family protein [Arabidopsis thaliana]
    877 19402 0 96 ref|NP_568408.1|F-box family protein/WD-40 repeat PP
    family protein [Arabidopsis thaliana]
    878 70559 0 98 ref|NP_181061.1|SUVH5 (SU(VAR)3-9 HOMOLOG 5) LN
    [Arabidopsis thaliana]
    879 15111 0 90 ref|NP_197821.1|ATXR6 (Arabidopsis thaliana Trithorax- DS
    related protein 6); DNA binding
    sp|Q9FNE9|ATXR6_ARATH Histone-lysine N-
    methyltransferase ATXR6 (Trithorax-related protein 6)
    (TRX-related protein 6)
    880 70832 0 100 ref|NP_172633.1|CYP51G1 (CYTOCHROME P450 51); HS
    oxygen binding [Arabidopsis thaliana]
    881 15129 4.00E−82 77 ref|NP_188372.1|PHD finger family protein [Arabidopsis LN
    thaliana]
    882 76086 0 91 ref|NP_192814.1|EMB1706 (EMBRYO DEFECTIVE 1706); PP
    S-adenosylmethionine-dependent methyltransferase
    [Arabidopsis thaliana]
    883 15203 1.00E−158 94 gb|AAD30650.1|AC006085_23Similar to human CGI-33 CK
    protein [Arabidopsis thaliana]
    884 70216 0 95 ref|NP_567665.2|CYP706A1 (cytochrome P450, family HS PP
    706, subfamily A, polypeptide 1); oxygen binding
    [Arabidopsis thaliana]
    885 14910 0 100 ref|NP_201191.1|UVR8 (UVB-RESISTANCE 8) DS
    [Arabidopsis thaliana]
    886 70318 0 92 ref|NP_172325.2|ATCPNIFS/ATNFS2/ATSUFS/CPNIFS/SUFS HS
    (CHLOROPLASTIC NIFS-LIKE CYSTEINE
    DESULFURASE); cysteine desulfurase/selenocysteine
    lyase/transaminase [Arabidopsis thaliana]
    887 15207 1.00E−44 99 gb|AAG51737.1|AC068667_16beta-1,3 glucanase, SP
    putative; 26636-27432 [Arabidopsis thaliana]
    888 14915 0 97 ref|NP_199393.1|CIPK19 (CIPK19); kinase [Arabidopsis LN
    thaliana]
    889 15132 1.00E−152 80 ref|NP_187881.1|ZIP1 (ZINC TRANSPORTER 1 LN
    PRECURSOR); zinc ion transporter [Arabidopsis thaliana]
    890 16229 0 100 gb|ABG54330.1|double HA-tagged mitogen activated SS
    protein kinase 3 [synthetic construct]
    891 14932 0 100 ref|NP_568748.1|nucleotide-binding family protein DS
    [Arabidopsis thaliana]
    892 76017 1.00E−180 100 ref|NP_568235.1|unknown protein [Arabidopsis thaliana] HS PP
    893 15964 1.00E−44 100 ref|NP_566894.1|unknown protein [Arabidopsis thaliana] DS
    894 17227 8.00E−83 73 gb|AAD03429.1|similar to nascent polypeptide associated CS
    complex alpha chain [Arabidopsis thaliana]
    895 72952 0 96 ref|NP_564480.1|unknown protein [Arabidopsis thaliana] CS
    896 73706 0 96 ref|NP_568221.1|protein kinase, putative [Arabidopsis HS SS
    thaliana]
    897 18203 0 92 ref|NP_568919.1|APRR3 (PSEUDO-RESPONSE HS
    REGULATOR 3); transcription regulator [Arabidopsis
    thaliana]
    898 16309 1.00E−163 88 ref|NP_195558.1|GGR (GERANYLGERANYL LN
    REDUCTASE); farnesyltranstransferase [Arabidopsis
    thaliana]
    899 15986 3.00E−99 84 dbj|BAF02216.1|hypothetical protein [Arabidopsis thaliana] DS
    900 15987 2.00E−54 79 ref|NP_174170.1|glutaredoxin family protein [Arabidopsis DS
    thaliana]
    901 16204 2.00E−59 100 ref|NP_566191.1|NADH-ubiquinone oxidoreductase- LN
    related [Arabidopsis thaliana]
    902 11133 1.00E−114 100 ref|NP_563897.1|alanine racemase family protein LN
    [Arabidopsis thaliana]
    903 73977 9.00E−67 100 ref|NP_194677.1|mitochondrial ATP synthase g subunit HS
    family protein [Arabidopsis thaliana]
    904 15995 1.00E−176 84 ref|NP_564660.1|unknown protein [Arabidopsis thaliana] DS
    904 18201 1.00E−176 84 ref|NP_564660.1|unknown protein [Arabidopsis thaliana] PP
    905 16887 1.00E−164 100 ref|NP_171820.1|phenazine biosynthesis PhzC/PhzF PP
    family protein [Arabidopsis thaliana]
    906 16213 1.00E−140 82 ref|NP_563991.1|unknown protein [Arabidopsis thaliana] HS
    907 15507 0 96 ref|NP_172255.1|cupin family protein [Arabidopsis LN
    thaliana]
    908 15508 3.00E−86 100 ref|NP_564937.1|unknown protein [Arabidopsis thaliana] LN
    909 15959 3.00E−56 74 ref|NP_180097.1|unknown protein [Arabidopsis thaliana] LN
    910 72427 0 93 ref|NP_568346.1|tubulin family protein [Arabidopsis HS
    thaliana]
    911 19041 2.00E−85 82 ref|NP_565723.1|unknown protein [Arabidopsis thaliana] HS LN
    912 17802 1.00E−118 100 ref|NP_187425.1|emp24/gp25L/p24 family protein HS
    [Arabidopsis thaliana]
    913 19042 0 94 ref|NP_569048.1|ARA12; subtilase [Arabidopsis thaliana] HS
    914 76053 0 94 ref|NP_172544.1|unknown protein [Arabidopsis thaliana] HS
    915 16120 1.00E−56 90 ref|NP_192997.1|ribosomal protein CK
    L7Ae/L30e/S12e/Gadd45 family protein [Arabidopsis
    thaliana]
    916 15424 1.00E−103 94 ref|NP_196647.1|CBS domain-containing protein HS
    [Arabidopsis thaliana]
    917 16401 0 90 ref|NP_179995.1|CYP71B6 (CYTOCHROME P450 71B6); PP
    oxygen binding [Arabidopsis thaliana]
    918 72417 0 100 gb|AAK25868.1|AF360158_1unknown protein [Arabidopsis CK
    thaliana]
    919 73702 0 90 ref|NP_564657.1|spliceosome protein-related [Arabidopsis HS SS
    thaliana]
    920 70706 0 100 gb|AAD17366.1|similar to human phosphotyrosyl HS
    phosphatase activator PTPA (GB: X73478) [Arabidopsis
    thaliana]
    921 71145 4.00E−57 86 gb|AAG40386.1|AF325034_1AT5g02160 [Arabidopsis HS
    thaliana]
    922 11609 0 97 gb|AAC34228.1|putative cytochrome P450 [Arabidopsis LN
    thaliana]
    923 71706 0 88 gb|AAF03464.1|AC009327_3 hypothetical protein CK
    [Arabidopsis thaliana]
    924 17325 1.00E−144 86 ref|NP_563896.1|unknown protein [Arabidopsis thaliana] PP
    925 70102 1.00E−166 100 ref|NP_353899.2|hypothetical protein Atu0877 HS
    [Agrobacterium tumefaciens str. C58]
    926 70106 1.00E−151 92 ref|NP_353321.1|hypothetical protein Atu0291 HS
    [Agrobacterium tumefaciens str. C58]
    927 70113 3.00E−94 94 ref|NP_013690.1|Adenine phosphoribosyltransferase, HS
    catalyzes the formation of AMP from adenine and 5-
    phosphoribosylpyrophosphate; involved in the salvage
    pathway of purine nucleotide biosynthesis; Apt1p
    [Saccharomyces cerevisiae]
    928 70115 0 100 ref|NP_116623.1|Alanine:glyoxylate aminotransferase HS
    (AGT), catalyzes the synthesis of glycine from glyoxylate,
    which is one of three pathways for glycine biosynthesis in
    yeast; has similarity to mammalian and plant
    alanine:glyoxylate aminotransferases; Agx1p
    [Saccharomyces cerevisiae]
    929 70118 0 94 ref|NP_012111.1|Mitochondrial glycerol-3-phosphate SP
    dehydrogenase; expression is repressed by both glucose
    and cAMP and derepressed by non-fermentable carbon
    sources in a Snf1p, Rsf1p, Hap2/3/4/5 complex dependent
    manner; Gut2p [Saccharomyces cerevisiae]
    930 70128 9.00E−85 70 ref|NP_638658.1|membrane-bound proton-translocating HS
    pyrophosphatase [Xanthomonas campestris pv.
    campestris str. ATCC 33913]
    931 70130 1.00E−161 99 ref|NP_639330.1|a-type carbonic anhydrase HS PEG
    [Xanthomonas campestris pv. campestris str. ATCC
    33913]
    932 17103 0 88 ref|NP_173155.1|CAT8 (CATIONIC AMINO ACID SS
    TRANSPORTER 8); cationic amino acid transporter
    [Arabidopsis thaliana]
    933 72748 1.00E−33 74 ref|NP_568635.1|unknown protein [Arabidopsis thaliana] HS
    934 17502 3.00E−94 74 ref|NP_565588.1|unknown protein [Arabidopsis thaliana] HS
    935 17503 1.00E−130 100 ref|NP_176178.1|ATGSTU16 (Arabidopsis thaliana HS
    Glutathione S-transferase (class tau) 16); glutathione
    transferase
    936 78708 1.00E−168 95 gb|AAK43902.1|AF370583_1Unknown protein LL
    [Arabidopsis thaliana]
    937 17504 1.00E−139 95 ref|NP_565634.1|harpin-induced protein-related/HIN1- HS LL PP
    related/harpin-responsive protein-related [Arabidopsis
    thaliana]
    938 17132 1.00E−127 100 ref|NP_187978.1|seven in absentia (SINA) family protein LN
    [Arabidopsis thaliana]
    939 72965 0 91 gb|AAN60250.1|unknown [Arabidopsis thaliana] LL
    940 72796 3.00E−61 100 ref|NP_201508.1|RALFL34 (RALF-LIKE 34) [Arabidopsis CS
    thaliana]
    941 16617 5.00E−96 100 ref|NP_355193.2|adenine phosphoribosyltransferase CS HS
    [Agrobacterium tumefaciens str. C58]
    942 16640 0 100 ref|NP_355113.2|alcohol dehydrogenase [Agrobacterium HS
    tumefaciens str. C58]
    943 16603 1.00E−132 85 ref|NP_357530.1|ribokinase [Agrobacterium tumefaciens HS
    str. C58]
    944 16612 1.00E−137 100 ref|NP_010335.1|Triose phosphate isomerase, abundant LN SP
    glycolytic enzyme; mRNA half-life is regulated by iron
    availability; transcription is controlled by activators Reb1p,
    Gcr1p, and Rap1p through binding sites in the 5′ non-
    coding region; Tpi1p [Saccharomyces cerevisiae]
    945 16614 1.00E−109 100 ref|NP_010741.1|Stress inducible cytoplasmic thioredoxin DS
    peroxidase; cooperates with Tsa1p in the removal of
    reactive oxygen, nitrogen and sulfur species using
    thioredoxin as hydrogen donor; deletion enhances the
    mutator phenotype of tsa1 mutants; Tsa2p
    [Saccharomyces cerevisiae]
    946 78354 7.00E−80 100 ref|NP_192392.1|methionine sulfoxide reductase domain- SS
    containing protein/SelR domain-containing protein
    [Arabidopsis thaliana]
    947 17818 6.00E−19 60 ref|NP_564780.1|TIM13 (TIM13); protein translocase PP
    [Arabidopsis thaliana]
    948 78370 3.00E−64 91 ref|NP_194900.1|TAFII15 (SALT TOLERANCE DURING HS
    GERMINATION 1); transcription factor [Arabidopsis
    thaliana]
    949 70411 0 90 ref|NP_849806.1|UBP1A; mRNA 3′-UTR binding SP
    [Arabidopsis thaliana]
    950 19154 1.00E−151 89 ref|NP_197310.1|transcriptional factor B3 family protein HS LN PP
    [Arabidopsis thaliana]
    951 19155 0 82 ref|NP_200906.2|nuclear transport factor 2 (NTF2) family HS
    protein/RNA recognition motif (RRM)-containing protein
    [Arabidopsis thaliana]
    952 18307 0 94 ref|NP_194507.1|ACBP2 (ACYL-COA BINDING PROTEIN HS
    ACBP 2) [Arabidopsis thaliana]
    953 72030 0 86 ref|NP_177367.1|zinc finger (C3HC4-type RING finger) LN
    family protein [Arabidopsis thaliana]
    954 17916 1.00E−173 95 ref|NP_568839.1|CSN6A (COP9 signalosome subunit 6A) PP
    [Arabidopsis thaliana]
    955 17917 0 96 ref|NP_188478.1|aspartyl protease family protein SS
    [Arabidopsis thaliana]
    956 17334 0 94 ref|NP_178146.1|chloroplast ADP, ATP carrier protein 1/ PP
    ADP, ATP translocase 1/adenine nucleotide translocase
    1 (AATP1) [Arabidopsis thaliana]
    957 71531 0 100 ref|NP_565656.1|aldo/keto reductase family protein HS
    [Arabidopsis thaliana]
    958 18441 7.00E−75 100 ref|NP_973779.1|lactoylglutathione lyase family protein/ HS
    glyoxalase I family protein [Arabidopsis thaliana]
    959 19162 2.00E−73 85 ref|NP_563687.1|photosystem II family protein DS
    [Arabidopsis thaliana]
    960 73205 0 98 ref|NP_190414.1|zinc finger (CCCH-type) family protein PEG
    [Arabidopsis thaliana]
    961 18306 1.00E−172 100 ref|NP_566769.1|LAG1 (Longevity assurance gene 1) SS
    [Arabidopsis thaliana]
    962 70808 0 97 ref|NP_196136.1|CESA3 (CELLULASE SYNTHASE 3); CS CK
    cellulose synthase/transferase, transferring glycosyl
    groups [Arabidopsis thaliana]
    963 17653 1.00E−178 95 ref|NP_199155.1|zinc finger (C3HC4-type RING finger) LN
    family protein [Arabidopsis thaliana]
    964 19535 0 81 ref|NP_567002.1|GCN5 (Histon acetyltransferase HAT1) HS
    [Arabidopsis thaliana]
    965 71719 0 99 ref|NP_192044.1|DC1 domain-containing protein HS LL PP
    [Arabidopsis thaliana]
    966 18546 1.00E−102 92 ref|NP_176285.1|AGL56 (AGAMOUS LIKE-56); DNA PP
    binding/transcription factor [Arabidopsis thaliana]
    967 19534 0 78 ref|NP_566721.1|binding [Arabidopsis thaliana] HS
    968 18421 0 96 gb|ABK06451.1|flag-tagged protein kinase domain of HS
    putative mitogen-activated protein kinase kinase kinase
    [synthetic construct]
    969 18422 0 100 ref|NP_194498.1|MSP1 protein, putative/ FIS
    intramitochondrial sorting protein, putative [Arabidopsis
    thaliana]
    970 19539 0 95 ref|NP_191747.1|CYP78A9 (CYTOCHROME P450 78A9); HS PP
    oxygen binding [Arabidopsis thaliana]
    971 19244 3.00E−74 88 ref|NP_565113.1|auxin-responsive family protein HS
    [Arabidopsis thaliana]
    972 15803 1.00E−142 100 ref|NP_199675.2|cyclin family protein [Arabidopsis HS
    thaliana]
    973 19545 0 100 ref|NP_568665.1|pentatricopeptide (PPR) repeat- HS
    containing protein [Arabidopsis thaliana]
    974 10222 0 94 ref|NP_190896.1|CYP71B5 (CYTOCHROME P450 71B5); LN
    oxygen binding [Arabidopsis thaliana]
    974 72356 0 94 ref|NP_190896.1|CYP71B5 (CYTOCHROME P450 71B5); CK PEG
    oxygen binding [Arabidopsis thaliana]
    975 70425 0 98 ref|NP_200201.3|unknown protein [Arabidopsis thaliana] HS
    976 19237 1.00E−150 95 ref|NP_199836.1|31 kDa ribonucleoprotein, chloroplast, HS
    putative/RNA-binding protein RNP-T, putative/RNA-
    binding protein 1/2/3, putative/RNA-binding protein cp31,
    putative [Arabidopsis thaliana]
    977 71303 0 82 ref|NP_199431.1|KH domain-containing protein HS
    [Arabidopsis thaliana]
    978 19240 1.00E−180 100 ref|NP_566576.1|meprin and TRAF homology domain- LN
    containing protein/MATH domain-containing protein
    [Arabidopsis thaliana]
    979 18535 0 100 ref|NP_196179.1|oxidoreductase, 2OG-Fe(II) oxygenase HS
    family protein [Arabidopsis thaliana]
    980 19450 0 94 ref|NP_565422.1|pentatricopeptide (PPR) repeat- LN
    containing protein [Arabidopsis thaliana]
    981 18221 1.00E−66 100 ref|NP_193992.1|protease inhibitor/seed storage/lipid PP
    transfer protein (LTP) family protein [Arabidopsis thaliana]
    982 18233 1.00E−110 87 ref|NP_193179.1|enoyl-CoA hydratase/isomerase family PP
    protein [Arabidopsis thaliana]
    983 18236 1.00E−31 70 ref|NP_565410.1|unknown protein [Arabidopsis thaliana] PP
    984 18238 1.00E−129 88 ref|NP_197105.1|3-oxo-5-alpha-steroid 4-dehydrogenase HS
    family protein/steroid 5-alpha-reductase family protein
    [Arabidopsis thaliana]
    985 18309 1.00E−128 93 gb|AAM61596.1|DNA-binding protein [Arabidopsis CS PEG
    thaliana]
    986 70337 0 85 gb|AAP84710.2|metacaspase 7 [Arabidopsis thaliana] HS
    987 18319 1.00E−105 89 ref|NP_172721.1|DDF1 (DWARF AND DELAYED LN
    FLOWERING 1); DNA binding/transcription factor
    [Arabidopsis thaliana]
    988 70338 1.00E−172 85 ref|NP_200445.1|zinc finger (C3HC4-type RING finger) LL
    family protein [Arabidopsis thaliana]
    989 10471 1.00E−114 84 dbj|BAF00210.1|hypothetical protein [Arabidopsis thaliana] DS
    990 18331 1.00E−114 63 ref|NP_565124.1|nucleic acid binding [Arabidopsis CS
    thaliana]
    991 10228 0 97 ref|NP_563880.1|TIF3H1 (eukaryotic translation initiation LN
    factor 3 subunit H1); translation initiation factor
    [Arabidopsis thaliana]
    991 10473 0 97 ref|NP_563880.1|TIF3H1 (eukaryotic translation initiation LN
    factor 3 subunit H1); translation initiation factor
    [Arabidopsis thaliana]
    992 18261 1.00E−167 91 ref|NP_563732.1|peroxidase, putative [Arabidopsis PP
    thaliana]
    993 18848 0 94 ref|NP_177805.1|O-methyltransferase family 2 protein LN
    [Arabidopsis thaliana]
    994 18268 1.00E−130 92 gb|AAM62813.1|unknown [Arabidopsis thaliana] PP
    995 18345 0 92 ref|NP_182320.1|SWA1 (SLOW WALKER1); nucleotide HS
    binding [Arabidopsis thaliana]
    996 73607 0 92 ref|NP_851068.1|WD-40 repeat family protein [Arabidopsis HS
    thaliana]
    997 18352 1.00E−166 83 ref|NP_201275.1|nodulin MtN21 family protein HS SS PEG
    [Arabidopsis thaliana]
    998 18357 1.00E−171 100 ref|NP_172866.1|mitochondrial substrate carrier family PP
    protein [Arabidopsis thaliana]
    999 19423 0 100 ref|NP_177020.1|CUT1 (CUTICULAR 1); acyltransferase DS
    [Arabidopsis thaliana]
    1000 78373 0 94 ref|NP_179537.1|CKL5 (Casein Kinase I-like 5); casein CK HS
    kinase I/kinase [Arabidopsis thaliana]
    1001 70603 0 100 ref|NP_175081.1|ALDH3H1 (ALDEHYDE HS LN
    DEHYDROGENASE 4); 3-chloroallyl aldehyde
    dehydrogenase/aldehyde dehydrogenase (NAD)
    [Arabidopsis thaliana]
    1002 19616 1.00E−159 100 ref|NP_563789.1|SMO2-2 (sterol 4-alpha-methyl-oxidase HS
    2); C-4 methylsterol oxidase [Arabidopsis thaliana]
    1003 19425 1.00E−164 91 ref|NP_564407.1|electron carrier/iron ion binding DS
    [Arabidopsis thaliana]
    1004 19426 1.00E−152 89 ref|NP_564428.1|unknown protein [Arabidopsis thaliana] PP
    1005 18382 2.00E−51 87 ref|NP_564651.1|unknown protein [Arabidopsis thaliana] PP
    1006 71536 4.00E−86 86 ref|NP_564747.1|ZCF37 [Arabidopsis thaliana] HS
    1007 70419 6.00E−88 66 ref|NP_564888.1|unknown protein [Arabidopsis thaliana] LL CK DS
    1008 70827 6.00E−85 100 ref|NP_189667.1|zinc finger (C3HC4-type RING finger) HS
    family protein [Arabidopsis thaliana]
    1009 19311 0 94 ref|NP_010849.1|Ferrioxamine B transporter, member of LN
    the ARN family of transporters that specifically recognize
    siderophore-iron chelates; transcription is induced during
    iron deprivation and diauxic shift; potentially
    phosphorylated by Cdc28p; Sit1p [Saccharomyces
    cerevisiae]
    1010 19323 0 92 ref|NP_354642.2|malic enzyme [Agrobacterium LL
    tumefaciens str. C58]
    1011 19320 0 100 ref|NP_012542.1|Glyceraldehyde-3-phosphate HS
    dehydrogenase, isozyme 2, involved in glycolysis and
    gluconeogenesis; tetramer that catalyzes the reaction of
    glyceraldehyde-3-phosphate to 1,3 bis-phosphoglycerate;
    detected in the cytoplasm and cell-wall; Tdh2p
    [Saccharomyces cerevisiae]
    1012 73613 0 95 ref|NP_197104.1|NIK1 (NSP-INTERACTING KINASE 1); CK
    kinase [Arabidopsis thaliana]
    1013 70432 1.00E−162 91 ref|NP_196709.1|GTP binding [Arabidopsis thaliana] SS
    1014 70433 0 100 ref|NP_196957.1|transducin family protein/WD-40 repeat HS
    family protein [Arabidopsis thaliana]
    1015 70434 1.00E−142 94 ref|NP_180497.1|tropinone reductase, putative/tropine HS
    dehydrogenase, putative [Arabidopsis thaliana]
    1016 72614 1.00E−128 79 ref|NP_197757.1|sterile alpha motif (SAM) domain- LL
    containing protein [Arabidopsis thaliana]
    1017 70436 7.00E−35 70 ref|NP_197966.1|early nodulin-related [Arabidopsis CS HS
    thaliana]
    1018 74226 0 92 dbj|BAB02016.1|MAP kinase [Arabidopsis thaliana] PP
    1019 70439 1.00E−123 91 ref|NP_191247.1|VQ motif-containing protein [Arabidopsis HS PEG
    thaliana]
    1020 70446 1.00E−128 100 ref|NP_568972.2|unknown protein [Arabidopsis thaliana] CS
    1021 70613 0 93 ref|NP_174145.1|unknown protein [Arabidopsis thaliana] PEG
    1022 70447 0 97 ref|NP_175977.1|uracil phosphoribosyltransferase, CK
    putative/UMP pyrophosphorylase, putative/UPRTase,
    putative [Arabidopsis thaliana] ref|NP_974037.1|uracil
    phosphoribosyltransferase, putative/UMP
    pyrophosphorylase, putative/UPRTase, putative
    [Arabidopsis thaliana]
    1023 71725 0 67 gb|ABE65946.1|nucleolin [Arabidopsis thaliana] CK
    1024 70462 9.00E−73 92 ref|NP_567037.1|ARR17 (response regulator 17); PEG
    transcription regulator/two-component response regulator
    [Arabidopsis thaliana]
    1025 70545 0 95 ref|NP_176108.3|bZIP family transcription factor SP
    [Arabidopsis thaliana]
    1026 70741 0 100 gb|AAM78097.1|AT4g18060/F15J5_30 [Arabidopsis HS
    thaliana]
    1027 19702 0 97 ref|NP_011904.1|Protein of unknown function, green HS
    fluorescent protein (GFP)-fusion protein localizes to the
    endoplasmic reticulum; msc7 mutants are defective in
    directing meiotic recombination events to homologous
    chromatids; Msc7p [Saccharomyces cerevisiae]
    1028 19985 1.00E−140 86 gb|AAA88792.1|nucleosome assembly protein 1 HS
    1029 19775 1.00E−80 54 ref|NP_175779.1|unknown protein [Arabidopsis thaliana] CK HS PP LN
    1030 19829 3.00E−56 42 ref|NP_565892.1|unknown protein [Arabidopsis thaliana] CS
    1031 19982 1.00E−123 79 gb|AAV49506.1|L-galactose-1-phosphate phosphatase HS PEG
    [Actinidia deliciosa]
    1032 19755 1.00E−110 63 emb|CAO23381.1|unnamed protein product [Vitis vinifera] HS
    1033 19732 0 96 dbj|BAA22559.1|squalene synthase [Glycine max] PP
    1034 70365 0 91 gb|AAQ84169.1|1-deoxy-D-xylulose 5-phosphate synthase CS
    [Pueraria montana var. lobata]
    1035 10476 1.00E−168 86 ref|NP_194096.1|CDPK6 (CALCIUM-DEPENDENT LN
    PROTEIN KINASE 6); anion channel/calcium- and
    calmodulin-dependent protein kinase/kinase [Arabidopsis
    thaliana]
    1036 19987 0 83 emb|CAO67062.1|unnamed protein product [Vitis vinifera] HS
    1037 19893 1.00E−166 85 gb|ABC75353.2|Intracellular chloride channel [Medicago HS
    truncatula]
    1038 19983 6.00E−92 60 emb|CAO39739.1|unnamed protein product [Vitis vinifera] HS LL
    1039 19825 1.00E−40 39 emb|CAO18125.1|unnamed protein product [Vitis vinifera] HS
    1040 19919 1.00E−121 77 emb|CAO61472.1|unnamed protein product [Vitis vinifera] HS
    1041 19979 0 67 emb|CAO68238.1|unnamed protein product [Vitis vinifera] HS
    1042 19786 2.00E−80 75 emb|CAO48404.1|unnamed protein product [Vitis vinifera] HS LN
    1043 70903 0 76 emb|CAO66035.1|unnamed protein product [Vitis vinifera] HS PP PEG
    1044 70970 1.00E−102 67 ref|NP_200538.1|unknown protein [Arabidopsis thaliana] HS
    1045 70980 0 89 dbj|BAE71243.1|putative galactose kinase [Trifolium CK
    pratense]
    1046 70936 1.00E−158 49 emb|CAO71465.1|unnamed protein product [Vitis vinifera] HS
    1047 71425 1.00E−160 74 emb|CAO14679.1|unnamed protein product [Vitis vinifera] DS
    1048 78666 3.00E−45 83 ref|NP_192698.1|GASA3 (GAST1 PROTEIN HOMOLOG LN
    3) [Arabidopsis thaliana]
    1049 71202 1.00E−163 95 ref|NP_194179.1|serine/threonine protein kinase, putative LN
    [Arabidopsis thaliana]
    1050 78973 0 90 ref|NP_565672.1|DRB2 (DSRNA-BINDING PROTEIN 2); LL
    double-stranded RNA binding [Arabidopsis thaliana]
    1051 76411 1.00E−179 99 ref|NP_172864.1|2-oxoglutarate-dependent dioxygenase, PP
    putative [Arabidopsis thaliana]
    1052 70635 4.00E−64 100 ref|NP_851278.1|senescence-associated family protein HS
    [Arabidopsis thaliana]
    1053 73715 0 92 ref|NP_198428.1|G6PD1 (GLUCOSE-6-PHOSPHATE PEG
    DEHYDROGENASE 1); glucose-6-phosphate 1-
    dehydrogenase [Arabidopsis thaliana]
    1054 70638 6.00E−79 89 ref|NP_197398.1|AWPM-19-like membrane family protein HS LN
    [Arabidopsis thaliana]
    1055 70642 1.00E−176 92 ref|NP_191315.1|aspartate/glutamate/uridylate kinase HS
    family protein [Arabidopsis thaliana]
    1056 70643 0 96 ref|NP_191703.1|ATCYSC1 (BETA-SUBSTITUTED ALA HS
    SYNTHASE 3; 1); L-3-cyanoalanine synthase/cysteine
    synthase [Arabidopsis thaliana]
    1057 71564 1.00E−121 95 emb|CAA47753.1|proteosome subunit [Arabidopsis HS SP
    thaliana]
    1058 75039 1.00E−175 90 ref|NP_188659.1|mitochondrial substrate carrier family LN
    protein [Arabidopsis thaliana]
    1059 70653 8.00E−82 100 ref|NP_566365.1|unknown protein [Arabidopsis thaliana] PEG
    1060 70655 4.00E−87 82 ref|NP_566619.1|unknown protein [Arabidopsis thaliana] LL PEG
    1061 78321 0 97 ref|NP_181404.1|MVD1 (mevalonate diphosphate DS HS
    decarboxylase 1) [Arabidopsis thaliana]
    1062 78307 0 100 ref|NP_182079.1|CYP76C4 (cytochrome P450, family 76, CK
    subfamily C, polypeptide 4); oxygen binding [Arabidopsis
    thaliana]
    1063 71808 0 91 ref|NP_182082.2|CYP76C3 (cytochrome P450, family 76, HS
    subfamily C, polypeptide 3); oxygen binding [Arabidopsis
    thaliana]
    1064 71810 0 97 gb|AAF88087.1|AC025417_15T12C24.27 [Arabidopsis LN
    thaliana]
    1065 71313 0 100 ref|NP_187667.1|CYP77A7 (cytochrome P450, family 77, CS
    subfamily A, polypeptide 7, unfertilized embryo sac 9);
    oxygen binding [Arabidopsis thaliana]
    1066 72349 1.00E−134 100 ref|NP_191072.1|TT5 (TRANSPARENT TESTA 5); SP
    chalcone isomerase [Arabidopsis thaliana]
    1067 71318 0 90 ref|NP_189261.1|CYP71B34 (cytochrome P450, family 71, HS
    subfamily B, polypeptide 34); oxygen binding [Arabidopsis
    thaliana]
    1068 71812 0 92 ref|NP_195705.1|CYP79B2 (cytochrome P450, family 79, LN
    subfamily B, polypeptide 2); oxygen binding [Arabidopsis
    thaliana]
    1069 74060 0 90 ref|NP_188731.1|CYP705A32 (cytochrome P450, family DS
    705, subfamily A, polypeptide 32); oxygen binding
    [Arabidopsis thaliana]
    1070 71816 0 93 ref|NP_568025.1|CYP81F3 (cytochrome P450, family 81, LL
    subfamily F, polypeptide 3); oxygen binding [Arabidopsis
    thaliana]
    1071 71569 1.00E−142 95 ref|NP_189364.1|ATPHB4 (PROHIBITIN 4) [Arabidopsis CS
    thaliana]
    1072 70672 0 100 ref|NP_567641.1|PRXR1 (peroxidase 42); peroxidase PP
    [Arabidopsis thaliana]
    1073 71336 0 96 ref|NP_563762.1|VHS domain-containing protein/GAT DS
    domain-containing protein [Arabidopsis thaliana]
    1074 71337 1.00E−179 100 ref|NP_179721.1|mannose 6-phosphate reductase HS
    (NADPH-dependent), putative [Arabidopsis thaliana]
    1075 71339 0 93 ref|NP_200747.1|XH/XS domain-containing protein CS
    [Arabidopsis thaliana] CS
    1076 71825 0 87 ref|NP_195998.2|TRFL10 (TRF-LIKE 10); DNA binding LN
    [Arabidopsis thaliana]
    1077 73696 1.00E−166 86 ref|NP_192864.1|MADS-box family protein [Arabidopsis SP
    thaliana]
    1078 70682 1.00E−129 94 ref|NP_001078595.1|RNA recognition motif (RRM)- HS
    containing protein [Arabidopsis thaliana]
    1079 70686 1.00E−117 75 ref|NP_199096.1|ATU2AF35B; RNA binding [Arabidopsis SP LL
    thaliana]
    1080 78316 0 100 ref|NP_192085.1|DC1 domain-containing protein SS
    [Arabidopsis thaliana]
    1081 71667 0 100 ref|NP_013976.1|Glutamate decarboxylase, converts DS
    glutamate into gamma-aminobutyric acid (GABA) during
    glutamate catabolism; involved in response to oxidative
    stress; Gad1p [Saccharomyces cerevisiae]
    1082 71695 0 77 emb|CAA75577.1|L-ascorbate oxidase [Medicago CK
    truncatula]
    1083 71696 0 96 gb|AAB03258.1|phosphoinositide-specific phospholipase C HS LN
    P13
    1084 72475 1.00E−111 83 gb|AAF21310.1|seed maturation protein PM24 [Glycine HS
    max]
    1085 71677 1.00E−125 77 gb|ABD28522.1|Cupin, RmlC-type [Medicago truncatula] CK
    1086 71691 7.00E−34 35 emb|CAO44124.1|unnamed protein product [Vitis vinifera] CS
    1087 72476 1.00E−122 70 emb|CAO47395.1|unnamed protein product [Vitis vinifera] HS
    1088 70803 0 97 ref|NP_850874.1|glutamate-tRNA ligase, putative/ SP LN
    glutamyl-tRNA synthetase, putatuve/GluRS, putative
    [Arabidopsis thaliana]
    1089 71612 0 94 ref|NP_192179.1|SULTR3; 2 (SULFATE TRANSPORTER LL
    3; 2); sulfate transporter [Arabidopsis thaliana]
    1090 71637 0 88 gb|AAD52696.1|AF087819_1auxin transport protein LN
    [Arabidopsis thaliana]
    1091 71629 0 97 ref|NP_565924.1|unknown protein [Arabidopsis thaliana] HS PEG
    1092 71622 0 97 ref|NP_566085.1|APRR9 (PSEUDO-RESPONSE LN
    REGULATOR 9); transcription regulator [Arabidopsis
    thaliana]
    1093 70810 0 91 ref|NP_175610.1|mitochondrial processing peptidase alpha HS SS
    subunit, putative [Arabidopsis thaliana]
    1094 72452 6.00E−76 77 ref|NP_199889.1|auxin-responsive family protein LN
    [Arabidopsis thaliana]
    1095 74071 0 93 ref|NP_174516.1|ribose-phosphate pyrophosphokinase 2/ LL
    phosphoribosyl diphosphate synthetase 2 (PRS2)
    [Arabidopsis thaliana]
    1096 11042 2.00E−89 93 ref|NP_179709.1|peptidyl-prolyl cis-trans isomerase/ LN
    cyclophilin (CYP2)/rotamase [Arabidopsis thaliana]
    1097 72510 0 89 ref|NP_196865.1|unknown protein [Arabidopsis thaliana] CK
    1098 72537 1.00E−124 82 ref|NP_851118.1|unknown protein [Arabidopsis thaliana] HS LN
    1099 72541 9.00E−57 88 ref|NP_568684.1|unknown protein [Arabidopsis thaliana] PP
    1100 72617 4.00E−88 100 ref|NP_568761.1|unknown protein [Arabidopsis thaliana] LL
    1101 73755 1.00E−132 100 ref|NP_200501.1|cysteine protease inhibitor [Arabidopsis PP SS
    thaliana]
    1102 72630 2.00E−86 93 ref|NP_201267.1|C/VIF2 (CELL WALL/VACUOLAR SP
    INHIBITOR OF FRUCTOSIDASE 2); pectinesterase
    inhibitor [Arabidopsis thaliana]
    1103 72645 5.00E−37 75 ref|NP_180615.1|photosystem II reaction center W (PsbW) LN
    protein-related [Arabidopsis thaliana]
    1104 72647 5.00E−43 100 ref|NP_566036.1|protease inhibitor/seed storage/lipid LN
    transfer protein (LTP) family protein [Arabidopsis thaliana]
    1105 14316 1.00E−55 86 ref|NP_188703.1|histone H2A, putative [Arabidopsis DS
    thaliana]
    1106 73689 6.00E−79 100 ref|NP_173037.1|transducin family protein/WD-40 repeat DS SS
    family protein [Arabidopsis thaliana]
    1107 73345 0 92 ref|NP_174226.1|transducin family protein/WD-40 repeat HS LN
    family protein [Arabidopsis thaliana]
    1108 73347 0 100 ref|NP_177513.2|transducin family protein/WD-40 repeat SP
    family protein [Arabidopsis thaliana]
    1109 73231 0 84 ref|NP_196332.1|leucine-rich repeat family protein PP
    [Arabidopsis thaliana]
    1110 78325 0 84 ref|NP_171637.1|aspartyl protease family protein HS
    [Arabidopsis thaliana]
    1111 72658 1.00E−138 93 ref|NP_172224.1|tropinone reductase, putative/tropine PEG
    dehydrogenase, putative [Arabidopsis thaliana]
    1112 72660 3.00E−78 82 ref|NP_564585.1|zinc finger (AN1-like) family protein LN
    [Arabidopsis thaliana]
    1113 72662 5.00E−49 100 ref|NP_179096.1|gibberellin-regulated family protein LN
    [Arabidopsis thaliana]
    1114 73352 0 97 ref|NP_566304.1|armadillo/beta-catenin repeat family LN
    protein/U-box domain-containing protein [Arabidopsis
    thaliana]
    1115 72814 0 100 ref|NP_566558.1|F-box family protein [Arabidopsis PP CS PEG
    thaliana]
    1116 72816 0 100 ref|NP_566824.1|CARA (CARBAMOYL PHOSPHATE PP
    SYNTHETASE A); carbamoyl-phosphate synthase
    (glutamine-hydrolyzing) [Arabidopsis thaliana]
    1117 72820 0 89 ref|NP_194653.1|leucine-rich repeat family protein/ LL
    extensin family protein [Arabidopsis thaliana]
    1118 73353 0 97 ref|NP_194713.1|MTO2 (METHIONINE OVER- HS PEG
    ACCUMULATOR); threonine synthase [Arabidopsis
    thaliana]
    1119 75066 1.00E−134 91 ref|NP_175644.1|ABA2 (ABA DEFICIENT 2); PEG
    oxidoreductase [Arabidopsis thaliana]
    1120 78337 2.00E−40 78 dbj|BAD43663.1|unknown protein [Arabidopsis thaliana] PEG
    1121 73317 0 96 ref|NP_200121.4|oxidoreductase [Arabidopsis thaliana] LN
    1122 73318 0 94 ref|NP_568145.1|short-chain dehydrogenase/reductase CS
    (SDR) family protein [Arabidopsis thaliana]
    1123 73749 0 97 gb|AAG51266.1|AC027135_7protein kinase, putative CS
    [Arabidopsis thaliana]
    1124 18704 0 88 ref|NP_201234.1|DCT/DIT2.1 (DICARBOXYLATE PEG
    TRANSPORT); oxoglutarate:malate antiporter [Arabidopsis
    thaliana]
    1125 73221 1.00E−162 82 ref|NP_563785.1|C2 domain-containing protein CK LL
    [Arabidopsis thaliana]
    1126 71125 1.00E−117 94 ref|NP_172671.1|Rho GDP-dissociation inhibitor family HS
    protein [Arabidopsis thaliana]
    1127 76203 0 97 ref|NP_200678.2|phosphoinositide-specific phospholipase PEG
    C family protein [Arabidopsis thaliana]
    1128 75067 0 100 ref|NP_566565.1|peroxidase, putative [Arabidopsis PEG
    thaliana]
    1129 73729 0 100 ref|NP_194944.1|CYP96A2 (cytochrome P450, family 96, LL
    subfamily A, polypeptide 2); oxygen binding [Arabidopsis
    thaliana]
    1130 75206 0 95 ref|NP_197962.1|GA3 (GA REQUIRING 3); oxygen HS
    binding [Arabidopsis thaliana]
    1131 73248 0 100 ref|NP_200532.1|CYP81F2 (cytochrome P450, family 81, HS
    subfamily F, polypeptide 2); oxygen binding [Arabidopsis
    thaliana]
    1132 73738 0 93 ref|NP_198641.1|serine/threonine protein kinase, putative DS
    [Arabidopsis thaliana]
    1133 73332 0 97 ref|NP_173685.1|SUC2 (SUCROSE-PROTON PP
    SYMPORTER 2); carbohydrate transporter/
    sucrose:hydrogen symporter/sugar porter [Arabidopsis
    thaliana]
    1134 78335 0 100 ref|NP_189582.1|UDP-glucose 6-dehydrogenase, putative HS LL PP
    [Arabidopsis thaliana]
    1135 75821 6.00E−76 90 ref|NP_190424.1|unknown protein [Arabidopsis thaliana] LL
    1136 72038 0 97 emb|CAA18501.1|Calcium-dependent serine/threonine HS
    protein kinase [Arabidopsis thaliana]
    1137 72027 0 91 ref|NP_849857.1|copine-related [Arabidopsis thaliana] DS
    1138 72016 0 97 ref|NP_200887.1|ATGCN1 (Arabidopsis thaliana general CS
    control non-repressible 1)
    1139 70835 1.00E−128 82 ref|NP_181461.1|PGPS1 SS
    (PHOSPHATIDYLGLYCEROLPHOSPHATE + SYNTHASE +
    1); CDP-alcohol phosphatidyltransferase [Arabidopsis
    thaliana]
    1140 72044 0 99 ref|NP_014446.1|Protein proposed to interact with CS
    phospholipid translocases, shares similarity to Cdc50p;
    Ynr048wp [Saccharomyces cerevisiae]
    1141 72092 0 92 ref|NP_010796.1|High-affinity glutamine permease, also CK
    transports Leu, Ser, Thr, Cys, Met and Asn; expression is
    fully dependent on Grr1p and modulated by the Ssy1p-
    Ptr3p-Ssy5p (SPS) sensor of extracellular amino acids;
    Gnp1p [Saccharomyces cerevisiae]
    1142 72124 1.00E−173 55 emb|CAO64952.1|unnamed protein product [Vitis vinifera] HS
    1143 72110 1.00E−172 63 emb|CAN75218.1|hypothetical protein [Vitis vinifera] HS
    1144 73916 1.00E−162 57 ref|NP_569047.1|SKIP2 (SKP1 INTERACTING PARTNER HS
    2); ubiquitin-protein ligase [Arabidopsis thaliana]
    1145 74268 0 100 ref|NP_186851.1|aspartate kinase, lysine-sensitive, HS LL
    putative [Arabidopsis thaliana]
    1146 74269 0 94 ref|NP_566764.1|bile acid:sodium symporter family protein DS
    [Arabidopsis thaliana]
    1147 77902 0 96 ref|NP_197021.2|tyrosyl-DNA phosphodiesterase-related SS
    [Arabidopsis thaliana]
    1148 74273 1.00E−180 100 ref|NP_199285.1|molybdenum cofactor sulfurase family HS
    protein [Arabidopsis thaliana]
    1149 74280 1.00E−165 94 emb|CAA58893.1|cysteine synthase [Arabidopsis thaliana] HS
    1150 74281 0 94 ref|NP_197655.1|prephenate dehydratase family protein LL
    [Arabidopsis thaliana]
    1151 74287 0 100 ref|NP_974217.1|SUVR4 [Arabidopsis thaliana] CK HS
    1152 73767 1.00E−156 100 ref|NP_194231.1|nodulin MtN3 family protein [Arabidopsis LN
    thaliana]
    1153 77304 0 100 ref|NP_175700.2|catalytic [Arabidopsis thaliana] CK HS PEG
    1154 73761 0 95 ref|NP_566683.1|mitochondrial substrate carrier family LL
    protein [Arabidopsis thaliana]
    1155 74721 0 93 ref|NP_194568.1|AAC3 (ADP/ATP CARRIER 3); ATP:ADP LL
    antiporter/binding [Arabidopsis thaliana]
    1156 74719 0 91 ref|NP_198474.1|protein phosphatase 2C, putative/PP2C, CK
    putative [Arabidopsis thaliana]
    1157 74257 0 98 ref|NP_179113.2|fatty acid elongase, putative [Arabidopsis DS HS
    thaliana]
    1158 72749 0 95 ref|NP_176767.1|regulator of chromosome condensation HS LL
    (RCC1) family protein/zinc finger protein-related
    [Arabidopsis thaliana]
    1159 72703 2.00E−77 92 ref|NP_013963.1|Subunit (17 kDa) of TFIID and SAGA PEG
    complexes, involved in RNA polymerase II transcription
    initiation and in chromatin modification, similar to histone
    H3; Taf9p [Saccharomyces cerevisiae]
    1160 72763 0 98 ref|NP_009691.1|Protein arginine N-methyltransferase that SS
    exhibits septin and Hsl1p-dependent bud neck localization
    and periodic Hsl1p-dependent phosphorylation; required
    along with Hsl1p for bud neck recruitment,
    phosphorylation, and degradation of Swe1p; Hsl7p
    [Saccharomyces cerevisiae]
    1161 72775 1.00E−172 100 ref|NP_009718.1|Catalytic subunit of the main cell cycle HS
    cyclin-dependent kinase (CDK); alternately associates with
    G1 cyclins (CLNs) and G2/M cyclins (CLBs) which direct
    the CDK to specific substrates; Cdc28p [Saccharomyces
    cerevisiae]
    1162 72728 0 96 ref|NP_013106.1|Cytoplasmic response regulator, part of a CS
    two-component signal transducer that mediates
    osmosensing via a phosphorelay mechanism;
    dephosphorylated form is degraded by the ubiquitin-
    proteasome system; potential Cdc28p substrate; Ssk1p
    [Saccharomyces cerevisiae]
    1163 72776 1.00E−101 92 gb|EDN62754.1|oxidant-induced cell cycle arrest HS
    [Saccharomyces cerevisiae YJM789]
    1164 72717 1.00E−131 100 ref|NP_011075.1|TATA-binding protein, general DS
    transcription factor that interacts with other factors to form
    the preinitiation complex at promoters, essential for
    viability; Spt15p [Saccharomyces cerevisiae]
    1165 72718 1.00E−159 90 ref|NP_011400.1|Activating gamma subunit of the AMP- DS
    activated Snf1p kinase complex (contains Snf1p and a
    Sip1p/Sip2p/Gal83p family member); activates glucose-
    repressed genes, represses glucose-induced genes; role
    in sporulation, and peroxisome biogenesis; Snf4p
    [Saccharomyces cerevisiae]
    1166 11715 0 93 ref|NP_187616.1|OMR1 (L-O-METHYLTHREONINE LN
    RESISTANT 1); threonine ammonia-lyase [Arabidopsis
    thaliana]
    1167 72779 0 93 ref|NP_011622.1|B-type cyclin involved in cell cycle DS
    progression; activates Cdc28p to promote the transition
    from G2 to M phase; accumulates during G2 and M, then
    targeted via a destruction box motif for ubiquitin-mediated
    degradation by the proteasome; Clb1p [Saccharomyces
    cerevisiae]
    1168 72791 0 100 ref|NP_009709.1|Protein of unknown function, required for DS HS
    normal localization of actin patches and for normal
    tolerance of sodium ions and hydrogen peroxide; localizes
    to both cytoplasm and nucleus; Apd1p [Saccharomyces
    cerevisiae]
    1169 72732 0 100 ref|NP_013662.1|Putative protein of unknown function; HS
    non-essential gene; null mutant displays increased
    frequency of mitochondrial genome loss (petite formation);
    Aim32p [Saccharomyces cerevisiae]
    1170 73027 1.00E−125 93 ref|NP_187445.1|Rho GDP-dissociation inhibitor family CS
    protein [Arabidopsis thaliana]
    1171 73058 0 96 ref|NP_175591.1|leucine-rich repeat protein kinase, CK
    putative [Arabidopsis thaliana]
    1172 73126 0 95 ref|NP_173076.1|protein kinase family protein [Arabidopsis PEG
    thaliana]
    1173 73138 0 91 ref|NP_356682.2|aldehyde dehydrogenase [Agrobacterium HS
    tumefaciens str. C58]
    1174 73174 0 94 ref|NP_241069.1|glycine betaine aldehyde dehydrogenase HS
    [Bacillus halodurans C-125]
    1175 73186 0 99 ref|NP_241405.1|NADP-dependent aldehyde HS LN
    dehydrogenase [Bacillus halodurans C-125]
    1176 11141 0 100 ref|NP_568064.1|AGT2 (ALANINE:GLYOXYLATE LN
    AMINOTRANSFERASE 2); alanine-glyoxylate
    transaminase [Arabidopsis thaliana]
    1177 73139 0 89 ref|NP_242876.1|aldehyde dehydrogenase [Bacillus CS
    halodurans C-125]
    1178 73128 0 97 ref|NP_388272.1|4-aminobutyrate aminotransferase HS
    [Bacillus subtilis subsp. subtilis str. 168]
    1179 73164 0 93 ref|NP_389241.1|transaminase [Bacillus subtilis subsp. PEG
    subtilis str. 168]
    1180 73117 0 97 ref|NP_391762.1|aldehyde dehydrogenase [Bacillus CS HS
    subtilis subsp. subtilis str. 168]
    1181 73142 0 99 ref|YP_585121.1|glyceraldehyde-3-phosphate PP SS
    dehydrogenase, type I [Ralstonia metallidurans CH34]
    1182 73990 1.00E−154 90 ref|NP_949547.1|glutaminase [Rhodopseudomonas HS
    palustris CGA009]
    1183 73166 1.00E−117 100 ref|NP_384268.1|phosphoglyceromutase [Sinorhizobium SS
    meliloti 1021]
    1184 73178 0 91 ref|NP_385430.1|PUTATIVE AMINOTRANSFERASE LL
    PROTEIN [Sinorhizobium meliloti 1021]
    1185 73190 1.00E−142 99 ref|NP_385544.1|PROBABLE TRIOSEPHOSPHATE PEG
    ISOMERASE PROTEIN [Sinorhizobium meliloti 1021]
    1186 73131 0 99 ref|NP_386510.1|beta amino acid--pyruvate transaminase CK
    [Sinorhizobium meliloti 1021]
    1187 73108 0 92 ref|NP_929378.1|pyruvate kinase [Photorhabdus CK
    luminescens subsp. laumondii TTO1]
    1188 73074 1.00E−171 87 gb|AAO17215.1|Epd [Photorhabdus luminescens] HS
    1189 73132 1.00E−80 100 ref|NP_390154.1|nucleoside diphosphate kinase [Bacillus CS
    subtilis subsp. subtilis str. 168]
    1190 73146 2.00E−94 93 ref|NP_931715.1|inorganic pyrophosphatase DS
    [Photorhabdus luminescens subsp. laumondii TTO1]
    1191 73147 0 97 ref|NP_015444.1|B-type cyclin involved in cell cycle HS
    progression; activates Cdc28p to promote the transition
    from G2 to M phase; accumulates during G2 and M, then
    targeted via a destruction box motif for ubiquitin-mediated
    degradation by the proteasome; C1b2p [Saccharomyces
    cerevisiae]
    1192 73080 0 92 gb|AAB17351.1|protein phosphatase type 2C LN
    [Saccharomyces cerevisiae]
    1193 73077 0 97 ref|NP_010018.1|Endosomal protein that regulates cell HS
    polarity, controls polarized growth; similar to Ynr048wp and
    Lem3p; Cdc50p [Saccharomyces cerevisiae]
    1194 73183 0 93 ref|NP_011895.1|Serine/threonine MAP kinase involved in CS HS
    regulating the maintenance of cell wall integrity and
    progression through the cell cycle; regulated by the PKC1-
    mediated signaling pathway; Slt2p [Saccharomyces
    cerevisiae]
    1195 73018 0 100 ref|NP_014582.1|NAD-dependent glycerol 3-phosphate HS
    dehydrogenase, homolog of Gpd1p, expression is
    controlled by an oxygen-independent signaling pathway
    required to regulate metabolism under anoxic conditions;
    located in cytosol and mitochondria; Gpd2p
    [Saccharomyces cerevisiae]
    1196 73112 0 97 ref|NP_014271.1|Homolog of human tumor suppressor HS
    gene PTEN/MMAC1/TEP1 that has lipid phosphatase
    activity and is linked to the phosphatidylinositol signaling
    pathway; plays a role in normal sporulation; Tep1p
    [Saccharomyces cerevisiae]
    1197 73988 0 83 ref|NP_013664.1|ER localized integral membrane protein SS PEG
    that may promote secretion of certain hexose transporters,
    including Gal2p; involved in glucose-dependent repression;
    Gsf2p [Saccharomyces cerevisiae]
    1198 10908 2.00E−61 100 ref|NP_199112.1|ATTRX3 (thioredoxin H-type 3); thiol- CK
    disulfide exchange intermediate [Arabidopsis thaliana]
    1198 11147 2.00E−61 100 ref|NP_199112.1|ATTRX3 (thioredoxin H-type 3); thiol- LN
    disulfide exchange intermediate [Arabidopsis thaliana]
    1199 72909 0 95 ref|NP_011569.1|High affinity methionine permease, HS
    integral membrane protein with 13 putative membrane-
    spanning regions; also involved in cysteine uptake; Mup1p
    [Saccharomyces cerevisiae]
    1200 73987 0 94 ref|NP_010444.1|Component of the SPS plasma PP SS
    membrane amino acid sensor system (Ssy1p-Ptr3p-
    Ssy5p), which senses external amino acid concentration
    and transmits intracellular signals that result in regulation
    of expression of amino acid permease genes; Ssy1p
    [Saccharomyces cerevisiae]
    1201 72922 0 91 ref|NP_010082.1|Putative transporter, member of the LL
    sugar porter family; Ydl199cp [Saccharomyces cerevisiae]
    1202 73036 0 95 ref|NP_010022.1|Plasma membrane permease, mediates CS HS
    uptake of glycerophosphoinositol and
    glycerophosphocholine as sources of the nutrients inositol
    and phosphate; expression and transport rate are
    regulated by phosphate and inositol availability; Git1p
    [Saccharomyces cerevisiae]
    1203 72958 0 94 ref|NP_014622.1|High affinity tryptophan and tyrosine HS PP
    permease, overexpression confers FK506 and FTY720
    resistance; Tat2p [Saccharomyces cerevisiae]
    1204 77006 1.00E−167 100 ref|NP_182073.1|ATAUR3 (ATAURORA3); ATP binding/ LL LN
    histone serine kinase(H3-S10 specific)/protein kinase
    [Arabidopsis thaliana]
    1205 74732 0 90 ref|NP_177415.1|casein kinase, putative [Arabidopsis CK
    thaliana]
    1206 74333 1.00E−158 100 ref|NP_180976.1|protein kinase family protein [Arabidopsis HS
    thaliana]
    1207 74735 0 100 ref|NP_173489.2|protein kinase [Arabidopsis thaliana] LN
    1208 74736 0 100 ref|NP_176353.1|protein kinase, putative [Arabidopsis LL
    thaliana]
    1209 74737 0 100 gb|AAF16665.1|AC012394_14putative protein kinase; HS
    59396-62219 [Arabidopsis thaliana]
    1210 76657 0 95 ref|NP_187827.1|protein kinase family protein [Arabidopsis SP LL
    thaliana]
    1211 76113 0 94 ref|NP_187165.2|protein kinase family protein [Arabidopsis CS
    thaliana]
    1212 74747 0 92 ref|NP_174161.1|protein kinase family protein [Arabidopsis HS
    thaliana]
    1213 77309 0 87 ref|NP_175879.2|protein kinase family protein [Arabidopsis PEG
    thaliana]
    1214 74322 0 94 gb|AAG52342.1|AC011663_21putative protein kinase; LL
    29119-30743 [Arabidopsis thaliana]
    1215 76212 1.00E−170 93 ref|NP_200959.2|NADP-dependent oxidoreductase, HS LN
    putative [Arabidopsis thaliana]
    1216 76514 1.00E−159 85 ref|NP_568357.1|AAA-type ATPase family protein LL DS
    [Arabidopsis thaliana]
    1217 75242 0 84 ref|NP_200318.1|2-oxoacid dehydrogenase family protein LL
    [Arabidopsis thaliana]
    1218 77324 0 97 gb|AAF79717.1|AC020889_25T1N15.3 [Arabidopsis PEG LN
    thaliana]
    1219 74350 3.00E−95 93 ref|NP_178122.1|APT2 (ADENINE PHOSPHORIBOSYL LN
    TRANSFERASE 2); adenine phosphoribosyltransferase
    [Arabidopsis thaliana]
    1220 77606 0 96 ref|NP_190925.1|AFC1 (ARABIDOPSIS FUS3- HS SS
    COMPLEMENTING GENE 1); kinase [Arabidopsis
    thaliana]
    1221 76530 0 92 ref|NP_567069.1|F-box family protein-related [Arabidopsis HS
    thaliana]
    1222 76716 1.00E−86 61 ref|NP_565175.1|RNA recognition motif (RRM)-containing HS
    protein [Arabidopsis thaliana]
    1223 77328 0 89 ref|NP_567904.1|RNA recognition motif (RRM)-containing HS
    protein [Arabidopsis thaliana]
    1224 12204 0 100 ref|NP_189366.1|G6PD5 (GLUCOSE-6-PHOSPHATE DS
    DEHYDROGENASE 5); glucose-6-phosphate 1-
    dehydrogenase [Arabidopsis thaliana]
    1225 77011 0 96 ref|NP_563818.1|strictosidine synthase family protein LL
    [Arabidopsis thaliana]
    1226 77607 0 94 ref|NP_175157.1|NRAMP2 (NRAMP metal ion transporter LL PEG
    2); metal ion transporter [Arabidopsis thaliana]
    1227 74612 1.00E−68 100 ref|NP_177750.1|unknown protein [Arabidopsis thaliana] HS
    1228 76126 1.00E−144 100 ref|NP_179467.1|signal recognition particle binding HS
    [Arabidopsis thaliana]
    1229 74376 1.00E−150 95 ref|NP_181340.1|DET2 (DE-ETIOLATED 2) [Arabidopsis DS
    thaliana]
    1230 74377 1.00E−46 100 ref|NP_181546.1|ATEM6 (ARABIDOPSIS EARLY DS LL PEG
    METHIONINE-LABELLED 6) [Arabidopsis thaliana]
    1231 74381 6.00E−63 100 ref|NP_181990.1|mtACP-1 (MITOCHONDRIAL ACYL CS
    CARRIER PROTEIN 1); acyl carrier [Arabidopsis thaliana]
    1232 78364 6.00E−88 87 ref|NP_566062.1|UBC6 (UBIQUITIN-CONJUGATING HS
    ENZYME 6); ubiquitin-protein ligase [Arabidopsis thaliana]
    1233 74623 1.00E−115 75 ref|NP_188379.1|late embryogenesis abundant domain- HS
    containing protein/LEA domain-containing protein
    [Arabidopsis thaliana]
    1234 74668 1.00E−122 88 ref|NP_188888.1|late embryogenesis abundant protein, DS
    putative/LEA protein, putative [Arabidopsis thaliana]
    1235 74629 5.00E−83 90 ref|NP_566782.1|unknown protein [Arabidopsis thaliana] LL
    1236 74635 1.00E−113 92 ref|NP_190864.1|peroxiredoxin type 2, putative CS
    [Arabidopsis thaliana]
    1237 74638 1.00E−100 100 ref|NP_191788.1|ATARFA1E (ADP-ribosylation factor HS SS
    A1E); GTP binding/phospholipase activator/protein
    binding [Arabidopsis thaliana]
    1238 76721 1.00E−148 77 ref|NP_192093.1|KCO5 (Ca2+ activated outward rectifying PEG
    K+ channel 5); outward rectifier potassium channel
    [Arabidopsis thaliana]
    1239 78365 2.00E−83 90 ref|NP_568004.1|UBC17 (UBIQUITIN-CONJUGATING CK HS
    ENZYME 17); ubiquitin-protein ligase [Arabidopsis
    thaliana]
    1240 74655 1.00E−132 91 ref|NP_195437.1|HCF164 (High chlorophyll fluorescence LN
    164); thiol-disulfide exchange intermediate [Arabidopsis
    thaliana]
    1241 74660 1.00E−160 92 ref|NP_196119.1|ATTOC34/OEP34 (Translocase of CS PEG
    chloroplast 34) [Arabidopsis thaliana]
    1242 74661 1.00E−180 96 ref|NP_197135.1|ubiquitin carboxyl-terminal hydrolase HS
    family
    1 protein [Arabidopsis thaliana]
    1243 75259 1.00E−101 85 ref|NP_198051.1|drought-responsive family protein HS
    [Arabidopsis thaliana]
    1244 75282 3.00E−93 100 ref|NP_201055.1|ATHVA22B (Arabidopsis thaliana HVA22 PEG
    homologue B)
    1245 76724 0 93 ref|NP_173089.1|organic cation transporter-related DS
    [Arabidopsis thaliana]
    1246 12350 1.00E−131 78 gb|AAM61424.1|serine O-acetyltransferase (EC 2.3.1.30) LN
    Sat-52 [Arabidopsis thaliana]
    1247 76522 0 93 ref|NP_001077495.1|unknown protein [Arabidopsis PP
    thaliana]
    1248 77903 0 96 ref|NP_194952.2|protein kinase family protein [Arabidopsis HS LL SS
    thaliana]
    1249 76653 0 100 ref|NP_568860.1|CIPK21 (CBL-INTERACTING PROTEIN CS
    KINASE 21); kinase [Arabidopsis thaliana]
    1250 76524 0 100 ref|NP_199469.1|protein kinase family protein [Arabidopsis CS
    thaliana]
    1251 11356 1.00E−172 100 ref|NP_181165.1|APG10 (ALBINO AND PALE GREEN LN
    10); 1-(5-phosphoribosyl)-5-[(5-
    phosphoribosylamino)methylideneamino]imidazole-4-
    carboxamide isomerase [Arabidopsis thaliana]
    1252 75275 0 94 ref|NP_199586.1|protein kinase, putative [Arabidopsis LL
    thaliana] dbj|BAA01715.1|serine/threonine protein kinase
    [Arabidopsis thaliana]
    1253 76225 0 94 ref|NP_195285.3|CONNEXIN 32; kinase [Arabidopsis PEG
    thaliana]
    1254 75281 0 94 ref|NP_568893.1|protein kinase family protein [Arabidopsis HS
    thaliana]
    1255 74384 1.00E−102 100 ref|NP_175960.1|prenylated rab acceptor (PRA1) family LL
    protein [Arabidopsis thaliana]
    1256 71238 1.00E−168 84 ref|NP_563814.1|DCP1 (DECAPPING 1) [Arabidopsis LN
    thaliana]
    1257 12354 0 100 ref|NP_172738.1|UGE1 (UDP-D-glucose/UDP-D-galactose DS
    4-epimerase 1); UDP-glucose 4-epimerase/protein
    dimerization [Arabidopsis thaliana]
    1258 76236 1.00E−157 100 ref|NP_201384.1|leucine-rich repeat family protein HS
    [Arabidopsis thaliana]
    1259 74682 4.00E−83 100 ref|NP_565581.1|unknown protein [Arabidopsis thaliana] CS
    1260 73425 0 95 ref|NP_391649.1|transaminase [Bacillus subtilis subsp. LL
    subtilis str. 168]
    1261 73438 0 99 ref|YP_351136.1|Glutamate--ammonia ligase SP
    [Pseudomonas fluorescens PfO-1]
    1262 73474 0 92 ref|NP_790236.1|phosphoglycerate kinase [Pseudomonas HS PP
    syringae pv. tomato str. DC3000]
    1263 70850 0 97 ref|NP_190853.1|ATELP1 (VACUOLAR SORTING HS
    RECEPTOR HOMOLOG) [Arabidopsis thaliana]
    1264 73429 1.00E−144 100 ref|ZP_01370194.1|pyrroline-5-carboxylate reductase HS SS CS
    [Desulfitobacterium hafniense DCB-2]
    1265 73441 0 94 ref|ZP_01370604.1|enolase [Desulfitobacterium hafniense PEG
    DCB-2]
    1266 73466 0 97 ref|ZP_00108577.1|COG1063: Threonine dehydrogenase LN
    and related Zn-dependent dehydrogenases [Nostoc
    punctiforme PCC 73102]
    1267 73455 1.00E−159 100 ref|NP_792905.1|UTP-glucose-1-phosphate HS
    uridylyltransferase [Pseudomonas syringae pv. tomato str.
    DC3000]
    1268 73432 0 94 ref|YP_582700.1|Alcohol dehydrogenase, zinc-binding CS
    [Ralstonia metallidurans CH34]
    1269 73435 0 97 ref|NP_391271.1|phosphoglyceromutase [Bacillus subtilis LN
    subsp. subtilis str. 168]
    1270 77726 0 99 ref|NP_391273.1|phosphoglycerate kinase [Bacillus subtilis HS
    subsp. subtilis str. 168]
    1271 73483 0 96 ref|NP_009362.1|Pyruvate kinase, functions as a LL
    homotetramer in glycolysis to convert
    phosphoenolpyruvate to pyruvate, the input for aerobic
    (TCA cycle) or anaerobic (glucose fermentation)
    respiration; Cdc19p [Saccharomyces cerevisiae]
    1272 73472 0 99 ref|NP_387397.1|ASPARTATE AMINOTRANSFERASE B DS
    PROTEIN [Sinorhizobium meliloti 1021]
    1273 73526 0 94 ref|NP_242877.1|benzyl alcohol dehydrogenase [Bacillus DS
    halodurans C-125]
    1274 73538 0 100 ref|NP_243126.1|hypothetical protein BH2260 [Bacillus HS
    halodurans C-125]
    1275 73574 1.00E−177 100 ref|NP_244591.1|2-keto-3-deoxygluconate kinase [Bacillus HS
    halodurans C-125]
    1276 73539 1.00E−170 100 ref|NP_287481.1|UTP--glucose-1-phosphate CS
    uridylyltransferase subunit GalU [Escherichia coil O157:H7
    EDL933]
    1277 73563 3.00E−62 90 ref|NP_743010.1|nucleoside diphosphate kinase CK
    [Pseudomonas putida KT2440]
    1278 73575 1.00E−175 100 ref|NP_792508.1|fructokinase [Pseudomonas syringae pv. LL
    tomato str. DC3000]
    1279 73565 0 95 ref|NP_011707.1|High-affinity histidine permease, also HS
    involved in the transport of manganese ions; Hip1p
    [Saccharomyces cerevisiae]
    1280 73531 0 93 ref|NP_388151.1|hypothetical protein BSU02690 [Bacillus DS
    subtilis subsp. subtilis str. 168]
    1281 73592 0 96 ref|NP_391888.1|6-phosphogluconate dehydrogenase LN
    [Bacillus subtilis subsp. subtilis str. 168]
    1282 74149 0 100 ref|NP_794093.1|pyruvate kinase [Pseudomonas syringae LL
    pv. tomato str. DC3000]
    1283 74174 0 99 ref|NP_41688.1|prediected aminotransferase, PLP- LL LN
    dependent [Escherichia coli K12]
    1284 74151 0 100 ref|NP_417148.1|4-aminobutyrate aminotransferase, PLP- PP
    dependent [Escherichia coli K12]
    1285 74104 0 100 ref|ZP_01369074.1|glucose-1-phosphate CS HS
    adenylyltransferase [Desulfitobacterium hafniense DCB-2]
    1286 74164 0 89 ref|NP_242876.1|aldehyde dehydrogenase [Bacillus DS
    halodurans C-125]
    1287 74129 0 77 ref|YP_001185919.1|methylmalonate-semialdehyde CK
    dehydrogenase [Pseudomonas mendocina ymp]
    1288 72340 0 97 ref|NP_195674.2|GGT1; gamma-glutamyltransferase/ HS
    glutathione gamma-glutamylcysteinyltransferase
    [Arabidopsis thaliana]
    1289 74155 0 100 ref|NP_385556.1|dihydrolipoamide dehydrogenase HS LL
    [Sinorhizobium meliloti 1021]
    1290 74168 0 87 ref|NP_927730.1|glutathione reductase [Photorhabdus LN
    luminescens subsp. laumondii TTO1]
    1291 74133 0 96 ref|ZP_00109554.2|COG1249: Pyruvate/2-oxoglutarate HS
    dehydrogenase complex, dihydrolipoamide dehydrogenase
    (E3) component, and related enzymes [Nostoc punctiforme
    PCC 73102]
    1292 74160 4.00E−95 99 ref|NP_441445.1|hypothetical protein slr0816 LL
    [Synechocystis sp. PCC 6803] dbj|BAA18125.1|slr0816
    [Synechocystis sp. PCC 6803]
    1293 74485 0 88 ref|NP_439939.1|hypothetical protein slr1495 HS
    [Synechocystis sp. PCC 6803]
    1294 74450 0 100 ref|NP_442868.1|LIM17 protein [Synechocystis sp. PCC CK
    6803]
    1295 74487 0 90 ref|NP_357138.2|branched-chain alpha-keto acid PP
    dehydrogenase subunit E2 [Agrobacterium tumefaciens
    str. C58]
    1296 74406 0 96 gb|AAN78639.1|AE016755_139Dihydrolipoamide LN
    dehydrogenase [Escherichia coli CFT073]
    1297 74454 1.00E−112 91 ref|NP_927456.1|ribulose-phosphate 3-epimerase LL
    (pentose-5-phosphate 3-epimerase) (PPE) (R5P3E)
    [Photorhabdus luminescens subsp. laumondii TTO1]
    1298 11361 6.00E−61 83 ref|NP_176291.1|FED A (FERREDOXIN 2); electron LN
    carrier/iron ion binding [Arabidopsis thaliana]
    1299 74431 0 99 ref|NP_390796.1|pyruvate kinase [Bacillus subtilis subsp. HS
    subtilis str. 168]
    1300 74411 0 94 ref|NP_949979.1|fructose-1,6-bisphosphatase SS
    [Rhodopseudomonas palustris CGA009]
    1301 74424 1.00E−172 92 ref|NP_386873.1|PROBABLE FRUCTOSE- PP
    BISPHOSPHATE ALDOLASE CLASS I PROTEIN
    [Sinorhizobium meliloti 1021]
    1302 74525 0 83 ref|NP_931210.1|glutamate synthase subunit beta HS
    [Photorhabdus luminescens subsp. laumondii TTO1]
    1303 74573 1.00E−75 38 ref|YP_720246.1|aspartate aminotransferase LN
    [Trichodesmium erythraeum IMS101]
    1304 75827 2.00E−44 82 ref|NP_565988.1|unknown protein [Arabidopsis thaliana] LL
    1305 77329 0 98 ref|NP_566005.1|mitochondrial transcription termination CK
    factor-related/mTERF-related [Arabidopsis thaliana]
    1306 77330 0 97 ref|NP_182296.1|auxin-responsive GH3 family protein PEG
    [Arabidopsis thaliana]
    1307 75830 6.00E−61 100 ref|NP_186754.1|MUB1 (MEMBRANE-ANCHORED CK
    UBIQUITIN-FOLD PROTEIN 1 PRECURSOR)
    [Arabidopsis thaliana]
    1308 75832 2.00E−42 85 ref|NP_186788.1|VMA10 (VACUOLAR MEMBRANE HS
    ATPASE 10) [Arabidopsis thaliana]
    1309 75836 7.00E−41 73 ref|NP_187208.1|unknown protein [Arabidopsis thaliana] CS
    1310 77034 4.00E−28 95 ref|NP_172702.1|unknown protein [Arabidopsis thaliana] HS PP
    1311 76255 0 92 ref|NP_566390.1|unknown protein [Arabidopsis thaliana] LL
    1312 76542 1.00E−77 69 ref|NP_188337.1|unknown protein [Arabidopsis thaliana] CS LL
    1313 77511 0 90 ref|NP_566642.1|unknown protein [Arabidopsis thaliana] SS CK
    1314 76261 1.00E−127 86 ref|NP_563649.1|unknown protein [Arabidopsis thaliana] HS
    1315 78456 0 97 ref|NP_189202.1|MAP1B (METHIONINE CK
    AMINOPEPTIDASE 1C); metalloexopeptidase
    [Arabidopsis thaliana]
    1316 77041 1.00E−125 95 ref|NP_189236.3|plastid-lipid associated protein PAP/ LN
    fibrillin family protein [Arabidopsis thaliana]
    1317 76546 0 90 gb|AAF79247.1|AC006917_32F10B6.11 [Arabidopsis LL
    thaliana]
    1318 75848 9.00E−96 100 ref|NP_189535.1|AIG2 (AVRRPT2-INDUCED GENE 2) CK HS
    [Arabidopsis thaliana]
    1319 77515 0 80 ref|NP_189945.1|zinc knuckle (CCHC-type) family protein HS
    [Arabidopsis thaliana]
    1320 76266 0 82 emb|CAB83070.1|putative protein [Arabidopsis thaliana] PEG
    1321 75852 1.00E−26 100 ref|NP_190227.1|unknown protein [Arabidopsis thaliana] HS
    1322 76556 0 86 ref|NP_190445.2|zinc finger (DHHC type) family protein PEG
    [Arabidopsis thaliana]
    1323 77523 1.00E−174 96 ref|NP_001078291.1|unknown protein [Arabidopsis HS
    thaliana]
    1324 75863 1.00E−120 100 ref|NP_191267.1|eukaryotic rpb5 RNA polymerase subunit CS
    family protein [Arabidopsis thaliana]
    1325 77052 1.00E−171 96 ref|NP_564000.2|unknown protein [Arabidopsis thaliana] PP
    1326 75865 1.00E−56 80 ref|NP_173123.1|ribosomal protein-related [Arabidopsis CS
    thaliana]
    1327 76551 0 92 ref|NP_173144.1|oxidoreductase, 2OG-Fe(II) oxygenase PEG
    family protein [Arabidopsis thaliana]
    1328 76280 0 86 ref|NP_564064.1|phytochrome kinase substrate-related LL
    [Arabidopsis thaliana]
    1329 75874 7.00E−96 100 ref|NP_193404.1|glycosyltransferase family protein 28 PP
    [Arabidopsis thaliana]
    1330 75879 9.00E−62 100 ref|NP_194229.1|ATGP4 (Arabidopsis thaliana HS
    geranylgeranylated protein)
    1331 75880 7.00E−59 65 ref|NP_173435.1|unknown protein [Arabidopsis thaliana] HS
    1332 77519 1.00E−176 90 ref|NP_196118.1|sad1/unc-84 protein-related [Arabidopsis HS CK
    thaliana]
    1333 76745 1.00E−111 88 dbj|BAB09403.1|unnamed protein product [Arabidopsis HS
    thaliana]
    1334 76554 1.00E−173 91 ref|NP_197092.1|unknown protein [Arabidopsis thaliana] DS
    1335 76746 3.00E−93 75 ref|NP_568333.1|unknown protein [Arabidopsis thaliana] CK
    1336 76750 1.00E−85 93 ref|NP_197746.1|unknown protein [Arabidopsis thaliana] LL
    1337 76621 3.00E−20 100 ref|NP_198912.1|unknown protein [Arabidopsis thaliana] HS
    1338 76623 1.00E−23 80 ref|NP_568739.1|unknown protein [Arabidopsis thaliana] LL
    1339 76461 1.00E−29 78 gb|AAB86938.1|NOI protein [Arabidopsis thaliana] CS
    1340 76462 5.00E−31 100 ref|NP_564277.1|unknown protein [Arabidopsis thaliana] HS PP
    1341 78987 1.00E−147 81 ref|NP_201096.1|protein binding/zinc ion binding HS
    [Arabidopsis thaliana]
    1342 76568 0 96 ref|NP_564484.1|unknown protein [Arabidopsis thaliana] HS
    1343 76176 0 95 ref|NP_565009.1|glycosyltransferase family 14 protein/ CK
    core-2/I-branching enzyme family protein [Arabidopsis
    thaliana]
    1344 76177 1.00E−97 100 ref|NP_177287.1|unknown protein [Arabidopsis thaliana] LN
    1345 78380 0 100 ref|NP_565058.1|eukaryotic translation initiation factor- LN
    related [Arabidopsis thaliana]
    1346 76629 2.00E−46 100 ref|NP_177894.1|unknown protein [Arabidopsis thaliana] HS
    1347 76189 2.00E−58 100 gb|AAD15467.2|unknown protein [Arabidopsis thaliana] CS
    1348 76761 1.00E−106 94 ref|NP_179133.1|ATARFB1A (ADP-ribosylation factor LL
    B1A); GTP binding [Arabidopsis thaliana]
    1349 78608 0 100 ref|NP_973624.1|ATORC2/ORC2 (ORIGIN PP
    RECOGNITION COMPLEX SECOND LARGEST
    SUBUNIT) [Arabidopsis thaliana]
    1350 78115 1.00E−153 100 ref|NP_181669.1|embryo-abundant protein-related CK DS
    [Arabidopsis thaliana]
    1351 74873 0 100 ref|NP_416275.1|glutamate dehydrogenase, NADP- DS
    specific [Escherichia coli K12]
    1352 74826 0 99 ref|NP_416651.1|predicted oxidoreductase [Escherichia HS
    coli K12]
    1353 74850 0 99 gb|AAN81953.1|AE016766_41D-erythrose 4-phosphate HS
    dehydrogenase [Escherichia coli CFT073]
    1354 74887 4.00E−76 90 gb|AAD25168.1|aquaporin [Saccharomyces cerevisiae] PEG
    1355 74804 0 95 gb|EDN59233.1|chromatin remodeling complex member, HS SS PEG
    RSC [Saccharomyces cerevisiae YJM789]
    1356 74831 1.00E−167 81 gb|EAY97794.1|hypothetical protein Osl_019027 [Oryza LN
    sativa (indica cultivar-group)]
    1357 74822 0 69 emb|CAO62934.1|unnamed protein product [Vitis vinifera] PEG
    1358 74836 1.00E−121 70 ref|NP_187378.1|transcriptional activator, putative LN
    [Arabidopsis thaliana]
    1359 74901 3.00E−31 61 ref|NP_001064928.1|Os10g0491900 [Oryza sativa HS
    (japonica cultivar-group)]
    1360 74974 1.00E−112 87 ref|NP_001063296.1|Os09g0443500 [Oryza sativa HS
    (japonica cultivar-group)]
    1361 74904 1.00E−149 82 ref|NP_001063966.1|Os09g0567900 [Oryza sativa HS
    (japonica cultivar-group)]
    1362 74916 8.00E−92 76 gb|EAZ28333.1|hypothetical protein OsJ_011816 [Oryza PEG
    sativa (japonica cultivar-group)]
    1363 74964 1.00E−158 95 ref|NP_417814.1|predicted phosphoribulokinase LL
    [Escherichia coli K12]
    1364 74918 6.00E−82 82 ref|NP_443015.1|hypothetical protein sll1109 LN
    [Synechocystis sp. PCC 6803]
    1365 74966 0 99 ref|NP_442146.1|hypothetical protein sll0209 HS
    [Synechocystis sp. PCC 6803]
    1366 74979 1.00E−142 82 ref|NP_440823.1|hypothetical protein slr1220 CK LL
    [Synechocystis sp. PCC 6803]
    1367 74934 0 96 ref|YP_350971.1|betaine aldehyde dehydrogenase PEG
    [Pseudomonas fluorescens PfO-1]
    1368 77814 0 92 ref|NP_116585.1|F-box protein required for G1/S and HS
    G2/M transition, associates with Skp1p and Cdc53p to
    form a complex, SCFCdc4, which acts as ubiquitin-protein
    ligase directing ubiquitination of the phosphorylated CDK
    inhibitor Sic1p; Cdc4p [Saccharomyces cerevisiae]
    1369 75387 1.00E−148 53 ref|NP_001067713.1|Os11g0293900 [Oryza sativa CK LL
    (japonica cultivar-group)]
    1370 75328 0 93 ref|NP_001050986.1|Os03g0699200 [Oryza sativa PP
    (japonica cultivar-group)]
    1371 77808 0 74 emb|CAO63310.1|unnamed protein product [Vitis vinifera] CS
    1372 75389 0 69 ref|NP_001045085.1|Os01g0897100 [Oryza sativa HS
    (japonica cultivar-group)]
    1373 75318 1.00E−126 49 emb|CAO40140.1|unnamed protein product [Vitis vinifera] CK
    1374 75330 0 70 emb|CAH66847.1|H0525C06.10 [Oryza sativa (indica CS HS
    cultivar-group)]
    1375 75342 1.00E−75 69 ref|NP_001056004.1|Os05g0509700 [Oryza sativa CK
    (japonica cultivar-group)]
    1376 75366 4.00E−59 74 ref|NP_001063106.1|Os09g0397700 [Oryza sativa HS
    (japonica cultivar-group)]
    1377 75319 1.00E−121 73 ref|NP_001050079.1|Os03g0343700 [Oryza sativa HS
    (japonica cultivar-group)]
    1378 75391 0 96 gb|ABU48662.1|G protein alpha subunit [Sorghum bicolor] HS
    1379 75334 4.00E−45 92 ref|NP_001049605.1|Os03g0257900 [Oryza sativa HS
    (japonica cultivar-group)]
    1380 75323 0 82 ref|NP_001053032.1|Os04g0466600 [Oryza sativa HS
    (japonica cultivar-group)]
    1381 75396 5.00E−84 77 ref|NP_001068537.1|Os11g0703400 [Oryza sativa PEG
    (japonica cultivar-group)]
    1382 75401 2.00E−72 93 ref|NP_001059557.1|Os07g0454700 [Oryza sativa HS
    (japonica cultivar-group)]
    1383 75413 1.00E−139 90 ref|NP_001050848.1|Os03g0666700 [Oryza sativa LL
    (japonica cultivar-group)]
    1384 75461 0 92 ref|NP_001066463.1|Os12g0236500 [Oryza sativa HS SS PP
    (japonica cultivar-group)]
    1385 75473 6.00E−50 71 ref|NP_001043914.1|Os01g0687600 [Oryza sativa DS
    (japonica cultivar-group)]
    1386 77817 8.00E−26 93 ref|NP_001045143.1|Os01g0908400 [Oryza sativa LL
    (japonica cultivar-group)]
    1387 75416 1.00E−165 81 gb|EAY92384.1|hypothetical protein Osl_013617 [Oryza CK
    sativa (indica cultivar-group)]
    1388 75464 0 68 gb|EAZ22667.1|hypothetical protein OsJ_006150 [Oryza HS
    sativa (japonica cultivar-group)]
    1389 75441 5.00E−46 68 gb|AAA33773.1|PVPR3 LN
    1390 75454 2.00E−82 73 ref|NP_001064989.1|Os10g0502000 [Oryza sativa HS
    (japonica cultivar-group)]
    1391 75493 4.00E−31 51 emb|CAO48835.1|unnamed protein product [Vitis vinifera] HS PP PEG
    1392 75446 2.00E−29 55 gb|ABU54835.1|defender against apoptotic death CS HS
    [Penaeus monodon]
    1393 75495 2.00E−86 82 gb|ABG23395.1|2C-methyl-D-erythritol 2,4- SS
    cyclodiphosphate synthase [Stevia rebaudiana]
    1394 75705 1.00E−102 71 ref|NP_001046126.1|Os02g0187100 [Oryza sativa SP
    (japonica cultivar-group)]
    1395 77818 0 100 ref|NP_241861.1|succinate-semialdehyde dehydrogenase HS PEG
    [Bacillus halodurans C-125]
    1396 75525 0 99 ref|NP_415448.1|aspartate aminotransferase, PLP- LN
    dependent [Escherichia coli K12]
    1397 75549 1.00E−115 37 dbj|BAC10067.1|hypothetical protein [Oryza sativa SS
    japonica Group]
    1398 75582 0 68 emb|CAO16731.1|unnamed protein product [Vitis vinifera] CS PEG
    1399 75535 6.00E−53 62 emb|CAO18074.1|unnamed protein product [Vitis vinifera] PEG
    1400 75547 1.00E−164 74 emb|CAO42486.1|unnamed protein product [Vitis vinifera] LL LN
    1401 75512 1.00E−141 63 emb|CAO40060.1|unnamed protein product [Vitis vinifera] CS HS
    1402 75673 1.00E−158 55 ref|NP_001050262.1|Os03g0387900 [Oryza sativa CK
    (japonica cultivar-group)]
    1403 75626 0 78 gb|EAZ07965.1|hypothetical protein Osl_029197 [Oryza HS
    sativa (indica cultivar-group)]
    1404 75674 4.00E−53 66 gb|EAY98259.1|hypothetical protein Osl_019492 [Oryza HS LN
    sativa (indica cultivar-group)]
    1405 75615 2.00E−46 59 gb|EAY75762.1|hypothetical protein Osl_003609 [Oryza CK
    sativa (indica cultivar-group)]
    1406 75627 1.00E−135 92 gb|EAZ15023.1|hypothetical protein OsJ_004848 [Oryza SS
    sativa (japonica cultivar-group)]
    1407 75628 1.00E−103 88 gb|AAQ24835.1|partner of Nob1 [Sorghum bicolor] PEG
    1408 75652 1.00E−139 85 gb|EAY93006.1|hypothetical protein Osl_014239 [Oryza CK
    sativa (indica cultivar-group)]
    1409 75605 1.00E−121 55 ref|NP_001047861.1|Os02g0704600 [Oryza sativa CK HS LN
    (japonica cultivar-group)]
    1410 70228 1.00E−83 100 ref|NP_189581.1|AHP2 (HISTIDINE-CONTAINING CK
    PHOSPHOTRANSMITTER 2); histidine phosphotransfer
    kinase/signal transducer [Arabidopsis thaliana]
    1411 13302 0 95 gb|AAF21885.1|AF101056_1MEI2 [Arabidopsis thaliana] LN
    1412 75610 0 86 ref|NP_001054248.1|Os04g0675500 [Oryza sativa CK
    (japonica cultivar-group)]
    1413 75623 0 95 ref|NP_194630.1|AIM1 (ABNORMAL INFLORESCENCE HS
    MERISTEM); enoyl-CoA hydratase [Arabidopsis thaliana]
    1414 75671 0 88 ref|NP_176918.1|leucine-rich repeat family protein PP
    [Arabidopsis thaliana]
    1415 75695 4.00E−78 63 emb|CAO21783.1|unnamed protein product [Vitis vinifera] HS
    1416 75648 2.00E−32 46 ref|NP_001054395.1|Os05g0103500 [Oryza sativa SS
    (japonica cultivar-group)] dbj|BAF16309.1|Os05g0103500
    [Oryza sativa (japonica cultivar-group)]
    1417 75672 0 84 ref|NP_196925.1|leucine-rich repeat transmembrane PP
    protein kinase, putative [Arabidopsis thaliana]
    dbj|BAB08300.1|receptor protein kinase-like protein
    [Arabidopsis thaliana]
    1418 75713 1.00E−141 43 emb|CAO21763.1|unnamed protein product [Vitis vinifera] CK
    1419 75714 7.00E−35 36 gb|ABK93511.1|unknown [Populus trichocarpa] HS PP
    1420 75762 1.00E−171 65 emb|CAN68895.1|hypothetical protein [Vitis vinifera] CK
    1421 77954 0 94 ref|NP_172684.1|flavin-containing monooxygenase family HS
    protein/FMO family protein [Arabidopsis thaliana]
    1422 77955 0 95 ref|NP_172680.1|flavin-containing monooxygenase family HS
    protein/FMO family protein [Arabidopsis thaliana]
    1423 77541 7.00E−85 100 gb|ABK28567.1|unknown [Arabidopsis thaliana] LN
    1424 78131 0 93 emb|CAB42923.1|putative mitochondrial protein HS
    [Arabidopsis thaliana]
    1425 78134 6.00E−95 91 ref|NP_192051.2|CBL5 (CALCINEURIN B-LIKE PROTEIN LN SS
    5) [Arabidopsis thaliana]
    1426 77554 1.00E−138 75 tpg|DAA00869.1|TPA_exp: PDR2 ABC transporter HS
    [Arabidopsis thaliana]
    1427 78992 1.00E−170 90 ref|NP_194508.1|calcium-binding EF hand family protein CK
    [Arabidopsis thaliana]
    1428 77557 0 84 ref|NP_196016.1|IQD12 (IQ-domain 12); calmodulin LL LN
    binding [Arabidopsis thaliana]
    1429 78128 0 96 ref|NP_196397.1|flavin-containing monooxygenase family HS
    protein/FMO family protein [Arabidopsis thaliana]
    1430 77560 0 94 ref|NP_568202.1|calcium-binding EF hand family protein CK HS
    [Arabidopsis thaliana]
    1431 77561 0 100 ref|NP_196694.1|monooxygenase family protein CS CK
    [Arabidopsis thaliana]
    1432 77958 1.00E−108 74 ref|NP_197694.1|TET12 (TETRASPANIN12) [Arabidopsis PP
    thaliana]
    1433 77563 0 92 ref|NP_197887.1|integral membrane transporter family CS CK
    protein [Arabidopsis thaliana]
    1434 78994 0 91 ref|NP_001032056.1|F-box family protein [Arabidopsis HS
    thaliana]
    1435 74508 0 90 ref|NP_850439.1|CYP76C1 (cytochrome P450, family 76, CS HS
    subfamily C, polypeptide 1); heme binding/iron ion
    binding/monooxygenase [Arabidopsis thaliana]
    1436 70229 0 100 ref|NP_194337.1|MEK1 (mitogen-activated protein kinase HS
    kinase 1); MAP kinase kinase/kinase [Arabidopsis
    thaliana]
    1437 77959 0 90 ref|NP_200937.1|flavin-containing monooxygenase family HS
    protein/FMO family protein [Arabidopsis thaliana]
    1438 77567 0 88 ref|NP_171951.2|integral membrane transporter family HS LN
    protein [Arabidopsis thaliana]
    1439 11749 2.00E−52 74 ref|NP_181812.1|PDF1 (PROTODERMAL FACTOR 1) CK
    [Arabidopsis thaliana]
    1440 77578 0 90 ref|NP_180886.1|integral membrane transporter family HS
    protein [Arabidopsis thaliana]
    1441 11751 1.00E−110 90 ref|NP_180871.1|SAR1 (SYNAPTOBREVIN-RELATED LN
    PROTEIN 1) [Arabidopsis thaliana]
    1442 77963 0 86 ref|NP_566652.1|unknown protein [Arabidopsis thaliana] LN
    1443 77925 1.00E−149 94 ref|NP_190985.1|ATFIP37 (ARABIDOPSIS THALIANA HS PP
    FKBP12 INTERACTING PROTEIN 37) [Arabidopsis
    thaliana]
    1444 77927 0 90 ref|NP_564083.1|unknown protein [Arabidopsis thaliana] HS
    1445 77345 2.00E−57 100 ref|NP_564113.1|unknown protein [Arabidopsis thaliana] HS
    1446 70230 0 96 gb|ABF55662.1|double MYC-tagged mitogen activated HS
    protein kinase kinase 2 [synthetic construct]
    1447 77353 1.00E−65 100 ref|NP_564301.1|unknown protein [Arabidopsis thaliana] HS
    1448 77354 6.00E−42 81 ref|NP_564312.1|unknown protein [Arabidopsis thaliana] LL
    1449 77355 1.00E−41 90 ref|NP_564515.1|unknown protein [Arabidopsis thaliana] PP
    1450 77588 1.00E−152 100 ref|NP_176415.1|unknown protein [Arabidopsis thaliana] CS
    1451 77591 1.00E−164 92 ref|NP_565628.1|unknown protein [Arabidopsis thaliana] LL
    1452 77594 1.00E−143 72 emb|CAB46003.1|RING-H2 finger protein RHF1a DS
    [Arabidopsis thaliana]
    1453 77595 1.00E−144 71 ref|NP_567661.1|SWIB complex BAF60b domain- LL
    containing protein [Arabidopsis thaliana]
    1454 77364 5.00E−76 84 ref|NP_194770.1|transcription factor [Arabidopsis thaliana] LN
    1455 78904 0 100 emb|CAB87764.1|putative protein [Arabidopsis thaliana] HS
    1456 77937 0 100 ref|NP_197133.1|acetolactate synthase small subunit, HS
    putative [Arabidopsis thaliana]
    1457 77369 1.00E−103 86 ref|NP_197494.1|plastid-lipid associated protein PAP- DS
    related/fibrillin-related [Arabidopsis thaliana]
    1458 77940 0 89 ref|NP_568648.1|transducin family protein/WD-40 repeat CK HS
    family protein [Arabidopsis thaliana]
    1459 78746 0 100 ref|NP_201387.2|ankyrin repeat family protein [Arabidopsis HS
    thaliana]
    1460 77372 1.00E−119 94 ref|NP_201515.1|F-box family protein [Arabidopsis DS
    thaliana]
    1461 78126 0 86 gb|AAF24593.1|AC007654_9T19E23.14 [Arabidopsis CK
    thaliana]
    1462 77951 0 100 ref|NP_565803.1|ATEYA (ARABIDOPSIS THALIANA LL PEG
    EYES ABSENT HOMOLOG); protein tyrosine
    phosphatase, metal-dependent [Arabidopsis thaliana]
    1463 75901 0 97 gb|EDN61448.1|F-box protein [Saccharomyces cerevisiae CS
    YJM789]
    1464 12123 1.00E−115 86 ref|NP_196598.1|EMB3010 (EMBRYO DEFECTIVE 3010); LN
    structural constituent of ribosome [Arabidopsis thaliana]
    1465 75987 9.00E−84 80 ref|NP_001105929.1|high affinity nitrate transporter [Zea CS
    mays]
    1466 75940 0 100 ref|NP_842265.1|Phosphoglucose isomerase (PGI) HS PP
    [Nitrosomonas europaea ATCC 19718]
    1467 75919 1.00E−175 95 ref|NP_780153.1|isocitrate dehydrogenase [Xylella HS LL SS
    fastidiosa Temecula1]
    1468 75908 0 99 ref|NP_440384.1|glutamate decarboxylase [Synechocystis HS
    sp. PCC 6803]
    1469 75920 0 100 ref|NP_440189.1|ferredoxin-sulfite reductase HS
    [Synechocystis sp. PCC 6803]
    1470 75992 0 94 ref|YP_001636715.1|pyruvate kinase [Chloroflexus HS
    aurantiacus J-10-fl]
    1471 75933 1.00E−116 94 ref|NP_442343.1|ribose-5-phosphate isomerase A HS PP
    [Synechocystis sp. PCC 6803]
    1472 77965 0 92 ref|NP_181991.1|kelch repeat-containing F-box family DS
    protein [Arabidopsis thaliana]
    1473 77966 0 89 ref|NP_186818.1|unknown protein [Arabidopsis thaliana] LN
    1474 77972 0 90 ref|NP_189657.1|unknown protein [Arabidopsis thaliana] HS
    1475 78522 0 96 ref|NP_175744.1|unknown protein [Arabidopsis thaliana] SP
    1476 12194 3.00E−78 91 ref|NP_176772.1|TPX2 (THIOREDOXIN-DEPENDENT CK
    PEROXIDASE 2); antioxidant [Arabidopsis thaliana]
    1477 78525 0 87 gb|AAC24050.1|Similar to S. cerevisiae SIK1P protein LN
    1478 78527 0 87 gb|AAC18814.1|Contains homology to serine/threonine PEG
    protein kinase gb|X99618 from Mycobacterium
    tuberculosis.
    1479 78917 0 95 ref|NP_177258.3|armadillo/beta-catenin repeat family LN
    protein/U-box domain-containing protein [Arabidopsis
    thaliana]
    1480 78920 0 100 ref|NP_565146.1|ACR3 (ACT Domain Repeat 3) PP
    [Arabidopsis thaliana]
    1481 78535 0 96 ref|NP_179324.2|pantothenate kinase-related [Arabidopsis CK
    thaliana]
    1482 78538 0 98 ref|NP_180538.1|kelch repeat-containing F-box family HS
    protein [Arabidopsis thaliana]
    1483 78922 0 95 ref|NP_181393.1|F-box family protein [Arabidopsis HS PP CS
    thaliana]
    1484 77984 1.00E−109 100 ref|NP_566068.1|unknown protein [Arabidopsis thaliana] LN CK
    1485 73938 0 100 ref|NP_201190.1|AAP4 (amino acid permease 4); amino DS CS
    acid permease [Arabidopsis thaliana]
    1486 78621 0 100 gb|AAD13704.1|hypothetical protein [Arabidopsis thaliana] HS
    1487 77990 1.00E−74 85 ref|NP_187290.1|integral membrane family protein DS
    [Arabidopsis thaliana]
    1488 78386 1.00E−132 100 ref|NP_187319.1|peptidyl-prolyl cis-trans isomerase SP
    cyclophilin-type family protein [Arabidopsis thaliana]
    1489 78001 1.00E−70 100 gb|AAF23196.1|AC016795_9unknown protein [Arabidopsis HS
    thaliana]
    1490 78543 0 90 ref|NP_187807.1|S-locus related protein SLR1, putative HS
    (S1) [Arabidopsis thaliana]
    1491 78002 1.00E−136 100 ref|NP_187847.1|unknown protein [Arabidopsis thaliana] LL
    1492 12259 1.00E−134 100 gb|AAM67061.1|ribosomal protein S2, putative LN
    [Arabidopsis thaliana]
    1493 78005 3.00E−93 96 ref|NP_172796.1|unknown protein [Arabidopsis thaliana] LL
    1494 78008 1.00E−135 88 ref|NP_188459.1|unknown protein [Arabidopsis thaliana] PEG
    1495 78019 1.00E−176 94 ref|NP_001031574.1|unknown protein [Arabidopsis CK HS
    thaliana]
    1496 78020 2.00E−74 89 gb|ABK28619.1|unknown [Arabidopsis thaliana] SS
    1497 78023 1.00E−121 94 ref|NP_173373.2|unknown protein [Arabidopsis thaliana] DS
    1498 78548 1.00E−146 86 ref|NP_564100.1|abscisic acid-responsive HVA22 family LN PP
    protein [Arabidopsis thaliana]
    1499 78161 1.00E−103 94 ref|NP_173738.2|caleosin-related family protein HS PEG
    [Arabidopsis thaliana]
    1500 78162 1.00E−179 100 ref|NP_564270.1|unknown protein [Arabidopsis thaliana] CK LN PP PEG
    1501 78033 1.00E−148 90 ref|NP_564297.1|unknown protein [Arabidopsis thaliana] LL
    1502 78622 0 95 ref|NP_564315.1|unknown protein [Arabidopsis thaliana] CK
    1503 78036 1.00E−67 100 ref|NP_174257.1|unknown protein [Arabidopsis thaliana] DS
    1504 78043 0 96 ref|NP_175182.2|endonuclease/exonuclease/phosphatase CS
    family protein [Arabidopsis thaliana]
    1505 78165 2.00E−92 84 ref|NP_564788.1|unknown protein [Arabidopsis thaliana] LL
    1506 78066 1.00E−116 86 gb|AAF68106.1|AC010793_1F20B17.2 [Arabidopsis PP
    thaliana]
    1507 78069 1.00E−124 64 ref|NP_178248.2|pentatricopeptide (PPR) repeat- PP
    containing protein [Arabidopsis thaliana]
    1508 78183 1.00E−115 100 ref|NP_180390.2|unknown protein [Arabidopsis thaliana] PP
    1509 78170 2.00E−37 100 gb|AAS47599.1|At2g33690 [Arabidopsis thaliana] PP
    1510 78953 1.00E−125 88 ref|NP_565921.1|unknown protein [Arabidopsis thaliana] PP
    1511 78929 0 97 ref|NP_182026.1|CCD7 (more axillary growth 3) LN
    [Arabidopsis thaliana]
    1512 78564 1.00E−63 100 ref|NP_188669.1|unknown protein [Arabidopsis thaliana] PEG
    1513 78566 0 100 ref|NP_566813.1|unknown protein [Arabidopsis thaliana] HS
    1514 78591 0 96 gb|AAG12668.1|AC027033_3hypothetical protein; 23726-25026 SS
    [Arabidopsis thaliana]
    1515 78181 3.00E−99 100 ref|NP_563968.1|unknown protein [Arabidopsis thaliana] LN
    1516 78190 2.00E−30 71 ref|NP_564173.1|unknown protein [Arabidopsis thaliana] LL
    1517 78571 0 93 gb|AAF79874.1|AC000348_27T7N9.16 [Arabidopsis CK
    thaliana]
    1518 78933 1.00E−107 84 gp|AAG51731.1|AC068667_10hypothetical protein; 69078-67980 LN
    [Arabidopsis thaliana]
    1519 78573 8.00E−73 80 ref|NP_174417.1|LOB domain protein 4/lateral organ CK
    boundaries domain protein 4 (LBD4) [Arabidopsis thaliana]
    1520 78632 0 100 ref|NP_564507.1|unknown protein [Arabidopsis thaliana] HS LL PP
    1521 78959 0 100 ref|NP_175985.1|pentatricopeptide (PPR) repeat- LN
    containing protein [Arabidopsis thaliana]
    1522 78191 3.00E−51 63 ref|NP_564986.1|ribosomal protein L12 family protein HS LN
    [Arabidopsis thaliana]
    1523 78595 1.00E−150 92 gb|AAB70396.1|Similar to ATP-dependent Clp protease HS PEG
    (gb|D90915).
    1524 78646 0 100 ref|NP_172453.1|pentatricopeptide (PPR) repeat- HS
    containing protein [Arabidopsis thaliana]
    1525 76325 1.00E−143 82 gb|EAY88291.1|hypothetical protein OsI_009524 [Oryza CS
    sativa (indica cultivar-group)]
    1526 76337 6.00E−76 87 ref|NP_001053732.1|Os04g0595200 [Oryza sativa HS
    (japonica cultivar-group)]
    1527 76349 1.00E−139 56 ref|NP_001066102.1|Os12g0136200 [Oryza sativa PP
    (japonica cultivar-group)]
    1528 76302 4.00E−75 82 ref|NP_001047161.1|Os02g0564500 [Oryza sativa LL
    (japonica cultivar-group)]
    1529 76329 0 92 ref|NP_014151.1|RNA polymerase I subunit A49; Rpa49p PEG PP
    [Saccharomyces cerevisiae]
    1530 76353 0 97 ref|NP_010937.1|Nucleotide binding alpha subunit of the SS
    heterotrimeric G protein that interacts with the receptor
    Gpr1p, has signaling role in response to nutrients; green
    fluorescent protein (GFP)-fusion protein localizes to the
    cell periphery; Gpa2p [Saccharomyces cerevisiae]
    1531 76389 0 83 ref|NP_014172.1|Co-chaperone that stimulates the CK
    ATPase activity of Ssa1p, required for a late step of
    ribosome biogenesis; associated with the cytosolic large
    ribosomal subunit; contains a J-domain; mutation causes
    defects in fluid-phase endocytosis; Jjj1p [Saccharomyces
    cerevisiae]
    1532 76378 1.00E−119 79 ref|NP_014726.1|Repressor of G1 transcription that binds HS PEG
    to SCB binding factor (SBF) at SCB target promoters in
    early G1; phosphorylation of Whi5p by the CDK,
    Cln3p/Cdc28p relieves repression and promoter binding by
    Whi5; periodically expressed in G1; Whi5p
    [Saccharomyces cerevisiae]
    1533 76392 1.00E−59 55 ref|NP_001045725.1|Os02g0122300 [Oryza sativa LL
    (japonica cultivar-group)]
    1534 76321 0 76 ref|NP_001058970.1|Os07g0166100 [Oryza sativa LN
    (japonica cultivar-group)]
    1535 76345 0 86 ref|NP_001043794.1|Os01g0665200 [Oryza sativa DS
    (japonica cultivar-group)]
    1536 76381 0 88 ref|NP_001058289.1|Os06g0663200 [Oryza sativa HS
    (japonica cultivar-group)]
    1537 76358 0 76 ref|NP_001050845.1|Os03g0666200 [Oryza sativa LN
    (japonica cultivar-group)]
    1538 12629 0 97 ref|NP_194110.2|unknown protein [Arabidopsis thaliana] HS
    1539 76335 1.00E−101 66 ref|NP_001065630.1|Os11g0127700 [Oryza sativa LL
    (japonica cultivar-group)]
    1540 76372 0 82 gb|EAY93387.1|hypothetical protein OsI_014620 [Oryza PP
    sativa (indica cultivar-group)]
    1541 76396 0 57 ref|NP_001047355.1|Os02g0602100 [Oryza sativa DS
    (japonica cultivar-group)]
    1542 72314 0 92 ref|NP_187714.1|steroid hormone receptor/transcription HS
    factor [Arabidopsis thaliana]
    1543 77840 1.00E−166 87 ref|NP_001066296.1|Os12g0176500 [Oryza sativa CS CK
    (japonica cultivar-group)]
    1544 76886 1.00E−143 85 dbj|BAC99390.1|putative U3 snoRNP protein IMP4 [Oryza PP PEG
    sativa japonica Group]
    1545 76803 1.00E−163 90 gb|EAY89818.1|hypothetical protein OsI_011051 [Oryza LL
    sativa (indica cultivar-group)]
    1546 10302 0 97 ref|NP_172288.1|ATNRT2:1 (Arabidopsis thaliana high HS
    affinity nitrate transporter 2.1); nitrate transporter
    1547 71107 0 96 ref|NP_030560.1|unknown protein [Arabidopsis thaliana] HS
    1548 76887 0 86 ref|NP_001044302.1|Os01g0758400 [Oryza sativa HS PP PEG
    (japonica cultivar-group)]
    1549 77842 0 76 ref|NP_001047779.1|0s02g0688500 [Oryza sativa LN
    (japonica cultivar-group)]
    1550 76805 1.00E−165 85 dbj|BAD08085.1|putative ornithine carbamoyltransferase HS
    [Oryza sativa japonica Group]
    1551 76817 2.00E−51 78 ref|NP_001063927.1|Os09g0560500 [Oryza sativa HS
    (japonica cultivar-group)]
    1552 77843 1.00E−68 66 ref|NP_001053206.1|Os04g0497400 [Oryza sativa CS
    (japonica cultivar-group)]
    1553 77844 0 94 ref|NP_001105843.1|sialyltransferase like protein [Zea PP
    mays]
    1554 76890 0 98 ref|NP_001044001.1|Os01g0703600 [Oryza sativa HS
    (japonica cultivar-group)]
    1555 77839 1.00E−155 74 ref|NP_001047096.1|Os02g0550700 [Oryza sativa DS PP
    (japonica cultivar-group)]
    1556 76868 0 83 ref|NP_001052270.1|Os04g0223000 [Oryza sativa HS PP PEG CS
    (japonica cultivar-group)]
    1557 76821 1.00E−144 80 ref|NP_001042197.1|Os01g0179200 [Oryza sativa LN
    (japonica cultivar-group)]
    1558 76869 3.00E−98 73 gb|EAZ29350.1|hypothetical protein OsJ_012833 [Oryza HS PP
    sativa (japonica cultivar-group)]
    1559 76881 0 88 ref|NP_001049165.1|Os03g0180700 [Oryza sativa PP
    (japonica cultivar-group)]
    1560 76894 4.00E−33 94 ref|NP_001066312.1|Os12g0180400 [Oryza sativa LN
    (japonica cultivar-group)]
    1561 11930 0 100 dbj|BAF01049.1|hypothetical protein [Arabidopsis thaliana] SS
    1562 76848 2.00E−80 90 ref|NP_001043542.1|Os01g0610100 [Oryza sativa HS
    (japonica cultivar-group)]
    1563 76901 2.00E−44 85 gb|EAY92619.1|hypothetical protein OsI_013852 [Oryza LN
    sativa (indica cultivar-group)]
    1564 76914 1.00E−139 78 gb|EAY79090.1|hypothetical protein OsI_033049 [Oryza PP
    sativa (indica cultivar-group)]
    1565 76939 1.00E−137 71 gb|EAY98958.1|hypothetical protein OsI_020191 [Oryza CK
    sativa (indica cultivar-group)]
    1566 76987 1.00E−150 72 gb|ABF93996.1|Integral membrane protein DUF6 CK
    containing protein, expressed [Oryza sativa (japonica
    cultivar-group)]
    1567 76904 4.00E−58 76 gb|EAZ05371.1|hypothetical protein OsI_026603 [Oryza HS LN
    sativa (indica cultivar-group)]
    1568 76941 4.00E−26 69 gb|EAY83408.1|hypothetical protein OsI_037367 [Oryza HS
    sativa (indica cultivar-group)]
    1569 77113 0 58 ref|NP_001064033.1|Os10g0110600 [Oryza sativa PEG
    (japonica cultivar-group)]
    1570 77185 0 80 dbj|BAD45738.1|thiF family protein-like [Oryza sativa DS
    japonica Group]
    1571 12911 0 100 ref|NP_001078414.1|binding [Arabidopsis thaliana] LN HS
    1572 77127 0 89 ref|NP_001062585.1|Os09g0115600 [Oryza sativa HS PEG
    (japonica cultivar-group)]
    1573 77177 0 85 gb|EAY84671.1|hypothetical protein OsI_005904 [Oryza PEG
    sativa (indica cultivar-group)]
    1574 77178 0 100 ref|NP_441510.1|bifunctional 3,4-dihydroxy-2-butanone 4- HS
    phosphate synthase/GTP cyclohydrolase II protein
    [Synechocystis sp. PCC 6803]
    1575 77179 2.00E−15 60 gb|EAY74575.1|hypothetical protein OsI_002422 [Oryza HS
    sativa (indica cultivar-group)]
    1576 77191 8.00E−61 81 ref|NP_001046564.1|Os02g0282100 [Oryza sativa PP
    (japonica cultivar-group)]
    1577 77145 2.00E−48 81 ref|NP_001051289.1|Os03g0751000 [Oryza sativa CK PP
    (japonica cultivar-group)]
    1578 77169 1.00E−137 87 gb|AAP50960.1|putative aurora-related kinase [Oryza PP
    sativa (japonica cultivar-group)]
    1579 77110 5.00E−30 56 ref|NP_001042508.1|Os01g0233000 [Oryza sativa LL LN
    (japonica cultivar-group)]
    1580 77146 0 100 ref|NP_353311.1|bifunctional GMP synthase/glutamine PP
    amidotransferase protein [Agrobacterium tumefaciens str.
    C58]
    1581 77170 7.00E−59 82 emb|CAH67592.1|OSIGBa0092M08.4 [Oryza sativa DS
    (indica cultivar-group)]
    1582 77171 0 95 ref|NP_244906.1|potassium/proton antiporter [Bacillus HS
    halodurans C-125]
    1583 77148 0 100 ref|NP_661081.1|bifunctional GMP synthase/glutamine CK
    amidotransferase protein [Chlorobium tepidum TLS]
    1584 11933 1.00E−149 94 ref|NP_849952.1|GONST1 (GOLGI NUCLEOTIDE LN
    SUGAR TRANSPORTER 1) [Arabidopsis thaliana]
    1585 77160 0 87 ref|NP_414589.1|potassium:proton antiporter [Escherichia DS
    coli K12]
    1586 77172 0 92 gb|AAC77846.1|mannose-1-P guanosyltransferase LL
    [Escherichia coli]
    1587 77184 0 92 ref|NP_243321.1|flagellum-specific ATP synthase [Bacillus HS
    halodurans C-125]
    1588 77225 0 94 ref|NP_662474.1|3,4-dihydroxy-2-butanone 4-phosphate LL
    synthase/GTP cyclohydrolase II [Chlorobium tepidum TLS]
    1589 77250 0 97 ref|NP_599940.1|detergent sensitivity rescuer dtsR1 LN
    [Corynebacterium glutamicum ATCC 13032]
    1590 77277 0 95 ref|NP_001048987.1|Os03g0151800 [Oryza sativa DS
    (japonica cultivar-group)] ica cultivar-group)]
    1591 77245 7.00E−45 64 gb|EAY86480.1|hypothetical protein OsI_007713 [Oryza SS
    sativa (indica cultivar-group)]
    1592 77246 4.00E−49 98 gb|EAZ21400.1|hypothetical protein OsJ_004883 [Oryza HS
    sativa (japonica cultivar-group)]
    1593 77462 0 75 ref|NP_001065111.1|Os10g0525000 [Oryza sativa CK
    (japonica cultivar-group)]
    1594 77414 0 82 ref|NP_001046919.1|Os02g0506500 [Oryza sativa HS
    (japonica cultivar-group)]
    1595 77439 0 82 ref|NP_001045101.1|Os01g0899500 [Oryza sativa PEG
    (japonica cultivar-group)]
    1596 77463 1.00E−106 89 ref|NP_001048776.1|Os03g0119000 [Oryza sativa HS
    (japonica cultivar-group)]
    1597 77488 0 80 gb|EAT84267.1|hypothetical protein SNOG_07991 DS
    [Phaeosphaeria nodorum SN15]
    1598 77441 5.00E−87 82 ref|NP_001053804.1|Os04g0606900 [Oryza sativa SS PEG
    (japonica cultivar-group)]
    1599 77464 1.00E−164 90 gb|EAT77502.1|hypothetical protein SNOG_14959 PEG
    [Phaeosphaeria nodorum SN15]
    1600 77442 0 83 ref|NP_013943.1|SR protein kinase (SRPK) involved in HS
    regulating proteins involved in mRNA metabolism and
    cation homeostasis; similar to human SRPK1; Sky1p
    [Saccharomyces cerevisiae]
    1601 77419 0 100 ref|NP_191311.1|ATSIP2 (ARABIDOPSIS THALIANA CK HS
    SEED IMBIBITION 2); hydrolase, hydrolyzing O-glycosyl
    compounds [Arabidopsis thaliana]
    1602 12444 1.00E−146 100 ref|NP_569036.1|GAMMA CA3 (GAMMA CARBONIC LN
    ANHYDRASE 3); carbonate dehydratase [Arabidopsis
    thaliana]
    1603 11791 0 87 ref|NP_188619.2|phototropic-responsive NPH3 family LN
    protein [Arabidopsis thaliana]
    1603 12445 0 87 ref|NP_188619.2|phototropic-responsive NPH3 family HS
    protein [Arabidopsis thaliana]
    1604 71249 0 96 ref|NP_189251.1|CYP71B22 (cytochrome P450, family 71, HS
    subfamily B, polypeptide 22); oxygen binding [Arabidopsis
    thaliana]
    1605 71237 0 95 ref|NP_192740.1|short-chain dehydrogenase/reductase CK
    (SDR) family protein [Arabidopsis thaliana]
    1606 12315 1.00E−97 100 ref|NP_567911.1|unknown protein [Arabidopsis thaliana] DS
    gb|AAM66960.1|unknown [Arabidopsis thaliana]
    1606 12366 1.00E−97 100 ref|NP_567911.1|unknown protein [Arabidopsis thaliana] DS
    gb|AAM66960.1|unknown [Arabidopsis thaliana]
    • Trait Enhancement Screens
  • DS-Enhancement of drought tolerance identified by a soil drought stress tolerance screen: Drought or water deficit conditions impose mainly osmotic stress on plants. Plants are particularly vulnerable to drought during the flowering stage. The drought condition in the screening process disclosed in Example 1B started from the flowering time and was sustained to the end of harvesting. The present invention provides recombinant DNA that can improve the plant survival rate under such sustained drought condition. Exemplary recombinant DNA for conferring such drought tolerance are identified as such in Table 3. Such recombinant DNA can find particular use in generating transgenic plants that are tolerant to the drought condition imposed during flowering time and in other stages of the plant life cycle. As demonstrated from the model plant screen, in some embodiments of transgenic plants with trait-improving recombinant DNA grown under such sustained drought condition can also have increased total seed weight per plant in addition to the increased survival rate within a transgenic population, providing a higher yield potential as compared to control plants.
  • PEG-Enhancement of drought tolerance identified by PEG induced osmotic stress tolerance screen: Various drought levels can be artificially induced by using various concentrations of polyethylene glycol (PEG) to produce different osmotic potentials (Pilon-Smits et al., (1995) Plant Physiol. 107:125-130). Several physiological characteristics have been reported as being reliable indications for selection of plants possessing drought tolerance. These characteristics include the rate of seed germination and seedling growth. The traits can be assayed relatively easily by measuring the growth rate of seedling in PEG solution. Thus, a PEG-induced osmotic stress tolerance screen can be a surrogate for drought tolerance screen. As demonstrated from the model plant screen, embodiments of transgenic plants with trait-improving recombinant DNA identified in the PEG-induced osmotic stress tolerance screen can survive better drought conditions providing a higher yield potential as compared to control plants.
  • SS-Enhancement of drought tolerance identified by high salinity stress tolerance screen: Three different factors are responsible for salt damages: (1) osmotic effects, (2) disturbances in the mineralization process, and (3) toxic effects caused by the salt ions, e.g., inactivation of enzymes. While the first factor of salt stress results in the wilting of the plants that is similar to drought effect, the ionic aspect of salt stress is clearly distinct from drought. The present invention provides genes that help plants maintain biomass, root growth, and/or plant development in high salinity conditions, which are identified as such in Table 3. Since osmotic effect is one of the major components of salt stress, which is common to the drought stress, trait-improving recombinant DNA identified in a high salinity stress tolerance screen can also provide transgenic crops with enhanced drought tolerance. As demonstrated from the model plant screen, embodiments of transgenic plants with trait-improving recombinant DNA identified in a high salinity stress tolerance screen can survive better drought conditions and/or high salinity conditions providing a higher yield potential as compared to control plants.
  • HS-Enhancement of drought tolerance identified by heat stress tolerance screen: Heat and drought stress often occur simultaneously, limiting plant growth. Heat stress can cause the reduction in photosynthesis rate, inhibition of leaf growth and osmotic potential in plants. Thus, genes identified by the present invention as heat stress tolerance conferring genes can also impart enhanced drought tolerance to plants. As demonstrated from the model plant screen, embodiments of transgenic plants with trait-improving recombinant DNA identified in a heat stress tolerance screen can survive better heat stress conditions and/or drought conditions providing a higher yield potential as compared to control plants.
  • CK and CS-Enhancement of tolerance to cold stress: Low temperature can immediately result in mechanical constraints, changes in activities of macromolecules, and reduced osmotic potential. In the present invention, two screening conditions, e.g., cold shock tolerance screen (CK) and cold germination tolerance screen (CS), were set up to look for transgenic plants that display visual growth advantage at lower temperature. In cold germination tolerance screen, the transgenic Arabidopsis plants were exposed to a constant temperature of 8° C. from planting until day 28 post plating. The trait-improving recombinant DNA identified by such screen can be used for the production of transgenic plant that can germinate more robustly in a cold temperature as compared to the wild type plants. In cold shock tolerance screen, the transgenic plants were first grown under the normal growth temperature of 22° C. until day 8 post plating, and subsequently were placed under 8° C. until day 28 post plating. As demonstrated from the model plant screen, embodiments of transgenic plants with trait-improving recombinant DNA identified in a cold shock stress tolerance screen and/or a cold germination stress tolerance screen can survive better cold conditions providing a higher yield potential as compared to control plants.
  • Enhancement of tolerance to multiple stresses: Different kinds of stresses often lead to identical or similar reaction in the plants. Genes that are activated or inactivated as a reaction to stress can either act directly in a way the genetic product reduces a specific stress, or they can act indirectly by activating other specific stress genes. By manipulating the activity of such regulatory genes, e.g., multiple stress tolerance genes, the plant can be enabled to react to different kinds of stresses. For examples, PEP SEQ ID NO: 1000 can be used to enhance both salt stress tolerance and heat stress tolerance in plants. Of particular interest, plants transformed with PEP SEQ ID NO: 1495 can resist salt and heat stress. Plants transformed with PEP SEQ ID NO: 1483 can also improve growth in early stage and under heat stress. In addition to these multiple stress tolerance genes, the stress tolerance conferring genes provided by the present invention can be used in combinations to generate transgenic plants that can resist multiple stress conditions.
  • PP-Enhancement of earl plant growth and development: It has been known in the art that to minimize the impact of disease on crop profitability, it is important to start the season with healthy and vigorous plants. This means avoiding seed and seedling diseases, leading to increased nutrient uptake and increased yield potential. Traditionally early planting and applying fertilizer are the methods used for promoting early seedling vigor. In early development stage, plant embryos establish only the basic root-shoot axis, a cotyledon storage organ(s), and stem cell populations, called the root and shoot apical meristems that continuously generate new organs throughout post-embryonic development. “Early growth and development” used herein encompasses the stages of seed imbibition through the early vegetative phase. The present invention provides genes that can be used to produce transgenic plants that have advantages in one or more processes including, but not limited to, germination, seedling vigor, root growth and root morphology under non-stressed conditions. The transgenic plants starting from a more robust seedling are less susceptible to the fungal and bacterial pathogens that attach germinating seeds and seedling. Furthermore, seedlings with advantage in root growth are more resistant to drought stress due to extensive and deeper root architecture. Therefore, it can be recognized by those skilled in the art that genes conferring the growth advantage in early stages to plants can also be used to generate transgenic plants that are more resistant to various stress conditions due to enhanced early plant development. The present invention provides such exemplary recombinant DNA that confer both the stress tolerance and growth advantages to plants, identified as such in Table 3, e.g., PEP SEQ ID NO: 1043 which can improve the plant early growth and development, and impart heat stress tolerance to plants. As demonstrated from the model plant screen, embodiments of transgenic plants with trait-improving recombinant DNA identified in the early plant development screen can grow better under non-stress conditions and/or stress conditions providing a higher yield potential as compared to control plants.
  • SP-Enhancement of late plant growth and development: “Late growth and development” used herein encompasses the stages of leaf development, flower production, and seed maturity. In certain embodiments, transgenic plants produced using genes that confer growth advantages to plants provided by the present invention, identified as such in Table 3, exhibit at least one phenotypic characteristics including, but not limited to, increased rosette radius, increased rosette dry weight, seed dry weight, silique dry weight, and silique length. On one hand, the rosette radius and rosette dry weight are used as the indexes of photosynthesis capacity, and thereby plant source strength and yield potential of a plant. On the other hand, the seed dry weight, silique dry weight and silique length are used as the indexes for plant sink strength, which are considered as the direct determinants of yield. As demonstrated from the model plant screen, embodiments of transgenic plants with trait-improving recombinant DNA identified in the late development screen can grow better and/or have enhanced development during leaf development and seed maturation providing a higher yield potential as compared to control plants.
  • LL-Enhancement of tolerance to shade stress identified in a low light screen: The effects of light on plant development are especially prominent at the seedling stage. Under normal light conditions with unobstructed direct light, a plant seeding develops according to a characteristic photomorphogenic pattern, in which plants have open and expanded cotyledons and short hypocotyls. Then the plant's energy is devoted to cotyledon and leaf development while longitudinal extension growth is minimized. Under low light condition where light quality and intensity are reduced by shading, obstruction or high population density, a seedling displays a shade-avoidance pattern, in which the seedling displays a reduced cotyledon expansion, and hypocotyls extension is greatly increased. As the result, a plant under low light condition increases significantly its stem length at the expanse of leaf, seed or fruit and storage organ development, thereby adversely affecting of yield. The present invention provides recombinant DNA that enable plants to have an attenuated shade avoidance response so that the source of plant can be contributed to reproductive growth efficiently, resulting higher yield as compared to the wild type plants. As demonstrated from the model plant screen, embodiments of transgenic plants with trait-improving recombinant DNA identified in a shade stress tolerance screen can have attenuated shade response under shade conditions providing a higher yield potential as compared to control plants. The transgenic plants generated by the present invention can be suitable for a higher density planting, thereby resulting increased yield per unit area.
  • LN-Enhancement of tolerance to low nitrogen availability stress
  • Nitrogen is a key factor in plant growth and crop yield. The metabolism, growth and development of plants are profoundly affected by their nitrogen supply. Restricted nitrogen supply alters shoot to root ratio, root development, activity of enzymes of primary metabolism and the rate of senescence (death) of older leaves. All field crops have a fundamental dependence on inorganic nitrogenous fertilizer. Since fertilizer is rapidly depleted from most soil types, it must be supplied to growing crops two or three times during the growing season. Enhanced nitrogen use efficiency by plants should enable crops cultivated under low nitrogen availability stress condition resulted from low fertilizer input or poor soil quality.
  • According to the present invention, transgenic plants generated using the recombinant nucleotides, which confer enhanced nitrogen use efficiency, identified as such in Table 3, exhibit one or more desirable traits including, but not limited to, increased seedling weight, greener leaves, increased number of rosette leaves, increased or decreased root length. One skilled in the art can recognize that the transgenic plants provided by the present invention with enhanced nitrogen use efficiency can also have altered amino acid or protein compositions, increased yield and/or better seed quality. The transgenic plants of the present invention can be productively cultivated under low nitrogen growth conditions, e.g., nitrogen-poor soils and low nitrogen fertilizer inputs, which would cause the growth of wild type plants to cease or to be so diminished as to make the wild type plants practically useless. The transgenic plants also can be advantageously used to achieve earlier maturing, faster growing, and/or higher yielding crops and/or produce more nutritious foods and animal feedstocks when cultivated using nitrogen non-limiting growth conditions.
  • Stacked Traits: The present invention also encompasses transgenic plants with stacked engineered traits, e.g., a crop having an enhanced phenotype resulting from expression of a trait-improving recombinant DNA, in combination with herbicide and/or pest resistance traits. For example, genes of the current invention can be stacked with other traits of agronomic interest, such as a trait providing herbicide resistance, for example a RoundUp Ready® trait, or insect resistance, such as using a gene from Bacillus thuringensis to provide resistance against lepidopteran, coliopteran, homopteran, hemiopteran, and other insects. Explementary herbicides include glyphosate herbicides, phosphinothricin herbicides, oxynil herbicides, imidazolinone herbicides, dinitroaniline herbicides, pyridine herbicides, sulfonylurea herbicides, bialaphos herbicides, sulfonamide herbicides and gluphosinate herbicides. To illustrate that the production of transgenic plants with herbicide resistance is a capability of those of ordinary skill in the art, reference is made to U.S. patent application publications 2003/0106096A1 and 2002/0112260A1 and U.S. Pat. Nos. 5,034,322; 5,776,760, 6,107,549 and 6,376,754, all of which are incorporated herein by reference. To illustrate that the production of transgenic plants with pest resistance is a capability of those of ordinary skill in the art reference is made to U.S. Pat. Nos. 5,250,515 and 5,880,275 which disclose plants expressing an endotoxin of Bacillus thuringiensis bacteria, to U.S. Pat. No. 6,506,599 which discloses control of invertebrates which feed on transgenic plants which express dsRNA for suppressing a target gene in the invertebrate, to U.S. Pat. No. 5,986,175 which discloses the control of viral pests by transgenic plants which express viral replicase, and to U.S. Patent Application Publication 2003/0150017 A1 which discloses control of pests by a transgenic plant which express a dsRNA targeted to suppressing a gene in the pest, all of is which are incorporated herein by reference.
  • Once one recombinant DNA has been identified as conferring an enhanced trait of interest in transgenic Arabidopsis plants, several methods are available for using the sequence of that recombinant DNA and knowledge about the protein it encodes to identify homologs of that sequence from the same plant or different plant species or other organisms, e.g., bacteria and yeast. Thus, in one aspect, the invention provides methods for identifying a homologous gene with a DNA sequence homologous to any of SEQ ID NO: 1 through SEQ ID NO: 803, or a homologous protein with an amino acid sequence homologous to any of SEQ ID NO: 804 to SEQ ID NO: 1606. In another aspect, the present invention provides the protein sequences of identified homologs for a sequence listed as SEQ ID NO: 1607 through SEQ ID NO: 94613. In yet another aspect, the present invention also includes linking or associating one or more desired traits, or gene function with a homolog sequence provided herein.
  • The trait-improving recombinant DNA and methods of using such trait-improving recombinant DNA for generating transgenic plants with enhanced traits provided by the present invention are not limited to any particular plant species. Indeed, the plants according to the present invention can be of any plant species, e.g., can be monocotyledonous or dicotyledonous. In one embodiment, they are agricultural plants, e.g., plants cultivated by man for purposes of food production or technical, particularly industrial applications. Of particular interest in the present invention are corn and soybean plants. The recombinant DNA constructs optimized for soybean transformation and recombinant DNA constructs optimized for corn transformation are provided by the present invention. Other plants of interest in the present invention for production of transgenic plants having enhanced traits include, without limitation, cotton, canola, wheat, sunflower, sorghum, alfalfa, barley, millet, rice, tobacco, fruit and vegetable crops, and turfgrass.
  • In certain embodiments, the present invention contemplates to use an orthologous gene in generating the transgenic plants with similarly enhanced traits as the transgenic Arabidopsis counterpart. Enhanced physiological properties in transgenic plants of the present invention can be confirmed in responses to stress conditions, for example in assays using imposed stress conditions to detect enhanced responses to drought stress, nitrogen deficiency, cold growing conditions, or alternatively, under naturally present stress conditions, for example under field conditions. Biomass measures can be made on greenhouse or field grown plants and can include such measurements as plant height, stem diameter, root and shoot dry weights, and, for corn plants, ear length and diameter.
  • Trait data on morphological changes can be collected by visual observation during the process of plant regeneration as well as in regenerated plants transferred to soil. Such trait data includes characteristics such as normal plants, bushy plants, taller plants, thicker stalks, narrow leaves, striped leaves, knotted phenotype, chlorosis, albino, anthocyanin production, or altered tassels, ears or roots. Other enhanced traits can be identified by measurements taken under field conditions, such as days to pollen shed, days to silking, leaf extension rate, chlorophyll content, leaf temperature, stand, seedling vigor, internode length, plant height, leaf number, leaf area, tillering, brace roots, stay green, stalk lodging, root lodging, plant health, barreness/prolificacy, green snap, and pest resistance. In addition, trait characteristics of harvested grain can be confirmed, including number of kernels per row on the ear, number of rows of kernels on the ear, kernel abortion, kernel weight, kernel size, kernel density and physical grain quality.
  • To confirm hybrid yield in transgenic corn plants expressing genes of the present invention, it can be desirable to test hybrids over multiple years at multiple locations in a geographical location where maize is conventionally grown, e.g., in Iowa, Ill. or other locations in the midwestern United States, under “normal” field conditions as well as under stress conditions, e.g., under drought or population density stress.
  • Transgenic plants can be used to provide plant parts according to the invention for regeneration or tissue culture of cells or tissues containing the constructs described herein. Plant parts for these purposes can include leaves, stems, roots, flowers, tissues, epicotyl, meristems, hypocotyls, cotyledons, pollen, ovaries, cells and protoplasts, or any other portion of the plant which can be used to regenerate additional transgenic plants, cells, protoplasts or tissue culture. Seeds of transgenic plants are provided by this invention can be used to propagate more plants containing the trait-improving recombinant DNA constructs of this invention. These descendants are intended to be included in the scope of this invention if they contain a trait-improving recombinant DNA construct of this invention, whether or not these plants are selfed or crossed with different varieties of plants.
  • The various aspects of the invention are illustrated by means of the following examples which are in no way intended to limit the full breath and scope of claims.
    • EXAMPLES Example 1 Identification of Recombinant DNA that Confers Enhanced Trait(s) to Plants A. Plant Expression Constructs for Arabidopsis Transformation
  • Each gene of interest was amplified from a genomic or cDNA library using primers specific to sequences upstream and downstream of the coding region. Transformation vectors were prepared to constitutively transcribe DNA in either sense orientation (for enhanced protein expression) or anti-sense orientation (for endogenous gene suppression) under the control of an enhanced Cauliflower Mosaic Virus 35S promoter (U.S. Pat. No. 5,359,142) directly or indirectly (Moore, et al., PNAS 95:376-381, 1998; Guyer, e.g., Genetics 149: 633-639, 1998; International patent application NO. PCT/EP98/07577). The transformation vectors also contain a bar gene as a selectable marker for resistance to glufosinate herbicide. The transformation of Arabidopsis plants was carried out using the vacuum infiltration method known in the art (Bethtold, et al., Methods Mol. Biol. 82:259-66, 1998). Seeds harvested from the plants, named as T1 seeds, were subsequently grown in a glufosinate-containing selective medium to select for plants which were actually transformed and which produced T2 transgenic seed.
    • B. Soil Drought Tolerance Screen
  • This example describes a soil drought tolerance screen to identify Arabidopsis plants transformed with recombinant DNA that wilt less rapidly and/or produce higher seed yield when grown in soil under drought conditions
  • T2 seeds were sown in flats filled with Metro/Mix® 200 (The Scotts® Company, USA). Humidity domes were added to each flat and flats were assigned locations and placed in climate-controlled growth chambers. Plants were grown under a temperature regime of 22° C. at day and 20° C. at night, with a photoperiod of 16 hours and average light intensity of 170 μmol/m2/s. After the first true leaves appeared, humidity domes were removed. The plants were sprayed with glufosinate herbicide and put back in the growth chamber for 3 additional days. Flats were watered for 1 hour the week following the herbicide treatment. Watering was continued every seven days until the flower bud primordia became apparent, at which time plants were watered for the last time.
  • To identify drought tolerant plants, plants were evaluated for wilting response and seed yield. Beginning ten days after the last watering, plants were examined daily until 4 plants/line had wilted. In the next six days, plants were monitored for wilting response. Five drought scores were assigned according to the visual inspection of the phenotypes: 1 for healthy, 2 for dark green, 3 for wilting, 4 severe wilting, and 5 for dead. A score of 3 or higher was considered as wilted.
  • At the end of this assay, seed yield measured as seed weight per plant under the drought condition was characterized for the transgenic plants and their controls and analyzed as a quantitative response according to example 1M.
  • Two approaches were used for statistical analysis on the wilting response. First, the risk score was analyzed for wilting phenotype and treated as a qualitative response according to the example 1L. Alternatively, the survival analysis was carried out in which the proportions of wilted and non-wilted transgenic and control plants were compared over each of the six days under scoring and an overall log rank test was performed to compare the two survival curves using S-PLUS statistical software (S-PLUS 6, Guide to statistics, Insightful, Seattle, Wash., USA). A list of recombinant DNA constructs which improve drought tolerance in transgenic plants is illustrated in Table 4
  • TABLE 4
    PEP Drought score Seed yield
    SEQ Construct Delta Delta
    ID ID Orientation mean P-value mean P-value
    989 10471 SENSE 0.069 0.285 0.368 0.021
    1224 12204 SENSE 0.152 0.018 −0.519 0.041
    1606 12315 ANTI-SENSE 0.067 0.029 −0.126 0.210
    1257 12354 ANTI-SENSE 0.118 0.334 −0.663 0.001
    1606 12366 SENSE −0.105 0.735 −0.072 0.403
    852 13623 SENSE 0.309 0.005 −0.202 0.403
    812 13638 ANTI-SENSE 0.195 0.047 −0.930 0.045
    838 13811 SENSE −0.037 0.729 −0.578 0.032
    860 14248 SENSE 0.205 0.013 −0.484 0.066
    885 14910 ANTI-SENSE −0.087 0.305 −0.261 0.220
    891 14932 ANTI-SENSE 0.222 0.011 −0.019 0.957
    879 15111 ANTI-SENSE 0.082 0.241 0.624 0.019
    893 15964 ANTI-SENSE 0.003 0.023 −0.396 0.028
    899 15986 ANTI-SENSE 0.199 0.128 −0.022 0.773
    900 15987 ANTI-SENSE 0.223 0.416 −0.156 0.576
    904 15995 ANTI-SENSE 0.281 0.196 −0.362 0.157
    945 16614 SENSE 0.136 0.001 0.059 0.440
    959 19162 SENSE 0.007 0.887 0.348 0.019
    999 19423 SENSE 0.222 0.024 −0.460 0.069
    1003 19425 SENSE 0.002 0.556 0.099 0.019
    1081 71667 SENSE 0.064 0.790 −0.314 0.101
    1164 72717 SENSE 0.043 0.031 −0.173 0.221
    1165 72718 SENSE 0.119 0.037 −0.272 0.359
    1167 72779 SENSE −0.026 0.491 0.395 0.006
    1168 72791 SENSE 0.284 0.046 −1.867 0.009
    1272 73472 SENSE 0.159 0.036 −0.223 0.511
    1273 73526 SENSE −0.219 0.141 −0.250 0.145
    1280 73531 SENSE −0.277 0.022 −0.097 0.740
    1132 73738 SENSE 0.386 0.022 −1.025 0.018
    1485 73938 SENSE 0.117 0.050 0.309 0.052
    1069 74060 SENSE 0.116 0.016 0.195 0.200
    1286 74164 SENSE 0.602 0.031 0.287 0.137
    1157 74257 SENSE −0.139 0.622 −0.366 0.059
    1146 74269 SENSE 0.176 0.057 −0.101 0.273
    1229 74376 SENSE −0.023 0.583 −0.747 0.053
    1234 74668 SENSE 0.112 0.018 −0.931 0.063
    1351 74873 SENSE 0.256 0.006 0.110 0.627
    1385 75473 SENSE 0.108 0.031 −1.469 0.015
    1535 76345 SENSE −0.024 0.476 0.318 0.017
    1541 76396 SENSE −0.146 0.218 −0.137 0.518
    1245 76724 SENSE 0.514 0.029 −1.467 0.021
    1581 77170 SENSE 0.258 0.026 −0.436 0.026
    1570 77185 SENSE 0.180 0.037 −0.602 0.086
    1457 77369 SENSE −0.117 0.194 −0.324 0.096
    1460 77372 SENSE 0.623 0.017 −0.108 0.028
    1597 77488 SENSE 0.001 0.973 −0.252 0.075
    1452 77594 SENSE 0.200 0.032 −0.334 0.096
    1555 77839 SENSE 0.082 0.021 −0.242 0.298
    1472 77965 SENSE 0.643 0.003 −0.157 0.456
    1487 77990 SENSE 0.246 0.022 −0.303 0.458
    1497 78023 SENSE 0.364 0.004 −3.072 0.012
    1503 78036 SENSE 0.651 0.010 −0.959 0.095
    1350 78115 SENSE 0.412 0.027 −0.024 0.880
    1061 78321 SENSE 0.254 0.044 −0.941 0.014
    1230 74377 SENSE 0.327 0.028 / /
    1007 70419 SENSE 0.007 0.047 −0.599 0.012

    Transgenic plants comprising recombinant DNA expressing protein as set forth in SEQ ID NO: 1047, 1073, 1105, 1106, 1137, 1190, 1216, 1334, 1585, or 1590 showed enhanced drought tolerance by the second criteria as illustrated in Example 1L.
    • C. Heat Stress Tolerance Screen
  • Under high temperatures, Arabidopsis seedlings become chlorotic and root growth is inhibited. This example sets forth the heat stress tolerance screen to identify Arabidopsis plants transformed with the gene of interest that are more resistant to heat stress based on primarily their seedling weight and root growth under high temperature.
  • T2 seeds were plated on ½ X MS salts, 1% phytagel, with 10 μg/ml BASTA (7 per plate with 2 control seeds; 9 seeds total per plate). Plates were placed at 4° C. for 3 days to stratify seeds. Plates were then incubated at room temperature for 3 hours and then held vertically for 11 additional days at temperature of 34° C. at day and 20° C. at night. Photoperiod was 16 h. Average light intensity was ˜140 μmol/m2/s. After 14 days of growth, plants were scored for glufosinate resistance, root length, final growth stage, visual color, and seedling fresh weight.
    A photograph of the whole plate was taken on day 14.
  • The seedling weight and root length were analyzed as quantitative responses according to example 1M. The final grow stage at day 14 was scored as success if 50% of the plants had reached 3 rosette leaves and size of leaves are greater than 1 mm (Boyes, et al., (2001) The Plant Cell 13, 1499-1510). The growth stage data was analyzed as a qualitative response according to example 1L. A list of recombinant DNA constructs that improve heat tolerance in transgenic plants illustrated in Table 5.
  • TABLE 5
    Root length Growth stage Seedling
    day 14 at day 14 weight
    PEP Construct Delta Risk score Delta
    SEQ ID ID Orientation mean P-value mean P-value mean P-value
    848 10706 ANTI- −0.080 0.577 −0.056 0.371 0.423 0.023
    SENSE
    822 13231 SENSE 0.267 0.037 1.633 0.010 1.492 0.000
    834 13914 SENSE 0.283 0.096 0.466 0.230 1.497 0.016
    827 15606 SENSE −0.107 0.459 0.032 0.889 0.658 0.049
    876 15623 SENSE 0.265 0.088 0.150 0.371 1.064 0.012
    906 16213 SENSE 0.020 0.917 0.048 0.579 0.681 0.013
    943 16603 SENSE 0.171 0.300 0.783 0.192 0.994 0.035
    941 16617 SENSE 0.327 0.055 0.179 0.312 1.362 0.007
    934 17502 SENSE −0.082 0.580 0.989 0.402 0.519 0.026
    935 17503 SENSE 0.149 0.052 0.015 0.828 0.697 0.003
    897 18203 SENSE −0.078 0.640 −0.221 0.300 0.728 0.041
    984 18238 SENSE 0.031 0.845 −0.077 0.457 0.820 0.047
    853 18302 SENSE 0.315 0.074 1.298 0.269 1.271 0.011
    851 18304 SENSE 0.346 0.222 0.374 0.381 1.111 0.043
    952 18307 SENSE 0.394 0.183 1.676 0.287 1.088 0.013
    997 18352 SENSE 0.239 0.055 0.036 0.894 0.924 0.019
    968 18421 SENSE 0.069 0.684 0.941 0.213 0.918 0.012
    969 18422 SENSE 0.236 0.243 / / 1.127 0.033
    958 18441 SENSE 0.175 0.289 0.832 0.497 0.907 0.043
    979 18535 SENSE −0.007 0.946 −0.100 0.496 0.853 0.015
    911 19041 ANTI- 0.160 0.012 −0.063 0.102 0.932 0.003
    SENSE
    913 19042 ANTI- 0.068 0.618 0.024 0.725 0.767 0.030
    SENSE
    950 19154 SENSE 0.109 0.609 1.642 0.111 0.877 0.041
    951 19155 SENSE 0.244 0.237 0.085 0.434 0.905 0.018
    976 19237 SENSE 0.094 0.296 0.492 0.362 0.663 0.047
    971 19244 SENSE 0.473 0.104 1.137 0.259 1.324 0.020
    1011 19320 SENSE −0.265 0.212 / / 0.329 0.043
    967 19534 SENSE 0.064 0.756 0.920 0.315 0.630 0.039
    964 19535 SENSE 0.190 0.158 −0.025 0.750 0.961 0.013
    970 19539 SENSE 0.083 0.373 0.521 0.256 0.466 0.031
    973 19545 SENSE −0.083 0.150 / / 0.609 0.038
    1002 19616 SENSE 0.288 0.094 −0.068 0.565 0.689 0.003
    1027 19702 SENSE −0.017 0.915 −0.033 0.798 0.783 0.043
    1032 19755 SENSE 0.312 0.129 1.611 0.029 1.285 0.008
    1029 19775 SENSE 0.126 0.362 2.093 0.172 0.775 0.004
    1042 19786 SENSE 0.226 0.265 0.580 0.372 1.083 0.040
    1039 19825 SENSE 0.053 0.662 −0.055 0.759 0.872 0.022
    1037 19893 SENSE −0.089 0.168 −0.130 0.249 0.787 0.023
    1040 19919 SENSE −0.214 0.277 0.198 0.435 0.814 0.050
    1041 19979 SENSE 0.202 0.080 0.738 0.222 1.048 0.047
    1031 19982 SENSE 0.241 0.111 0.933 0.263 1.127 0.025
    1038 19983 SENSE 0.238 0.218 0.834 0.367 0.876 0.002
    1028 19985 SENSE 0.216 0.057 0.414 0.306 0.860 0.001
    1036 19987 SENSE 0.052 0.568 0.584 0.442 0.834 0.028
    925 70102 SENSE −0.013 0.877 −0.115 0.461 0.779 0.012
    926 70106 SENSE 0.038 0.667 −0.016 0.692 0.869 0.028
    927 70113 SENSE 0.163 0.289 1.098 0.222 1.005 0.012
    930 70128 SENSE 0.025 0.785 0.347 0.302 0.920 0.016
    931 70130 SENSE 0.238 0.111 −0.041 0.447 1.275 0.000
    884 70216 SENSE 0.012 0.932 0.165 0.689 0.708 0.007
    1436 70229 SENSE −0.074 0.761 0.228 0.259 0.494 0.034
    1446 70230 SENSE 0.068 0.053 −0.005 0.908 0.554 0.008
    804 70244 SENSE 0.019 0.894 / / 0.468 0.036
    845 70253 SENSE −0.080 0.196 −0.189 0.436 1.085 0.004
    856 70412 SENSE 0.151 0.185 1.151 0.374 0.757 0.023
    975 70425 SENSE −0.056 0.712 / / 0.815 0.011
    1014 70433 SENSE 0.196 0.242 / / 0.737 0.021
    1015 70434 SENSE 0.136 0.106 / / 0.814 0.000
    1017 70436 SENSE 0.199 0.196 0.008 0.918 0.969 0.017
    1019 70439 SENSE 0.188 0.127 0.846 0.311 1.250 0.012
    1001 70603 SENSE 0.430 0.028 0.301 0.281 1.573 0.004
    1052 70635 SENSE −0.199 0.020 −0.185 0.234 0.381 0.045
    1054 70638 SENSE 0.004 0.943 −0.069 0.197 0.788 0.036
    1055 70642 SENSE −0.100 0.336 −0.278 0.049 0.385 0.003
    1056 70643 SENSE 0.160 0.445 −0.001 0.423 0.947 0.021
    1078 70682 SENSE −0.203 0.156 −0.278 0.057 0.404 0.024
    920 70706 ANTI- −0.354 0.066 −0.162 0.208 0.517 0.010
    SENSE
    843 70716 ANTI- 0.098 0.240 0.013 0.970 0.858 0.001
    SENSE
    837 70721 ANTI- 0.254 0.047 0.346 0.068 0.859 0.008
    SENSE
    859 70723 ANTI- 0.180 0.341 1.110 0.253 0.990 0.016
    SENSE
    1026 70741 SENSE 0.046 0.693 0.469 0.265 0.927 0.008
    1093 70810 SENSE 0.168 0.053 −0.072 0.275 0.897 0.013
    1008 70827 SENSE −0.106 0.519 0.878 0.158 0.646 0.045
    880 70832 SENSE 0.224 0.152 1.398 0.318 0.912 0.008
    1263 70850 SENSE −0.002 0.986 0.312 0.296 0.887 0.035
    1043 70903 SENSE 0.065 0.734 0.623 0.454 0.776 0.002
    1046 70936 SENSE 0.393 0.063 0.889 0.020 1.352 0.008
    1044 70970 SENSE 0.335 0.231 0.520 0.444 1.429 0.031
    1547 71107 SENSE −0.257 0.177 0.027 0.685 0.528 0.045
    1126 71125 SENSE 0.236 0.091 1.197 0.112 1.308 0.029
    921 71145 SENSE 0.093 0.534 / / 0.535 0.030
    1604 71249 SENSE −0.150 0.372 0.056 0.768 0.866 0.035
    977 71303 SENSE 0.103 0.377 / / 0.858 0.025
    1067 71318 SENSE 0.100 0.212 0.498 0.324 1.190 0.004
    957 71531 SENSE −0.087 0.696 −0.085 0.224 0.718 0.048
    1006 71536 SENSE 0.021 0.831 −0.134 0.725 0.922 0.047
    1057 71564 SENSE 0.305 0.153 0.033 0.795 0.793 0.013
    1091 71629 SENSE 0.084 0.202 1.387 0.044 1.001 0.019
    1083 71696 SENSE 0.222 0.304 0.850 0.296 0.885 0.043
    965 71719 SENSE 0.113 0.605 0.088 0.689 0.989 0.046
    1063 71808 SENSE 0.158 0.043 0.589 0.172 0.956 0.011
    1143 72110 SENSE −0.031 0.607 −0.114 0.565 0.329 0.041
    1142 72124 SENSE −0.211 0.255 −0.100 0.411 0.568 0.049
    1542 72314 SENSE 0.127 0.271 1.270 0.224 0.943 0.002
    1288 72340 SENSE 0.089 0.574 0.893 0.258 0.864 0.032
    910 72427 ANTI- −0.024 0.813 −0.019 0.423 0.658 0.006
    SENSE
    1084 72475 SENSE −0.129 0.192 0.024 0.896 0.697 0.013
    1087 72476 SENSE −0.136 0.228 −0.168 0.134 0.729 0.007
    1098 72537 SENSE −0.124 0.341 −0.254 0.011 0.352 0.025
    1169 72732 SENSE 0.191 0.165 0.090 0.641 0.700 0.020
    933 72748 SENSE 0.125 0.369 1.403 0.138 1.010 0.000
    1158 72749 SENSE 0.053 0.642 0.625 0.250 0.881 0.027
    1161 72775 SENSE −0.050 0.707 −0.157 0.333 0.861 0.049
    1163 72776 SENSE 0.091 0.358 1.128 0.239 1.244 0.006
    1168 72791 SENSE −0.095 0.672 / / 0.763 0.034
    1199 72909 SENSE 0.254 0.065 −0.033 0.348 0.818 0.048
    1203 72958 SENSE −0.030 0.774 −0.052 0.358 0.840 0.034
    1195 73018 SENSE 0.053 0.638 0.057 0.895 0.856 0.042
    1202 73036 SENSE −0.005 0.957 0.282 0.386 0.783 0.007
    1188 73074 SENSE −0.146 0.202 −0.081 0.319 0.667 0.028
    1193 73077 SENSE 0.028 0.770 0.495 0.459 0.944 0.001
    1196 73112 SENSE 0.021 0.846 / / 0.886 0.019
    1180 73117 SENSE −0.060 0.537 0.124 0.759 0.996 0.018
    1178 73128 SENSE 0.149 0.075 0.248 0.598 0.934 0.038
    1191 73147 SENSE 0.689 0.024 0.822 0.293 1.572 0.010
    1174 73174 SENSE 0.305 0.027 0.532 0.480 0.779 0.046
    1194 73183 SENSE 0.113 0.617 0.180 0.573 0.969 0.004
    1175 73186 SENSE 0.101 0.628 1.230 0.130 0.714 0.014
    1131 73248 SENSE 0.289 0.103 0.455 0.104 1.034 0.018
    1118 73353 SENSE 0.108 0.504 0.947 0.218 0.864 0.024
    1264 73429 SENSE 0.305 0.067 0.867 0.057 1.190 0.003
    1267 73455 SENSE 0.133 0.064 0.299 0.033 0.559 0.018
    1262 73474 SENSE −0.433 0.105 −0.164 0.092 0.433 0.024
    1274 73538 SENSE −0.003 0.962 0.241 0.339 0.741 0.003
    1279 73565 SENSE 0.182 0.325 0.650 0.525 1.279 0.021
    1275 73574 SENSE 0.067 0.721 0.363 0.636 0.758 0.043
    996 73607 SENSE −0.070 0.388 0.401 0.673 0.636 0.024
    896 73706 SENSE 0.064 0.744 0.294 0.124 1.082 0.012
    1144 73916 SENSE −0.004 0.980 0.495 0.265 1.060 0.024
    903 73977 SENSE 0.230 0.065 0.096 0.370 0.596 0.014
    1182 73990 SENSE 0.133 0.346 / / 1.140 0.025
    1291 74133 SENSE −0.170 0.121 −0.027 0.729 0.635 0.013
    1289 74155 SENSE 0.211 0.210 0.458 0.428 0.945 0.017
    1148 74273 SENSE 0.050 0.756 0.694 0.467 0.837 0.026
    1149 74280 SENSE 0.117 0.251 −0.103 0.271 0.785 0.002
    1151 74287 SENSE 0.044 0.644 −0.148 0.027 0.928 0.000
    1206 74333 SENSE 0.144 0.114 0.144 0.521 0.748 0.023
    1299 74431 SENSE 0.002 0.987 −0.190 0.282 0.674 0.012
    1293 74485 SENSE −0.007 0.920 −0.098 0.273 0.923 0.007
    1435 74508 SENSE 0.409 0.104 0.221 0.394 0.825 0.001
    1302 74525 SENSE 0.110 0.261 0.080 0.467 0.967 0.004
    1227 74612 SENSE −0.319 0.220 −0.591 0.063 0.563 0.017
    1233 74623 SENSE −0.167 0.140 / / 0.521 0.000
    1237 74638 SENSE 0.036 0.848 0.418 0.399 0.828 0.049
    1209 74737 SENSE 0.004 0.959 0.877 0.414 0.972 0.008
    1212 74747 SENSE 0.254 0.074 1.728 0.157 0.961 0.027
    1355 74804 SENSE 0.615 0.095 1.179 0.314 1.685 0.019
    1352 74826 SENSE −0.062 0.460 / / 0.655 0.009
    1353 74850 SENSE 0.167 0.271 0.910 0.352 0.950 0.040
    1359 74901 SENSE 0.117 0.664 0.258 0.353 0.897 0.041
    1361 74904 SENSE −0.030 0.814 −0.030 0.791 0.866 0.016
    1365 74966 SENSE −0.041 0.658 0.114 0.770 0.671 0.015
    1360 74974 SENSE 0.142 0.382 −0.117 0.116 0.793 0.047
    1130 75206 SENSE 0.044 0.484 −0.217 0.093 0.671 0.010
    1254 75281 SENSE 0.207 0.020 0.046 0.795 0.827 0.009
    1380 75323 SENSE 0.041 0.684 −0.202 0.074 0.473 0.006
    1374 75330 SENSE −0.005 0.712 −0.001 0.998 0.753 0.001
    1379 75334 SENSE 0.427 0.107 0.050 0.599 1.040 0.004
    1376 75366 SENSE −0.013 0.883 / / 0.832 0.008
    1372 75389 SENSE 0.304 0.038 0.181 0.377 0.923 0.005
    1378 75391 SENSE 0.076 0.434 0.109 0.434 0.918 0.020
    1382 75401 SENSE 0.020 0.910 / / 0.854 0.005
    1392 75446 SENSE 0.431 0.174 0.231 0.269 0.967 0.021
    1390 75454 SENSE 0.055 0.585 0.288 0.378 0.770 0.022
    1384 75461 SENSE 0.032 0.434 0.020 0.936 0.931 0.034
    1388 75464 SENSE −0.117 0.288 0.085 0.651 0.717 0.014
    1391 75493 SENSE 0.007 0.891 −0.021 0.738 1.080 0.013
    1401 75512 SENSE 0.089 0.652 0.860 0.279 0.806 0.032
    1409 75605 SENSE 0.153 0.136 −0.016 0.721 1.065 0.014
    1413 75623 SENSE 0.151 0.321 −0.030 0.721 0.751 0.000
    1403 75626 SENSE 0.364 0.001 0.619 0.475 1.127 0.014
    1404 75674 SENSE −0.028 0.530 / / 0.893 0.021
    1415 75695 SENSE 0.132 0.300 0.072 0.640 1.108 0.010
    1419 75714 SENSE −0.049 0.701 0.169 0.588 0.853 0.025
    1308 75832 SENSE 0.043 0.229 −0.006 0.944 0.691 0.013
    1318 75848 SENSE 0.117 0.485 0.324 0.491 0.953 0.035
    1321 75852 SENSE −0.218 0.196 −0.017 0.895 0.468 0.039
    1330 75879 SENSE 0.126 0.570 −0.007 0.937 0.863 0.042
    1331 75880 SENSE 0.198 0.119 0.331 0.249 0.842 0.011
    1468 75908 SENSE 0.057 0.686 −0.064 0.759 0.916 0.015
    1467 75919 SENSE −0.063 0.562 −0.056 0.586 0.640 0.036
    1471 75933 SENSE 0.126 0.099 0.431 0.238 0.905 0.004
    1466 75940 SENSE 0.147 0.429 1.316 0.343 0.872 0.049
    830 75958 SENSE 0.036 0.515 −0.144 0.102 1.048 0.001
    826 75969 SENSE 0.164 0.316 0.002 0.990 0.696 0.025
    1470 75992 SENSE 0.103 0.525 0.101 0.605 0.853 0.005
    832 76002 SENSE −0.016 0.860 0.032 0.815 0.868 0.023
    892 76017 SENSE 0.107 0.424 0.359 0.280 0.978 0.022
    843 76039 SENSE 0.226 0.299 0.039 0.656 1.072 0.008
    914 76053 SENSE 0.293 0.058 0.940 0.022 1.142 0.004
    1215 76212 SENSE 0.006 0.732 0.105 0.829 0.808 0.012
    1258 76236 SENSE −0.062 0.693 0.941 0.453 0.871 0.031
    1314 76261 SENSE 0.065 0.490 0.699 0.344 0.901 0.039
    1526 76337 SENSE 0.121 0.439 0.454 0.199 0.924 0.010
    1532 76378 SENSE −0.077 0.500 0.220 0.481 0.829 0.034
    1536 76381 SENSE −0.011 0.954 0.712 0.324 0.806 0.004
    1340 76462 SENSE −0.019 0.861 −0.004 0.959 0.716 0.038
    1221 76530 SENSE 0.260 0.305 −0.053 0.801 1.088 0.004
    1342 76568 SENSE −0.008 0.748 0.059 0.677 0.610 0.016
    1337 76621 SENSE −0.098 0.270 0.001 0.995 0.622 0.006
    1346 76629 SENSE 0.154 0.603 0.550 0.509 0.982 0.049
    1222 76716 SENSE −0.007 0.945 / / 0.792 0.024
    1333 76745 SENSE 0.044 0.738 −0.010 0.927 0.695 0.021
    1550 76805 SENSE 0.369 0.113 0.041 0.519 0.950 0.018
    1551 76817 SENSE 0.126 0.645 0.007 0.790 0.861 0.024
    1562 76848 SENSE −0.080 0.699 −0.112 0.185 0.804 0.006
    1558 76869 SENSE 0.345 0.160 1.378 0.130 1.205 0.030
    1548 76887 SENSE 0.319 0.292 / / 0.812 0.036
    1554 76890 SENSE 0.226 0.007 −0.032 0.300 0.659 0.027
    1567 76904 SENSE 0.178 0.268 / / 0.917 0.004
    1310 77034 SENSE −0.033 0.843 0.479 0.109 0.953 0.001
    1572 77127 SENSE 0.061 0.705 −0.026 0.704 0.769 0.043
    1582 77171 SENSE 0.054 0.519 −0.133 0.026 0.698 0.000
    1575 77179 SENSE 0.146 0.392 0.039 0.517 1.072 0.010
    1587 77184 SENSE 0.025 0.782 / / 0.979 0.012
    1153 77304 SENSE 0.174 0.297 1.437 0.321 1.010 0.047
    1223 77328 SENSE 0.116 0.253 / / 1.016 0.024
    1445 77345 SENSE 0.222 0.005 0.215 0.529 0.833 0.010
    1447 77353 SENSE 0.124 0.184 0.043 0.702 0.830 0.007
    1594 77414 SENSE 0.115 0.229 / / 0.965 0.002
    1601 77419 SENSE 0.309 0.205 0.762 0.199 1.166 0.013
    1600 77442 SENSE 0.112 0.214 0.779 0.067 0.825 0.019
    1596 77463 SENSE −0.027 0.865 −0.143 0.007 0.674 0.045
    1319 77515 SENSE 0.242 0.195 0.088 0.276 1.411 0.014
    1332 77519 SENSE 0.667 0.043 1.824 0.173 1.142 0.021
    1323 77523 SENSE 0.190 0.379 1.044 0.059 1.312 0.014
    1426 77554 SENSE 0.358 0.257 1.126 0.108 0.949 0.034
    1430 77560 SENSE −0.047 0.095 0.786 0.380 0.583 0.012
    1438 77567 SENSE −0.178 0.220 / / 0.437 0.020
    1440 77578 SENSE 0.213 0.119 1.089 0.387 0.931 0.013
    1270 77726 SENSE −0.060 0.338 / / 0.990 0.007
    1368 77814 SENSE −0.032 0.843 −0.117 0.556 0.885 0.025
    1395 77818 SENSE 0.094 0.220 0.336 0.311 0.879 0.004
    1248 77903 SENSE 0.014 0.798 0.015 0.874 0.675 0.017
    1443 77925 SENSE 0.005 0.960 0.085 0.472 0.911 0.001
    1444 77927 SENSE −0.167 0.181 −0.114 0.590 0.638 0.002
    1456 77937 SENSE 0.231 0.151 0.815 0.062 1.368 0.001
    1458 77940 SENSE −0.017 0.859 / / 0.706 0.004
    1421 77954 SENSE 0.326 0.111 1.981 0.208 1.139 0.014
    1422 77955 SENSE −0.078 0.652 −0.062 0.104 0.529 0.029
    1437 77959 SENSE 0.345 0.055 0.505 0.429 1.016 0.038
    1474 77972 SENSE 0.101 0.481 0.125 0.606 1.030 0.008
    1495 78019 SENSE 0.030 0.321 0.320 0.481 0.931 0.034
    1429 78128 SENSE 0.341 0.052 0.016 0.764 1.007 0.021
    1424 78131 SENSE 0.042 0.138 0.018 0.829 0.687 0.005
    1499 78161 SENSE 0.156 0.202 0.170 0.418 0.898 0.000
    1522 78191 SENSE 0.177 0.313 0.964 0.512 0.854 0.020
    1061 78321 SENSE 0.196 0.245 −0.007 0.773 1.013 0.048
    1110 78325 SENSE 0.046 0.345 0.123 0.609 0.643 0.007
    1232 78364 SENSE 0.054 0.615 0.837 0.243 0.475 0.038
    1239 78365 SENSE 0.083 0.384 / / 1.153 0.030
    948 78370 SENSE 0.016 0.854 0.310 0.456 0.826 0.036
    1000 78373 SENSE 0.018 0.774 0.595 0.263 1.046 0.009
    1482 78538 SENSE 0.123 0.332 1.152 0.342 0.921 0.024
    1490 78543 SENSE −0.003 0.979 / / 0.934 0.008
    1513 78566 SENSE 0.131 0.429 0.479 0.532 0.820 0.017
    1523 78595 SENSE 0.182 0.295 0.005 0.938 0.766 0.014
    1520 78632 SENSE 0.394 0.058 0.997 0.314 1.143 0.017
    1459 78746 SENSE 0.192 0.256 1.115 0.346 1.025 0.013
    1455 78904 SENSE 0.150 0.222 0.970 0.084 0.946 0.030
    1483 78922 SENSE 0.162 0.307 2.327 0.024 1.156 0.007
    1341 78987 SENSE −0.034 0.626 0.689 0.246 0.828 0.005
    1434 78994 SENSE 0.282 0.000 2.384 0.009 0.940 0.002
  • Transgenic plants comprising recombinant DNA expressing protein as set forth in SEQ ID NO: 823, 825, 873, 886, 912, 916, 919, 928, 937, 942, 972, 986, 995, 1074, 1107, 1134, 1136, 1145, 1157, 1173, 1220, 1228, 1242, 1243, 1285, 1377, 1469, 1486, 1489, 1524, 1538, 1546, 1556, 1568, 1571, 1574, 1592, or 1603 showed enhanced heat stress tolerance by the second criteria as illustrated in Example 1L and 1M.
    • D. Salt Stress Tolerance Screen
  • This example sets forth the high salinity stress screen to identify Arabidopsis plants transformed with the gene of interest that are tolerant to high levels of salt based on their rate of development, root growth and chlorophyll accumulation under high salt conditions.
  • T2 seeds were plated on glufosinate selection plates containing 90 mM NaCl and grown under standard light and temperature conditions. All seedlings used in the experiment were grown at a temperature of 22° C. at day and 20° C. at night, a 16-hour photoperiod, an average light intensity of approximately 120 umol/m2. On day 11, plants were measured for primary root length. After 3 more days of growth (day 14), plants were scored for transgenic status, primary root length, growth stage, visual color, and the seedlings were pooled for fresh weight measurement. A photograph of the whole plate was also taken on day 14.
  • The seedling weight and root length were analyzed as quantitative responses according to example 1M. The final growth stage at day 14 was scored as success if 50% of the plants reached 3 rosette leaves and size of leaves are greater than 1 mm (Boyes, D. C., et al., (2001), The Plant Cell 13, 1499/1510). The growth stage data was analyzed as a qualitative response according to example 1L. A list of recombinant DNA constructs that improve high salinity tolerance in transgenic plants illustrated in Table 6.
  • TABLE 6
    Root length Root length Growth stage Seedling
    PEP at day 11 at day 14 at day 14 weight at day 14
    SEQ Delta Delta Delta Delta
    ID Orientation mean P-value mean P-value mean P-value mean P-value
    932 ANTI- 0.305 0.019 0.360 0.093 0.583 0.428 0.835 0.050
    SENSE
    955 SENSE 0.028 0.336 0.085 0.047 −0.038 0.866 0.060 0.036
    1093 SENSE 0.097 0.010 0.046 0.488 0.605 0.172 0.166 0.016
    1139 SENSE 0.187 0.011 0.092 0.015 −0.038 0.923 −0.002 0.987
    1183 SENSE 0.251 0.118 0.328 0.016 / / 0.404 0.148
    1106 SENSE 0.093 0.383 0.169 0.030 0.370 0.357 0.215 0.053
    896 SENSE 0.349 0.000 0.270 0.069 0.057 0.797 0.421 0.047
    1416 SENSE 0.062 0.516 0.081 0.035 −0.159 0.513 −0.076 0.670
    1591 SENSE 0.034 0.592 0.051 0.003 0.255 0.623 0.194 0.052
    1598 SENSE 0.227 0.004 0.224 0.002 1.203 0.316 0.281 0.258
    1425 SENSE −0.107 0.327 −0.028 0.724 −0.215 0.425 0.384 0.029
    1384 SENSE −0.088 0.195 −0.0557 0.531 −0.009 0.980 0.101 0.025
  • Transgenic plants comprising recombinant DNA expressing protein as set forth in SEQ ID NO: 821, 834, 890, 919, 946, 961, 997, 1013, 1080, 1101, 1147, 1160, 1181, 1197, 1200, 1220, 1237, 1248, 1264, 1300, 1313, 1355, 1393, 1397, 1406, 1467, 1496, 1514, 1530 or 1561 showed enhanced salt stress tolerance by the second criteria as illustrated in Example 1L and 1M.
    • E. Polyethylene Glycol (PEG) Induced Osmotic Stress Tolerance Screen
  • There are numerous factors, which can influence seed germination and subsequent seedling growth, one being the availability of water. Genes, which can directly affect the success rate of germination and early seedling growth, are usable agronomic traits for improving the germination and growth of crop plants under drought stress. In this assay, PEG was used to induce osmotic stress on germinating transgenic lines of Arabidopsis thaliana seeds in order to screen for osmotically resistant seed lines.
  • T2 seeds were plated on BASTA selection plates containing 3% PEG and grown under standard light and temperature conditions. Seeds were plated on each plate containing 3% PEG, ½ X MS salts, 1% phytagel, and 10 μg/ml glufosinate. Plates were placed at 4° C. for 3 days to stratify seeds. On day 11, plants were measured for primary root length. After 3 more days of growth, e.g., at day 14, plants were scored for transgenic status, primary root length, growth stage, visual color, and the seedlings were pooled for fresh weight measurement. A photograph of the whole plate was taken on day14.
  • Seedling weight and root length were analyzed as quantitative responses according to example 1M. The final growth stage at day 14 was scored as success or failure based on whether the plants reached 3 rosette leaves and size of leaves are greater than 1 mm. The growth stage data was analyzed as a qualitative response according to example 1L. A list of recombinant DNA constructs that improve osmotic stress tolerance in transgenic plants illustrated in Table 7.
  • TABLE 7
    Root length Root length Growth stage Seedling
    PEP at day 11 at day 14 at day 14 weight at day 14
    Seq Delta Delta Delta Delta
    ID Orientation mean P-value mean P-value mean P-value mean P-value
    1019 SENSE 0.003 0.883 0.068 0.022 0.113 0.715 −0.139 0.215
    960 SENSE 0.139 0.278 0.065 0.010 2.264 0.322 0.197 0.256
    1241 SENSE 0.061 0.690 0.096 0.044 1.011 0.569 −0.095 0.666
    1119 SENSE 0.002 0.978 −0.107 0.415 2.760 0.156 0.156 0.000
    1391 SENSE 0.602 0.012 0.533 0.044 / / 0.866 0.005
    1322 SENSE 0.062 0.041 0.150 0.020 / / −0.132 0.218
    1238 SENSE 0.099 0.387 0.118 0.004 2.693 0.175 −0.187 0.005
    1556 SENSE 0.153 0.116 0.271 0.081 / / 0.331 0.019
    1153 SENSE 0.063 0.067 0.081 0.134 2.964 0.104 0.280 0.020
    1218 SENSE 0.040 0.067 −0.089 0.170 0.492 0.806 0.198 0.030
    1599 SENSE 0.099 0.168 0.103 0.237 / / 0.292 0.031
    1478 SENSE 0.216 0.115 0.197 0.041 1.353 0.414 0.234 0.388
    1512 SENSE −0.167 0.071 −0.230 0.141 −1.066 0.090 0.085 0.012
    1572 SENSE 0.447 0.005 0.352 0.025 4 / 0.656 0.046
  • Transgenic plants comprising recombinant DNA expressing protein as set forth in SEQ ID NO: 832, 833, 871, 874, 931, 974, 985, 997, 1021, 1024, 1031, 1043, 1053, 1059, 1060, 1091, 1111, 1115, 1118, 1120, 1124, 1127, 1128, 1159, 1172, 1179, 1185, 1197, 1213, 1226, 1230, 1244, 1253, 1265, 1306, 1320, 1327, 1354, 1355, 1357, 1362, 1367, 1381, 1395, 1398, 1399, 1407, 1462, 1494, 1499, 1500, 1523, 1529, 1532, 1544, 1548, 1569, 1572, 1573, 1595, or 1598 showed enhanced PEG osmotic stress tolerance by the second criteria as illustrated in Example 1L and 1M.
    • F. Cold Shock Tolerance Screen
  • This example set forth a screen to identify Arabidopsis plants transformed with the genes of interest that are more tolerant to cold stress subjected during day 8 to day 28 after seed planting. During these crucial early stages, seedling growth and leaf area increase were measured to assess tolerance when Arabidopsis seedlings were exposed to low temperatures. Using this screen, genetic alterations can be found that enable plants to germinate and grow better than wild type plants under sudden exposure to low temperatures.
  • Eleven seedlings from T2 seeds of each transgenic line plus one control line were plated together on a plate containing ½ X Gamborg Salts with 0.8 Phytagel™, 1% Phytagel, and 0.3% Sucrose. Plates were then oriented horizontally and stratified for three days at 4° C. At day three, plates were removed from stratification and exposed to standard conditions (16 hr photoperiod, 22° C. at day and 20° C. at night) until day 8. At day eight, plates were removed from standard conditions and exposed to cold shock conditions (24 hr photoperiod, 8° C. at both day and night) until the final day of the assay, e.g., day 28. Rosette areas were measured at day 8 and day 28, which were analyzed as quantitative responses according to example 1M. A list of recombinant nucleotides that improve cold shock stress tolerance in plants illustrated in Table 8.
  • TABLE 8
    Rosette area Rosette area Rosette area
    PEP at day 8 at day 28 difference
    SEQ Construct Delta Risk score Delta
    ID ID Orientation mean P-value mean P-value mean P-value
    814 72361 SENSE 0.172 0.712 0.657 0.000 0.757 0.001
    816 71626 SENSE 0.634 0.013 0.456 0.032 0.513 0.003
    861 13965 ANTI- 0.414 0.077 0.248 0.117 0.274 0.012
    SENSE
    915 16120 SENSE 0.494 0.247 0.758 0.042 0.722 0.077
    918 72417 SENSE 0.984 0.041 0.125 0.023 0.114 0.051
    923 71706 SENSE 0.010 0.943 0.231 0.064 0.459 0.019
    962 70808 SENSE 0.394 0.285 0.290 0.014 0.362 0.072
    974 72356 SENSE 0.570 0.057 0.823 0.044 0.888 0.096
    1000 78373 SENSE −0.020 0.948 0.846 0.006 0.923 0.005
    1012 73613 SENSE 0.574 0.024 0.579 0.010 0.570 0.012
    1022 70447 SENSE 0.294 0.369 0.195 0.015 0.106 0.089
    1023 71725 SENSE 0.201 0.492 0.199 0.026 0.225 0.055
    1085 71677 SENSE 0.596 0.003 0.741 0.021 0.425 0.226
    1097 72510 SENSE 0.813 0.250 0.891 0.009 1.105 0.015
    1125 73221 SENSE 0.582 0.016 0.412 0.027 0.425 0.117
    1141 72092 SENSE 0.092 0.750 0.568 0.006 0.480 0.027
    1151 74287 SENSE 0.692 0.065 0.795 0.017 0.774 0.015
    1153 77304 SENSE 0.664 0.194 1.164 0.014 1.479 0.014
    1156 74719 SENSE 0.350 0.133 0.393 0.083 0.449 0.013
    1171 73058 SENSE 0.500 0.180 0.322 0.027 0.329 0.049
    1186 73131 SENSE 0.369 0.286 0.725 0.031 0.907 0.052
    1187 73108 SENSE 0.579 0.065 0.725 0.018 0.644 0.025
    1198 10908 ANTI- −0.549 0.086 0.112 0.095 0.136 0.050
    SENSE
    1205 74732 SENSE 0.348 0.082 0.457 0.059 0.513 0.019
    1239 78365 SENSE 0.430 0.141 0.621 0.035 0.600 0.043
    1307 75830 SENSE 0.865 0.113 1.430 0.003 1.558 0.002
    1315 78456 SENSE −0.352 0.118 0.534 0.077 0.650 0.049
    1335 76746 SENSE 0.552 0.112 0.508 0.071 0.734 0.041
    1343 76176 SENSE 0.435 0.095 1.337 0.018 1.472 0.018
    1350 78115 SENSE 0.136 0.464 0.413 0.016 0.421 0.018
    1375 75342 SENSE 1.019 0.029 1.486 0.039 1.752 0.046
    1408 75652 SENSE −0.425 0.454 0.388 0.005 0.415 0.009
    1409 75605 SENSE 0.424 0.100 0.703 0.041 0.808 0.010
    1420 75762 SENSE 1.078 0.039 0.558 0.037 0.480 0.011
    1430 77560 SENSE 0.378 0.128 0.261 0.028 0.288 0.041
    1431 77561 SENSE −0.191 0.296 0.446 0.054 0.511 0.047
    1439 11749 ANTI- −0.458 0.494 0.622 0.028 0.710 0.008
    SENSE
    1458 77940 SENSE 0.498 0.200 0.305 0.167 0.573 0.009
    1461 78126 SENSE −0.708 0.080 0.426 0.046 0.485 0.071
    1500 78162 SENSE 1.502 0.000 1.496 0.025 1.778 0.024
    1502 78622 SENSE 0.550 0.221 0.722 0.018 0.752 0.016
    1517 78571 SENSE 1.529 0.033 1.204 0.001 1.303 0.001
    1519 78573 SENSE 0.292 0.457 0.603 0.007 0.542 0.038
    1543 77840 SENSE −0.182 0.173 0.232 0.030 0.299 0.020
    1565 76939 SENSE 0.598 0.154 0.520 0.037 0.597 0.035
    1566 76987 SENSE 0.953 0.052 0.845 0.010 0.936 0.007
    1577 77145 SENSE 0.408 0.180 0.403 0.041 0.368 0.140
    1593 77462 SENSE 1.157 0.052 1.077 0.012 0.969 0.003
    1601 77419 SENSE 0.156 0.513 0.763 0.010 0.844 0.031
    1605 71237 SENSE 0.836 0.009 0.825 0.005 1.041 0.007
    845 70253 SENSE 0.578 0.007 0.571 0.064 0.459 0.007
    1007 70419 SENSE −0.079 0.646 0.197 0.126 0.266 0.012
    1313 77511 SENSE 0.822 0.011 0.131 0.013 0.063 0.189
    1332 77519 SENSE 0.275 0.286 0.911 0.034 1.020 0.031
    1484 77984 SENSE −0.104 0.724 0.255 0.055 0.274 0.048

    Transgenic plants comprising recombinant DNA expressing protein as set forth in SEQ ID NO: 818, 836, 844, 848, 883, 1029, 1045, 1062, 1082, 1277, 1287, 1294, 1305, 1318, 1366, 1369, 1373, 1387, 1402, 1405, 1410, 1412, 1418, 1427, 1433, 1476, 1481, 1495, 1531, or 1583 showed enhanced cold stress tolerance by the second criterial as illustrated in Example 1L and 1M.
    • G. Cold Germination Tolerance Screen
  • This example sets forth a screen to identify Arabidopsis plants transformed with the genes of interests are resistant to cold stress based on their rate of development, root growth and chlorophyll accumulation under low temperature conditions.
  • T2 seeds were plated and all seedlings used in the experiment were grown at 8° C. Seeds were first surface disinfested using chlorine gas and then seeded on assay plates containing an aqueous solution of ½ X Gamborg's B/5 Basal Salt Mixture (Sigma/Aldrich Corp., St. Louis, Mo., USA G/5788), 1% Phytagel™ (Sigma-Aldrich, P-8169), and 10 ug/ml glufosinate with the final pH adjusted to 5.8 using KOH. Test plates were held vertically for 28 days at a constant temperature of 8° C., a photoperiod of 16 hr, and average light intensity of approximately 100 umol/m2/s. At 28 days post plating, root length was measured, growth stage was observed, the visual color was assessed, and a whole plate photograph was taken.
  • The root length at day 28 was analyzed as a quantitative response according to example 1M. The growth stage at day 7 was analyzed as a qualitative response according to example 1L. A list of recombinant DNA constructs that improve cold stress tolerance in transgenic plants illustrated in Table 9.
  • TABLE 9
    Root
    NUC PEP length at Growth stage
    Seq SEQ day 28 at day 28
    ID ID Construct Nomination Delta Delta
    NO NO ID ID Orientation mean P-value mean P-value
    187 990 18331 CGPG3338 SENSE / / / /
    227 1030 19829 CGPG3981 SENSE −0.021 0.389 0.597 0.031
    231 1034 70365 CGPG4028 SENSE −0.088 0.312 0.725 0.013
    214 1017 70436 CGPG3703 SENSE 0.051 0.747 1.952 0.005
    217 1020 70446 CGPG3730 SENSE −0.064 0.784 1.572 0.009
    159 962 70808 CGPG289 SENSE 0.090 0.637 2.318 0.003
    262 1065 71313 CGPG4401 SENSE 0.160 0.542 1.654 0.001
    272 1075 71339 CGPG4551 SENSE / / / /
    283 1086 71691 CGPG4656 SENSE −0.048 0.305 1.121 0.003
    335 1138 72016 CGPG5246 SENSE 0.385 0.012 1.855 0.161
    337 1140 72044 CGPG5268 SENSE 0.442 0.044 1.908 0.003
    359 1162 72728 CGPG5530 SENSE 0.243 0.300 2.142 0.002
    137 940 72796 CGPG2451 SENSE 0.187 0.063 0.775 0.014
    92 895 72952 CGPG2095 SENSE / / / /
    399 1202 73036 CGPG5796 SENSE 0.246 0.127 2.235 0.001
    64 867 73075 CGPG1797 SENSE 0.046 0.788 1.242 0.007
    377 1180 73117 CGPG5657 SENSE 0.384 0.033 1.764 0.001
    386 1189 73132 CGPG5705 SENSE 0.208 0.283 2.646 0.003
    374 1177 73139 CGPG5641 SENSE 0.040 0.536 1.183 0.002
    473 1276 73539 CGPG6475 SENSE 0.004 0.967 1.052 0.002
    482 1285 74104 CGPG6566 SENSE 0.107 0.490 1.060 0.003
    428 1231 74381 CGPG6111 SENSE 0.060 0.631 0.457 0.049
    632 1435 74508 CGPG8 SENSE 0.323 0.009 1.197 0.387
    433 1236 74635 CGPG6147 SENSE 0.165 0.172 1.596 0.006
    438 1241 74660 CGPG6177 SENSE 0.358 0.007 1.518 0.001
    571 1374 75330 CGPG7508 SENSE 0.019 0.906 0.570 0.026
    589 1392 75446 CGPG7637 SENSE / / / /
    598 1401 75512 CGPG7752 SENSE 0.057 0.576 1.652 0.001
    595 1398 75582 CGPG7742 SENSE 0.213 0.374 1.883 0.003
    506 1309 75836 CGPG6827 SENSE 0.228 0.076 1.314 0.041
    521 1324 75863 CGPG6942 SENSE 0.162 0.132 1.468 0.002
    523 1326 75865 CGPG6949 SENSE 0.046 0.615 1.742 0.006
    660 1463 75901 CGPG8211 SENSE 0.437 0.015 1.733 0.070
    59 862 75912 CGPG1726 SENSE −0.035 0.550 0.265 0.000
    37 840 76050 CGPG1463 SENSE −0.146 0.404 0.213 0.043
    408 1211 76113 CGPG5862 SENSE 0.135 0.014 0.615 0.453
    544 1347 76189 CGPG7253 SENSE 0.015 0.018 0.333 0.645
    722 1525 76325 CGPG8870 SENSE −0.141 0.553 0.557 0.026
    447 1250 76524 CGPG6266 SENSE 0.099 0.300 1.123 0.015
    446 1249 76653 CGPG6254 SENSE 0.507 0.101 3.257 0.004
    628 1431 77561 CGPG7972 SENSE 0.278 0.061 1.265 0.009
    647 1450 77588 CGPG8108 SENSE 0.063 0.677 1.028 0.032
    749 1552 77843 CGPG9017 SENSE 0.382 0.011 1.325 0.006
    701 1504 78043 CGPG8606 SENSE 0.237 0.204 0.859 0.003
    91 894 17227 CGPG2077 SENSE 0.071 0.621 0.820 0.006
    319 1122 73318 CGPG5029 SENSE 0.004 0.989 0.532 0.011
    465 1268 73432 CGPG6421 SENSE −0.038 0.743 0.532 0.011
    568 1371 77808 CGPG7499 SENSE 0.170 0.037 1.138 0.023
    312 1115 72814 CGPG4982 SENSE 0.080 0.592 1.467 0.013
    461 1264 73429 CGPG6397 SENSE 0.320 0.206 1.589 0.017
    682 1485 73938 CGPG85 SENSE 0.029 0.927 1.140 0.005
    680 1483 78922 CGPG8489 SENSE 0.260 0.123 1.326 0.004
  • Transgenic plants comprising recombinant DNA expressing protein as set forth in 826, 863, 864, 941, 985, 1071, 1123, 1170, 1194, 1259, 1312, 1339, 1433, 1465, 1543, 1556 showed enhanced cold stress tolerance by the second criterial as illustrated in Example 1L and 1M.
    • H. Shade Tolerance Screen
  • Plants undergo a characteristic morphological response in shade that includes the elongation of the petiole, a change in the leaf angle, and a reduction in chlorophyll content. While these changes can confer a competitive advantage to individuals, in a monoculture the shade avoidance response is thought to reduce the overall biomass of the population. Thus, genetic alterations that prevent the shade avoidance response can be associated with higher yields. Genes that favor growth under low light conditions can also promote yield, as inadequate light levels frequently limit yield. This protocol describes a screen to look for Arabidopsis plants that show an attenuated shade avoidance response and/or grow better than control plants under low light intensity. Of particular interest, we were looking for plants that didn't extend their petiole length, had an increase in seedling weight relative to the reference and had leaves that were more close to parallel with the plate surface.
  • T2 seeds were plated on glufosinate selection plates with ½ MS medium. Seeds were sown on ½ X MS salts, 1% Phytagel, 10 ug/ml BASTA. Plants were grown on vertical plates at a temperature of 22° C. at day, 20° C. at night and under low light (approximately 30 uE/m2/s, far/red ratio (655/665/725/735)-0.35 using PLAQ lights with GAM color filter #680). Twenty-three days after seedlings were sown, measurements were recorded including seedling status, number of rosette leaves, status of flower bud, petiole leaf angle, petiole length, and pooled fresh weights. A digital image of the whole plate was taken on the measurement day. Seedling weight and petiole length were analyzed as quantitative responses according to example 1M. The number of rosette leaves, flowering bud formation and leaf angel were analyzed as qualitative responses according to example 1L.
  • A list of recombinant DNA constructs that improve shade tolerance in plants illustrated in Table 10.
  • TABLE 10
    Seedling Petiole
    weight length
    NUC PEP at day 23 at day 23
    Seq SEQ Construct Delta P- Delta P-
    ID ID ID Orientation mean value mean value
    52 855 15624 SENSE 0.327 0.041 0.141 0.189
    398 1201 72922 SENSE 0.421 0.049 0.339 0.070
    427 1230 74377 SENSE 0.411 0.039 0.374 0.067
    405 1208 74736 SENSE 0.268 0.024 0.147 0.141
    566 1369 75387 SENSE 0.329 0.008 0.342 0.010
    59 862 75912 SENSE 0.470 0.035 0.572 0.058
    664 1467 75919 SENSE 0.453 0.007 0.114 0.063
    736 1539 76335 SENSE −1.012 0.081 −0.594 0.007
    783 1586 77172 SENSE 0.426 0.044 0.218 0.164
    698 1501 78033 SENSE 0.060 0.033 −0.129 0.612
  • For “seeding weight”, if p<0.05 and delta or risk score mean >0, the transgenic plants showed statistically significant trait enhancement as compared to the reference. If p<0.2 and delta or risk score mean >0, the transgenic plants showed a trend of trait enhancement as compared to the reference with p<0.2.
  • For “petiole length”, if p<0.05 and delta <0, the transgenic plants showed statistically significant trait enhancement as compared to the reference. If p<0.2 and delta <0, the transgenic plants showed a trend of trait enhancement as compared to the reference.
  • Transgenic plants comprising recombinant DNA expressing protein as set forth in SEQ ID NO: 805, 828, 833, 870, 936, 937, 939, 965, 988, 1007, 1010, 1016, 1038, 1050, 1060, 1070, 1079, 1089, 1095, 1100, 1117, 1125, 1129, 1134, 1135, 1145, 1150, 1154, 1155, 1158, 1184, 1204, 1210, 1214, 1216, 1217, 1225, 1226, 1235, 1248, 1252, 1255, 1260, 1271, 1278, 1282, 1283, 1289, 1292, 1297, 1304, 1311, 1312, 1317, 1328, 1336, 1338, 1348, 1363, 1366, 1383, 1386, 1400, 1428, 1448, 1451, 1453, 1462, 1491, 1493, 1505, 1516, 1520, 1528, 1533, 1545, 1579, or 1588 showed enhanced tolerance to shade or low light condition by the second criteria as illustrated in Example 1L and 1M.
    • I. Early Plant Growth and Development Screen
  • This example sets forth a plate based phenotypic analysis platform for the rapid detection of phenotypes that are evident during the first two weeks of growth. In this screen, we were looking for genes that confer advantages in the processes of germination, seedling vigor, root growth and root morphology under non-stressed growth conditions to plants. The transgenic plants with advantages in seedling growth and development were determined by the seedling weight and root length at day14 after seed planting.
  • T2 seeds were plated on glufosinate selection plates and grown under standard conditions (˜100 uE/m2/s, 16 h photoperiod, 22° C. at day, 20° C. at night). Seeds were stratified for 3 days at 4° C. Seedlings were grown vertically (at a temperature of 22° C. at day 20° C. at night). Observations were taken on day 10 and day 14. Both seedling weight and root length at day 14 were analyzed as quantitative responses according to example 1M.
  • A list recombinant DNA constructs that improve early plant growth and development illustrated in Table 11.
  • TABLE 11
    Root length Root length Seedling weight
    PEP at day 10 at day 14 at day 14
    NUC SEQ Delta Delta Delta
    SEQ ID ID Orientation mean P-value mean P-value mean P-value
    52 855 SENSE 0.091 0.027 0.071 0.018 0.037 0.744
    102 905 SENSE 0.188 0.210 0.104 0.247 0.308 0.021
    121 924 SENSE 0.242 0.015 0.128 0.063 0.203 0.078
    153 956 SENSE 0.153 0.027 0.122 0.197 0.256 0.010
    134 937 SENSE 0.329 0.048 0.250 0.085 0.712 0.020
    144 947 SENSE 0.127 0.146 0.045 0.566 0.371 0.023
    101 904 SENSE 0.537 0.026 0.356 0.004 0.634 0.021
    178 981 SENSE 0.372 0.136 0.273 0.033 0.346 0.082
    179 982 SENSE 0.404 0.001 0.222 0.051 0.288 0.111
    191 994 SENSE 0.282 0.008 0.285 0.009 0.445 0.012
    163 966 SENSE 0.132 0.219 0.121 0.035 0.135 0.439
    74 877 SENSE 0.282 0.033 0.166 0.015 0.143 0.363
    162 965 SENSE 0.320 0.119 0.253 0.035 0.458 0.109
    296 1099 SENSE 0.047 0.653 0.057 0.369 0.141 0.013
    313 1116 SENSE 0.222 0.124 0.166 0.039 0.187 0.202
    400 1203 SENSE 0.103 0.336 0.171 0.067 0.263 0.049
    459 1262 SENSE 0.278 0.081 0.273 0.027 0.308 0.121
    215 1018 SENSE 0.138 0.023 0.088 0.068 0.167 0.092
    498 1301 SENSE 0.248 0.245 0.203 0.100 0.435 0.002
    492 1295 SENSE 0.066 0.018 −0.052 0.334 0.215 0.171
    567 1370 SENSE −0.134 0.218 0.030 0.770 −0.132 0.305
    611 1414 SENSE 0.232 0.220 0.168 0.035 0.165 0.319
    614 1417 SENSE 0.142 0.277 0.147 0.174 0.167 0.562
    616 1419 SENSE 0.038 0.549 0.046 0.130 −0.028 0.873
    526 1329 SENSE −0.044 0.135 0.070 0.044 −0.026 0.085
    663 1466 SENSE 0.075 0.043 −0.065 0.418 0.047 0.639
    79 882 SENSE 0.127 0.094 0.117 0.041 0.111 0.266
    724 1527 SENSE 0.512 0.024 0.437 0.010 0.634 0.001
    737 1540 SENSE −0.011 0.931 0.120 0.151 −0.090 0.487
    248 1051 SENSE 0.197 0.003 0.145 0.007 0.020 0.783
    444 1247 SENSE 0.369 0.009 0.279 0.012 0.255 0.004
    741 1544 SENSE 0.205 0.011 0.129 0.350 0.168 0.158
    522 1325 SENSE 0.134 0.354 0.160 0.069 0.085 0.653
    777 1580 SENSE 0.218 0.022 0.064 0.601 0.067 0.770
    775 1578 SENSE −0.192 0.322 0.019 0.780 −0.333 0.091
    629 1432 SENSE −0.042 0.151 0.075 0.016 −0.184 0.176
    704 1507 SENSE −0.074 0.546 0.123 0.058 0.113 0.433
    697 1500 SENSE 0.173 0.049 0.078 0.546 0.109 0.054
    706 1509 SENSE 0.074 0.018 0.076 0.301 0.059 0.664
    331 1134 SENSE 0.107 0.013 0.050 0.569 0.202 0.178
    546 1349 SENSE −0.182 0.037 −0.050 0.104 −0.150 0.613
    717 1520 SENSE 0.297 0.085 0.223 0.029 0.292 0.213
    22 825 SENSE / / / / 0.444 0.025
    581 1384 SENSE 0.116 0.126 0.193 0.013 0.181 0.175
    726 1529 SENSE 0.375 0.012 0.088 0.188 0.353 0.015
    755 1558 SENSE 0.409 0.031 0.203 0.091 0.346 0.198
  • Transgenic plants comprising recombinant DNA expressing a protein as set forth in 810, 831, 844, 857, 865, 884, 892, 917, 950, 954, 970, 983, 992, 998, 1004, 1005, 1029, 1033, 1043, 1072, 1101, 1109, 1115, 1133, 1181, 1200, 1284, 1310, 1340, 1384, 1391, 1443, 1449, 1471, 1480, 1483, 1498, 1506, 1508, 1510, 1529, 1548, 1553, 1555, 1556, 1558, 1559, 1564, 1576, or 1577 showed enhanced tolerance to shade or low light condition by the second criterial as illustrated in Example 1L and 1M.
    • J. Late Plant Growth and Development Screen
  • This example sets forth a soil based phenotypic platform to identify genes that confer advantages in the processes of leaf development, flowering production and seed maturity to plants.
  • Arabidopsis plants were grown on a commercial potting mixture (Metro Mix 360, Scotts Co., Marysville, Ohio) consisting of 30-40% medium grade horticultural vermiculite, 35-55% sphagnum peat moss, 10-20% processed bark ash, 1-15% pine bark and a starter nutrient charge. Soil was supplemented with Osmocote time-release fertilizer at a rate of 30 mg/ft3. T2 seeds were imbibed in 1% agarose solution for 3 days at 4° C. and then sown at a density of −5 per 2½″ pot. Thirty-two pots were ordered in a 4 by 8 grid in standard greenhouse flat. Plants were grown in environmentally controlled rooms under a 16 h day length with an average light intensity of ˜200 μmoles/m2/s. Day and night temperature set points were 22° C. and 20° C., respectively. Humidity was maintained at 65%. Plants were watered by sub-irrigation every two days on average until mid-flowering, at which point the plants were watered daily until flowering was complete.
  • Application of the herbicide glufosinate was performed to select T2 individuals containing the target transgene. A single application of glufosinate was applied when the first true leaves were visible. Each pot was thinned to leave a single glufosinate-resistant seedling ˜3 days after the selection was applied.
  • The rosette radius was measured at day 25. The silique length was measured at day 40. The plant parts were harvested at day 49 for dry weight measurements if flowering production was stopped. Otherwise, the dry weights of rosette and silique were carried out at day 53. The seeds were harvested at day 58. All measurements were analyzed as quantitative responses according to example 1M. A list of recombinant DNA constructs that improve late plant growth and development illustrated in Table 12.
  • TABLE 12
    Rosette dry Rosette Seed net Silique dry Silique
    weight at radius at dry weight weight length at
    PEP day 53 day 25 at day 62 at day 53 day 40
    SEQ Construct Delta P- Delta P- Delta P- Delta Delta P-
    ID ID mean value mean value mean value mean P-value mean value
    835 14405 0.110 0.430 / / 0.557 0.001 0.200 0.214 0.043 0.252
    869 14833 0.247 0.382 / / 1.126 0.021 0.587 0.044 0.075 0.340
    887 15207 0.238 0.023 −0.407 0.087 0.047 0.785 0.343 0.046 −0.015 0.540
    949 70411 0.181 0.008 / / −0.268 0.192 0.061 0.025 −0.039 0.240
    1057 71564 0.397 0.049 0.190 0.205 0.440 0.005 0.342 0.035 0.070 0.043
    1066 72349 0.174 0.011 / / −0.526 0.049 −0.292 0.131 0.041 0.265
    1102 72630 0.200 0.022 / / 0.537 0.030 −0.257 0.034 −0.297 0.015
    1108 73347 0.063 0.559 −0.046 0.475 0.848 0.035 0.243 0.188 −0.005 0.706
    944 16612 −0.438 0.116 −0.280 0.026 0.493 0.023 −0.746 0.034 −0.023 0.289
    929 70118 −0.186 0.237 −0.004 0.944 1.043 0.042 / / 0.040 0.279
    1025 70545 0.057 0.434 0.111 0.355 1.228 0.021 / / −0.060 0.418
    1079 70686 −0.071 0.644 0.136 0.109 0.700 0.004 / / 0.014 0.571
    1088 70803 0.173 0.197 −0.207 0.053 0.691 0.008 / / 0.067 0.094
    1261 73438 0.397 0.057 −0.251 0.005 0.733 0.014 −0.056 0.542 −0.012 0.809
    1077 73696 −0.384 0.425 −0.284 0.129 0.666 0.020 / / −0.097 0.154
    1394 75705 0.570 0.049 0.019 0.797 0.477 0.165 0.213 0.337 −0.164 0.018
    1210 76657 0.091 0.481 −0.370 0.031 0.744 0.019 −0.016 0.927 −0.038 0.395
    1488 78386 0.092 0.010 −0.118 0.227 −0.578 0.034 / / 0.017 0.502
    1475 78522 0.386 0.003 0.728 0.001 1.532 0.007 / / 0.170 0.038
  • If p<0.05 and delta or risk score mean >0, the transgenic plants showed statistically significant trait enhancement as compared to the reference. If p<0.2 and delta or risk score mean >0, the transgenic plants showed a trend of trait enhancement as compared to the reference.
    • K. Limited Nitrogen Tolerance Screen
  • Under low nitrogen conditions, Arabidopsis seedlings become chlorotic and have less biomass. This example sets forth the limited nitrogen tolerance screen to identify Arabidopsis plants transformed with the gene of interest that are altered in their ability to accumulate biomass and/or retain chlorophyll under low nitrogen condition.
  • T2 seeds were plated on glufosinate selection plates containing 0.5×N-Free Hoagland's T 0.1 mM NH4NO3 T 0.1% sucrose T 1% phytagel media and grown under standard light and temperature conditions. At 12 days of growth, plants were scored for seedling status (e.g., viable or non-viable) and root length. After 21 days of growth, plants were scored for BASTA resistance, visual color, seedling weight, number of green leaves, number of rosette leaves, root length and formation of flowering buds. A photograph of each plant was also taken at this time point.
  • The seedling weight and root length were analyzed as quantitative responses according to example 1M. The number green leaves, the number of rosette leaves and the flowerbud formation were analyzed as qualitative responses according to example 1L. The leaf color raw data were collected on each plant as the percentages of five color elements (Green, DarkGreen, LightGreen, RedPurple, YellowChlorotic) using a computer imaging system. A statistical logistic regression model was developed to predict an overall value based on five colors for each plant.
  • A list of recombinant DNA constructs that improve low nitrogen availability tolerance in plants illustrated in Table 13.
  • TABLE 13
    Leaf color Rosette weight
    at day 21 at day 21
    NUC PEP Construct Risk score Delta
    SEQ ID SEQ ID ID Orientation mean P-value mean P-value
    188 991 10473 SENSE 4.078 0.017 −0.181 0.023
    373 1176 11141 SENSE 4.800 0.027 −0.059 0.513
    395 1198 11147 SENSE 3.499 0.012 −0.157 0.323
    10 813 11860 ANTI-SENSE −3.108 0.157 0.345 0.017
    781 1584 11933 ANTI-SENSE 0.412 0.024 0.004 0.902
    661 1464 12123 ANTI-SENSE 4.867 0.025 0.036 0.750
    8 811 12147 ANTI-SENSE 2.164 0.134 0.074 0.007
    6 809 12217 SENSE 3.494 0.047 0.086 0.245
    12 815 12230 SENSE 1.878 0.077 0.111 0.015
    799 1602 12444 SENSE 0.144 0.926 0.014 0.010
    21 824 12749 ANTI-SENSE 0.315 0.022 0.109 0.325
    3 806 12816 SENSE −0.989 0.012 0.098 0.002
    38 841 13038 ANTI-SENSE 2.207 0.450 0.074 0.040
    39 842 13040 ANTI-SENSE 3.223 0.039 0.137 0.241
    608 1411 13302 ANTI-SENSE 2.956 0.013 0.040 0.100
    35 838 13828 ANTI-SENSE 3.733 0.002 −0.043 0.188
    46 849 14340 ANTI-SENSE 3.417 0.023 −0.113 0.049
    32 835 14405 SENSE 2.350 0.158 0.097 0.031
    43 846 14415 SENSE 3.195 0.006 −0.131 0.066
    85 888 14915 ANTI-SENSE 3.923 0.005 −0.081 0.079
    78 881 15129 SENSE 3.751 0.002 0.096 0.164
    104 907 15507 ANTI-SENSE 8.130 0.013 −0.086 0.312
    106 909 15959 ANTI-SENSE 5.694 0.032 −0.165 0.121
    98 901 16204 SENSE 7.476 0.013 −0.012 0.416
    95 898 16309 SENSE 0.678 0.046 0.072 0.436
    65 868 16323 SENSE 2.085 0.019 −0.008 0.779
    16 819 17806 ANTI-SENSE 3.639 0.036 −0.087 0.208
    184 987 18319 SENSE 1.043 0.023 −0.100 0.061
    147 950 19154 SENSE −1.213 0.201 0.146 0.033
    175 978 19240 SENSE 0.175 0.828 0.098 0.002
    289 1092 71622 SENSE 0.222 0.357 0.082 0.003
    287 1090 71637 SENSE 0.074 0.772 0.061 0.001
    261 1064 71810 SENSE 2.561 0.010 −0.038 0.111
    416 1219 74350 SENSE 8.315 0.006 0.020 0.504
    500 1303 74573 SENSE 4.232 0.015 0.093 0.207
    555 1358 74836 SENSE 1.278 0.002 −0.133 0.018
    561 1364 74918 SENSE 5.122 0.022 0.414 0.346
    27 830 75958 SENSE 1.827 0.046 −0.078 0.101
    731 1534 76321 SENSE 5.099 0.004 −0.120 0.313
    754 1557 76821 SENSE 4.293 0.011 −0.157 0.044
    757 1560 76894 SENSE 3.806 0.048 0.123 0.102
    513 1316 77041 SENSE 1.772 0.042 −0.186 0.098
    786 1589 77250 SENSE 7.658 0.015 0.035 0.664
    620 1423 77541 SENSE 1.896 0.045 −0.189 0.081
    746 1549 77842 SENSE 4.863 0.048 −0.184 0.037
    670 1473 77966 SENSE 1.716 0.120 0.218 0.022
    719 1522 78191 SENSE 2.686 0.037 0.121 0.113
    695 1498 78548 SENSE 1.766 0.191 0.116 0.027
    226 1029 19775 SENSE 0.037 0.858 0.240 0.042
    34 837 70721 ANTI-SENSE 1.858 0.012 0.052 0.047
    280 1083 71696 SENSE −0.133 0.002 0.085 0.049
  • For rosette weight, if p<0.05 and delta or risk score mean >0, the transgenic plants showed statistically significant trait enhancement as compared to the reference. If p<0.2 and delta or risk score mean >0, the transgenic plants showed a trend of trait enhancement as compared to the reference with p<0.2. For root length, if p<0.05, the transgenic plants showed statistically significant trait enhancement as compared to the reference. If p<0.2, the transgenic plants showed a trend of trait enhancement as compared to the reference.
  • Transgenic plants comprising recombinant DNA expressing a protein as set forth in 807, 808, 817, 820, 829, 839, 847, 848, 850, 854, 858, 859, 866, 872, 875, 878, 889, 902, 908, 911, 922, 938, 944, 953, 963, 974, 980, 993, 1001, 1009, 1035, 1042, 1048, 1049, 1054, 1058, 1068, 1076, 1088, 1094, 1096, 1098, 1103, 1104, 1107, 1112, 1113, 1114, 1121, 1152, 1166, 1175, 1192, 1204, 1207, 1215, 1218, 1240, 1246, 1251, 1256, 1266, 1269, 1281, 1283, 1290, 1296, 1298, 1344, 1345, 1356, 1389, 1396, 1400, 1404, 1409, 1425, 1428, 1438, 1441, 1442, 1454, 1477, 1479, 1484, 1492, 1500, 1511, 1515, 1518, 1521, 1537, 1563, 1567, 1571, 1579, or 1603 showed enhanced tolerance to shade or low light condition by the second criterial as illustrated in Example 1L and 1M.
    • L. Statistic Analysis for Qualitative Responses
  • A list of responses that were analyzed as qualitative responses illustrated in Table 14.
  • TABLE 14
    response Screen categories (success vs. failure)
    Wilting response Risk Soil drought tolerance screen non-wilted vs. wilted
    Score
    growth stage at day 14 heat stress tolerance screen 50% of plants reach stage1.03 vs.
    not
    growth stage at day 14 salt stress tolerance screen 50% of plants reach stage1.03 vs.
    not
    growth stage at day 14 PEG induced osmotic stress 50% of plants reach stage1.03 vs.
    tolerance screen not
    growth stage at day 7 cold germination tolerance screen 50% of plants reach stage 0.5 vs.
    not
    number of rosette Shade tolerance screen 5 leaves appeared vs. not
    leaves at day 23
    Flower bud formation at Shade tolerance screen flower buds appear vs. not
    day 23
    leaf angle at day 23 Shade tolerance screen >60 degree vs. <60 degree
    number of green leaves limited nitrogen tolerance screen 6 or 7 leaves appeared vs. not
    at day 21
    number of rosette limited nitrogen tolerance screen 6 or 7 leaves appeared vs. not
    leaves at day 21
    Flower bud formation at limited nitrogen tolerance screen flower buds appear vs. not
    day 21
  • Plants were grouped into transgenic and reference groups and were scored as success or failure according to Table 14. First, the risk (R) was calculated, which is the proportion of plants that were scored as of failure plants within the group. Then the relative risk (RR) was calculated as the ratio of R (transgenic) to R (reference). Risk score (RS) was calculated as — log2 RR. Two criteria were used to determine a transgenic with enhanced trait(s). Transgenic plants comprising recombinant DNA disclosed herein showed trait enhancement according to either or both of the two criteria.
  • For the first criteria, the risk scores from multiple events of the transgene of interest were evaluated for statistical significance by t-test using SAS statistical software (SAS 9, SAS/STAT User's Guide, SAS Institute Inc, Cary, N.C., USA). RS with a value greater than 0 indicates that the transgenic plants perform better than the reference. RS with a value less than 0 indicates that the transgenic plants perform worse than the reference. The RS with a value equal to 0 indicates that the performance of the transgenic plants and the reference don't show any difference. If p<0.05 and risk score mean >0, the transgenic plants showed statistically significant trait enhacement as compared to the reference. If p<0.2 and risk score mean >0, the transgenic plants showed a trend of trait enhancement as compared to the reference.
  • For the second criteria, the RS from each event was evaluated for statistical significance by t-test using SAS statistical software (SAS 9, SAS/STAT User's Guide, SAS Institute Inc, Cary, N.C., USA). The RS with a value greater than 0 indicates that the transgenic plants from this event\perform better than the reference. The RS with a value less than 0 indicates that the transgenic plants from this event perform worse than the reference. The RS with a value equal to 0 indicates that the performance of the transgenic plants from this event and the reference don't show any difference. If p<0.05 and risk score mean >0, the transgenic plants from this event showed statistically significant trait enhancement as compared to the reference. If p<0.2 and risk score mean >0, the transgenic plants showed a trend of trait enhancement as compared to the reference. If two or more events of the transgene of interest showed improvement in the same response, the transgene was deemed to show trait enhancement.
    • M. Statistic Analysis for Quantitative Responses
  • A list of responses that were analyzed as quantitative responses illustrated in Table 15.
  • TABLE 15
    response screen
    seed yield Soil drought stress tolerance screen
    seedling weight at day 14 heat stress tolerance screen
    root length at day 14 heat stress tolerance screen
    seedling weight at day 14 salt stress tolerance screen
    root length at day 14 salt stress tolerance screen
    root length at day 11 salt stress tolerance screen
    seedling weight at day 14 PEG induced osmotic stress tolerance
    screen
    root length at day 11 PEG induced osmotic stress tolerance
    screen
    root length at day 14 PEG induced osmotic stress tolerance
    screen
    rosette area at day 8 cold shock tolerance screen
    rosette area at day 28 cold shock tolerance screen
    difference in rosette area cold shock tolerance screen
    from day 8 to day 28
    root length at day 28 cold germination tolerance screen
    seedling weight at day 23 Shade tolerance screen
    petiole length at day 23 Shade tolerance screen
    root length at day 14 Early plant growth and development screen
    Seedling weight at day14 Early plant growth and development screen
    Rosette dry weight at Late plant growth and development screen
    day 53
    rosette radius at day 25 Late plant growth and development screen
    seed dry weight at day 58 Late plant growth and development screen
    silique dry weight at day 53 Late plant growth and development screen
    silique length at day 40 Late plant growth and development screen
    Seedling weight at day 21 Limited nitrogen tolerance screen
    Root length at day 21 Limited nitrogen tolerance screen
  • The measurements (M) of each plant were transformed by log2 calculation. The Delta was calculated as log2M(transgenic)−log2M(reference). Two criteria were used to determine trait enhancement. A transgene of interest could show trait enhancement according to either or both of the two criteria. The measurements (M) of each plant were transformed by log2 calculation. The Delta was calculated as log2M(transgenic)−log2M(reference). If the measured response was Petiole Length for the Low Light assay, Delta was subsequently multiplied by −1, to account for the fact that a shorter petiole length is considered an indication of trait enhancement.
  • For the first criteria, the Deltas from multiple events of the transgene of interest were evaluated for statistical significance by t-test using SAS statistical software (SAS 9, SAS/STAT User's Guide, SAS Institute Inc, Cary, N.C., USA). Delta with a value greater than 0 indicates that the transgenic plants perform better than the reference. Delta with a value less than 0 indicates that the transgenic plants perform worse than the reference. The Delta with a value equal to 0 indicates that the performance of the transgenic plants and the reference don't show any difference. If p<0.05 and risk score mean >0, the transgenic plants showed statistically significant trait enhancement as compared to the reference. If p<0.2 and risk score mean >0, the transgenic plants showed a trend of trait enhancement as compared to the reference.
  • For the second criteria, the delta from each event was evaluated for statistical significance by t-test using SAS statistical software (SAS 9, SAS/STAT User's Guide, SAS Institute Inc, Cary, N.C., USA). The Delta with a value greater than 0 indicates that the transgenic plants from this event perform better than the reference. The Delta with a value less than 0 indicates that the transgenic plants from this event perform worse than the reference. The Delta with a value equal to 0 indicates that the performance of the transgenic plants from this event and the reference don't show any difference. If p<0.05 and delta mean >0, the transgenic plants from this event showed statistically significant trait improvement as compared to the reference. If p<0.2 and delta mean >0, the transgenic plants showed a trend of trait enhancement as compared to the reference. If two or more events of the transgene of interest showed enhancement in the same response, the transgene was deemed to show trait improvement.
    • Example 2 Plant Expression Constructs
  • This example illustrates the construction of plasmids for transferring recombinant DNA into a plant cell nucleus that can be regenerated into transgenic plants.
    • Plant Expression Constructs for Corn Transformation
  • A base corn transformation vector pMON93039, as set forth in SEQ ID NO: 94614, illustrated in Table 16 and FIG. 1, is made for use in preparing recombinant DNA for Agrobacterium-mediated transformation into corn tissue.
  • TABLE 16
    Coordinates of
    SEQ ID NO:
    Function Name Annotation 94614
    Agrobacterium B-AGRtu.right Agro right border sequence, 11364-11720
    T-DNA border essential for transfer of T-DNA.
    transfer
    Gene of E-Os.Act1 Upstream promoter region  19-775
    interest of the rice actin 1 gene
    expression E- Duplicated35S A1-B3  788-1120
    cassette CaMV.35S.2xA1- domain without TATA box
    B3
    P-Os.Act1 Promoter region of the rice 1125-1204
    actin 1 gene
    L-Ta.Lhcb1 5′ untranslated leader of 1210-1270
    wheat major chlorophyll a/b
    binding protein
    I-Os.Act1 First intron and flanking 1287-1766
    UTR exon sequences from
    the rice actin 1 gene
    T-St.Pis4 3′ non-translated region of 1838-2780
    the potato proteinase
    inhibitor II gene which
    functions to direct
    polyadenylation of the
    mRNA
    Plant P-Os.Act1 Promoter from the rice actin 2830-3670
    selectable 1 gene
    marker L-Os.Act1 First exon of the rice actin 1 3671-3750
    expression gene
    cassette I-Os.Act1 First intron and flanking 3751-4228
    UTR exon sequences from
    the rice actin 1 gene
    TS-At.ShkG-CTP2 Transit peptide region of 4238-4465
    Arabidopsis EPSPS
    CR-AGRtu.aroA- Coding region for bacterial 4466-5833
    CP4.nat strain CP4 native aroA gene.
    T-AGRtu.nos A 3′ non-translated region of 5849-6101
    the nopaline synthase gene
    of Agrobacterium
    tumefaciens Ti plasmid
    which functions to direct
    polyadenylation of the
    mRNA.
    Agrobacterium B-AGRtu.left Agro left border sequence, 6168-6609
    T-DNA border essential for transfer of T-
    transfer DNA.
    Maintenance OR-Ec.oriV-RK2 The vegetative origin of 6696-7092
    in E. coli replication from plasmid
    RK2.
    CR-Ec.rop Coding region for repressor 8601-8792
    of primer from the ColE1
    plasmid. Expression of this
    gene product interferes with
    primer binding at the origin
    of replication, keeping
    plasmid copy number low.
    OR-Ec.ori-ColE1 The minimal origin of 9220-9808
    replication from the E. coli
    plasmid ColE1.
    P-Ec.aadA- Promoter for Tn7 10339-10380
    SPC/STR adenylyltransferase
    (AAD(3″))
    CR-Ec.aadA- Coding region for Tn7 10381-11169
    SPC/STR adenylyltransferase
    (AAD(3″)) conferring
    spectinomycin and
    streptomycin resistance.
    T-Ec.aadA- 3′ UTR from the Tn7 11170-11227
    SPC/STR adenylyltransferase
    (AAD(3″)) gene of E. coli.
  • Primers for PCR amplification of protein coding nucleotides of recombinant DNA are designed at or near the start and stop codons of the coding sequence in order to eliminate most of the 5′ and 3′ untranslated regions. Each recombinant DNA coding for or suppressing a protein identified in Table 2 is amplified by PCR prior to insertion into the insertion site within the gene of interest expression cassette of the base vector.
    • B. Plant Expression Constructs for Soy and Canola Transformation
  • Vectors for use in transformation of soybean and canola can also be prepared. Elements of an exemplary common expression vector pMON82053 (SEQ ID NO: 94615) are shown in Table 17 below and FIG. 2.
  • TABLE 17
    Coordinates of
    SEQ ID NO:
    Function Name Annotation 94615
    Agrobacterium B-AGRtu.left Agro left border sequence, essential 6144-6585
    T-DNA transfer border for transfer of T-DNA.
    Plant selectable P-At.Act7 Promoter from the Arabidopsis actin 6624-7861
    marker 7 gene
    expression L-At.Act7 5′UTR of Arabidopsis Act7 gene
    cassette I-At.Act7 Intron from the Arabidopsis actin7
    gene
    TS-At.ShkG- Transit peptide region of 7864-8091
    CTP2 Arabidopsis EPSPS
    CR-AGRtu.aroA- Synthetic CP4 coding region with 8092-9459
    CP4.nno_At dicot preferred codon usage.
    T-AGRtu.nos A 3′ non-translated region of the 9466-9718
    nopaline synthase gene of
    Agrobacterium tumefaciens Ti
    plasmid which functions to direct
    polyadenylation of the mRNA.
    Gene of interest P-CaMV.35S-enh Promoter for 35S RNA from CaMV  1-613
    expression containing a duplication of the −90 to
    cassette −350 region.
    T-Gb.E6-3b 3′ untranslated region from the fiber  688-1002
    protein E6 gene of sea-island cotton.
    Agrobacterium B-AGRtu.right Agro right border sequence, 1033-1389
    T-DNA transfer border essential for transfer of T-DNA.
    Maintenance in OR-Ec.oriV-RK2 The vegetative origin of replication 5661-6057
    E. coli from plasmid RK2.
    CR-Ec.rop Coding region for repressor of 3961-4152
    primer from the ColE1 plasmid.
    Expression of this gene product
    interferes with primer binding at the
    origin of replication, keeping
    plasmid copy number low.
    OR-Ec.ori-ColE1 The minimal origin of replication 2945-3533
    from the E. coli plasmid ColE1.
    P-Ec.aadA- Promoter for Tn7 2373-2414
    SPC/STR adenylyltransferase (AAD(3″))
    CR-Ec.aadA- Coding region for Tn7 1584-2372
    SPC/STR adenylyltransferase (AAD(3″))
    conferring spectinomycin and
    streptomycin resistance.
    T-Ec.aadA- 3′ UTR from the Tn7 1526-1583
    SPC/STR adenylyltransferase (AAD(3″)) gene
    of E. coli.

    Primers for PCR amplification of protein coding nucleotides of recombinant DNA are designed at or near the start and stop codons of the coding sequence in order to eliminate most of the 5′ and 3′ untranslated regions. Each recombinant DNA coding for or suppressing a protein identified in Table 2 is amplified by PCR prior to insertion into the insertion site within the gene of interest expression cassette of the base vector.
    • C. Cotton Transformation Vector
  • Plasmids for use in transformation of cotton tissue are prepared with elements of expression vector pMON99053 (SEQ ID NO: 94616) are shown in Table 18 below and FIG. 3. Primers for PCR amplification of protein coding nucleotides of recombinant DNA are designed at or near the start and stop codons of the coding sequence in order to eliminate most of the 5′ and 3′ untranslated regions. Each recombinant DNA coding for or suppressing a protein identified in Table 2 is amplified by PCR prior to insertion into the insertion site within the gene of interest expression cassette of the base vector.
  • TABLE 18
    Coordinates
    of SEQ ID
    Function Name Annotation NO: 94616
    Agrobacterium B-AGRtu.right border Agro right border sequence,  1-357
    T-DNA transfer essential for transfer of T-
    DNA.
    Gene of interest Exp-CaMV.35S- Enhanced version of the 35S  388-1091
    expression enh + Ph. DnaK RNA promoter from CaMV
    cassette plus the petunia hsp70 5′
    untranslated region
    T-Ps.RbcS2-E9 The 3′ non-translated region of 1165-1797
    the pea RbcS2 gene which
    functions to direct
    polyadenylation of the mRNA.
    Plant selectable Exp-CaMV.35S Promoter and 5′ untranslated 1828-2151
    marker region from the 35S RNA of
    expression CaMV
    cassette CR-Ec.nptII-Tn5 Coding region for neomycin 2185-2979
    phosphotransferase gene from
    transposon Tn5 which confers
    resistance to neomycin and
    kanamycin.
    T-AGRtu.nos A 3′ non-translated region of 3011-3263
    the nopaline synthase gene of
    Agrobacterium tumefaciens Ti
    plasmid which functions to
    direct polyadenylation of the
    mRNA.
    Agrobacterium B-AGRtu.left border Agro left border sequence, 3309-3750
    T-DNA transfer essential for transfer of T-
    DNA.
    Maintenance in OR-Ec.oriV-RK2 The vegetative origin of 3837-4233
    E. coli replication from plasmid RK2.
    CR-Ec.rop Coding region for repressor of 5742-5933
    primer from the ColE1
    plasmid. Expression of this
    gene product interferes with
    primer binding at the origin of
    replication, keeping plasmid
    copy number low.
    OR-Ec.ori-ColE1 The minimal origin of 6363-6949
    replication from the E. coli
    plasmid ColE1.
    P-Ec.aadA-SPC/STR Promoter for Tn7 7480-7521
    adenylyltransferase (AAD(3″))
    CR-Ec.aadA-SPC/STR Coding region for Tn7 7522-8310
    adenylyltransferase (AAD(3″))
    conferring spectinomycin and
    streptomycin resistance.
    T-Ec.aadA-SPC/STR 3′ UTR from the Tn7 8311-8368
    adenylyltransferase (AAD(3″))
    gene of E. coli.
    • Example 3 Corn Transformation
  • This example illustrates transformation methods in producing a transgenic nucleus in a corn plant cell and the plants, seeds and pollen produced from a transgenic cell with such a nucleus having an enhanced trait, e.g. enhanced water use efficiency, enhanced cold tolerance, increased yield, enhanced nitrogen use efficiency, enhanced seed protein and enhanced seed oil. Plasmid vectors are prepared by cloning DNA identified in Table 2 in the base vector for use in corn transformation of corn tissue.
  • For Agrobacterium-mediated transformation of corn embryo cells corn plants of a readily transformable line are grown in the greenhouse and ears are harvested when the embryos are 1.5 to 2.0 mm in length. Ears are surface sterilized by spraying or soaking the ears in 80% ethanol, followed by air drying. Immature embryos are isolated from individual kernels on surface sterilized ears. Prior to inoculation of maize cells, Agrobacterium cells are grown overnight at room temperature. Immature maize embryo cells are inoculated with Agrobacterium shortly after excision, and incubated at room temperature with Agrobacterium for 5-20 minutes. Immature embryo plant cells are then co-cultured with Agrobacterium for 1 to 3 days at 23° C. in the dark. Co-cultured embryos are transferred to selection media and cultured for approximately two weeks to allow embryogenic callus to develop. Embryogenic callus is transferred to culture medium containing 100 mg/L paromomycin and subcultured at about two week intervals. Transformed plant cells are recovered 6 to 8 weeks after initiation of selection.
  • For Agrobacterium-mediated transformation of maize callus immature embryos are cultured for approximately 8-21 days after excision to allow callus to develop. Callus is then incubated for about 30 minutes at room temperature with the Agrobacterium suspension, followed by removal of the liquid by aspiration. The callus and Agrobacterium are co-cultured without selection for 3-6 days followed by selection on paromomycin for approximately 6 weeks, with biweekly transfers to fresh media. Paromomycin resistant calli are identified about 6-8 weeks after initiation of selection.
  • For transformation by microprojectile bombardment maize immature embryos are isolated and cultured 3-4 days prior to bombardment. Prior to microprojectile bombardment, a suspension of gold particles is prepared onto which the desired recombinant DNA expression cassettes are precipitated. DNA is introduced into maize cells as described in U.S. Pat. Nos. 5,550,318 and 6,399,861 using the electric discharge particle acceleration gene delivery device. Following microprojectile bombardment, tissue is cultured in the dark at 27° C. Additional transformation methods and materials for making transgenic plants of this invention, for example, various media and recipient target cells, transformation of immature embryos and subsequence regeneration of fertile transgenic plants are disclosed in U.S. Pat. Nos. 6,194,636, 6,232,526 and 7,151,204, which are incorporated herein by reference.
  • To regenerate transgenic corn plants a callus of transgenic plant cells resulting from transformation and selection is placed on media to initiate shoot development into plantlets which are transferred to potting soil for initial growth in a growth chamber at 26° C. followed by a mist bench before transplanting to 5 inch pots where plants are grown to maturity. The regenerated plants are self-fertilized and seed is harvested for use in one or more methods to select seeds, seedlings or progeny second generation transgenic plants (R2 plants) or hybrids, e.g. by selecting transgenic plants exhibiting an enhanced trait as compared to a control plant.
  • Transgenic corn plant cells are transformed with recombinant DNA from each of the genes identified in Table 2. Progeny transgenic plants and seed of the transformed plant cells are screened for enhanced water use efficiency, enhanced cold tolerance, increased yield, enhanced nitrogen use efficiency, enhanced seed protein and enhanced seed oil as obtained in Example 7.
    • Example 4 Soybean Transformation
  • This example illustrates plant transformation in producing the transgenic soybean plants of this invention and the production and identification of transgenic seed for transgenic soybean having enhanced water use efficiency, enhanced cold tolerance, increased yield, enhanced nitrogen use efficiency, enhanced seed protein and enhanced seed oil.
  • For Agrobacterium mediated transformation, soybean seeds are imbided overnight and the meristem explants excised. The explants are placed in a wounding vessel. Soybean explants and induced Agrobacterium cells from a strain containing plasmid DNA with the gene of interest cassette and a plant selectable marker cassette are mixed no later than 14 hours from the time of initiation of seed imbibition, and wounded using sonication. Following wounding, explants are placed in co-culture for 2-5 days at which point they are transferred to selection media for 6-8 weeks to allow selection and growth of transgenic shoots. Resistant shoots are harvested approximately 6-8 weeks and placed into selective rooting media for 2-3 weeks. Shoots producing roots are transferred to the greenhouse and potted in soil. Shoots that remain healthy on selection, but do not produce roots are transferred to non-selective rooting media for an additional two weeks. Roots from any shoots that produce roots off selection are tested for expression of the plant selectable marker before they are transferred to the greenhouse and potted in soil. Additionally, a DNA construct can be transferred into the genome of a soybean cell by particle bombardment and the cell regenerated into a fertile soybean plant as described in U.S. Pat. No. 5,015,580, herein incorporated by reference.
  • Transgenic soybean plant cells are transformed with recombinant DNA from each of the genes identified in Table 2. Transgenic progeny plants and seed of the transformed plant cells are screened for enhanced water use efficiency, enhanced cold tolerance, increased yield, enhanced nitrogen use efficiency, enhanced seed protein and enhanced seed oil as obtained in Example 10.
    • Example 5 Cotton Transgenic Plants with Enhanced Agronomic Traits
  • Cotton transformation is performed as generally described in WO0036911 and in U.S. Pat. No. 5,846,797. Transgenic cotton plants containing each recombinant DNA having a sequence of SEQ ID NO: 1 through SEQ ID NO: 803 are obtained by transforming with recombinant DNA from each of the genes identified in Table 2. Progeny transgenic plants are selected from a population of transgenic cotton events under specified growing conditions and are compared with control cotton plants. Control cotton plants are substantially the same cotton genotype but without the recombinant DNA, for example, either a parental cotton plant of the same genotype that was not transformed with the identical recombinant DNA or a negative isoline of the transformed plant. Additionally, a commercial cotton cultivar adapted to the geographical region and cultivation conditions, e.g. cotton variety ST474, cotton variety FM 958, and cotton variety Siokra L-23, are used to compare the relative performance of the transgenic cotton plants containing the recombinant DNA. The specified culture conditions are growing a first set of transgenic and control plants under “wet” conditions, e.g. irrigated in the range of 85 to 100 percent of evapotranspiration to provide leaf water potential of −14 to −18 bars, and growing a second set of transgenic and control plants under “dry” conditions, e.g. irrigated in the range of 40 to 60 percent of evapotranspiration to provide a leaf water potential of −21 to −25 bars. Pest control, such as weed and insect control is applied equally to both wet and dry treatments as needed. Data gathered during the trial includes weather records throughout the growing season including detailed records of rainfall; soil characterization information; any herbicide or insecticide applications; any gross agronomic differences observed such as leaf morphology, branching habit, leaf color, time to flowering, and fruiting pattern; plant height at various points during the trial; stand density; node and fruit number including node above white flower and node is above crack boll measurements; and visual wilt scoring. Cotton boll samples are taken and analyzed for lint fraction and fiber quality. The cotton is harvested at the normal harvest timeframe for the trial area. Enhanced water use efficiency is indicated by increased yield, improved relative water content, enhanced leaf water potential, increased biomass, enhanced leaf extension rates, and improved fiber parameters.
  • The transgenic cotton plants of this invention are identified from among the transgenic cotton plants by agronomic trait screening as having increased yield and enhanced water use efficiency.
    • Example 6 Canola Transformation
  • This example illustrates plant transformation in producing the transgenic canola plants of this invention and the production and identification of transgenic seed for transgenic canola having enhanced water use efficiency, enhanced cold tolerance, increased yield, enhanced nitrogen use efficiency, enhanced seed protein and enhanced seed oil.
  • Tissues from in vitro grown canola seedlings are prepared and inoculated with overnight-grown Agrobacterium cells containing plasmid DNA with the gene of interest cassette and a plant selectable marker cassette. Following co-cultivation with Agrobacterium, the infected tissues are allowed to grow on selection to promote growth of transgenic shoots, followed by growth of roots from the transgenic shoots. The selected plantlets are then transferred to the greenhouse and potted in soil. Molecular characterization is performed to confirm the presence of the gene of interest, and its expression in transgenic plants and progenies. Progeny transgenic plants are selected from a population of transgenic canola events under specified growing conditions and are compared with control canola plants. Control canola plants are substantially the same canola genotype but without the recombinant DNA, for example, either a parental canola plant of the same genotype that is not transformed with the identical recombinant DNA or a negative isoline of the transformed plant
  • Transgenic canola plant cells are transformed with recombinant DNA from each of the genes identified in Table 1. Transgenic progeny plants and seed of the transformed plant cells are screened for enhanced water use efficiency, enhanced cold tolerance, increased yield, enhanced nitrogen use efficiency, enhanced seed protein and enhanced seed oil as obtained in Example 7.
    • Example 7 Identification of Homologs
  • This example illustrates the identification of homologs of proteins encoded by the DNA identified in Table 1 which is used to provide transgenic seed and plants having enhanced agronomic traits. From the sequence of the homologs, homologous DNA sequence can be identified for preparing additional transgenic seeds and plants of this invention with enhanced agronomic traits.
  • An “All Protein Database” is constructed of known protein sequences using a proprietary sequence database and the National Center for Biotechnology Information (NCBI) non-redundant amino acid database (nr.aa). For each organism from which a polynucleotide sequence provided herein was obtained, an “Organism Protein Database” is constructed of known protein sequences of the organism; it is a subset of the All Protein Database based on the NCBI taxonomy ID for the organism.
  • The All Protein Database is queried using amino acid sequences provided herein as SEQ ID NO: 804 through SEQ ID NO: 1606 using NCBI “blastp” program with E-value cutoff of 1 e−8. Up to 1000 top hits are kept, and separated by organism names. For each organism other than that of the query sequence, a list is kept for hits from the query organism itself with a more significant E-value than the best hit of the organism. The list contains likely duplicated genes of the polynucleotides provided herein, and is referred to as the Core List. Another list is kept for all the hits from each organism, sorted by E-value, and referred to as the Hit List.
  • The Organism Protein Database is queried using polypeptide sequences provided herein as SEQ ID NO: 804 through SEQ ID NO: 1606 using NCBI “blastp” program with E-value cutoff of 1 e−4. Up to 1000 top hits are kept. A BLAST searchable database is constructed based on these hits, and is referred to as “SubDB”. SubDB is queried with each sequence in the Hit List using NCBI “blastp” program with E-value cutoff of leg. The hit with the best E-value is compared with the Core List from the corresponding organism. The hit is deemed a likely ortholog if it belongs to the Core List, otherwise it is deemed not a likely ortholog and there is no further search of sequences in the Hit List for the same organism. Likely orthologs from a large number of distinct organisms were identified and are reported by amino acid sequences of SEQ ID NO: 1607 to SEQ ID NO: 94613. These orthologs are reported in Tables 19 as homologs to the proteins cognate to genes used in trait-improving recombinant DNA
    • Example 8 Consensus Sequence Build
  • ClustalW program is selected for multiple sequence alignments of an amino acid sequence of SEQ ID NO: 804 and its homologs, through SEQ ID NO: 1606 and its homologs. Three major factors affecting the sequence alignments dramatically are (1) protein weight matrices; (2) gap open penalty; (3) gap extension penalty. Protein weight matrices available for ClustalW program include Blosum, Pam and Gonnet series. Those parameters with gap open penalty and gap extension penalty were extensively tested. On the basis of the test results, Blosum weight matrix, gap open penalty of 10 and gap extension penalty of 1 were chosen for multiple sequence alignment. The consensus sequence of SEQ ID NO: 1325 and its 30 homologs were derived according to the procedure described above and is displayed in FIG. 4.
    • Example 9 Pfam Module Annoation
  • This example illustrates the identification of domain and domain module by Pfam analysis.
  • The amino acid sequence of the expressed proteins that were shown to be associated with an enhanced trait were analyzed for Pfam protein family against the current Pfam collection of multiple sequence alignments and hidden Markov models using the HMMER software in the appended computer listing. The Pfam domain modules and individual protein domain for the proteins of SEQ ID NO: 804 through 1606 are shown in Table 20 and Table 21 respectively. The Hidden Markov model databases for the identified patent families are also in the appended computer listing allowing identification of other homologous proteins and their cognate encoding DNA to enable the full breadth of the invention for a person of ordinary skill in the art. Certain proteins are identified by a single Pfam domain and others by multiple Pfam domains. For instance, the protein with amino acids of SEQ ID NO: 830 is characterized by two Pfam domains, e.g. “Lectin_legB” and “Pkinase”. See also the protein with amino acids of SEQ ID NO: 817 which is characterized by four copies of the Pfam domain “Arm”. In Table 21 “score” is the gathering score for the Hidden Markov Model of the domain which exceeds the gathering cutoff reported in Table 22.
  • TABLE 20
    PEP
    Seq
    ID No. Construct ID Pfam module Position
    804 CGPG10.pep p450 31-495
    805 CGPG1008.pep Tryp_alpha_amyl 23-95
    806 CGPG1023.pep Na_Ca_ex::Na_Ca_ex 104-255::299-432
    807 CGPG1038.pep DUF1475 1-256
    812 CGPG1113.pep DUF1350 49-370
    814 CGPG1163.pep DSPc 49-182
    817 CGPG1205.pep Arm::Arm::Arm::Arm 94-134::135-175
    ::176-216::258-298
    818 CGPG1207.pep NifU_N 26-105
    820 CGPG1223.pep ATP_bind_1 7-250
    821 CGPG1250.pep DUF822 12-160
    824 CGPG1319.pep DUF599 10-233
    826 CGPG1329.pep Cullin 29-631
    827 CGPG133.pep Cyclin_N::Cyclin_C 168-293::295-422
    828 CGPG1332.pep Cullin 12-646
    829 CGPG1343.pep LRR_1 389-412
    830 CGPG1348.pep Lectin_legB::Pkinase 27-248::334-604
    831 CGPG1349.pep B_lectin::S_locus_glycop::PAN_1::Pkinase 65-171::180-312
    ::327-404::484-731
    832 CGPG1373.pep Pkinase 12-291
    833 CGPG1377.pep Pkinase 4-258
    834 CGPG1412.pep TPP_enzyme_N::TPP_enzyme_M::TPP_enzyme_C 45-221::243-376
    ::431-578
    835 CGPG1421.pep Biotin_lipoyl::E3_binding::2-oxoacid_dh 76-149::180-218
    ::249-480
    836 CGPG1426.pep Aminotran_1_2 48-432
    837 CGPG1433.pep Pyr_redox_2::Pyr_redox_dim 45-359::388-497
    838 CGPG1453.pep malic::Malic_M 171-360::362-615
    839 CGPG1454.pep Ribul_P_3_epim 7-207
    840 CGPG1463.pep Alpha-amylase::Alpha-amyl_C2 26-361::362-422
    841 CGPG1464.pep Glycolytic 11-358
    842 CGPG1471.pep IF4E 1-198
    843 CGPG1481.pep Pkinase 4-260
    844 CGPG1499.pep PPDK_N::PEP-utilizers::PEP-utilizers_C 85-445::496-586
    ::598-955
    845 CGPG150.pep p450 30-507
    846 CGPG1536.pep CRAL_TRIO_N::CRAL_TRIO 73-142::159-345
    847 CGPG1539.pep UPF0139 8-107
    848 CGPG155.pep GlutR_N::Shikimate_DH::GlutR_dimer 100-251::255-407
    ::420-526
    849 CGPG1583.pep PLAC8 88-187
    850 CGPG1588.pep PLAC8 75-214
    851 CGPG16.pep MIP 14-235
    852 CGPG1609.pep MMR_HSR1::DUF933 54-190::337-420
    853 CGPG1629.pep WD40::WD40::WD40 262-301::307-346
    ::356-395
    854 CGPG1637.pep DUF220 163-262
    855 CGPG1653.pep TBC 200-415
    856 CGPG1658.pep Nodulin-like 14-260
    857 CGPG1663.pep BT1 30-441
    858 CGPG1682.pep OPT 62-685
    859 CGPG1701.pep Glyco_transf_8 76-299
    861 CGPG1724.pep Per1 63-334
    862 CGPG1726.pep DUF607 111-291
    863 CGPG1736.pep Usp 1-148
    864 CGPG1741.pep mTERF 279-627
    865 CGPG1783.pep PB1 42-132
    866 CGPG1790.pep PB1 59-153
    868 CGPG1845.pep TFIID-18 kDa 29-119
    869 CGPG1855.pep CAF1 3-227
    870 CGPG1870.pep Pkinase 406-572
    871 CGPG1879.pep Pkinase::NAF 21-277::303-364
    872 CGPG1886.pep Pkinase 26-325
    873 CGPG1903.pep F-box 320-367
    874 CGPG1905.pep F-box::Kelch_2::Kelch_2 4-51::104-150
    ::255-306
    875 CGPG1914.pep F-box::Kelch_1::Kelch_1 42-89::170-215
    ::217-266
    876 CGPG193.pep WD40::WD40::WD40::WD40 167-205::268-307
    ::318-355::363-401
    877 CGPG1939.pep F-box::WD40::WD40::WD40 66-113::152-190
    ::247-283::325-364
    878 CGPG1949.pep YDG_SRA::Pre-SET::SET 360-519::543-639
    ::641-771
    879 CGPG1959.pep PHD::SET 34-82::208-344
    880 CGPG197.pep p450 40-481
    882 CGPG1981.pep MT-A70 476-636
    883 CGPG1999.pep Nfu_N::NifU 78-193::221-291
    884 CGPG2.pep p450 71-531
    885 CGPG2006.pep RCC1::RCC1::RCC1::RCC1 32-82::138-187
    ::190-239::294-343
    886 CGPG2010.pep Aminotran_5 74-448
    887 CGPG2011.pep X8 128-209
    888 CGPG2014.pep Pkinase::NAF 28-282::341-398
    889 CGPG2023.pep Zip 48-352
    890 CGPG2026.pep Pkinase 38-324
    892 CGPG2064.pep Cenp-O 123-201
    894 CGPG2077.pep NAC::UBA 88-147::195-232
    895 CGPG2095.pep AARP2CN::DUF663 228-309::483-780
    896 CGPG2105.pep Pkinase::Pkinase_C 102-404::422-471
    897 CGPG2108.pep Response_reg::CCT 64-180::442-484
    898 CGPG2111.pep polyprenyl_synt 74-324
    899 CGPG2124.pep UIM::efhand 139-156::220-248
    900 CGPG2125.pep Glutaredoxin 44-110
    903 CGPG2134.pep ATP-synt_G 8-122
    904 CGPG2139.pep DUF1517 94-391
    905 CGPG2140.pep PhzC-PhzF 6-282
    907 CGPG2163.pep Cupin_1::Cupin_1 5-157::190-339
    908 CGPG2165.pep ClpS 76-152
    910 CGPG2218.pep Spc97_Spc98 67-555
    912 CGPG2225.pep EMP24_GP25L 52-116
    913 CGPG2229.pep Subtilisin_N::PA 30-106::362-461
    915 CGPG2254.pep Ribosomal_L7Ae 20-114
    916 CGPG2268.pep CBS 66-188
    917 CGPG227.pep p450 37-494
    918 CGPG2312.pep UPF0061 75-571
    919 CGPG2315.pep SIP1 286-514
    920 CGPG2316.pep PTPA 98-396
    922 CGPG235.pep p450 74-510
    923 CGPG2358.pep Branch 54-278
    925 CGPG2361.pep Metallophos 9-231
    926 CGPG2365.pep Epimerase 3-211
    927 CGPG2372.pep Pribosyltran 29-169
    928 CGPG2374.pep Aminotran_5 8-370
    929 CGPG2377.pep DAO 69-466
    930 CGPG2387.pep H_PPase 1-239
    931 CGPG2389.pep Carb_anhydrase 52-275
    932 CGPG2395.pep AA_permease 89-526
    934 CGPG2409.pep DUF862 17-154
    935 CGPG2410.pep GST_N::GST_C 5-79::101-204
    937 CGPG2416.pep Hin1 97-235
    938 CGPG2441.pep Sina 5-205
    939 CGPG2450.pep Epimerase 114-371
    940 CGPG2451.pep RALF 57-129
    941 CGPG2492.pep Pribosyltran 80-216
    942 CGPG2495.pep ADH_N::ADH_zinc_N 25-134::165-307
    943 CGPG2506.pep PfkB 5-289
    944 CGPG2515.pep TIM 5-244
    945 CGPG2531.pep AhpC-TSA 5-138
    946 CGPG2581.pep SelR 12-133
    947 CGPG2584.pep zf-Tim10_DDP 22-86
    948 CGPG2592.pep TFIID_30 kDa 30-80
    949 CGPG2612.pep RRM_1::RRM_1::RRM_I 65-132::150-225
    ::275-343
    950 CGPG2660.pep B3::B3 17-115::211-301
    951 CGPG2663.pep NTF2::RRM_1 15-131::295-365
    952 CGPG2679.pep ACBP::Ank::Ank 104-190::265-297
    ::298-330
    953 CGPG2696.pep zf-C3HC4 177-218
    954 CGPG2772.pep Mov34 6-136
    955 CGPG2773.pep Asp 161-498
    956 CGPG281.pep TLC 91-574
    957 CGPG2846.pep Aldo_ket_red 49-365
    958 CGPG2852.pep Glyoxalase 9-132
    960 CGPG2870.pep zf-CCCH::zf-CCCH::zf-CCCH::zf-CCCH::zf- 111-137::159-185
    CCCH ::205-231::347-373
    ::393-419
    961 CGPG2877.pep LAG1 96-307
    962 CGPG289.pep Cellulose_synt 243-1060
    963 CGPG2924.pep zf-C3HC4 138-179
    964 CGPG2947.pep Acetyltransf_1::Bromodomain 265-343::460-548
    965 CGPG2963.pep C1_2::C1_3::C1_3::C1_2::C1_3::C1_3::C1_2 81-108::136-164
    ::194-223::305-335
    ::391-420::494-522
    ::552-581
    966 CGPG2987.pep SRF-TF Nov-66
    968 CGPG3045.pep Pkinase_Tyr 82-356
    969 CGPG3046.pep AAA 121-305
    970 CGPG3060.pep p450 67-528
    971 CGPG3075.pep Auxin_inducible 7-106
    972 CGPG310.pep Cyclin_N 18-143
    973 CGPG3103.pep PPR::PPR::PPR::PPR::PPR::PPR::PPR::PPR::PPR 14-48::49-83::84-118
    ::PPR::PPR ::119-153::155-188
    ::189-223::224-258
    ::259-293::295-329
    ::330-364::365-398
    974 CGPG315.pep p450 29-491
    976 CGPG3189.pep RRM_1::RRM_1 115-186::209-280
    977 CGPG3204.pep KH_1::KH_1::KH_1::KH_1::KH_1 45-104::151-221
    ::318-381::400-467
    ::575-637
    978 CGPG3208.pep MATH::MATH 26-153::180-302
    979 CGPG3219.pep 2OG-FeII_Oxy 220-320
    980 CGPG3233.pep PPR::PPR::PPR::PPR::PPR::PPR::PPR::PPR 160-194::195-229
    ::231-265::266-300
    ::301-335::336-370
    ::371-405::406-440
    981 CGPG3263.pep Tryp_alpha_amyl 28-104
    982 CGPG3276.pep ECH 11-186
    984 CGPG3282.pep Steroid_dh 117-268
    985 CGPG3300.pep zf-CCHC::zf-CCHC::zf-CCHC::zf-CCHC::zf- 55-72::74-91::93-110
    CCHC::zf-CCHC::zf-CCHC ::112-129::138-155
    ::157-174::229-246
    986 CGPG3318.pep Peptidase_C14 3-416
    987 CGPG3319.pep AP2 28-79
    988 CGPG3326.pep zf-C3HC4 259-299
    989 CGPG333.pep PTS_2-RNA 48-239
    990 CGPG3338.pep Alba 17-87
    991 CGPG334.pep Mov34 20-128
    992 CGPG3374.pep peroxidase 42-286
    993 CGPG3402.pep Dimerisation::Methyltransf_2 30-89::99-342
    995 CGPG3413.pep WD40::U3_snoRNA_C 168-207::377-523
    996 CGPG3422.pep WD40::WD40::WD40 241-279::387-425
    ::519-559
    997 CGPG3436.pep DUF6::DUF6 17-144::198-327
    998 CGPG3539.pep Mito_carr::Mito_carr::Mito_carr 11-105::113-209
    ::214-303
    999 CGPG3550.pep FAE1_CUT1_RppA::ACP_syn_III_C 81-370::384-468
    1000 CGPG3551.pep Pkinase 9-273
    1001 CGPG3552.pep Aldedh 23-441
    1002 CGPG3572.pep FA_hydroxylase 112-225
    1004 CGPG3599.pep DUF579 51-289
    1008 CGPG364.pep zf-C3HC4 97-137
    1010 CGPG3679.pep malic::Malic_M::PTA_PTB 36-179::181-418
    ::446-768
    1011 CGPG3686.pep Gp_dh_N::Gp_dh_C 2-150::155-312
    1012 CGPG3694.pep LRRNT_2::LRR_1::LRR_1::LRR_1::LRR_1::Pkinase_Tyr 38-78::106-128
    ::130-152::154-176
    ::178-201::312-583
    1013 CGPG3696.pep MMR_HSR1 136-257
    1014 CGPG3698.pep WD40::WD40 104-142::234-272
    1015 CGPG3699.pep adh_short 19-187
    1016 CGPG3702.pep SAM_1 228-291
    1017 CGPG3703.pep ENOD93 25-103
    1018 CGPG3707.pep Pkinase 42-333
    1019 CGPG3710.pep VQ 118-148
    1020 CGPG3730.pep DUF167 140-216
    1021 CGPG3731.pep DUF616 194-508
    1022 CGPG3734.pep PRK::Pribosyltran 46-233::280-425
    1023 CGPG3745.pep RRM_1::RRM_1 386-455::481-553
    1024 CGPG3764.pep Response_reg 20-145
    1026 CGPG3851.pep SH3_1 284-338
    1027 CGPG3911.pep Aldedh 104-587
    1028 CGPG3948.pep NAP 50-295
    1031 CGPG3996.pep Inositol_P 6-267
    1032 CGPG4006.pep ENT 1-74
    1033 CGPG4025.pep SQS_PSY 44-331
    1034 CGPG4028.pep Transket_pyr::Transketolase_C 398-565::579-702
    1035 CGPG403.pep Pkinase 78-336
    1036 CGPG4041.pep DEAD::Helicase_C 141-315::386-462
    1037 CGPG4078.pep GST_C 180-283
    1038 CGPG4079.pep RRS1 1-178
    1041 CGPG4104.pep LRRNT_2::LRR_1::LRR_1::LRR_1::LRR_1::Pkinase 30-67::95-117
    ::119-141::143-165
    ::167-188::367-633
    1042 CGPG4127.pep Hydrolase 43-239
    1043 CGPG4135.pep Pkinase::efhand::efhand::efhand::efhand 118-376::423-451
    ::459-487::495-523
    ::529-557
    1044 CGPG4161.pep Methyltransf_11 56-159
    1045 CGPG4180.pep GHMP_kinases_N::GHMP_kinases_C 152-219::382-466
    1046 CGPG4191.pep Bombesin 163-176
    1047 CGPG4199.pep Copine::zf-C3HC4 117-265::385-417
    1048 CGPG4241.pep GASA 3-99
    1049 CGPG427.pep Pkinase_Tyr 8-262
    1050 CGPG4273.pep dsrm::dsrm 2-68::88-153
    1051 CGPG4301.pep 2OG-FeII_Oxy 151-253
    1052 CGPG4303.pep Rhodanese 13-114
    1053 CGPG4313.pep G6PD_N::G6PD_C 94-273::276-573
    1054 CGPG4314.pep AWPM-19 15-156
    1055 CGPG4329.pep AA_kinase 86-324
    1056 CGPG4330.pep PALP 53-341
    1057 CGPG4338.pep Proteasome 21-217
    1058 CGPG4341.pep Mito_carr::Mito_carr::Mito_carr 51-134::158-246
    ::252-343
    1061 CGPG4386.pep GHMP_kinases_N::GHMP_kinases_C 113-171::245-338
    1062 CGPG4394.pep p450 39-503
    1063 CGPG4396.pep p450 39-504
    1064 CGPG4400.pep p450 32-474
    1065 CGPG4401.pep p450 47-511
    1066 CGPG441.pep Chalcone 14-225
    1067 CGPG4413.pep p450 32-547
    1068 CGPG4427.pep p450 57-530
    1069 CGPG4446.pep p450 43-504
    1070 CGPG4448.pep p450 32-486
    1071 CGPG4474.pep Band_7 33-212
    1072 CGPG4482.pep peroxidase 47-291
    1073 CGPG4511.pep VHS::GAT 36-166::227-315
    1074 CGPG4517.pep Aldo_ket_red 5-292
    1075 CGPG4551.pep XS::XH 30-148::418-557
    1077 CGPG4567.pep SRF-TF 3-53
    1078 CGPG4586.pep RRM_1 8-73
    1079 CGPG4600.pep zf-CCCH::zf-CCCH 13-39::149-174
    1080 CGPG4631.pep C1_2::C1_2::C1_3::C1_2::C1_3::C1_2 88-115::209-237
    ::264-292::319-349
    ::404-433::566-595
    1081 CGPG4642.pep Pyridoxal_deC 63-412
    1082 CGPG4645.pep Cu-oxidase_3::Cu-oxidase::Cu-oxidase_2 31-148::157-325
    ::414-551
    1083 CGPG4646.pep efhand_like::PI-PLC-X::PI-PLC-Y::C2 27-105::108-251
    ::332-450::471-563
    1084 CGPG4649.pep SMP::SMP::SMP 14-72::130-191
    ::195-256
    1085 CGPG4653.pep DUF1637 47-280
    1087 CGPG4668.pep SYF2 140-306
    1088 CGPG469.pep tRNA-synt_1c::tRNA-synt_1c_C 213-518::520-697
    1089 CGPG4708.pep Sulfate_transp::STAS 172-482::505-623
    1090 CGPG4712.pep Mem_trans 9-565
    1091 CGPG4714.pep DUF231 248-423
    1092 CGPG4719.pep Response_reg::CCT 37-153::417-461
    1093 CGPG473.pep Peptidase_M16::Peptidase_M16_C 88-234::239-423
    1094 CGPG4734.pep Auxin_inducible 19-119
    1095 CGPG4736.pep Pribosyltran 225-358
    1096 CGPG474.pep Pro_isomerase 6-172
    1102 CGPG4850.pep PMEI 25-174
    1103 CGPG4868.pep PsbW 1-133
    1104 CGPG4871.pep Tryp_alpha_amyl 52-133
    1105 CGPG488.pep Histone 19-92
    1106 CGPG4908.pep WD40::WD40 16-54::63-101
    1108 CGPG4921.pep WD40::WD40::WD40::WD40::WD40 202-241::253-
    291::295-333::337-375
    ::472-510
    1109 CGPG4954.pep LRRNT_2::LRR_1::LRR_1::LRR_1 33-72::76-98::100-122
    ::124-145
    1110 CGPG4956.pep Asp 141-482
    1111 CGPG4959.pep adh_short 15-183
    1112 CGPG4965.pep zf-A20::zf-AN1 15-39::114-154
    1113 CGPG4970.pep GASA 1-108
    1114 CGPG4980.pep U-box::Arm::Arm 73-147::246-287
    ::288-328
    1115 CGPG4982.pep F-box::FBA_1 2-49::209-387
    1116 CGPG4985.pep CPSase_sm_chain::GATase 56-203::245-422
    1117 CGPG4990.pep LRRNT_2::LRR_1::LRR_1::LRR_1::LRR_1::LRR_1 73-112::139-161
    ::163-183::187-206
    ::210-232::306-328
    1118 CGPG4991.pep PALP 164-473
    1119 CGPG5007.pep adh_short 21-192
    1120 CGPG5015.pep adh_short 13-126
    1121 CGPG5026.pep adh_short 46-221
    1122 CGPG5029.pep adh_short 80-252
    1123 CGPG5046.pep LRRNT_2::LRR_1::LRR_1::LRR_1::Pkinase 30-70::99-121
    ::123-145::147-169
    ::306-573
    1124 CGPG508.pep Na_sulph_symp 93-563
    1125 CGPG5103.pep C2 9-95
    1126 CGPG511.pep Rho_GDI 22-222
    1127 CGPG5121.pep efhand_like::PI-PLC-X::PI-PLC-Y::C2 30-113::116-258
    ::331-449::470-562
    1128 CGPG5126.pep peroxidase 54-303
    1129 CGPG5136.pep p450 35-500
    1130 CGPG5146.pep p450 45-501
    1131 CGPG5149.pep p450 31-478
    1132 CGPG5181.pep Pkinase 278-540
    1133 CGPG52.pep Sugar_tr 32-472
    1134 CGPG5206.pep UDPG_MGDP_dh_N::UDPG_MGDP_dh::UDPG_MGDP_dh_C 2-200::209-306
    ::328-452
    1136 CGPG5232.pep Pkinase 71-328
    1137 CGPG5239.pep Copine 136-284
    1138 CGPG5246.pep ABC_tran::ABC_tran 94-285::406-571
    1139 CGPG525.pep CDP-OH_P_transf 138-277
    1140 CGPG5268.pep CDC50 65-368
    1141 CGPG5272.pep AA_permease 153-621
    1142 CGPG5333.pep MFS_1 55-468
    1143 CGPG5338.pep RRM_1::RRM_1 8-77::108-178
    1144 CGPG5341.pep F-box 33-79
    1145 CGPG5369.pep AA_kinase::ACT::ACT 83-366::400-469
    ::477-539
    1146 CGPG5372.pep SBF 142-322
    1147 CGPG5380.pep Tyr-DNA_phospho 137-581
    1148 CGPG5386.pep MOSC_N::MOSC 4-132::138-296
    1149 CGPG5396.pep PALP 9-297
    1150 CGPG5397.pep PDT 128-307
    1151 CGPG5421.pep Pre-SET::SET 119-267::269-414
    1152 CGPG5433.pep MtN3_slv::MtN3_slv 10-98::132-218
    1153 CGPG5439.pep LANC_like 69-410
    1154 CGPG5453.pep Mito_carr::Mito_carr::Mito_carr 14-116::125-215
    ::233-334
    1155 CGPG5456.pep Mito_carr::Mito_carr::Mito_carr 78-175::183-279
    ::283-373
    1156 CGPG5483.pep PP2C 66-369
    1157 CGPG5492.pep FAE1_CUT1_RppA::ACP_syn_III_C 61-358::372-456
    1158 CGPG5508.pep RCC1::RCC1::RCC1::RCC1::FYVE::DZC 310-359::413-462
    ::478-526::582-630
    ::633-701::967-1002
    1159 CGPG5520.pep TFIID-31 kDa 19-152
    1160 CGPG5525.pep PRMT5 187-679
    1161 CGPG5526.pep Pkinase 8-295
    1162 CGPG5530.pep Response_reg 504-644
    1163 CGPG5534.pep Y_phosphatase2 3-169
    1164 CGPG5537.pep TBP::TBP 62-147::152-238
    1165 CGPG5545.pep CBS::CBS 35-175::193-318
    1166 CGPG555.pep PALP::Thr_dehydrat_C::Thr_dehydrat_C 104-396::409-498
    498::504-591
    1167 CGPG5558.pep Cyclin_N::Cyclin_C 212-337::339-458
    1168 CGPG5559.pep Suc_Fer-like 69-311
    1169 CGPG5562.pep Suc_Fer-like 59-308
    1170 CGPG5592.pep Rho_GDI 35-239
    1171 CGPG5625.pep LRR_1::LRR_1::Pkinase 433-455::457-476
    ::586-854
    1172 CGPG5631.pep WAK::Pkinase 171-270::390-658
    1173 CGPG5632.pep Aldedh 29-491
    1174 CGPG5636.pep Aldedh 15-476
    1175 CGPG5637.pep Aldedh 32-493
    1176 CGPG564.pep Aminotran_3 80-413
    1177 CGPG5641.pep Aldedh 14-472
    1178 CGPG5650.pep Aminotran_3 32-374
    1179 CGPG5653.pep Aminotran_1_2 32-383
    1180 CGPG5657.pep Aldedh 15-474
    1181 CGPG5671.pep Gp_dh_N::Gp_dh_C 3-151::156-313
    1182 CGPG5672.pep Glutaminase 24-309
    1183 CGPG5677.pep PGAM 4-165
    1184 CGPG5678.pep Aminotran_1_2 35-385
    1185 CGPG5679.pep TIM 7-248
    1186 CGPG5682.pep Aminotran_3 31-384
    1187 CGPG5691.pep PK::PK_C 5-350::362-478
    1188 CGPG5699.pep Gp_dh_N::Gp_dh_C 3-155::160-316
    1189 CGPG5705.pep NDK 3-137
    1190 CGPG5722.pep Pyrophosphatase 17-175
    1191 CGPG5734.pep Cyclin_N::Cyclin_C 232-357::359-478
    1192 CGPG5736.pep PP2C 22-280
    1193 CGPG5744.pep CDC50 63-365
    1194 CGPG5747.pep Pkinase 23-318
    1195 CGPG5748.pep NAD_Gly3P_dh_N::NAD_Gly3P_dh_C 84-259::282-432
    1198 CGPG577.pep Thioredoxin 7-111
    1199 CGPG5780.pep AA_permease 68-517
    1200 CGPG5793.pep AA_permease 285-815
    1201 CGPG5795.pep Sugar_tr 123-565
    1202 CGPG5796.pep Sugar_tr 43-466
    1203 CGPG5800.pep AA_permease 86-546
    1204 CGPG5812.pep Pkinase 22-273
    1205 CGPG5815.pep Pkinase 9-272
    1206 CGPG5838.pep Pkinase 1-264
    1207 CGPG5844.pep Pkinase 78-351
    1208 CGPG5846.pep Pkinase 99-376
    1209 CGPG5851.pep Pkinase 121-401
    1210 CGPG5857.pep Pkinase 19-273
    1211 CGPG5862.pep Pkinase 181-447
    1212 CGPG5863.pep Pkinase 52-330
    1213 CGPG5867.pep Pkinase 142-423
    1214 CGPG5872.pep Pkinase 18-288
    1215 CGPG5913.pep ADH_N::ADH_zinc_N 28-109::140-284
    1217 CGPG5961.pep Biotin_lipoyl::2-oxoacid_dh 94-167::232-462
    1219 CGPG5968.pep Pribosyltran 36-172
    1220 CGPG5984.pep Pkinase 115-443
    1221 CGPG5991.pep LRR_1 266-293
    1222 CGPG6006.pep RRM_1 19-89
    1223 CGPG6015.pep La::RRM_1::RRM_3 14-85::118-188
    ::302-404
    1224 CGPG603.pep G6PD_N::G6PD_C 35-222::224-508
    1225 CGPG6046.pep Str_synth 179-266
    1226 CGPG6063.pep Nramp 88-451
    1228 CGPG6092.pep SRPRB 53-235
    1229 CGPG6104.pep Steroid_dh 111-262
    1230 CGPG6106.pep LEA_5 1-92
    1231 CGPG6111.pep PP-binding 48-115
    1232 CGPG6113.pep UQ_con 7-143
    1234 CGPG6132.pep SMP::SMP::SMP 13-71::135-196
    ::200-262
    1236 CGPG6147.pep Redoxin 74-234
    1237 CGPG6152.pep Arf 5-177
    1238 CGPG6154.pep Ion_trans_2::Ion_trans_2 122-204::253-328
    1239 CGPG6170.pep UQ_con 19-158
    1240 CGPG6171.pep Thioredoxin 120-227
    1241 CGPG6177.pep AIG1 39-236
    1242 CGPG6181.pep Peptidase_C12 2-214
    1243 CGPG6188.pep Di19 10-217
    1244 CGPG6202.pep TB2_DP1_HVA22 9-106
    1245 CGPG6217.pep MFS_1::Sugar_tr 40-460::90-507
    1246 CGPG623.pep SATase_N::Hexapep::Hexapep::Hexapep 45-149::203-220
    ::229-246::247-264
    1247 CGPG6239.pep Sugar_tr 27-458
    1248 CGPG6244.pep Pkinase 39-303
    1249 CGPG6254.pep Pkinase::NAF 12-264::292-352
    1251 CGPG627.pep His_biosynth 48-289
    1252 CGPG6271.pep Pkinase 191-527
    1253 CGPG6278.pep Pkinase 86-368
    1254 CGPG6288.pep Pkinase_Tyr 207-463
    1255 CGPG6309.pep PRA1 29-181
    1256 CGPG633.pep DCP1 12-134
    1257 CGPG635.pep Epimerase 9-273
    1258 CGPG6350.pep LRRNT_2::LRR_1::LRR_1::LRR_1:LRR_1 32-78::105-127
    ::129-151::153-175
    ::177-196
    1260 CGPG6365.pep Aminotran_1_2 32-384
    1261 CGPG6374.pep Gln-synt_C 120-380
    1262 CGPG6377.pep PGK 2-383
    1263 CGPG638.pep PA 51-163
    1264 CGPG6397.pep F420_oxidored 3-246
    1265 CGPG6398.pep Enolase_N::Enolase_C 5-135::140-430
    1266 CGPG6408.pep ADH_N::ADH_zinc_N 25-155::185-350
    1267 CGPG6415.pep NTP_transferase 4-271
    1268 CGPG6421.pep ADH_N::ADH_zinc_N 25-148::179-318
    1269 CGPG6442.pep iPGM_N::Metalloenzyme 2-363::373-488
    1270 CGPG6443.pep PGK 1-391
    1271 CGPG6446.pep PK::PK_C 106-453::467-587
    1272 CGPG6453.pep Aminotran_1_2 41-402
    1273 CGPG6466.pep ADH_N::ADH_zinc_N 27-153::184-322
    1274 CGPG6467.pep Aminotran_3 19-366
    1275 CGPG6470.pep PfkB 1-302
    1276 CGPG6475.pep NTP_transferase 10-282
    1277 CGPG6477.pep NDK 4-138
    1278 CGPG6478.pep PfkB 1-308
    1279 CGPG6493.pep AA_permease 94-561
    1280 CGPG6506.pep Asparaginase 140-457
    1281 CGPG6518.pep NAD_binding_2::6PGD 2-173::177-467
    1282 CGPG6546.pep PK::PK_C 3-348::360-477
    1283 CGPG6556.pep Aminotran_1_2 124-475
    1284 CGPG6562.pep Aminotran_3 116-451
    1285 CGPG6566.pep NTP_transferase::Hexapep::Hexapep::Hexapep 95-350::398-415
    ::432-449::460-477
    1286 CGPG6571.pep Aldedh 102-560
    1287 CGPG6576.pep Aldedh 99-565
    1288 CGPG659.pep G_glu_transpept 48-567
    1289 CGPG6594.pep Pyr_redox_2::Pyr_redox_dim 94-419::450-559
    1290 CGPG6603.pep Pyr_redox_2::Pyr_redox_dim 94-397::427-538
    1291 CGPG6608.pep Pyr_redox_2::Pyr_redox_dim 93-394::423-532
    1292 CGPG6634.pep DUF177 100-252
    1294 CGPG6667.pep Invertase_neut 89-577
    1295 CGPG6678.pep Biotin_lipoyl::E3_binding::2-oxoacid_dh 92-165::225-263
    ::281-512
    1296 CGPG6695.pep Pyr_redox_2::Pyr_redox_dim 97-408::436-545
    1297 CGPG6699.pep Ribul_P_3_epim 94-295
    1298 CGPG670.pep Fer2 60-135
    1299 CGPG6705.pep PK::PK_C::PEP-utilizers 89-433::445-559
    ::584-663
    1300 CGPG6735.pep FBPase 93-413
    1301 CGPG6744.pep Glycolytic 92-429
    1302 CGPG6753.pep Pyr_redox_2 236-538
    1303 CGPG6757.pep Aminotran_1_2 127-473
    1305 CGPG6806.pep mTERF 110-457
    1306 CGPG6811.pep GH3 10-567
    1308 CGPG6815.pep V-ATPase_G 5-109
    1310 CGPG6830.pep Tbf5 13-76
    1313 CGPG6864.pep DUF620 190-438
    1314 CGPG6877.pep Hep_59 101-194
    1315 CGPG6878.pep Peptidase_M24 107-343
    1316 CGPG6880.pep PAP_fibrillin 72-232
    1318 CGPG6887.pep AIG2 12-111
    1319 CGPG6895.pep zf-CCHC::zf-CCHC::zf-CCHC::zf-CCHC 166-183::208-225
    ::325-342::356-373
    1322 CGPG6912.pep zf-DHHC 149-213
    1324 CGPG6942.pep RNA_pol_Rpb5_N::RNA_pol_Rpb5_C 18-108::149-222
    1327 CGPG6969.pep 2OG-FeII_Oxy 223-323
    1329 CGPG6991.pep Glyco_tran_28_C 11-170
    1332 CGPG7037.pep Sad1_UNC 313-416
    1333 CGPG7051.pep PAP_fibrillin 84-236
    1336 CGPG7086.pep SFT2 44-163
    1339 CGPG7136.pep NOI 1-72
    1340 CGPG7147.pep RAMP4 1-64
    1343 CGPG7222.pep Branch 49-274
    1345 CGPG7233.pep eIF2A 214-407
    1346 CGPG7238.pep UPF0185 5-80
    1347 CGPG7253.pep ArfGap 15-117
    1348 CGPG7255.pep Arf 5-177
    1349 CGPG7286.pep ORC2 20-345
    1350 CGPG7292.pep Methyltransf_11 38-135
    1351 CGPG7301.pep ELFV_dehydrog_N::ELFV_dehydrog 57-187::202-445
    1352 CGPG7305.pep Pyr_redox_2 126-386
    1353 CGPG7307.pep Gp_dh_N::Gp_dh_C 11-163::168-324
    1354 CGPG7318.pep MIP 1-142
    1355 CGPG7319.pep SNF5 172-400
    1356 CGPG7345.pep Lipase_3 97-237
    1357 CGPG7368.pep MT-A70 516-676
    1358 CGPG7385.pep FHA 32-107
    1359 CGPG7391.pep G-patch 6-50
    1360 CGPG7405.pep TATA_RF 1-216
    1361 CGPG7415.pep IU_nuc_hydro 1-312
    1362 CGPG7416.pep GLTP 52-233
    1363 CGPG7420.pep PRK 95-302
    1366 CGPG7445.pep PRC::PRC 92-169::171-252
    1367 CGPG7465.pep Aldedh 103-567
    1368 CGPG7473.pep F-box::WD40::WD40::WD40::WD40 273-320::412-449
    ::453-493::520-556
    ::560-598
    1369 CGPG7489.pep UBX 295-376
    1370 CGPG7492.pep Pescadillo_N::BRCT 8-291::337-414
    1371 CGPG7499.pep G-alpha 423-839
    1374 CGPG7508.pep Smg4_UPF3 1-170
    1375 CGPG7509.pep SSB 76-187
    1376 CGPG7511.pep GFA 31-125
    1377 CGPG7515.pep Brix 45-297
    1378 CGPG7521.pep G-alpha 23-386
    1380 CGPG7547.pep PAD_porph 14-368
    1381 CGPG7561.pep Snf7 17-187
    1382 CGPG7562.pep Sybindin 6-136
    1383 CGPG7563.pep DUF887 40-279
    1384 CGPG7567.pep Peptidase_M18 14-461
    1389 CGPG7597.pep zf-AN1 76-116
    1390 CGPG7606.pep Pentapeptide::Pentapeptide 127-166::172-211
    1392 CGPG7637.pep DAD 2-112
    1393 CGPG7649.pep YgbB 71-227
    1394 CGPG7658.pep Cyclase 56-256
    1395 CGPG7664.pep Aldedh 9-463
    1396 CGPG7666.pep Aminotran_1_2 26-392
    1397 CGPG7668.pep DUF594 660-719
    1399 CGPG7746.pep UPF0153 49-139
    1400 CGPG7747.pep Copine 113-261
    1401 CGPG7752.pep zf-MYND::PDCD2_C 176-214::241-403
    1403 CGPG7770.pep YTH 263-353
    1406 CGPG7778.pep Ubie_methyltran 51-304
    1407 CGPG7786.pep KH_1 141-193
    1408 CGPG7788.pep YIF1 34-263
    1410 CGPG78.pep Hpt 46-132
    1411 CGPG783.pep RRM_1::RRM_2 288-354::682-778
    1412 CGPG7832.pep STT3 26-670
    1413 CGPG7841.pep ECH::3HCDH_N::3HCDH 17-186::311-490
    ::492-585
    1414 CGPG7845.pep LRRNT_2::LRR_1::LRR_1::LRR_1::LRR_1::LRR_1 23-64::97-119
    ::121-143::145-167
    ::169-192::194-216
    1415 CGPG7847.pep Peptidase_C48 30-225
    1417 CGPG7853.pep LRR_1::LRR_1::LRR_1::LRR_1:LRR_1::LRR_1::LRR_1 142-164::166-188
    ::190-212::214-235
    ::258-280::282-304
    ::306-325
    1418 CGPG7857.pep Response_reg::CCT 79-195::689-736
    1420 CGPG7869.pep Acyltransferase 117-264
    1421 CGPG7891.pep FMO-like 11-427
    1422 CGPG7892.pep FMO-like 9-416
    1423 CGPG7906.pep Skp1_POZ::Skp1 4-65::76-153
    1424 CGPG7924.pep AAA 249-462
    1428 CGPG7964.pep IQ::IQ 108-128::130-150
    1429 CGPG7968.pep FMO-like 13-427
    1431 CGPG7972.pep FAD_binding_3 5-372
    1432 CGPG7982.pep Tetraspannin 4-241
    1433 CGPG7985.pep BT1 57-469
    1434 CGPG7993.pep F-box::LRR_2 27-73::278-304
    1435 CGPG8.pep p450 39-503
    1436 CGPG80.pep Pkinase 68-328
    1437 CGPG8001.pep FMO-like 13-433
    1438 CGPG8009.pep BT1 41-511
    1440 CGPG8049.pep BT1 1-436
    1441 CGPG806.pep Synaptobrevin 127-215
    1442 CGPG8060.pep DUF829 161-425
    1446 CGPG81.pep Pkinase 70-330
    1452 CGPG8125.pep zf-C3HC4 46-86
    1453 CGPG8134.pep DEK_C::SWIB::SWIB 3-57::197-272
    ::305-382
    1455 CGPG8156.pep PCI 258-362
    1456 CGPG8159.pep ACT::ACT 77-141::308-374
    1458 CGPG8179.pep WD40::WD40 138-177::264-305
    1459 CGPG8193.pep Ank::Ank 22-54::55-87
    1460 CGPG8197.pep F-box 5-53
    1461 CGPG8198.pep F-box::Kelch_2::Kelch_1::Kelch_2 74-119::174-221
    ::223-278::329-369
    1463 CGPG8211.pep F- 182-229::292-328
    box::WD40::WD40::WD40::WD40::WD40::WD40 ::332-368::372-408
    ::411-449::453-538
    ::542-578
    1464 CGPG823.pep Ribosomal_S6e 1-129
    1466 CGPG8238.pep PGI 49-537
    1467 CGPG8260.pep Iso_dh 4-331
    1468 CGPG8267.pep Pyridoxal_deC 34-383
    1469 CGPG8268.pep NTR_SIR_ferr:NIR_SER::NIR_SIR_ferr 62-131::164-345
    ::360-432
    1470 CGPG8274.pep PK::PK_C 5-347::363-476
    1471 CGPG8277.pep Rib_5-P_isom_A 55-229
    1472 CGPG8279.pep F-box::Kelch_1::Kelch_1 22-69::124-168
    ::170-213
    1475 CGPG8408.pep DUF641 60-192
    1476 CGPG842.pep Redoxin 5-162
    1477 CGPG8421.pep NOSIC::Nop 121-173::213-361
    1478 CGPG8435.pep NHL::NHL 55-82::115-142
    1479 CGPG8440.pep U-box::Arm::Arm::Arm::Arm 242-316::372-413
    ::455-495::496-537
    ::538-578
    1480 CGPG8453.pep ACT::ACT::ACT::ACT 36-99::129-201
    ::265-332::343-406
    1481 CGPG8470.pep DUF89 18-357
    1482 CGPG8479.pep F-box::Kelch_1::Kelch_1 31-78::124-170
    ::172-216
    1483 CGPG8489.pep F-box::FBA_1 3-50::219-384
    1484 CGPG8498.pep Fcf1 87-185
    1485 CGPG85.pep Aa_trans 19-454
    1486 CGPG8501.pep PPR::PPR::PPR::PPR::PPR::PPR 149-183::189-223
    ::224-258::259-292
    ::330-364::401-435
    1487 CGPG8507.pep DUF588 31-185
    1488 CGPG8509.pep Pro_isomerase 80-233
    1490 CGPG8517.pep B_lectin::S_locus_glycop::PAN_2 84-197::211-339
    ::356-422
    1492 CGPG852.pep Ribosomal_S5::Ribosomal_S5_C 94-160::177-250
    1498 CGPG8567.pep TB2_DP1_HVA22 3-98
    1499 CGPG8580.pep Caleosin 22-195
    1501 CGPG8590.pep DUF579 42-289
    1503 CGPG8594.pep DUF584 1-139
    1504 CGPG8606.pep Exo_endo_phos 56-327
    1505 CGPG8628.pep DUF584 32-203
    1507 CGPG8654.pep PPR::PPR 73-107::141-175
    1508 CGPG8668.pep TATA_RF 1-200
    1511 CGPG8702.pep RPE65 50-622
    1514 CGPG8748.pep AAA 201-357
    1516 CGPG8770.pep DUF543 1-73
    1517 CGPG8777.pep DUF569::DUF569 1-144::227-368
    1519 CGPG8786.pep DUF260 13-113
    1520 CGPG8792.pep Abhydrolase_3 75-290
    1521 CGPG8801.pep PPR::PPR::PPR::PPR::PPR::PPR::PPR 110-144::145-179
    ::181-215::216-250
    ::251-285::286-320
    ::321-355
    1522 CGPG8809.pep Ribosomal_L12 141-208
    1523 CGPG8840.pep CLP_protease 115-289
    1524 CGPG8850.pep PPR::PPR::PPR::PPR::PPR::PPR::PPR::PPR::PPR 189-223::224-258
    ::PPR ::297-331::332-366
    ::367-401::402-436
    ::437-470::471-505
    ::506-540::542-576
    1525 CGPG8870.pep Fructosamin_kin 54-339
    1526 CGPG8871.pep DUF59 36-115
    1527 CGPG8872.pep RRM_1::RRM_1::RRM_1 138-205::214-288
    ::308-378
    1528 CGPG8876.pep SFT2 43-162
    1529 CGPG8902.pep RNA_pol_I_A49 31-415
    1530 CGPG8904.pep G-alpha 103-447
    1531 CGPG8907.pep DnaJ::zf-C2H2 4-67::338-362
    1532 CGPG8914.pep Whi5 181-205
    1533 CGPG8931.pep eIF3_subunit 1-231
    1534 CGPG8933.pep MACPF 126-322
    1535 CGPG8935.pep Pkinase 33-324
    1536 CGPG8938.pep Pkinase 71-348
    1537 CGPG8944.pep PH 31-134
    1538 CGPG895.pep DUF231 251-427
    1540 CGPG8961.pep Dus 59-392
    1541 CGPG8963.pep Pkinase 319-612
    1542 CGPG898.pep DUF231 276-448
    1543 CGPG8993.pep AAA::Rep_fac_C 44-226::237-326
    1544 CGPG8994.pep Brix 86-262
    1545 CGPG8995.pep Porin_3 54-326
    1546 CGPG90.pep MFS_1 68-427
    1547 CGPG900.pep DUF231 241-420
    1548 CGPG9002.pep CTP_transf_1 51-382
    1549 CGPG9009.pep Alg6_Alg8 22-514
    1550 CGPG9011.pep OTCace_N::OTCace 70-212::216-369
    1551 CGPG9012.pep FolB 16-129
    1552 CGPG9017.pep DMRL_synthase 70-213
    1553 CGPG9025.pep Glyco_transf_29 105-355
    1554 CGPG9026.pep Adap_comp_sub 160-428
    1555 CGPG9032.pep RNase_PH::RNase_PH_C 33-165::194-262
    1556 CGPG9040.pep Sec1 35-592
    1557 CGPG9044.pep Syntaxin::SNARE 57-163::256-318
    1558 CGPG9048.pep RNase_PH 15-135
    1559 CGPG9049.pep Glycos_transf_1 244-442
    1560 CGPG9058.pep RNA_pol_N 1-60
    1561 CGPG906.pep PPR::PPR 210-244::245-279
    1562 CGPG9070.pep ATP-synt_C::ATP-synt_C 20-85::104-169
    1564 CGPG9084.pep CH::EB1 15-116::209-255
    1566 CGPG9098.pep DUF6::DUF6 32-165::208-337
    1567 CGPG9099.pep Rick_17 kDa_Anti 66-110
    1568 CGPG9110.pep RALF 53-118
    1569 CGPG9119.pep PTR2 115-504
    1570 CGPG9125.pep ThiF 98-233
    1571 CGPG913.pep PPR::PPR::PPR::PPR::PPR::PPR 86-120::188-222
    ::223-257::289-323
    ::325-358::361-395
    1574 CGPG9164.pep DHBP_synthase::GTP_cyclohydro2 5-202::207-377
    1575 CGPG9172.pep Sec61_beta 32-77
    1577 CGPG9185.pep DUF423 10-115
    1578 CGPG9187.pep Pkinase 12-263
    1579 CGPG9190.pep DREPP 2-203
    1580 CGPG9193.pep GATase::GMP_synt_C 11-196::432-524
    1581 CGPG9195.pep DUF1279 91-193
    1582 CGPG9203.pep Na_H_Exchanger::TrkA_C 13-391::418-486
    1583 CGPG9209.pep GATase::GMP_synt_C 9-197::423-515
    1585 CGPG9210.pep Na_H_Exchanger::TrkA_N 10-376::402-517
    1586 CGPG9211.pep NTP_transferase::MannoseP_isomer 7-296::307-473
    1587 CGPG9212.pep ATP-synt_ab_N::ATP-synt_ab 22-87::143-353
    1588 CGPG9216.pep DHBP_synthase::GTP_cyclohydro2 10-206::211-379
    1589 CGPG9226.pep Carboxyl_trans 40-541
    1590 CGPG9252.pep CDC48_N::AAA::AAA 28-114::245-429
    ::518-705
    1592 CGPG9289.pep LSM 10-75
    1593 CGPG9298.pep p450 41-516
    1594 CGPG9299.pep ThiF 82-227
    1597 CGPG9316.pep ATP-grasp_2::Ligase_CoA 34-242::285-421
    1598 CGPG9317.pep DUF163 43-196
    1599 CGPG9318.pep Aldo_ket_red 20-285
    1600 CGPG9324.pep Pkinase 158-706
    1601 CGPG9357.pep Raffinose_syn 7-757
    1602 CGPG965.pep Hexapep::Hexapep::Hexapep::Hexapep 70-87::119-136
    ::142-159::160-177
    1603 CGPG970.pep NPH3 206-441
    1604 CGPG982.pep p450 29-495
    1605 CGPG994.pep adh_short 50-218
    1606 CGPG996.pep DUF866 1-167
  • TABLE 21
    PEP Seq
    ID No. Construct ID Pfam domain name Begin Stop score E-value
    806 CGPG1023.pep Na_Ca_ex 104 255 94.2 4.10E−25
    806 CGPG1023.pep Na_Ca_ex 299 432 128.4 2.10E−35
    807 CGPG1038.pep DUF1475 1 256 709.5 2.40E−210
    812 CGPG1113.pep DUF1350 49 370 64.5 3.50E−16
    814 CGPG1163.pep DSPc 49 182 103 9.00E−28
    817 CGPG1205.pep Arm 94 134 37.2 5.90E−08
    817 CGPG1205.pep Arm 135 175 32.9 1.10E−06
    817 CGPG1205.pep Arm 176 216 31.7 2.60E−06
    817 CGPG1205.pep Arm 258 298 18.8 0.02
    818 CGPG1207.pep NifU_N 26 105 78.3 2.60E−20
    820 CGPG1223.pep ATP_bind_1 7 250 425.9 5.70E−125
    821 CGPG1250.pep DUF822 12 160 323.6 3.70E−94
    824 CGPG1319.pep DUF599 10 233 464.2 1.70E−136
    826 CGPG1329.pep Cullin 29 631 966.3 1.20E−287
    827 CGPG133.pep Cyclin_N 168 293 232.6 9.20E−67
    827 CGPG133.pep Cyclin_C 295 422 170.5 4.50E−48
    828 CGPG1332.pep Cullin 12 646 709.1 3.20E−210
    829 CGPG1343.pep LRR_1 389 412 9.2 6
    830 CGPG1348.pep Lectin_legB 27 248 295 1.40E−85
    830 CGPG1348.pep Pkinase 334 604 170.2 5.30E−48
    830 CGPG1348.pep Pkinase_Tyr 334 604 134.8 2.50E−37
    831 CGPG1349.pep B_lectin 65 171 95.8 1.30E−25
    831 CGPG1349.pep S_locus_glycop 180 312 105 2.40E−28
    831 CGPG1349.pep PAN_1 327 404 38.5 2.40E−08
    831 CGPG1349.pep Pkinase 484 731 167.1 4.70E−47
    831 CGPG1349.pep Pkinase_Tyr 484 731 89.6 1.00E−23
    832 CGPG1373.pep Pkinase 12 291 356.7 3.80E−104
    833 CGPG1377.pep Pkinase 4 258 247.3 3.30E−71
    834 CGPG1412.pep TPP_enzyme_N 45 221 286.5 5.40E−83
    834 CGPG1412.pep TPP_enzyme_M 243 376 82.9 1.00E−21
    834 CGPG1412.pep TPP_enzyme_C 431 578 35 3.50E−09
    835 CGPG1421.pep Biotin_lipoyl 76 149 85.1 2.30E−22
    835 CGPG1421.pep E3_binding 180 218 58.5 2.20E−14
    835 CGPG1421.pep 2-oxoacid_dh 249 480 358.5 1.10E−104
    836 CGPG1426.pep Aminotran_1_2 48 432 525 8.50E−155
    837 CGPG1433.pep HI0933_like 44 365 −247.2 0.002
    837 CGPG1433.pep GIDA 45 369 −206 0.00022
    837 CGPG1433.pep Pyr_redox_2 45 359 241.5 1.90E−69
    837 CGPG1433.pep Pyr_redox 216 313 115.7 1.40E−31
    837 CGPG1433.pep Pyr_redox_dim 388 497 213.1 6.50E−61
    838 CGPG1453.pep malic 171 360 412.3 7.10E−121
    838 CGPG1453.pep Malic_M 362 615 468.8 7.10E−138
    839 CGPG1454.pep Ribul_P_3_epim 7 207 331.5 1.50E−96
    840 CGPG1463.pep Alpha-amylase 26 361 224.3 2.80E−64
    840 CGPG1463.pep Alpha-amyl_C2 362 422 132.9 9.40E−37
    841 CGPG1464.pep Glycolytic 11 358 852.5 2.20E−253
    842 CGPG1471.pep IF4E 1 198 287.7 2.20E−83
    843 CGPG1481.pep Pkinase 4 260 292.7 7.40E−85
    844 CGPG1499.pep PPDK_N 85 445 654.8 6.90E−194
    844 CGPG1499.pep PEP-utilizers 496 586 165.9 1.10E−46
    844 CGPG1499.pep PEP-utilizers_C 598 955 688.7 4.30E−204
    845 CGPG150.pep p450 30 507 128 2.80E−35
    846 CGPG1536.pep CRAL_TRIO_N 73 142 46.4 1.00E−10
    846 CGPG1536.pep CRAL_TRIO 159 345 145.1 2.00E−40
    847 CGPG1539.pep UPF0139 8 107 215.9 9.60E−62
    848 CGPG155.pep GlutR_N 100 251 288.2 1.70E−83
    848 CGPG155.pep Shikimate_DH 255 407 208.3 1.80E−59
    848 CGPG155.pep GlutR_dimer 420 526 180.6 4.10E−51
    849 CGPG1583.pep PLAC8 88 187 176.8 5.40E−50
    850 CGPG1588.pep PLAC8 75 214 156.3 8.30E−44
    851 CGPG16.pep MIP 14 235 396.7 3.60E−116
    852 CGPG1609.pep MMR_HSR1 54 190 118.9 1.50E−32
    852 CGPG1609.pep DUF933 337 420 205.4 1.40E−58
    853 CGPG1629.pep WD40 262 301 31.1 4.20E−06
    853 CGPG1629.pep WD40 307 346 36 1.30E−07
    853 CGPG1629.pep WD40 356 395 41.3 3.50E−09
    854 CGPG1637.pep DUF220 163 262 148.5 1.80E−41
    855 CGPG1653.pep TBC 200 415 −15 1.60E−06
    856 CGPG1658.pep Nodulin-like 14 260 516.4 3.30E−152
    857 CGPG1663.pep MFS_1 22 387 26.3 0.00011
    857 CGPG1663.pep BT1 30 441 633.5 1.90E−187
    858 CGPG1682.pep OPT 62 685 688.8 4.20E−204
    859 CGPG1701.pep Glyco_transf_8 76 299 13.5 1.90E−07
    861 CGPG1724.pep Per1 63 334 669.6 2.50E−198
    862 CGPG1726.pep DUF607 111 291 388.6 9.80E−114
    863 CGPG1736.pep Usp 1 148 64.9 2.70E−16
    864 CGPG1741.pep mTERF 279 627 84.1 4.40E−22
    865 CGPG1783.pep PB1 42 132 85 2.40E−22
    866 CGPG1790.pep PB1 59 153 109.6 9.20E−30
    868 CGPG1845.pep TFIID-18 kDa 29 119 145.5 1.50E−40
    869 CGPG1855.pep CAF1 3 227 330.9 2.30E−96
    870 CGPG1870.pep Pkinase 406 572 74.8 2.90E−19
    871 CGPG1879.pep Pkinase 21 277 357.5 2.30E−104
    871 CGPG1879.pep Pkinase_Tyr 21 275 88.2 2.60E−23
    871 CGPG1879.pep NAF 303 364 98.7 1.80E−26
    872 CGPG1886.pep Pkinase 26 325 337.3 2.70E−98
    873 CGPG1903.pep F-box 320 367 41 4.30E−09
    874 CGPG1905.pep F-box 4 51 41.7 2.60E−09
    874 CGPG1905.pep Kelch_2 104 150 27.4 5.30E−05
    874 CGPG1905.pep Kelch_2 255 306 41.6 2.80E−09
    875 CGPG1914.pep F-box 42 89 39.8 9.50E−09
    875 CGPG1914.pep Kelch_2 170 215 26.3 0.00011
    875 CGPG1914.pep Kelch_1 170 215 52.2 1.80E−12
    875 CGPG1914.pep Kelch_2 217 266 31.3 3.60E−06
    875 CGPG1914.pep Kelch_1 217 266 59.1 1.50E−14
    876 CGPG193.pep WD40 167 205 28.5 2.40E−05
    876 CGPG193.pep WD40 268 307 24.4 0.00041
    876 CGPG193.pep WD40 318 355 25.1 0.00026
    876 CGPG193.pep WD40 363 401 39.3 1.40E−08
    877 CGPG1939.pep F-box 66 113 36.2 1.20E−07
    877 CGPG1939.pep WD40 152 190 26.2 0.00012
    877 CGPG1939.pep WD40 247 283 33.6 7.10E−07
    877 CGPG1939.pep WD40 325 364 22.9 0.0012
    878 CGPG1949.pep YDG_SRA 360 519 403.5 3.10E−118
    878 CGPG1949.pep Pre-SET 543 639 156.7 6.30E−44
    878 CGPG1949.pep SET 641 771 178.4 1.80E−50
    879 CGPG1959.pep PHD 34 82 54.3 4.30E−13
    879 CGPG1959.pep SET 208 344 105.1 2.20E−28
    880 CGPG197.pep p450 40 481 169.2 1.10E−47
    882 CGPG1981.pep MT-A70 476 636 321.4 1.70E−93
    883 CGPG1999.pep Nfu_N 78 193 145 2.10E−40
    883 CGPG1999.pep NifU 221 291 121.1 3.30E−33
    884 CGPG2.pep p450 71 531 324.3 2.20E−94
    885 CGPG2006.pep RCC1 32 82 31.3 3.60E−06
    885 CGPG2006.pep RCC1 138 187 40 8.30E−09
    885 CGPG2006.pep RCC1 190 239 33 1.10E−06
    885 CGPG2006.pep RCC1 294 343 42.8 1.20E−09
    886 CGPG2010.pep Aminotran_5 74 448 681.1 8.90E−202
    886 CGPG2010.pep Beta_elim_lyase 77 389 −107.3 0.0021
    887 CGPG2011.pep X8 128 209 153.5 5.60E−43
    888 CGPG2014.pep Pkinase 28 282 339.2 7.00E−99
    888 CGPG2014.pep NAF 341 398 86.9 6.70E−23
    889 CGPG2023.pep Zip 48 352 371 1.90E−108
    890 CGPG2026.pep Pkinase 38 324 328.9 9.40E−96
    892 CGPG2064.pep Cenp-O 123 201 107.6 3.80E−29
    894 CGPG2077.pep NAC 88 147 81.6 2.50E−21
    894 CGPG2077.pep UBA 195 232 29.8 1.00E−05
    895 CGPG2095.pep AARP2CN 228 309 121.6 2.30E−33
    895 CGPG2095.pep DUF663 483 780 615.9 3.60E−182
    896 CGPG2105.pep Pkinase 102 404 274.6 2.00E−79
    896 CGPG2105.pep Pkinase_C 422 471 39.6 1.10E−08
    897 CGPG2108.pep Response_reg 64 180 86.8 6.80E−23
    897 CGPG2108.pep CCT 442 484 65 2.50E−16
    898 CGPG2111.pep polyprenyl_synt 74 324 156.4 7.70E−44
    899 CGPG2124.pep UIM 139 156 20.6 0.0057
    899 CGPG2124.pep efhand 220 248 35.7 1.70E−07
    900 CGPG2125.pep Glutaredoxin 44 110 40.7 5.10E−09
    903 CGPG2134.pep ATP-synt_G 8 122 170.2 5.30E−48
    904 CGPG2139.pep DUF1517 94 391 709.7 2.10E−210
    905 CGPG2140.pep PhzC-PhzF 6 282 506.2 3.90E−149
    907 CGPG2163.pep Cupin_1 5 157 105.9 1.20E−28
    907 CGPG2163.pep Cupin_1 190 339 83.5 6.80E−22
    908 CGPG2165.pep CIpS 76 152 131.5 2.40E−36
    910 CGPG2218.pep Spc97_Spc98 67 555 750.6 1.10E−222
    912 CGPG2225.pep EMP24_GP25L 52 116 55.6 1.80E−13
    913 CGPG2229.pep Subtilisin_N 30 106 89.6 9.70E−24
    913 CGPG2229.pep Peptidase_S8 119 600 52.4 1.60E−12
    913 CGPG2229.pep PA 362 461 112 1.80E−30
    915 CGPG2254.pep Ribosomal_L7Ae 20 114 110.3 5.80E−30
    916 CGPG2268.pep CBS 66 188 107.9 3.00E−29
    917 CGPG227.pep p450 37 494 364.2 2.20E−106
    918 CGPG2312.pep UPF0061 75 571 361.8 1.20E−105
    919 CGPG2315.pep SIP1 286 514 516.5 3.10E−152
    920 CGPG2316.pep PTPA 98 396 696.6 1.80E−206
    922 CGPG235.pep p450 74 510 203.2 6.10E−58
    923 CGPG2358.pep Branch 54 278 425.3 8.70E−125
    925 CGPG2361.pep Metallophos 9 231 49.7 1.00E−11
    926 CGPG2365.pep Epimerase 3 211 −25.8 3.00E−05
    927 CGPG2372.pep Pribosyltran 29 169 147.9 2.70E−41
    928 CGPG2374.pep Aminotran_5 8 370 −92.6 4.20E−07
    929 CGPG2377.pep DAO 69 466 243.4 5.00E−70
    929 CGPG2377.pep FAD_binding_2 69 457 −124 0.0024
    930 CGPG2387.pep H_PPase 1 239 −188.8 6.80E−17
    931 CGPG2389.pep Carb_anhydrase 52 275 117.4 4.30E−32
    932 CGPG2395.pep AA_permease 89 526 −4.2 1.30E−05
    934 CGPG2409.pep DUF862 17 154 252.5 8.90E−73
    935 CGPG2410.pep GST_N 5 79 68.9 1.70E−17
    935 CGPG2410.pep GST_C 101 204 30.1 8.30E−06
    937 CGPG2416.pep Hin1 97 235 198.2 2.10E−56
    938 CGPG2441.pep Sina 5 205 188 2.30E−53
    939 CGPG2450.pep adh_short 112 282 −38.2 0.004
    939 CGPG2450.pep Epimerase 114 371 191.5 2.10E−54
    939 CGPG2450.pep 3Beta_HSD 115 402 −72.8 1.60E−05
    939 CGPG2450.pep NAD_binding_4 116 342 −62.5 9.90E−05
    940 CGPG2451.pep RALF 57 129 123.9 4.80E−34
    941 CGPG2492.pep Pribosyltran 80 216 144.1 3.80E−40
    942 CGPG2495.pep ADH_N 25 134 143.2 7.40E−40
    942 CGPG2495.pep ADH_zinc_N 165 307 138 2.60E−38
    943 CGPG2506.pep PfkB 5 289 140.3 5.30E−39
    944 CGPG2515.pep TIM 5 244 446 5.10E−131
    945 CGPG2531.pep Redoxin 4 160 43.7 6.60E−10
    945 CGPG2531.pep AhpC-TSA 5 138 178.9 1.30E−50
    946 CGPG2581.pep SelR 12 133 289.3 7.50E−84
    947 CGPG2584.pep zf-Tim10_DDP 22 86 115.1 2.00E−31
    948 CGPG2592.pep TFIID_30kDa 30 80 135.9 1.10E−37
    949 CGPG2612.pep RRM_1 65 132 43 1.10E−09
    949 CGPG2612.pep RRM_1 150 225 83.9 5.30E−22
    949 CGPG2612.pep RRM_1 275 343 53.1 9.50E−13
    950 CGPG2660.pep B3 17 115 77.8 3.60E−20
    950 CGPG2660.pep B3 211 301 61.4 3.10E−15
    951 CGPG2663.pep NTF2 15 131 168.8 1.50E−47
    951 CGPG2663.pep RRM_1 295 365 45.3 2.10E−10
    952 CGPG2679.pep ACBP 104 190 54.4 3.80E−13
    952 CGPG2679.pep Ank 265 297 49.7 1.00E−11
    952 CGPG2679.pep Ank 298 330 35.5 2.00E−07
    953 CGPG2696.pep zf-C3HC4 177 218 43.9 5.70E−10
    954 CGPG2772.pep Mov34 6 136 111.9 1.90E−30
    955 CGPG2773.pep Asp 161 498 −73.6 3.00E−09
    956 CGPG281.pep TLC 91 574 1046.6 0
    957 CGPG2846.pep Aldo_ket_red 49 365 248 2.00E−71
    958 CGPG2852.pep Glyoxalase 9 132 37.4 5.20E−08
    960 CGPG2870.pep zf-CCCH 111 137 49.3 1.30E−11
    960 CGPG2870.pep zf-CCCH 159 185 34.6 3.60E−07
    960 CGPG2870.pep zf-CCCH 205 231 49.5 1.20E−11
    960 CGPG2870.pep zf-CCCH 347 373 29.9 9.60E−06
    960 CGPG2870.pep zf-CCCH 393 419 42.5 1.50E−09
    961 CGPG2877.pep LAG1 96 307 430.8 1.90E−126
    962 CGPG289.pep Cellulose_synt 243 1060 2161.1 0
    963 CGPG2924.pep zf-C3HC4 138 179 33.3 9.10E−07
    964 CGPG2947.pep Acetyltransf_1 265 343 50.6 5.60E−12
    964 CGPG2947.pep Bromodomain 460 548 122.2 1.50E−33
    965 CGPG2963.pep C1_3 80 108 35.7 1.60E−07
    965 CGPG2963.pep C1_2 81 108 37.1 6.10E−08
    965 CGPG2963.pep C1_1 122 172 14.3 0.00058
    965 CGPG2963.pep C1_3 136 164 36.3 1.10E−07
    965 CGPG2963.pep C1_3 194 223 27.2 6.10E−05
    965 CGPG2963.pep C1_2 305 335 40.5 5.90E−09
    965 CGPG2963.pep C1_3 391 420 40.1 8.20E−09
    965 CGPG2963.pep C1_3 494 522 25.6 0.00018
    965 CGPG2963.pep C1_3 551 581 27.5 5.00E−05
    965 CGPG2963.pep C1_2 552 581 47.9 3.50E−11
    966 CGPG2987.pep SRF-TF 11 66 24.4 0.00041
    968 CGPG3045.pep Pkinase 82 356 192 1.50E−54
    968 CGPG3045.pep Pkinase_Tyr 82 356 254 3.20E−73
    969 CGPG3046.pep AAA 121 305 245.7 1.00E−70
    970 CGPG3060.pep p450 67 528 268 1.90E−77
    971 CGPG3075.pep Auxin_inducible 7 106 121 3.50E−33
    972 CGPG310.pep Cyclin_N 18 143 31.8 1.80E−07
    973 CGPG3103.pep PPR 14 48 10.8 0.4
    973 CGPG3103.pep PPR 49 83 37.5 4.80E−08
    973 CGPG3103.pep PPR 84 118 38.8 1.90E−08
    973 CGPG3103.pep PPR 119 153 11.8 0.31
    973 CGPG3103.pep PPR 155 188 27.6 4.50E−05
    973 CGPG3103.pep PPR 189 223 34.8 3.20E−07
    973 CGPG3103.pep PPR 224 258 36.8 7.80E−08
    973 CGPG3103.pep PPR 259 293 7.7 0.95
    973 CGPG3103.pep PPR 295 329 39.7 1.10E−08
    973 CGPG3103.pep PPR 330 364 12.6 0.25
    973 CGPG3103.pep PPR 365 398 30.4 6.70E−06
    974 CGPG315.pep p450 29 491 346.8 3.80E−101
    976 CGPG3189.pep RRM_1 115 186 101.9 2.00E−27
    976 CGPG3189.pep RRM_1 209 280 104.9 2.40E−28
    977 CGPG3204.pep KH_1 45 104 53.4 7.60E−13
    977 CGPG3204.pep KH_1 151 221 58.6 2.20E−14
    977 CGPG3204.pep KH_1 318 381 44.6 3.60E−10
    977 CGPG3204.pep KH_2 318 365 11.3 0.019
    977 CGPG3204.pep KH_1 400 467 63.4 7.50E−16
    977 CGPG3204.pep KH_1 575 637 53.3 8.70E−13
    978 CGPG3208.pep MATH 26 153 47.1 6.00E−11
    978 CGPG3208.pep MATH 180 302 18.3 0.0015
    979 CGPG3219.pep 2OG-FeII_Oxy 220 320 161.1 2.90E−45
    980 CGPG3233.pep PPR 160 194 21.8 0.0026
    980 CGPG3233.pep PPR 195 229 9.6 0.56
    980 CGPG3233.pep PPR 231 265 24.1 0.00052
    980 CGPG3233.pep PPR 266 300 40.7 5.10E−09
    980 CGPG3233.pep PPR 301 335 44 5.30E−10
    980 CGPG3233.pep PPR 336 370 45.3 2.20E−10
    980 CGPG3233.pep PPR 371 405 44.7 3.30E−10
    980 CGPG3233.pep PPR 406 440 7.4 1
    981 CGPG3263.pep Tryp_alpha_amyl 28 104 36.6 8.90E−08
    982 CGPG3276.pep ECH 11 186 48.1 3.10E−11
    984 CGPG3282.pep Steroid_dh 117 268 65.5 1.80E−16
    985 CGPG3300.pep zf-CCHC 55 72 30.4 6.40E−06
    985 CGPG3300.pep zf-CCHC 74 91 26.8 7.80E−05
    985 CGPG3300.pep zf-CCHC 93 110 29.8 1.00E−05
    985 CGPG3300.pep zf-CCHC 112 129 27.3 5.70E−05
    985 CGPG3300.pep zf-CCHC 138 155 23.8 0.00038
    985 CGPG3300.pep zf-CCHC 157 174 24.9 0.00026
    985 CGPG3300.pep zf-CCHC 229 246 26.5 9.70E−05
    986 CGPG3318.pep Peptidase_C14 3 416 273.4 4.50E−79
    987 CGPG3319.pep AP2 28 79 61.2 3.40E−15
    988 CGPG3326.pep zf-C3HC4 259 299 36.8 7.90E−08
    989 CGPG333.pep PTS_2-RNA 48 239 409.9 3.80E−120
    990 CGPG3338.pep Alba 17 87 114.8 2.50E−31
    991 CGPG334.pep Mov34 20 128 65.2 2.20E−16
    992 CGPG3374.pep peroxidase 42 286 426.2 4.60E−125
    993 CGPG3402.pep Dimerisation 30 89 93.1 8.60E−25
    993 CGPG3402.pep Methyltransf_2 99 342 287.6 2.40E−83
    995 CGPG3413.pep WD40 168 207 41.5 3.10E−09
    995 CGPG3413.pep U3_snoRNA_C 377 523 212.3 1.10E−60
    996 CGPG3422.pep WD40 241 279 41.2 3.70E−09
    996 CGPG3422.pep WD40 387 425 35.3 2.20E−07
    996 CGPG3422.pep WD40 519 559 21.9 0.0024
    997 CGPG3436.pep DUF6 17 144 33.8 6.40E−07
    997 CGPG3436.pep DUF6 198 327 50.4 6.10E−12
    998 CGPG3539.pep Mito_carr 11 105 84.6 3.10E−22
    998 CGPG3539.pep Mito_carr 113 209 115.7 1.40E−31
    998 CGPG3539.pep Mito_carr 214 303 102.2 1.60E−27
    999 CGPG3550.pep FAE1_CUT1_RppA 81 370 700.9 9.60E−208
    999 CGPG3550.pep Chal_sti_synt_C 327 470 2.6 0.0011
    999 CGPG3550.pep ACP_syn_III_C 384 468 21.5 8.90E−08
    1000 CGPG3551.pep Pkinase 9 273 145.9 1.10E−40
    1001 CGPG3552.pep Aldedh 23 441 176.5 6.90E−50
    1002 CGPG3572.pep FA_hydroxylase 112 225 133.2 7.50E−37
    1004 CGPG3599.pep DUF579 51 289 588.5 6.70E−174
    1008 CGPG364.pep zf-C3HC4 97 137 51 4.30E−12
    1010 CGPG3679.pep malic 36 179 249.1 9.50E−72
    1010 CGPG3679.pep Malic_M 181 418 426.3 4.30E−125
    1010 CGPG3679.pep PTA_PTB 446 768 457.7 1.60E−134
    1011 CGPG3686.pep Gp_dh_N 2 150 334.5 1.80E−97
    1011 CGPG3686.pep Gp_dh_C 155 312 388.4 1.10E−113
    1012 CGPG3694.pep LRRNT_2 38 78 64.2 4.40E−16
    1012 CGPG3694.pep LRR_1 106 128 11.7 2.1
    1012 CGPG3694.pep LRR_1 130 152 14.2 0.48
    1012 CGPG3694.pep LRR_1 154 176 16.7 0.089
    1012 CGPG3694.pep LRR_1 178 201 11.7 2.1
    1012 CGPG3694.pep Pkinase 312 583 104.7 2.80E−28
    1012 CGPG3694.pep Pkinase_Tyr 312 583 110.8 4.20E−30
    1013 CGPG3696.pep MMR_HSR1 136 257 120.2 5.90E−33
    1014 CGPG3698.pep WD40 104 142 31.6 2.80E−06
    1014 CGPG3698.pep WD40 234 272 22.5 0.0016
    1015 CGPG3699.pep adh_short 19 187 111.6 2.30E−30
    1015 CGPG3699.pep KR 19 203 −54.2 0.00034
    1016 CGPG3702.pep SAM_2 227 293 48.9 1.80E−11
    1016 CGPG3702.pep SAM_1 228 291 52.7 1.30E−12
    1017 CGPG3703.pep ENOD93 25 103 190.1 5.50E−54
    1018 CGPG3707.pep Pkinase 42 333 296.2 6.30E−86
    1019 CGPG3710.pep VQ 118 148 45.7 1.60E−10
    1020 CGPG3730.pep DUF167 140 216 99.7 9.10E−27
    1021 CGPG3731.pep DUF616 194 508 769.9 1.60E−228
    1022 CGPG3734.pep PRK 46 233 177.1 4.40E−50
    1022 CGPG3734.pep Pribosyltran 280 425 5.8 0.00083
    1023 CGPG3745.pep RRM_1 386 455 66.7 7.80E−17
    1023 CGPG3745.pep RRM_1 481 553 49.6 1.10E−11
    1024 CGPG3764.pep Response_reg 20 145 67.1 5.90E−17
    1026 CGPG3851.pep SH3_1 284 338 42.4 1.60E−09
    1026 CGPG3851.pep SH3_2 285 338 30.1 8.10E−06
    1027 CGPG3911.pep Aldedh 104 587 526.9 2.20E−155
    1028 CGPG3948.pep NAP 50 295 467.9 1.30E−137
    1031 CGPG3996.pep Inositol_P 6 267 363.1 4.60E−106
    1032 CGPG4006.pep ENT 1 74 140.3 5.60E−39
    1033 CGPG4025.pep SQS_PSY 44 331 455.8 5.80E−134
    1034 CGPG4028.pep Transket_pyr 398 565 233 6.90E−67
    1034 CGPG4028.pep Transketolase_C 579 702 152.2 1.40E−42
    1035 CGPG403.pep Pkinase 78 336 354.1 2.40E−103
    1036 CGPG4041.pep DEAD 141 315 219 1.10E−62
    1036 CGPG4041.pep Helicase_C 386 462 120.8 4.10E−33
    1037 CGPG4078.pep GST_C 180 283 23.1 0.00038
    1038 CGPG4079.pep RRS1 1 178 271.1 2.30E−78
    1041 CGPG4104.pep LRRNT_2 30 67 33.1 1.00E−06
    1041 CGPG4104.pep LRR_1 95 117 11.4 2.3
    1041 CGPG4104.pep LRR_1 119 141 15.5 0.21
    1041 CGPG4104.pep LRR_1 143 165 12.1 1.8
    1041 CGPG4104.pep LRR_1 167 188 16.1 0.13
    1041 CGPG4104.pep Pkinase 367 633 99.2 1.30E−26
    1042 CGPG4127.pep Hydrolase 43 239 93.3 7.50E−25
    1043 CGPG4135.pep Pkinase 118 376 357.9 1.70E−104
    1043 CGPG4135.pep efhand 423 451 41.5 3.10E−09
    1043 CGPG4135.pep efhand 459 487 24.8 0.00033
    1043 CGPG4135.pep efhand 495 523 30.6 5.70E−06
    1043 CGPG4135.pep efhand 529 557 40.3 7.00E−09
    1044 CGPG4161.pep Methyltransf_11 56 159 48 3.30E−11
    1044 CGPG4161.pep Methyltransf_12 56 157 31.8 2.40E−06
    1045 CGPG4180.pep GHMP_kinases_N 152 219 64.2 4.40E−16
    1045 CGPG4180.pep GHMP_kinases_C 382 466 58.4 2.50E−14
    1046 CGPG4191.pep Bombesin 163 176 14.8 0.16
    1047 CGPG4199.pep Copine 117 265 295.3 1.20E−85
    1047 CGPG4199.pep zf-C3HC4 385 417 16.2 0.0013
    1048 CGPG4241.pep GASA 3 99 179.9 6.40E−51
    1049 CGPG427.pep Pkinase 8 262 210 5.80E−60
    1049 CGPG427.pep Pkinase_Tyr 8 262 248 2.10E−71
    1050 CGPG4273.pep dsrm 2 68 70 7.70E−18
    1050 CGPG4273.pep dsrm 88 153 66.9 6.90E−17
    1051 CGPG4301.pep 2OG-Fell_Oxy 151 253 97 6.00E−26
    1052 CGPG4303.pep Rhodanese 13 114 64.9 2.70E−16
    1053 CGPG4313.pep G6PD_N 94 273 322.4 8.50E−94
    1053 CGPG4313.pep G6PD_C 276 573 522.2 6.00E−154
    1054 CGPG4314.pep AWPM-19 15 156 335.5 9.50E−98
    1055 CGPG4329.pep AA_kinase 86 324 201.9 1.60E−57
    1056 CGPG4330.pep PALP 53 341 418.6 9.40E−123
    1057 CGPG4338.pep Proteasome 21 217 157.3 4.00E−44
    1058 CGPG4341.pep Mito_carr 51 134 78 3.10E−20
    1058 CGPG4341.pep Mito_carr 158 246 81.5 2.80E−21
    1058 CGPG4341.pep Mito_carr 252 343 82.8 1.10E−21
    1061 CGPG4386.pep GHMP_kinases_N 113 171 55.4 1.90E−13
    1061 CGPG4386.pep GHMP_kinases_C 245 338 29.5 1.20E−05
    1062 CGPG4394.pep p450 39 503 389.1 7.00E−114
    1063 CGPG4396.pep p450 39 504 355.6 8.20E−104
    1064 CGPG4400.pep p450 32 474 146.7 6.70E−41
    1065 CGPG4401.pep p450 47 511 383.1 4.60E−112
    1066 CGPG441.pep Chalcone 14 225 498.4 8.60E−147
    1067 CGPG4413.pep p450 32 547 286.5 5.20E−83
    1068 CGPG4427.pep p450 57 530 225.1 1.60E−64
    1069 CGPG4446.pep p450 43 504 275.6 1.00E−79
    1070 CGPG4448.pep p450 32 486 332.3 8.70E−97
    1071 CGPG4474.pep Band_7 33 212 136.8 5.90E−38
    1072 CGPG4482.pep peroxidase 47 291 314.4 2.10E−91
    1073 CGPG4511.pep VHS 36 166 58.2 2.80E−14
    1073 CGPG4511.pep GAT 227 315 18.1 2.80E−05
    1074 CGPG4517.pep Aldo_ket_red 5 292 460.6 2.10E−135
    1075 CGPG4551.pep XS 30 148 250.2 4.60E−72
    1075 CGPG4551.pep XH 418 557 251.6 1.70E−72
    1077 CGPG4567.pep SRF-TF 3 53 85.4 1.80E−22
    1078 CGPG4586.pep RRM_1 8 73 41.5 2.90E−09
    1079 CGPG4600.pep zf-CCCH 13 39 35.4 2.00E−07
    1079 CGPG4600.pep zf-CCCH 149 174 24.1 0.00053
    1080 CGPG4631.pep C1_3 87 115 40.8 4.80E−09
    1080 CGPG4631.pep C1_2 88 115 41.2 3.80E−09
    1080 CGPG4631.pep C1_3 208 237 39.4 1.30E−08
    1080 CGPG4631.pep C1_2 209 237 45.5 1.80E−10
    1080 CGPG4631.pep C1_3 264 292 48.3 2.70E−11
    1080 CGPG4631.pep C1_2 319 349 41.5 2.90E−09
    1080 CGPG4631.pep C1_3 404 433 55.4 1.90E−13
    1080 CGPG4631.pep C1_2 566 595 40.8 4.70E−09
    1081 CGPG4642.pep Pyridoxal_deC 63 412 126.5 7.90E−35
    1082 CGPG4645.pep Cu-oxidase_3 31 148 198.9 1.30E−56
    1082 CGPG4645.pep Cu-oxidase 157 325 222.3 1.10E−63
    1082 CGPG4645.pep Cu-oxidase_2 414 551 155.1 2.00E−43
    1083 CGPG4646.pep efhand_like 27 105 109.6 9.60E−30
    1083 CGPG4646.pep PI-PLC-X 108 251 143.6 5.60E−40
    1083 CGPG4646.pep PI-PLC-Y 332 450 93.9 5.20E−25
    1083 CGPG4646.pep C2 471 563 82.3 1.50E−21
    1084 CGPG4649.pep SMP 14 72 102 1.90E−27
    1084 CGPG4649.pep SMP 130 191 127.6 3.60E−35
    1084 CGPG4649.pep SMP 195 256 62.7 1.30E−15
    1085 CGPG4653.pep DUF1637 47 280 366.2 5.30E−107
    1087 CGPG4668.pep SYF2 140 306 301.7 1.50E−87
    1088 CGPG469.pep tRNA-synt_1c 213 518 428.8 7.70E−126
    1088 CGPG469.pep tRNA-synt_1c_C 520 697 229.4 8.00E−66
    1089 CGPG4708.pep Sulfate_transp 172 482 504.9 9.60E−149
    1089 CGPG4708.pep STAS 505 623 142.8 9.80E−40
    1090 CGPG4712.pep Mem_trans 9 565 715.3 4.30E−212
    1091 CGPG4714.pep DUF231 248 423 336.8 3.80E−98
    1092 CGPG4719.pep Response_reg 37 153 91.6 2.50E−24
    1092 CGPG4719.pep CCT 417 461 85 2.40E−22
    1093 CGPG473.pep Peptidase_M16 88 234 184 3.90E−52
    1093 CGPG473.pep Peptidase_M16_C 239 423 161.3 2.70E−45
    1094 CGPG4734.pep Auxin_inducible 19 119 55.4 1.90E−13
    1095 CGPG4736.pep Pribosyltran 225 358 139.9 7.20E−39
    1096 CGPG474.pep Pro_isomerase 6 172 426 5.20E−125
    1102 CGPG4850.pep PMEI 25 174 138.8 1.60E−38
    1103 CGPG4868.pep PsbW 1 133 333 5.40E−97
    1104 CGPG4871.pep Tryp_alpha_amyl 52 133 98.3 2.30E−26
    1105 CGPG488.pep Histone 19 92 110.5 5.00E−30
    1105 CGPG488.pep CBFD_NFYB_HMF 25 89 20.6 0.002
    1106 CGPG4908.pep WD40 16 54 22.1 0.002
    1106 CGPG4908.pep WD40 63 101 22.2 0.002
    1108 CGPG4921.pep WD40 202 241 26.8 7.90E−05
    1108 CGPG4921.pep WD40 253 291 41.3 3.40E−09
    1108 CGPG4921.pep WD40 295 333 33.5 7.40E−07
    1108 CGPG4921.pep WD40 337 375 47.3 5.20E−11
    1108 CGPG4921.pep WD40 472 510 25.7 0.00017
    1109 CGPG4954.pep LRRNT_2 33 72 38.6 2.20E−08
    1109 CGPG4954.pep LRR_1 76 98 9 6.5
    1109 CGPG4954.pep LRR_1 100 122 12.7 1.4
    1109 CGPG4954.pep LRR_1 124 145 8 10
    1110 CGPG4956.pep Asp 141 482 −61.6 5.90E−10
    1111 CGPG4959.pep adh_short 15 183 94.8 2.80E−25
    1111 CGPG4959.pep KR 16 200 −64.6 0.0014
    1112 CGPG4965.pep zf-A20 15 39 32.9 1.20E−06
    1112 CGPG4965.pep zf-AN1 114 154 64.5 3.50E−16
    1113 CGPG4970.pep GASA 1 108 225.3 1.40E−64
    1114 CGPG4980.pep U-box 73 147 95.4 1.80E−25
    1114 CGPG4980.pep Arm 246 287 20.1 0.0085
    1114 CGPG4980.pep Arm 288 328 22.4 0.0017
    1115 CGPG4982.pep F-box 2 49 42.8 1.20E−09
    1115 CGPG4982.pep FBA_1 209 387 313.8 3.20E−91
    1116 CGPG4985.pep CPSase_sm_chain 56 203 298.5 1.30E−86
    1116 CGPG4985.pep GATase 245 422 238.5 1.50E−68
    1117 CGPG4990.pep LRRNT_2 73 112 28.9 1.90E−05
    1117 CGPG4990.pep LRR_1 139 161 13.9 0.59
    1117 CGPG4990.pep LRR_1 163 183 13.6 0.73
    1117 CGPG4990.pep LRR_1 187 206 13.9 0.62
    1117 CGPG4990.pep LRR_1 210 232 8.2 9.1
    1117 CGPG4990.pep LRR_1 306 328 9.8 4.6
    1118 CGPG4991.pep PALP 164 473 254.7 2.00E−73
    1119 CGPG5007.pep adh_short 21 192 65.9 1.30E−16
    1119 CGPG5007.pep Epimerase 23 271 −42.4 0.00053
    1120 CGPG5015.pep adh_short 13 126 −22.3 0.00036
    1121 CGPG5026.pep adh_short 46 221 22.7 4.00E−07
    1122 CGPG5029.pep adh_short 80 252 70.7 4.90E−18
    1123 CGPG5046.pep LRRNT_2 30 70 51.2 3.60E−12
    1123 CGPG5046.pep LRR_1 99 121 9.2 6
    1123 CGPG5046.pep LRR_1 123 145 10.5 3.4
    1123 CGPG5046.pep LRR_1 147 169 15.8 0.16
    1123 CGPG5046.pep Pkinase_Tyr 306 573 109.4 1.10E−29
    1123 CGPG5046.pep Pkinase 306 573 145.6 1.40E−40
    1124 CGPG508.pep Na_sulph_symp 93 563 619 4.30E−183
    1125 CGPG5103.pep C2 9 95 64.8 3.00E−16
    1126 CGPG511.pep Rho_GDI 22 222 43.8 6.70E−12
    1127 CGPG5121.pep efhand_like 30 113 41.4 3.20E−09
    1127 CGPG5121.pep PI-PLC-X 116 258 140.7 4.20E−39
    1127 CGPG5121.pep PI-PLC-Y 331 449 88.6 2.00E−23
    1127 CGPG5121.pep C2 470 562 81.3 3.00E−21
    1128 CGPG5126.pep peroxidase 54 303 312 1.10E−90
    1129 CGPG5136.pep p450 35 500 88.4 2.30E−23
    1130 CGPG5146.pep p450 45 501 209 1.10E−59
    1131 CGPG5149.pep p450 31 478 306.7 4.40E−89
    1132 CGPG5181.pep Pkinase 278 540 112.7 1.10E−30
    1133 CGPG52.pep Sugar_tr 32 472 −75.6 5.00E−06
    1134 CGPG5206.pep UDPG_MGDP_dh_N 2 200 331.6 1.40E−96
    1134 CGPG5206.pep UDPG_MGDP_dh 209 306 189.1 1.10E−53
    1134 CGPG5206.pep UDPG_MGDP_dh_C 328 452 183.7 4.70E−52
    1136 CGPG5232.pep Pkinase 71 328 295.9 8.10E−86
    1137 CGPG5239.pep Copine 136 284 331.7 1.30E−96
    1138 CGPG5246.pep ABC_tran 94 285 132.8 9.70E−37
    1138 CGPG5246.pep ABC_tran 406 571 146.2 9.10E−41
    1139 CGPG525.pep CDP-OH_P_transf 138 277 132.1 1.60E−36
    1140 CGPG5268.pep CDC50 65 368 681.3 7.50E−202
    1141 CGPG5272.pep AA_permease 153 621 569.2 4.10E−168
    1142 CGPG5333.pep MFS_1 55 468 76 1.30E−19
    1142 CGPG5333.pep Sugar_tr 89 515 21.1 8.20E−10
    1143 CGPG5338.pep RRM_1 8 77 90.6 5.10E−24
    1143 CGPG5338.pep RRM_1 108 178 82.6 1.30E−21
    1144 CGPG5341.pep F-box 33 79 31.7 2.60E−06
    1145 CGPG5369.pep AA_kinase 83 366 213.4 5.30E−61
    1145 CGPG5369.pep ACT 400 469 20.9 0.0047
    1145 CGPG5369.pep ACT 477 539 9.7 0.71
    1146 CGPG5372.pep SBF 142 322 125.7 1.30E−34
    1147 CGPG5380.pep Tyr-DNA_phospho 137 581 1043.5 0
    1148 CGPG5386.pep MOSC_N 4 132 245 1.70E−70
    1148 CGPG5386.pep MOSC 138 296 66.5 8.80E−17
    1149 CGPG5396.pep PALP 9 297 469.3 5.00E−138
    1150 CGPG5397.pep PDT 128 307 347.9 1.70E−101
    1151 CGPG5421.pep Pre-SET 119 267 14.7 2.20E−05
    1151 CGPG5421.pep SET 269 414 151.3 2.60E−42
    1152 CGPG5433.pep MtN3_slv 10 98 144.3 3.30E−40
    1152 CGPG5433.pep MtN3_slv 132 218 145.4 1.50E−40
    1153 CGPG5439.pep LANC_like 69 410 459.8 3.60E−135
    1154 CGPG5453.pep Mito_carr 14 116 102 1.80E−27
    1154 CGPG5453.pep Mito_carr 125 215 98.8 1.60E−26
    1154 CGPG5453.pep Mito_carr 233 334 104 4.60E−28
    1155 CGPG5456.pep Mito_carr 78 175 128.9 1.50E−35
    1155 CGPG5456.pep Mito_carr 183 279 100.4 5.50E−27
    1155 CGPG5456.pep Mito_carr 283 373 91.5 2.70E−24
    1156 CGPG5483.pep PP2C 66 369 92.8 1.10E−24
    1157 CGPG5492.pep FAE1_CUT1_RppA 61 358 683.7 1.40E−202
    1157 CGPG5492.pep Chal_sti_synt_C 312 458 −1.1 0.0023
    1157 CGPG5492.pep ACP_syn_III_C 372 456 4.3 5.30E−06
    1158 CGPG5508.pep RCC1 310 359 23.9 0.00059
    1158 CGPG5508.pep RCC1 413 462 39 1.70E−08
    1158 CGPG5508.pep RCC1 478 526 32.5 1.50E−06
    1158 CGPG5508.pep RCC1 582 630 28.9 1.80E−05
    1158 CGPG5508.pep FYVE 633 701 44.7 3.30E−10
    1158 CGPG5508.pep DZC 967 1002 74 4.80E−19
    1159 CGPG5520.pep TFIID-31 kDa 19 152 319.5 6.10E−93
    1160 CGPG5525.pep PRMT5 187 679 1145.5 0
    1161 CGPG5526.pep Pkinase 8 295 335.7 8.20E−98
    1162 CGPG5530.pep Response_reg 504 644 85.4 1.80E−22
    1163 CGPG5534.pep Y_phosphatase2 3 169 331.1 2.00E−96
    1164 CGPG5537.pep TBP 62 147 136.9 5.90E−38
    1164 CGPG5537.pep TBP 152 238 157.1 4.70E−44
    1165 CGPG5545.pep CBS 35 175 26.9 7.50E−05
    1165 CGPG5545.pep CBS 193 318 80.7 4.60E−21
    1166 CGPG555.pep PALP 104 396 325.8 7.90E−95
    1166 CGPG555.pep Thr_dehydrat_C 409 498 105.4 1.70E−28
    1166 CGPG555.pep Thr_dehydrat_C 504 591 126.4 8.20E−35
    1167 CGPG5558.pep Cyclin_N 212 337 208.5 1.60E−59
    1167 CGPG5558.pep Cyclin_C 339 458 141 3.30E−39
    1168 CGPG5559.pep Suc_Fer-like 69 311 370.5 2.70E−108
    1169 CGPG5562.pep Suc_Fer-like 59 308 60.7 4.90E−15
    1170 CGPG5592.pep Rho_GDI 35 239 71.2 3.40E−18
    1171 CGPG5625.pep LRR_1 433 455 20.5 0.0061
    1171 CGPG5625.pep LRR_1 457 476 11.7 2.1
    1171 CGPG5625.pep Pkinase 586 854 138.6 1.80E−38
    1171 CGPG5625.pep Pkinase_Tyr 587 854 123.3 7.00E−34
    1172 CGPG5631.pep WAK 171 270 186.4 7.00E−53
    1172 CGPG5631.pep Pkinase_Tyr 390 660 146.8 5.90E−41
    1172 CGPG5631.pep Pkinase 390 658 159.5 9.00E−45
    1173 CGPG5632.pep Aldedh 29 491 831.6 4.30E−247
    1174 CGPG5636.pep Aldedh 15 476 794.5 6.10E−236
    1175 CGPG5637.pep Aldedh 32 493 925.9 1.70E−275
    1176 CGPG564.pep Aminotran_3 80 413 293.8 3.30E−85
    1177 CGPG5641.pep Aldedh 14 472 720.7 1.10E−213
    1178 CGPG5650.pep Aminotran_3 32 374 476.5 3.50E−140
    1179 CGPG5653.pep Aminotran_1_2 32 383 268.2 1.70E−77
    1180 CGPG5657.pep Aldedh 15 474 701.6 5.70E−208
    1181 CGPG5671.pep Gp_dh_N 3 151 356.5 4.40E−104
    1181 CGPG5671.pep Gp_dh_C 156 313 350.1 3.90E−102
    1182 CGPG5672.pep Glutaminase 24 309 615.7 4.20E−182
    1183 CGPG5677.pep PGAM 4 165 177.7 3.10E−50
    1184 CGPG5678.pep Aminotran_1_2 35 385 204 3.60E−58
    1185 CGPG5679.pep TIM 7 248 398.9 8.00E−117
    1186 CGPG5682.pep Aminotran_3 31 384 432.3 7.00E−127
    1187 CGPG5691.pep PK 5 350 699.4 2.60E−207
    1187 CGPG5691.pep PK_C 362 478 198.7 1.40E−56
    1188 CGPG5699.pep Gp_dh_N 3 155 274 3.00E−79
    1188 CGPG5699.pep Gp_dh_C 160 316 231.1 2.60E−66
    1189 CGPG5705.pep NDK 3 137 354.1 2.40E−103
    1190 CGPG5722.pep Pyrophosphatase 17 175 197.9 2.50E−56
    1191 CGPG5734.pep Cyclin_N 232 357 208.7 1.40E−59
    1191 CGPG5734.pep Cyclin_C 359 478 150 6.70E−42
    1192 CGPG5736.pep PP2C 22 280 398.6 9.20E−117
    1193 CGPG5744.pep CDC50 63 365 697.3 1.20E−206
    1194 CGPG5747.pep Pkinase 23 318 294 2.90E−85
    1195 CGPG5748.pep NAD_Gly3P_dh_N 84 259 271 2.50E−78
    1195 CGPG5748.pep NAD_Gly3P_dh_C 282 432 282.8 6.90E−82
    1198 CGPG577.pep Thioredoxin 7 111 138.6 1.70E−38
    1199 CGPG5780.pep AA_permease 68 517 −83.3 0.0017
    1200 CGPG5793.pep AA_permease 285 815 226.5 5.90E−65
    1201 CGPG5795.pep Sugar_tr 123 565 30.1 3.70E−10
    1202 CGPG5796.pep Sugar_tr 43 466 340.9 2.30E−99
    1202 CGPG5796.pep MFS_1 47 417 74.4 3.70E−19
    1203 CGPG5800.pep AA_permease 86 546 489 5.90E−144
    1204 CGPG5812.pep Pkinase 22 273 334.2 2.30E−97
    1204 CGPG5812.pep Pkinase_Tyr 22 271 85.2 2.10E−22
    1205 CGPG5815.pep Pkinase 9 272 136.6 6.90E−38
    1206 CGPG5838.pep Pkinase 1 264 137.8 3.10E−38
    1207 CGPG5844.pep Pkinase 78 351 159.7 7.80E−45
    1207 CGPG5844.pep Pkinase_Tyr 78 351 122.7 1.10E−33
    1208 CGPG5846.pep Pkinase_Tyr 92 376 128.5 2.00E−35
    1208 CGPG5846.pep Pkinase 99 376 136.1 9.90E−38
    1209 CGPG5851.pep Pkinase_Tyr 121 401 138.2 2.30E−38
    1209 CGPG5851.pep Pkinase 121 401 139.5 9.70E−39
    1210 CGPG5857.pep Pkinase 19 273 159.1 1.20E−44
    1211 CGPG5862.pep Pkinase 181 447 99.8 8.50E−27
    1211 CGPG5862.pep Pkinase_Tyr 181 447 95.5 1.70E−25
    1212 CGPG5863.pep Pkinase 52 330 86.5 8.60E−23
    1213 CGPG5867.pep Pkinase_Tyr 142 423 94.1 4.50E−25
    1213 CGPG5867.pep Pkinase 142 423 104 4.70E−28
    1214 CGPG5872.pep Pkinase_Tyr 18 288 125.8 1.20E−34
    1214 CGPG5872.pep Pkinase 18 288 153 7.90E−43
    1215 CGPG5913.pep ADH_N 28 109 95.4 1.80E−25
    1215 CGPG5913.pep ADH_zinc_N 140 284 151 3.30E−42
    1217 CGPG5961.pep Biotin_lipoyl 94 167 79.7 9.50E−21
    1217 CGPG5961.pep 2-oxoacid_dh 232 462 478 1.20E−140
    1219 CGPG5968.pep Pribosyltran 36 172 151.2 2.90E−42
    1220 CGPG5984.pep Pkinase 115 443 246.8 4.70E−71
    1221 CGPG5991.pep LRR_1 266 293 9.3 5.7
    1222 CGPG6006.pep RRM_1 19 89 81.3 3.10E−21
    1223 CGPG6015.pep La 14 85 101.3 3.00E−27
    1223 CGPG6015.pep RRM_1 118 188 37.1 6.40E−08
    1223 CGPG6015.pep RRM_3 302 404 142.2 1.40E−39
    1224 CGPG603.pep G6PD_N 35 222 342 1.00E−99
    1224 CGPG603.pep G6PD_C 224 508 655.5 4.50E−194
    1225 CGPG6046.pep Str_synth 179 266 137.2 4.80E−38
    1226 CGPG6063.pep Nramp 88 451 733.6 1.40E−217
    1228 CGPG6092.pep SRPRB 53 235 117.6 3.70E−32
    1229 CGPG6104.pep Steroid_dh 111 262 337.7 2.00E−98
    1230 CGPG6106.pep LEA_5 1 92 209.3 9.10E−60
    1231 CGPG6111.pep PP-binding 48 115 75.2 2.10E−19
    1232 CGPG6113.pep UQ_con 7 143 205.4 1.40E−58
    1234 CGPG6132.pep SMP 13 71 121.1 3.30E−33
    1234 CGPG6132.pep SMP 135 196 113.9 4.90E−31
    1234 CGPG6132.pep SMP 200 262 105 2.30E−28
    1236 CGPG6147.pep Redoxin 74 234 181.5 2.20E−51
    1236 CGPG6147.pep AhpC-TSA 75 214 65.2 2.30E−16
    1237 CGPG6152.pep Arf 5 177 434.6 1.40E−127
    1237 CGPG6152.pep SRPRB 15 177 −23.5 7.20E−06
    1237 CGPG6152.pep Miro 19 129 20.4 0.00012
    1237 CGPG6152.pep Ras 19 179 −47.2 8.20E−06
    1238 CGPG6154.pep Ion_trans_2 122 204 70 7.90E−18
    1238 CGPG6154.pep Ion_trans_2 253 328 48.9 1.80E−11
    1239 CGPG6170.pep UQ_con 19 158 187.1 4.50E−53
    1240 CGPG6171.pep Thioredoxin 120 227 55.8 1.50E−13
    1241 CGPG6177.pep AIG1 39 236 212.9 7.60E−61
    1241 CGPG6177.pep MMR_HSR1 39 154 31.5 1.40E−06
    1242 CGPG6181.pep Peptidase_C12 2 214 311.3 1.80E−90
    1243 CGPG6188.pep Di19 10 217 479 6.00E−141
    1244 CGPG6202.pep TB2_DP1_HVA22 9 106 191.2 2.60E−54
    1245 CGPG6217.pep MFS_1 40 460 86.7 7.20E−23
    1245 CGPG6217.pep Sugar_tr 90 507 −7.3 1.10E−08
    1246 CGPG623.pep SATase_N 45 149 210 5.60E−60
    1246 CGPG623.pep Hexapep 203 220 19.7 0.011
    1246 CGPG623.pep Hexapep 229 246 15.6 0.18
    1246 CGPG623.pep Hexapep 247 264 8 16
    1247 CGPG6239.pep Sugar_tr 27 458 289.4 7.10E−84
    1247 CGPG6239.pep MFS_1 32 413 90.4 5.50E−24
    1248 CGPG6244.pep Pkinase 39 303 81.8 2.10E−21
    1249 CGPG6254.pep Pkinase 12 264 310.9 2.40E−90
    1249 CGPG6254.pep Pkinase_Tyr 12 261 75.1 2.20E−19
    1249 CGPG6254.pep NAF 292 352 103 9.50E−28
    1251 CGPG627.pep His_biosynth 48 289 33.3 4.00E−12
    1252 CGPG6271.pep Pkinase 191 527 227.5 3.00E−65
    1253 CGPG6278.pep Pkinase_Tyr 86 365 146.9 5.60E−41
    1253 CGPG6278.pep Pkinase 86 368 158.7 1.60E−44
    1254 CGPG6288.pep Pkinase 207 463 183.7 4.70E−52
    1254 CGPG6288.pep Pkinase_Tyr 207 463 207.1 4.10E−59
    1255 CGPG6309.pep PRA1 29 181 233.1 6.50E−67
    1256 CGPG633.pep DCP1 12 134 258.3 1.70E−74
    1257 CGPG635.pep RmID_sub_bind 7 338 −145.7 0.00034
    1257 CGPG635.pep adh_short 7 177 −35.3 0.0026
    1257 CGPG635.pep Epimerase 9 273 226.4 6.40E−65
    1257 CGPG635.pep Polysacc_synt_2 9 319 −162.6 0.0011
    1257 CGPG635.pep 3Beta_HSD 10 299 −79 3.60E−05
    1257 CGPG635.pep NAD_binding_4 11 240 −73 0.00047
    1258 CGPG6350.pep LRRNT_2 32 78 22.6 0.0015
    1258 CGPG6350.pep LRR_1 105 127 20.8 0.0051
    1258 CGPG6350.pep LRR_1 129 151 13.6 0.74
    1258 CGPG6350.pep LRR_1 153 175 13.4 0.84
    1258 CGPG6350.pep LRR_1 177 196 10.9 2.9
    1260 CGPG6365.pep Aminotran_1_2 32 384 403.5 3.20E−118
    1261 CGPG6374.pep Gln-synt_C 120 380 370.8 2.30E−108
    1262 CGPG6377.pep PGK 2 383 466.4 3.70E−137
    1263 CGPG638.pep PA 51 163 106 1.10E−28
    1264 CGPG6397.pep NAD_binding_2 1 157 −57 0.00027
    1264 CGPG6397.pep NAD_Gly3P_dh_N 2 121 −33.4 0.0009
    1264 CGPG6397.pep F420_oxidored 3 246 249.4 7.60E−72
    1265 CGPG6398.pep Enolase_N 5 135 212.4 1.10E−60
    1265 CGPG6398.pep Enolase_C 140 430 405 1.10E−118
    1266 CGPG6408.pep ADH_N 25 155 153.5 6.00E−43
    1266 CGPG6408.pep ADH_zinc_N 185 350 101.5 2.50E−27
    1267 CGPG6415.pep NTP_transferase 4 271 71.9 2.10E−18
    1268 CGPG6421.pep ADH_N 25 148 131.4 2.60E−36
    1268 CGPG6421.pep ADH_zinc_N 179 318 163.9 4.30E−46
    1269 CGPG6442.pep iPGM_N 2 363 870.1 1.10E−258
    1269 CGPG6442.pep Metalloenzyme 373 488 191.4 2.20E−54
    1270 CGPG6443.pep PGK 1 391 727.8 7.60E−216
    1271 CGPG6446.pep PK 106 453 901.2 4.70E−268
    1271 CGPG6446.pep PK_C 467 587 259.4 7.60E−75
    1272 CGPG6453.pep Aminotran_1_2 41 402 404.3 1.80E−118
    1273 CGPG6466.pep ADH_N 27 153 129.2 1.20E−35
    1273 CGPG6466.pep ADH_zinc_N 184 322 135.3 1.80E−37
    1274 CGPG6467.pep Aminotran_3 19 366 361.7 1.20E−105
    1275 CGPG6470.pep PfkB 1 302 230 5.40E−66
    1276 CGPG6475.pep NTP_transferase 10 282 35.5 1.90E−09
    1277 CGPG6477.pep NDK 4 138 268.7 1.20E−77
    1278 CGPG6478.pep PfkB 1 308 70.6 5.30E−18
    1279 CGPG6493.pep AA_permease 94 561 594.7 9.00E−176
    1280 CGPG6506.pep Asparaginase 140 457 525.4 6.50E−155
    1281 CGPG6518.pep NAD_binding_2 2 173 303 5.60E−88
    1281 CGPG6518.pep 6PGD 177 467 700.7 1.10E−207
    1282 CGPG6546.pep PK 3 348 560.5 1.80E−165
    1282 CGPG6546.pep PK_C 360 477 86.8 6.80E−23
    1283 CGPG6556.pep Aminotran_1_2 124 475 223.7 4.30E−64
    1284 CGPG6562.pep Aminotran_3 116 451 628.8 4.90E−186
    1285 CGPG6566.pep NTP_transferase 95 350 301.4 1.80E−87
    1285 CGPG6566.pep Hexapep 398 415 6.4 25
    1285 CGPG6566.pep Hexapep 432 449 16.6 0.097
    1285 CGPG6566.pep Hexapep 460 477 5.5 31
    1286 CGPG6571.pep Aldedh 102 560 720.7 1.10E−213
    1287 CGPG6576.pep Aldedh 99 565 569.2 4.30E−168
    1288 CGPG659.pep G_glu_transpept 48 567 839.1 2.30E−249
    1289 CGPG6594.pep DAO 94 524 −28.6 0.00082
    1289 CGPG6594.pep GIDA 94 429 −226.6 0.0045
    1289 CGPG6594.pep Pyr_redox_2 94 419 229.8 6.20E−66
    1289 CGPG6594.pep Pyr_redox 278 374 119.5 9.90E−33
    1289 CGPG6594.pep Pyr_redox_dim 450 559 194.7 2.20E−55
    1290 CGPG6603.pep Pyr_redox_2 94 397 239.1 9.60E−69
    1290 CGPG6603.pep Pyr_redox 257 350 101.2 3.10E−27
    1290 CGPG6603.pep Pyr_redox_dim 427 538 189.7 7.10E−54
    1291 CGPG6608.pep DAO 93 497 −33.9 0.0018
    1291 CGPG6608.pep Pyr_redox_2 93 394 145.4 1.60E−40
    1291 CGPG6608.pep Pyr_redox 256 348 92.2 1.70E−24
    1291 CGPG6608.pep Pyr_redox_dim 423 532 89.3 1.20E−23
    1292 CGPG6634.pep DUF177 100 252 152.3 1.30E−42
    1294 CGPG6667.pep Invertase_neut 89 577 1313.4 0
    1295 CGPG6678.pep Biotin_lipoyl 92 165 75.9 1.30E−19
    1295 CGPG6678.pep E3_binding 225 263 51.7 2.60E−12
    1295 CGPG6678.pep 2-oxoacid_dh 281 512 374.6 1.60E−109
    1296 CGPG6695.pep GIDA 97 428 −211.9 0.00053
    1296 CGPG6695.pep Pyr_redox_2 97 408 266.1 7.40E−77
    1296 CGPG6695.pep Pyr_redox 266 361 90.1 7.20E−24
    1296 CGPG6695.pep Pyr_redox_dim 436 545 184.3 3.20E−52
    1297 CGPG6699.pep Ribul_P_3_epim 94 295 491.3 1.20E−144
    1298 CGPG670.pep Fer2 60 135 120.2 6.20E−33
    1299 CGPG6705.pep PK 89 433 788.8 3.30E−234
    1299 CGPG6705.pep PK_C 445 559 164.3 3.30E−46
    1299 CGPG6705.pep PEP-utilizers 584 663 122.9 9.40E−34
    1300 CGPG6735.pep FBPase 93 413 525 8.60E−155
    1301 CGPG6744.pep Glycolytic 92 429 576.6 2.40E−170
    1302 CGPG6753.pep Pyr_redox 236 328 10.7 0.00051
    1302 CGPG6753.pep Pyr_redox_2 236 538 72.9 1.10E−18
    1303 CGPG6757.pep Aminotran_1_2 127 473 234 3.30E−67
    1305 CGPG6806.pep mTERF 110 457 550.4 2.00E−162
    1306 CGPG6811.pep GH3 10 567 1341 0
    1308 CGPG6815.pep V-ATPase_G 5 109 183.9 4.00E−52
    1310 CGPG6830.pep Tbf5 13 76 113.7 5.40E−31
    1313 CGPG6864.pep DUF620 190 438 698.7 4.50E−207
    1314 CGPG6877.pep Hep_59 101 194 198.3 1.90E−56
    1315 CGPG6878.pep Peptidase_M24 107 343 229.5 7.80E−66
    1316 CGPG6880.pep PAP_fibrillin 72 232 178.2 2.20E−50
    1318 CGPG6887.pep AIG2 12 111 89.1 1.40E−23
    1319 CGPG6895.pep zf-CCHC 166 183 26 0.00014
    1319 CGPG6895.pep zf-CCHC 208 225 24.9 0.00026
    1319 CGPG6895.pep zf-CCHC 325 342 38.1 3.30E−08
    1319 CGPG6895.pep zf-CCHC 356 373 32 2.20E−06
    1322 CGPG6912.pep zf-DHHC 149 213 119.1 1.30E−32
    1324 CGPG6942.pep RNA_pol_Rpb5_N 18 108 174.3 3.20E−49
    1324 CGPG6942.pep RNA_pol_Rpb5_C 149 222 68.2 2.80E−17
    1327 CGPG6969.pep 2OG-Fell_Oxy 223 323 152.3 1.30E−42
    1329 CGPG6991.pep Glyco_tran_28_C 11 170 171.7 1.90E−48
    1332 CGPG7037.pep Sad1_UNC 313 416 −3.4 0.0011
    1333 CGPG7051.pep PAP_fibrillin 84 236 218.7 1.40E−62
    1336 CGPG7086.pep SFT2 44 163 182.6 9.70E−52
    1339 CGPG7136.pep NOI 1 72 159.7 8.10E−45
    1340 CGPG7147.pep RAMP4 1 64 152.5 1.20E−42
    1343 CGPG7222.pep Branch 49 274 399.8 4.00E−117
    1345 CGPG7233.pep eIF2A 214 407 415.3 8.90E−122
    1346 CGPG7238.pep UPF0185 5 80 214.1 3.30E−61
    1347 CGPG7253.pep ArfGap 15 117 58.4 2.40E−14
    1348 CGPG7255.pep Arf 5 177 365.3 1.00E−106
    1348 CGPG7255.pep SRPRB 15 200 −3.7 2.60E−07
    1348 CGPG7255.pep Miro 19 129 40.3 7.10E−09
    1348 CGPG7255.pep Ras 19 179 −43.7 4.50E−06
    1349 CGPG7286.pep ORC2 20 345 558.7 6.00E−165
    1350 CGPG7292.pep Methyltransf_11 38 135 44.1 5.00E−10
    1350 CGPG7292.pep Methyltransf_12 38 133 38.4 2.60E−08
    1351 CGPG7301.pep ELFV_dehydrog_N 57 187 294.9 1.50E−85
    1351 CGPG7301.pep ELFV_dehydrog 202 445 484.3 1.50E−142
    1352 CGPG7305.pep DAO 126 401 −31.6 0.0013
    1352 CGPG7305.pep Pyr_redox_2 126 386 66.3 1.00E−16
    1352 CGPG7305.pep Pyr_redox 255 345 55.7 1.60E−13
    1353 CGPG7307.pep Gp_dh_N 11 163 300.6 3.00E−87
    1353 CGPG7307.pep Gp_dh_C 168 324 258.5 1.50E−74
    1354 CGPG7318.pep MIP 1 142 −31.2 9.10E−08
    1355 CGPG7319.pep SNF5 172 400 471.8 9.00E−139
    1356 CGPG7345.pep Lipase_3 97 237 131.1 3.30E−36
    1357 CGPG7368.pep MT-A70 516 676 316.4 5.20E−92
    1358 CGPG7385.pep FHA 32 107 51 4.10E−12
    1359 CGPG7391.pep G-patch 6 50 71.2 3.40E−18
    1360 CGPG7405.pep TATA_RF 1 216 160.8 3.70E−45
    1361 CGPG7415.pep IU_nuc_hydro 1 312 255.3 1.30E−73
    1362 CGPG7416.pep GLTP 52 233 208 2.30E−59
    1363 CGPG7420.pep PRK 95 302 426.6 3.60E−125
    1366 CGPG7445.pep PRC 92 169 37.2 5.70E−08
    1366 CGPG7445.pep PRC 171 252 48.6 2.20E−11
    1367 CGPG7465.pep Aldedh 103 567 834.4 6.30E−248
    1368 CGPG7473.pep F-box 273 320 35.1 2.60E−07
    1368 CGPG7473.pep WD40 412 449 41.5 2.90E−09
    1368 CGPG7473.pep WD40 453 493 49.7 1.00E−11
    1368 CGPG7473.pep WD40 520 556 30.6 5.70E−06
    1368 CGPG7473.pep WD40 560 598 41.7 2.70E−09
    1369 CGPG7489.pep UBX 295 376 70.8 4.50E−18
    1370 CGPG7492.pep Pescadillo_N 8 291 519 5.30E−153
    1370 CGPG7492.pep BRCT 337 414 50.7 5.00E−12
    1371 CGPG7499.pep G-alpha 423 839 50.2 3.20E−22
    1374 CGPG7508.pep Smg4_UPF3 1 170 236.2 7.10E−68
    1375 CGPG7509.pep SSB 76 187 95.3 1.90E−25
    1376 CGPG7511.pep GFA 31 125 74.2 4.20E−19
    1377 CGPG7515.pep Brix 45 297 232.5 9.60E−67
    1378 CGPG7521.pep G-alpha 23 386 560.5 1.80E−165
    1380 CGPG7547.pep PAD_porph 14 368 695.7 3.40E−206
    1381 CGPG7561.pep Snf7 17 187 219.6 7.40E−63
    1382 CGPG7562.pep Sybindin 6 136 253.6 4.30E−73
    1382 CGPG7562.pep Sedlin_N 11 135 −21.6 0.00015
    1383 CGPG7563.pep DUF887 40 279 394.2 2.10E−115
    1384 CGPG7567.pep Peptidase_M18 14 461 680 1.90E−201
    1389 CGPG7597.pep zf-AN1 76 116 78.4 2.40E−20
    1390 CGPG7606.pep Pentapeptide 127 166 29.2 1.50E−05
    1390 CGPG7606.pep Pentapeptide 172 211 42.7 1.30E−09
    1392 CGPG7637.pep DAD 2 112 168.4 1.90E−47
    1393 CGPG7649.pep YgbB 71 227 244.8 2.00E−70
    1394 CGPG7658.pep Cyclase 56 256 109.9 7.70E−30
    1395 CGPG7664.pep Aldedh 9 463 801 7.20E−238
    1396 CGPG7666.pep Aminotran_1_2 26 392 491 1.50E−144
    1397 CGPG7668.pep DUF594 660 719 97.6 3.90E−26
    1399 CGPG7746.pep UPF0153 49 139 59.7 9.90E−15
    1400 CGPG7747.pep Copine 113 261 308.5 1.30E−89
    1401 CGPG7752.pep zf-MYND 176 214 48.9 1.80E−11
    1401 CGPG7752.pep PDCD2_C 241 403 38.2 1.00E−10
    1403 CGPG7770.pep YTH 263 353 218.6 1.40E−62
    1406 CGPG7778.pep Ubie_methyltran 51 304 393.3 3.70E−115
    1406 CGPG7778.pep Methyltransf_11 105 222 75 2.50E−19
    1406 CGPG7778.pep Methyltransf_12 105 220 43.1 1.00E−09
    1407 CGPG7786.pep KH_1 141 193 27.6 4.60E−05
    1408 CGPG7788.pep YIF1 34 263 341.8 1.20E−99
    1410 CGPG78.pep Hpt 46 132 55.5 1.80E−13
    1411 CGPG783.pep RRM_1 288 354 40 8.40E−09
    1411 CGPG783.pep RRM_2 682 778 232.4 1.00E−66
    1412 CGPG7832.pep STT3 26 670 626.4 2.50E−185
    1413 CGPG7841.pep ECH 17 186 192.8 8.40E−55
    1413 CGPG7841.pep 3HCDH_N 311 490 295.4 1.10E−85
    1413 CGPG7841.pep 3HCDH 492 585 116.2 9.50E−32
    1414 CGPG7845.pep LRRNT_2 23 64 49.2 1.50E−11
    1414 CGPG7845.pep LRR_1 97 119 10.5 3.5
    1414 CGPG7845.pep LRR_1 121 143 14.5 0.39
    1414 CGPG7845.pep LRR_1 145 167 12.1 1.7
    1414 CGPG7845.pep LRR_1 169 192 13.1 1.1
    1414 CGPG7845.pep LRR_1 194 216 14 0.55
    1415 CGPG7847.pep Peptidase_C48 30 225 −1.9 0.00023
    1417 CGPG7853.pep LRR_1 142 164 17.4 0.052
    1417 CGPG7853.pep LRR_1 166 188 9.9 4.4
    1417 CGPG7853.pep LRR_1 190 212 10 4.3
    1417 CGPG7853.pep LRR_1 214 235 13.8 0.65
    1417 CGPG7853.pep LRR_1 258 280 10.5 3.5
    1417 CGPG7853.pep LRR_1 282 304 14 0.56
    1417 CGPG7853.pep LRR_1 306 325 11.7 2.1
    1418 CGPG7857.pep Response_reg 79 195 89.7 9.40E−24
    1418 CGPG7857.pep CCT 689 736 62.1 1.80E−15
    1420 CGPG7869.pep Acyltransferase 117 264 81.9 2.00E−21
    1421 CGPG7891.pep FMO-like 11 427 −207 1.20E−16
    1421 CGPG7891.pep DAO 13 268 −9.4 4.70E−05
    1422 CGPG7892.pep FMO-like 9 416 −157.4 2.80E−19
    1423 CGPG7906.pep Skp1_POZ 4 65 96.7 7.50E−26
    1423 CGPG7906.pep Skp1 76 153 154.3 3.40E−43
    1424 CGPG7924.pep AAA 249 462 54.2 4.60E−13
    1428 CGPG7964.pep IQ 108 128 25.7 0.00017
    1428 CGPG7964.pep IQ 130 150 12.2 1.9
    1429 CGPG7968.pep FMO-like 13 427 −229.9 2.10E−15
    1429 CGPG7968.pep DAO 15 291 −34.2 0.0019
    1429 CGPG7968.pep Pyr_redox_2 15 321 −18 0.00054
    1431 CGPG7972.pep FAD_binding_3 5 372 −97.4 5.20E−06
    1432 CGPG7982.pep Tetraspannin 4 241 241.9 1.40E−69
    1433 CGPG7985.pep BT1 57 469 419.2 6.00E−123
    1434 CGPG7993.pep F-box 27 73 15.1 0.26
    1434 CGPG7993.pep LRR_2 278 304 16.8 0.084
    1435 CGPG8.pep p450 39 503 399 7.30E−117
    1436 CGPG80.pep Pkinase 68 328 277.6 2.60E−80
    1437 CGPG8001.pep FMO-like 13 433 −243.5 1.10E−14
    1437 CGPG8001.pep Pyr_redox 215 295 5.3 0.0016
    1438 CGPG8009.pep BT1 41 511 517.8 1.30E−152
    1440 CGPG8049.pep BT1 1 436 331.8 1.20E−96
    1441 CGPG806.pep Synaptobrevin 127 215 146.7 6.20E−41
    1442 CGPG8060.pep DUF829 161 425 426 5.30E−125
    1446 CGPG81.pep Pkinase 70 330 287.7 2.30E−83
    1452 CGPG8125.pep zf-C3HC4 46 86 31.1 4.00E−06
    1453 CGPG8134.pep DEK_C 3 57 60.4 6.10E−15
    1453 CGPG8134.pep SWIB 197 272 140.9 3.60E−39
    1453 CGPG8134.pep SWIB 305 382 112.9 9.40E−31
    1455 CGPG8156.pep PCI 258 362 69.4 1.20E−17
    1456 CGPG8159.pep ACT 77 141 51.9 2.10E−12
    1456 CGPG8159.pep ACT 308 374 51.5 3.00E−12
    1458 CGPG8179.pep WD40 138 177 23.7 0.00069
    1458 CGPG8179.pep WD40 264 305 42.5 1.50E−09
    1459 CGPG8193.pep Ank 22 54 5.5 5.2
    1459 CGPG8193.pep Ank 55 87 36.4 1.00E−07
    1460 CGPG8197.pep F-box 5 53 22 0.0022
    1461 CGPG8198.pep F-box 74 119 15 0.28
    1461 CGPG8198.pep Kelch_2 174 221 19.7 0.011
    1461 CGPG8198.pep Kelch_1 223 278 15.6 0.041
    1461 CGPG8198.pep Kelch_2 329 369 14.2 0.51
    1463 CGPG8211.pep F-box 182 229 48.8 2.00E−11
    1463 CGPG8211.pep WD40 292 328 30.3 6.90E−06
    1463 CGPG8211.pep WD40 332 368 37.7 4.30E−08
    1463 CGPG8211.pep WD40 372 408 43.4 8.30E−10
    1463 CGPG8211.pep WD40 411 449 40.9 4.60E−09
    1463 CGPG8211.pep WD40 453 538 32.2 1.90E−06
    1463 CGPG8211.pep WD40 542 578 38.9 1.80E−08
    1464 CGPG823.pep Ribosomal_S6e 1 129 258.3 1.70E−74
    1466 CGPG8238.pep PGI 49 537 857.4 7.40E−255
    1467 CGPG8260.pep Iso_dh 4 331 460.7 1.90E−135
    1468 CGPG8267.pep Pyridoxal_deC 34 383 352.2 8.70E−103
    1469 CGPG8268.pep NIR_SIR_ferr 62 131 43.9 5.60E−10
    1469 CGPG8268.pep NIR_SIR 164 345 193.4 5.50E−55
    1469 CGPG8268.pep NIR_SIR_ferr 360 432 76.9 6.80E−20
    1470 CGPG8274.pep PK 5 347 589.9 2.50E−174
    1470 CGPG8274.pep PK_C 363 476 81.9 2.10E−21
    1471 CGPG8277.pep Rib_5-P_isom_A 55 229 345 1.30E−100
    1472 CGPG8279.pep F-box 22 69 43 1.10E−09
    1472 CGPG8279.pep Kelch_1 124 168 35.2 2.40E−07
    1472 CGPG8279.pep Kelch_1 170 213 29.4 1.40E−05
    1472 CGPG8279.pep Kelch_2 170 213 24.3 0.00045
    1475 CGPG8408.pep DUF641 60 192 237.3 3.40E−68
    1476 CGPG842.pep Redoxin 5 162 182.6 9.80E−52
    1476 CGPG842.pep AhpC-TSA 6 142 38.6 2.20E−08
    1477 CGPG8421.pep NOSIC 121 173 90.1 6.90E−24
    1477 CGPG8421.pep Nop 213 361 257.3 3.20E−74
    1478 CGPG8435.pep NHL 55 82 5.9 3.4
    1478 CGPG8435.pep NHL 115 142 37.2 5.80E−08
    1479 CGPG8440.pep U-box 242 316 70.2 6.80E−18
    1479 CGPG8440.pep Arm 372 413 47.5 4.70E−11
    1479 CGPG8440.pep Arm 455 495 32.1 2.00E−06
    1479 CGPG8440.pep Arm 496 537 22.3 0.0018
    1479 CGPG8440.pep Arm 538 578 25.5 0.0002
    1480 CGPG8453.pep ACT 36 99 33.5 7.90E−07
    1480 CGPG8453.pep ACT 129 201 54.1 4.90E−13
    1480 CGPG8453.pep ACT 265 332 28.6 2.40E−05
    1480 CGPG8453.pep ACT 343 406 43.5 7.50E−10
    1481 CGPG8470.pep DUF89 18 357 −103.6 0.0022
    1482 CGPG8479.pep F-box 31 78 22.6 0.0015
    1482 CGPG8479.pep Kelch_1 124 170 35.4 2.00E−07
    1482 CGPG8479.pep Kelch_1 172 216 44.6 3.40E−10
    1482 CGPG8479.pep Kelch_2 172 216 21.7 0.0027
    1483 CGPG8489.pep F-box 3 50 44.4 3.90E−10
    1483 CGPG8489.pep FBA_1 219 384 291.3 2.00E−84
    1484 CGPG8498.pep Fcf1 87 185 245.9 9.10E−71
    1485 CGPG85.pep Aa_trans 19 454 556.5 2.80E−164
    1486 CGPG8501.pep PPR 149 183 11.6 0.32
    1486 CGPG8501.pep PPR 189 223 29 1.70E−05
    1486 CGPG8501.pep PPR 224 258 25.6 0.00019
    1486 CGPG8501.pep PPR 259 292 6.5 1.3
    1486 CGPG8501.pep PPR 330 364 4.2 2.5
    1486 CGPG8501.pep PPR 401 435 12.3 0.27
    1487 CGPG8507.pep DUF588 31 185 202.1 1.30E−57
    1488 CGPG8509.pep Pro_isomerase 80 233 18.3 3.90E−10
    1490 CGPG8517.pep B_lectin 84 197 191 2.90E−54
    1490 CGPG8517.pep S_locus_glycop 211 339 250 5.20E−72
    1490 CGPG8517.pep PAN_2 356 422 105.1 2.10E−28
    1492 CGPG852.pep Ribosomal_S5 94 160 140.9 3.60E−39
    1492 CGPG852.pep Ribosomal_S5_C 177 250 134.4 3.30E−37
    1498 CGPG8567.pep TB2_DP1_HVA22 3 98 59.4 1.20E−14
    1499 CGPG8580.pep Caleosin 22 195 434.3 1.70E−127
    1501 CGPG8590.pep DUF579 42 289 571.9 6.60E−169
    1503 CGPG8594.pep DUF584 1 139 248.7 1.30E−71
    1504 CGPG8606.pep Exo_endo_phos 56 327 125 2.30E−34
    1505 CGPG8628.pep DUF584 32 203 125.8 1.30E−34
    1507 CGPG8654.pep PPR 73 107 13.2 0.21
    1507 CGPG8654.pep PPR 141 175 38.6 2.30E−08
    1508 CGPG8668.pep TATA_RF 1 200 306.9 3.90E−89
    1511 CGPG8702.pep RPE65 50 622 19.9 1.70E−17
    1514 CGPG8748.pep AAA 201 357 13.1 1.30E−06
    1516 CGPG8770.pep DUF543 1 73 107.6 3.90E−29
    1517 CGPG8777.pep DUF569 1 144 377.9 1.70E−110
    1517 CGPG8777.pep DUF569 227 368 391.4 1.40E−114
    1519 CGPG8786.pep DUF260 13 113 247.6 2.70E−71
    1520 CGPG8792.pep Abhydrolase_3 75 290 228.4 1.60E−65
    1521 CGPG8801.pep PPR 110 144 18.7 0.022
    1521 CGPG8801.pep PPR 145 179 9.1 0.64
    1521 CGPG8801.pep PPR 181 215 42.6 1.40E−09
    1521 CGPG8801.pep PPR 216 250 19.5 0.012
    1521 CGPG8801.pep PPR 251 285 23.6 0.00076
    1521 CGPG8801.pep PPR 286 320 37.2 6.10E−08
    1521 CGPG8801.pep PPR 321 355 12 0.3
    1522 CGPG8809.pep Ribosomal_L12 141 208 61.2 3.50E−15
    1523 CGPG8840.pep CLP_protease 115 289 45.1 1.30E−11
    1524 CGPG8850.pep PPR 189 223 17.3 0.057
    1524 CGPG8850.pep PPR 224 258 48.5 2.40E−11
    1524 CGPG8850.pep PPR 297 331 34.6 3.50E−07
    1524 CGPG8850.pep PPR 332 366 46.2 1.20E−10
    1524 CGPG8850.pep PPR 367 401 40.7 5.40E−09
    1524 CGPG8850.pep PPR 402 436 50 8.00E−12
    1524 CGPG8850.pep PPR 437 470 36.5 9.50E−08
    1524 CGPG8850.pep PPR 471 505 39.8 9.60E−09
    1524 CGPG8850.pep PPR 506 540 23.2 0.00094
    1524 CGPG8850.pep PPR 542 576 46.6 8.80E−11
    1525 CGPG8870.pep Fructosamin_kin 54 339 208 2.30E−59
    1525 CGPG8870.pep APH 69 308 80.1 7.30E−21
    1526 CGPG8871.pep DUF59 36 115 57.6 4.20E−14
    1527 CGPG8872.pep RRM_1 138 205 78 3.00E−20
    1527 CGPG8872.pep RRM_1 214 288 32.4 1.70E−06
    1527 CGPG8872.pep RRM_1 308 378 60 8.10E−15
    1528 CGPG8876.pep SFT2 43 162 194.7 2.40E−55
    1529 CGPG8902.pep RNA_pol_I_A49 31 415 702.7 2.70E−208
    1530 CGPG8904.pep G-alpha 103 447 513.2 3.10E−151
    1531 CGPG8907.pep DnaJ 4 67 128.7 1.70E−35
    1531 CGPG8907.pep zf-C2H2 338 362 28 3.40E−05
    1532 CGPG8914.pep Whi5 181 205 50.1 7.80E−12
    1533 CGPG8931.pep eIF3_subunit 1 231 272.1 1.20E−78
    1534 CGPG8933.pep MACPF 126 322 60.6 5.20E−15
    1535 CGPG8935.pep Pkinase 33 324 308.5 1.30E−89
    1536 CGPG8938.pep Pkinase 71 348 187.5 3.40E−53
    1536 CGPG8938.pep Pkinase_Tyr 71 348 128.4 2.10E−35
    1537 CGPG8944.pep PH 31 134 48.5 2.40E−11
    1538 CGPG895.pep DUF231 251 427 223.7 4.30E−64
    1540 CGPG8961.pep Dus 59 392 236.5 5.90E−68
    1541 CGPG8963.pep Pkinase 319 612 332 1.10E−96
    1542 CGPG898.pep DUF231 276 448 289.8 5.30E−84
    1543 CGPG8993.pep AAA 44 226 54.9 2.80E−13
    1543 CGPG8993.pep Rep_fac_C 237 326 113.5 6.50E−31
    1544 CGPG8994.pep Brix 86 262 264.3 2.50E−76
    1545 CGPG8995.pep Porin_3 54 326 280.1 4.30E−81
    1546 CGPG90.pep MFS_1 68 427 55 2.50E−13
    1547 CGPG900.pep DUF231 241 420 229.6 6.90E−66
    1548 CGPG9002.pep CTP_transf_1 51 382 443.1 3.90E−130
    1549 CGPG9009.pep Alg6_Alg8 22 514 439.6 4.30E−129
    1550 CGPG9011.pep OTCace_N 70 212 188.6 1.60E−53
    1550 CGPG9011.pep OTCace 216 369 198.1 2.20E−56
    1551 CGPG9012.pep FoIB 16 129 125 2.10E−34
    1552 CGPG9017.pep DMRL_synthase 70 213 195.5 1.30E−55
    1553 CGPG9025.pep Glyco_transf_29 105 355 −11 1.90E−06
    1554 CGPG9026.pep Adap_comp_sub 160 428 469.4 4.70E−138
    1555 CGPG9032.pep RNase_PH 33 165 135.6 1.40E−37
    1555 CGPG9032.pep RNase_PH_C 194 262 44.9 2.70E−10
    1556 CGPG9040.pep Sec1 35 592 217.7 2.70E−62
    1557 CGPG9044.pep Syntaxin 57 163 93.9 5.10E−25
    1557 CGPG9044.pep SNARE 256 318 79.5 1.10E−20
    1558 CGPG9048.pep RNase_PH 15 135 53.3 8.30E−13
    1559 CGPG9049.pep Glycos_transf_1 244 442 16 3.70E−05
    1560 CGPG9058.pep RNA_pol_N 1 60 125.6 1.40E−34
    1561 CGPG906.pep PPR 210 244 28.2 3.10E−05
    1561 CGPG906.pep PPR 245 279 13.7 0.19
    1562 CGPG9070.pep ATP-synt_C 20 85 42.4 1.60E−09
    1562 CGPG9070.pep ATP-synt_C 104 169 21.7 0.00014
    1564 CGPG9084.pep CH 15 116 47.4 5.20E−11
    1564 CGPG9084.pep EB1 209 255 79.7 9.20E−21
    1566 CGPG9098.pep DUF6 32 165 22.6 0.0015
    1566 CGPG9098.pep TPT 199 337 −10.3 0.0023
    1566 CGPG9098.pep DUF6 208 337 66.1 1.20E−16
    1567 CGPG9099.pep Rick_17kDa_Anti 66 110 24.9 0.00029
    1568 CGPG9110.pep RALF 53 118 122.9 9.30E−34
    1569 CGPG9119.pep PTR2 115 504 350.4 3.10E−102
    1570 CGPG9125.pep ThiF 98 233 171.7 1.90E−48
    1571 CGPG913.pep PPR 86 120 32.9 1.20E−06
    1571 CGPG913.pep PPR 188 222 51.1 4.00E−12
    1571 CGPG913.pep PPR 223 257 7.4 1
    1571 CGPG913.pep PPR 289 323 26 0.00014
    1571 CGPG913.pep PPR 325 358 12 0.29
    1571 CGPG913.pep PPR 361 395 12.8 0.24
    1574 CGPG9164.pep DHBP_synthase 5 202 475.9 5.10E−140
    1574 CGPG9164.pep GTP_cyclohydro2 207 377 431.4 1.30E−126
    1575 CGPG9172.pep Sec61_beta 32 77 83 9.60E−22
    1577 CGPG9185.pep DUF423 10 115 84.7 2.90E−22
    1578 CGPG9187.pep Pkinase 12 263 298.2 1.60E−86
    1579 CGPG9190.pep DREPP 2 203 280.3 3.80E−81
    1580 CGPG9193.pep GATase 11 196 175.1 1.90E−49
    1580 CGPG9193.pep GMP_synt_C 432 524 172.7 9.30E−49
    1581 CGPG9195.pep DUF1279 91 193 127 5.60E−35
    1582 CGPG9203.pep Na_H_Exchanger 13 391 242.3 1.00E−69
    1582 CGPG9203.pep TrkA_C 418 486 58.4 2.50E−14
    1583 CGPG9209.pep GATase 9 197 199.6 7.80E−57
    1583 CGPG9209.pep GMP_synt_C 423 515 201.4 2.20E−57
    1585 CGPG9210.pep Na_H_Exchanger 10 376 229 1.10E−65
    1585 CGPG9210.pep TrkA_N 402 517 131 3.50E−36
    1586 CGPG9211.pep NTP_transferase 7 296 508.1 1.00E−149
    1586 CGPG9211.pep MannoseP_isomer 307 473 454 2.00E−133
    1586 CGPG9211.pep Cupin_2 388 458 48.1 3.10E−11
    1587 CGPG9212.pep ATP-synt_ab_N 22 87 53.4 7.60E−13
    1587 CGPG9212.pep ATP-synt_ab 143 353 429.3 5.40E−126
    1588 CGPG9216.pep DHBP_synthase 10 206 377.8 1.70E−110
    1588 CGPG9216.pep GTP_cyclohydro2 211 379 395.3 9.20E−116
    1589 CGPG9226.pep Carboxyl_trans 40 541 967.5 5.20E−288
    1590 CGPG9252.pep CDC48_N 28 114 132.1 1.60E−36
    1590 CGPG9252.pep AAA 245 429 330.3 3.40E−96
    1590 CGPG9252.pep AAA_5 245 377 9.8 0.00052
    1590 CGPG9252.pep AAA 518 705 344.1 2.40E−100
    1592 CGPG9289.pep LSM 10 75 64.8 3.00E−16
    1593 CGPG9298.pep p450 41 516 138.8 1.60E−38
    1594 CGPG9299.pep ThiF 82 227 145.2 1.80E−40
    1597 CGPG9316.pep ATP-grasp_2 34 242 405.7 7.10E−119
    1597 CGPG9316.pep Ligase_CoA 285 421 229 1.10E−65
    1598 CGPG9317.pep DUF163 43 196 205.3 1.50E−58
    1599 CGPG9318.pep Aldo_ket_red 20 285 408 1.40E−119
    1600 CGPG9324.pep Pkinase 158 706 150.9 3.40E−42
    1601 CGPG9357.pep Raffinose_syn 7 757 1669.7 0
    1602 CGPG965.pep Hexapep 70 87 10.5 6.4
    1602 CGPG965.pep Hexapep 119 136 16.4 0.11
    1602 CGPG965.pep Hexapep 142 159 5.9 28
    1602 CGPG965.pep Hexapep 160 177 2.6 71
    1603 CGPG970.pep NPH3 206 441 272 1.20E−78
    1604 CGPG982.pep p450 29 495 389.8 4.30E−114
    1605 CGPG994.pep adh_short 50 218 46.7 8.30E−11
    1606 CGPG996.pep DUF866 1 167 456.5 3.60E−134
  • TABLE 22
    Pfam domain gathering
    name Accession # cutoff domain description
    2OG-Fell_Oxy PF03171.11 11.5 2OG-Fe(II) oxygenase superfamily
    3Beta_HSD PF01073.10 −135.9 3-beta hydroxysteroid dehydrogenase/isomerase family
    3HCDH PF00725.13 −8.9 3-hydroxyacyl-CoA dehydrogenase, C-terminal domain
    3HCDH_N PF02737.9 −82.1 3-hydroxyacyl-CoA dehydrogenase, NAD binding domain
    6PGD PF00393.10 −232.3 6-phosphogluconate dehydrogenase, C-terminal domain
    AAA PF00004.20 12.3 ATPase family associated with various cellular activities (AAA)
    AAA_5 PF07728.5 4 ATPase family associated with various cellular activities (AAA)
    AARP2CN PF08142.3 25 AARP2CN (NUC121) domain
    AA_kinase PF00696.19 −40 Amino acid kinase family
    AA_permease PF00324.12 −120.8 Amino acid permease
    ABC_tran PF00005.18 9.5 ABC transporter
    ACBP PF00887.10 −14 Acyl CoA binding protein
    ACP_syn_III_C PF08541.1 −21.6 3-Oxoacyl-[acyl-carrier-protein (ACP)] synthase III C terminal
    ACT PF01842.16 0.7 ACT domain
    ADH_N PF08240.3 −14.5 Alcohol dehydrogenase GroES-like domain
    ADH_zinc_N PF00107.17 23.8 Zinc-binding dehydrogenase
    AIG1 PF04548.7 −40 AIG1 family
    AIG2 PF06094.3 12.7 AIG2-like family
    AP2 PF00847.11 21.7 AP2 domain
    APH PF01636.14 32.5 Phosphotransferase enzyme family
    ATP-grasp_2 PF08442.1 −118.8 ATP-grasp domain
    ATP-synt_C PF00137.12 5 ATP synthase subunit C
    ATP-synt_G PF04718.6 −7.9 Mitochondrial ATP synthase g subunit
    ATP-synt_ab PF00006.16 −37.5 ATP synthase alpha/beta family, nucleotide-binding domain
    ATP-synt_ab_N PF02874.14 17 ATP synthase alpha/beta family, beta-barrel domain
    ATP_bind_1 PF03029.8 -19 Conserved hypothetical ATP binding protein
    AWPM-19 PF05512.2 25 AWPM-19-like family
    Aa_trans PF01490.9 −128.4 Transmembrane amino acid transporter protein
    Abhydrolase_3 PF07859.4 25.8 alpha/beta hydrolase fold
    Acetyltransf_1 PF00583.15 18.6 Acetyltransferase (GNAT) family
    Acyltransferase PF01553.12 2.2 Acyltransferase
    Adap_comp_sub PF00928.12 −5.4 Adaptor complexes medium subunit family
    AhpC-TSA PF00578.12 4.8 AhpC/TSA family
    Alba PF01918.12 20 Alba
    Aldedh PF00171.13 −208.2 Aldehyde dehydrogenase family
    Aldo_ket_red PF00248.12 −97 Aldo/keto reductase family
    Alg6_Alq8 PF03155.6 −235.5 ALG6, ALG8 glycosyltransferase family
    Alpha-amyl_C2 PF07821.3 25 Alpha-amylase C-terminal beta-sheet domain
    Alpha-amylase PF00128.15 −92.6 Alpha amylase, catalytic domain
    Aminotran_1_2 PF00155.12 −57.5 Aminotransferase class I and II
    Aminotran_3 PF00202.12 −206.1 Aminotransferase class-III
    Aminotran_5 PF00266.10 −164.4 Aminotransferase class-V
    Ank PF00023.21 0 Ankyrin repeat
    Arf PF00025.12 40 ADP-ribosylation factor family
    ArfGap PF01412.9 −17 Putative GTPase activating protein for Arf
    Arm PF00514.14 17 Armadillo/beta-catenin-like repeat
    Asp PF00026.14 −153.8 Eukaryotic aspartyl protease
    Asparaginase PF00710.11 25 Asparaginase
    Auxin_inducible PF02519.5 −15 Auxin responsive protein
    B3 PF02362.12 26.5 B3 DNA binding domain
    BRCT PF00533.17 27.8 BRCA1 C Terminus (BRCT) domain
    BT1 PF03092.7 −148.6 BT1 family
    B_lectin PF01453.15 28.2 D-mannose binding lectin
    Band_7 PF01145.16 10.3 SPFH domain/Band 7 family
    Beta_elim_lyase PF01212.12 −110.3 Beta-eliminating lyase
    Biotin _lipoyl PF00364.13 −2.3 Biotin-requiring enzyme
    Bombesin PF02044.8 11.4 Bombesin-like peptide
    Branch PF02485.12 −83.5 Core-2/I-Branching enzyme
    Brix PF04427.9 11.4 Brix domain
    Bromodomain PF00439.16 8.9 Bromodomain
    C1_1 PF00130.13 11.4 Phorbol esters/diacylglycerol binding domain (C1 domain)
    C1_2 PF03107.7 26.4 C1 domain
    C1_3 PF07649.3 25 C1-like domain
    C2 PF00168.21 3.7 C2 domain
    CAF1 PF04857.11 −100.5 CAF1 family ribonuclease
    CBFD_NFYB_HMF PF00808.14 18.4 Histone-like transcription factor (CBF/NF-Y) and archaeal histone
    CBS PF00571.19 17.5 CBS domain pair
    CCT P F06203.5 25 CCT motif
    CDC48_N PF02359.9 −2 Cell division protein 48 (CDC48), N-terminal domain
    CDC50 PF03381.6 25 LEM3 (ligand-effect modulator 3) family/CDC50 family
    CD P-OH_P_transf PF01066.12 0 CDP-alcohol phosphatidyltransferase
    CH PF00307.22 22.5 Calponin homology (CH) domain
    CLP_protease PF00574.14 −77.2 Clp protease
    CPSase_sm_chain PF00988.13 25 Carbamoyl-phosphate synthase small chain, CPSase domain
    CRAL_TRIO PF00650.11 −26 CRAL/TRIO domain
    CRAL_TRIO_N PF03765.6 16 CRAL/TRIO, N-terminus
    CTP_transf_1 PF01148.11 −35.9 Cytidylyltransferase family
    Caleosin PF05042.4 25 Caleosin related protein
    Carb_anhydrase PF00194.12 −105 Eukaryotic-type carbonic anhydrase
    Carboxyl_trans PF01039.13 −262.3 Carboxyl transferase domain
    Cellulose_synt PF03552.5 −257.9 Cellulose synthase
    Cenp-O PF09496.1 25 Cenp-O kinetochore centromere component
    Chal_sti_synt_C PF02797.6 −6.1 Chalcone and stilbene synthases, C-terminal domain
    Chalcone PF02431.6 25 Chalcone-flavanone isomerase
    ClpS PF02617.8 −15 ATP-dependent Clp protease adaptor protein ClpS
    Copine PF07002.7 −36.5 Copine
    Cu-oxidase PF00394.13 −18.9 Multicopper oxidase
    Cu-oxidase_2 PF07731.5 −5.8 Multicopper oxidase
    Cu-oxidase_3 PF07732.6 10 Multicopper oxidase
    Cullin PF00888.13 −33.3 Cullin family
    Cupin_1 PF00190.13 −13 Cupin
    Cupin_2 PF07883.2 19.4 Cupin domain
    Cyclase PF04199.4 −31.7 Putative cyclase
    Cyclin_C PF02984.10 −13 Cyclin, C-terminal domain
    Cyclin_N PF00134.14 −14.7 Cyclin, N-terminal domain
    DAD PF02109.7 25 DAD family
    DAO PF01266.15 −34.9 FAD dependent oxidoreductase
    DCP1 PF06058.4 −16.8 Dcp1-like decapping family
    DEAD PF00270.20 7.2 DEAD/DEAH box helicase
    DEK_C PF08766.2 25 DEK C terminal domain
    DHBP_synthase PF00926.10 −95.1 3,4-dihydroxy-2-butanone 4-phosphate synthase
    DMRL_synthase PF00885.10 −43 6,7-dimethyl-8-ribityllumazine synthase
    DREPP PF05558.3 25 DREPP plasma membrane polypeptide
    DSPc PF00782.11 −21.8 Dual specificity phosphatase, catalytic domain
    DUF1279 PF06916.4 25 Protein of unknown function (DUF1279)
    DUF1350 PF07082.2 −145.7 Protein of unknown function (DUF1350)
    DUF1475 PF07343.2 25 Protein of unknown function (DUF1475)
    DUF1517 PF07466.2 25 Protein of unknown function (DUF1517)
    DUF163 PF02590.8 −48.6 Uncharacterized ACR, COG1576
    DUF1637 PF07847.3 25 Protein of unknown function (DUF1637)
    DUF167 PF02594.7 −3.4 Uncharacterised ACR, YggU family COG1872
    DUF177 PF02620.8 25 Uncharacterized ACR, COG1399
    DUF220 PF02713.5 25 Domain of unknown function DUF220
    DUF231 PF03005.6 −58 Arabidopsis proteins of unknown function
    DUF260 PF03195.5 0.8 Protein of unknown function DUF260
    DUF423 PF04241.6 −17.6 Protein of unknown function (DUF423)
    DUF543 PF04418.3 25 Domain of unknown function (DUF543)
    DUF569 PF04601.4 −47.6 Protein of unknown function (DUF569)
    DUF579 PF04669.4 25 Protein of unknown function (DUF579)
    DUF584 PF04520.4 25 Protein of unknown function, DUF584
    DUF588 PF04535.3 25 Domain of unknown function (DUF588)
    DUF59 PF01883.10 −7.9 Domain of unknown function DUF59
    DUF594 PF04578.4 25 Protein of unknown function, DUF594
    DUF599 PF04654.3 25 Protein of unknown function, DUF599
    DUF6 PF00892.11 21.7 Integral membrane protein DUF6
    DUF607 PF04678.4 25 Protein of unknown function, DUF607
    DUF616 PF04765.4 25 Protein of unknown function (DUF616)
    DUF620 PF04788.3 25 Protein of unknown function (DUF620)
    DUF641 PF04859.3 25 Plant protein of unknown function (DUF641)
    DUF663 PF04950.3 25 Protein of unknown function (DUF663)
    DUF822 PF05687.4 25 Plant protein of unknown function (DUF822)
    DUF829 PF05705.5 25 Eukaryotic protein of unknown function (DUF829)
    DUF862 PF05903.5 −21.4 PPPDE putative peptidase domain
    DUF866 PF05907.4 30.1 Eukaryotic protein of unknown function (DUF866)
    DUF887 PF05967.2 −72.3 Eukaryotic protein of unknown function (DUF887)
    DUF89 PF01937.10 −113.8 Protein of unknown function DUF89
    DUF933 PF06071.4 20 Protein of unknown function (DUF933)
    DZC PF08381.2 15.3 Disease resistance/zinc finger/chromosome condensation-like region
    Di19 PF05605.3 25 Drought induced 19 protein (Di19)
    Dimerisation PF08100.2 25 Dimerisation domain
    DnaJ PF00226.22 −8 DnaJ domain
    Dus PF01207.8 −82.1 Dihydrouridine synthase (Dus)
    E3_binding PF02817.8 10 e3 binding domain
    EB1 PF03271.8 25 EB1-like C-terminal motif
    ECH PF00378.11 −57.6 Enoyl-CoA hydratase/isomerase family
    ELFV_dehydrog PF00208.12 −26.4 Glutamate/Leucine/Phenylalanine/Valine dehydrogenase
    ELFV_dehydrog_N PF02812.9 31.8 Glu/Leu/Phe/Val dehydrogenase, dimerisation domain
    EMP24_GP25L PF01105.15 10.4 emp24/gp25L/p24 family/GOLD
    ENOD93 PF03386.5 25 Early nodulin 93 ENOD93 protein
    ENT PF03735.5 25 ENT domain
    Enolase_C PF00113.13 −71.2 Enolase, C-terminal TIM barrel domain
    Enolase_N PF03952.7 11.3 Enolase, N-terminal domain
    Epimerase PF01370.12 −46.3 NAD dependent epimerase/dehydratase family
    Exo_endo_phos PF03372.14 11 Endonuclease/Exonuclease/phosphatase family
    F-box PF00646.24 14.4 F-box domain
    F420_oxidored PF03807.8 −34.5 NADP oxidoreductase coenzyme F420-dependent
    FAD_binding_2 PF00890.15 −124.8 FAD binding_ domain
    FAD_binding_3 PF01494.10 −136.6 FAD binding domain
    FAE1_CUT1_RppA PF08392.3 −192.7 FAE1/Type III polyketide synthase-like protein
    FA_hydroxylase PF04116.4 −15.3 Fatty acid hydroxylase superfamily
    FBA_1 PF07734.4 −39.4 F-box associated
    FBPase PF00316.11 −170.3 Fructose-1-6-bisphosphatase
    FHA PF00498.17 25 FHA domain
    FMO-like PF00743.10 −381.6 Flavin-binding_monooxygenase-like
    FYVE PF01363.12 28.5 FYVE zinc finger
    Fcf1 PF04900.3 −7.6 Fcf1
    Fer2 PF00111.18 7 2Fe-2S iron-sulfur cluster binding domain
    FolB PF02152.9 25 Dihydroneopterin aldolase
    Fructosamin_kin PF03881.5 −125.6 Fructosamine kinase
    G-alpha PF00503.11 −230 G-protein alpha subunit
    G-patch PF01585.14 18.4 G-patch domain
    G6PD_C PF02781.7 −175 Glucose-6-phosphate dehydrogenase, C-terminal domain
    G6PD_N PF00479.13 -99 Glucose-6-phosphate dehydrogenase, NAD binding domain
    GASA PF02704.5 25 Gibberellin regulated protein
    GAT PF03127.5 −7 GAT domain
    GATase PF00117.19 −38.1 Glutamine amidotransferase class-I
    GFA PF04828.5 12.4 Glutathione-dependent formaldehyde-activating enzyme
    GH3 PF03321.4 −336 GH3 auxin-responsive promoter
    GHMP_kinases_C PF08544.4 20.8 GHMP kinases C terminal
    GHMP_kinases_N PF00288.17 17.1 GI-IMP kinases N terminal domain
    GIDA PF01134.13 −226.7 Glucose inhibited division protein A
    GLTP PF08718.2 −71.1 Glycolipid transfer protein (GLTP)
    GMP_synt_C PF00958.13 25 GMP synthase C terminal domain
    GST_C PF00043.16 22.3 Glutathione S-transferase, C-terminal domain
    GST_N PF02798.11 14.6 Glutathione S-transferase, N-terminal domain
    GTP_cyclohydro2 PF00925.11 −49 GTP cyclohydrolase II
    G_glu_transpept PF01019.12 −236.1 Gamma-glutamyltranspeptidase
    Gln-synt_C PF00120.15 −124 Glutamine synthetase, catalytic domain
    GlutR_N PF05201.6 −37.8 Glutamyl-tRNAGlu reductase, N-terminal domain
    GlutR_dimer PF00745.11 25 Glutamyl-tRNAGlu reductase, dimerisation domain
    Glutaminase PF04960.6 −143.6 Glutaminase
    Glutaredoxin PF00462.15 17.2 Glutaredoxin
    Glyco_tran_28_C PF04101.7 −10.4 Glycosyltransferase family 28 C-terminal domain
    Glyco_transf_29 PF00777.9 −74 Glycosyltransferase family 29 (sialyltransferase)
    Glyco_transf_8 PF01501.11 −43.2 Glycosyl transferase family 8
    Glycolytic PF00274.10 −174.5 Fructose-bisphosphate aldolase class-I
    Glycos_transf_1 PF00534.11 −7.3 Glycosyl transferases group 1
    Glyoxalase PF00903.16 12.1 Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily
    Gp_dh_C PF02800.11 −64.1 Glyceraldehyde 3-phosphate dehydrogenase, C-terminal domain
    Gp_dh_N PF00044.15 −74.2 Glyceraldehyde 3-phosphate dehydrogenase, NAD binding domain
    Hl0933_like PF03486.5 −255.8 Hl0933-like protein
    H_PPase PF03030.7 −377 Inorganic H+ pyrophosphatase
    Helicase_C PF00271.22 2.4 Helicase conserved C-terminal domain
    Hep_59 PF07052.2 25 Hepatocellular carcinoma-associated antigen 59
    Hexapep PF00132.15 0.3 Bacterial transferase hexapeptide (three repeats)
    Hin1 PF07320.4 25 Harpin-induced protein 1 (Hint)
    His_biosynth PF00977.12 −102.4 Histidine biosynthesis protein
    Histone PF00125.15 17.4 Core histone H2A/H2B/H3/H4
    Hpt PF01627.14 25 Hpt domain
    Hydrolase PF00702.17 13.6 haloacid dehalogenase-like hydrolase
    IF4E PF01652.9 −35 Eukaryotic initiation factor 4E
    IQ PF00612.18 11.9 IQ calmodulin-binding motif
    IU_nuc_hydro PF01156.10 −154 Inosine-uridine preferring nucleoside hydrolase
    Inositol_P PF00459.16 −55.6 Inositol monophosphatase family
    Invertase_neut PF04853.3 −233.6 Plant neutral invertase
    Ion_trans_2 PF07885.7 24.9 Ion channel
    Iso_dh PF00180.11 −97 Isocitrate/isopropylmalate dehydrogenase
    KH_1 PF00013.20 12.5 KH domain
    KH_2 PF07650.8 5 KH domain
    KR PF08659.1 −74.3 KR domain
    Kelch_1 PF01344.16 11.7 Kelch motif
    Kelch_2 PF07646.6 14 Kelch motif
    LAG1 PF03798.7 −57.5 Longevity-assurance protein (LAG1)
    LANC_like PF05147.4 −76.9 Lanthionine synthetase C-like protein
    LEA_5 PF00477.8 25 Small hydrophilic plant seed protein
    LRRNT_2 PF08263.3 18.6 Leucine rich repeat N-terminal domain
    LRR_1 PF00560.24 7.7 Leucine Rich Repeat
    LRR_2 PF07723.4 6 Leucine Rich Repeat
    LSM PF01423.13 13.7 LSM domain
    La PF05383.8 25 La domain
    Lectin_legB PF00139.10 −110.1 Legume lectin domain
    Ligase_CoA PF00549.10 −43.3 CoA-ligase
    Lipase_3 PF01764.16 −8 Lipase (class 3)
    MACPF PF01823.10 −24.6 MAC/Perforin domain
    MATH PF00917.17 0.5 MATH domain
    MFS_1 PF07690.7 23.5 Major Facilitator Superfamily
    MIP PF00230.11 −62 Major intrinsic protein
    MMR_HSR1 PF01926.14 31.2 GTPase of unknown function
    MOSC PF03473.8 25 MOSC domain
    MOSC_N PF03476.7 25 MOSC N-terminal beta barrel domain
    MT-A70 PF05063.5 −40.8 MT-A70
    Malic_M PF03949.6 −143.9 Malic enzyme, NAD binding domain
    MannoseP_isomer PF01050.9 −70 Mannose-6-phosphate isomerase
    Mem_trans PF03547.9 −73.4 Membrane transport protein
    Metalloenzyme PF01676.9 −14.4 Metalloenzyme superfamily
    Metallophos PF00149.19 22 Calcineurin-like phosphoesterase
    Methyltransf_11 PF08241.3 21 Methyltransferase domain
    Methyltransf_12 PF08242.3 23 Methyltransferase domain
    Methyltransf_2 PF00891.9 −103.8 O-methyltransferase
    Miro PF08477.4 10.8 Miro-like protein
    Mito_carr PF00153.18 0 Mitochondrial carrier protein
    Mov34 PF01398.12 0.9 Mov34/MPN/PAD-1 family
    MtN3_slv PF03083.7 9.7 MtN3/saliva family
    NAC PF01849.9 0 NAC domain
    NAD_Gly3P_dh_C PF07479.5 −50.8 NAD-dependent glycerol-3-phosphate dehydrogenase C-terminus
    NAD_Gly3P_dh_N PF01210.14 −44 NAD-dependent glycerol-3-phosphate dehydrogenase N-terminus
    NAD_binding_2 PF03446.6 −63.5 NAD binding domain of 6-phosphogluconate dehydrogenase
    NAD_binding_4 PF07993.3 −87.7 Male sterility protein
    NAF PF03822.5 4.5 NAF domain
    NAP PF00956.9 −122 Nucleosome assembly protein (NAP)
    NDK PF00334.10 −59.9 Nucleoside diphosphate kinase
    NHL PF01436.12 3.8 NHL repeat
    NIR_SIR PF01077.13 −19.6 Nitrite and sulphite reductase 4Fe-4S domain
    NIR_SIR_ferr PF03460.8 2.4 Nitrite/Sulfite reductase ferredoxin-like half domain
    NOI PF05627.2 0.3 Nitrate-induced NOI protein
    NOSIC PF08060.4 25 NOSIC (NUC001) domain
    NPH3 PF03000.5 25 NPH3 family
    NTF2 PF02136.11 6 Nuclear transport factor 2 (NTF2) domain
    NTP_transferase PF00483.14 −39.9 Nucleotidyl transferase
    Na_Ca_ex PF01699.15 25 Sodium/calcium exchanger protein
    Na_H_Exchanger PF00999.12 −67.9 Sodium/hydrogen exchanger family
    Na_sulph_symp PF00939.10 −259 Sodium: sulfate symporter transmembrane region
    Nfu_N PF08712.2 20 Scaffold protein Nfu/NifU N terminal
    NifU PF01106.8 −5.6 NifU-like domain
    NifU_N PF01592.7 −27.4 NifU-like N terminal domain
    Nodufin-like PF06813.4 −57.8 Nodulin-like
    Nop PF01798.9 25 Putative snoRNA binding domain
    Nramp PF01566.9 −171.4 Natural resistance-associated macrophage protein
    OPT PF03169.6 −238.6 OPT oligopeptide transporter protein
    ORC2 PF04084.5 −181.2 Origin recognition complex subunit 2
    OTCace PF00185.15 −42 Aspartate/omithine carbamoyltransferase, Asp/Om binding domain
    OTCace_N PF02729.12 −55 Aspartate/omithine carbamoyltransferase, carbamoyl-P binding
    domain
    PA PF02225.13 13 PA domain
    PAD_porph PF04371.6 −180.8 Porphyromonas-type peptidyl-arginine deiminase
    PALP PF00291.16 −70 Pyridoxal-phosphate dependent enzyme
    PAN_1 PF00024.17 1.4 PAN domain
    PAN_2 PF08276.2 −4.9 PAN-like domain
    PAP _fibrillin PF04755.3 25 PAP _fibrillin
    PB1 PF00564.15 12.3 PB1 domain
    PCl PF01399.18 25 PCl domain
    PDCD2_C PF04194.4 −40.9 Programmed cell death protein 2, C-terminal putative domain
    PDT PF00800.9 25 Prephenate dehydratase
    PEP-utilizers PF00391.14 0.6 PEP-utilising enzyme, mobile domain
    PEP-utilizers_C PF02896.9 −173 PEP-utilising enzyme, TIM barrel domain
    PGAM PF00300.13 −3 Phosphoglycerate mutase family
    PGI P F00342.10 −168.9 Phosphoglucose isomerase
    PGK PF00162.10 −39.3 Phosphoglycerate kinase
    PH P F00169.20 25.1 PH domain
    PHD PF00628.20 26.2 PHD-finger
    Pl-PLC-X PF00388.10 18.8 Phosphatidylinositol-specific phospholipase C, X domain
    Pl-PLC-Y PF00387.10 −11 Phosphatidylinositol-specific phospholipase C, Y domain
    PK PF00224.12 −244 Pyruvate kinase, barrel domain
    PK_C PF02887.7 −44 Pyruvate kinase, alpha/beta domain
    PLAC8 PF04749.8 −1.1 PLAC8 family
    PMEI PF04043.6 25 Plant invertase/pectin methylesterase inhibitor
    PP-binding PF00550.16 25.3 Phosphopantetheine attachment site
    PP2C PF00481.12 −36.3 Protein phosphatase 2C
    PPDK_N PF01326.10 −150.2 Pyruvate phosphate dikinase, PEP/pyruvate binding domain
    PPR PF01535.11 0 PPR repeat
    PRA1 PF03208.10 25 PRA1 family protein
    PRC PF05239.7 25 PRC-barrel domain
    PRK PF00485.9 −28.5 Phosphoribulokinase/Uridine kinase family
    PRMT5 PF05185.7 25 PRMT5 arginine-N-methyltransferase
    PTA_PTB PF01515.10 −165.5 Phosphate acetyl/butaryl transferase
    PTPA PF03095.6 −106 Phosphotyrosyl phosphate activator (PTPA) protein
    PTR2 PF00854.12 −50 POT family
    PTS_2-RNA PF01885.7 −48 RNA 2′-phosphotransferase, Tpt1/KptA family
    Pentapeptide PF00805.13 0 Pentapeptide repeats (8 copies)
    Peptidase_C12 PF01088.12 10 Ubiquitin carboxyl-terminal hydrolase, family 1
    Peptidase_C14 PF00656.13 −22.5 Caspase domain
    Peptidase_C48 PF02902.10 −13.1 Ulp1 protease family, C-terminal catalytic domain
    Peptidase_M16 PF00675.11 −38 Insulinase (Peptidase family M16)
    Peptidase_M16_C PF05193.12 7.9 Peptidase M16 inactive domain
    Peptidase_M18 PF02127.6 −250.8 Aminopeptidase I zinc metalloprotease (M18)
    Peptidase_M24 PF00557.15 −70.7 metallopeptidase family M24
    Peptidase_S8 PF00082.13 −51 Subtilase family
    Per1 PF04080.4 25 Per1-like
    Pescadillo_N PF06732.2 −167.1 Pescadillo N-terminus
    PfkB PF00294.15 −67.8 pfkB family carbohydrate kinase
    PhzC-PhzF PF02567.7 −66 Phenazine biosynthesis-like protein
    Pkinase P F00069.16 70.3 Protein kinase domain
    Pkinase_C PF00433.15 14.1 Protein kinase C terminal domain
    Pkinase_Tyr PF07714.8 65 Protein tyrosine kinase
    Polysacc_synt_2 PF02719.6 −176 Polysaccharide biosynthesis protein
    Porin_3 PF01459.13 −53 Eukaryotic porin
    Pre-SET PF05033.7 3.9 Pre-SET motif
    Pribosyltran PF00156.18 2 Phosphoribosyl transferase domain
    Pro _isomerase PF00160.12 −37 Cyclophilin type peptidyl-prolyl cis-trans isomerase/CLD
    Proteasome PF00227.17 −36.7 Proteasome A-type and B-type
    PsbW PF07123.3 6.7 Photosystem II reaction centre W protein (PsbW)
    Pyr_redox P F00070.18 5 Pyridine nucleotide-disulphide oxidoreductase
    Pyr_redox_2 PF07992.5 −20 Pyridine nucleotide-disulphide oxidoreductase
    Pyr_redox_dim PF02852.13 −13 Pyridine nucleotide-disulphide oxidoreductase, dimerisation domain
    Pyridoxal_deC P F00282.10 −158.6 Pyridoxal-dependent decarboxylase conserved domain
    Pyrophosphatase PF00719.10 −41 Inorganic pyrophosphatase
    RALF PF05498.2 25 Rapid ALkalinization Factor (RALF)
    RAMP4 PF06624.3 25 Ribosome associated membrane protein RAMP4
    RCC1 PF00415.9 21.2 Regulator of chromosome condensation (RCC1)
    RNA_pol_I_A49 PF06870.3 25 A49-like RNA polymerase I associated factor
    RNA_pol_N PF01194.8 25 RNA polymerases N/8 kDa subunit
    RNA_pol_Rpb5_C PF01191.10 25 RNA polymerase Rpb5, C-terminal domain
    RNA_pol_Rpb5_N PF03871.5 −8.9 RNA polymerase Rpb5, N-terminal domain
    RNase_PH PF01138.12 4 3′ exoribonuclease family, domain 1
    RNase_PH_C PF03725.6 20 3′ exoribonuclease family, domain 2
    RPE65 PF03055.6 −156.5 Retinal pigment epithelial membrane protein
    RRM_1 PF00076.13 17.7 RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain)
    RRM_2 PF04059.3 25 RNA recognition motif 2
    RRM_3 PF08777.2 0.5 RNA binding motif
    RRS1 PF04939.3 −60.5 Ribosome biogenesis regulatory protein (RRS1)
    Raffinose_syn PF05691.3 −395.7 Raffinose synthase or seed imbibition protein Sip1
    Ras PF00071.13 −69.9 Ras family
    Redoxin PF08534.1 −1 Redoxin
    Rep_fac_C PF08542.2 −0.4 Replication factor C
    Response_reg PF00072.15 4 Response regulator receiver domain
    Rho_GDI PF02115.8 −55 RHO protein GDP dissociation inhibitor
    Rhodanese PF00581.11 25 Rhodanese-like domain
    Rib_5-P_isom_A PF06026.5 −84.5 Ribose 5-phosphate isomerase A (phosphoriboisomerase A)
    Ribosomal_L12 PF00542.10 25 Ribosomal protein L7/L12 C-terminal domain
    Ribosomal_L7Ae PF01248.17 6 Ribosomal protein L7Ae/L30e/S12e/Gadd45 family
    Ribosomal_S5 PF00333.11 25 Ribosomal protein S5, N-terminal domain
    Ribosomal_S5_C PF03719.6 0 Ribosomal protein S5, C-terminal domain
    Ribosomal_S6e PF01092.10 25 Ribosomal protein S6e
    Ribul_P_3_epim PF00834.10 −97.3 Ribulose-phosphate 3 epimerase family
    Rick_17 kDa_Anti PF05433.6 23.2 Rickettsia 17 kDa surface antigen
    RmID_sub_bind PF04321.8 −171.8 RmID substrate binding domain
    SAM_1 PF00536.21 11.3 SAM domain (Sterile alpha motif)
    SAM_2 PF07647.8 0 SAM domain (Sterile alpha motif)
    SATase_N PF06426.5 25 Serine acetyltransferase, N-terminal
    SBF PF01758.7 −27.8 Sodium Bile acid symporter family
    SET PF00856.19 23.5 SET domain
    SFT2 PF07770.3 −14.4 SFT2-like protein
    SH3_1 PF00018.19 −8 SH3 domain
    SH3_2 PF07653.8 0 Variant SH3 domain
    SIP1 PF04938.3 25 Survival motor neuron (SMN) interacting protein 1 (SIP1)
    SMP PF04927.3 25 Seed maturation protein
    SNARE PF05739.10 23.8 SNARE domain
    SNF5 PF04855.3 25 SNF5/SMARCB1/INI1
    SQS_PSY PF00494.10 −78 Squalene/phytoene synthase
    SRF-TF PF00319.9 11 SRF-type transcription factor (DNA-binding and dimerisation domain)
    SRPRB PF09439.1 −45.6 Signal recognition particle receptor beta subunit
    SSB PF00436.16 0.4 Single-strand binding protein family
    STAS PF01740.12 0 STAS domain
    STT3 PF02516.5 −175 Oligosaccharyl transferase STT3 subunit
    SWIB PF02201.9 −5.7 SW IB/MDM2 domain
    SYF2 PF08231.3 25 SYF2 splicing factor
    S_locus_glycop PF00954.11 −12.7 S-locus glycoprotein family
    Sad1_UNC PF07738.4 −20.4 Sad1/UNC-like C-terminal
    Sect PF00995.14 −272 Sec1 family
    Sec61_beta PF03911.7 25 Sec61beta family
    Sedlin_N PF04628.4 −22.1 Sedlin, N-terminal conserved region
    SeIR PF01641.9 −66.5 SeIR domain
    Shikimate_DH PF01488.11 −4.4 Shikimate/quinate 5-dehydrogenase
    Sina PF03145.7 −48.4 Seven in absentia protein family
    Skp1 PF01466.10 −2 Skp1 family, dimerisation domain
    Skp1_POZ PF03931.6 14.9 Skp1 family, tetramerisation domain
    Smg4_UPF3 PF03467.6 −27.5 Smg-4/UPF3 family
    Snf7 PF03357.12 −22.9 Snf7
    Spc97_Spc98 PF04130.4 −136.8 Spc97/Spc98 family
    Steroid_dh PF02544.7 −44.7 3-oxo-5-alpha-steroid 4-dehydrogenase
    Str_synth PF03088.7 4.7 Strictosidine synthase
    Subtilisin_N PF05922.7 26.1 Subtilisin N-terminal Region
    Suc_Fer-like PF06999.3 −42.4 Sucrase/ferredoxin-like
    Sugar_tr PF00083.15 −85 Sugar (and other) transporter
    Sulfate_transp PF00916.11 −131.5 Sulfate transporter family
    Sybindin PF04099.3 −44.4 Sybindin-like family
    Synaptobrevin PF00957.12 25 Synaptobrevin
    Syntaxin PF00804.16 11.4 Syntaxin
    TATA_RF PF08612.2 25 TATA-binding related factor (TRF)
    TB2_DP1J-IVA22 PF03134.10 −6.9 TB2/DP1, HVA22 family
    TBC PF00566.9 −58 TBC domain
    TBP PF00352.12 −8 Transcription factor TFIID (or TATA-binding protein, TBP)
    TFIID-18 kDa PF02269.7 −7.3 Transcription initiation factor IID, 18 kD subunit
    TFIID-31 kDa PF02291.6 25 Transcription initiation factor IID, 31 kD subunit
    TFIID_30 kDa PF03540.4 25 Transcription initiation factor TFIID 23-30 kDa subunit
    TIM PF00121.9 −97 Triosephosphate isomerase
    TLC PF03219.5 25 TLC ATP/ADP transporter
    TPP_enzyme_C PF02775.12 19.7 Thiaminepyrophosphate enzyme, C-terminal TPP binding domain
    TPP_enzyme_M PF00205.13 −8.1 Thiamine pyrophosphate enzyme, central domain
    TPP_enzyme_N PF02776.9 −70 Thiamine pyrophosphate enzyme, N-terminal TPP binding domain
    TPT PF03151.7 −15.3 Triose-phosphate Transporter family
    Tbf5 PF06331.3 25 Transcription factor TFIIH complex subunit Tfb5
    Tetraspannin PF00335.11 −15.4 Tetraspanin family
    ThiF PF00899.12 −38.4 ThiF family
    Thioredoxin PF00085.11 −25.7 Thioredoxin
    Thr_dehydrat_C PF00585.9 −7.9 C-terminal regulatory domain of Threonine dehydratase
    Transket_pyr PF02779.15 −49 Transketolase, pyrimidine binding domain
    Transketolase_C PF02780.11 −15.5 Transketolase, C-terminal domain
    TrkA_C PF02080.12 25 TrkA-C domain
    TrkA_N PF02254.9 4.7 TrkA-N domain
    Tryp_alpha_amyl PF00234.13 −0.2 Protease inhibitor/seed storage/LTP family
    Tyr-DNA_phospho PF06087.3 −152.8 Tyrosyl-DNA phosphodiesterase
    U-box PF04564.6 −7.6 U-box domain
    U3_snoRNA_C PF09384.1 25 U3 small nucleolar RNA C terminal
    UBA PF00627.22 20.7 UBA/TS-N domain
    UBX PF00789.11 10 UBX domain
    UDPG_MGDP_dh PF00984.10 −6.9 UDP-glucose/GDP-mannose dehydrogenase family, central domain
    UDPG_MGDP_dh_C PF03720.6 0.8 UDP-glucose/GDP-mannose dehydrogenase family, UDP binding
    domain
    UDPG_MGDP_dh_N PF03721.5 −74.8 UDP-glucose/GDP-mannose dehydrogenase family, NAD binding
    domain
    UIM PF02809.11 16.6 Ubiquitin interaction motif
    UPF0061 PF02696.5 −200 Uncharacterized ACR, YdiU/UPF0061 family
    UPF0139 PF03669.4 25 Uncharacterised protein family (UPF0139)
    UPF0153 PF03692.6 11.7 Uncharacterised protein family (UPF0153)
    UPF0185 PF03671.5 11.6 Uncharacterised protein family (UPF0185)
    UQ_con PF00179.17 −30 Ubiquitin-conjugating enzyme
    Ubie_methyltran PF01209.9 −117 ubiE/COQ5 methyltransferase family
    Usp PF00582.17 21.6 Universal stress protein family
    V-ATPase_G PF03179.6 −19.8 Vacuolar (H+)-ATPase G subunit
    VHS PF00790.10 −13.2 VHS domain
    VQ PF05678.5 25 VQ motif
    WAK PF08488.2 25 Wall-associated kinase
    WD40 PF00400.23 21.5 WD domain, G-beta repeat
    Whi5 PF08528.2 25 Whi5 like
    X8 P F07983.4 −28.8 X8 domain
    XH PF03469.5 25 XH domain
    XS PF03468.5 25 XS domain
    YDG_SRA PF02182.8 25 YDG/SRA domain
    YIF1 PF03878.6 −81.2 YIF1
    YTH PF04146.6 25 YT521-B-like family
    Y_phosphatase2 PF03162.4 −47.6 Tyrosine phosphatase family
    YgbB PF02542.7 25 YqbB family
    Zip PF02535.13 −25.6 ZIP Zinc transporter
    adh_short PF00106.16 −40.2 short chain dehydrogenase
    dsrm PF00035.16 24.6 Double-stranded RNA binding motif
    eIF2A PF08662.2 0 Eukaryotic translation initiation factor eIF2A
    eIF3_subunit PF08597.1 11.9 Translation initiation factor eIF3 subunit
    efhand PF00036.23 21.7 EF hand
    efhand_like PF09279.2 8.8 Phosphoinositide-specific phospholipase C, efhand-like
    iPGM_N PF06415.4 −263.4 BPG-independent PGAM N-terminus (iPGM_N)
    mTERF PF02536.5 −60 mTERF
    malic P F00390.10 25 Malic enzyme, N-terminal domain
    p450 PF00067.13 −105 Cytochrome P450
    peroxidase PF00141.14 −10 Peroxidase
    polyprenyl_synt PF00348.8 −43 Polyprenyl synthetase
    tRNA-synt_1c P F00749.12 −130.2 tRNA synthetases class I (E and Q), catalytic domain
    tRNA-synt_1c_C PF03950.9 25 tRNA synthetases class I (E and Q), anti-codon binding domain
    zf-A20 PF01754.7 25 A20-like zinc finger
    zf-AN1 PF01428.7 0 AN1-like Zinc finger
    zf-C2H2 PF00096.17 17.7 Zinc finger, C2H2 type
    zf-C3HC4 PF00097.16 16 Zinc finger, C3HC4 type (RING finger)
    zf-CCCH PF00642.15 0 Zinc finger C-x8-C-x5-C-x3-H type (and similar)
    zf-CCHC PF00098.14 17.9 Zinc knuckle
    zf-DHHC PF01529.11 −11 DHHC zinc finger domain
    zf-MYND PF01753.9 11 MYND finger
    zf-Tim10_DDP PF02953.6 −5 Tim10/DDP family zinc finger
    • Example 10 Selection of Transgenic Plants with Enhanced Agronomic Trait(s)
  • This example illustrates identification of plant cells of the invention by screening derived plants and seeds for enhanced trait. Transgenic seed and plants in corn, soybean, cotton or canola with recombinant DNA identified in Table 2 are prepared by plant cells transformed with DNA that is stably integrated into the genome of the corn cell. Transgenic corn plant cells are transformed with recombinant DNA from each of the genes identified in Table 2. Progeny transgenic plants and seed of the transformed plant cells are screened for enhanced water use efficiency, enhanced cold tolerance, increased yield, enhanced nitrogen use efficiency, enhanced seed protein and enhanced seed oil as compared to control plants
    • A. Selection for Enhanced Nitrogen Use Efficiency
  • Transgenic corn seeds provided by the present invention are planted in fields with three levels of nitrogen (N) fertilizer being applied, e.g. low level (0 N), medium level (80 lb/ac) and high level (180 lb/ac). A variety of physiological traits are monitored. Plants with enhanced NUE provide higher yield as compared to control plants.
    • B. Selection for Increased Yield
  • Effective selection of enhanced yielding transgenic plants uses hybrid progeny of the transgenic plants for corn, cotton, and canola, or inbred progeny of transgenic plants for soybeanplants plant such as corn, cotton, canola, or inbred plant such as soy, canola and cottoncotton over multiple locations with plants grown under optimal production management practices, and maximum pest control. A target for improved yield is about a 5% to 10% increase or more in yield as compared to yield produced by plants grown from seed for a control plant. Selection methods can be applied in multiple and diverse geographic locations, for example up to 16 or more locations, over one or more planting seasons, for example at least two planting seasons, to statistically distinguish yield improvement from natural environmental effects.
    • C. Selection for Enhanced Water Use Efficiency (WUE)
  • The selection process imposes a water withholding period to induce stressdrought followed by watering. For example, for corn, a selection process imposes 3 drought/re-water cycles on plants over a total period of 15 days after an initial stress free growth period of 11 days. Each cycle consists of 5 days, with no water being applied for the first four days and a water quenching on the 5th day of the cycle. The primary phenotypes analyzed by the selection method are the changes in plant growth rate as determined by height and biomass during a vegetative drought treatment.
    • D. Selection for Growth Under Cold Stress
  • (1) Cold germination assay—Trays of transgenic and control seeds are placed in a growth chamber at 9.7° C. for 24 days (no light). Seeds having higher germination rates as compared to the control are identified.
  • (2) Cold field efficacy trial—A cold field efficacy trial is used to identify gene constructs that confer enhanced cold vigor at germination and early seedling growth under early spring planting field conditions in conventional-till and simulated no-till environments. Seeds are planted into the ground around two weeks before local farmers begin to plant corn so that a significant cold stress is exerted onto the crop, named as cold treatment. Seeds also are planted under local optimal planting conditions such that the crop has little or no exposure to cold condition, named as normal treatment. At each location, seeds are planted under both cold and normal conditions with 3 repetitions per treatment. Two temperature monitors are set up at each location to monitor both air and soil temperature daily.
  • Seed emergence is defined as the point when the growing shoot breaks the soil surface. The number of emerged seedlings in each plot is counted everyday from the day the earliest plot begins to emerge until no significant changes in emergence occur. In addition, for each planting date, the latest date when emergence is 0 in all plots is also recorded. Seedling vigor is also rated at V3-V4 stage before the average of corn plant height reaches 10 inches, with 1=excellent early growth, 5=Average growth and 9=poor growth. Days to 50% emergence, maximum percent emergence and seedling vigor are used to determine plants with enhanced cold tolerance.
  • E. Screens for Transgenic Plant Seeds with Increased Protein and/or Oil Levels
  • This example sets forth a high-throughput selection for identifying plant seeds with improvement in seed composition using the Infratec 1200 series Grain Analyzer, which is a near-infrared transmittance spectrometer used to determine the composition of a bulk seed sample (Table 26). Near infrared analysis is a non-destructive, high-throughput method that can analyze multiple traits in a single sample scan. An NIR calibration for the analytes of interest is used to predict the values of an unknown sample. The NIR spectrum is obtained for the sample and compared to the calibration using a complex chemometric software package that provides predicted values as well as information on how well the sample fits in the calibration.
  • Infratec Model 1221, 1225, or 1227 with transport module by Foss North America is used with cuvette, item #1000-4033, Foss North America or for small samples with small cell cuvette, Foss standard cuvette modified by Leon Girard Co. Corn and soy check samples of varying composition maintained in check cell cuvettes are supplied by Leon Girard Co. NIT collection software is provided by Maximum Consulting Inc. Software. Calculations are performed automatically by the software. Seed samples are received in packets or containers with barcode labels from the customer. The seed is poured into the cuvettes and analyzed as received.
  • TABLE 23
    Typical sample(s): Whole grain corn and soybean seeds
    Analytical time to Less than 0.75 min per sample
    run method:
    Total elapsed time per run: 1.5 minute per sample
    Typical and minimum Corn typical: 50 cc; minimum 30 cc
    sample size: Soybean typical: 50 cc; minimum 5 cc
    Typical analytical range: Determined in part by the specific
    calibration.
    Corn - moisture 5-15%, oil 5-20%,
    protein 5-30%, starch 50-75%, and density
    1.0-1.3%.
    Soybean - moisture 5-15%, oil 15-25%,
    and protein 35-50%.
    • Example 11 Cotton Transgenic Plants with Enhanced Agronomic Traits
  • Cotton transformation is performed as generally described in WO0036911 and in U.S. Pat. No. 5,846,797. Transgenic cotton plants containing each of the recombinant DNA having a sequence of SEQ ID NO: 1 through SEQ ID NO: 803 are obtained by transforming with recombinant DNA from each of the genes identified in Table 2. Progeny transgenic plants are selected from a population of transgenic cotton events under specified growing conditions and are compared with control cotton plants. Control cotton plants are substantially the same cotton genotype but without the recombinant DNA, for example, either a parental cotton plant of the same genotype that was not transformed with the identical recombinant DNA or a negative isoline of the transformed plant. Additionally, a commercial cotton cultivar adapted to the geographical region and cultivation conditions, e.g. cotton variety ST474, cotton variety FM 958, and cotton variety Siokra L-23, are used to compare the relative performance of the transgenic cotton plants containing the recombinant DNA. The specified culture conditions are growing a first set of transgenic and control plants under “wet” conditions, e.g. irrigated in the range of 85 to 100 percent of evapotranspiration to provide leaf water potential of −14 to −18 bars, and growing a second set of transgenic and control plants under “dry” conditions, e.g. irrigated in the range of 40 to 60 percent of evapotranspiration to provide a leaf water potential of −21 to −25 bars. Pest control, such as weed and insect control is applied equally to both wet and dry treatments as needed. Data gathered during the trial includes weather records throughout the growing season including detailed records of rainfall; soil characterization information; any herbicide or insecticide applications; any gross agronomic differences observed such as leaf morphology, branching habit, leaf color, time to flowering, and fruiting pattern; plant height at various points during the trial; stand density; node and fruit number including node above white flower and node above crack boll measurements; and visual wilt scoring. Cotton boll samples are taken and analyzed for lint fraction and fiber quality. The cotton is harvested at the normal harvest timeframe for the trial area. Enhanced water use efficiency is indicated by increased yield, improved relative water content, enhanced leaf water potential, increased biomass, enhanced leaf extension rates, and improved fiber parameters.
  • The transgenic cotton plants of this invention are identified from among the transgenic cotton plants by agronomic trait screening as having increased yield and enhanced water use efficiency.
    • Example 12 Canola Plants with Enhanced Agrominic Traits
  • This example illustrates plant transformation in producing the transgenic canola plants of this invention and the production and identification of transgenic seed for transgenic canola having enhanced water use efficiency, enhanced cold tolerance, increased yield, enhanced nitrogen use efficiency, enhanced seed protein and enhanced seed oil.
  • Tissues from in vitro grown canola seedlings are prepared and inoculated with a suspension of overnight grown Agrobacterium containing plasmid DNA with the gene of interest cassette and a plant selectable marker cassette. Following co-cultivation with Agrobacterium, the infected tissues are allowed to grow on selection to promote growth of transgenic shoots, followed by growth of roots from the transgenic shoots. The selected plantlets are then transferred to the greenhouse and potted in soil. Molecular characterizations are performed to confirm the presence of the gene of interest, and its expression in transgenic plants and progenies. Progeny transgenic plants are selected from a population of transgenic canola events under specified growing conditions and are compared with control canola plants. Control canola plants are substantially the same canola genotype but without the recombinant DNA, for example, either a parental canola plant of the same genotype that is not transformed with the identical recombinant DNA or a negative isoline of the transformed plant
  • Transgenic canola plant cells are transformed with recombinant DNA from each of the genes identified in Table 2. Transgenic progeny plants and seed of the transformed plant cells are screened for enhanced water use efficiency, enhanced cold tolerance, increased yield, enhanced nitrogen use efficiency, enhanced seed protein and enhanced seed oil.
    • Example 13 Selection of Transgenic Plants with Enhanced Agronomic Trait(s)
  • This example illustrates the preparation and identification by selection of transgenic seeds and plants derived from transgenic plant cells of this invention where the plants and seed are identified by screening for a transgenic plant having an enhanced agronomic trait imparted by expression or suppression of a protein selected from the group including the homologous proteins identified in Example 7. Transgenic plant cells of corn, soybean, cotton, canola, alfalfa, wheat and rice are transformed with recombinant DNA for expressing or suppressing each of the homologs identified in Example 7. Plants are regenerated from the transformed plant cells and used to produce progeny plants and seed that are screened for enhanced water use efficiency, enhanced cold tolerance, increased yield, enhanced nitrogen use efficiency, enhanced seed protein and enhanced seed oil. Plants are identified exhibiting enhanced traits imparted by expression or suppression of the homologous proteins.
    • Example 14 Monocot and Dicot Plant Transformation for the Suppression of Endogeneous Protein
  • This example illustrates monocot and dicot plant transformation to produce nuclei of this invention in cells of a transgenic plant by transformation where the recombinant DNA suppresses the expression of an endogenous protein identified in Table 24.
  • Corn, soybean, cotton, or canola tissue are transformed as described in Examples 2-5 using recombinant DNA in the nucleus with DNA that is transcribed into RNA that forms double-stranded RNA targeted to an endogenous gene with DNA encoding the protein. The genes for which the double-stranded RNAs are targeted are the native gene in corn, soybean, cotton or canola that are homologs of the genes encoding the protein that has the function of the protein of Arabidopsis thaliana as identified in Table 24.
  • Populations of transgenic plants prepared in Examples 3, 4, 5, 6, or 13 with DNA for suppressing a gene identified in Table 2 as providing an enhanced trait by gene suppression are screened to identify an event from those plants with a nucleus of the invention by selecting the trait identified in this specification.
  • TABLE 24
    PEP
    SEQ Construct
    ID Pfam module ID Traits
    115 AP2 10177 LN
    116 zf-C2H2 12155 CS SS
    118 F-box::Tub 11873 LN PEG
    154 Pex2_Pex12::zf-C3HC4 11113 CS
    Myb_DNA-binding::Myb_DNA-
    188 binding 12325 LN
    200 bZIP_1 71228 CK

Claims (14)

What is claimed is:
1. A plant cell nucleus with stably-integrated, recombinant DNA comprising a promoter that is functional in plant cells and that is operably linked to protein coding DNA encoding a protein having an amino acid sequence comprising a Pfam domain module NTP_transferase::Hexapep::Hexapep::Hexapep;
wherein said plant cell nucleus is selected by screening a population of transgenic plants that have said recombinant DNA in its nuclei and express said protein for an enhanced trait as compared to control plants that do not have said recombinant DNA in their nuclei; and
wherein said enhanced trait is selected from group of enhanced traits consisting of enhanced water use efficiency, enhanced cold tolerance, enhanced heat tolerance, increased yield, enhanced nitrogen use efficiency, enhanced seed protein and enhanced seed oil.
2. A plant cell nucleus with stably integrated, recombinant DNA, wherein
(a) said recombinant DNA comprises a promoter that is functional in said plant cell and that is operably linked to a protein coding DNA encoding a protein having an amino acid sequence comprising a Pfam domain module selected from the group consisting of Syntaxin::SNARE, Pro_isomerase, Pkinase, ATP-synt_G, Carboxyl_trans, CDC50, GATase::GMP_synt_C, F-box::WD40::WD40::WD40, dsrm::dsrm, Pyr_redox—2::Pyr_redox_dim, WAK::Pkinase, Pkinase_Tyr, PTPA, Biotin_lipoyl::E3_binding::2-oxoacid_dh, AAA, LRRNT—2::LRR—1::LRR—1::LRR—1, PRA1, TIM, YTH, ThiF, Hep—59, Pkinase, PALP::Thr_dehydrat_C::Thr_dehydrat_C, zf-Tim10_DDP, CAF1, Pkinase, Pyr_redox—2::Pyr_redox_dim, Response_reg, YIF1, NPH3, LRRNT—2::LRR—1::LRR—1::LRR—1::LRR—1::Pkinase_Tyr, NOI, Fer2, AA_permease, Caleosin, IF4E, Pkinase, Ribul_P—3_epim, F-box::WD40::WD40::WD40::WD40::WD40::WD40, MIP, p450, Ribosomal_S5::Ribosomal_S5_C, Hpt, TBC, Acyltransferase, Epimerase, Pkinase, Dus, Se1R, PH, Tyr-DNA_phospho, RRM—1, Pkinase, ECH, SRPRB, DUF599, Pkinase::efhand::efhand::efhand::efhand, ORC2, PMEI, p450, GLTP, Suc_Fer-like, CBS::CBS, ADH_N::ADH_zinc_N, LRRNT—2::LRR—1::LRR—1::LRR—1::Pkinase, F-box, adh_short, polyprenyl_synt, GHMP_kinases_N::GHMP_kinases_C, PsbW, Na_H_Exchanger::TrkA_C, Ribosomal_L12, CDC50, DCP1, Pyr_redox—2::Pyr_redox_dim, Steroid_dh, tRNA-synt—1c:::tRNA-synt—1c_C, Cupin—1::Cupin—1, peroxidase, Sugar_tr, Pro_isomerase, Iso_dh, PTS—2-RNA, Aminotran—5, ENOD93, KH—1::KH—1::KH—1::KH—1::KH—1, Mito_carr::Mito_carr::Mito_carr, DUF569::DUF569, C1—2::C1—2::C1—3::C1—2::C1—3::C1—2, DnaJ::zf-C2H2, Aldedh, AAA::Rep_fac_C, DUF641, Aminotran—1—2, TB2_DP1_HVA22, zf-C3HC4, RRM—1::RRM—2, Pkinase, PPR::PPR::PPR::PPR::PPR::PPR::PPR::PPR::PPR::PPR::PPR, Pyr_redox—2, IQ::IQ, SMP::SMP::SMP, AWPM-19, CLP_protease, Pkinase::NAF, PRMT5, PPR::PPR::PPR::PPR::PPR::PPR, Aldedh, ATP-synt_C::ATP-synt_C, adh_short, RCC1::RCC1::RCC1::RCC1::FYVE::DZC, p450, PfkB, PB1, Hexapep::Hexapep::Hexapep::Hexapep, Aminotran—1—2, DUF862, Aldedh, ADH_N::ADH_zinc_N, CDC48—N::AAA::AAA, AA_permease, UQ_con, Mem_trans, GFA, OPT, DUF887, Di19, U-box::Arm::Arm, DAO, G-alpha, Aminotran—3, 2OG-FeII_Oxy, Lectin_legB::Pkinase, NAC::UBA, efhand_like::PI-PLC-X::PI-PLC-Y::C2, TLC, ATP-grasp—2::Ligase_CoA, Pkinase, PRC::PRC, MFS—1::Sugar_tr, Copine::zf-C3HC4, RRM—1::RRM—1::RRM—1, Pribosyltran, AA_kinase, PhzC-PhzF, Gp_dh_N::Gp_dh_C, Sugar_tr, Pre-SET::SET, Alpha-amylase::Alpha-amyl_C2, Cyclin_N, FAE1_CUT1_RppA::ACP_syn_III_C, RPE65, efhand_like::PI-PLC-X::PI-PLC-Y::C2, Mito_carr::Mito_carr::Mito_carr, Invertase_neut, DSPc, LANC_like, Aminotran—5, Glutaminase, PPR::PPR::PPR::PPR::PPR::PPR::PPR::PPR, PGI, SSB, p450, La::RRM—1::RRM—3, Methyltransf—11, SBF, NTP_transferase::Hexapep::Hexapep::Hexapep, Mov34, Hydrolase, AAA, RRM—1::RRM—1, Pkinase::NAF, F-box::FBA—1, p450, F-box::LRR—2, zf-DHHC, TBP::TBP, DUF607, FMO-like, adh_short, ATP-synt_ab_N::ATP-synt_ab, RNase_PH, PP2C, UQ_con, Aminotran—1—2, p450, FMO-like, Gp_dh_N::Gp_dh_C, Mito_carr::Mito_carr::Mito_carr, zf-CCCH::zf-CCCH::zf-CCCH::zf-CCCH::zf-CCCH, GST_C, GH3, PAP_fibrillin, ThiF, Ribul_P—3_epim, DUF260, p450, MACPF, Steroid_dh, Response_reg, Carb_anhydrase, Aldedh, Pkinase, Methyltransf—11, PK::PK_C, Pkinase, DEK_C::SWIB::SWIB, TATA_RF, Tryp_alpha_amyl, Y_phosphatase2, TATA_RF, NifU_N, ENT, Pkinase, F-box::Kelch—2::Kelch—2, WD40::WD40, MtN3_slv::MtN3_slv, TB2_DP1_HVA22, Pkinase, Aldedh, AAA, Pyridoxal_deC, zf-CCHC::zf-CCHC::zf-CCHC::zf-CCHC, Peptidase_M24, LRRNT—2::LRR—1::LRR—1::LRR—1::LRR—1::Pkinase, Arf, DUF1279, UPF0185, Rhodanese, adh_short, Tryp_alpha_amyl, Pkinase, UPF0139, CBS, Glyco_transf—29, iPGM_N::Metalloenzyme, Proteasome, Pkinase, UBX, ELFV_dehydrog_N::ELFV_dehydrog, p450, ADH_N::ADH_zinc_N, zf-C3HC4, NDK, NAD_Gly3P_dh_N::NAD_Gly3P_dh_C, GlutR_N::Shikimate_DH::GlutR_dimer, p450, SNF5, p450, Pribosyltran, AIG1, Response_reg::CCT, mTERF, DUF220, Pkinase::NAF, zf-CCCH::zf-CCCH, Pkinase, Pkinase, MATH::MATH, Asparaginase, Pkinase, Gp_dh_N::Gp_dh_C, Pkinase, KH—1, Fcf1, PK::PK_C::PEP-utilizers, CRAL_TRIO_N::CRAL_TRIO, Raffinose_syn, DUF584, BT1, Aminotran—1—2, C1—2::C1—3::C1—3::C1—2::C1—3::C1—3::C1—2, FMO-like, PLACE, F-box::Kelch—2::Kelch—1::Kelch—2, XS::XH, STT3, ABC_tran::ABC_tran, Aldo_ket_red, NTF2::RRM—1, DUF594, Biotin_lipoyl::2-oxoacid_dh, RRM—1, FHA, Mov34, MT-A70, Brix, X8, Auxin_inducible, Peptidase_M18, Sec61_beta, F-box::Kelch—1::Kelch—1, Brix, TIM, CTP_transf—1, Tetraspannin, PALP, DUF822, Pkinase, B3::B3, MFS—1, SFT2, F-box::Kelch—1::Kelch—1, DUF588, Thioredoxin, Alba, Ion_trans—2::Ion_trans—2, Peptidase_C48, YDG_SRA::Pre-SET::SET, Aldedh, Abhydrolase—3, p450, U-box::Arm::Arm::Arm::Arm, AA_permease, LAG1, peroxidase, PAD_porph, Pkinase, F-box, AIG2, p450, AARP2CN::DUF663, UPF0153, NAD_binding—2::6 PGD, Pkinase, B_lectin::S_locus_glycop::PAN—1::Pkinase, EMP24_GP25L, DUF6::DUF6, DUF163, Sina, adh_short, Rho_GDI, zf-CCHC::zf-CCHC::zf-CCHC::zf-CCHC::zf-CCHC::zf-CCHC::zf-CCHC, VHS::GAT, Pyrophosphatase, DMRL_synthase, Cyclin_N::Cyclin_C, NDK, TPP_enzyme_N::TPP_enzyme_M::TPP_enzyme_C, SH3—1, UDPG_MGDP_dh_N::UDPG_MGDP_dh::UDPG_MGDP_dh_C, UIM::efhand, DUF579, Pkinase, DHBP_synthase::GTP_cyclohydro2, Peptidase_C14, Glycolytic, Pkinase, Lipase—3, LRRNT—2::LRR—1::LRR—1::LRR—1::LRR—1, Snf7, BT1, PPDK_N::PEP-utilizers::PEP-utilizers_C, V-ATPase_G, RNA_pol_I_A49, Zip, WD40::WD40::WD40, Branch, RCC1::RCC1::RCC1::RCC1, TFIID-18kDa, Pkinase, Cullin, TFIID-31 kDa, Asp, Pkinase, Ubie_methyltran, PPR::PPR, PPR::PPR::PPR::PPR::PPR::PPR::PPR, Fructosamin_kin, PPR::PPR::PPR::PPR::PPR::PPR, Pkinase_Tyr, p450, AA_permease, Glycos_transf—1, ECH::3HCDH_N::3HCDH, MIP, ADH_N::ADH_zinc_N, Aa_trans, DUF1517, Redoxin, RRS1, Pribosyltran, Sulfate_transp::STAS, DUF167, MMR_HSR1::DUF933, Aminotran—1—2, AA_permease, DUF620, Aldedh, Aminotran—1—2, LRR—1, CDP-OH_P_transf, DHBP_synthase::GTP_cyclohydro2, NHL::NHL, WD40::U3_snoRNA_C, Na_sulph_symp, adh_short, Thioredoxin, Ribosomal_L7Ae, OTCace_N::OTCace, Mito_carr::Mito_carr::Mito_carr, Pescadillo_N::BRCT, PPR::PPR::PPR::PPR::PPR::PPR::PPR::PPR::PPR::PPR, mTERF, Chalcone, Per1, PPR::PPR, Na_H_Exchanger::TrkA_N, DEAD::Helicase_C, Cyclin_N::Cyclin_C, PP-binding, SRF-TF, SATase_N::Hexapep::Hexapep::Hexapep, PK::PK_C, adh_short, DUF6::DUF6, Pyr_redox—2, G-patch, WD40::WD40::WD40::WD40, G-alpha, VQ, WD40::WD40::WD40::WD40::WD40, Aminotran—3, Pribosyltran, LRRNT—2::LRR—1::LRR—1::LRR—1::LRR—1::LRR—1, elF3_subunit, H_PPase, Nodulin-like, Whi5, Tryp_alpha_amyl, NIR_SIR_ferr::NIR_SIR::NIR_SIR_ferr, RRM—1::RRM—1, Band—7, Asp, MFS—1, F420_oxidored, Pkinase, PRK, Na_Ca_ex::Na_Ca_ex, Bombesin, Pkinase, Epimerase, Pkinase, Inositol_P, Arm::Arm::Arm::Arm, PB1, Hin1, p450, RNA_pol_Rpb5_N::RNA_pol_Rpb5_C, Adap_comp_sub, Peptidase_M16::Peptidase_M16—C, Pkinase, PGK, Biotin_lipoyl::E3_binding::2-oxoacid_dh, Alg6_Alg8, F-box, MMR_HSR1, G6PD_N::G6PD_C, DAD, malic::Malic_M::PTA_PTB, ADH_N::ADH_zinc_N, LRR—1::LRR—1::LRR—1::LRR—1:LRR—1::LRR—1::LRR—1, PfkB, PA, Pyr_redox—2::Pyr_redox_dim, SIP1, PP2C, BT1, AhpC-TSA, GASA, Aminotran—3, Sad1_UNC, Pkinase, zf-MYND::PDCD2—C, Pkinase, PGK, ArfGap, GATase::GMP_synt_C, p450, DUF1637, 2OG-FeII_Oxy, Aldedh, DUF231, Glyco_transf—8, Sec1, DUF1475, Cellulose_synt, RRM—1::RRM—1::RRM—1, Usp, AA_permease, Acetyltransf—1::Bromodomain, Glyco_tran—28_C, RNA_pol_N, NTP_transferase, malic::Malic_M, Histone, Epimerase, UPF0061, ClpS, LEA—5, Auxin_inducible, PAP_fibrillin, Aldo_ket_red, Gln-synt_C, DREPP, p450, SFT2, eIF2A, Cenp-O, CPSase_sm_chain::GATase, WD40::WD40::WD40, Pkinase, Porin—3, Pkinase, Aminotran—1—2, GST_N::GST_C, F-box::Kelch—1::Kelch—1, IU_nuc_hydro, SYF2, PDT, Subtilisin_N::PA, Sugar_tr, WD40::WD40, p450, DUF829, Pyr_redox—2::Pyr_redox_dim, Aminotran—1—2, Cyclin_N::Cyclin_C, YgbB, Sugar_tr, SRF-TF, DUF231, DUF584, BT1, zf-C3HC4, Metallophos, FA_hydroxylase, p450, ACBP::Ank::Ank, LSM, SAM—1, LRR—1::LRR—1::Pkinase, Cullin, F-box::FBA—1, peroxidase, Rib—5-P_isom_A, zf-A20::zf-AN1, Dimerisation::Methyltransf—2, PGAM, PTR2, Copine, PALP, Exo_endo_phos, G6PD_N::G6PD_C, PLAC8, Aldo_ket_red, Ank::Ank, FBPase, zf-C3HC4, ACT::ACT, Suc_Fer-like, Pkinase_Tyr, G-alpha, RAMP4, Glutaredoxin, RRM—1::RRM—1, MT-A70, Response_reg::CCT, Arf, AP2, DUF177, 200-FeII_Oxy, LRRNT—2::LRR—1::LRR—1::LRR—1::LRR—1::LRR—1, LRR—1, Aldedh, DUF1350, FAE1_CUT1_RppA::ACP_syn_III_C, Sybindin, zf-C3HC4, Nfu_N::NifU, Rho_GDI, PK::PK_C, NOSIC::Nop, PK::PK_C, PRK::Pribosyltran, PfkB, p450, DUF231, TFIID—30 kDa, Aldedh, zf-AN1, GHMP_kinases_N::GHMP_kinases_C, DUF423, Pkinase, Cu-oxidase—3::Cu-oxidase::Cu-oxidase—2, PCI, RNase_PH::RNase_PH_C, DUF59, NTP_transferase, CH::EB1, Pkinase::Pkinase_C, DUF866, SMP::SMP::SMP, Aminotran—3, Transket_pyr::Transketolase_C, Copine, His_biosynth, Tbf5, DUF543, p450, C2, DUF616, Gp_dh_N::Gp_dh_C, Smg4_UPF3, DUF231, DUF89, WD40::WD40, Aldedh, ACT::ACT::ACT::ACT, Pkinase, Pyridoxal_deC, Skp1_POZ::Skp1, NAP, FolB, p450, Pentapeptide::Pentapeptide, NTP_transferase::MannoseP_isomer, SQS_PSY, Cyclase, GASA, Rick—17 kDa_Anti, FMO-like, B_lectin::S_locus_glycop::PAN—2, Peptidase_C12, Ribosomal_S6e, Glyoxalase, Response_reg::CCT, PHD::SET, Redoxin, G_glu_transpept, Synaptobrevin, p450, RALF, PALP, Branch, DUF579, Aminotran—3, Nramp, Enolase_N::Enolase_C, Str_synth, FAD_binding—3, MOSC_N::MOSC, Spc97_Spc98, Glycolytic, F-box::WD40::WD40::WD40::WD40, AA_kinase::ACT::ACT, RALF, and ATP_bind—1;
(b) said recombinant DNA comprises a promoter that is functional in said plant cell and that is operably linked to a protein coding DNA encoding a protein comprising an amino acid sequence with at least 90% identity to a consensus amino acid sequence selected from the group consisting of SEQ ID NO: 94617 through 94734;
(c) said recombinant DNA comprises a promoter that is functional in plant cells and that is operably linked to a protein coding DNA encoding a protein comprising an amino acid sequence selected from the group consisting of 819, 867, 906, 914, 967, 1009, 1040, 1086, 1107, 1227, 1233, 1250, 1293, 1311, 1320, 1342, 1364, 1365, 1373, 1398, 1402, 1439, 1443, 1473, 1495, 1539, 1596, and homologs thereof listed in table 19;
(d) said recombinant DNA comprises a promoter that is functional in said plant cell and that is operably linked to a protein coding recombinant DNA encoding a protein having an amino acid sequence having at least 70% identity to an amino acid sequence of SEQ ID NO 1227;
(e) said recombinant DNA suppresses comprises a promoter that is functional in said plant cell and operably linked to DNA that transcribe into RNA that suppresses the level of an endogenous protein wherein said endogenous protein has an amino acid sequence comprising a pfam domain module selected from the group consisting of DUF1475, DUF1350, Arm::Arm::Arm::Arm, NifU_N, ATP_bind—1, DUF599, LRR—1, Pyr_redox—2::Pyr_redox_dim, malic::Malic_M, Glycolytic, IF4E, Pkinase, UPF0139, GlutR_N::Shikimate_DH::GlutR_dimer, PLAC8, PLAC8, DUF220, OPT, Glyco_transf—8, Per1, Usp, mTERF, PB1, CAF1, Pkinase, F-box::Kelch—1::Kelch—1, PHD::SET, Nfu_N::NifU, RCC1::RCC1::RCC1::RCC1, X8, Pkinase::NAF, UIM::effiand, Glutaredoxin, DUF1517, Cupin—1::Cupin—1, ClpS, Spc97_Spc98, Subtilisin_N::PA, CBS, PTPA, p450, AA_permease, Sina, p450, Mov34, Thioredoxin, SATase_N::Hexapep::Hexapep::Hexapep, Epimerase, RRM—1::RRM—2, Synaptobrevin, Ribosomal_S6e, Redoxin, MFS—1, PPR::PPR, NPH3, and DUF866; or
(f) said recombinant DNA comprises a promoter that is functional in said plant cell and operably linked to DNA that transcribe into RNA that suppresses the level of an endogenous protein wherein said endogenous protein has an amino acid sequence with at least 70% identity to an amino acid sequence selected from the group consisting of SEQ ID NO: 811, 813, 819, 891, 893, 909, 911, 1439, 1584, and homologs thereof listed in table 16;
and wherein said plant cell nucleus is selected by screening a population of transgenic plants that have said recombinant DNA and an enhanced trait as compared to control plants that do not have said recombinant DNA in their nuclei; and wherein said enhanced trait is selected from group of enhanced traits consisting of enhanced water use efficiency, enhanced cold tolerance, enhanced heat tolerance, enhanced resistance to salt exposure, enhanced shade tolerance, increased yield, enhanced nitrogen use efficiency, enhanced seed protein and enhanced seed oil.
3. The plant cell nucleus of claim 2 wherein said protein coding DNA encodes a protein having an amino acid sequence selected from the group consisting of SEQ ID NO: 804 through SEQ ID NO: 94613.
4. The plant cell nucleus of claim 2 further comprising DNA expressing a protein that provides tolerance from exposure to an herbicide applied at levels that are lethal to a wild type of said plant cell.
5. The plant cell nucleus of claim 4 wherein said herbicide is a glyphosate, dicamba, or glufosinate compound.
6. A transgenic plant cell or plant comprising a plurality of plant cells with the plant cell nucleus of claim 2.
7. The transgenic plant cell or plant of claim 6 which is homozygous for said recombinant DNA.
8. A transgenic seed comprising a plurality of plant cells with a plant cell nucleus of claim 2.
9. The transgenic seed of claim 8 from a corn, soybean, cotton, canola, alfalfa, wheat or rice plant.
10. A transgenic pollen grain comprising a haploid derivative of a plant cell nucleus of claim 2.
11. A method for manufacturing non-natural, transgenic seed that can be used to produce a crop of transgenic plants with an enhanced trait resulting from expression of recombinant DNA in a nucleus of claim 2, wherein said method for manufacturing said transgenic seed comprising:
(a) screening a population of plants for said enhanced trait and said recombinant DNA, wherein individual plants in said population can exhibit said trait at a level less than, essentially the same as or greater than the level that said trait is exhibited in control plants which do not contain the recombinant DNA, wherein said enhanced trait is selected from the group of enhanced traits consisting of enhanced water use efficiency, enhanced cold tolerance, enhanced heat tolerance, enhanced high salinity tolerance, enhanced shade tolerance, increased yield, enhanced nitrogen use efficiency, enhanced seed protein and enhanced seed oil,
(b) selecting from said population one or more plants that exhibit said trait at a level greater than the level that said trait is exhibited in control plants, and
(c) collecting seeds from selected plant selected from step b.
12. The method of claim 11 wherein said method for manufacturing said transgenic seed further comprising
(a) verifying that said recombinant DNA is stably integrated in said selected plants, and
(b) analyzing tissue of said selected plant to determine the expression or suppression of a protein having the function of a protein having an amino acid sequence selected from the group consisting of SEQ ID NO:804-1606.
13. The method of claim 11 wherein said seed is corn, soybean, cotton, alfalfa, canola wheat or rice seed.
14. A method of producing hybrid corn seed comprising:
(a) acquiring hybrid corn seed from a herbicide tolerant corn plant which also has stably-integrated, recombinant DNA in a nucleus of claim 2;
(b) producing corn plants from said hybrid corn seed, wherein a fraction of the plants produced from said hybrid corn seed is homozygous for said recombinant DNA, a fraction of the plants produced from said hybrid corn seed is hemizygous for said recombinant DNA, and a fraction of the plants produced from said hybrid corn seed has none of said recombinant DNA;
(c) selecting corn plants which are homozygous and hemizygous for said recombinant DNA by treating with an herbicide;
(d) collecting seed from herbicide-treated-surviving corn plants and planting said seed to produce further progeny corn plants;
(e) repeating steps (c) and (d) at least once to produce an inbred corn line; and
(f) crossing said inbred corn line with a second corn line to produce hybrid seed.
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