Transgenic plants with enhanced agronomic traits

Abstract
This invention provides transgenic plant cells with recombinant DNA for expression of proteins that are useful for imparting enhanced agronomic trait(s) to transgenic crop plants. This invention also provides transgenic plants and progeny seed comprising the transgenic plant cells where the plants are selected for having an enhanced trait selected from the group of traits consisting of enhanced water use efficiency, enhanced cold tolerance, increased yield, enhanced nitrogen use efficiency, enhanced seed protein and enhanced seed oil. Also disclosed are methods for manufacturing transgenic seed and plants with enhanced traits.
Description
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 text file named 3126.015US2.txt, which is 103,067,648 bytes (measured in MS-WINDOWS), were created on Sep. 24, 2014, and are herein incorporated by reference.


INCORPORATION OF COMPUTER PROGRAM LISTING

Two copies of the Computer Program Listing (Copy 1 and Copy 2) and a computer readable form (CRF) containing folders hmmer-2.3.2 and 248pfamDir, all on CD-Rs are 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 248pfamDir contains 248 Pfam Hidden Markov Models. Both folders were created on CD-R on Sep. 24, 2014, having a total size of 20,111,360 bytes (measured in MS-WINDOWS).


INCORPORATION OF TABLE

Two copies of Table 9 (Copy 1 and Copy 2) and a computer readable form (CRF), all on CD-Rs, each containing the file named 38-21(54146)APCT_table9.txt, which is 319,488 bytes (measured in MS-WINDOWS), were created on Sep. 24, 2014, and comprise 74 pages when viewed in MS Word, are herein incorporated by reference.


FIELD OF THE INVENTION

Disclosed herein are inventions in the filed of plant genetics and developmental biology. More specifically, the present inventions provide plant cells with recombinant DNA for providing an enhanced trait in a transgenic plant, plants comprising such cells, seed and pollen derived from such plants, methods of making and using such cells, plants, seeds and pollen.


BACKGROUND OF THE INVENTION

Transgenic plants with improved agronomic traits such as yield, environmental stress tolerance, pest resistance, herbicide tolerance, improved seed compositions, and the like are desired by both farmers and consumers. Although considerable efforts in plant breeding have provided significant gains in desired traits, the ability to introduce specific DNA plant genomes provides further opportunities for generation of plants with improved and/or unique traits. Merely introducing recombinant DNA into a plant genome doesn't always produce a transgenic plant with an enhanced agronomic trait. Methods to select individual transgenic events from a population are required to identify those transgenic events that are characterized by the enhanced agronomic trait.


SUMMARY OF THE INVENTION

This invention provides plant cell nuclei with recombinant DNA that imparts enhanced agronomic traits in transgenic plants having the nuclei in their cells, e.g. enhanced water use efficiency, enhanced cold tolerance, increased yield, enhanced nitrogen use efficiency, enhanced seed protein or enhanced seed oil. Such recombinant DNA in a plant cell nucleus 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. 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 9. 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: 30328, and SEQ ID NO: 30377 through SEQ ID NO: 30418. Alternatively, in other cases where neither a Pfam domain module nor a consensus amino acid sequence is available, such DNA in the construct is defined by the sequence of a specific encoded and/or its homologous proteins.


Other aspects of the invention are specifically directed to transgenic plant cells comprising the recombinant DNA of the invention, transgenic plants comprising a plurality of such plant cells, progeny transgenic seed, embryo and transgenic pollen from such plants. Such plant cells are selected from a population of transgenic plants regenerated from plant cells transformed with recombinant DNA and that express the protein by screening transgenic plants in the population for an enhanced trait as compared to control plants that do not have said recombinant DNA, where the enhanced trait is selected from group of enhanced traits consisting of enhanced water use efficiency, enhanced cold tolerance, increased yield, enhanced nitrogen use efficiency, enhanced seed protein and enhanced seed oil.


In yet another aspect of the invention the plant cells, plants, seeds, embryo 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 of said plant cell. Such tolerance is especially useful not only as an advantageous trait in such plants but is also useful in a selection step in the methods of the invention. In aspects of the invention the agent of such herbicide is a glyphosate, dicamba, or glufosinate compound.


Yet other aspects of the invention provide transgenic plants which are homozygous for the recombinant DNA and transgenic seed of the invention from corn, soybean, cotton, canola, alfalfa, wheat or rice plants.


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 (d) verifying that the recombinant DNA is stably integrated in said selected plants; and (e) 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: 1-358; 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 transgenic plants are selected by identifying plants with the enhanced trait. The methods are especially useful for manufacturing corn, soybean, cotton, alfalfa, wheat or rice seed 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 stably-integrated, recombinant DNA comprising a promoter that is (a) functional in plant cells and (b) is operably linked to DNA that encodes a protein. Such protein is 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 9. Alternatively, e.g. where a Pfam domain module is not available, such protein is defined by 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: 30328, and SEQ ID NO: 30377 through SEQ ID NO: 30418. Alternatively, in other cases where neither a Pfam domain module nor a consensus amino acid sequence is available, such DNA in the construct is defined by the sequence of a specific encoded and/or its homologous proteins. The methods further comprise 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; 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.





BRIEF DESCRIPTION OF THE DRAWINGS


FIG. 1 is a consensus amino acid sequence of SEQ ID NO: 561 and its homologs.



FIGS. 2-5 are plasmid maps.





DETAILED DESCRIPTION OF THE INVENTION

In the attached sequence listing:


SEQ ID NO:1-358 are nucleotide sequences of the coding strand of DNA for “genes” used in the recombinant DNA imparting an enhanced trait in plant cells, i.e. each represents a coding sequence for a protein;


SEQ ID NO: 359-716 are amino acid sequences of the cognate protein of the “genes” with nucleotide coding sequences 1-358;


SEQ ID NO: 717-30327 are amino acid sequences of homologous proteins;


SEQ ID NO: 30328 is a consensus sequence of SEQ ID NO: 561 and its homologs;


SEQ ID NO: 30329 is the nucleotide sequence of a plasmid base vector pMON93039 useful for corn transformation;


SEQ ID NO: 30330 is the nucleotide sequence of a plasmid base vector pMON92705 useful for corn transformation;


SEQ ID NO: 30331 is the nucleotide sequence of a plasmid base vector pMON82053 useful for soybean and canola transformation;


SEQ ID NO: 30332-30375 are nucleotide sequences of the regulatory elements in base vectors;


SEQ ID NO: 30376 is the nucleotide sequence of a plasmid base vector pMON99053 useful for cotton transformation; and


SEQ ID NO: 30377-30418 are consensus sequences.


Table 1 lists the protein SEQ ID Nos and their corresponding consensus SEQ ID Nos.











TABLE 1





PEP

Consensus


SEQ ID

SEQ ID


NO
Gene ID
NO

















371
PHE0002860_7494
30377


372
PHE0002860_8694
30378


378
PHE0004013_9281
30379


401
PHE0004780_5752
30380


402
PHE0004782_5754
30381


420
PHE0004859_5896
30382


421
PHE0004859_5917
30383


427
PHE0004889_7961
30384


436
PHE0004903_5960
30385


446
PHE0004948_6003
30386


470
PHE0006047_7234
30387


471
PHE0006047_8766
30388


474
PHE0006049_7107
30389


480
PHE0006062_7058
30390


485
PHE0006072_7071
30391


486
PHE0006074_7060
30392


487
PHE0006076_7052
30393


488
PHE0006076_7331
30394


514
PHE0006176_7147
30395


544
PHE0006286_7314
30396


545
PHE0006286_8011
30397


546
PHE0006288_7310
30398


547
PHE0006288_8023
30399


558
PHE0006346_8132
30400


561
PHE0006351_8200
30328


562
PHE0006353_8098
30401


563
PHE0006355_8084
30402


567
PH E0006378_7667
30403


568
PHE0006378_8715
30404


615
PHE0006593_8245
30405


616
PHE0006593_8256
30406


654
PHE0006740_8446
30407


655
PHE0006740_8596
30408


679
PHE0006816_8560
30409


680
PHE0006844_8839
30410


683
PHE0006908_9016
30411


699
PHE0006941_9117
30412


707
PH E0006954_9154
30413


708
PH E0006954_9161
30414


712
PHE0006970_9141
30415


714
PHE0006986_9183
30416


715
PHE0006992_9140
30417


716
PHE0006992_9184
30418









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 baombardment 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 “consensus sequence” means an artificial sequence of amino acids in a conserved region of an alignment of amino acid sequences of homologous proteins, e.g. as determined by a CLUSTALW alignment of amino acid sequence of homolog proteins.


As used herein “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 useful in the present invention may have any base sequence that has been changed from SEQ ID NO:1 through SEQ ID NO: 358 substitution in accordance with degeneracy of the genetic code. Homologs are proteins that, when optimally aligned, have at least 60% identity, more preferably about 70% or higher, more preferably at least 80% and even more preferably at least 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 90% identity to a consensus amino acid sequence of proteins and homologs disclosed herein.


Homologs are be 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 may not necessarily 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 is a likely 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 invention comprises functional homolog proteins that differ in one or more amino acids from those of disclosed protein as the result of conservative amino acid substitutions, for example substitutions are among: acidic (negatively charged) amino acids such as aspartic acid and glutamic acid; basic (positively charged) amino acids such as arginine, histidine, and lysine; neutral polar amino acids such as glycine, serine, threonine, cysteine, tyrosine, asparagine, and glutamine; neutral nonpolar (hydrophobic) amino acids such as alanine, leucine, isoleucine, valine, proline, phenylalanine, tryptophan, and methionine; amino acids having aliphatic side chains such as glycine, alanine, valine, leucine, and isoleucine; amino acids having aliphatic-hydroxyl side chains such as serine and threonine; amino acids having amide-containing side chains such as asparagine and glutamine; amino acids having aromatic side chains such as phenylalanine, tyrosine, and tryptophan; amino acids having basic side chains such as lysine, arginine, and histidine; amino acids having sulfur-containing side chains such as cysteine and methionine; naturally conservative amino acids such as valine-leucine, valine-isoleucine, phenylalanine-tyrosine, lysine-arginine, alanine-valine, aspartic acid-glutamic acid, and asparagine-glutamine. A further aspect of the homologs encoded by DNA useful 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.


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.


The “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 are useful 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 useful 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: 359 through SEQ ID NO: 716. All DNA encoding proteins that have scores higher than the gathering cutoff disclosed in Table 16 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 Pfams modules for use in this invention, as more specifically disclosed below, are Gp_dh_N::Gp_dh_C, Mg_chelatase::VWA, zf-CCCH::zf-CCCH::zf-CCCH::zf-CCCH::zf-CCCH, WD40, tRNA-synt2b::HGTP_anticodon, RNase_PH::RNase_PH_C, F-box::Kelch1::Kelch1, Peptidase_C54, Iso_dh, Metallophos, OTU, Rotamase, Sugar_tr, Glyoxalase::Glyoxalase, Ras, Brix, S6PP::S6PP_C, PsbR, Pkinase, p450, PP2C, CH::EB1, DUF537, Histone, PPR::PPR::PPR::PPR::PPR, TFIIS_M::TFIIS_C, DUF751, RRM1::RRM1, ETC_C1_NDUFA4, SRF-TF, CCT, Globin::FAD_binding6::NAD_binding1, FAE1_CUT1_RppA::ACP_syn_III_C, Frataxin_Cyay, F-box::LRR2, Tryp_alpha_amyl, PFK::PFK, Dehydrin, RLI::Fer4::ABC_tran::ABC_tran, CTP_transf2, GTP_EFTU::GTP_EFTU_D2::GTP_EFTU_D3, PfkB, IPT, TPR1::TPR2::TPR1::TPR2::TPR1::TPR1::TPR1::TPR1::TPR1, Globin, Porphobil_deam::Porphobil_deamC, NB-ARC::LRR1::LRR1::LRR1, Bromodomain, DUF1365, PTS2-RNA, Pkinase::UBA::KA1, MATH::BTB, DUF6::TPT, Cyclin_N::Cyclin_C, zf-AN 1, Methyltransf6, Thioredoxin, DNA_photolyase::FAD_binding7, vATP-synt_E, Bac_globin, B_lectin::S_locus_glycop::PAN2::Pkinase_Tyr, Sigma70_r2::Sigma70_r3::Sigma70_r4, Ribosomal_L10, zf-C3HC4::WD40::WD40::WD40, PGM_PMM_I:PGM_PMM_II:PGM_PMM_III::PGM_PMM_IV, Hydrolase, Peptidase_C1, DS, Carotene_hydrox, Aa_trans, Mov34, zf-MYND::UCH, Heme_oxygenase, S6PP, SSB, Peptidase_M16::Peptidase_M16-C, Bet_v_I, Auxin_inducible, Response_reg, Di19, DUF125, GDC-P, Pyr_redox2::Fer2_BFD::NIR_SIR_ferr::NIR_SIR, KOW::eIF-5a, MtN3_slv::MtN3_slv, Ribul_P3_epim, NPH3, DnaJ::DnaJ_C, UQ_con, RRM1::RRM1::RRM1, F-box, CoA_binding::Ligase_CoA, adh_short, Ribosomal_L22, AA_permease, Acyltransferase, AMPKBI, RRM1, Chalcone, GATase2::Asn_synthase, Peptidase_M24, DUF498, DAGAT, PFK, DUF1677, Glyco_transf43, zf-DNL, DHBP_synthase::GTP_cyclohydro2, PseudoU_synth2, Glyoxalase, DUF21::CBS, Ribosomal_S30AE, Glycolytic, Chloroa_b-bind, ZF-HD_dimer, Usp, Ferrochelatase, Pyridoxal_deC, Glyco_transf8, Pyr_redox2::Glutaredoxin, Epimerase, UPF0113, RNase_PH, AIG1, Phi1, CorA, HD::RelA_SpoT, P-II, GSHPx, PGAM, PGI, DUF868, Lung7-TM_R, F-box::FBA1, TPP_enzyme_N::TPP_enzyme_M::TPP_enzyme_C, DnaJ::zf-CSL, DEAD::Helicase_C, 2OG-FeII_Oxy, HMGL-like::LeuA_dimer, VQ, DUF298, DREPP, ketoacyl-synt::Ketoacyl-synt_C, THF_DHG_CYH::THF_DHG_CYH_C, DNA_pol_E_B, UPF0051, Pkinase::efhand::efhand::efhand::efhand, malic::Malic_M, ThiF, Transket_pyr::Transketolase_C, Ribosomal_L37ae, PEPcase, Glyco_hydro32N::Glyco_hydro32C, GASA, DnaJ, AA_kinase::ACT::ACT, Pkinase_Tyr, Cupin1, zf-LSD1::zf-LSD1::zf-LSD1, Cupin3, GAF::HisKA::HATPase_c::Response_reg, Methyltransf12::Mg-por_mtran_C, DUF516, PTR2, Ammonium_transp, eIF-5a, ECH, Aldedh, zf-C3HC4, SAM_decarbox, X8, Mg_chelatase, PurA, Ribosomal_S6e, Molybdop_Fe4S4::Molybdopterin::Molydop_binding, CP12, Biotin_lipoyl::E3_binding::2-oxoacid_dh, NOI, Tubulin::Tubulin_C, V-SNARE, AP2, ELFV_dehydrog_N::ELFV_dehydrog, Ribosomal_L32e, and FAD_binding3.


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 may 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” means the association of two or more DNA fragments in a DNA construct so that the function of one, e.g. protein-encoding DNA, is controlled by the other, e.g. a promoter.


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 a “control plant” means a plant that does not contain the recombinant DNA that expressed a protein that impart 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 nontransgenic plant of the parental line used to generate a transgenic plant, i.e. devoid of recombinant DNA. A suitable control plant may 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.


As used herein an “enhanced trait” means a characteristic of a transgenic plant that includes, but is not limited to, an enhance agronomic trait characterized by enhanced plant morphology, physiology, growth and development, yield, nutritional enhancement, disease or pest resistance, or environmental or chemical tolerance. In more specific aspects of this invention enhanced trait is selected from group of enhanced traits consisting of enhanced water use efficiency, enhanced cold tolerance, increased yield, enhanced nitrogen use efficiency, enhanced seed protein and enhanced seed oil. In an important aspect of the invention the enhanced trait is enhanced yield including increased yield under non-stress conditions and increased yield under environmental stress conditions. Stress conditions may 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 and high plant density. “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 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 (i.e. seeds, or weight of seeds, per acre), bushels per acre, tonnes per acre, tons per acre, kilo per hectare. For example, maize yield may 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 may 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 may or may not 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 may be manifest by an alterations in the ratios of seed components.


A subset of the nucleic molecules of this invention includes fragments of the disclosed recombinant DNA consisting of oligonucleotides of at least 15, preferably at least 16 or 17, more preferably at least 18 or 19, and even more preferably at least 20 or more, consecutive nucleotides. Such oligonucleotides are fragments of the larger molecules having a sequence selected from the group consisting of SEQ ID NO:1 through SEQ ID NO: 358, and find use, for example as probes and primers for detection of the polynucleotides of the present invention.


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 may include additional regulatory elements, such as 5′ leasders 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, caulimovirus promoters such as the cauliflower mosaic virus. For instance, see U.S. Pat. Nos. 5,858,742 and 5,322,938, which disclose versions of the constitutive promoter derived from cauliflower mosaic virus (CaMV35S), U.S. Pat. No. 5,641,876, which discloses a rice actin promoter, U.S. Patent Application Publication 2002/0192813A1, which discloses 5′, 3′ and intron elements useful in the design of effective plant expression vectors, U.S. patent application Ser. No. 09/757,089, which discloses a maize chloroplast aldolase promoter, U.S. patent application Ser. No. 08/706,946, which discloses a rice glutelin promoter, U.S. patent application Ser. No. 09/757,089, which discloses a maize aldolase (FDA) promoter, and U.S. patent application Ser. No. 60/310,370, 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 may 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 may 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. Particularly useful as 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 effect 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 I (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′, tins 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 may also include a transit peptide for targeting of a gene target 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 useful in the present invention, see Klee, H. J. et al (MGG (1987) 210:437-442).


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 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 imparting 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 is 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.


Plant Cell Transformation Methods

Numerous methods for transforming plant cells with recombinant DNA are known in the art and may be used in the present invention. Two commonly used methods for plant transformation are Agrobacterium-mediated transformation and microprojectile bombardment. Microprojectile bombardment methods are illustrated in U.S. Pat. No. 5,015,580 (soybean); U.S. Pat. No. 5,550,318 (corn); U.S. Pat. No. 5,538,880 (corn); U.S. Pat. No. 5,914,451 (soybean); U.S. Pat. No. 6,160,208 (corn); U.S. Pat. No. 6,399,861 (corn); U.S. Pat. No. 6,153,812 (wheat) and U.S. Pat. No. 6,365,807 (rice) and Agrobacterium-mediated transformation is described in U.S. Pat. No. 5,159,135 (cotton); U.S. Pat. No. 5,824,877 (soybean); U.S. Pat. No. 5,463,174 (canola); U.S. Pat. No. 5,591,616 (corn); U.S. Pat. No. 6,384,301 (soybean), U.S. Pat. No. 7,026,528 (wheat) and U.S. Pat. No. 6,329,571 (rice), all of which are incorporated herein by reference. For Agrobacterium tumefaciens based plant transformation systems, additional elements present on transformation constructs will include T-DNA left and right border sequences to facilitate incorporation of the recombinant polynucleotide into the plant genome.


In general it is useful to introduce recombinant DNA randomly, i.e. at a non-specific location, in the genome of a target plant line. In special cases it may be useful to target recombinant DNA insertion in order to achieve site-specific integration, for example, to replace an existing gene in the genome, to use an existing promoter in the plant genome, or to insert a recombinant polynucleotide at a predetermined site known to be active for gene expression. Several site specific recombination systems exist which are known to function in plants including cre-lox as disclosed in U.S. Pat. No. 4,959,317 and FLP-FRT as disclosed in U.S. Pat. No. 5,527,695, both incorporated herein by reference.


Transformation methods of this invention are preferably practiced in tissue culture on media and in a controlled environment. “Media” refers to the numerous nutrient mixtures that are used to grow cells in vitro, that is, outside of the intact living organism. 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. It is contemplated that any cell from which a fertile plant may be regenerated is useful as a recipient cell. Callus may be initiated from tissue sources including, but not limited to, immature embryos, hypocotyls, seedling apical meristems, microspores and the like. Cells capable of proliferating as callus are also recipient cells for genetic transformation. Practical transformation methods and materials for making transgenic plants of this invention, for example various media and recipient target cells, transformation of immature embryo cells and subsequent regeneration of fertile transgenic plants are disclosed in U.S. Pat. Nos. 6,194,636 and 6,232,526, which are incorporated herein by reference.


The seeds of transgenic plants can be harvested from fertile transgenic plants and be used to grow progeny generations of transformed plants of this invention including hybrid plants line for selection of plants having an enhanced trait. In addition to direct transformation of a plant with a recombinant DNA, transgenic plants can be prepared by crossing a first plant having a recombinant DNA with a second plant lacking the DNA. For example, recombinant DNA can be introduced into a first plant line that is amenable to transformation to produce 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 the practice of transformation DNA is typically introduced into only a small percentage of target plant cells in any one transformation experiment. Marker genes are used to provide an efficient system for identification of those cells that are stably transformed by receiving and integrating a recombinant DNA molecule into their genomes. Preferred marker genes provide selective markers which confer resistance to a selective agent, such as an antibiotic or a herbicide. Any of the herbicides to which plants of this invention may be resistant are useful agents for selective markers. Potentially transformed cells are exposed to the selective agent. In the population of surviving cells will be those cells where, generally, the resistance-conferring gene is integrated and expressed at sufficient levels to permit cell survival. Cells may be tested further to confirm stable integration of the exogenous DNA. Commonly used selective marker genes include those conferring resistance to antibiotics such as kanamycin and paromomycin (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 (aroA or 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. Selectable markers which provide an ability to visually identify transformants can also be employed, for example, 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.


Plant cells that survive exposure to the selective agent, or plant cells that have been scored positive in a screening assay, may 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−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 may 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 the plant cells 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.


Table 2 provides a list of protein encoding DNA (“genes”) that are useful 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: 359 to 716.


“NUC SEQ ID NO” identifies a DNA sequence from SEQ ID NO: 1 to 358.


“BV id” is a reference to the identifying number in Table 4 of base vectors used for construction of the transformation vectors of the recombinant DNA. Construction of plant transformation constructs is illustrated in Example 1.


“Gene Name” which is a common name for protein encoded by the recombinant DNA.


“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;


“% 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 (-F T) between the sequence of interest provided herein and the hit sequence in GenBank;














TABLE 2







nuc
pep






seq
seq


ID
ID

BV

Annotation














NO
NO
Gene ID
id
Gene Name
% id
GenBank id
desciption

















1
359
PHE0001295_7469
4
rice cryptochrome 1 -
95
gi|50909767|
ref|XP_466372.1|cryptochrome






AB073546


la [Oryza sativa









(japonica cultivar-group)]


2
360
PHE0002129_8308
16

Nostoc sp. PCC 7120

93
gi|17133998|
ref|NP_488901.1|






phosphoenolpyruvate


phosphoenolpyruvate






carboxylase


carboxylase [Nostoc sp.









PCC 7120]


3
361
PHE0002132_4965
4
maize
80
gi|59803710|
gb|AAX07936.1|phospho-






phosphoenolpyruvate


enolpyruvate carboxylase






carboxylase kinase 2


kinase 2 [Zea mays]


4
362
PHE0002132_8653
19
maize
80
gi|59803710|
gb|AAX07936.1|phospho-






phosphoenolpyruvate


enolpyruvate carboxylase






carboxylase kinase 2


kinase 2 [Zea mays]


5
363
PHE0002133_7497
4
maize
82
gi|59803708|
gb|AAX07935.1|phospho-






phosphoenopyruvate


enolpyruvate carboxylase






carboxylase kinase 3


kinase 1 [Zea mays]


6
364
PHE0002693_8516
17
wheat geranylgeranyl
93
gi|23397035|
gb|AAN31803.1|putative






reductase like 1


geranylgeranyl reductase






sequence


[Arabidopsis thaliana]


7
365
PHE0002777_7490
4
maize ferrochelatase-I
85
gi|50725080|
dbj|BAD33213.1|putative






like 2 sequence


ferrochelatase [Oryza










sativa (japonica cultivar-










group)]


8
366
PHE0002777_8472
6
maize ferrochelatase-I
85
gi|50725080|
dbj|BAD33213.1|putative






like 2 sequence


ferrochelatase [Oryza










sativa (japonica cultivar-










group)]


9
367
PHE0002777_8726
19
maize ferrochelatase-I
85
gi|50725080|
dbj|BAD33213.1|putative






like 2 sequence


ferrochelatase [Oryza










sativa (japonica cultivar-










group)]


10
368
PHE0002779_7478
4
soybean
89
gi|6272281|
emb|CAB60127.1|cytosolic






phosphoglucomutase


phosphoglucomutase






like 1 sequence


[Pisum sativum]


11
369
PHE0002810_5803
9
maize cytochrome
92
gi|1870201|
emb|CAA72208.1|cytochrome






P450 monooxygenase


p450 [Zea mays]






(CYP71B3) like 4


emb|CAA57423.1|






sequence


cytochrome P450 [Zea










mays]



12
370
PHE0002857_7502
4

Zea Mays putative low

61
gi|50934635|
ref|XP_476845.1|putative






molecular early light-


low molecular mass early






inducible protein


light-induced









protein, chloroplast









precursor (ELIP) [Oryza










sativa (japonica cultivar-










group)]


13
371
PHE0002860_7494
4

Zea Mays Unknown

25
gi|15237638|
ref|NP_201222.1|unknown






protein


protein [Arabidopsis










thaliana]



14
372
PHE0002860_8694
19

Zea Mays Unknown

25
gi|15237638|
ref|NP_201222.1|unknown






protein


protein [Arabidopsis










thaliana]



15
373
PHE0003814_7802
17
rice PsbS like
85
gi|34908652|
ref|NP_915673.1|putative









photosystem II subunit









(22 KDa) precursor [Oryza










sativa (japonica cultivar-










group)]


16
374
PHE0003838_5934
1
soy G2604 like 1
79
gi|18398482|
|AAQ55219.1|LSD1-like









[Arabidopsis thaliana]


17
375
PHE0003845_5806
11

Arabidopsis DWF4

88
gi|15229822|
emb|CAB62435.1|steroid









22-alpha-hydroxylase









(DWF4) [Arabidopsis










thaliana]



18
376
PHE0003845_7028
17

Arabidopsis DWF4

88
gi|15229822|
ref|NP_190635.1|DWF4









(DWARF 4) [Arabidopsis










thaliana]



19
377
PHE0003845_7413
2

Arabidopsis DWF4

88
gi|15229822|
reflNP_l90635.1|DWF4









(DWARF 4) [Arabidopsis










thaliana]



20
378
PHE0004013_9281
9
ARGOS-like
68
gi|62734659|
gb|AAX96768.1|expressed









protein [Oryza sativa









(japonica cultivar-group)]









g


21
379
PHE0004021_4654
10

Galdieria sulphuraria

45
gi|83769256|
dbj|BAE59393.1|unnamed






asparagine synthetase


protein product









[Aspergillus oryzae]


22
380
PHE0004143_7850
1

Arabidopsis putative

100
gi|7267860|
emb|CAB78203.1|phospho-






glutathione peroxidase


lipid hydroperoxide









glutathione peroxidase









[Arabidopsis thaliana]


23
381
PHE0004143_8160
19

Arabidopsis putative

92
gi|30681827|
ref|NP_192897.2|ATGPX






glutathione peroxidase


6 (GLUTATHIONE









PEROXIDASE 6);









glutathione peroxidase









[Arabidopsis thaliana]


24
382
PHE0004311_5022
1

Arabidopsis

99
gi|24209881|
gb|AAN41402.1|aminopep-






aminopeptidase P


tidase P [Arabidopsis










thaliana]



25
383
PHE0004398_5136
4
rice NPK1 kinase
95
gi|50900060|
ref|XP_450818.1|putative






domain only


protein kinase (Oryza










sativa (japonica cultivar-










group)]


26
384
PHE0004398_5757
13
rice NPK1 kinase
95
gi|50900060|
ref|XP_450818.1|putative






domain only


protein kinase [Oryza










sativa (japonica cultivar-










group)]


27
385
PHE0004473_5214
4

Arabidopsis putative

69
gi|15241016|
ref|NP_198119.1|DNA






histone H2A


binding [Arabidopsis










thaliana]



28
386
PHE0004473_8803
19

Arabidopsis putative

69
gi|15241016|
ref|NP_198119.1|DNA






histone H2A


binding [Arabidopsis










thaliana]



29
387
PHE0004503_5244
4

Arabidopsis nodulin

100
gi|15240040|
emb|CAC05445.1|






MtN3 family protein


senescence-associated









protein (SAG29)









[Arabidopsis thaliana]


30
388
PHE0004503_8801
19

Arabidopsis nodulin

100
gi|15240040|
emb|CAC05445.1|






MtN3 family protein


senescence-associated









protein (SAG29)









[Arabidopsis thaliana]


31
389
PHE0004641_5519
9
corn photosynthetic
90
gi|126737|
gb|AAA33487.1|NADP-






NADP-dependent


dependent malic enzyme






malic enzyme


(EC 1.1.1.40)


32
390
PHE0004642_5520
9
corn non-
85
gi|37147841|
gb|AAQ88396.1|non-






photosynthetic NADP-


photosynthetic NADP-






dependent malic


malic enzyme [Zea mays]






enzyme


33
391
PHE0004670_6044
9

Arabidopsis putative

100
gi|15225103|
ref|NP_180715.1|ATGPX






glutathione peroxidase


2 (GLUTATHIONE









PEROXIDASE 2);









glutathione peroxidase


34
392
PHE0004683_8693
19

Arabidopsis SUMO

100
gi|18416454|
gb|AAN15413.1|






activating enzyme 1a


ubiquitin activating









enzyme - like protein


35
393
PHE0004742_5691
13
rice putative
67
gi|50948187|
ref|XP_483621.1|putative






CRT/DRE binding


CRT/DRE binding factor






factor


[Oryza sativa (japonica









cultivar-group)]


36
394
PHE0004747_5708
16

Xenorhabdus

75
gi|87120270|
ref|ZP_01076165.1|methyl-







nematophilus



malonate-semialdehyde






MMSDH-like


dehydrogenase









[Marinomonas sp.









MED121]


37
395
PHE0004761_5728
4

Arabidopsis

92
gi|15218889|
ref|NP_174226.1|nucleotide






transducin family


binding [Arabidopsis






protein/WD-40



thaliana]







repeat family protein


38
396
PHE0004762_5729
4

Arabidopsis F-box

89
gi|56790216|
dbj|BAB09749.1|






family protein


unnamed protein product









[Arabidopsis thaliana]


39
397
PHE0004762_7997
19

Arabidopsis F-box

89
gi|56790216|
dbj|BAB09749.1|






family protein


unnamed protein product









[Arabidopsis thaliana]


40
398
PHE0004766_5733
4
soy ATP-binding-
76
gi|15234447|
gb|AAD03441.1| contains






cassette transporter


similarity to Guillardia










theta ABC transporter










(GB: AF041468)









[Arabidopsis thaliana]


41
399
PHE0004779_5749
4

Arabidobpsis

89
gi|15230092|
ref|NP_189073.1|ATAMT






ammonium transporter


1; 3; ammonium









transporter [Arabidopsis










thaliana]



42
400
PHE0004779_8394
1

Arabidopsis

89
gi|15230092|
ref|NP_189073.1|ATAMT






ammonium transporter


1; 3; ammonium









transporter [Arabidopsis










thaliana]



43
401
PHE0004780_5752
4
Arabidopsisexpressed
92
gi|21536499|
gb|AAM60831.1|unknown






protein


[Arabidopsis thaliana]


44
402
PHE0004782_5754
4

Arabidopsis

65
gi|18404589|
ref|NP_565874.1|EMB15






hypothetical protein


13; copper ion transporter









[Arabidopsis thaliana]


45
403
PHE0004784_5760
1
soy S-
72
gi|21239731|
gb|AAM44307.1|S-






adenosylmethionine


adenosylmethionine






decarboxylase


decarboxylase [x










Citrofortunella mitis]



46
404
PHE0004787_7988
19
rice Nitrogen
73
gi|50878396|
gb|AAT85171.1|putative






regulatory protein P-II


P-II nitrogen sensing









protein


47
405
PHE0004791_5771
4

Xenorhabdus

73
gi|36786606|
emb|CAE15666.1|Flavo-







nematophila



hemoprotein (hemoglobin-






Flavohemoprotein


like protein)









(flavohemoglobin)









(dihydropteridine









reductase)









(ferrisiderophore









reductase B) (nitric oxide









dioxygenase) (NOD)









[Photorhabdus










luminescens subsp.











laumondii TTO1]



48
406
PHE0004805_5791
17
corn hypothetical
51
gi|50509855|
dbj|BAD32027.1|unknown






protein


protein [Oryza sativa









(japonica cultivar-group)]


49
407
PHE0004806_5792
17
rice OTU-like cysteine
90
gi|50915926|
ref|XP_468427.1|OTU-






protease-like


like cysteine protease-like









[Oryza sativa (japonica









cultivar-group)]


50
408
PHE0004807_5793
17
corn cleavage
97
gi|62733690|
gb|AAX95801.1|RNA






stimulation factor 64


recognition motif, (a.k.a.









RRM, RBD, or RNP









domain), putative [Oryza










sativa (japonica cultivar-










group)]


51
409
PHE0004808_5794
17
corn cysteine
63
gi|2224810|
emb|CAB09698.1|cysteine






proteinase


proteinase [Hordeum










vulgare subsp. vulgare]



52
410
PHE0004809_5795
17
corn
71
gi|34898886|
ref|NP_910789.1|putative






MRT4577_261462


protein phosphatase 2C






putative protein


(PP2C) [Oryza sativa






phosphatase 2C


(japonica cultivar-group)]


53
411
PHE0004810_5796
17
rice MRT4577_41500
90
gi|50948089|
ref|XP_483572.1|putative






putative calcium-


calcium-dependent






dependent protein


protein kinase [Oryza






kinase



sativa (japonica cultivar-










group)]


54
412
PHE0004811_5798
17
rice MRT4577_35987
78
gi|50911677|
ref|XP_467246.1|zinc






C3HC4-type RING


finger (C3HC4-type






finger


RING finger)-like [Oryza










sativa (japonica cultivar-










group)]


55
413
PHE0004812_5799
17
rice
80
gi|30698518|
dbj|BAC76607.1|plastid






MRT4577_148933


sigma factor SIG5 [Oryza






plastid sigma factor



sativa (japonica cultivar-







SIG5


group)]


56
414
PHE0004813_5800
17
corn putative zinc
85
gi|57900442|
sp|Q5JLB5|ZFNL2_ORY






finger protein


SA Zinc finger CCCH









type domain containing









protein ZFN-like 2


57
415
PHE0004815_5802
17
corn protein kinase
51
gi|15237684|
ref|NP_200660.1|ATP






family protein


binding/kinase/protein









kinase/protein









serine/threonine kinase/









protein-tyrosine kinase









[Arabidopsis thaliana]


58
416
PHE0004827_5825
4
corn phosphate-
74
gi|50912943|
ref|XP_467879.1|putative






induced protein 1-like


phi-1 [Oryza sativa






(EXORDIUM)


(japonica cultivar-group)]


59
417
PHE0004830_5828
4

Arabidopsis putative

91
gi|15231772|
ref|NP_188021.1|RSH2






RelA/SpoT protein


(RELA-SPOT









HOMOLOG); catalytic









[Arabidopsis thaliana]









dbj|BAB02337.1|









unnamed protein product









[Arabidopsis thaliana]


60
418
PHE0004845_5852
4

Arabidopsis Beta

96
gi|15235959|
ref|NP_194300.1|BETA-






carotene hydroxilase


OHASE 1 (BETA-









HYDROXYLASE 1);]


61
419
PHE0004856_7855
1

Arabidopsis

93
gi|22331730|
ref|NP_190653.2|protein






phototropic-responsive


binding/signal






NPH3 family protein


transducer [Arabidopsis










thaliana]



62
420
PHE0004859_5896
4

Arabidopsis thaliana

77
gi|15236062|
ref|NP_194901.1|GDU1






Glutamine dumper 1


(GLUTAMINE









DUMPER 1)









[Arabidopsis thaliana]


63
421
PHE0004859_5917
8

Arabidopsis thaliana

77
gi|15236062|
ref|NP_194901.1|GDU1






Glutamine dumper 1


(GLUTAMINE









DUMPER 1)









[Arabidopsis thaliana]


64
422
PHE0004883_5935
1

Arabidopsis

89
gi|15240864|
ref|NP_198641.1|ATP






serine/threonine


binding/kinase/protein






protein kinase


kinase/protein









serine/threonine kinase/









protein-tyrosine kinase









[Arabidopsis thaliana]


65
423
PHE0004886_5938
4

Arabidopsis thaliana

94
gi|4406770|
gb|AAD20081.1|unknown






GEK1


protein [Arabidopsis










thaliana]



66
424
PHE0004887_5939
4

Zea mays GEK1-like

74
gi|50944457|
ref|XP_481756.1|putative









GEKO1 [Oryza sativa









(japonica cultivar-group)]


67
425
PHE0004887_5940
16

Zea mays GEK1-like

74
gi|50944457|
ref|XP_481756.1|putative









GEKO1 [Oryza sativa









(japonica cultivar-group)]


68
426
PHE0004887_8704
19

Zea mays GEK1-like

74
gi|50944457|
ref|XP_481756.1|putative









GEKO1 [Oryza sativa









(japonica cultivar-group)]


69
427
PHE0004889_7961
19
Corn OsRAA1-like
75
gi|34902924|
dbj|BAB07982.1| FPF1









protein-like [Oryza sativa









(japonica cultivar-group)]


70
428
PHE0004894_5948
17
corn plastid division
79
gi|50929441|
gb|AAK64282.1| plastid






protein FtsZ


division protein FtsZ









[Oryza sativa]


71
429
PHE0004894_5950
10
corn plastid division
79
gi|50929441|
gb|AAK64282.1| plastid






protein FtsZ


division protein FtsZ









[Oryza sativa]


72
430
PHE0004894_5951
4
corn plastid division
79
gi|50929441|
gb|AAK64282.1| plastid






protein FtsZ


division protein FtsZ









[Oryza sativa]


73
431
PHE0004895_5952
4
corn deoxyhypusine
79
gi|1019423|
gb|AAC49075.1|deoxyhy-






synthase 3


pusine synthase


74
432
PHE0004895_7135
15
corn deoxyhypusine
79
gi|1019423|
gb|AAC49075.1|deoxyhy-






synthase 3


pusine synthase


75
433
PHE0004895_7137
17
corn deoxyhypusine
79
gi|1019423|
gb|AAC49075.l|deoxyhy-






synthase 3


pusine synthase


76
434
PHE0004895_8610
19
corn deoxyhypusine
79
gi|1019423|
gb|AAC49075.1|deoxyhy-






synthase 3


pusine synthase


77
435
PHE0004902_5959
4

Glycine max soy type-

59
gi|33330864|
gb|AAQ10675.1|type-A






A response regulator


response regulator









[Catharanthus roseus]


78
436
PHE0004903_5960
4

Arabidopsis

82
gi|18412607|
ref|NP_565228.1|unknown






expressed protein


protein [Arabidopsis










thaliana]



79
437
PHE0004905_5962
4

Arabidopsis calcium-

86
gi|15236560|
ref|NP_194096.1|CDPK6






dependent protein


(CALCIUM-






kinase


DEPENDENT PROTEIN









KINASE 6);


80
438
PHE0004909_5966
4

Arabidopsis protein

83
gi|42561860|
ref|NP_172415.2|ATP






kinase family protein


binding/kinase/protein









kinase/protein









serine/threonine kinase/









protein-tyrosine kinase









[Arabidopsis thaliana]


81
439
PHE0004911_5968
4

Arabidopsis

91
gi|15235475|
ref|NP_195437.1|HCF164;






thioredoxin family


thiol-disulfide exchange






protein


intermediate [Arabidopsis










thaliana]



82
440
PHE0004912_5969
4

Arabidopsis putative

87
gi|15235432|
ref|NP_192172.1|ATP






serine/threonine


binding/kinase/protein






protein kinase


kinase/protein









serine/threonine kinase/









protein-tyrosine kinase









[Arabidopsis thaliana]


83
441
PHE0004918_5975
4

Arabidopsis expressed

90
gi|42571697|
ref|NP_973939.1|unknown






protein


protein [Arabidopsis










thaliana]



84
442
PHE0004921_5979
4
corn hypothetical
80
gi|50917557|
ref|XP_469175.1|hypothetical






protein


protein [Oryza sativa









(japonica cultivar-group)]


85
443
PHE0004928_5986
4

Arabidopsis putative

100
gi|15227956|
gb|AAL07163.1| putative






peptidyl-prolyl cis-


peptidyl-prolyl cis-trans






trans isomerase


isomerase [Arabidopsis










thaliana]



86
444
PHE0004932_6045
9

Arabidopsis PUR

92
gi|30685174|
ref|NP_850182.1|PUR






alpha-1 protein


ALPHA-1; nucleic acid









binding [Arabidopsis










thaliana]]



87
445
PHE0004941_5997
4

Arabidopsis dehydrin

42
gi|30693389|
sp|P25863|XERO1_ARATH









Dehydrin Xero 1









gb|AAB00375.1| dehydrin


88
446
PHE0004948_6003
9
corn PUR alpha-1
97
gi|34902984|
ref|NP_912839.1|unnamed






protein


protein product [Oryza










sativa (japonica cultivar-










group)]


89
447
PHE0004966_6028
4

Arabidopsis sugar

97
gi|56381949|
ref|NP_200733.2|






transporter family


carbohydrate transporter/






protein


sugar porter [Arabidopsis










thaliana]



90
448
PHE0004968_6030
4

Arabidopsis RNase L

100
gi|22328793|
gb|AAN15617.1| RNase L






inhibitor-like protein


inhibitor-like protein









[Arabidopsis thaliana]


91
449
PHE0004977_6043
9

Mortierella

95
gi|15099959|
gb|AAK84179.1|diacylglyc-







ramanniana



erol acyltransferase type






diacylglycerol


2A [Mortierella






acyltransferase type



ramanniana]







2A


92
450
PHE0004979_6047
3
yeast SUC2
100
gi|50554053|
ref|XP_504435.1|Y1XPR2:









SUC2 [Yarrowia










lipolytica]



93
451
PHE0004984_7235
4

Arabidopsis putative

100
gi|15232838|
ref|NP_186851.1|amino






aspartate kinase


acid binding/aspartate









kinase [Arabidopsis










thaliana]



94
452
PHE0004984_8782
19

Arabidopsis putative

100
gi|15232838|
ref|NP_186851.1|amino






aspartate kinase


acid binding/aspartate









kinase [Arabidopsis










thaliana]



95
453
PHE0004989_8115
19

Arabidopsis CBS

96
gi|42569036|
ref|NP_179058.3|unknown






domain-containing


protein [Arabidopsis






protein



thaliana]



96
454
PHE0004991_8092
19

Arabidopsis auxin-

77
gi|15241259|
ref|NP_199889.1|unknown






responsive family


protein [Arabidopsis






protein



thaliana]



97
455
PHE0004993_6062
4
soy putative protein
50
gi|18423511|
ref|NP_568793.1|unknown









protein [Arabidopsis










thaliana]



98
456
PHE0004993_8014
19
soy putative protein
50
gi|18423511|
ref|NP_568793.1|unknown









protein [Arabidopsis










thaliana]



99
457
PHE0004993_8682
19
soy putative protein
50
gi|18423511|
ref|NP_568793.1|unknown









protein [Arabidopsis










thaliana]



100
458
PHE0005002_6071
4
corn putative
79
gi|33321009|
gb|AAQ06256.1|putative






magnesium-


magnesium-






protoporphyrin IX


protoporphyrin IX






methyltransferase


methyltransferase









[Sorghum bicolor]


101
459
PHE0005003_7032
4
corn putative
83
gi|50905547|
ref|XP_464262.1|putative






porphobilinogen


porphobilinogen






deaminase


deaminase [Oryza sativa









(japonica cultivar-group)]


102
460
PHE0005008_6077
4

Arabidopsis two-

91
gi|30679083|
ref|NP_850511.1|ARR22






component responsive


(ARABIDOPSIS






regulator family


RESPONSE






protein


REGULATOR 22); two-









component response









regulator [Arabidopsis










thaliana]



103
461
PHE0005009_6078
4

Arabidopsis ubiquitin-

100
gi|223311064|
ref|NP_566459.2|FUS9






conjugating enzyme


(FUSCA 9); ubiquitin









conjugating enzyme









[Arabidopsis thaliana]


104
462
PHE0005010_6079
4
corn ETCHED1
94
gi|48596293|
emb|CAD45039.1|ETCHED1






protein


protein [Zea mays]


105
463
PHE0006003_7195
13
rice OSISAP1
71
gi|37548823|
gb|AAN15744.1|multiple









stress-associated zinc-









finger protein


106
464
PHE0006003_7205
1
rice OSISAP1
71
gi|37548823|
gb|AAN15744.1|multiple









stress-associated zinc-









finger protein


107
465
PHE0006018_7098
4
corn translational
90
gi|11181616|
gb|AAG3266l.1|translational






elongation factor EF-


elongation factor EF-






TuM


TuM [Zea mays]


108
466
PHE0006021_7077
4
rice root specific
100
gi|38678114|
dbj|BAD03969.1|root






pathogenesis-related


specific pathogenesis-






protein 10


related protein 10 [Oryza










sativa (japonica cultivar-










group)]


109
467
PHE0006021_8737
19
rice root specific
100
gi|38678114|
dbj|BAD03969.1|root






pathogenesis-related


specific pathogenesis-






protein 10


related protein 10


110
468
PHE0006043_7080
4

Arabidopsis glycosyl

100
gi|18409445|
ref|NP_564983.1|transferase,






transferase family 8


transferring glycosyl






protein


groups/transferase,









transferring hexosyl









groups


111
469
PHE0006043_8788
19

Arabidopsis glycosyl

100
gi|18409445|
ref|NP_564983.1|transferase,






transferase family 8


transferring glycosyl






protein


groups/transferase,









transferring hexosyl









groups


112
470
PHE0006047_7234
4
soy hydroperoxide
69
gi|5830465|
emb|CAB54847.1|hydroper-






lyase


oxide lyase [Medicago










sativa]



113
471
PHE0006047_8766
19
soy hydroperoxide
69
gi|5830465|
emb|CAB54847.1|hydroper-






lyase


oxide lyase [Medicago










sativa]



114
472
PHE0006048_7094
4
soy
90
gi|13124865|
gb|AAK11734.1|serine/






serine/threonine/tyrosine


threonine/tyrosine kinase






kinase


[Arachis hypogaea]


115
473
PHE0006048_8785
19
soy
90
gi|13124865|
gb|AAKH734.1|serine/






serine/threonine/tyrosine


threonine/tyrosine kinase






kinase


[Arachis hypogaea]


116
474
PHE0006049_7107
4
soy putative non-green
42
gi|18404784|
gb|AAC67363.2| putative






plastid inner envelope


non-green plastid inner






membrane protein


envelope membrane









protein [Arabidopsis










thaliana]



117
475
PHE0006051_7097
4

Arabidopsis ubiquitin

91
gi|15238468|
ref|NP_201348.1|cysteine-






carboxyl-terminal


type endopeptidase/






hydrolase family


ubiquitin thiolesterase






protein


[Arabidopsis thaliana]


118
476
PHE0006054_7095
4

Arabidopsis GTP-

92
gi|30680751|
dbj|BAB11522.1| GTP-






binding protein


binding protein









[Arabidopsis thaliana]


119
477
PHE0006054_8779
19

Arabidopsis GTP-

92
gi|30680751|
dbj|BAB11522.1| GTP-






binding protein


binding protein









[Arabidopsis thaliana]


120
478
PHE0006059_7042
4
corn heat-shock
74
gi|51964000|
ref|XP_465165.1| putative






protein


DnaJ-like protein [Oryza










sativa (japonica cultivar-










group)]


121
479
PHE0006061_7051
4
corn calcineurin-like
94
gi|50251955|
dbj|BAD27890.1|putative






phosphoesterase


vacuolar protein sorting;






family protein


Vps29p [Oryza sativa









(japonica cultivar-group)]


122
480
PHE0006062_7058
4
corn putative ATP
70
gi|50905037|
ref|XP_464007.1|putative






synthase


ATP synthase [Oryza










sativa (japonica cultivar-










group)]


123
481
PHE0006063_7049
4
corn putative pyruvate
85
gi|77557068|
gb|ABA99864.1|pyruvate






dehydrogenase E1


dehydrogenase E1 beta






beta subunit


subunit [Oryza sativa









(japonica cultivar-group)]


124
482
PHE0006068_7064
4
corn protein kinase
80
gi|50924460|
ref|XP_472590.1|OSJNBa






family protein


0006B20.13 [Oryza sativa









(japonica cultivar-group)]


125
483
PHE0006069_7065
4
corn unknown protein
75
gi|50924572|
ref|XP_472645.1|OSJNBa









0027P08.10 [Oryza sativa









(japonica cultivar-group)]


126
484
PHE0006071_7068
4
corn pentatricopeptide
44
gi|50905575|
ref|XP_464276.1|putative






(PPR) repeat-


pentatricopeptide (PPR)






containing protein


repeat-containing protein









[Oryza sativa (japonica









cultivar-group)]


127
485
PHE0006072_7071
4
corn unknown protein
53
gi|77554714|
gb|ABA97510.1|transposon









protein, putative,









CACTA, En/Spm sub-









class [Oryza sativa









(japonica cultivar-group)]


128
486
PHE0006074_7060
4
corn putative
44
gi|18568267|
gb|AAL75999.1|putative






polyprotein


polyprotein [Zea mays]


129
487
PHE0006076_7052
4

Arabidopsis Clavata3/

100
gi|18390629|
ref|NP_563763.1|CLE3






ESR-Related-3


(CLAVATA3/ESR-









RELATED 3); receptor









binding [Arabidopsis










thaliana]



130
488
PHE0006076_7331
1

Arabidopsis Clavata3/

100
gi|18390629|
ref|NP_563763.1|CLE3






ESR-Related-3


(CLAVATA3/ESR-









RELATED 3); receptor









binding [Arabidopsis










thaliana]



131
489
PHE0006077_7045
4

Arabidopsis

100
gi|15242249|
sp|P46690|GASA4_ARATH






gibberellin-regulated


Gibberellin-regulated






protein 4


protein 4 precursor


132
490
PHE0006077_7343
1

Arabidopsis

100
gi|15242249|
emb|CAA66909.1|






gibberellin-regulated


GASA4 [Arabidopsis






protein 4



thaliana]










sp|P46690|GASA4_ARATH









Gibberellin-regulated









protein 4 precursor


133
491
PHE0006079_7044
4

Arabidopsis sucrose-

100
gi|18409555|
ref|NP_566964.1|SPP2






phosphatase


(sucrose-phosphatase 2);









catalytic/sucrose-









phosphatase [Arabidopsis










thaliana]



134
492
PHE0006079_7337
1

Arabidopsis sucrose-

100
gi|18409555|
ref|NP_566964.1|SPP2






phosphatase


(sucrose-phosphatase 2);









catalytic/sucrose-









phosphatase [Arabidopsis










thaliana]



135
493
PHE0006082_7330
1
soy stress-induced
66
gi|79325071|
emb|CAB78283.1| stress-






protein sti1-like


induced protein sti1-like






protein


protein [Arabidopsis










thaliana]



136
494
PHE0006088_7063
14
CTP-RtACL
70
gi|71004972|
ref|XP_757152.1|hypothetical









protein UM01005.1









[Ustilago maydis 521]


137
495
PHE0006089_7061
4

Arabidopsis brix

94
gi|18404250|
ref|NP_564618.1|unknown






domain-containing


protein [Arabidopsis






protein



thaliana]



138
496
PHE0006089_7334
1

Arabidopsis brix

94
gi|18404250|
ref|NP_564618.1|unknown






domain-containing


protein [Arabidopsis






protein



thaliana]



139
497
PHE0006091_7074
4

Arabidopsis putative

94
gi|15224901|
ref|NP_181390.1|DNA






elongation factor


binding/transcription









factor [Arabidopsis










thaliana]



140
498
PHE0006091_7341
1

Arabidopsis putative

94
gi|15224901|
ref|NP_181390.1|DNA






elongation factor


binding/transcription









factor [Arabidopsis










thaliana]



141
499
PHE0006092_7062
4

Arabidopsis

90
gi|30695647|
ref|NP_849806.1|mRNA






oligouridylate-binding


3′-UTR binding






protein


[Arabidopsis thaliana]


142
500
PHE0006092_7336
1

Arabidopsis

90
gi|30695647|
ref|NP_849806.1|mRNA






oligouridylate-binding


3′-UTR binding






protein


[Arabidopsis thaliana]


143
501
PHE0006093_7066
4

Arabidopsis putative

84
gi|2583121|
gb|AAB82630.1|unknown






tRNA


protein [Arabidopsis






2″phosphotransferase



thaliana]



144
502
PHE0006093_7327
1

Arabidopsis putative

84
gi|2583121|
gb|AAB82630.1|unknown






tRNA


protein [Arabidopsis






2″phosphotransferase



thaliana]



145
503
PHE0006094_7231
4

Arabidopsis chalcone

100
gi|15233190|
ref|NP_191072.1|TT5






flavanone isomerase


(TRANSPARENT









TESTA 5); chalcone









isomerase [Arabidopsis










thaliana]



146
504
PHE0006094_7333
1

Arabidopsis chalcone

100
gi|15233190|
ref|NP_191072.1|TT5






flavanone isomerase


(TRANSPARENT









TESTA 5); chalcone









isomerase [Arabidopsis










thaliana]



147
505
PHE0006154_7204
14

E. coli ATP-dependent

100
gi|85675091|
dbj|BAA15500.2|6-






phosphofructokinase


phosphofructokinase II






B (pfkB)


[Escherichia coli W3110]


148
506
PHE0006160_7265
14
pyrophosphate-
92
gi|1346693|
sp|P29495|PFP_PROFRP






dependent


yrophosphate--fructose 6-






phosphofructokinase


phosphate 1-






(PPi-PFK)


phosphotransferase


149
507
PHE0006160_7286
9
pyrophosphate-
92
gi|1346693|
gb|AAA25675.1|






dependent


pyrophosphate-frustose 6-






phosphofructokinase


phosphate 1-






(PPi-PFK)


phosphotransferase


150
508
PHE0006160_8851
14
pyrophosphate-
92
gi|1346693|
sp|P29495|PFP_PROFRP






dependent


yrophosphate--fructose 6-






phosphofructokinase


phosphate 1-






(PPi-PFK)


phosphotransferase


151
509
PHE0006161_7215
9
ATP-dependent
96
gi|2956754|
sp|O42938|K6PF_SCHPO






phosphofructokinase 1


6-phosphofructokinase






(Pfk-1)


(Phosphofructokinase)









(Phosphohexokinase)









(6PF-1-K)


152
510
PHE0006161_7221
14
ATP-dependent
97
gi|2956754|
sp|O42938|K6PF_SCHPO






phosphofructokinase 1


6-phosphofructokinase






(Pfk-1)


(Phosphofructokinase)









(Phosphohexokinase)









(6PF-1-K)


153
511
PHE0006173_7211
12

Glycine max

81
gi|44662864|
gb|AAS47511.1|ribosomal






ribosomal protein S6


protein S6 [Glycine










max]



154
512
PHE0006174_7208
12
Yeast NSR1
62
gi|1323271|
ref|NP_011675.1|









Nucleolar protein that









binds nuclear localization









sequences, required for









pre-rRNA processing and









ribosome biogenesis;









Nsr1p [Saccharomyces










cerevisiae]



155
513
PHE0006175_7210
4
Corn eIF-5A-2
87
gi|34915268|
ref|NP_919091.1|putative









translation initiation









factor 5A [Oryza sativa









(japonica cultivar-group)]


156
514
PHE0006176_7147
9
EEM1


157
515
PHE0006178_7139
4
Corn eIF-5A-3
63
gi|4204352|
gb|AAD10697.1|eIF-5A









[Candida albicans]


158
516
PHE0006178_8626
19
Corn eIF-5A-3
63
gi|4204352|
gb|AAD10697.1|eIF-5A









[Candida albicans]









sp|O94083|IF5A_CANAL









Eukaryotic translation









initiation factor 5A (eIF-









5A) (eIF-4D)


159
517
PHE0006184_7245
9
EEM11
58
gi|50924850|
ref|XP_472770.1|B1358B









12.19 [Oryza sativa









(japonica cultivar-group)]


160
518
PHE0006201_7184
14
ZmKASICTP-AtKAS
94
gi|22325473|
ref|NP_178533.2|catalytic/









fatty-acid synthase









[Arabidopsis thaliana]


161
519
PHE0006201_7187
9
ZmKASICTP-AtKAS
94
gi|22325473|
ref|NP_178533.2|catalytic/









fatty-acid synthase









[Arabidopsis thaliana]


162
520
PHE0006202_7182
4
MAML-4
94
gi|42562149|
ref|NP_173285.2|2-






(At1g18500)


isopropylmalate synthase/









catalytic/transferase,









transferring acyl groups,









acyl groups converted









into alkyl on transfer









[Arabidopsis thaliana]


163
521
PHE0006204_7183
17
soy Cyclin D
45
gi|15236274|
ref|NP_192236.1|CYCD6;









1; cyclin-dependent









protein kinase









[Arabidopsis thaliana]


164
522
PHE0006204_7189
4
soy Cyclin D
45
gi|15236274|
ref|NP_192236.1|CYCD6;









1; cyclin-dependent









protein kinase









[Arabidopsis thaliana]


165
523
PHE0006204_8634
19
soy Cyclin D
45
gi|15236274|
ref|NP_192236.1|CYCD6;









1; cyclin-dependent









protein kinase









[Arabidopsis thaliana]


166
524
PHE0006208_7223
4
rice Microtubule-
92
gi|50929089|
ref|XP_474072.1|OSJNBb






associated EB1


0079B02.14 [Oryza sativa









(japonica cultivar-group)]


167
525
PHE0006209_7991
19
rice 2-isopropylmalate
96
gi|77548611|
gb|ABA91408.1|2-






synthase


isopropylmalate synthase









[Oryza sativa (japonica









cultivar-group)]


168
526
PHE0006212_7196
4
corn Heme oxygenase-
89
gi|51090890|
dbj|BAD35463.1|putative






like


heme oxygenase 1 [Oryza










sativa (japonica cultivar-










group)]


169
527
PHE0006213_7198
4
corn ATG4a-like
69
gi|50929729|
gb|ABB77259.1|









autophagy 4 [Oryza sativa









(indica cultivar-group)]


170
528
PHE0006214_7213
17
corn Cyclin D
61
gi|50508578|
dbj|BAD30903.1|putative









cyclin D1 [Oryza sativa









(japonica cultivar-group)]


171
529
PHE0006214_7219
4
corn Cyclin D
61
gi|50508578|
dbj|BAD30903.1|putative









cyclin D1 [Oryza sativa









(japonica cultivar-group)]


172
530
PHE0006215_7280
9
ATP-dependent
92
gi|396136|
emb|CAA50526.1|6-






phosphofructokinase 1


phosphofructokinase






(Pfk-l)


[Lactobacillus










delbrueckii]



173
531
PHE0006221_7201
13
OsNTRC
94
gi|34576294|
emb|CAE46765.1|NADPH









thioredoxin reductase









[Oryza sativa (japonica









cultivar-group)]


174
532
PHE0006221_7241
5
OsNTRC
94
gi|34576294|
emb|CAE46765.1|NADPH









thioredoxin reductase









[Oryza sativa (japonica









cultivar-group)]


175
533
PHE0006221_7937
19
OsNTRC
94
gi|34576294|
emb|CAE46765.1|NADPH









thioredoxin reductase









[Oryza sativa (japonica









cultivar-group)]


176
534
PHE0006227_7282
1
ADR1
100
gi|30692890|
emb|CAE46486.1|CC-









NBS-LRR disease









resistance protein









[Arabidopsis thaliana]


177
535
PHE0006232_7454
4
rice Kinase
95
gi|34896978|
ref|NP_909835.1|putative









receptor-like kinase









[Oryza sativa (japonica









cultivar-group)]


178
536
PHE0006232_8756
19
rice Kinase
95
gi|34896978|
ref|NP_909835.1|putative









receptor-like kinase









[Oryza sativa (japonica









cultivar-group)]


179
537
PHE0006233_7220
4
corn bchI
88
gi|70905055|
gb|AAZ14053.1|magnesium









chelatase subunit I









precursor [Zea mays]


180
538
PHE0006234_7281
4
bchD -Mg Chelatase
87
gi|30680676|
ref|NP_563821.2|PDE166;









magnesium chelatase/









nucleoside-









triphosphatase/nucleotide









binding [Arabidopsis










thaliana]



181
539
PHE0006254_7312
1
glycosyl hydroxylase
90
gi|15238600|
ref|NP_198423.1|unknown









protein [Arabidopsis










thaliana]



182
540
PHE0006263_7271
9
OsDGAT2
95
gi|50912089|
ref|XP_467452.1|putative









mono- or diacylglycerol









acyltransferase [Oryza










sativa (japonica cultivar-










group)]


183
541
PHE0006264_7285
9
NcDGAT2
100
gi|38567182|
emb|CAE76475.1|related









to diacylglycerol









acyltransferase type 2a









[Neurospora crassa]


184
542
PHE0006265_7990
19

Arabidopsis thaliana

100
gi|15225771|
ref|NP_180235.1|HY1






cultivar Col-0 heme


(HEME OXYGENASE 1)






oxygenase 1 (HO1)


[Arabidopsis thaliana]






gene,


185
543
PHE0006281_7526
7
AtETR
95
gi|30697334|
ref|NP_176808.3|ETR1









(ETHYLENE









RESPONSE 1); two-









component response









regulator [Arabidopsis










thaliana]



186
544
PHE0006286_7314
1

Arabidopsis allene

97
gi|15239032|
ref|NP_199079.1|AOS






oxide synthase (AOS)/


(ALLENE OXIDE






hydroperoxide


SYNTHASE); hydro-






dehydrase/cyt


lyase/oxygen binding









[Arabidopsis thaliana]


187
545
PHE0006286_8011
19

Arabidopsis allene

97
gi|15239032|
ref|NP_199079.1|AOS






oxide synthase (AOS)/


(ALLENE OXIDE






hydroperoxide


SYNTHASE); hydro-






dehydrase/cyt


lyase/oxygen binding









[Arabidopsis thaliana]


188
546
PHE0006288_7310
1

Arabidopsis unknown

80
gi|15219363|
ref|NP_173123.1|unknown






protein


protein [Arabidopsis










thaliana]



189
547
PHE0006288_8023
19

Arabidopsis unknown

80
gi|15219363|
ref|NP_173123.1|unknown






protein


protein [Arabidopsis










thaliana]



190
548
PHE0006296_7515
9
EEM9
87
gi|63087722|
emb|CAI93176.1|glycosyl









transferase [Zea mays]


191
549
PHE0006309_7570
4

E. coli Glyoxalase I

100
gi|24052010|
gb|AAN43259.1|lactoyl-









glutathione lyase [Shigella










flexneri 2a str. 301]



192
550
PHE0006309_8148
19

E. coli Glyoxalase I

100
gi|24052010|
gb|AAN43259.1|lactoyl-









glutathione lyase [Shigella










flexneri 2a str. 301]










dbj|BAE76494.1|









glyoxalase I, Ni-









dependent [Escherichia










coli W3110]



193
551
PHE0006309_8620
19

E. coli Glyoxalase I

100
gi|24052010|
gb|AAN43259.1|lactoyl-









glutathione lyase [Shigella










flexneri 2a str. 301]










dbj|BAE76494.1|









glyoxalase I, Ni-









dependent [Escherichia










coli W3110]



194
552
PHE0006310_7574
12
rice BWMK1
95
gi|6689924|
gb|AAF23902.1|MAP









kinase homolog [Oryza










sativa]



195
553
PHE0006311_7976
19
AtRrp4p
96
gi|15218790|
ref|NP_171835.1|RNA









binding/exonuclease









[Arabidopsis thaliana]


196
554
PHE0006312_7579
4
yeast Nip7p
100
gi|45270008|
ref|NP_015113.1|









Nucleolar protein required









for 60S ribosome subunit









biogenesis, constituent of









66S pre-ribosomal









particles; physically









interacts with Nop8p and









the exosome subunit









Rrp43p; Nip7p









[Saccharomyces










cerevisiae]



197
555
PHE0006312_8644
19
yeast Nip7p
100
gi|45270008|
ref|NP_015113.1|









Nucleolar protein required









for 60S ribosome subunit









biogenesis, constituent of









66S pre-ribosomal









particles; physically









interacts with Nop8p and









the exosome subunit









Rrp43p; Nip7p









[Saccharomyces










cerevisiae]



198
556
PHE0006342_8182
19
1
91
gi|6320905|
ref|NP_010984.1|One of









two redundant DL-









glycerol-3-phosphatases









(RHR2/GPP1 encodes the









other) involved in









glycerol biosynthesis;









induced in response to









hyperosmotic stress and









oxidative stress, and









during the diauxic









transition; Hor2p









[Saccharomyces










cerevisiae]



199
557
PHE0006344_8188
19
SIB1 (SIGMA
89
gi|15228994|
ref|NP_191230.1|SIBl






FACTOR BINDING


(SIGMA FACTOR






PROTEIN 1); binding


BINDING PROTEIN 1);









binding [Arabidopsis










thaliana]



200
558
PHE0006346_8132
19

100
gi|18410491|
ref|NP_565076.1|unknown









protein [Arabidopsis










thaliana]



201
559
PHE0006348_8203
19
antiporter/glucose-6-
92
gi|18407336|
ref|NP_564785.1|antiporter/






phosphate transporte


glucose-6-phosphate









transporter [Arabidopsis










thaliana]



202
560
PHE0006349_8204
19

100
gi|45270642|
sp|P40001|YEA8_YEAST









Hypothetical 14.0 kDa









protein in GCN4-WBP1









intergenic region


203
561
PHE0006351_8200
19
rice hypothetical
58
gi|34897644|
ref|NP_910168.1|hypothetical






protein


protein [Oryza sativa]


204
562
PHE0006353_8098
19

91
gi|18418660|
ref|NP_567982.1|unknown









protein [Arabidopsis










thaliana]



205
563
PHE0006355_8084
19

Arabidopsis unknown

84
gi|18403871|
ref|NP_564601.1|unknown






protein


protein [Arabidopsis










thaliana]



206
564
PHE0006356_8103
19

78
gi|15240413|
ref|NP_198048.1|unknown









protein [Arabidopsis










thaliana]



207
565
PHE0006377_7592
4

Saccharomyces

91
gi|14588945|
cmb|CAC42984.1|rRNA







cerevisiae Rrp44p



processing protein









[Saccharomyces










cerevisiae]



208
566
PHE0006377_8683
19

Saccharomyces

91
gi|14588945|
sp|P25359|RRP43_YEAST







cerevisiae Rrp44p



Exosome complex









exonuclease RRP43









(Ribosomal RNA-









processing protein 43)


209
567
PHE0006378_7667
4

Saccharomyces

94
gi|51013303|
gb|AAT92945.1|YOL142W







cerevisiae Rrp40p



[Saccharomyces










cerevisiae]



210
568
PHE0006378_8715
19

Saccharomyces

94
gi|51013303|
gb|AAT92945.l|YOL142W







cerevisiae Rrp40p



[Saccharomyces










cerevisiae]



211
569
PHE0006380_7658
4

Saccharomyces

100
gi|1323143|
sp|P53256|RRP46_YEAST







cerevisiae Rrp46p



Exosome complex









exonuclease RRP46









(Ribosomal RNA-









processing protein 46)


212
570
PHE0006380_8719
19

Saccharomyces

100
gi|1323143|
sp|P53256|RRP46_YEAST







cerevisiae Rrp46p



Exosome complex









exonuclease RRP46









(Ribosomal RNA-









processing protein 46)


213
571
PHE0006381_7655
4

Saccharomyces

88
gi|1045263|
ref|NP_011674.1|3′5′







cerevisiae mtr3p



exoribornuclease, exosome









subunit; nucleolar protein









involved in export of









mRNA and ribosomal









subunits; homologous to









the E. coli exonuclease









RNase PH; Mtr3p









[Saccharomyces










cerevisiae]



214
572
PHE0006381_8695
19

Saccharomyces

88
gi|1045263|
ref|NP_011674.1|3′5′







cerevisiae mtr3p



exoribonuclease, exosome









subunit; nucleolar protein









involved in export of









mRNA and ribosomal









subunits; homologous to









the E. coli exonuclease









RNase PH; Mtr3p









[Saccharomyces










cerevisiae]



215
573
PHE0006382_7652
4
PHE0006382
100
gi|6321225|
ref|NP_011302.1|Protein







Saccharomyces cerevisiae



involved in exosome






SKI8


mediated 3′ to 5′ mRNA









degradation and









translation inhibition of









non-poly(A) mRNAs as









well as double-strand









break formation during









meiotic recombination;









required for repressing









propagation of dsRNA









viruses; Ski8p









[Saccharomyces










cerevisiae]



216
574
PHE0006382_8678
19

Saccharomyces

100
gi|6321225|
ref|NP_011302.1|Protein







cerevisiae SKI8



involved in exosome









mediated 3′ to 5′ mRNA









degradation and









translation inhibition of









non-poly(A) mRNAs as









well as double-strand









break formation during









meiotic recombination;









required for repressing









propagation of dsRNA









viruses; Ski8p









[Saccharomyces










cerevisiae]



217
575
PHE0006425_7646
4
corn CAT2
86
gi|77556625|
gb|ABA99421.1|Amino









acid permease [Oryza










sativa (japonica cultivar-










group)]


218
576
PHE0006426_8056
19
corn CAT5
76
gi|50881438|
gb|AAT85283.1|amino









acid permease domain









containing protein [Oryza










sativa (japonica cultivar-










group)]


219
577
PHE0006428_7651
4

Oryza sativa

100
gi|34902308|
ref|NP_912500.1|Putative






hemoglobin 2


non-symbiotic









hemoglobin 2 (rHb2)









[Oryza sativa (japonica









cultivar-group)]


220
578
PHE0006429_7671
4

Oryza sativa

100
gi|50920543|
ref|XP_470632.1|Putative






hemoglobin 1


Non-symbiotic









hemoglobin 1 [Oryza










sativa (japonica cultivar-










group)]


221
579
PHE0006433_8307
19
Pseudouridine
90
gi|56744228|
ref|NP_190794.2| RNA






synthase


binding/pseudouridine









synthase/pseudouridylate









synthase [Arabidopsis










thaliana]



222
580
PHE0006439_8108
19
corn putative RNA-
56
gi|15231311|
ref|NP_190188.1|RNA






binding protein


binding/nucleic acid









binding [Arabidopsis










thaliana]



223
581
PHE0006449_7865
1
dihydrolipoamide
90
gi|17741871|
ref|NP_533968.1|






acetyltransferase


dihydrolipoamide









acetyltransferase









[Agrobacterium










tumefaciens str. C58]



224
582
PHE0006449_8165
19
lipoamide
90
gi|17741871|
gb|AAL44284.1|lipoamide






acyltransferase


acyltransferase






component of


component of branched-






branched-chain alpha-


chain alpha-keto acid






keto acid


dehydrogenase complex






dehydrogenase


E2 [Agrobacterium






complex E2



tumefaciens str. C58]



225
583
PHE0006450_7624
1
FtsZ1
83
gi|7672161|
emb|CAB89287.1|chloroplast









FtsZ-like protein









[Nicotiana tabacum]


226
584
PHE0006464_8089
19
corn unnamed protein
56
gi|34904362|
dbj|BAA96588.1| plasma






product


membrane polypeptide -









like [Oryza sativa









(japonica cultivar-group)]









sp|P83649|SRS1_ORYSA









Salt-stress root protein









RS1


227
585
PHE0006468_7903
1

100
gi|18401231|
ref|NP_566558.1|unknown









protein [Arabidopsis










thaliana]



228
586
PHE0006477_7809
17
AtPsbR
81
gi|15219268|
sp|P27202|PSBR_ARATH









Photosystem II 10 kDa









polypeptide, chloroplast









precursor


229
587
PHE0006478_8190
19
adenosylmethionine: 2-
94
gi|34910724|
ref|NP_916709.1|S-






demethylmenaquinone


adenosylmethionine: 2-






methyltransferase-like


demethylmenaquinone






protein


methyltransferase-like









protein [Oryza sativa









(japonica cultivar-group)]


230
588
PHE0006497_8355
19

Arabidopsis unknown

72
gi|15238921|
ref|NP_196661.1|unknown






protein


protein [Arabidopsis










thaliana]



231
589
PHE0006498_7795
18
soy Glutamate
100
gi|32493114|
gb|AAP85548.1|putative






Decarboxylase


glutamate decarboxylase









[Glycine max]


232
590
PHE0006498_7796
2
soy Glutamate
100
gi|32493114|
gb|AAP85548.1|putative






Decarboxylase


glutamate decarboxylase









[Glycine max]


233
591
PHE0006505_7871
1
soy Thioredoxin X
68
gi|18403021|
ref|NP_564566.1|ATHX;









electron transporter/thiol-









disulfide exchange









intermediate [Arabidopsis










thaliana]



234
592
PHE0006506_7818
1

Arabidopsis SRK2C

100
gi|42572557|
ref|NP_974374.1|AKIN11;






like


protein kinase









[Arabidopsis thaliana]


235
593
PHE0006514_7926
10
Truncated Beta GDH
99
gi|18273|
emb|CAA41636.1|glutamate









dehydrogenase









(NADP+) [Chlorella










sorokiniana]



236
594
PHE0006516_7866
17
Corn Magnesium
80
gi|78708975|
gb|ABB47950.1|CorA-






transporter


like Mg2+ transporter









protein, putative [Oryza










sativa (japonica cultivar-










group)]


237
595
PHE0006516_7882
8
Corn Magnesium
80
gi|78708975|
gb|ABB47950.1|CorA-






transporter


like Mg2+ transporter









protein, putative [Oryza










sativa (japonica cultivar-










group)]


238
596
PHE0006516_7887
16
Corn Magnesium
80
gi|78708975|
gb|ABB47950.1|CorA-






transporter


like Mg2+ transporter









protein, putative [Oryza










sativa (japonica cultivar-










group)]


239
597
PHE0006516_8363
19
Corn Magnesium
80
gi|78708975|
gb|ABB47950.1|CorA-






transporter


like Mg2+ transporter









protein, putative [Oryza










sativa (japonica cultivar-










group)]


240
598
PHE0006517_7858
16
Rice Magnesium
95
gi|78708975|
gb|ABB47950.1|CorA-






transporter


like Mg2+ transporter









protein, putative [Oryza










sativa (japonica cultivar-










group)]


241
599
PHE0006517_7879
17
Rice Magnesium
95
gi|78708975|
gb|ABB47950.1|CorA-






transporter


like Mg2+ transporter









protein, putative [Oryza










sativa (japonica cultivar-










group)]


242
600
PHE0006517_7897
8
Rice Magnesium
95
gi|78708975|
gb|ABB47950.1|CorA-






transporter


like Mg2+ transporter









protein, putative [Oryza










sativa (japonica cultivar-










group)]


243
601
PHE0006521_7840
15

Anabaena SPP

100
gi|14594809|
emb|CAC43285.1|sucrose-









phosphate phosphatase









[Nostoc sp. PCC 7120]


244
602
PHE0006545_8320
9
ARG1-like protein
79
gi|51535811|
dbj|BAD37896.1|ARG1-









like protein [Oryza sativa









(japonica cultivar-group)]


245
603
PHE0006549_8255
19
methylenetetrahydrofolate
83
gi|54291831|
gb|AAV32199.1|unknown






dehydrogenase


protein [Oryza sativa






(NADP+)


(japonica cultivar-group)]


246
604
PHE0006555_8283
19
G3PB_PEA
84
gi|50948907|
ref|XP_493811.1|EST






Glyceraldehyde 3-


C74302(E30840)






phosphate


corresponds to a region of






dehydrogenase B,


the predicted






chloroplast


gene. ~similar to









glyceraldehyde-3-









phosphate dehydrogenase.









(M64118) [Oryza sativa









(japonica cultivar-group)]


247
605
PHE0006559_8227
16
phosphoenolpyruvate
98
gi|34904868|
ref|NP_913781.1|phospho-






carboxylase


enolpyruvate carboxylase









[Oryza sativa (japonica









cultivar-group)]


248
606
PHE0006564_8298
17
corn asparagine
95
gi|28395526|
gb|AAO39048.1|asparagine






synthetase 2


synthetase 2 [Hordeum










vulgare]



249
607
PHE0006565_8300
17
corn glutamine-
97
gi|53680379|
gb|AAU89392.1|glutamine-






dependent asparagines


dependent asparagine






synthetase.


synthetase [Triticum










aestivum]



250
608
PHE0006571_8279
19

Arabidopsis thaliana

95
gi|15223870|
gb|AAN12902.1| putative






phosphoenolpyruvate


calcium-dependent






carboxylase kinase


protein kinase









[Arabidopsis thaliana]


251
609
PHE0006574_8224
19
Glyoxalase I
100
gi|984219|
sp|Q09751|LGUL_SCHPO









Lactoylglutathione









lyase (Methylglyoxalase)









(Aldoketomutase)









(Glyoxalase 1)


252
610
PHE0006586_8271
19

Arabidopsis

83
gi|51860727|
gb|AAU11485.1|mitochondrial






mitochondrial


frataxin-like






frataxin-like


[Arabidopsis thaliana]


253
611
PHE0006587_8277
19

Arabidopsis CP12

100
gi|15228752|
gb|AAM45071.1|






domain-containing


putative CP12 protein






protein


precursor [Arabidopsis










thaliana]



254
612
PHE0006590_8258
19

Arabidopsis

89
gi|30678634|
ref|NP_849585.1|ATHM1;






thioredoxin M-type 1


electron transporter/









thiol-disulfide exchange









intermediate [Arabidopsis










thaliana]



255
613
PHE0006591_8264
19

Arabidopsis

94
gi|15236327|
ref|NP_192261.1|ATHM2;






thioredoxin M-type 2


electron transporter/









thiol-disulfide exchange









intermediate [Arabidopsis










thaliana]



256
614
PHE0006592_8278
19
thioredoxin M-type 4
80
gi|15232567|
ref|NP_188155.1|ATHM4;









electron transporter/









thiol-disulfide exchange









intermediate [Arabidopsis










thaliana]



257
615
PHE0006593_8245
1

Arabidopsis putative

100
gi|15236013|
ref|NP_193460.1|unknown






protein


protein [Arabidopsis










thaliana]



258
616
PHE0006593_8256
19

Arabidopsis putative

100
gi|15236013|
ref|NP_193460.1|unknown






protein


protein [Arabidopsis










thaliana]



259
617
PHE0006595_8250
1

Arabidopsis unknown

100
gi|18417658|
ref|NP_567853.1|unknown






protein


protein [Arabidopsis










thaliana]



260
618
PHE0006595_8265
19

Arabidopsis unknown

100
gi|18417658|
ref|NP_567853.1|unknown






protein


protein [Arabidopsis










thaliana]



261
619
PHE0006596_8236
1

Arabidopsis

93
gi|15224138|
ref|NP_179417.1|nucleoti-






hypothetical protein


dyltransferase









[Arabidopsis thaliana]


262
620
PHE0006596_8257
19

Arabidopsis

93
gi|15224138|
ref|NP_179417.1|nucleoti-






hypothetical protein


dyltransferase









[Arabidopsis thaliana]


263
621
PHE0006597_8242
1

Arabidopsis putative

94
gi|22330852|
ref|NP_187165.2|ATP






serine/threonine


binding/kinase/protein






protein kinase


kinase/protein









serine/threonine kinase/









protein-tyrosine kinase









[Arabidopsis thaliana]


264
622
PHE0006598_8240
1

Arabidopsis drought-

77
gi|22137252|
gb|AAM91471.1|AT3g06






responsive family


760/F3E22_10






protein


[Arabidopsis thaliana]









gb|AAL67123.1|









AT3g06760/F3E22_10









[Arabidopsis thaliana]


265
623
PHE0006598_8268
19

Arabidopsis drought-

77
gi|22137252|
gb|AAM91471.1|AT3g06






responsive family


760/F3E22_10






protein


[Arabidopsis thaliana]


266
624
PHE0006599_8230
1

Arabidopsis zinc

79
gi|18410665|
ref|NP_565088.1|transcription






finger homeobox


factor [Arabidopsis






family protein



thaliana]



267
625
PHE0006599_8262
19

Arabidopsis zinc

79
gi|18410665|
ref|NP_565088.1|transcription






finger homeobox


factor [Arabidopsis






family protein



thaliana]



268
626
PHE0006600_8249
1

Xenorhabdus putative

83
gi|75208732|
ref|ZP_00709024.1|COG0






tartrate dehydrogenase


473:









Isocitrate/isopropylmalate









dehydrogenase









[Escherichia coli B171]


269
627
PHE0006607_8231
1

Arabidopsis MADS-

92
gi|15219825|
ref|NP_176285.1|AGL56;






box family protein


DNA binding/transcription factor









[Arabidopsis thaliana]


270
628
PHE0006609_8234
1
Soy Glutathione
71
gi|18407538|
ref|NP_566128.1|ATGPX






Peroxidase


4 (GLUTATHIONE









PEROXIDASE 4);









glutathione peroxidase









[Arabidopsis thaliana]


271
629
PHE0006610_8239
1
Soy Glutathione
75
gi|2632109|
emb|CAA04142.1|phospho-






Peroxidase


lipid glutathione









peroxidase [Pisum










sativum]



272
630
PHE0006613_8238
1
Soy Glutathione
64
gi|11544696|
emb|CAC17628.1|putative






Peroxidase


phospholipid









hydroperoxide glutathione









peroxidase [Oryza sativa









(japonica cultivar-group)]


273
631
PHE0006617_8463
19
corn oxalate oxidase
86
gi|6996619|
gb|AAF34811.1|oxalate









oxidase [Triticum










aestivum]



274
632
PHE0006620_8462
19
corn NADPH-
96
gi|78172239|
gb|ABB29303.1|NADPH-






dependent reductase


dependent reductase [Zea










mays]



275
633
PHE0006648_8356
19
corn putative protease
44
gi|50919133|
ref|XP_469963.1|putative






inhibitor


protease inhibitor [Oryza










sativa (japonica cultivar-










group)]


276
634
PHE0006666_8414
19
corn putative plastidic
93
gi|34895322|
ref|NP_909004.1|putative






aldolase


plastidic aldolase [Oryza










sativa (japonica cultivar-










group)] ]


277
635
PHE0006669_8357
14

Schizosaccharomyces

97
gi|2956754|
sp|O42938|K6PF_SCHPO







pombe ATP-PFK



6-phosphofructokinase









(Phosphofructokinase)









(Phosphohexokinase)









(6PF-1-K)


278
636
PHE0006670_8346
21

E. coli ATP-dependent

100
gi|85675091|
dbj|BAA15500.2|6-






phosphofructokinase


phosphofructokinase II






B with CTP2


[Escherichia coli W3110]


279
637
PHE0006673_8992
17

Arabidopsis peptide

88
gi|18409391|
ref|NP_564979.1|transporter






transporter


[Arabidopsis thaliana]


280
638
PHE0006676_8410
19
corn pyruvate
94
gi|3850999|
gb|AAC72192.1|pyruvate






dehydrogenase E1


dehydrogenase E1 beta






beta subunit


subunit isoform 1 [Zea










mays]



281
639
PHE0006684_8413
19
corn probable 60S
88
gi|77548268|
gb|ABA91065.1|ribosomal






acidic ribosomal


protein L10, putative






protein


[Oryza sativa (japonica









cultivar-group)]


282
640
PHE0006685_8415
19
corn Ribosomal
63
gi|50932757|
ref|XP_475906.1|unknown






protein L1p/L10e


protein [Oryza sativa






family


(japonica cultivar-group)]


283
641
PHE0006686_8416
19
corn ribosomal protein
98
gi|3914685|
sp|O48557|RL17_MAIZE






L17.2, cytosolic


60S ribosomal protein









L17 gb|AAB88619.1|









ribosomal protein L17









[Zea mays]


284
642
PHE0006687_8471
19
corn ribosomal protein
98
gi|5236757|
sp|P49211|RL32A_ARATH






L32-like protein.


60S ribosomal protein









L32-1


285
643
PHE0006706_8434
1
soy PDH45 (DNA
100
gi|15223841|
ref|NP_175549.1|ATP






helicase 45)


binding/ATP-dependent









helicase/helicase/nucleic









acid binding [Arabidopsis










thaliana]



286
644
PHE0006709_8432
1
Corn protein similar to
80
gi|34912462|
ref|NP_917578.1|MtN3-






nodulin Mt N3 Protein


like protein [Oryza sativa









(japonica cultivar-group)]









dbj|BAB92465.1|









senescence-associated









protein-like [Oryza sativa









(japonica cultivar-group)]


287
645
PHE0006715_8477
1
AKIN beta2
100
gi|56744220|
sp|Q9SCY5|KINB2_ARATH









SNF1-related protein









kinase regulatory beta









subunit 2 (AKIN beta2)









(AKINB2)


288
646
PHE0006716_8482
1
putative nitrate-
78
gi|20465673|
gb|AAM20305.1|putative






induced NOI protein


nitrate-induced NOI









protein [Arabidopsis










thaliana]



289
647
PHE0006727_8435
1
corn NADH-
91
gi|50509945|
dbj|BAD30267.1|NADH-






ubiquinone


ubiquinone






oxidoreductase-


oxidoreductase-related-






related-like protein


like protein [Oryza sativa









(japonica cultivar-group)]


290
648
PHE0006727_8595
19
NADH-ubiquinone
91
gi|50509945|
dbj|BAD30267.1|NADH-






oxidoreductase-


ubiquinone






related-like protein


oxidoreductase-related-









like protein [Oryza sativa









(japonica cultivar-group)]


291
649
PHE0006728_8430
1

Arabidopsis RNA

95
gi|15231193|
ref|NP_190149.1|RNA






recognition motif


binding/nucleic acid






(RRM)-containing


binding/ubiquitin-protein






protein


ligase/zinc ion binding









[Arabidopsis thaliana]


292
650
PHE0006729_8433
1
corn DNAJ heat shock
67
gi|51536221|
dbj|BAD38392.1|DNAJ






N-terminal domain-


heat shock N-terminal






containing protein-like


domain-containing









protein-like [Oryza sativa









(japonica cultivar-group)]


293
651
PHE0006730_8428
1
corn membrane
77
gi|51091402|
dbj|BAD36145.1|membrane






protein PTM1-like


protein PTM1-like









[Oryza sativa (japonica









cultivar-group)]


294
652
PHE0006737_8455
1

Arabidopsis putative

100
gi|15221544|
gb|AAK64077.1| putative






oxidoreductase


oxidoreductase









[Arabidopsis thaliana]


295
653
PHE0006737_8527
19

Arabidopsis putative

100
gi|15221544|
gb|AAK25895.1| putative






oxidoreductase


oxidoreductase









[Arabidopsis thaliana]


296
654
PHE0006740_8446
1
corn unknown protein
70
gi|50931847|
ref|XP_475451.1|unknown









protein [Oryza sativa









(japonica cultivar-group)]


297
655
PHE0006740_8596
19
corn unknown protein
70
gi|50931847|
ref|XP_475451.1|unknown









protein [Oryza sativa









(japonica cultivar-group)]


298
656
PHE0006741_8448
1

Arabidopsis unknown

90
gi|30678912|
ref|NP_566212.2|ATBPM






protein


4; protein binding









[Arabidopsis thaliana]


299
657
PHE0006741_8589
19

Arabidopsis unknown

90
gi|30678912|
ref|NP_566212.2|ATBPM






protein


4; protein binding









[Arabidopsis thaliana]


300
658
PHE0006742_8440
1

Pseudomonas

98
gi|77385037|
ref|YP_350541.1|







fluorescens Glucose-



glucose-6-phosphate






6-phosphate isomerase


isomerase [Pseudomonas










fluorescens PfO-1]



301
659
PHE0006742_8591
19

Pseudomonas

98
gi|77385037|
gb|ABA76550.1|Glucose-







fluorescens Glucose-



6-phosphate isomerase






6-phosphate isomerase


[Pseudomonas










fluorescens PfO-l]



302
660
PHE0006744_8449
1

Arabidopsis ribitol

95
gi|18423110|
ref|NP_568721.1|oxidore-






dehydrogenase-like


ductase [Arabidopsis










thaliana]










gb|AAM13036.1| ribitol









dehydrogenase-like









[Arabidopsis thaliana]


303
661
PHE0006745_8590
19
corn putative 28 kDa
81
gi|50904959|
ref|XP_463968.1|putative






Golgi SNARE protein


28 kDa Golgi SNARE









protein [Oryza sativa









(japonica cultivar-group)]


304
662
PHE0006746_8453
1

Arabidopsis

93
gi|18421106|
ref|NP_568493.1|SFP1






CGPG6223 sugar-


(sugar-porter family






porter family protein 1


protein 1); carbohydrate









transporter/sugar porter









[Arabidopsis thaliana]


305
663
PHE0006750_8523
12

Arabidopsis Cop1

100
gi|15225760|
ref|NP_180854.1|COP1









(CONSTITUTIVE









PHOTOMORPHOGENIC









1) [Arabidopsis










thaliana]



306
664
PHE0006757_8530
12

Arabidopsis

92
gi|18390661|
ref|NP_563768.1|ATGPAT1/






phospholipid/glycerol


GPAT1; 1-






acyltransferase family


acylglycerol-3-phosphate






protein


O-acyltransferase/acyltransferase









[Arabidopsis thaliana]


307
665
PHE0006760_8529
19

Arabidopsis vacuolar

100
gi|15237054|
ref|NP_192853.1|TUF






ATP synthase subunit


(TUFF) [Arabidopsis






E/V-ATPase E



thaliana]







subunit/vacuolar prot


emb|CAB81216.1|H+-









transporting ATPase









chain E, vacuolar









[Arabidopsis thaliana]


308
666
PHE0006765_8536
20

Arabidopsis IMB1

92
gi|30686240|
ref|NP_181036.2|IMB1









(IMBIBITION-









INDUCIBLE 1); DNA









binding [Arabidopsis










thaliana]



309
667
PHE0006766_8867
9
AGRtu.Isopentyl
94
gi|15163474|
gb|AAK90970.1|AGR_pT






transferase-0:2:1


i_50p [Agrobacterium










tumefaciens str. C58]



310
668
PHE0006769_8865
14
Pyruvate oxidase
97
gi|1651398|
dbj|BAA35585.1|pyruvate






(POXB)


dehydrogenase (pyruvate









oxidase), thiamin-









dependent, FAD-binding









[Escherichia coli W3110]


311
669
PHE0006770_8553
19
corn PDH45
99
gi|84322402|
gb|ABC55720.1|putative









RH2 protein [Zea mays]


312
670
PHE0006770_8568
13
corn PDH45
99
gi|84322402|
gb|ABC55720.1|putative









RH2 protein [Zea mays]


313
671
PHE0006771_8551
19

Arabidopsis HIC

94
gi|15226428|
gb|AAC69929.1| putative






(High CO2)


beta-ketoacyl-CoA









synthase [Arabidopsis










thaliana]



314
672
PHE0006775_8548
19
RabG3e/Rab7
100
gi|15222098|
ref|NP_175355.1|GTP









binding [Arabidopsis










thaliana]



315
673
PHE0006775_8555
13
RabG3e/Rab7
100
gi|15222098|
ref|NP_175355.1|GTP









binding [Arabidopsis










thaliana]



316
674
PHE0006788_8581
13

Lycopersicon

72
gi|71360930|
emb|CAJ19706.1|non-







esculentum non



specific lipid transfer






specific lipid transfer


protein [Lycopersicon






protein



esculentum]



317
675
PHE0006793_8580
13

Arabidopsis

97
gi|15236789|
ref|NP_191946.1|CYP86






cytochrome P450


A2; oxygen binding









[Arabidopsis thaliana]









emb|CAB80794.1|









probable cytochrome









P450 [Arabidopsis










thaliana]



318
676
PHE0006794_8578
13

Arabidopsis single-

100
gi|30681642|
ref|NP_192844.2|single-






strand-binding family


stranded DNA binding






protein


[Arabidopsis thaliana]


319
677
PHE0006805_8531
12

E. coli yf1a

100
gi|24053042|
gb|AAN44153.1|putative









yhbH sigma 54 modulator









[Shigella flexneri 2a str.









301]


320
678
PHE0006811_8506
19
Cyanoglobin
91
gi|1653074|
dbj|BAA17991.1|cyanoglobin









[Synechocystis sp.









PCC 6803]


321
679
PHE0006816_8560
19
Corn HO2-Like
71
gi|14485573|
gb|AAK63011.1|heme









oxygenase 2 [Sorghum










bicolor]



322
680
PHE0006844_8839
22

Arabidopsis RNA-

100
gi|15232735|
ref|NP_190300.1|ubiquitin-






binding protein-like


protein ligase/zinc ion






protein


binding [Arabidopsis










thaliana]



323
681
PHE0006847_8860
19

Agrobacterium 3,4-

100
gi|17739122|
gb|AAL41769.1|3,4-






dihydroxy-2-


dihydroxy-2-butanone-4-






butanone-4-phoshate


phoshate synthase/GTP






synthase/GTP


cyclohydrolase II






cyclohyd


[Agrobacterium










tumefaciens str. C58]



324
682
PHE0006870_8846
19
60S ribosomal protein
100
gi|18411538|
gb|AAM65721.1|60S






L37a


ribosomal protein L37a









[Arabidopsis thaliana]


325
683
PHE0006908_9016
19
Thioredoxin_MON_Z
67
gi|10178282|
emb|CAC08340.1|putative






M33301


protein [Arabidopsis










thaliana]



326
684
PHE0006909_9003
19
A1ZM000889_at_Cup
75
gi|50924572|
ref|XP_472645.1|OSJNBa






in_3


0027P08.10 [Oryza sativa









(japonica cultivar-group)]


327
685
PHE0006910_9019
19
A1ZM009835_at_Mo
75
gi|55773965|
dbj|BAD72492.1|ALM






v34


beta-like [Oryza sativa









(japonica cultivar-group)]


328
686
PHE0006912_9000
19
A1ZM000998_a_at_putative
79
gi|50911385|
ref|XP_467100.1|putative






enoyl-CoA


enoyl-CoA hydratase






hydratase


[Oryza sativa (japonica









cultivar-group)]


329
687
PHE0006919_9008
19
putative mitochondrial
76
gi|57899480|
dbj|BAD86941.1|putative






processing peptidase


milochondrial processing






alpha subuunit, mitoch


peptidase [Oryza sativa









(japonica cultivar-group)]


330
688
PHE0006929_9151
22
COP1-interacting
46
gi|15238295|
ref|NP_201297.1|CIP8






protein CIP8


(COP1-INTERACTING









PROTEIN 8); protein









binding/zinc ion binding









[Arabidopsis thaliana]


331
689
PHE0006929_9185
19
COP1-interacting
46
gi|15238295|
ref|NP_201297.1|CIP8






protein CIP8


(COP1-INTERACTING









PROTEIN 8); protein









binding/zinc ion binding









[Arabidopsis thaliana]


332
690
PHE0006931_9148
22
glycine dehydrogenase
93
gi|10175436|
dbj|BAB06534.1|glycine






subunit 1


dehydrogenase subunit 1









[Bacillus halodurans C-









125]


333
691
PHE0006931_9168
19
glycine dehydrogenase
93
gi|10175436|
dbj|BAB06534.1|glycine






subunit 1


dehydrogenase subunit 1









[Bacillus halodurans C-









125]


334
692
PHE0006932_9147
22
expressed protein
100
gi|18406559|
ref|NP_566020.1|unknown









protein [Arabidopsis










thaliana]



335
693
PHE0006932_9174
19
Unknown protein
100
gi|18406559|
ref|NP_566020.1|unknown









protein [Arabidopsis










thaliana]



336
694
PHE0006933_9139
22
short-chain
92
gi|30686197|
ref|NP_849428.1|oxidore-






dehydrogenase/reductase


ductase [Arabidopsis






(SDR) family



thaliana]







protein_CGPG5025


337
695
PHE0006934_9145
22
OsPol delta small
91
gi|9188572|
dbj|BAA99574.1|OsPol






subunit


delta small subunit [Oryza










sativa (japonica cultivar-










group)]


338
696
PHE0006937_9126
22
putative leucine zipper
77
gi|51535194|
dbj|BAD38167.1|putative






protein


leucine zipper protein









[Oryza sativa (japonica









cultivar-group)]


339
697
PHE0006938_9149
22
TPA: actin-related
98
gi|30696705|
ref|NP_568836.2|ATARP






protein 8B


8 (ACTIN-RELATED









PROTEIN 8); structural









constituent of









cytoskeleton [Arabidopsis










thaliana]



340
698
PHE0006940_9122
22
NADP-dependent
100
gi|10174856|
dbj|BAB05956.1|NADP-






glyceraldehyde-3-


dependent






phosphate


glyceraldehyde-3-






dehydrogenase


phosphate dehydrogenase









[Bacillus halodurans C-









125]


341
699
PHE0006941_9117
22
Unknown protein
90
gi|18401933|
ref|NP_564515.1|unknown









protein [Arabidopsis










thaliana]



342
700
PHE0006943_9124
22
amino acid
94
gi|18395471|
ref|NP_564217.1|AATL2






transporter-like


(AMINO ACID






protein 2


TRANSPORTER-LIKE









PROTEIN 2); amino acid









permease [Arabidopsis










thaliana]



343
701
PHE0006948_9125
22
Similar to glycine-rich
100
gi|15221825|
ref|NP_173298.1|RNA






RNA-binding proteins_CGPG4960


binding/nucleic acid









binding [Arabidopsis










thaliana]



344
702
PHE0006948_9160
19
glycine-rich RNA-
100
gi|15221825|
ref|NP_173298.1|RNA






binding proteins


binding/nucleic acid









binding [Arabidopsis










thaliana]



345
703
PHE0006949_9133
22
PROBABLE
97
gi|15072942|
ref|NP_384120.1|






SUCCINATE-


PROBABLE






SEMIALDEHYDE


SUCCINATE-






DEHYDROGENASE


SEMIALDEHYDE






[NADP] PROTEIN


DEHYDROGENASE









[NADP+] PROTEIN









[Sinorhizobium meliloti









1021]


346
704
PHE0006949_9179
19
PROBABLE
97
gi|15072942|
emb|CAC41401.1|PROBABLE






SUCCINATE-


SUCCINATE-






SEMIALDEHYDE


SEMIALDEHYDE






DEHYDROGENASE


DEHYDROGENASE






[NADP] PROTEIN


[NADP+] PROTEIN









[Sinorhizobium meliloti]


347
705
PHE0006952_9233
22
Gpm1p with ctp
95
gi|407495|
ref|NP_012770.1|









Tetrameric









phosphoglycerate mutase,









[Saccharomyces










cerevisiae]



348
706
PHE0006953_9121
22
universal stress
93
gi|30678807|
ref|NP_850506.1|unknown






protein (USP) family


protein [Arabidopsis






protein



thaliana]



349
707
PHE0006954_9154
22
unnamed protein
80
gi|22327694|
ref|NP_680415.1|unknown






product


protein [Arabidopsis










thaliana]



350
708
PHE0006954_9161
19
unnamed protein
80
gi|22327694|
ref|NP_680415.1|unknown






product


protein [Arabidopsis










thaliana]



351
709
PHE0006962_9114
15
nitrate reductase
94
gi|85675313|
dbj|BAA15989.2|nitrate









reductase, periplasmic,









large subunit [Escherichia










coli W3110]



352
710
PHE0006963_9131
15
nitrite reductase
97
gi|85676675|
dbj|BAE77925.1|nitrite









reductase, large subunit,









NAD(P)H-binding









[Escherichia coli W3110]


353
711
PHE0006965_9119
17
glutaminyl-tRNA
86
gi|77554943|
gb|ABA97739.1|prolyl-






synthetase


tRNA synthetase [Oryza










sativa (japonica cultivar-










group)]


354
712
PHE0006970_9141
19
DNA binding/
100
gi|15242227|
ref|NP_197020.1|DNA






transcription factor


binding/transcription









factor [Arabidopsis










thaliana]



355
713
PHE0006977_9163
19
ribulose-phosphate 3-
96
gi|15221735|
ref|NP_176518.1|ribulose-






epimerase


phosphate 3-epimerase









[Arabidopsis thaliana]


356
714
PHE0006986_9183
19
Unknown protein
82
gi|50932819|
ref|XP_475937.1|unknown









protein [Oryza sativa









(japonica cultivar-group)]


357
715
PHE0006992_9140
22
unknown protein
93
gi|15234800|
ref)NP_194792.1|unknown









protein [Arabidopsis










thaliana]



358
716
PHE0006992_9184
19
Unknown protein
93
gi|15234800|
ref|NP_194792.1|unknown









protein [Arabidopsis










thaliana]











Selection Methods for Transgenic Plants with Enhanced Agronomic Trait


Within a population of transgenic plants regenerated from plant cells transformed with the recombinant DNA many plants that survive to fertile transgenic plants that produce seeds and progeny plants will not exhibit an enhanced agronomic trait. Selection from the population is necessary to identify one or more transgenic plant cells that can provide plants with the enhanced trait. Transgenic plants having enhanced traits are selected from populations of plants regenerated or derived from plant cells transformed as described herein by evaluating the plants in a variety of assays to detect 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. These assays also may take many forms including, but not limited to, direct screening for the trait in a greenhouse or field trial or by screening for a surrogate trait. Such analyses can be directed to detecting changes in the chemical composition, biomass, physiological properties, morphology of the plant. Changes in chemical compositions such as nutritional composition of grain can be detected by analysis of the seed composition and content of protein, free amino acids, oil, free fatty acids, starch or tocopherols. Changes in biomass characteristics can be made on greenhouse or field grown plants and can include plant height, stem diameter, root and shoot dry weights; and, for corn plants, ear length and diameter. Changes in physiological properties can be identified by evaluating responses to stress conditions, for example assays using imposed stress conditions such as water deficit, nitrogen deficiency, cold growing conditions, pathogen or insect attack or light deficiency, or increased plant density. Changes in morphology can be measured by visual observation of tendency of a transformed plant with an enhanced agronomic trait to also appear to be a normal plant as compared to changes toward bushy, taller, thicker, narrower leaves, striped leaves, knotted trait, chlorosis, albino, anthocyanin production, or altered tassels, ears or roots. Other selection properties include 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, phenotypic characteristics of harvested grain may be evaluated, 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. Although the plant cells and methods of this invention can be applied to any plant cell, plant, seed or pollen, e.g. any fruit, vegetable, grass, tree or ornamental plant, the various aspects of the invention are preferably applied to corn, soybean, cotton, canola, alfalfa, wheat and rice plants. In many cases the invention is applied to corn plants that are inherently resistant to disease from the Mal de Rio Cuarto virus or the Puccina sorghi fungus or both.


The following examples are included to demonstrate aspects of the invention, those of skill in the art should, in light of the present disclosure, appreciate that many changes can be made in the specific aspects which are disclosed and still obtain a like or similar results without departing from the spirit and scope of the invention.


Example 1
Plant Expression Constructs

This example illustrates the construction of plasmids for transferring recombinant DNA into plant cells which can be regenerated into transgenic plants of this invention


A. Plant Expression Constructs for Corn Transformation

A base corn plant transformation vector pMON93039, as set forth in SEQ ID NO: 30329, illustrated in Table 3 and FIG. 2, was fabricated for use in preparing recombinant DNA for Agrobacterium-mediated transformation into corn tissue.












TABLE 3








Coordinates of





SEQ ID NO:


function
name
annotation
30329







Agro
B-AGRtu.right
Agro right border
11364-11720


transforamtion
border
sequence, essential for





transfer of T-DNA.



Gene of
E-Os.Act1
upstream promoter
  19-775


interest

region of the rice actin



expression

1 gene



cassette
E-CaMV.35S.
duplicated35S A1-B3
 788-1120



2xA1-B3
domain without TATA





box




P-Os.Act1
promoter region of the
 1125-1204




rice actin 1 gene




L-Ta.Lhcb1
5′ untranslated leader
 1210-1270




of 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
 1838-2780




of the potato proteinase





inhibitor II gene which





functions to direct





polyadenylation of the





mRNA



Plant
P-Os.Act1
Promoter from the rice
 2830-3670


selectable

actin 1 gene



marker
L-Os.Act1
first exon of the rice
 3671-3750


expression

actin 1 gene



cassette
I-Os.Act1
first intron and flanking
 3751-4228




UTR exon sequences





from the rice actin 1





gene




TS-At.ShkG-
Transit peptide region
 4238-4465



CTP2
of Arabidopsis EPSPS




CR-AGRtu.
Synthetic CP4 coding
 4466-5833



aroA-CP4.nat
region with dicot





preferred codon usage.




T-AGRtu.nos
A 3′ non-translated
 5849-6101




region of the nopaline





synthase gene of






Agrobacterium







tumefaciens Ti plasmid






which functions to





direct polyadenylation





of the mRNA.



Agro
B-AGRtu.left
Agro left border
 6168-6609


transformation
border
sequence, essential for





transfer of T-DNA.



Maintenance
OR-Ec.oriV-
The vegetative origin of
 6696-7092


in E. coli
RK2
replication from





plasmid RK2.




CR-Ec.rop
Coding region for
 8601-8792




repressor 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-
The minimal origin of
 9220-9808



ColE1
replication from the E.






coli plasmid ColE1.





P-Ec.aadA-
romoter 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.










Another embodiment of corn plant transformation base vector is pMON92705, as set forth in SEQ ID NO: 30330, illustrated in Table 4 and FIG. 3, which was fabricated for use in preparing recombinant DNA for Agrobacterium-mediated transformation into corn tissue.












TABLE 4








Coordinates





of SEQ ID


function
name
annotation
NO: 30330







Agro
B-AGRtu.right
Agro right border
 5206-5526


transforamtion
border
sequence, essential for
  




transfer of T-DNA.
  


Gene of
P-Os.Act1
Promoter from the rice
 5580-6423


interest

actin 1 gene
  


expression
L-Os.Act1
5′UTR of riceAct1 gene
 6424-6503


cassette
I-Os.Act1
Intron from the rice
 6504-6980




actin1 gene
  



T-St.Pis4
3′ non-translated region of
 7055-7997




the potato proteinase
  




inhibitor II gene which
  




functions to direct
  




polyadenylation of the
  




mRNA
  


Plant
P-Os.Act1
Promoter from the rice
 8047-8887


selectable

actin 1 gene



marker
L-Os.Act1
first exon of the rice actin
 8888-8967


expression

1 gene



cassette
I-Os.Act1
first intron and flanking
 8968-9445




UTR exon sequences





from the rice actin 1 gene




TS-At.ShkG-
Transit peptide region of
 9455-9682



CTP2

Arabidopsis EPSPS





CR-AGRtu.
Synthetic CP4 coding
 9683-11050



aroA-CP4.nat
region with dicot





preferred codon usage.




T-AGRtu.nos
A 3′ non-translated region
11066-11318




of the nopaline synthase





gene of Agrobacterium






tumefaciens Ti plasmid






which functions to direct





polyadenylation of the





mRNA.



Agro
B-AGRtu.left
Agro left border
  10-451


transformation
border
sequence, essential for





transfer of T-DNA.



Maintenance
OR-Ec.oriV-
The vegetative origin of
 538-934


in E. coli
RK2
replication from plasmid





RK2.




CR-Ec.rop
Coding region for
 2443-2634




repressor 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-
The minimal origin of
 3062-3650



ColE1
replication from the E.






coli plasmid ColE1.





P-Ec.aadA-
romoter for Tn7
 4181-4222



SPC/STR
adenylyltransferase





(AAD(3″))




CR-Ec.aadA-
Coding region for Tn7
 4223-5011



SPC/STR
adenylyltransferase





(AAD(3″)) conferring






spectinomycin and







streptomycin resistance.





T-Ec.aadA-
3″ UTR from the Tn7
 5012-5562



SPC/STR
adenylyltransferase





(AAD(3″)) gene of E.






coli.










Other base vectors similar to those described above were also constructed as listed in Table 5. See Table 5 for a summary of base vector plasmids and base vector ID's which are referenced in Table 2. Also see Table 5 for a summary of regulatory elements used in the gene expression cassette for these base vectors and SEQ ID NOs for elements.


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 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 one of the base vectors as referenced in Table 2.












TABLE 5









Base
Base



Vector
Vector for



ID
Corn







4
pMON92705



5
pMON92708



6
pMON92709



7
pMON92713



8
pMON92714



9
pMON92715



10
pMON92716



11
pMON92717



12
pMON92718



13
pMON92719



14
pMON92721



15
pMON92722



16
pMON92723



17
pMON92724



19
pMON93039



20
pMON93043



21
pMON94781







Base
Base



Vector
Vector for



ID
Soybean







1
pMON82053



2
pMON92671



3
pMON92672



18
pMON93007



22
pMON99006























TABLE 6







SEQ ID

SEQ ID

SEQ ID


vector
promoter
NO
leader
NO
intron
NO







pMON82053
P-CaMV.35S-enh
30332
NONE
/
NONE
/


pMON92671
P-At.SAMS3
30333
L-At.SAMS3
30352
I-At.SAMS3
30371


pMON92672
P-At.Stm
30334
L-At.Stm
30353
NONE
/


pMON92705
P-Os.Act1
30335
L-Os.Act1
30354
I-Os.Act1
30372


pMON92708
P-Zm.CA4H
30336
L-Zm.CA4H
30355
NONE
/


pMON92709
P-Os.GT1
30337
L-Os.GT1
30356
I-Zm.DnaK
30373


pMON92713
P-Zm.P39486
30338
L-Zm.39486
30357
I-Zm.DnaK
30373


pMON92714
P-RTBV
30339
L-RTBV
30358
I-Zm.DnaK
30373


pMON92715
P-Hv.Per1
30340
L-Hv.Per1
30359
I-Zm.DnaK
30373


pMON92716
P-Zm.FDA
30341
L-Zm.FDA
30360
I-Zm.DnaK
30373


pMON92717
P-At.SAMS3
30334
L-At.SAMS3
30352
I-At.SAMS3
30371


pMON92718
P-Zm.CLK1
30342
L-Zm.Cik1
30361
I-Zm.Cik1
30374


pMON92719
P-Zm.RAB17
30343
L-Zm.RAB17
30362
I-Zm.DnaK
30373


pMON92721
P-Zm.SzeinC1
30344
L-Zm.SzeinC1
30363
I-Zm.DnaK
30373


pMON92722
P-CaMV.35S-enh
30345
L-CaMV.35S
30364
I-Zm.DnaK
30373


pMON92723
P-Zm.Nicotianamine
30346
L-Zm.NAS2
30365
I-Zm.DnaK
30373



Synthase


pMON92724
P-Zm.-636aldolase-
30347
L-Zm.PPDK
30366
I-Zm.DnaK
30373



0:1:2 + P-Zm.PPDK


pMON93007
P-At.rd29a
30348
L-At.rd29a
30367
NONE
/


pMON93039
E-Os.Act1 + E-
30349
L-Ta.Lhcb1
30368
I-Os.Act1
30375



CaMV.35S.2xA1-B3 +



P-Os.Act1


pMON93043
P-Zm.EM
30350
L-Zm.EM
30369
I-Zm.DnaK
30373


pMON94781
P-Zm.Brittle-2
30351
L-Zm.Brittle-2
30370
I-Zm.DnaK
30373


pMON99006
P-CaMV.35S-enh
30332
NONE
/
NONE
/










B. Plasmids for Use in Transformation of Soybean were Also Prepared.


Elements of an exemplary common expression vector plasmid pMON82053 are shown in Table 7 below and FIG. 4.












TABLE 7








Coordinates





of SEQ ID


function
name
annotation
NO: 30331







Agro
B-AGRtu.left
Agro left border
6144-6585


transforamtion
border
sequence, essential





for transfer of T-DNA.



Plant
P-At.Act7
Promoter from the
6624-7861


selectable


arabidopsis actin




marker

7 gene



expression
L-At.Act7
5′UTR of Arabidopsis



cassette

Act7 gene




I-At.Act7
Intron from the






Arabidopsis actin7 gene





TS-At.ShkG-
Transit peptide region of
7864-8091



CTP2

Arabidopsis EPSPS





CR-AGRtu.
Synthetic CP4 coding
8092-9459



aroA-
region with dicot




CP4.nno_At
preferred codon usage.




T-AGRtu.nos
A 3′ non-translated
9466-9718




region of the nopaline





synthase gene of






Agrobacterium







tumefaciens Ti plasmid






which functions to direct





polyadenylation





of the mRNA.



Gene of
P-CaMV.
Promoter for 35S RNA
  1-613


interest
35S-enh
from CaMV containing



expression

a duplication of the



cassette

−90 to −350 region.




T-Gb.E6-3b
3′ untranslated region from
 688-1002




the fiber protein E6 gene





of sea-island cotton;



Agro
B-AGRtu.right
Agro right border
1033-1389


transformation
border
sequence, essential





for transfer of T-DNA.



Maintenance
OR-Ec.oriV-
The vegetative origin
5661-6057


in E. coli
RK2
of replication





from plasmid RK2.




CR-Ec.rop
Coding region for repressor
3961-4152




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-
The minimal origin of
2945-3533



ColE1
replication from the






E. coli plasmid ColE1.





P-Ec.aadA-
romoter 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 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 one of the base vectors as referenced in Table 2.


C. Cotton Transformation Vector

Plasmids for use in transformation of cotton are also prepared. Elements of an exemplary common expression vector plasmid pMON99053 are shown in Table 8 below and FIG. 5. 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 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 one of the base vectors as referenced in Table 2.












TABLE 8








Coordinates





of SEQ ID


function
name
annotation
NO: 30376







Agro
B-AGRtu.right
Agro right border
11364-11720


transforamtion
border
sequence, essential for





transfer of T-DNA.



Gene of interest
Exp-CaMV.
Enhanced version
 7794-8497


expression
35S-
of the 35S



cassette
enh+ph.DnaK
RNA promoter from





CaMV plus the





petunia hsp70 5′





untranslated region




T-Ps.RbcS2-E9
The 3′ non-translated
  67-699




region of the pea





RbcS2 gene which





functions to direct





polyadenylation





of the mRNA.



Plant selectable
Exp-CaMV.
Promoter from the rice
  730-1053


marker
35S
actin 1 gene



expression
CR-Ec.nptII-
first exon of the rice
 1087-1881


cassette
Tn5
actin 1 gene




T-AGRtu.nos
A 3′ non-translated
 1913-2165




region of the nopaline





synthase gene of






Agrobacterium







tumefaciens Ti plasmid






which functions to





direct polyadenylation





of the mRNA.



Agro
B-AGRtu.left
Agro left border sequence,
 2211-2652


transformation
border
essential for transfer of T-





DNA.



Maintenance in
OR-Ec.oriV-
The vegetative origin of
 2739-3135



E. coli

RK2
replication from





plasmid RK2.




CR-Ec.rop
Coding region for
 4644-4835




repressor 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-
The minimal origin of
 5263-5851



ColE1
replication from





the E. coli





plasmid ColE1.




P-Ec.aadA-
romoter for Tn7
 6382-6423



SPC/STR
adenylyltransferase





(AAD(3″))




CR-Ec.aadA-
Coding region for Tn7
 6424-7212



SPC/STR
adenylyltransferase





(AAD(3″)) conferring






spectinomycin and







streptomycin resistance.





T-Ec.aadA-
3′ UTR from the Tn7
 7213-7270



SPC/STR
adenylyltransferase





(AAD(3″)) gene of E. coli.









Example 2
Corn Transformation

This example illustrates plant cell transformation methods useful in producing transgenic corn plant cells, plants, seeds and pollen of this invention and the production and identification of transgenic corn plants and seed with an enhanced trait, i.e. enhanced water use efficiency, enhanced cold tolerance, increased yield, enhanced nitrogen use efficiency, enhanced seed protein and enhanced seed oil. Plasmid vectors were prepared by cloning DNA identified in Table 2 in the identified base vectors for use in corn transformation of corn plant cells to produce transgenic corn plants and progeny plants, seed and pollen.


For Agrobacterium-mediated transformation of corn embryo cells corn plants of a readily transformable line (designated LH59) is grown in the greenhouse and ears 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, and paromomycin resistant callus identified as containing the recombinant DNA in an expression cassette.


For transformation by microprojectile bombardment immature maize 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 degrees 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 and 6,232,526 and U.S. patent application Ser. No. 09/757,089, which are incorporated herein by reference.


To regenerate transgenic corn plants a callus of transgenic plant cells resulting from transformation is placed on media to initiate shoot development in plantlets which are transferred to potting soil for initial growth in a growth chamber at 26 degrees 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 seed, 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 reported in Example 7.


Example 3
Soybean Transformation

This example illustrates plant transformation useful 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 germinated overnight and the meristem explants excised. The meristems and 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 germination 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. Trait positive 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. 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 reported in Example 7.


Example 4
Cotton Transgenic Plants with Enhanced

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: 358 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, i.e. 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, i.e. 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, i.e. 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 5
Canola Transformation

This example illustrates plant transformation useful 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 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 as reported in Example 7.


Example 6
Homolog Identification

This example illustrates the identification of homologs of proteins encoded by the DNA identified in Table 2 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” was 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” was 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 was queried using amino acid sequences provided herein as SEQ ID NO: 359 through SEQ ID NO: 716 using NCBI “blastp” program with E-value cutoff of 1e-8. Up to 1000 top hits were kept, and separated by organism names. For each organism other than that of the query sequence, a list was 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 was kept for all the hits from each organism, sorted by E-value, and referred to as the Hit List.


The Organism Protein Database was queried using polypeptide sequences provided herein as SEQ ID NO: 359 through SEQ ID NO: 716 using NCBI “blastp” program with E-value cutoff of 1e-4. Up to 1000 top hits were kept. A BLAST searchable database was constructed based on these hits, and is referred to as “SubDB”. SubDB was queried with each sequence in the Hit List using NCBI “blastp” program with E-value cutoff of 1e-8. The hit with the best E-value was 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. Homologs from a large number of distinct organisms were identified and are reported by amino acid sequences of SEQ ID NO: 717 through SEQ ID NO: 30327. These relationship of proteins of SEQ ID NO: 358 through 716 and homologs of SEQ ID NO: 717 through 30327 is identified in Table 9. The source organism for each homolog is found in the Sequence Listing.


Example 7
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 corn seed and plants 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 1. 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

The physiological efficacy of transgenic corn plants (tested as hybrids) can be tested for nitrogen use efficiency (NUE) traits in a high-throughput nitrogen (N) selection method. The collected data are compared to the measurements from wildtype controls using a statistical model to determine if the changes are due to the transgene. Raw data were analyzed by SAS software. Results shown herein are the comparison of transgenic plants relative to the wildtype controls.


(1) Media Preparation for Planting a NUE Protocol

Planting materials used: Metro Mix 200 (vendor: Hummert) Cat. #10-0325, Scotts Micro Max Nutrients (vendor: Hummert) Cat. #07-6330, OS 4⅓″×3⅞″ pots (vendor: Hummert) Cat. #16-1415, OS trays (vendor: Hummert) Cat. #16-1515, Hoagland's macronutrients solution, Plastic 5″ stakes (vendor: Hummert) yellow Cat. #49-1569, white Cat. #49-1505, Labels with numbers indicating material contained in pots. Fill 500 pots to rim with Metro Mix 200 to a weight of ˜140 g/pot. Pots are filled uniformly by using a balancer. Add 0.4 g of Micro Max nutrients to each pot. Stir ingredients with spatula to a depth of 3 inches while preventing material loss.


(2) Planting a NUE Selection in the Greenhouse

(a) Seed Germination—Each pot is lightly atered twice using reverse osmosis purified water. The first watering is scheduled to occur just before planting; and the second watering, after the seed has been planted in the pot. Ten Seeds of each entry (1 seed per pot) are planted to select eight healthy uniform seedlings. Additional wild type controls are planted for use as border rows. Alternatively, 15 seeds of each entry (1 seed per pot) are planted to select 12 healthy uniform seedlings (this larger number of plantings is used for the second, or confirmation, planting). Place pots on each of the 12 shelves in the Conviron growth chamber for seven days. This is done to allow more uniform germination and early seedling growth. The following growth chamber settings are 25° C./day and 22° C./night, 14 hours light and ten hours dark, humidity ˜80%, and light intensity ˜350 μmol/m2/s (at pot level). Watering is done via capillary matting similar to greenhouse benches with duration of ten minutes three times a day.


(b) Seedling transfer—After seven days, the best eight or 12 seedlings for the first or confirmation pass runs, respectively, are chosen and transferred to greenhouse benches. The pots are spaced eight inches apart (center to center) and are positioned on the benches using the spacing patterns printed on the capillary matting. The Vattex matting creates a 384-position grid, randomizing all range, row combinations. Additional pots of controls are placed along the outside of the experimental block to reduce border effects.


Plants are allowed to grow for 28 days under the low N run or for 23 days under the high N run. The macronutrients are dispensed in the form of a macronutrient solution (see composition below) containing precise amounts of N added (2 mM NH4NO3 for limiting N selection and 20 mM NH4NO3 for high N selection runs). Each pot is manually dispensed 100 ml of nutrient solution three times a week on alternate days starting at eight and ten days after planting for high N and low N runs, respectively. On the day of nutrient application, two 20 min waterings at 05:00 and 13:00 are skipped. The vattex matting should be changed every third run to avoid N accumulation and buildup of root matter. Table 10 shows the amount of nutrients in the nutrient solution for either the low or high nitrogen selection.











TABLE 10






2 mM NH4NO3
20 mM NH4NO3 (high



(Low Nitrogen Growth
Nitrogen Growth



Condition, Low N)
Condition, High N)


Nutrient Stock
mL/L
mL/L

















1 M NH4NO3
2
20


1 M KH2PO4
0.5
0.5


1 M MgSO4 · 7H2O
2
2


1 M CaCl2
2.5
2.5


1 M K2SO4
1
1





Note:


Adjust pH to 5.6 with HCl or KOH






(c) Harvest Measurements and Data Collection—After 28 days of plant growth for low N runs and 23 days of plant growth for high N runs, the following measurements are taken (phenocodes in parentheses): total shoot fresh mass (g) (SFM) measured by Sartorius electronic balance, V6 leaf chlorophyll measured by Minolta SPAD meter (relative units) (LC), V6 leaf area (cm2) (LA) measured by a Li-Cor leaf area meter, V6 leaf fresh mass (g) (LFM) measured by Sartorius electronic balance, and V6 leaf dry mass (g) (LDM) measured by Sartorius electronic balance. Raw data were analyzed by SAS software. Results shown are the comparison of transgenic plants relative to the wildtype controls.


To take a leaf reading, samples were excised from the V6 leaf. Since chlorophyll meter readings of corn leaves are affected by the part of the leaf and the position of the leaf on the plant that is sampled, SPAD meter readings were done on leaf six of the plants. Three measurements per leaf were taken, of which the first reading was taken from a point one-half the distance between the leaf tip and the collar and halfway from the leaf margin to the midrib while two were taken toward the leaf tip. The measurements were restricted in the area from ½ to ¾ of the total length of the leaf (from the base) with approximately equal spacing between them. The average of the three measurements was taken from the SPAD machine.


Leaf fresh mass is recorded for an excised V6 leaf, the leaf is placed into a paper bag. The paper bags containing the leaves are then placed into a forced air oven at 80° C. for 3 days. After 3 days, the paper bags are removed from the oven and the leaf dry mass measurements are taken.


From the collected data, two derived measurements are made: (1) Leaf chlorophyll area (LCA), which is a product of V6 relative chlorophyll content and its leaf area (relative units). Leaf chlorophyll area=leaf chlorophyll X leaf area. This parameter gives an indication of the spread of chlorophyll over the entire leaf area; (2) specific leaf area (LSA) is calculated as the ratio of V6 leaf area to its dry mass (cm2/g dry mass), a parameter also recognized as a measure of NUE.


Nitrogen Use Field Efficacy Assay

Level I. Transgenic plants provided by the present invention are planted in field without any nitrogen source being applied. Transgenic plants and control plants are grouped by genotype and construct with controls arranged randomly within genotype blocks. Each type of transgenic plants are tested by 3 replications and across 5 locations. Nitrogen levels in the fields are analyzed in early April pre-planting by collecting 30 sample soil cores from 0-24″ and 24 to 48″ soil layer. Soil samples are analyzed for nitrate-nitrogen, phosphorus (P), Potassium (K), organic matter and pH to provide baseline values. P, K and micronutrients are applied based upon soil test recommendations.


Level II. Transgenic plants provided by the present invention are planted in field with three levels of nitrogen (N) fertilizer being applied, i.e. low level (0 N), medium level (80 lb/ac) and high level (180 lb/ac). Liquid 28% or 32% UAN (Urea, Ammonium Nitrogen) are used as the N source and apply by broadcast boom and incorporate with a field cultivator with rear rolling basket in the same direction as intended crop rows. Although there is no N applied to the 0 N treatment the soil should still be disturbed in the same fashion as the treated area. Transgenic plants and control plants are grouped by genotype and construct with controls arranged randomly within genotype blocks. Each type of transgenic plants is tested by 3 replications and across 4 locations. Nitrogen levels in the fields are analyzed in early April pre-planting by collecting 30 sample soil cores from 0-24″ and 24 to 48″ soil layer. Soil samples are analyzed for nitrate-nitrogen, phosphorus (P), Potassium (K), organic matter and pH to provide baseline values. P, K and micronutrients are applied based upon soil test recommendations.


B. Selection for Increased Yield

Many transgenic plants of this invention exhibit improved yield as compared to a control plant. Improved yield can result from enhanced seed sink potential, i.e. the number and size of endosperm cells or kernels and/or enhanced sink strength, i.e. the rate of starch biosynthesis. Sink potential can be established very early during kernel development, as endosperm cell number and size are determined within the first few days after pollination.


Much of the increase in corn yield of the past several decades has resulted from an increase in planting density. During that period, corn yield has been increasing at a rate of 2.1 bushels/acre/year, but the planting density has increased at a rate of 250 plants/acre/year. A characteristic of modern hybrid corn is the ability of these varieties to be planted at high density. Many studies have shown that a higher than current planting density should result in more biomass production, but current germplasm does not perform. well at these higher densities. One approach to increasing yield is to increase harvest index (HI), the proportion of biomass that is allocated to the kernel compared to total biomass, in high density plantings.


Effective yield selection of enhanced yielding transgenic corn events uses hybrid progeny of the transgenic event over multiple locations with plants grown under optimal production management practices, and maximum pest control. A useful target for improved yield is a 5% to 10% increase in yield as compared to yield produced by plants grown from seed for a control plant. Selection methods may be applied in multiple and diverse geographic locations, for example up to 16 or more locations, over one or more plating seasons, for example at least two planting seasons to statistically distinguish yield improvement from natural environmental effects. It is to plant multiple transgenic plants, positive and negative control plants, and pollinator plants in standard plots, for example 2 row plots, 20 feet long by 5 feet wide with 30 inches distance between rows and a 3 foot alley between ranges. Transgenic events can be grouped by recombinant DNA constructs with groups randomly placed in the field. A pollinator plot of a high quality corn line is planted for every two plots to allow open pollination when using male sterile transgenic events. A useful planting density is about 30,000 plants/acre. High planting density is greater than 30,000 plants/acre, preferably about 40,000 plants/acre, more preferably about 42,000 plants/acre, most preferably about 45,000 plants/acre. Surrogate indicators for yield improvement include source capacity (biomass), source output (sucrose and photosynthesis), sink components (kernel size, ear size, starch in the seed), development (light response, height, density tolerance), maturity, early flowering trait and physiological responses to high density planting, for example at 45,000 plants per acre, for example as illustrated in Table 11 and 12.












TABLE 11





Timing
Evaluation
Description
comments







V2-3
Early stand
Can be taken any time after





germination and prior to





removal of any plants.



Pollen shed
GDU to 50%
GDU to 50% plants




shed
shedding 50% tassel.



Silking
GDU to 50%
GDU to 50% plants




silk
showing silks.



Maturity
Plant height
Height from soil surface to
10 plants per




flag leaf attachment (inches).
plot-Yield





team assistance


Maturity
Ear height
Height from soil surface to
10 plants per




primary ear attachment node.
plot-Yield





team assistance


Maturity
Leaves above
visual scores: erect, size,




ear
rolling



Maturity
Tassel size
Visual scores +/− vs. WT



Pre-Harvest
Final Stand
Final stand count prior to





harvest, exclude tillers



Pre-Harvest
Stalk lodging
No. of stalks broken below





the primary ear attachment.





Exclude leaning tillers



Pre-Harvest
Root lodging
No. of stalks leaning >45°





angle from perpendicular.



Pre-Harvest
Stay green
After physiological maturity





and when differences among





genotypes are evident: Scale





1 (90-100% tissue green)-9





(0-19% tissue green).



Harvest
Grain Yield
Grain yield/plot (Shell





weight)


















TABLE 12





Timing
Evaluation
Description







V8-V12
Chlorophyll



V12-VT
Ear leaf area



V15-15DAP
Chl fluorescence



V15-15DAP
CER



15-25 DAP
Carbohydrates
sucrose, starch


Pre-Harvest
1st internode diameter



Pre-Harvest
Base 3 internode diameter



Pre-Harvest
Ear internode diameter



Maturity
Ear traits
diameter, length, kernel




number, kernel weight









Electron transport rates (ETR) and CO2 exchange rates (CER): ETR and CER are measured with Li6400LCF (Licor, Lincoln, Nebr.) around V9-R1 stages. Leaf chlorophyll fluorescence is a quick way to monitor the source activity and is reported to be highly correlated with CO2 assimilation under varies conditions (Photosyn Research, 37: 89-102). The youngest fully expanded leaf or 2 leaves above the ear leaf is measured with actinic light 1500 (with 10% blue light) micromol m−2 s−1, 28° C., CO2 levels 450 ppm. Ten plants are measured in each event. There are 2 readings for each plant.


A hand-held chlorophyll meter SPAD-502 (Minolta—Japan) is used to measure the total chlorophyll level on live transgenic plants and the wild type counterparts a. Three trifoliates from each plant are analyzed, and each trifoliate were analyzed three times. Then 9 data points are averaged to obtain the chlorophyll level. The number of analyzed plants of each genotype ranges from 5 to 8.


When selecting for yield improvement a useful statistical measurement approach comprises three components, i.e. modeling spatial autocorrelation of the test field separately for each location, adjusting traits of recombinant DNA events for spatial dependence for each location, and conducting an across location analysis. The first step in modeling spatial autocorrelation is estimating the covariance parameters of the semivariogram. A spherical covariance model is assumed to model the spatial autocorrelation. Because of the size and nature of the trial, it is likely that the spatial autocorrelation may change. Therefore, anisotropy is also assumed along with spherical covariance structure. The following set of equations describes the statistical form of the anisotropic spherical covariance model.








C


(

h
;
θ

)


=


vI


(

h
=
0

)


+



σ
2



(

1
-


3
2


h

+


1
2



h
3



)




I


(

h
<
1

)





,




where I(•) is the indicator function, h=√{square root over ({dot over (x)}2+{dot over (y)}2)}, and






{dot over (x)}=[cos(ρπ/180)(x1−x2)−sin(ρπ/180)(y1−y2)]/ωx






{dot over (y)}=[sin(πρ/180)(x1−x2)+cos(ρπ/180)(y1−y2)]/ωy


where s1=(x1, y1) are the spatial coordinates of one location and s2=(x2, y2) are the spatial coordinates of the second location. There are 5 covariance parameters, θ=(ν, σ2, ρ, ωn, ωj), where ν is the nugget effect, σ2 is the partial sill, ρ is a rotation in degrees clockwise from north, ωn is a scaling parameter for the minor axis and ωj is a scaling parameter for the major axis of an anisotropical ellipse of equal covariance. The five covariance parameters that defines the spatial trend will then be estimated by using data from heavily replicated pollinator plots via restricted maximum likelihood approach. In a multi-location field trial, spatial trend are modeled separately for each location.


After obtaining the variance parameters of the model, a variance-covariance structure is generated for the data set to be analyzed. This variance-covariance structure contains spatial information required to adjust yield data for spatial dependence. In this case, a nested model that best represents the treatment and experimental design of the study is used along with the variance-covariance structure to adjust the yield data. During this process the nursery or the seed batch effects can also be modeled and estimated to adjust the yields for any yield parity caused by seed batch differences. After spatially adjusted data from different locations are generated, all adjusted data is combined and analyzed assuming locations as replications. In this analysis, intra and inter-location variances are combined to estimate the standard error of yield from transgenic plants and control plants. Relative mean comparisons are used to indicate statistically significant yield improvements.


C. Selection for Enhanced Water Use Efficiency (WUE)

Described in this example is a high-throughput method for greenhouse selection of transgenic corn plants to wild type corn plants (tested as inbreds or hybrids) for water use efficiency. This 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. The hydration status of the shoot tissues following the drought is also measured. The plant height are measured at three time points. The first is taken just prior to the onset drought when the plant is 11 days old, which is the shoot initial height (SIH). The plant height is also measured halfway throughout the drought/re-water regimen, on day 18 after planting, to give rise to the shoot mid-drought height (SMH). Upon the completion of the final drought cycle on day 26 after planting, the shoot portion of the plant is harvested and measured for a final height, which is the shoot wilt height (SWH) and also measured for shoot wilted biomass (SWM). The shoot is placed in water at 40 degree Celsius in the dark. Three days later, the shoot is weighted to give rise to the shoot turgid weight (STM). After drying in an oven for four days, the shoots are weighted for shoot dry biomass (SDM). The shoot average height (SAH) is the mean plant height across the 3 height measurements. The procedure described above may be adjusted for +/−˜one day for each step given the situation.


To correct for slight differences between plants, a size corrected growth value is derived from SIH and SWH. This is the Relative Growth Rate (RGR). Relative Growth Rate (RGR) is calculated for each shoot using the formula [RGR%=(SWH−SIH)/((SWH+SIH)/2)*100]. Relative water content (RWC) is a measurement of how much (%) of the plant was water at harvest. Water Content (RWC) is calculated for each shoot using the formula [RWC%=(SWM−SDM)/(STM−SDM)*100]. Fully watered corn plants of this age run around 98% RWC.


D. Selection for Growth Under Cold Stress

(1) Cold germination assay—Three sets of seeds are used for the assay. The first set consists of positive transgenic events (F1 hybrid) where the genes of the present invention are expressed in the seed. The second seed set is nontransgenic, wild-type negative control made from the same genotype as the transgenic events. The third set consisted of two cold tolerant and one cold sensitive commercial check lines of corn. All seeds are treated with a fungicide “Captan” (MAESTRO® 80DF Fungicide, Arvesta Corporation, San Francisco, Calif., USA). 0.43 mL Captan is applied per 45 g of corn seeds by mixing it well and drying the fungicide prior to the experiment.


Corn kernels are placed embryo side down on blotter paper within an individual cell (8.9×8.9 cm) of a germination tray (54×36 cm). Ten seeds from an event are placed into one cell of the germination tray. Each tray can hold 21 transgenic events and 3 replicates of wildtype (LH244SDms+LH59), which is randomized in a complete block design. For every event there are five replications (five trays). The trays are placed at 9.7 C for 24 days (no light) in a Convrion growth chamber (Conviron Model PGV36, Controlled Environments, Winnipeg, Canada). Two hundred and fifty milliliters of deionized water are added to each germination tray. Germination counts are taken 10th, 11th, 12th, 13th, 14th, 17th, 19th, 21st, and 24th day after start date of the experiment. Seeds are considered germinated it the emerged radicle size is 1 cm. From the germination counts germination index is calculated.


The germination index is calculated as per:





Germination index=(Σ([T+1−ni]*[Pi−Pi-1]))/T


Where T is the total number of days for which the germination assay is performed. The number of days after planting is defined by n. “i” indicated the number of times the germination had been counted, including the current day. P is the percentage of seeds germinated during any given rating. Statistical differences are calculated between transgenic events and wild type control. After statistical analysis, the events that show a statistical significance at the p level of less than 0.1 relative to wild-type controls will advance to a secondary cold selection. The secondary cold screen is conducted in the same manner of the primary selection only increasing the number of repetitions to ten. Statistical analysis of the data from the secondary selection is conducted to identify the events that show a statistical significance at the p level of less than 0.05 relative to wild-type controls.


(2) Cold Shock assay—The experimental set-up for the cold shock assay is the same as described in the above cold germination assay except seeds were grown in potted media for the cold shock assay.


The desired numbers of 2.5″ square plastic pots are placed on flats (n=32, 4×8). Pots were filled with Metro Mix 200 soil-less media containing 19:6:12 fertilizer (6 lbs/cubic yard) (Metro Mix, Pots and Flat are obtained from Hummert International, Earth City, Mo.). After planting seeds, pots are placed in a growth chamber set at 23° C., relative humidity of 65% with 12 hour day and night photoperiod (300 uE/m2-min). Planted seeds are watered for 20 minute every other day by sub-irrigation and flats were rotated every third day in a growth chamber for growing corn seedlings.


On the 10th day after planting the transgenic positive and wild-type negative (WT) plants are positioned in flats in an alternating pattern. Chlorophyll fluorescence of plants is measured on the 10th day during the dark period of growth by using a PAM-2000 portable fluorometer as per the manufacturer's instructions (Walz, Germany). After chlorophyll measurements, leaf samples from each event are collected for confirming the expression of genes of the present invention. For expression analysis six V1 leaf tips from each selection are randomly harvested. The flats are moved to a growth chamber set at 5° C. All other conditions such as humidity, day/night cycle and light intensity are held constant in the growth chamber. The flats are sub-irrigated every day after transfer to the cold temperature. On the 4th day chlorophyll fluorescence is measured. Plants are transferred to normal growth conditions after six days of cold shock treatment and allowed to recover for the next three days. During this recovery period the length of the V3 leaf is measured on the 1st and 3rd days. After two days of recovery V2 leaf damage is determined visually by estimating percent of green V2 leaf.


Statistical differences in V3 leaf growth, V2 leaf necrosis and fluorescence during pre-shock and cold shock can be used for estimation of cold shock damage on corn plants. (3) Early seedling growth assay—Three sets of seeds are used for the experiment. The first set consists of positive transgenic events (F1 hybrid) where the genes of the present invention are expressed in the seed. The second seed set is nontransgenic, wild-type negative control made from the same genotype as the transgenic events. The third seed set consists of two cold tolerant and two cold sensitive commercial check lines of corn. All seeds are treated with a fungicide “Captan”, (3a,4,7,a-tetrahydro-2-[(trichloromethyl)thio]-1H-isoindole-1,3(2H)-dione, Drex Chemical Co. Memphis, Tenn.). Captan (0.43 mL) was applied per 45 g of corn seeds by mixing it well and drying the fungicide prior to the experiment.


Seeds are grown in germination paper for the early seedling growth assay. Three 12″×18″ pieces of germination paper (Anchor Paper #SD7606) are used for each entry in the test (three repetitions per transgenic event). The papers are wetted in a solution of 0.5% KNO3 and 0.1% Thyram.


For each paper fifteen seeds are placed on the line evenly spaced down the length of the paper. The fifteen seeds are positioned on the paper such that the radical would grow downward, for example longer distance to the paper's edge. The wet paper is rolled, up starting from one of the short ends. The paper is rolled evenly and tight enough to hold the seeds in place. The roll is secured into place with two large paper clips, one at the top and one at the bottom. The rolls are incubated in a growth chamber at 23° C. for three days in a randomized complete block design within an appropriate container. The chamber is set for 65% humidity with no light cycle. For the cold stress treatment the rolls are then incubated in a growth chamber at 12° C. for twelve days. The chamber is set for 65% humidity with no light cycle.


After the cold treatment the germination papers are unrolled and the seeds that did not germinate are discarded. The lengths of the radicle and coleoptile for each seed are measured through an automated imaging program that automatically collects and processes the images. The imaging program automatically measures the shoot length, root length, and whole seedling length of every individual seedling and then calculates the average of each roll.


After statistical analysis, the events that show a statistical significance at the p level of less than 0.1 relative to wild-type controls will advance to a secondary cold selection. The secondary cold selection is conducted in the same manner of the primary selection only increasing the number of repetitions to five. Statistical analysis of the data from the secondary selection is conducted to identify the events that show a statistical significance at the p level of less than 0.05 relative to wild-type controls.


4. Cold Field Efficacy Trial

This example sets forth a cold field efficacy trial 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 are beginning 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. The cold field efficacy trials are carried out in five locations, including Glyndon Minn., Mason Mich., Monmouth Ill., Dayton Iowa, Mystic Conn. At each location, seeds are planted under both cold and normal conditions with 3 repetitions per treatment, 20 kernels per row and single row per plot. Seeds are planted 1.5 to 2 inch deep into soil to avoid muddy conditions. 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 seedling 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 calculated using SAS software for the data within each location or across all locations.


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. 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 a 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 13





Typical sample(s):
Whole grain corn and soybean seeds







Analytical time to run method:
Less than 0.75 min per sample


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 8
Consensus Sequence

This example illustrates the identification of consensus amino acid sequence for the proteins and homologs encoded by DNA that is used to prepare the transgenic seed and plants of this invention having enhanced agronomic traits.


ClustalW program was selected for multiple sequence alignments of the amino acid sequence of SEQ ID NO: 561 and its 10 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. FIG. 1 shows the sequences of SEQ ID NO: 561, its homologs and the consensus sequence (SEQ ID NO: 30328) at the end. The symbols for consensus sequence are (1) uppercase letters for 100% identity in all positions of multiple sequence alignment output; (2) lowercase letters for >=70% identity; symbol; (3) “X” indicated <70% identity; (4) dashes “—” meaning that gaps were in >=70% sequences.


The consensus amino acid sequence can be used to identify DNA corresponding to the full scope of this invention that is useful in providing transgenic plants, for example corn and soybean plants with enhanced agronomic traits, for example improved nitrogen use efficiency, improved yield, improved water use efficiency and/or improved growth under cold stress, due to the expression in the plants of DNA encoding a protein with amino acid sequence identical to the consensus amino acid sequence.


Example 9
Identification of Amino Acid Domain by Pfam Analysis

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: 359 through 716 are shown in Table 14 and Table 15 respectively. The Hidden Markov model databases for the identified protein 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, t For instance, the protein with amino acids of SEQ ID NO: 417 is characterized by two Pfam domains, i.e. HD and RelA_Spot.


In Table 15 “score” is the gathering score for the Hidden Markov Model of the domain which exceeds the gathering cutoff reported in Table 16.












TABLE 14





PEP





SEQ





ID

Pfam domain
domain


NO
Gene ID
module
coordinates


















591
PHE0006505_7871.pep
Thioredoxin
 69-174


541
PHE0006264_7285.pep
DAGAT
 48-349


359
PHE0001295_7469.pep
DNA_photolyase::
 18-190::223-501




FAD_binding_7



665
PHE0006760_8529.pep
vATP-synt_E
 16-225


639
PHE0006684_8413.pep
Ribosomal_L10
 19-123


645
PHE0006715_8477.pep
AMPKBI
197-287


626
PHE0006600_8249.pep
Iso_dh
 6-355


484
PHE0006071_7068.pep
PPR::PPR::
 30-63::64-98::99-




PPR::PPR::PPR
132::138-





172::173-207


417
PHE0004830_5828.pep
HD::RelA_SpoT
233-337::427-537


576
PHE0006426_8056.pep
AA_permease
 2-454


571
PHE0006381_7655.pep
RNase_PH
 42-186


570
PHE0006380_8719.pep
RNase_PH::
 1-126::129-201




RNase_PH_C



713
PHE0006977_9163.pep
Ribul_P_3_epim
 7-207


466
PHE0006021_7077.pep
Bet_v_I
 1-155


596
PHE0006516_7887.pep
CorA
 90-474


632
PHE0006620_8462.pep
Epimerase
 13-259


631
PHE0006617_8463.pep
Cupin_1
 65-215


585
PHE0006468_7903.pep
F-box::FBA_1
 2-49::209-387


424
PHE0004887_5939.pep
DUF516
 49-310


478
PHE0006059_7042.pep
DnaJ::DnaJ_C
 4-67::222-344


671
PHE0006771_8551.pep
FAE1_CUT1_
 52-341::356-439




RppA::





ACP_syn_III_C



606
PHE0006564_8298.pep
GATase_2::
 2-161::209-450




Asn_synthase



695
PHE0006934_9145.pep
DNA_pol_E_B
178-389


391
PHE0004670_6044.pep
GSHPx
 9-117


647
PHE0006727_8435.pep
ETC_C1_
 54-156




NDUFA4



441
PHE0004918_5975.pep
DUF1365
 44-255


704
PHE0006949_9179.pep
Aldedh
 19-478


409
PHE0004808_5794.pep
Peptidase_C1
 8-205


582
PHE0006449_8165.pep
Biotin_llpoyl::
 92-165::229-




E3_binding::2-
265::281-512




oxoacid_dh



538
PHE0006234_7281.pep
Mg_chelatase::
 85-295::559-754




VWA



383
PHE0004398_5136.pep
Pkinase
 7-269


687
PHE0006919_9008.pep
Peptidase_M16::
 80-226::231-417




Peptidase_M16_C



379
PH E0004021_4654.pep
GATase_2::
 2-173::227-460




Asn_synthase



387
PHE0004503_5244.pep
MtN3_slv::
 12-99::134-220




MtN3_slv



648
PHE0006727_8595.pep
ETC_C1_
 54-156




NDUFA4



601
PHE0006521_7840.pep
S6PP
 2-247


569
PHE0006380_7658.pep
RNase_PH::
 1-126::129-201




RNase_PH_C



525
PHE0006209_7991.pep
HMGL-like:
 28-305::398-542




LeuA_dimer



556
PHE0006342_8182.pep
Hydrolase
 12-200


550
PHE0006309_8148.pep
Glyoxalase
 2-123


515
PHE0006178_7139.pep
elF-5a
 82-149


453
PHE0004989_8115.pep
DUF21::CBS
 14-191::210-325


443
PHE0004928_5986.pep
Rotamase
 11-119


681
PHE0006847_8860.pep
DHBP_synthase::
 8-203::208-366




GTP_cyclohydro2



510
PHE0006161_7221.pep
PFK::PFK
195-506::585-877


468
PHE0006043_7080.pep
Glyco_transf_8
 83-345


710
PHE0006963_9131.pep
Pyr_redox_2::Fer2_
 5-287::422-




BFD::NIR_SIR_
474::556-




ferr:NIR_SIR
623::631-777


565
PHE0006377_7592.pep
RNase_PH::
 48-244::322-384




RNase_PH_C



535
PHE0006232_7454.pep
B_lectin::S_locus_
 74-187::201-




glycop::PAN_2::
327::344-




Pkinase_Tyr
411::552-824


494
PHE0006088_7063.pep
CoA_binding::
634-743::784-929




Ligase_CoA



438
PHE0004909_5966.pep
Pkinase
157-428


619
PHE0006596_8236.pep
CTP_transf_2
 19-159


536
PHE0006232_8756.pep
B_lectin::S_locus_
 74-187::201-




glycop::PAN_2::
327::344-




Pkinase_Tyr
411::552-824


407
PHE0004806_5792.pep
OTU
156-268


502
PHE0006093_7327.pep
PTS_2-RNA
 48-239


411
PHE0004810_5796.pep
Pkinase::efhand::
 77-358::405-




efhand::efhand::
433::441-




efhand
469::477-





505::508-536


586
PHE0006477_7809.pep
PsbR
 42-140


507
PHE0006160_7286.pep
PFK
 3-309


362
PHE0002132_8653.pep
Pkinase
 9-285


505
PHE0006154_7204.pep
PfkB
 7-299


700
PHE0006943_9124.pep
Aa_trans
 29-428


479
PHE0006061_7051.pep
Metallophos
 2-120


492
PHE0006079_7337.pep
S6PP::S6PP_C
 8-262::263-395


661
PHE0006745_8590.pep
V-SNARE
 71-221


653
PHE0006737_8527.pep
2OG-Fell_Oxy
217-317


688
PHE0006929_9151.pep
zf-C3HC4
259-299


422
PHE0004883_5935.pep
Pkinase
314-581


686
PHE0006912_9000.pep
ECH
 57-226


685
PHE0006910_9019.pep
Mov34
 92-201


674
PHE0006788_8581.pep
Tryp_alpha_amyl
 27-110


599
PHE0006517_7879.pep
CorA
 81-456


429
PHE0004894_5950.pep
Tubulin::
 52-245::247-369




Tubulin_C



439
PHE0004911_5968.pep
Thioredoxin
120-227


666
PHE0006765_8536.pep
Bromodomain
110-199


489
PHE0006077_7045.pep
GASA
 5-106


590
PHE0006498_7796.pep
Pyridoxal_deC
 34-381


396
PHE0004762_5729.pep
F-box::LRR_2
 62-108::314-340


369
PHE0002810_5803.pep
p450
 59-531


432
PHE0004895_7135.pep
DS
 44-349


448
PHE0004968_6030.pep
RLI::Fer4::ABC_
 6-37::48-71::103-




tran::ABC_tran
292::374-544


477
PHE0006054_8779.pep
AIG1
 39-236


380
PHE0004143_7850.pep
GSHPx
 21-129


491
PHE0006079_7044.pep
S6PP::S6PP_C
 8-262::263-395


442
PHE0004921_5979.pep
DUF1677
 3-107


412
PHE0004811_5798.pep
zf-C3HC4
164-205


469
PHE0006043_8788.pep
Glyco_transf_8
 83-345


435
PHE0004902_5959.pep
Response_reg
 21-146


437
PHE0004905_5962.pep
Pkinase
 78-336


635
PHE0006669_8357.pep
PFK:: PFK
271-582::661-953


364
PHE0002693_8516.pep
FAD_binding_3
 55-374


454
PHE0004991_8092.pep
Auxin _inducible
 19-119


460
PHE0005008_6077.pep
Response_reg
 22-137


425
PHE0004887_5940.pep
DUF516
 49-310


467
PHE0006021_8737.pep
Bet_v_l
 1-155


511
PHE0006173_7211.pep
Ribosomal_S6e
 1-129


361
PHE0002132_4965.pep
Pkinase
 9-285


587
PHE0006478_8190.pep
Methyltransf_6
 4-161


526
PHE0006212_7196.pep
Heme_oxygenase
 74-278


431
PHE0004895_5952.pep
DS
 44-349


709
PHE0006962_9114.pep
Molybdop_Fe4S4::
 39-93::96-




Molybdopterin::
568::714-822




Molydop_binding



696
PHE0006937_9126.pep
DUF298
127-242


610
PHE0006586_8271.pep
Frataxin_Cyay
 76-187


385
PHE0004473_5214.pep
Histone
 28-101


483
PHE0006069_7065.pep
Cupin_3
 62-137


659
PHE0006742_8591.pep
PGI
 55-545


637
PHE0006673_8992.pep
PTR2
123-530


604
PHE0006555_8283.pep
Gp_dh_N::
 83-236::241-398




Gp_dh_C



475
PHE0006051_7097.pep
zf-MYND::UCH
 57-94::326-630


638
PHE0006676_8410.pep
Transket_pyr::
 39-215::232-354




Transketolase_C



612
PHE0006590_8258.pep
Thioredoxin
 75-178


539
PHE0006254_7312.pep
X8
 29-115


513
PHE0006175_7210.pep
KOW::elF-5a
 27-63::85-154


428
PHE0004894_5948.pep
Tubulin::
 52-245::247-369




Tubulin_C



532
PHE0006221_7241.pep
Pyr_redox_2::
 44-329::405-467




Glutaredoxin



501
PHE0006093_7066.pep
PTS_2-RNA
 48-239


609
PHE0006574_8224.pep
Glyoxalase::
 11-150::166-298




Glyoxalase



543
PHE0006281_7526.pep
GAF::HisKA::
158-307::343-




HATPase_c::
408::455-




Response_reg
582::610-726


497
PHE0006091_7074.pep
TFIIS_M::
206-327::338-376




TFIIS_C



520
PHE0006202_7182.pep
HMGL-like::
 97-374::467-612




LeuA_dimer



462
PHE0005010_6079.pep
zf-DNL
 96-159


373
PHE0003814_7802.pep
Chloroa_b-bind
 66-217


530
PHE0006215_7280.pep
PFK
 2-277


493
PHE0006082_7330.pep
TPR_1::TPR_2::
 2-35::36-69::




TPR_1::TPR_2::
 70-103::257-




TPR_1::TPR_1::
290::291-324::332-




TPR_1::
369::396-429::430-




TPR_1::TPR_1
463::464-497


368
PHE0002779_7478.pep
PGM_PMM_
 16-165::199-




I::PGM_
314::316-




PMM_II::PGM_
439::477-571




PMM_III::PGM_





PMM_IV



593
PHE0006514_7926.pep
ELFV_dehydrog_
 57-187::202-447




N::ELFV_





dehydrog



548
PHE0006296_7515.pep
Glyco_transf_43
 89-312


691
PHE0006931_9168.pep
GDC-P
 3-443


621
PHE0006597_8242.pep
Pkinase
143-409


628
PHE0006609_8234.pep
GSHPx
 12-120


630
PHE0006613_8238.pep
GSHPx
 12-120


504
PHE0006094_7333.pep
Chalcone
 14-225


634
PHE0006666_8414.pep
Glycolytic
 43-387


698
PHE0006940_9122.pep
Aldedh
 18-477


617
PHE0006595_8250.pep
DUF537
 18-156


527
PHE0006213_7198.pep
Peptidase_C54
142-436


399
PHE0004779_5749.pep
Ammonium_transp
 47-471


419
PHE0004856_7855.pep
NPH3
193-435


549
PHE0006309_7570.pep
Glyoxalase
 2-123


451
PHE0004984_7235.pep
AA_kinase::
 83-366::403-




ACT::ACT
478::479-546


588
PHE0006497_8355.pep
DUF868
 28-304


677
PHE0006805_8531.pep
Ribosomal_S30AE
 2-95


574
PHE0006382_8678.pep
WD40
282-319


705
PHE0006952_9233.pep
PGAM
 91-277


652
PHE0006737_8455.pep
2OG-Fel l_Oxy
217-317


367
PHE0002777_8726.pep
Ferrochelatase
108-432


405
PHE0004791_5771.pep
Globin::FAD_
 7-131::154-




binding_
254::263-373




6::NAD_binding_1



575
PHE0006425_7646.pep
AA_permease
 36-537


578
PHE0006429_7671.pep
Globin
 18-158


522
PHE0006204_7189.pep
Cyclin_N::
 18-151::153-284




Cyclin_C



684
PHE0006909_9003.pep
Cupin_3
 62-137


559
PHE0006348_8203.pep
DUF6::TPT
106-231::240-385


650
PHE0006729_8433.pep
DnaJ::zf-CSL
 12-81::96-174


703
PHE0006949_9133.pep
Aldedh
 19-478


533
PHE0006221_7937.pep
Pyr_redox_2::
 44-329::405-467




Glutaredoxin



458
PHE0005002_6071.pep
Methyltransf_12::
155-252::223-319




Mg-por_mtran_C



690
PHE0006931_9148.pep
GDC-P
 3-443


416
PHE0004827_5825.pep
Phi_1
 40-315


583
PHE0006450_7624.pep
Tubulin::
 57-250::252-369




Tubulin_C



605
PHE0006559_8227.pep
PEPcase
 1-948


433
PHE0004895_7137.pep
DS
 44-349


669
PHE0006770_8553.pep
DEAD::Helicase_C
 58-224::292-368


667
PHE0006766_8867.pep
IPT
 1-235


594
PHE0006516_7866.pep
CorA
 90-474


473
PHE0006048_8785.pep
Pkinase_Tyr
135-389


374
PHE0003838_5934.pep
zf-LSD1::zf-
 28-52::67-




LSD1::zf-LSD1
 91::105-129


464
PHE0006003_7205.pep
zf-AN1
105-145


618
PHE0006595_8265.pep
DUF537
 18-156


365
PHE0002777_7490.pep
Ferrochelatase
108-432


629
PHE0006610_8239.pep
GSHPx
 77-185


531
PHE0006221_7201.pep
Pyr_redox_2::
 44-329::405-467




Glutaredoxin



476
PHE0006054_7095.pep
AIG1
 39-236


393
PHE0004742_5691.pep
AP2
 43-108


404
PHE0004787_7988.pep
P-II
 85-187


410
PHE0004809_5795.pep
PP2C
 46-324


434
PHE0004895_8610.pep
DS
 44-349


415
PHE0004815_5802.pep
Pkinase_Tyr
334-585


613
PHE0006591_8264.pep
Thioredoxin
 81-184


455
PHE0004993_6062.pep
CCT
237-275


689
PHE0006929_9185.pep
zf-C3HC4
259-299


375
PHE0003845_5806.pep
p450
 40-509


498
PHE0006091_7341.pep
TFIIS_M::
206-327::338-376




TFIIS_C



592
PHE0006506_7818.pep
Pkinase::
 20-272::294-




UBA::KA1
333::463-511


384
PHE0004398_5757.pep
Pkinase
 7-269


557
PHE0006344_8188.pep
VQ
 44-74


702
PHE0006948_9160.pep
RRM_1
 38-109


682
PHE0006870_8846.pep
Ribosomal_L37ae
 2-91


423
PHE0004886_5938.pep
DUF516
 49-313


589
PHE0006498_7795.pep
Pyridoxal_deC
 34-381


602
PHE0006545_8320.pep
DnaJ
 31-93


641
PHE0006686_8416.pep
Ribosomal_L22
 17-153


572
PHE0006381_8695.pep
RNase_PH
 42-186


529
PHE0006214_7219.pep
Cyclin_N::
 32-158::160-289




Cyclin_C



581
PHE0006449_7865.pep
Biotin_lipoyl::E3_
 92-165::229-




binding::2-
265::281-512




oxoacid_dh



607
PHE0006565_8300.pep
GATase_2::Asn_
 2-161::209-450




synthase



664
PHE0006757_8530.pep
Acyltransferase
375-496


603
PHE0006549_8255.pep
THF_DHG_CYH::
 3-120::123-290




THF_DHG_





CYH_C



658
PHE0006742_8440.pep
PGI
 55-545


524
PHE0006208_7223.pep
CH::EB1
 19-120::204-251


657
PHE0006741_8589.pep
MATH::BTB
 53-182::206-328


408
PHE0004807_5793.pep
RRM_1
 13-84


456
PHE0004993_8014.pep
CCT
237-275


693
PHE0006932_9174.pep
DUF498
 56-164


414
PHE0004813_5800.pep
zf-CCCH::zf-
 74-100::119-




CCCH::
145::165-




zf-CCCH::zf-
191::317-




CCCH::zf-CCCH
343::363-389


512
PHE0006174_7208.pep
RRM_1::RRM_1
170-241::269-340


670
PHE0006770_8568.pep
DEAD::
 58-224::292-368




Helicase_C



506
PHE0006160_7265.pep
PFK
 3-309


646
PHE0006716_8482.pep
NOI
 1-72


392
PHE0004683_8693.pep
ThiF
 30-167


500
PHE0006092_7336.pep
RRM_1::RRM_
 65-132::150-




1::RRM_1
225::275-343


388
PHE0004503_8801.pep
MtN3_slv::
 12-99::134-220




MtN3_slv



452
PHE0004984_8782.pep
AA_kinase::
 83-366::403-




ACT::ACT
478::479-546


516
PHE0006178_8626.pep
elF-5a
 82-149


521
PHE0006204_7183.pep
Cyclin_N::
 18-151::153-284




Cyclin_C



636
PHE0006670_8346.pep
PfkB
 83-375


366
PHE0002777_8472.pep
Ferrochelatase
108-432


376
PHE0003845_7028.pep
p450
 40-509


598
PHE0006517_7858.pep
CorA
 81-456


651
PHE0006730_8428.pep
Lung_7-TM_R
168-423


381
PHE0004143_8160.pep
GSHPx
 23-131


428
PHE0004887_8704.pep
DUF516
 49-310


440
PHE0004912_5969.pep
Pkinase
162-434


620
PHE0006596_8257.pep
CTP_transf_2
 19-159


692
PHE0006932_9147.pep
DUF498
 56-164


418
PHE0004845_5852.pep
Carotene_hydrox
136-295


406
PHE0004805_5791.pep
DUF751
125-188


540
PHE0006263_7271.pep
DAGAT
 48-324


398
PHE0004766_5733.pep
UPF0051
275-515


643
PHE0006706_8434.pep
DEAD::
 46-212::280-356




Helicase_C



495
PHE0006089_7061.pep
Brix
 60-255


519
PHE0006201_7187.pep
ketoacyl-synt::
 47-309::317-477




Ketoacyl-synt_C



447
PHE0004966_6028.pep
Sugar_tr
101-556


577
PHE0006428_7651.pep
Globin
 21-161


449
PHE0004977_6043.pep
DAGAT
 54-352


509
PHE0006161_7215.pep
PFK::PFK
195-506::585-877


706
PHE0006953_9121.pep
Usp
 3-157


413
PHE0004812_5799.pep
Sigma70_r2::
267-340::343-




Sigma70_
424::436-489




r3::Sigma70_r4



389
PHE0004641_5519.pep
malic::Malic_M
162-350::352-605


668
PHE0006769_8865.pep
TPP_enzyme_N::
 3-172::190-




TPP_enzyme_M
336::379-525




::TPP_enzyme_C



496
PHE0006089_7334.pep
Brix
 60-255


649
PHE0006728_8430.pep
RRM_1
111-190


663
PHE0006750_8523.pep
zf-C3HC4::
 52-89::454-




WD40::
492::496-




WD40::WD40
534::540-576


463
PHE0006003_7195.pep
zf-AN1
105-145


597
PHE0006516_8363.pep
CorA
 90-474


461
PHE0005009_6078.pep
UQ_con
 40-177


534
PHE0006227_7282.pep
NB-ARC::LRR_1::
152-421::652-




LRR_1::LRR_1
674::676-





698::700-722


551
PHE0006309_8620.pep
Glyoxalase
 2-123


554
PHE0006312_7579.pep
UPF0113
 1-175


608
PHE0006571_8279.pep
Pkinase
 15-273


382
PHE0004311_5022.pep
Peptidase_M24
354-577


472
PHE0006048_7094.pep
Pkinase_Tyr
135-389


397
PHE0004762_7997.pep
F-box:: LRR_2
 62-108::314-340


390
PHE0004642_5520.pep
malic::Malic_M
170-358::360-613


518
PHE0006201_7184.pep
ketoacyl-synt::
 47-309::317-477




Ketoacyl-synt_C



662
PHE0006746_8453.pep
Sugar_tr
 33-464


528
PHE0006214_7213.pep
Cyclin_N::
 32-158::160-289




Cyclin_C



503
PHE0006094_7231.pep
Chalcone
 14-225


445
PHE0004941_5997.pep
Dehydrin
 14-128


370
PHE0002857_7502.pep
Chloroa_b-bind
 66-183


627
PHE0006607_8231.pep
SRF-TF
 11-66


676
PHE0006794_8578.pep
SSB
 71-182


600
PHE0006517_7897.pep
CorA
 81-456


694
PHE0006933_9139.pep
adh_short
 30-212


555
PHE0006312_8644.pep
UPF0113
 1-175


624
PHE0006599_8230.pep
2F-HD_dimer
 34-93


580
PHE0006439_8108.pep
RRM_1
 23-94


430
PHE0004894_5951.pep
Tubulin::
 52-245::247-369




Tubulin_C



377
PHE0003845_7413.pep
p450
 40-509


482
PHE0006068_7064.pep
Pkinase
 2-222


656
PHE0006741_8448.pep
MATH::BTB
 53-182::206-328


579
PHE0006433_8307.pep
PseudoU_synth_2
105-284


675
PHE0006793_8580.pep
p450
 27-508


508
PHE0006160_8851.pep
PFK
 3-309


595
PHE0006516_7882.pep
CorA
 90-474


614
PHE0006592_8278.pep
Thioredoxin
 87-190


633
PHE0006648_8356.pep
Tryp_alpha_amyl
 36-114


678
PHE0006811_8506.pep
Bac_globin
 3-122


672
PHE0006775_8548.pep
Ras
 10-178


403
PHE0004784_5760.pep
SAM_decarbox
 3-333


542
PHE0006265_7990.pep
Heme_oxygenase
 88-279


566
PHE0006377_8683.pep
RNase_PH::
 48-244::322-384




RNase_PH_C



459
PHE0005003_7032.pep
Porphobil_
 47-263::271-347




deam::P





orphobil_deamC



450
PHE0004979_6047.pep
Glyco_hydro_
 32-342::395-492




32N::Glyco_





hydro_32C



363
PHE0002133_7497.pep
Pkinase
 13-273


644
PHE0006709_8432.pep
MtN3_slv::
 9-98::132-218




MtN3_slv



490
PHE0006077_7343.pep
GASA
 5-106


537
PHE0006233_7220.pep
Mg_chelatase
 87-295


552
PHE0006310_7574.pep
Pkinase
 13-304


623
PHE0006598_8268.pep
Di19
 11-219


564
PHE0006356_8103.pep
F-box::Kelch_1::
 42-89::180-




Kelch_1
225::227-282


673
PHE0006775_8555.pep
Ras
 10-178


394
PHE0004747_5708.pep
Aldedh
 99-565


523
PHE0006204_8634.pep
Cyclin_N::
 18-151::153-284




Cyclin_C



697
PHE0006938_9149.pep
F-box
 41-88


465
PHE0006018_7098.pep
GTP_EFTU::
 64-260::281-




GTP_EFTU_
352::357-451




D2::GTP_





EFTU _D3



642
PHE0006687_8471.pep
Ribosomal_L32e
 14-123


611
PHE0006587_8277.pep
CP12
 60-131


622
PHE0006598_8240.pep
Di19
 11-219


625
PHE0006599_8262.pep
ZF-HD_dimer
 34-93


457
PHE0004993_8682.pep
CCT
237-275


584
PHE0006464_8089.pep
DREPP
 2-203


573
PHE0006382_7652.pep
WD40
282-319


701
PHE0006948_9125.pep
RRM_1
 38-109


499
PHE0006092_7062.pep
RRM_1::RRM_
 65-132::150-




1::RRM_1
225::275-343


481
PHE0006063_7049.pep
Transket_pyr::
 76-252::265-387




Transketolase_C



400
PHE0004779_8394.pep
Ammonium_transp
 47-471


711
PHE0006965_9119.pep
tRNA-synt_2b::
 67-243::312-409




HGTP_anticodon



517
PHE0006184_7245.pep
DUF125
 34-247


360
PHE0002129_8308.pep
PEPcase
 3-982


444
PHE0004932_6045.pep
PurA
 28-275


386
PHE0004473_8803.pep
Histone
 28-101


660
PHE0006744_8449.pep
adh_short
 37-225






















TABLE 15





PEP








SEQ ID

Pfam domain


NO
GENE ID
name
begin
stop
score
E-value





















359
PHE0001295_7469.pep
DNA_photolyase
18
190
254.3
2.30E−73


359
PHE0001295_7469.pep
FAD_binding_7
223
501
503
 3.20E−148


360
PHE0002129_8308.pep
PEPcase
3
982
425.8
 5.30E−125


361
PHE0002132_4965.pep
Pkinase
9
285
234.9
1.60E−67


362
PHE0002132_8653.pep
Pkinase
9
285
234.9
1.60E−67


363
PHE0002133_7497.pep
Pkinase
13
273
288.2
1.40E−83


364
PHE0002693_8516.pep
FAD_binding_3
55
374
−131.4
0.0029


365
PHE0002777_7490.pep
Ferrochelatase
108
432
598.9
 4.30E−177


366
PHE0002777_8472.pep
Ferrochelatase
108
432
598.9
 4.30E−177


367
PHE0002777_8726.pep
Ferrochelatase
108
432
598.9
 4.30E−177


368
PHE0002779_7478.pep
PGM_PMM_I
16
165
154.6
2.40E−43


368
PHE0002779_7478.pep
PGM_PMM_II
199
314
108.5
1.80E−29


368
PHE0002779_7478.pep
PGM_PMM_III
316
439
136.8
5.30E−38


368
PHE0002779_7478.pep
PGM_PMM_IV
477
571
77.3
4.30E−20


369
PHE0002810_5803.pep
p450
59
531
323.8
2.80E−94


370
PHE0002857_7502.pep
Chloroa_b-bind
66
183
−26.1
0.0016


373
PHE0003814_7802.pep
Chloroa_b-bind
66
217
66.4
8.20E−17


374
PHE0003838_5934.pep
zf-LSD1
28
52
40.3
6.10E−09


374
PHE0003838_5934.pep
zf-LSD1
67
91
54.8
2.60E−13


374
PHE0003838_5934.pep
zf-LSD1
105
129
54.1
4.30E−13


375
PHE0003845_5806.pep
p450
40
509
127.1
4.50E−35


376
PHE0003845_7028.pep
p450
40
509
127.1
4.50E−35


377
PHE0003845_7413.pep
p450
40
509
127.1
4.50E−35


379
PHE0004021_4654.pep
GATase_2
2
173
−29
7.60E−09


379
PHE0004021_4654.pep
Asn_synthase
227
460
295.7
7.70E−86


380
PHE0004143_7850.pep
Redoxin
12
176
4.9
0.0016


380
PHE0004143_7850.pep
GSHPx
21
129
246.5
5.10E−71


381
PHE0004143_8160.pep
Redoxin
14
178
4.9
0.0016


381
PHE0004143_8160.pep
GSHPx
23
131
246.5
5.10E−71


382
PHE0004311_5022.pep
Peptidase_M24
354
577
12.2
3.20E−09


383
PHE0004398_5136.pep
Pkinase
7
269
341.5
1.30E−99


383
PHE0004398_5136.pep
Pkinase_Tyr
7
269
155.9
9.80E−44


384
PHE0004398_5757.pep
Pkinase
7
269
341.5
1.30E−99


384
PHE0004398_5757.pep
Pkinase_Tyr
7
269
155.9
9.80E−44


385
PHE0004473_5214.pep
Histone
28
101
104.2
3.60E−28


386
PHE0004473_8803.pep
Histone
28
101
104.2
3.60E−28


387
PHE0004503_5244.pep
MtN3_slv
12
99
135.1
1.80E−37


387
PHE0004503_5244.pep
MtN3_slv
134
220
135.4
1.40E−37


388
PHE0004503_8801.pep
MtN3_slv
12
99
135.1
1.80E−37


388
PHE0004503_8801.pep
MtN3_slv
134
220
135.4
1.40E−37


389
PHE0004641_5519.pep
malic
162
350
392.4
 6.10E−115


389
PHE0004641_5519.pep
Malic_M
352
605
486.9
 2.20E−143


390
PHE0004642_5520.pep
malic
170
358
402.6
 5.40E−118


390
PHE0004642_5520.pep
Malic_M
360
613
483.8
 1.90E−142


391
PHE0004670_6044.pep
GSHPx
9
117
230.9
2.60E−66


392
PHE0004683_8693.pep
ThiF
30
167
−12.5
3.60E−05


393
PHE0004742_5691.pep
AP2
43
108
93.1
7.50E−25


394
PHE0004747_5708.pep
Aldedh
99
565
568.6
 5.60E−168


396
PHE0004762_5729.pep
F-box
62
108
15.1
0.22 


396
PHE0004762_5729.pep
LRR_2
314
340
17.1
0.058 


397
PHE0004762_7997.pep
F-box
62
108
15.1
0.22 


397
PHE0004762_7997.pep
LRR_2
314
340
17.1
0.058 


398
PHE0004766_5733.pep
UPF0051
275
515
465.7
 5.30E−137


399
PHE0004779_5749.pep
Ammonium_transp
47
471
644.8
 6.60E−191


400
PHE0004779_8394.pep
Ammonium_transp
47
471
644.8
 6.60E−191


403
PHE0004784_5760.pep
SAM_decarbox
3
333
694.5
 7.10E−206


404
PHE0004787_7988.pep
P-II
85
187
176
8.50E−50


405
PHE0004791_5771.pep
Globin
7
131
80.7
4.20E−21


405
PHE0004791_5771.pep
FAD_binding_6
154
254
44.1
4.20E−10


405
PHE0004791_5771.pep
NAD_binding_1
263
373
45
2.40E−10


406
PHE0004805_5791.pep
DUF751
125
188
62.4
1.40E−15


407
PHE0004806_5792.pep
OTU
156
268
141.1
2.60E−39


408
PHE0004807_5793.pep
RRM_1
13
84
114.1
3.80E−31


409
PHE0004808_5794.pep
Peptidase_C1
8
205
327.1
2.80E−95


410
PHE0004809_5795.pep
PP2C
46
324
111.1
3.00E−30


411
PHE0004810_5796.pep
Pkinase
77
358
332.4
7.00E−97


411
PHE0004810_5796.pep
efhand
405
433
26
 0.00012


411
PHE0004810_5796.pep
efhand
441
469
26.3
9.80E−05


411
PHE0004810_5796.pep
efhand
477
505
21
0.0038


411
PHE0004810_5796.pep
efhand
508
536
34.1
4.40E−07


412
PHE0004811_5798.pep
zf-C3HC4
164
205
37.6
3.90E−08


413
PHE0004812_5799.pep
Sigma70_r2
267
340
49.2
1.30E−11


413
PHE0004812_5799.pep
Sigma70_r3
343
424
52.3
1.50E−12


413
PHE0004812_5799.pep
Sigma70_r4
436
489
66.5
7.70E−17


414
PHE0004813_5800.pep
zf-CCCH
74
100
42.6
1.20E−09


414
PHE0004813_5800.pep
zf-CCCH
119
145
42.4
1.40E−09


414
PHE0004813_5800.pep
zf-CCCH
165
191
38
2.90E−08


414
PHE0004813_5800.pep
zf-CCCH
317
343
46.8
6.70E−11


414
PHE0004813_5800.pep
zf-CCCH
363
389
48.2
2.60E−11


415
PHE0004815_5802.pep
Pkinase
334
585
35.3
4.90E−10


415
PHE0004815_5802.pep
Pkinase_Tyr
334
585
77.5
1.60E−20


416
PHE0004827_5825.pep
Phi_1
40
315
567.5
 1.20E−167


417
PHE0004830_5828.pep
HD
233
337
53.6
6.10E−13


417
PHE0004830_5828.pep
RelA_SpoT
427
537
165
1.80E−46


418
PHE0004845_5852.pep
Carotene_hydrox
136
295
339.2
6.30E−99


419
PHE0004856_7855.pep
NPH3
193
435
469.9
 2.90E−138


422
PHE0004883_5935.pep
Pkinase
314
581
148.8
1.30E−41


422
PHE0004883_5935.pep
Pkinase_Tyr
315
581
104
4.10E−28


423
PHE0004886_5938.pep
DUF516
49
313
561.2
 9.10E−166


424
PHE0004887_5939.pep
DUF516
49
310
356.9
 2.90E−104


425
PHE0004887_5940.pep
DUF516
49
310
356.9
 2.90E−104


426
PHE0004887_8704.pep
DUF516
49
310
356.9
 2.90E−104


428
PHE0004894_5948.pep
Tubulin
52
245
339.5
5.20E−99


428
PHE0004894_5948.pep
Tubulin_C
247
369
96.5
7.20E−26


429
PHE0004894_5950.pep
Tubulin
52
245
339.5
5.20E−99


429
PHE0004894_5950.pep
Tubulin_C
247
369
96.5
7.20E−26


430
PHE0004894_5951.pep
Tubulin
52
245
339.5
5.20E−99


430
PHE0004894_5951.pep
Tubulin_C
247
369
96.5
7.20E−26


431
PHE0004895_5952.pep
DS
44
349
713.1
 1.80E−211


432
PHE0004895_7135.pep
DS
44
349
713.1
 1.80E−211


433
PHE0004895_7137.pep
DS
44
349
713.1
 1.80E−211


434
PHE0004895_8610.pep
DS
44
349
713.1
 1.80E−211


435
PHE0004902_5959.pep
Response_reg
21
146
77.4
4.00E−20


437
PHE0004905_5962.pep
Pkinase
78
336
354.5
 1.50E−103


438
PHE0004909_5966.pep
Pkinase
157
428
148.5
1.60E−41


438
PHE0004909_5966.pep
Pkinase_Tyr
157
428
139.3
9.50E−39


439
PHE0004911_5968.pep
Thloredoxin
120
227
56.1
1.10E−13


440
PHE0004912_5969.pep
Pkinase
162
434
125.2
1.70E−34


440
PHE0004912_5969.pep
Pkinase_Tyr
162
434
115.7
1.20E−31


441
PHE0004918_5975.pep
DUF1365
44
255
407.9
 1.30E−119


442
PHE0004921_5979.pep
DUF1677
3
107
192.2
1.20E−54


443
PHE0004928_5986.pep
Rotamase
11
119
143.6
4.90E−40


444
PHE0004932_6045.pep
PurA
28
275
44.4
5.80E−12


445
PHE0004941_5997.pep
Dehydrin
14
128
165.3
1.40E−46


447
PHE0004966_6028.pep
Sugar_tr
101
556
315.4
9.20E−92


447
PHE0004966_6028.pep
MFS_1
105
515
81.2
2.90E−21


448
PHE0004968_6030.pep
RLI
6
37
55.4
1.70E−13


448
PHE0004968_6030.pep
Fer4
48
71
39.3
1.20E−08


448
PHE0004968_6030.pep
ABC_tran
103
292
96.8
5.90E−26


448
PHE0004968_6030.pep
ABC_tran
374
544
85.8
1.30E−22


449
PHE0004977_6043.pep
DAGAT
54
352
405.8
 5.80E−119


450
PHE0004979_6047.pep
Glyco_hydro_32N
32
342
430.7
 1.80E−126


450
PHE0004979_6047.pep
Glyco_hydro_32C
395
492
42.6
1.20E−09


451
PHE0004984_7235.pep
AA_kinase
83
366
224.7
1.80E−64


451
PHE0004984_7235.pep
ACT
403
478
28.1
2.80E−05


451
PHE0004984_7235.pep
ACT
479
546
24
0.0005


452
PHE0004984_8782.pep
AA_kinase
83
366
224.7
1.80E−64


452
PHE0004984_8782.pep
ACT
403
478
28.1
2.80E−05


452
PHE0004984_8782.pep
ACT
479
546
24
0.0005


453
PHE0004989_8115.pep
DUF21
14
191
174.7
2.10E−49


453
PHE0004989_8115.pep
CBS
210
325
33.9
5.30E−07


454
PHE0004991_8092.pep
Auxin_inducible
19
119
55.4
1.70E−13


455
PHE0004993_6062.pep
CCT
237
275
74
4.40E−19


456
PHE0004993_8014.pep
CCT
237
275
74
4.40E−19


457
PHE0004993_8682.pep
CCT
237
275
74
4.40E−19


458
PHE0005002_6071.pep
Methyltransf_11
155
252
44.7
3.00E−10


458
PHE0005002_6071.pep
Methyltransf_12
155
252
59.7
8.50E−15


458
PHE0005002_6071.pep
Mg-por_mtran_C
223
319
198.4
1.50E−56


459
PHE0005003_7032.pep
Porphobil_deam
47
263
451.7
 8.90E−133


459
PHE0005003_7032.pep
Porphobil_deamC
271
347
100.4
4.80E−27


460
PHE0005008_6077.pep
Response_reg
22
137
70.4
5.10E−18


461
PHE0005009_6078.pep
UQ_con
40
177
216.1
7.20E−62


462
PHE0005010_6079.pep
zf-DNL
96
159
102.2
1.40E−27


463
PHE0006003_7195.pep
zf-AN1
105
145
73.2
7.60E−19


464
PHE0006003_7205.pep
zf-AN1
105
145
73.2
7.60E−19


465
PHE0006018_7098.pep
GTP_EFTU
64
260
334.6
1.60E−97


465
PHE0006018_7098.pep
GTP_EFTU_D2
281
352
87
5.30E−23


465
PHE0006018_7098.pep
GTP_EFTU_D3
357
451
186.5
5.80E−53


466
PHE0006021_7077.pep
Bet_v_I
1
155
11.1
6.70E−07


467
PHE0006021_8737.pep
Bet_v_I
1
155
11.1
6.70E−07


468
PHE0006043_7080.pep
Glyco_transf_8
83
345
341.2
1.60E−99


469
PHE0006043_8788.pep
Glyco_transf_8
83
345
341.2
1.60E−99


472
PHE0006048_7094.pep
Pkinase
135
389
219.6
6.60E−63


472
PHE0006048_7094.pep
Pkinase_Tyr
135
389
257.1
3.40E−74


473
PHE0006048_8785.pep
Pkinase
135
389
219.6
6.60E−63


473
PHE0006048_8785.pep
Pkinase_Tyr
135
389
257.1
3.40E−74


475
PHE0006051_7097.pep
zf-MYND
57
94
50.2
6.20E−12


475
PHE0006051_7097.pep
UCH
326
630
176.1
8.20E−50


476
PHE0006054_7095.pep
AIG1
39
236
212.9
6.60E−61


476
PHE0006054_7095.pep
MMR_HSR1
39
154
31.5
1.20E−06


477
PHE0006054_8779.pep
AIG1
39
236
212.9
6.60E−61


477
PHE0006054_8779.pep
MMR_HSR1
39
154
31.5
1.20E−06


478
PHE0006059_7042.pep
DnaJ
4
67
144.7
2.20E−40


478
PHE0006059_7042.pep
DnaJ_C
222
344
47
5.90E−11


479
PHE0006061_7051.pep
Metallophos
2
120
28.2
2.60E−05


481
PHE0006063_7049.pep
Transket_pyr
76
252
249.7
5.40E−72


481
PHE0006063_7049.pep
Transketolase_C
265
387
161.6
1.80E−45


482
PHE0006068_7064.pep
Pkinase_Tyr
1
222
68.5
7.00E−20


482
PHE0006068_7064.pep
Pkinase
2
222
219.7
5.90E−63


483
PHE0006069_7065.pep
Cupin_3
62
137
130
6.10E−36


484
PHE0006071_7068.pep
PPR
30
63
4.4
2.1  


484
PHE0006071_7068.pep
PPR
64
98
19.6
0.011 


484
PHE0006071_7068.pep
PPR
99
132
18.3
0.025 


484
PHE0006071_7068.pep
PPR
138
172
29.2
1.40E−05


484
PHE0006071_7068.pep
PPR
173
207
39.2
1.30E−08


489
PHE0006077_7045.pep
GASA
5
106
226.6
5.10E−65


490
PHE0006077_7343.pep
GASA
5
106
226.6
5.10E−65


491
PHE0006079_7044.pep
S6PP
8
262
519.2
 4.00E−153


491
PHE0006079_7044.pep
Hydrolase_3
12
257
−20.6
5.00E−06


491
PHE0006079_7044.pep
S6PP_C
263
395
320.8
2.20E−93


492
PHE0006079_7337.pep
S6PP
8
262
519.2
 4.00E−153


492
PHE0006079_7337.pep
Hydrolase_3
12
257
−20.6
5.00E−06


492
PHE0006079_7337.pep
S6PP_C
263
395
320.8
2.20E−93


493
PHE0006082_7330.pep
TPR_1
2
35
28.1
2.80E−05


493
PHE0006082_7330.pep
TPR_2
2
35
27.1
5.70E−05


493
PHE0006082_7330.pep
TPR_2
36
69
22.3
0.0016


493
PHE0006082_7330.pep
TPR_1
36
69
15.7
0.066 


493
PHE0006082_7330.pep
TPR_1
70
103
40.8
4.40E−09


493
PHE0006082_7330.pep
TPR_2
70
103
32.2
1.70E−06


493
PHE0006082_7330.pep
TPR_1
255
290
25.7
 0.00015


493
PHE0006082_7330.pep
TPR_2
257
290
26
 0.00013


493
PHE0006082_7330.pep
TPR_1
291
324
30.4
5.90E−06


493
PHE0006082_7330.pep
TPR_2
291
324
21.2
0.0034


493
PHE0006082_7330.pep
TPR_1
332
369
19.6
0.01 


493
PHE0006082_7330.pep
TPR_1
396
429
26.1
 0.00012


493
PHE0006082_7330.pep
TPR_2
396
429
20.9
0.0042


493
PHE0006082_7330.pep
TPR_1
430
463
35.5
1.70E−07


493
PHE0006082_7330.pep
TPR_2
430
463
23.6
 0.00062


493
PHE0006082_7330.pep
TPR_3
461
497
16.6
0.066 


493
PHE0006082_7330.pep
TPR_1
464
497
33.3
7.70E−07


493
PHE0006082_7330.pep
TPR_2
464
497
24.5
 0.00034


494
PHE0006088_7063.pep
CoA_binding
634
743
52.5
1.30E−12


494
PHE0006088_7063.pep
Ligase_CoA
784
929
149.1
1.10E−41


495
PHE0006089_7061.pep
Brix
60
255
136.1
8.50E−38


496
PHE0006089_7334.pep
Brix
60
255
136.1
8.50E−38


497
PHE0006091_7074.pep
TFIIS_M
206
327
203.5
4.50E−58


497
PHE0006091_7074.pep
TFIIS_C
338
376
83.3
7.00E−22


498
PHE0006091_7341.pep
TFIIS_M
206
327
203.5
4.50E−58


498
PHE0006091_7341.pep
TFIIS_C
338
376
83.3
7.00E−22


499
PHE0006092_7062.pep
RRM_1
65
132
43
9.10E−10


499
PHE0006092_7062.pep
RRM_1
150
225
83.8
4.80E−22


499
PHE0006092_7062.pep
RRM_1
275
343
53.1
8.60E−13


500
PHE0006092_7336.pep
RRM_1
65
132
43
9.10E−10


500
PHE0006092_7336.pep
RRM_1
150
225
83.8
4.80E−22


500
PHE0006092_7336.pep
RRM_1
275
343
53.1
8.60E−13


501
PHE0006093_7066.pep
PTS_2-RNA
48
239
409.9
 3.30E−120


502
PHE0006093_7327.pep
PTS_2-RNA
48
239
409.9
 3.30E−120


503
PHE0006094_7231.pep
Chalcone
14
225
498.4
 7.50E−147


504
PHE0006094_7333.pep
Chalcone
14
225
498.4
 7.50E−147


505
PHE0006154_7204.pep
PfkB
7
299
260.8
2.50E−75


506
PHE0006160_7265.pep
PFK
3
309
−70.5
1.40E−08


507
PHE0006160_7286.pep
PFK
3
309
−70.5
1.40E−08


508
PHE0006160_8851.pep
PFK
3
309
−70.5
1.40E−08


509
PHE0006161_7215.pep
PFK
195
506
618.8
 4.20E−183


509
PHE0006161_7215.pep
PFK
585
877
69.6
9.40E−18


510
PHE0006161_7221.pep
PFK
195
506
621.1
 8.90E−184


510
PHE0006161_7221.pep
PFK
585
877
69.6
9.40E−18


511
PHE0006173_7211.pep
Ribosomal_S6e
1
129
266.2
6.00E−77


512
PHE0006174_7208.pep
RRM_1
170
241
103.1
7.30E−28


512
PHE0006174_7208.pep
RRM_1
269
340
101.6
2.10E−27


513
PHE0006175_7210.pep
KOW
27
63
31.3
3.10E−06


513
PHE0006175_7210.pep
eIF-5a
85
154
122.5
1.10E−33


515
PHE0006178_7139.pep
eIF-5a
82
149
97.8
3.00E−26


516
PHE0006178_8626.pep
eIF-5a
82
149
97.8
3.00E−26


517
PHE0006184_7245.pep
DUF125
34
247
255.9
7.60E−74


518
PHE0006201_7184.pep
ketoacyl-synt
47
309
215.6
1.00E−61


518
PHE0006201_7184.pep
Ketoacyl-synt_C
317
477
227.3
3.00E−65


519
PHE0006201_7187.pep
ketoacyl-synt
47
309
215.6
1.00E−61


519
PHE0006201_7187.pep
Ketoacyl-synt_C
317
477
227.3
3.00E−65


520
PHE0006202_7182.pep
HMGL-like
97
374
377.5
 1.90E−110


520
PHE0006202_7182.pep
LeuA_dimer
467
612
180.7
3.20E−51


521
PHE0006204_7183.pep
Cyclin_N
18
151
53.6
6.20E−13


521
PHE0006204_7183.pep
Cyclin_C
153
284
17.1
 0.00056


522
PHE0006204_7189.pep
Cyclin_N
18
151
53.6
6.20E−13


522
PHE0006204_7189.pep
Cyclin_C
153
284
17.1
 0.00056


523
PHE0006204_8634.pep
Cyclin_N
18
151
53.6
6.20E−13


523
PHE0006204_8634.pep
Cyclin_C
153
284
17.1
 0.00056


524
PHE0006208_7223.pep
CH
19
120
54.8
2.50E−13


524
PHE0006208_7223.pep
EB1
204
251
79.3
1.10E−20


525
PHE0006209_7991.pep
HMGL-like
28
305
371.7
 1.00E−108


525
PHE0006209_7991.pep
LeuA_dimer
398
542
165.2
1.50E−46


526
PHE0006212_7196.pep
Heme_oxygenase
74
278
−13.8
4.40E−06


527
PHE0006213_7198.pep
Peptidase_C54
142
436
555.2
 6.10E−164


528
PHE0006214_7213.pep
Cyclin_N
32
158
43.2
7.80E−10


528
PHE0006214_7213.pep
Cyclin_C
160
289
−2.8
0.029 


529
PHE0006214_7219.pep
Cvclin_N
32
158
43.2
7.80E−10


529
PHE0006214_7219.pep
Cyclin_C
160
289
−2.8
0.029 


530
PHE0006215_7280.pep
PFK
2
277
650.2
 1.50E−192


531
PHE0006221_7201.pep
Pyr_redox_2
44
329
169.5
7.60E−48


531
PHE0006221_7201.pep
Pyr_redox
190
284
94.9
2.20E−25


531
PHE0006221_7201.pep
Thioredoxin
384
487
22.9
2.10E−06


531
PHE0006221_7201.pep
Glutaredoxin
405
467
35
2.40E−07


532
PHE0006221_7241.pep
Pyr_redox_2
44
329
169.5
7.60E−48


532
PHE0006221_7241.pep
Pyr_redox
190
284
94.9
2.20E−25


532
PHE0006221_7241.pep
Thioredoxin
384
487
22.9
2.10E−06


532
PHE0006221_7241.pep
Glutaredoxin
405
467
35
2.40E−07


533
PHE0006221_7937.pep
Pyr_redox_2
44
329
169.5
7.60E−48


533
PHE0006221_7937.pep
Pyr_redox
190
284
94.9
2.20E−25


533
PHE0006221_7937.pep
Thioredoxin
384
487
22.9
2.10E−06


533
PHE0006221_7937.pep
Glutaredoxin
405
467
35
2.40E−07


534
PHE0006227_7282.pep
NB-ARC
152
421
72.5
1.20E−18


534
PHE0006227_7282.pep
LRR_1
652
674
9.6
4.2  


534
PHE0006227_7282.pep
LRR_1
676
698
8.1
7.8  


534
PHE0006227_7282.pep
LRR_1
700
722
10.3
3   


535
PHE0006232_7454.pep
B_lectin
74
187
129.9
6.60E−36


535
PHE0006232_7454.pep
S_locus_glycop
201
327
180.6
3.60E−51


535
PHE0006232_7454.pep
PAN_2
344
411
108.4
2.00E−29


535
PHE0006232_7454.pep
Pkinase
552
823
142.3
1.20E−39


535
PHE0006232_7454.pep
Pkinase_Tyr
552
824
143.8
4.30E−40


536
PHE0006232_8756.pep
B_lectin
74
187
129.9
6.60E−36


536
PHE0006232_8756.pep
S_locus_glycop
201
327
180.6
3.60E−51


536
PHE0006232_8756.pep
PAN_2
344
411
108.4
2.00E−29


536
PHE0006232_8756.pep
Pkinase_Tyr
552
824
143.8
4.30E−40


536
PHE0006232_8756.pep
Pkinase
552
823
142.3
1.20E−39


537
PHE0006233_7220.pep
Mg_chelatase
87
295
−123
 0.00014


538
PHE0006234_7281.pep
Mg_chelatase
85
295
−105.3
5.10E−06


538
PHE0006234_7281.pep
VWA
559
754
−2.7
0.0079


539
PHE0006254_7312.pep
X8
29
115
168.4
1.70E−47


540
PHE0006263_7271.pep
DAGAT
48
324
279.6
5.70E−81


541
PHE0006264_7285.pep
DAGAT
48
349
391.3
 1.30E−114


542
PHE0006265_7990.pep
Heme_oxygenase
88
279
−46.8
 0.00098


543
PHE0006281_7526.pep
GAF
158
307
83.2
7.40E−22


543
PHE0006281_7526.pep
HisKA
343
408
84.2
3.60E−22


543
PHE0006281_7526.pep
HATPase_c
455
582
126.8
5.50E−35


543
PHE0006281_7526.pep
Response_req
610
726
51.5
2.60E−12


548
PHE0006296_7515.pep
Glyco_transf_43
89
312
227.4
2.90E−65


549
PHE0006309_7570.pep
Glyoxalase
2
123
153.5
4.90E−43


550
PHE0006309_8148.pep
Glyoxalase
2
123
153.5
4.90E−43


551
PHE0006309_8620.pep
Glyoxalase
2
123
153.5
4.90E−43


552
PHE0006310_7574.pep
Pkinase
13
304
294.9
1.40E−85


554
PHE0006312_7579.pep
UPF0113
1
175
14.8
1.10E−06


555
PHE0006312_8644.pep
UPF0113
1
175
14.8
1.10E−06


556
PHE0006342_8182.pep
Hydrolase
12
200
106.3
8.10E−29


557
PHE0006344_8188.pep
VQ
44
74
46
1.10E−10


559
PHE0006348_8203.pep
UAA
97
388
−141.8
0.0019


559
PHE0006348_8203.pep
DUF6
106
231
27.4
4.60E−05


559
PHE0006348_8203.pep
TPT
240
385
193.4
5.10E−55


564
PHE0006356_8103.pep
F-box
42
89
41.3
3.00E−09


564
PHE0006356_8103.pep
Kelch_1
180
225
43.1
8.70E−10


564
PHE0006356_8103.pep
Kelch_2
180
225
22.6
0.0012


564
PHE0006356_8103.pep
Kelch_1
227
282
21.5
0.0027


565
PHE0006377_7592.pep
RNase_PH
48
244
131.7
1.80E−36


565
PHE0006377_7592.pep
RNase_PH_C
322
384
36.2
1.00E−07


566
PHE0006377_8683.pep
RNase_PH
48
244
131.7
1.80E−36


566
PHE0006377_8683.pep
RNase_PH_C
322
384
36.2
1.00E−07


569
PHE0006380_7658.pep
RNase_PH
1
126
104.2
3.60E−28


569
PHE0006380_7658.pep
RNase_PH_C
129
201
61.5
2.40E−15


570
PHE0006380_8719.pep
RNase_PH
1
126
104.2
3.60E−28


570
PHE0006380_8719.pep
RNase_PH_C
129
201
61.5
2.40E−15


571
PHE0006381_7655.pep
RNase_PH
42
186
112.2
1.40E−30


572
PHE0006381_8695.pep
RNase_PH
42
186
112.2
1.40E−30


573
PHE0006382_7652.pep
WD40
282
319
33.7
5.70E−07


574
PHE0006382_8678.pep
WD40
282
319
33.7
5.70E−07


575
PHE0006425_7646.pep
AA_permease
36
537
76.4
8.40E−20


576
PHE0006426_8056.pep
AA_permease
2
454
−41.6
2.20E−05


577
PHE0006428_7651.pep
Globin
21
161
110.6
4.10E−30


578
PHE0006429_7671.pep
Globin
18
158
110.2
5.60E−30


579
PHE0006433_8307.pep
PseudoU_synth_2
105
284
150.2
5.00E−42


580
PHE0006439_8108.pep
RRM_1
23
94
105.3
1.70E−28


581
PHE0006449_7865.pep
Biotin_lipoyl
92
165
76.9
6.00E−20


581
PHE0006449_7865.pep
E3_binding
229
265
50.4
5.70E−12


581
PHE0006449_7865.pep
2-oxoacid_dh
281
512
373.8
 2.40E−109


582
PHE0006449_8165.pep
Biotin_lipoyl
92
165
76.9
6.00E−20


582
PHE0006449_8165.pep
E3_binding
229
265
50.4
5.70E−12


582
PHE0006449_8165.pep
2-oxoacid_dh
281
512
373.8
 2.40E−109


583
PHE0006450_7624.pep
Tubulin
57
250
351.6
 1.20E−102


583
PHE0006450_7624.pep
Tubulin_C
252
369
102.7
9.80E−28


584
PHE0006464_8089.pep
DREPP
2
203
280.3
3.30E−81


585
PHE0006468_7903.pep
F-box
2
49
42.7
1.20E−09


585
PHE0006468_7903.pep
FBA_1
209
387
311.9
1.00E−90


586
PHE0006477_7809.pep
PsbR
42
140
242.1
1.10E−69


587
PHE0006478_8190.pep
Methyltransf_6
4
161
171.6
1.70E−48


588
PHE0006497_8355.pep
DUF868
28
304
175.5
1.20E−49


589
PHE0006498_7795.pep
Pyridoxal_deC
34
381
515
 7.40E−152


590
PHE0006498_7796.pep
Pyridoxal_deC
34
381
515
 7.40E−152


591
PHE0006505_7871.pep
Thioredoxin
69
174
120.9
3.30E−33


592
PHE0006506_7818.pep
Pkinase_Tyr
20
270
87.1
4.90E−23


592
PHE0006506_7818.pep
Pkinase
20
272
381.9
 9.00E−112


592
PHE0006506_7818.pep
UBA
294
333
35.7
1.50E−07


592
PHE0006506_7818.pep
KA1
463
511
95.6
1.40E−25


593
PHE0006514_7926.pep
ELFV_dehydrog_N
57
187
298.9
8.40E−87


593
PHE0006514_7926.pep
ELFV_dehydrog
202
447
469.7
 3.30E−138


594
PHE0006516_7866.pep
CorA
90
474
403.1
 3.80E−118


595
PHE0006516_7882.pep
CorA
90
474
403.1
 3.80E−118


596
PHE0006516_7887.pep
CorA
90
474
403.1
 3.80E−118


597
PHE0006516_8363.pep
CorA
90
474
403.1
 3.80E−118


598
PHE0006517_7858.pep
CorA
81
456
344
 2.30E−100


599
PHE0006517_7879.pep
CorA
81
456
344
 2.30E−100


600
PHE0006517_7897.pep
CorA
81
456
344
 2.30E−100


601
PHE0006521_7840.pep
S6PP
2
247
493.5
 2.30E−145


601
PHE0006521_7840.pep
Hydrolase_3
6
242
−20.7
5.00E−06


602
PHE0006545_8320.pep
DnaJ
31
93
128.9
1.30E−35


603
PHE0006549_8255.pep
THF_DHG_CYH
3
120
222.5
8.50E−64


603
PHE0006549_8255.pep
THF_DHG_CYH_C
123
290
366.5
 3.90E−107


604
PHE0006555_8283.pep
Gp_dh_N
83
236
280.2
3.80E−81


604
PHE0006555_8283.pep
Gp_dh_C
241
398
333
4.80E−97


605
PHE0006559_8227.pep
PEPcase
1
948
2506
0   


606
PHE0006564_8298.pep
GATase_2
2
161
98.9
1.40E−26


606
PHE0006564_8298.pep
Asn_synthase
209
450
340.2
3.20E−99


607
PHE0006565_8300.pep
GATase_2
2
161
102.1
1.50E−27


607
PHE0006565_8300.pep
Asn_synthase
209
450
325.3
9.70E−95


608
PHE0006571_8279.pep
Pkinase
15
273
308.5
1.10E−89


609
PHE0006574_8224.pep
Glyoxalase
11
150
144.4
2.80E−40


609
PHE0006574_8224.pep
Glyoxalase
166
298
109.9
6.70E−30


610
PHE0006586_8271.pep
Frataxin_Cyay
76
187
128.3
2.00E−35


611
PHE0006587_8277.pep
CP12
60
131
155.6
1.20E−43


612
PHE0006590_8258.pep
Thioredoxin
75
178
170.4
4.10E−48


613
PHE0006591_8264.pep
Thioredoxin
81
184
162.9
7.80E−46


614
PHE0006592_8278.pep
Thioredoxin
87
190
157.4
3.50E−44


617
PHE0006595_8250.pep
DUF537
18
156
206.9
4.30E−59


618
PHE0006595_8265.pep
DUF537
18
156
206.9
4.30E−59


619
PHE0006596_8236.pep
CTP_transf_2
19
159
48.1
2.80E−11


620
PHE0006596_8257.pep
CTP_transf_2
19
159
48.1
2.80E−11


621
PHE0006597_8242.pep
Pkinase
143
409
98.7
1.60E−26


621
PHE0006597_8242.pep
Pkinase_Tyr
143
409
97.2
4.50E−26


622
PHE0006598_8240.pep
Di19
11
219
487.1
 1.90E−143


623
PHE0006598_8268.pep
Di19
11
219
487.1
 1.90E−143


624
PHE0006599_8230.pep
ZF-HD_dimer
34
93
141.6
2.00E−39


625
PHE0006599_8262.pep
ZF-HD_dimer
34
93
141.6
2.00E−39


626
PHE0006600_8249.pep
Iso_dh
6
355
346.2
 4.90E−101


627
PHE0006607_8231.pep
SRF-TF
11
66
24.4
 0.00036


628
PHE0006609_8234.pep
GSHPx
12
120
221.4
1.80E−63


629
PHE0006610_8239.pep
GSHPx
77
185
234.2
2.60E−67


630
PHE0006613_8238.pep
GSHPx
12
120
200.6
3.30E−57


631
PHE0006617_8463.pep
Cupin_1
65
215
171.2
2.40E−48


631
PHE0006617_8463.pep
Cupin_2
100
177
26.7
7.30E−05


632
PHE0006620_8462.pep
Epimerase
13
259
78.2
2.40E−20


632
PHE0006620_8462.pep
NmrA
13
313
−88.1
0.004 


632
PHE0006620_8462.pep
3Beta_HSD
14
287
−65.2
3.00E−08


632
PHE0006620_8462.pep
NAD_binding_4
15
243
−13.5
8.50E−08


633
PHE0006648_8356.pep
Tryp_alpha_amyl
36
114
56
1.20E−13


634
PHE0006666_8414.pep
Glycolytic
43
387
859
 2.20E−255


635
PHE0006669_8357.pep
PFK
271
582
621.1
 8.90E−184


635
PHE0006669_8357.pep
PFK
661
953
69.6
9.40E−18


636
PHE0006670_8346.pep
PfkB
83
375
260.8
2.50E−75


637
PHE0006673_8992.pep
PTR2
123
530
305.8
7.40E−89


638
PHE0006676_8410.pep
Transket_pyr
39
215
267.6
2.30E−77


638
PHE0006676_8410.pep
Transketolase_C
232
354
203.9
3.50E−58


639
PHE0006684_8413.pep
Ribosomal_L10
19
123
4.8
0.0008


641
PHE0006686_8416.pep
Ribosomal_L22
17
153
267.2
3.00E−77


642
PHE0006687_8471.pep
Ribosomal_L32e
14
123
200.6
3.30E−57


643
PHE0006706_8434.pep
DEAD
46
212
190.3
4.20E−54


643
PHE0006706_8434.pep
Helicase_C
280
356
128.7
1.50E−35


644
PHE0006709_8432.pep
MtN3_slv
9
98
96.7
6.30E−26


644
PHE0006709_8432.pep
MtN3_slv
132
218
116.8
5.80E−32


645
PHE0006715_8477.pep
AMPKBI
197
287
161.8
1.60E−45


646
PHE0006716_8482.pep
NOI
1
72
159.7
7.10E−45


647
PHE0006727_8435.pep
ETC_C1_NDUFA4
54
156
168.1
2.00E−47


648
PHE0006727_8595.pep
ETC_C1_NDUFA4
54
156
168.1
2.00E−47


649
PHE0006728_8430.pep
RRM_1
111
190
32.8
1.10E−06


650
PHE0006729_8433.pep
DnaJ
12
81
66.1
1.00E−16


650
PHE0006729_8433.pep
zf-CSL
96
174
25.2
 0.00021


651
PHE0006730_8428.pep
Lung_7-TM_R
168
423
385.2
 8.80E−113


652
PHE0006737_8455.pep
2OG-Fell_Oxy
217
317
139.1
1.10E−38


653
PHE0006737_8527.pep
2OG-Fell_Oxy
217
317
139.1
1.10E−38


656
PHE0006741_8448.pep
MATH
53
182
61.8
2.10E−15


656
PHE0006741_8448.pep
BTB
206
328
86.7
6.70E−23


657
PHE0006741_8589.pep
MATH
53
182
61.8
2.10E−15


657
PHE0006741_8589.pep
BTB
206
328
86.7
6.70E−23


658
PHE0006742_8440.pep
PGI
55
545
770.4
 1.00E−228


659
PHE0006742_8591.pep
PGI
55
545
770.4
 1.00E−228


660
PHE0006744_8449.pep
adh_short
37
225
8.4
1.00E−06


661
PHE0006745_8590.pep
V-SNARE
71
221
154.6
2.40E−43


662
PHE0006746_8453.pep
Sugar_tr
33
464
275.2
1.10E−79


662
PHE0006746_8453.pep
MFS_1
38
424
80
6.90E−21


663
PHE0006750_8523.pep
zf-C3HC4
52
89
35.8
1.40E−07


663
PHE0006750_8523.pep
WD40
454
492
34
4.90E−07


663
PHE0006750_8523.pep
WD40
496
534
22.1
0.0018


663
PHE0006750_8523.pep
WD40
540
576
38.3
2.50E−08


664
PHE0006757_8530.pep
Acyltransferase
375
496
38.8
1.70E−08


665
PHE0006760_8529.pep
vATP-synt_E
16
225
389.4
 4.90E−114


666
PHE0006765_8536.pep
Bromodomain
110
199
136.3
7.50E−38


667
PHE0006766_8867.pep
IPT
1
235
515.1
 6.90E−152


668
PHE0006769_8865.pep
TPP_enzyme_N
3
172
280.5
2.90E−81


668
PHE0006769_8865.pep
TPP_enzyme_M
190
336
193
6.40E−55


668
PHE0006769_8865.pep
TPP_enzyme_C
379
525
201.8
1.50E−57


669
PHE0006770_8553.pep
DEAD
58
224
201.3
2.10E−57


669
PHE0006770_8553.pep
Helicase_C
292
368
128.3
2.00E−35


670
PHE0006770_8568.pep
DEAD
58
224
201.3
2.10E−57


670
PHE0006770_8568.pep
Helicase_C
292
368
128.3
2.00E−35


671
PHE0006771_8551.pep
FAE1_CUT1_RppA
52
341
682.1
 3.70E−202


671
PHE0006771_8551.pep
Chal_sti_synt_C
298
441
13.6
 0.00012


671
PHE0006771_8551.pep
ACP_syn_III_C
356
439
6
3.10E−06


672
PHE0006775_8548.pep
Miro
9
128
68.3
2.20E−17


672
PHE0006775_8548.pep
Ras
10
178
279.3
7.00E−81


673
PHE0006775_8555.pep
Miro
9
128
68.3
2.20E−17


673
PHE0006775_8555.pep
Ras
10
178
279.3
7.00E−81


674
PHE0006788_8581.pep
Tryp_alpha_amyl
27
110
118.8
1.50E−32


675
PHE0006793_8580.pep
p450
27
508
156.6
5.80E−44


676
PHE0006794_8578.pep
SSB
71
182
121.5
2.20E−33


677
PHE0006805_8531.pep
Ribosomal_S30AE
2
95
173.7
4.20E−49


678
PHE0006811_8506.pep
Bac_globin
3
122
108.1
2.30E−29


681
PHE0006847_8860.pep
DHBP_synthase
8
203
370.6
 2.20E−108


681
PHE0006847_8860.pep
GTP_cyclohydro2
208
366
−2.3
3.80E−10


682
PHE0006870_8846.pep
Ribosomal_L37ae
2
91
220.3
3.90E−63


684
PHE0006909_9003.pep
Cupin_3
62
137
130
6.10E−36


685
PHE0006910_9019.pep
Mov34
92
201
58
2.80E−14


686
PHE0006912_9000.pep
ECH
57
226
208.9
1.10E−59


687
PHE0006919_9008.pep
Peptidase_M16
80
226
191.7
1.70E−54


687
PHE0006919_9008.pep
Peptidase_M16_C
231
417
152.9
7.70E−43


688
PHE0006929_9151.pep
zf-C3HC4
259
299
47.2
5.00E−11


689
PHE0006929_9185.pep
zf-C3HC4
259
299
47.2
5.00E−11


690
PHE0006931_9148.pep
GDC-P
3
443
700.9
 8.30E−208


691
PHE0006931_9168.pep
GDC-P
3
443
700.9
 8.30E−208


692
PHE0006932_9147.pep
DUF498
56
164
153.1
6.90E−43


693
PHE0006932_9174.pep
DUF498
56
164
153.1
6.90E−43


694
PHE0006933_9139.pep
adh_short
30
212
5.7
1.50E−06


695
PHE0006934_9145.pep
DNA_pol_E_B
178
389
249.9
5.00E−72


696
PHE0006937_9126.pep
DUF298
127
242
222.4
9.20E−64


697
PHE0006938_9149.pep
F-box
41
88
34.3
3.80E−07


698
PHE0006940_9122.pep
Aldedh
18
477
674.3
 8.70E−200


700
PHE0006943_9124.pep
Aa_trans
29
428
516.5
 2.80E−152


701
PHE0006948_9125.pep
RRM_1
38
109
98.5
1.80E−26


702
PHE0006948_9160.pep
RRM_1
38
109
98.5
1.80E−26


703
PHE0006949_9133.pep
Aldedh
19
478
778.3
 4.10E−231


704
PHE0006949_9179.pep
Aldedh
19
478
778.3
 4.10E−231


705
PHE0006952_9233.pep
PGAM
91
277
153.2
6.30E−43


706
PHE0006953_9121.pep
Usp
3
157
85.3
1.80E−22


709
PHE0006962_9114.pep
Molybdop_Fe4S4
39
93
88.2
2.40E−23


709
PHE0006962_9114.pep
Molybdopterin
96
568
478.2
 9.20E−141


709
PHE0006962_9114.pep
Molydop_binding
714
822
121.4
2.40E−33


710
PHE0006963_9131.pep
Pyr_redox_2
5
287
191.2
2.30E−54


710
PHE0006963_9131.pep
Pyr_redox
147
242
100.4
4.80E−27


710
PHE0006963_9131.pep
Fer2_BFD
422
474
92.1
1.50E−24


710
PHE0006963_9131.pep
NIR_SIR_ferr
556
623
82
1.70E−21


710
PHE0006963_9131.pep
NIR_SIR
631
777
166.4
6.70E−47


711
PHE0006965_9119.pep
tRNA-synt_2b
67
243
57.5
3.90E−14


711
PHE0006965_9119.pep
HGTP_anticodon
312
409
100
6.40E−27


713
PHE0006977_9163.pep
Ribul_P_3_epim
7
207
332.8
5.30E−97



















TABLE 16





Pfam domain
accession
gathering



name
number
cutoff
domain description


















2-Hacid_dh
PF00389.18
13.2
D-isomer specific





2-hydroxyacid





dehydrogenase,





catalytic domain


2-Hacid_dh_C
PF02826.6
−75.7
D-isomer specific





2-hydroxyacid





dehydrogenase, NAD





binding domain


3Beta_HSD
PF01073.8
−135.9
3-beta hydroxysteroid





dehydrogenase/





isomerase family


3_5_exonuc
PF01612.10
−32
3′-5′ exonuclease


AAA
PF00004.17
10
ATPase family associated





with various





cellular activities (AAA)


AA_kinase
PF00696.16
−40
Amino acid kinase family


AA_permease
PF00324.10
−120.8
Amino acid permease


ABC1
PF03109.6
−27.6
ABC1 family


ABC_tran
PF00005.14
8.6
ABC transporter


ADH_N
PF08240.1
−14.5
Alcohol dehydrogenase





GroES-like domain


ADH_zinc_N
PF00107.15
23.8
Zinc-binding dehydrogenase


AMP-binding
PF00501.15
0
AMP-binding enzyme


AMPKBI
PF04739.4
25
5′-AMP-activated protein





kinase, beta





subunit, complex-





interacting region


AP2
PF00847.9
0
AP2 domain


APS_kinase
PF01583.9
25
Adenylylsulphate kinase


ARID
PF01388.10
−8
ARID/BRIGHT DNA





binding domain


AT_hook
PF02178.7
14.2
AT hook motif


AUX_IAA
PF02309.6
−83
AUX/IAA family


Aa_trans
PF01490.7
−128.4
Transmembrane amino





acid transporter protein


Abhydrolase_1
PF00561.9
5.5
alpha/beta hydrolase fold


Acetyltransf_1
PF00583.12
18.6
Acetyltransferase





(GNAT) family


Acyltransferase
PF01553.10
6
Acyltransferase


Aldedh
PF00171.11
−295
Aldehyde dehydrogenase





family


Aldo_ket_red
PF00248.10
−97
Aldo/keto reductase family


Alpha-amylase
PF00128.11
−93
Alpha amylase,





catalytic domain


Alpha_adaptinC2
PF02883.9
−12
Adaptin C-terminal domain


Aminotran_1_2
PF00155.9
−57.5
Aminotransferase





class I and II


Aminotran_3
PF00202.10
−207.6
Aminotransferase class-III


Aminotran_5
PF00266.8
−92.9
Aminotransferase class-V


Ammonium_
PF00909.10
−144
Ammonium


transp


Transporter Family


Ank
PF00023.17
21.6
Ankyrin repeat


Annexin
PF00191.8
8
Annexin


ArfGap
PF01412.8
−17
Putative GTPase activating





protein for Arf


Asn_synthase
PF00733.10
−52.8
Asparagine synthase


Asp
PF00026.13
−186.1
Eukaryotic aspartyl protease


Auxin_inducible
PF02519.4
−15
Auxin responsive protein


Auxin_resp
PF06507.3
25
Auxin response factor


B12D
PF06522.1
25
B12D protein


B3
PF02362.11
26.5
B3 DNA binding domain


B56
PF01603.8
−210
Protein phosphatase





2A regulatory B





subunit (B56 family)


BAH
PF01426.6
7
BAH domain


BRO1
PF03097.6
25
BRO1-like domain


BURP
PF03181.5
−52
BURP domain


Bromodomain
PF00439.13
8.9
Bromodomain


CAF1
PF04857.8
−100.5
CAF1 family ribonuclease


CBFD_NFYB_
PF00808.12
18.4
Histone-like transcription


HMF


factor (CBF/NF-





Y) and archaeal histone


CBS
PF00571.16
15.8
CBS domain pair


CCT
PF06203.3
25
CCT motif


CH
PF00307.18
22.5
Calponin homology





(CH) domain


CMAS
PF02353.9
−177.9
Cyclopropane-fatty-acyl-





phospholipid synthase


CN_hydrolase
PF00795.11
−13.9
Carbon-nitrogen hydrolase


CTP_synth_N
PF06418.2
25
CTP synthase N-terminus


CTP_transf_2
PF01467.15
−11.8
Cytidylyltransferase


Carb_kinase
PF01256.7
−66.3
Carbohydrate kinase


Catalase
PF00199.8
−229
Catalase


Cation_efflux
PF01545.10
−95.7
Cation efflux family


Chal_sti_synt_C
PF02797.5
−6.1
Chalcone and stilbene





synthases, C-terminal





domain


Chromo
PF00385.11
27.5
‘chromo’ (CHRromatin





Organisation





MOdifier) domain


Citrate_synt
PF00285.10
−101.5
Citrate synthase


CobW_C
PF07683.3
18
Cobalamin synthesis protein





cobW C-terminal domain


ComA
PF02679.5
25
(2R)-phospho-3-sulfolactate





synthase (ComA)


CorA
PF01544.8
−61.3
CorA-like Mg2+





transporter protein


Cpn10
PF00166.11
−7.8
Chaperonin 10 Kd subunit


Cpn60_TCP1
PF00118.13
−223.4
TCP-1/cpn60





chaperonin family


Cu-oxidase
PF00394.11
−18.9
Multicopper oxidase


Cu-oxidase_2
PF07731.3
−5.8
Multicopper oxidase


Cu-oxidase_3
PF07732.4
10
Multicopper oxidase


Cyclin_C
PF02984.7
−13
Cyclin, C-terminal domain


Cyclin _N
PF00134.12
−14.7
Cyclin, N-terminal domain


Cyclotide
PF03784.3
25
Cyclotide family


Cys_Met_
PF01053.9
−278.4
Cys/Met metabolism


Meta_PP


PLP-dependent





enzyme


Cystatin
PF00031.10
17.5
Cystatin domain


DAO
PF01266.11
−36.5
FAD dependent





oxidoreductase


DNA_photolyase
PF00875.7
−10
DNA photolyase


DSPc
PF00782.9
−21.8
Dual specificity





phosphatase, catalytic





domain


DUF125
PF01988.8
−10.1
Integral membrane





protein DUF125


DUF1423
PF07227.1
25
Protein of unknown





function (DUF1423)


DUF1530
PF07060.1
25
ProFAR isomerase





associated


DUF1685
PF07939.1
25
Protein of unknown





function (DUF1685)


DUF246
PF03138.4
−15
Plant protein family


DUF250
PF03151.6
125
Domain of unknown





function, DUF250


DUF296
PF03479.4
−11
Domain of unknown





function (DUF296)


DUF393
PF04134.2
25
Protein of unknown





function, DUF393


DUF581
PF04570.4
−3.1
Protein of unknown





function (DUF581)


DUF6
PF00892.9
30
Integral membrane





protein DUF6


DUF641
PF04859.2
25
Plant protein of





unknown function





(DUF641)


DUF760
PF05542.1
25
Protein of unknown function





(DUF760)


DUF788
PF05620.1
25
Protein of unknown





function (DUF788)


Dehydrin
PF00257.8
−4.4
Dehydrin


Di19
PF05605.2
25
Drought induced 19





protein (Di19)


Dirigent
PF03018.4
25
Dirigent-like protein


DnaJ
PF00226.18
−8
DnaJ domain


E1_dh
PF00676.9
−90
Dehydrogenase E1





component


E2F_TDP
PF02319.9
17
E2F/DP family





winged-helix DNA-





binding domain


EB1
PF03271.6
25
EB1-like C-terminal motif


EF1_GNE
PF00736.8
20
EF-1 guanine nucleotide





exchange domain


ELFV_dehydrog
PF00208.10
−27
Glutamate/Leucine/





Phenylalanine/Valine





dehydrogenase


ELFV_
PF02812.7
31.8
Glu/Leu/Phe/Val


dehydrog_N


dehydrogenase,





dimerisation domain


ERO1
PF04137.5
−179.5
Endoplasmic Reticulum





Oxidoreductin 1 (ERO1)


ERp29
PF07749.2
10.5
Endoplasmic reticulum





protein





ERp29, C-terminal domain


Epimerase
PF01370.10
−46.3
NAD dependent epimerase/





dehydratase family


F-box
PF00646.20
12.4
F-box domain


FAD_binding_3
PF01494.8
−136.6
FAD binding domain


FAD_binding_4
PF01565.12
−8.1
FAD binding domain


FAD_binding_7
PF03441.3
25
FAD binding domain of





DNA photolyase


FAE_3-kCoA_
PF07168.1
25
Fatty acid elongase


syn1


3-ketoacyl-CoA





synthase 1


FA _desaturase
PF00487.13
−46
Fatty acid desaturase


FBA_1
PF07734.2
−39.4
F-box associated


FBPase
PF00316.9
−170.3
Fructose-1-6-





bisphosphatase


FGGY_N
PF00370.10
−104.7
FGGY family





of carbohydrate





kinases, N-





terminal domain


FHA
PF00498.13
25
FHA domain


Fer4
PF00037.14
8
4Fe-4S binding domain


GAF
PF01590.14
23
GAF domain


GAT
PF03127.4
−7
GAT domain


GATA
PF00320.15
28.5
GATA zinc finger


GATase
PF00117.15
−38.1
Glutamine amidotransferase





class-I


GATase_2
PF00310.10
−106.2
Glutamine





amidotransferases





class-II


GFO_IDH_
PF01408.11
−7.2
Oxidoreductase family,


MocA


NAD-binding





Rossmann fold


GFO_IDH_
PF02894.7
6
Oxidoreductase family,


MocA_C


C-terminal





alpha/beta domain


GH3
PF03321.3
−336
GH3 auxin-responsive





promoter


GIDA
PF01134.11
−226.7
Glucose inhibited





division protein A


GRAS
PF03514.4
−78
GRAS family





transcription factor


GRIM-19
PF06212.1
25
GRIM-19 protein


GSHPx
PF00255.9
−16
Glutathione peroxidase


GST_C
PF00043.13
22.3
Glutathione S-transferase,





C-terminal





domain


GST _N
PF02798.8
14.6
Glutathione S-transferase,





N-terminal





domain


GTP_EFTU
PF00009.14
8
Elongation factor Tu





GTP binding domain


GTP_EFTU_D2
PF03144.13
25
Elongation factor





Tu domain 2


GTP_EFTU_D3
PF03143.6
14.3
Elongation factor Tu





C-terminal domain


Gamma-thionin
PF00304.10
9.6
Gamma-thionin family


Gln-synt_C
PF00120.13
−124
Glutamine synthetase,





catalytic domain


Gln-synt_N
PF03951.8
9
Glutamine synthetase,





beta-Grasp domain


Globin
PF00042.11
−8.8
Globin


Glyco_hydro_l
PF00232.8
−301.8
Glycosyl hydrolase family 1


Glyco_hydro_14
PF01373.7
−231.4
Glycosyl hydrolase





family 14


Glyco_hydro_16
PF00722.9
−65
Glycosyl hydrolases





family 16


Glyco_hydro_38
PF01074.11
−125.3
Glycosyl hydrolases





family 38 N-terminal





domain


Glyco_
PF07748.2
−93.1
Glycosyl hydrolases


hydro_38C


family 38 C-terminal





domain


Glyco_transf_20
PF00982.9
−243.6
Glycosyltransferase





family 20


Glycogen_syn
PF05693.2
−492.3
Glycogen synthase


Glycolytic
PF00274.8
−158
Fructose-bisphosphate





aldolase class-I


Glycos_transf_l
PF00534.9
−7.3
Glycosyl transferases





group 1


Glycos_transf_2
PF00535.14
17.6
Glycosyl transferase





family 2


Glyoxalase
PF00903.14
12.1
Glyoxalase/Bleomycin





resistance





protein/Dioxygenase





superfamily


Got1
PF04178.2
25
Got1-like family


Gp_dh_C
PF02800.8
−64.1
Glyceraldehyde 3-phosphate





dehydrogenase,





C-terminal domain


Gp_dh_N
PF00044.11
−74.2
Glyceraldehyde 3-phosphate





dehydrogenase,





NAD binding domain


HALZ
PF02183.7
17
Homeobox associated





leucine zipper


HAMP
PF00672.13
17
HAMP domain


HATPase_c
PF02518.13
22.4
Histidine kinase-, DNA





gyrase B-, and





HSP90-like ATPase


HEAT
PF02985.9
17.6
HEAT repeat


HEM4
PF02602.5
−12
Uroporphyrinogen-III





synthase HemD


HGTP_
PF03129.9
−2
Anticodon binding domain


anticodon





HI0933_like
PF03486.4
−255.8
HI0933-like protein


HLH
PF00010.15
8.2
Helix-loop-helix





DNA-binding domain


HMA
PF00403.14
17.4
Heavy-metal-associated





domain


HMG_box
PF00505.8
4.1
HMG (high mobility





group) box


HSF_DNA-bind
PF00447.7
−70
HSF-type DNA-binding


HSP20
PF00011.9
13
Hsp20/alpha crystallin family


H_PPase
PF03030.5
−377
Inorganic H+





pyrophosphatase


Heme_
PF01126.10
−58
Heme oxygenase


oxygenase





Hexapep
PF00132.11
20
Bacterial transferase





hexapeptide (three repeats)


Hexokinase_l
PF00349.10
−110.3
Hexokinase


Hexokinase_2
PF03727.5
−131.3
Hexokinase


HisKA
PF00512.13
10.2
His Kinase A





(phosphoacceptor) domain


Hist_deacetyl
PF00850.9
−71
Histone deacetylase domain


Histone
PF00125.12
17.4
Core histone H2A/





H2B/H3/H4


Homeobox
PF00046.17
-4.1
Homeobox domain


Hpt
PF01627.11
25
Hpt domain


Hydrolase
PF00702.13
13.6
haloacid dehalogenase-





like hydrolase


ICL
PF00463.9
−234
Isocitrate lyase family


IF4E
PF01652.8
−35
Eukaryotic initiation





factor 4E


IPK
PF03770.6
25
Inositol polyphosphate kinase


IlvC
PF01450.8
−33.8
Acetohydroxy acid





isomeroreductase,





catalytic domain


IlvN
PF07991.1
−75.8
Acetohydroxy acid





isomeroreductase,





catalytic domain


Inhibitor_I29
PF08246.1
4.9
Cathepsin propeptide





inhibitor domain (129)


Ion_trans
PF00520.18
−4.5
Ion transport protein


Isoamylase_N
PF02922.7
−6.5
Isoamylase N-terminal





domain


Jacalin
PF01419.6
20
Jacalin-like lectin domain.


JmjC
PF02373.11
−8
JmjC domain


JmjN
PF02375.6
25
jmjN domain


K-box
PF01486.7
0
K-box region


KA1
PF02149.9
25
Kinase associated domain 1


KH _l
PF00013.17
8.1
KH domain


Kelch_l
PF01344.13
20
Kelch motif


Kelch_2
PF07646.4
20
Kelch motif


Ketoacyl-synt_C
PF02801.10
−54.9
Beta-ketoacyl synthase,





C-terminal





domain


Kunitz_legume
PF00197.8
−32
Trypsin and protease





inhibitor


LEA_5
PF00477.7
25
Small hydrophilic





plant seed protein


LIM
PF00412.10
0
LIM domain


LRR_2
PF07723.2
8.7
Leucine Rich Repeat


Lactamase_B
PF00753.15
22.3
Metallo-beta-lactamase





superfamily


Ldh_1_C
PF02866.6
−13
lactate/malate





dehydrogenase, alpha/beta





C-terminal domain


Ldh_1_N
PF00056.11
−31.3
lactate/malate





dehydrogenase, NAD





binding domain


Lectin_legA
PF00138.7
19
Legume lectins alpha domain


Lectin_legB
PF00139.9
−77
Legume lectins beta domain


Lig_chan
PF00060.16
8.2
Ligand-gated ion channel


Lipase_GDSL
PF00657.11
10.9
GDSL-like Lipase/





Acylhydrolase


M20_dimer
PF07687.3
12
Peptidase dimerisation





domain


MAP1_LC3
PF02991.5
−18.8
Microtubule associated





protein 1A/1B,





light chain 3


MFMR
PF07777.1
−46.7
G-box binding protein





MFMR


MFS_1
PF07690.4
23.5
Major Facilitator Superfamily


MIP
PF00230.8
−62
Major intrinsic protein


Malic_M
PF03949.4
−143.9
Malic enzyme, NAD





binding domain


MatE
PF01554.8
59.6
MatE


Metallophos
PF00149.16
22
Calcineurin-like





phosphoesterase


Metallothio_2
PF01439.7
−3
Metallothionein


Meth_synt_1
PF08267.1
−167.8
Cobalamin-independent





synthase, N-





terminal domain


Meth_synt_2
PF01717.7
−155
Cobalamin-independent





synthase,





Catalytic domain


Methyltransf_11
PF08241.1
17.1
Methyltransferase domain


Methyltransf_12
PF08242.1
21.4
Methyltransferase domain


Methyltransf_2
PF00891.7
−103.8
O-methyltransferase


Methyltransf_3
PF01596.7
−120.6
O-methyltransferase


Mpv17_PMP22
PF04117.2
−5.4
Mpv17/PMP22 family


MtN3_slv
PF03083.5
−0.8
MtN3/saliva family


Myb_DNA-
PF00249.18
19.1
Myb-like DNA-


binding


binding domain


NAC
PF01849.6
0
NAC domain


NAD_binding_4
PF07993.1
−87.7
Male sterility protein


NAF
PF03822.4
25
NAF domain


NAM
PF02365.5
−19
No apical meristem





(NAM) protein


NDK
PF00334.8
−59.9
Nucleoside diphosphate





kinase


NIF
PF03031.7
−81
NLI interacting factor-





like phosphatase


NPH3
PF03000.4
25
NPH3 family


NTF2
PF02136.10
6
Nuclear transport factor





2 (NTF2) domain


NTP_transferase
PF00483.12
−90.5
Nucleotidyl transferase


NUDIX
PF00293.16
0
NUDIX domain


Na_Ca_ex
PF01699.12
25
Sodium/calcium





exchanger protein


NifU_N
PF01592.6
−13
NifU-like N terminal domain


NmrA
PF05368.2
−90.6
NmrA-like family


Om_Arg_deC_N
PF02784.6
−76
Pyridoxal-dependent





decarboxylase,





pyridoxal binding domain


Orn_DAP_
PF00278.11
−34.9
Pyridoxal-dependent


Arg_deC


decarboicylase, C-





terminal sheet domain


Oxidored_FMN
PF00724.8
−147.7
NADH:flavin





oxidoreductase/NADH





oxidase family


PA
PF02225.10
13
PA domain


PAD_porph
PF04371.4
−180.8
Porphyromonas-type





peptidyl-arginine





deiminase


PARP
PF00644.9
−55.5
Poly(ADP-ribose)





polymerase catalytic





domain


PAS
PF00989.12
20
PAS fold


PB1
PF00564.12
12.1
PB1 domain


PBD
PF00786.16
12.1
P21-Rho-binding domain


PCI
PF01399.14
25
PCI domain


PDZ
PF00595.11
12.1
PDZ domain (Also





known as DHR or





GLGF)


PEP-utilizers
PF00391.12
10
PEP-utilising enzyme,





mobile domain


PEP-utilizers_C
PF02896.7
−173
PEP-utilising enzyme,





TIM barrel domain


PEPcase
PF00311.7
25
Phosphoenolpyruvate





carboxylase


PGAM
PF00300.1 I
−3
Phosphoglycerate





mutase family


PHD
PF00628.16
25.9
PHD-finger


PK
PF00224.10
−244
Pyruvate kinase,





barrel domain


PK_C
PF02887.5
−44
Pyruvate kinase, alpha/





beta domain


PMSR
PF01625.9
−62
Peptide methionine





sulfoxide reductase


PP2C
PF00481.10
−44
Protein phosphatase 2C


PPDK_N
PF01326.8
−87
Pyruvate phosphate dikinase,





PEP/pyruvate





binding domain


PRA1
PF03208.8
25
PRA1 family protein


PSI_PsaF
PF02507.5
25
Photosystem I reaction





centre subunit III


PTR2
PF00854.1 I
−50
POT family


PUA
PF01472.8
2.2
PUA domain


Peptidase_A22B
PF04258.3
−137.3
Signal peptide peptidase


Peptidase_C1
PF00112.11
−115.8
Papain family





cysteine protease


Peptidase_C15
PF01470.7
−100
Pyroglutamyl peptidase


Peptidase_M20
PF01546.16
−14.4
Peptidase family M20/





M25/M40


Peptidase_S10
PF00450.11
−198
Serine carboxypeptidase


Peptidase_S41
PF03572.7
−25.8
Peptidase family S41


PfkB
PF00294.12
−67.8
pfkB family carbohydrate





kinase


Phytochrome
PF00360.9
11
Phytochrome region


Pkinase
PF00069.14
−70.8
Protein kinase domain


Pkinase_C
PF00433.11
14
Protein kinase C





terminal domain.


Pkinase_Tyr
PF07714.4
65
Protein tyrosine kinase


Polysacc_synt_2
PF02719.5
−176
Polysaccharide





biosynthesis protein


Pro_CA
PF00484.8
−45
Carbonic anhydrase


Pro_dh
PF01619.7
−120.5
Proline dehydrogenase


Pyr_redox
PF00070.16
5
Pyridine nucleotide-





disulphide





oxidoreductase


Pyr_redox_2
PF07992.2
−20
Pyridine nucleotide-





disulphide





oxidoreductase


Pyr_redox_dim
PF02852.11
−13
Pyridine nucleotide-





disulphide





oxidoreductase,





dimerisation domain


Pyridoxal_deC
PF00282.8
-158.6
Pyridoxal-dependent





decarboxylase





conserved domain


RHD3
PF05879.2
25
Root hair defective 3





GTP-binding protein





(RHD3)


RIO1
PF01163.11
−89.1
RIO1 family


RRM_1
PF00076.10
15.2
RNA recognition





motif. (a.k.a. RRM,





RBD, or RNP domain)


RTC
PF01137.11
−36.9
RNA 3′-terminal





phosphate cyclase


RTC_insert
PF05189.3
25
RNA 3′-terminal





phosphate cyclase





(RTC), insert domain


RWP-RK
PF02042.5
25
RWP-RK domain


Ran_BPI
PF00638.8
−38
RanBPI domain


Ras
PF00071.11
18
Ras family


Remorin_C
PF03763.3
25
Remorin, C-terminal region


Response_reg
PF00072.11
−14.4
Response regulator





receiver domain


Reticulon
PF02453.7
−40
Reticulon


Ribonuclease_T2
PF00445.8
−53
Ribonuclease T2 family


Ribosomal_L1
PF00687.10
−101
Ribosomal protein





L1p/L10e family


Ribosomal_L10e
PF00826.7
25
Ribosomal L10


Ribosomal_L12
PF00542.8
25
Ribosomal protein L7/L12





dC-terminal omain


Ribosomal_L19e
PF01280.9
−28
Ribosomal protein L19e


Ribosomal_L39
PF00832.9
25
Ribosomal L39 protein


Ribosomal_L7Ae
PF01248.13
6
Ribosomal protein





L7Ae/L30e/S12e/





Gadd45 family


Ribosomal_S11
PF00411.7
−4
Ribosomal protein S11


Ribosomal_S17
PF00366.9
1.7
Ribosomal protein S17


Ribosomal_S2
PF00318.9
−22
Ribosomal protein S2


Ribosomal_S27
PF01599.8
50
Ribosomal protein S27a


Rieske
PF00355.15
−7
Rieske [2Fe-2S] domain


RmID_sub_bind
PF04321.6
−171.8
RmID substrate





binding domain


RuBisCO_small
PF00101.9
−20.1
Ribulose bisphosphate





carboxylase, small





chain


Rubrerythrin
PF02915 .7
−4.8
Rubrerythrin


SAM_1
PF00536.17
11.3
SAM domain





(Sterile alpha motif)


SAM_2
PF07647.5
20
SAM domain





(Sterile alpha motif)


SPC25
PF06703.1
25
Microsomal signal





peptidase 25 kDa





subunit (SPC25)


SPX
PF03105.9
−20
SPX domain


SRF-TF
PF00319.8
11
SRF-type transcription





factor (DNA-binding and





dimerisation domain)


START
PF01852.8
25
START domain


SapB_1
PF05184.4
20
Saposin-like type B, region 1


SapB_2
PF03489.5
20
Saposin-like type B, region 2


SecY
PF00344.9
−210
eubacterial secY protein


SelR
PF01641.8
−66.5
SelR domain


Sigma70_r1_2
PF00140.9
25
Sigma-70 factor, re:ion 1.2


Sigma70_r2
PF04542.3
11
Sigma-70 region 2


Sigma70_r3
PF04539.4
10
Sigma-70 region 3


Sigma70_r4
PF04545.5
20.7
Sigma-70, region 4


Sina
PF03145.6
−48.4
Seven in absentia





protein family


Steroid_dh
PF02544.6
−44.7
3-oxo-5-alpha-steroid





4-dehydrogenase


Suc_Fer-like
PF06999.2
−42.4
Sucrase/ferredoxin-like


Succ_DH_
PF02910.9
−42
Fumarate reductase/succinate


flav_C


dehydrogenase





flavoprotein C-terminal





domain


Sucrose_synth
PF00862.9
−134
Sucrose synthase


Sugar_tr
PF00083.12
−85
Sugar (and other) transporter


Synaptobrevin
PF00957.9
25
Synaptobrevin


TPP_enzyme_C
PF02775.9
19.7
Thiamine pyrophosphate





enzyme, C-





terminal TPP binding domain


TPP_enzyme_M
PF00205.11
−23.9
Thiamine pyrophosphate





enzyme, central





domain


TPP_enzyme_N
PF02776.7
−70
Thiamine





pyrophosphate enzyme, N-





terminal TPP binding domain


Thiolase_C
PF02803.6
−30.7
Thiolase, C-terminal domain


Thiolase_N
PF00108.1
−129.5
Thiolase, N-terminal domain


Thioredoxin
PF00085.8
−25.7
Thioredoxin


Tic22
PF04278.2
25
Tic22-like family


Transaldolase
PF00923.8
−49
Transaldolase


Transferase
PF02458.5
−161.2
Transferase family


Transket_pyr
PF02779.12
−50
Transketolase, pyridine





binding domain


Transketolase_C
PF02780.9
−15.5
Transketolase,





C-terminal domain


Transketolase_N
PF00456.10
−98
Transketolase,





thiamine diphosphate





binding domain


Trehalase
PF01204.8
25
Trehalase


Trehalase_Ca-bi
PF07492.1
20
Neutral trehalase Ca2+





binding domain


Trehalose_PPase
PF02358.6
−49.4
Trehalose-phosphatase


Trp_Tyr_perm
PF03222.3
−232.6
Tryptophan/tyrosine





permease family


Trp_syntA
PF00290.10
−149.8
Tryptophan synthase





alpha chain


Trypsin
PF00089.13
−33.2
Trypsin


Tub
PF01167.7
−98
Tub family


Tubulin
PF00091.14
−55.7
Tubulin/FtsZ family,





GTPase domain


Tubulin_C
PF03953.6
−10
Tubulin/FtsZ family,





C-terminal domain


UBA
PF00627.18
20.5
UBA/TS-N domain


UDPGP
PF01704.7
−265.2
UTP--glucose-1-phosphate





uridylyltransferase


UDPGT
PF00201.8
−151
UDP-glucoronosyl





and UDP-glucosyl





transferase


UPF0057
PF01679.7
25
Uncharacterized protein





family UPF0057


UbiA
PF01040.8
−45
UbiA prenyltransferase





family


Ubie_methyltran
PF01209.8
−117
ubiE/COQ5





methyltransferase family


Usp
PF00582.15
25.7
Universal stress protein





family


VHS
PF00790.8
−13.2
VHS domain


VQ
PF05678.3
25
VQ motif


W2
PF02020.7
25
eIF4-gamma/eIF5/





eIF2-epsilon


WD40
PF00400.19
21.4
WD domain, G-beta repeat


WHEP-TRS
PF00458.9
10
WHEP-TRS domain


WRKY
PF03106.5
25
WRKY DNA-binding





domain


Wzy_C
PF04932.4
25
O-Antigen Polymerase


XET_C
PF06955.2
11.4
Xyloglucan endo-





transglycosylase (XET)





C-terminus


Xan_ur_
PF00860.10
−151.2
Permease family


permease





YL1
PF05764.3
25
YL1 nuclear protein


YL1_C
PF08265.1
18.6
YL1 nuclear protein





C-terminal domain


YTH
PF04146.5
25
YT521-B-like family


Yippee
PF03226.4
25
Yippee putative





zinc-binding protein


YjeF_N
PF03853.3
25
YjeF-related protein





N-terminus


ZF-HD_dimer
PF04770.2
25
ZF-HD protein





dimerisation region


Zip
PF02535.10
−28
ZIP Zinc transporter


adh_short
PF00106.13
−46.6
short chain dehydrogenase


bZIP_1
PF00170.10
16.5
bZIP transcription factor


bZIP_2
PF07716.4
15
Basic region leucine zipper


cNMP_binding
PF00027.17
20.6
Cyclic nucleotide-binding





domain


cobW
PF02492.8
−10
CobW/HypB/UreG,





nucleotide-binding domain


efhand
PF00036.19
17.5
EF hand


ketoacyl-synt
PF00109.14
−73.6
Beta-ketoacyl synthase,





N-terminal





domain


malic
PF00390.8
25
Malic enzyme,





N-terminal domain


p450
PF00067.11
−105
Cytochrome P450


peroxidase
PF00141.12
−10
Peroxidase


tRNA-synt_2b
PF00587.14
−40.5
tRNA synthetase class





II core domain (G,





H, P, S and T)


ubiquitin
PF00240.12
19.4
Ubiquitin family


zf-B_box
PF00643.13
11.1
B-box zinc finger


zf-C2H2
PF00096.14
19
Zinc finger, C2H2 type


zf-C3HC4
PF00097.12
16.9
Zinc finger, C3HC4





type (RING finger)


zf-Dof
PF02701.5
25
Dof domain, zinc finger


zf-LSD1
PF06943.2
25
LSD1 zinc finger









Example 10
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 a having an enhanced agronomic trait imparted by expression of a protein selected from the group including the homologous proteins identified in Example 6. Transgenic plant cells of corn, soybean, cotton, canola, wheat and rice are transformed with recombinant DNA for expressing each of the homologs identified in Example 6. 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 of the homologous proteins.

Claims
  • 1. 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 Gp_dh_N::Gp_dh_C, Mg_chelatase::VWA, zf-CCCH::zf-CCCH::zf-CCCH::zf-CCCH::zf-CCCH, WD40, tRNA-synt—2b::HGTP_anticodon, RNase_PH::RNase_PH_C, F-box::Kelch—1::Kelch—1, Peptidase_C54, Iso_dh, Metallophos, OTU, Rotamase, Sugar_tr, Glyoxalase::Glyoxalase, Ras, Brix, S6PP::S6PP_C, PsbR, Pkinase, p450, PP2C, CH::EB1, DUF537, Histone, PPR::PPR::PPR::PPR::PPR, DUF751, RRM—1::RRM—1, ETC_C1_NDUFA4, SRF-TF, CCT, Globin::FAD_binding—6::NAD_binding—1, FAE1_CUT1_RppA::ACP_syn_III_C, Frataxin_Cyay, F-box::LRR—2, Tryp_alpha_amyl, PFK::PFK, Dehydrin, RLI::Fer4::ABC_tran::ABC_tran, CTP_transf—2, GTP_EFTU::GTP_EFTU_D2::GTP_EFTU_D3, PfkB, IPT, TPR—1::TPR—2::TPR—1::TPR—2::TPR—1::TPR—1::TPR—1::TPR—1::TPR—1, Globin, Porphobil_deam::Porphobil_deamC, NB-ARC::LRR—1::LRR—1::LRR—1, Bromodomain, DUF1365, PTS—2-RNA, Pkinase::UBA::KA1, MATH::BTB, DUF6::TPT, Cyclin_N::Cyclin_C, zf-AN1, Methyltransf—6, Thioredoxin, DNA_photolyase::FAD_binding—7, vATP-synt_E, Bac_globin, B_lectin::S_locus_glycop::PAN—2::Pkinase_Tyr, Sigma70_r2::Sigma70_r3::Sigma70_r4, Ribosomal_L10, zf-C3HC4::WD40::WD40::WD40, PGM_PMM_I::PGM_PMM_II::PGM_PMM_III::PGM_PMM_IV, Hydrolase, Peptidase_C1, DS, Carotene_hydrox, Aa_trans, Mov34, zf-MYND::UCH, Heme_oxygenase, S6PP, SSB, Peptidase_M16::Peptidase_M16_C, Bet_v_I, Auxin_inducible, Response_reg, Di19, DUF125, GDC-P, Pyr_redox—2::Fer2_BFD::NIR_SIR_ferr:NIR_SIR, KOW::eIF-5a, MtN3_slv::MtN3_slv, Ribul_P—3_epim, NPH3, DnaJ::DnaJ_C, UQ_con, RRM—1::RRM—1::RRM—1, F-box, CoA_binding::Ligase_CoA, adh_short, Ribosomal_L22, AA_permease, Acyltransferase, AMPKBI, RRM—1, Chalcone, GATase—2::Asn_synthase, Peptidase_M24, DUF498, DAGAT, PFK, DUF1677, Glyco_transf—43, zf-DNL, DHBP_synthase::GTP_cyclohydro2, PseudoU_synth—2, Glyoxalase, DUF21::CBS, Ribosomal_S30AE, Glycolytic, Chloroa_b-bind, ZF-HD_dimer, Usp, Ferrochelatase, Pyridoxal_deC, Glyco_transf—8, Pyr_redox—2::Glutaredoxin, Epimerase, UPF0113, RNase_PH, AIG1, Phi—1, CorA, HD::RelA_SpoT, P-II, GSHPx, PGAM, PGI, DUF868, Lung—7-TM_R, F-box::FBA—1, TPP_enzyme_N::TPP_enzyme_M::TPP_enzyme_C, DnaJ::zf-CSL, DEAD::Helicase_C, 2OG-FeII_Oxy, HMGL-like::LeuA_dimer, VQ, DUF298, DREPP, ketoacyl-synt::Ketoacyl-synt_C, THF_DHG_CYH::THF_DHG_CYH_C, DNA_pol_E_B, UPF0051, Pkinase::efhand::efhand::efhand::efhand, malic::Malic_M, ThiF, Transket_pyr:Transketolase_C, Ribosomal_L37ae, PEPcase, Glyco_hydro—32N::Glyco_hydro—32C, CASA, DnaJ, AA_kinase::ACT::ACT, Pkinase_Tyr, Cupin—1, zf-LSD1::zf-LSD1::zf-LSD1, Cupin—3, GAF::HisKA::HATPase_c::Response_reg, Methyltransf—12::Mg-por_mtran_C, DUF516, PTR2, Ammonium_transp, eIF-5a, ECH, Aldedh, zf-C3HC4, SAM_decarbox, X8, Mg_chelatase, PurA, Ribosomal_S6e, Molybdop_Fe4S4::Molybdopterin::Molydop_binding, CP12, Biotin_lipoyl::E3_binding::2-oxoacid_dh, NOI, Tubulin::Tubulin_C, V-SNARE, AP2, ELFV_dehydrog_N::ELFV_dehydrog, Ribosomal_L32e, and FAD_binding—3;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: 30377 through SEQ ID NO: 30418;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 395, 553, 640, and homologs thereof listed in table 9; ord. 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 selected from the group consisting of 560;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.
  • 2. The plant cell nucleus of claim 1 wherein said protein coding DNA encodes a protein having an amino acid sequence selected from the group consisting of SEQ ID NO: 350 through SEQ ID NO: 30327.
  • 3. The plant cell nucleus of claim 1 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.
  • 4. The plant cell nucleus of claim 3 wherein the agent of said herbicide is a glyphosate, dicamba, or glufosinate compound.
  • 5. A transgenic plant cell or plant comprising a plurality of plant cells with the plant cell nucleus of claim 1.
  • 6. The transgenic plant cell or plant of claim 5 which is homozygous for said recombinant DNA.
  • 7. A transgenic seed comprising a plurality of plant cells with the plant cell nucleus of claim 1.
  • 8. The transgenic seed of claim 7 from a corn, soybean, cotton, canola, alfalfa, wheat or rice plant.
  • 9. A transgenic pollen grain comprising a haploid derivative of the plant cell nucleus of claim 1.
  • 10. A method for manufacturing non-natural, transgenic seed of claim 7 that can be used to produce a crop of transgenic plants with an enhanced trait resulting from expression of stably-integrated recombinant DNA 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 express 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 resistance to salt exposure, 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 seed from selected plants selected from step b.
  • 11. The method of claim 10 further comprising (d) verifying that said recombinant DNA is stably integrated in said selected plants; and(e) analyzing tissue of said selected plant to determine the expression or suppression of a gene that encodes an protein having the function of a protein having an amino acid sequence selected from the group consisting of one of SEQ ID NO:358-716.
  • 12. 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 1;(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.
CROSS REFERENCE TO RELATED APPLICATIONS

This application is a continuation of U.S. application Ser. No. 11/893,915, filed Aug. 17, 2007, which claims benefit under 35 USC §119(e) of U.S. provisional Application Ser. No. 60/838,415, filed Aug. 17, 2006, which is herein incorporated by reference.

Provisional Applications (1)
Number Date Country
60838415 Aug 2006 US
Continuations (1)
Number Date Country
Parent 11893915 Aug 2007 US
Child 14121611 US