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Table S2
Protein spots were excised from high-resolution 2-D reference gels and identified using LC-MS/MS.  Identified soybean NR proteins were classified into functional classes basically as described by Bevan et al. (1998) with some modification.  Classes were slightly modified to be more suitable for a seed development study (see text for details).  For example, polysaccharide catabolism and seed maturation subclasses were added into the main categories of primary metabolism and cell growth/division, respectively.  Acquired MS data were searched against plant NCBI NR protein databse (for details see Materials and Methods).  This NR protein table includes the pI range of the high-resolution 2-D reference gels used for excision of protein spots, spot ID (both Phoretix and ImageMaster), protein description, accession number, probability, theoretical and experimental molecular mass (MM) and isoelectric point (pI), score, coverage (%), unique peptide (Uni. Pep.), transmembrane domain (TM), transmembrane length (TML), and GRAVY.
Gel Spot ID   Accession Proba- Theoretical Experimental Score Cove- Uni. TM TML GRAVY
pI Phoretix Image Protein Description   bility MM pI MM pI   rage Pep.
Range   Master       (kDa)   (kDa)     (%)  
01 Primary Metabolism                        
01.01 Amino acids and polyamines                              
4-7 105 281 Methionine synthase [Glycine max]  33325957 4.05E-09 84.3 5.9 96.64 6.34 198.29 31.59 20 0 0 -0.161
4-7 299   S-adenosylmethionine synthetase [Oryza sativa] 100801542 2.33E-09 42.7 5.9 52.22 5.77 30.21 9.77 3 0 0 -0.322
4-7 475 984 Cysteine synthase [Glycine max]  18252506 8.57E-05 34.3 5.6 38.21 5.73 38.25 22.77 4 0 0 0.116
4-7 425 889 Spermidine Synthase [Arabidopsis Thaliana] 55670893 8.99E-07 36.4 4.6 43.36 4.77 20.19 4.19 2 0 0 -0.233
4-7 335 733 Aminotransferases class-I pyridoxal-phosphate-binding site [Medicago truncatula] 92882071 7.16E-07 50.0 7 48.02 4.17 30.20 7.41 3 0 0 -0.113
4-7 339 740 Glutamate 1-semialdehyde aminotransferase enzyme [Brassica napus] 28972461 5.67E-06 50.3 6.5 51.91 5.72 30.20 9.51 3 0 0 0
4-7 353 760 Glutamate dehydrogenase 1 [Glycine max]  59668638 4.26E-04 44.5 6 53.18 4.60 20.15 5.35 2 0 0 -0.189
4-7 362 763 Glutamate dehydrogenase 2 [Arabidopsis thaliana] 15240793 2.11E-05 44.7 6.1 52.38 5.63 18.19 7.79 2 0 0 -0.148
4-7 389 829 Cytosolic glutamine synthetase [Glycine max] 256143 1.86E-07 38.8 5.4 46.19 5.44 30.24 14.08 3 0 0 -0.413
3-10 172 2573 Gamma-glutamyl hydrolase precursor (Gamma-Glu-X carboxypeptidase) [Glycine max] 6016129 3.87E-07 37.7 6.1 34.01 8.94 20.22 8.48 2 1 13 -0.176
3-10 101 2375 Adenylosuccinate synthetase [Medicago truncatula] 92897609 7.14E-08 53.0 7.2 47.59 7.06 20.14 5.15 2 0 0 -0.113
3-10 121 2423 Aspartate aminotransferase glyoxysomal isozyme AAT1 precursor [Glycine max] 2654094 6.78E-10 49.7 8.6 45.17 8.02 30.19 8.55 3 0 0 -0.034
3-10 124 2445 Phosphoserine aminotransferase [Medicago truncatula]  92867333 7.03E-07 47.2 8 43.68 7.55 40.23 10.05 4 0 0 -0.283
3-10 181 2802 Serine acetyltransferase [Glycine max]  18252508 1.76E-04 30.5 7.7 32.39 7.55 18.16 8.07 2 0 0 -0.09
01.02 Nitrogen and sulfur                              
4-7 55 204 Embryo-specific urease [Glycine max]  32170829 1.42E-08 90.2 5.6 110.23 6.18 30.18 4.53 3 1 8 -0.094
4-7 462 946 Ni-binding urease accessory protein UreG [Glycine max]  5524682 3.78E-07 30.1 5.9 39.68 6.24 30.23 17.52 3 0 0 -0.443
4-7 254 549 Ferric leghemoglobin reductase-2 precursor [Glycine max]  3309269 3.96E-08 53.0 7 58.41 6.49 106.35 28.00 11 0 0 0.008
4-7 332 719 ATP sulfurylase [Glycine max]  90194295 2.81E-07 51.8 7.7 50.71 6.01 40.18 11.04 4 0 0 -0.289
01.03 Nucleotides                        
3-10 36   ATP binding / ATPase/ hydrolase/ nucleoside-triphosphatase/ nucleotide  [Arabidopsis thaliana] 18414193 1.06E-05 90.0 4.9 61.76 6.97 30.16 3.70 3 0 0 -0.384  
4-7 185 442 ATP binding / protein binding [Arabidopsis thaliana]  42571633 1.20E-06 51.1 5.2 69.27 5.67 60.19 11.76 6 0 0 -0.175
4-7 186 443 ATP binding / protein binding [Arabidopsis thaliana]  15232923 8.15E-08 58.9 5.8 69.27 5.85 60.28 12.15 6 0 0 -0.172
4-7 411 866 Adenosine kinase [Medicago truncatula] 92880884 4.44E-13 37.5 5 44.35 5.21 20.22 9.68 2 0 0 -0.159
3-10 288   Nucleoside diphosphate kinase [Glycine max] 1236951 8.46E-10 16.4 5.9 17.13 6.90 20.21 11.41 2 0 0 -0.144
4-7 248 534 Uridine monophosphate kinase [Medicago truncatula] 92874915 4.74E-05 53.5 5.9 58.98 6.28 20.16 3.78 2 0 0 -0.189
4-7 36 177 Formate-tetrahydrofolate ligase, FTHFS [Medicago truncatula]  92892664 6.89E-10 68.1 6.6 61.76 6.97 40.26 7.97 4 1 6 0.007
4-7 426 880 Ribose-phosphate pyrophosphokinase [Medicago truncatula]  92898315 2.85E-08 35.7 6.2 43.36 6.19 20.29 7.48 2 1 13 0.094
01.04 Phosphate                        
01.05 Sugars and polysaccharides                              
4-7 243 560 UDP-glucose/GDP-mannose dehydrogenase [Oryza sativa] 77554940 3.75E-06 52.9 5.7 59.74 6.33 18.15 4.58 2 0 0 -0.066
3-10 144 2492 UDP-glucose 4-epimerase [Arabidopsis thaliana] 15222072 2.08E-08 39.2 6.1 37.65 8.13 20.19 7.69 2 0 0 -0.344
3-10 28 2146 Similar to dTDP-glucose 4,6-dehydratase [Arabidopsis thaliana] 15218420 4.18E-09 75.4 6.9 65.31 7.11 20.22 2.54 2 0 0 -0.417
3-10 29 2172 Similar to dTDP-glucose 4,6-dehydratase [Oryza sativa] 50253123 4.05E-09 34.6 5.9 65.08 7.24 34.24 10.29 4 0 0 -0.24
4-7 278 609 UTP--glucose-1-phosphate uridylyltransferase [Medicago truncatula]  92875142 4.27E-07 51.4 5.1 55.00 5.06 50.20 11.91 5 0 0 -0.149
4-7 79 237 Sucrose synthase [Medicago sativa] 3169544 5.58E-07 92.3 5.8 104.13 6.48 40.17 5.09 4 0 0 -0.27
3-10 66 2271 Sucrose synthase [Glycine max] 2606081 1.12E-06 92.2 6 106.50 6.29 20.17 2.73 2 1 6 -0.292
4-7 280 605 Phosphogluconate dehydrogenase (decarboxylating) [Arabidopsis thaliana] 15222639 8.93E-08 53.4 5.2 54.76 6.57 20.20 3.49 2 0 0 -0.272
3-10 123 2414 D-galactoside/L-rhamnose binding SUEL lectin; Galactose-binding like [Medicago truncatula] 92868127 1.67E-06 93.3 5.5 44.34 6.94 28.17 2.89 3 1 13 -0.406
4-7 523 1057 Phosphomannomutase [Glycine max]  90762150 1.17E-04 28.0 5.8 33.15 6.04 20.19 12.96 2 0   -0.311
01.06 Fatty acids and lipids                              
4-7 297 682 Acetyl-CoA carboxylase carboxyltransferase beta subunit [Glycine max] 91214152 5.77E-06 49.0 4.7 53.73 5.93 30.21 7.41 3 0 0 -0.385
4-7 306 672 Beta-ketoacyl-ACP synthetase I [Glycine max]  7385201 7.25E-09 49.7 7.2 52.94 6.43 40.23 8.74 4 1 8 -0.11
4-7 431 899 Pyruvate dehydrogenase E1 beta subunit, mitochondrion [Arabidopsis thaliana] 21431823 7.73E-05 39.0 5.6 42.63 5.18 20.17 7.58 2 0 0 -0.098
4-7 259 559 Pyruvate/2-oxoglutarate dehydrogenase complex, dihydrolipoamide dehydrogenase (E3), mitochondrion [Pisum sativa] 9955324 2.36E-09 49.7 6 57.47 6.61 76.23 15.53 8 0 0 -0.019
4-7 480 982 Malonyltransferase [Glycine max]  82618886 1.83E-06 36.4 6.4 37.64 6.42 80.21 31.40 8 0 0 0.018
3-10 131 2438 3-ketoacyl-CoA thiolase [Glycine max]  37549269 1.03E-05 47.0 8.5 42.37 8.45 20.19 5.84 2 1 6 0.045
4-7 232 530 Myo-inositol-1-phosphate synthase [Glycine max]  84311235 1.14E-09 56.4 5.3 61.26 5.42 108.26 29.41 11 1 10 -0.158
3-10 8 2081 Lipoxygenase L-4 [Glycine max] 2160320 4.95E-07 96.5 5.6 92.32 6.87 40.24 6.68 4 2 11 -0.361
4-7 41 187 Lipoxygenase [Glycine max] 18746 7.71E-09 96.8 5.7 112.95 6.03 130.25 20.14 13 1 9 -0.28
3-10 7   Lipoxygenase-2 [Glycine max]  505138 6.84E-10 97.3 6.2 93.10 6.73 150.35 22.63 15 1 12 -0.297
4-7 64 221 Lipoxygenase [Glycine max] 18675 6.03E-09 94.4 5.9 107.86 6.24 60.18 7.87 6 1 19 -0.309
3-10 12 2092 Lipoxygenase [Glycine max] 18677 9.85E-07 96.8 6.3 89.46 7.06 30.14 3.73 3 1 10 -0.337
3-10 9 2923 Lipoxygenase [Medicago truncatula] 92871486 2.91E-06 96.9 5.9 91.54 6.80 20.16 2.77 2 1 12 -0.269
01.07 Cofactors                              
4-7 468   Pyridoxine biosynthesis protein-like [Arabidopsis thaliana]  21617922 9.83E-07 33.2 5.7 38.95 5.87 60.22 19.09 6 0 0 0.024
01.08 Polysaccharide catabolism                              
4-7 261 576 Beta-amylase [Glycine max]  71673371 6.87E-09 56.1 5.4 57.28 5.28 68.32 20.77 7 1 9 -0.359
01.99 Others                              
4-7 461 943 Aldo/keto reductase [Medicago truncatula]  92870669 1.80E-07 34.8 5.9 39.76 6.14 40.26 10.36 4 0   -0.213
4-7 206 480 Acetohydroxy acid isomeroreductase [Medicago truncatula]  92874663 1.04E-08 62.9 6.3 64.67 5.92 20.27 5.69 2 1 10 -0.052
3-10 129 2425 Similar to Glycine cleavage system T protein [Medicago truncatula] 144924918 1.24E-04 44.3 8.7 43.02 7.91 20.14 5.90 2 0   -0.237
02 Energy                              
02.01 Glycolysis                              
4-7 133 338 Phosphoglucomutase [Medicago truncatula] 92868958 3.84E-07 63.2 5.4 88.69 5.51 68.29 14.26 7 0 0 -0.16
4-7 199 462 Cytosolic phosphoglucose isomerase [Arabidopsis thaliana]  11094236 1.38E-04 61.7 6.3 65.81 6.13 30.20 6.25 3 3 10 -0.108
4-7 446 934 Fructokinase 1 [Zea mays] 31652274 1.63E-09 34.7 4.7 40.83 5.17 20.19 7.43 2 0 0 0.139
3-10 53 2247 6-phosphofructokinase [Arabidopsis thaliana]  30679628 2.24E-04 64.5 5.3 57.87 6.75 18.25 4.44 2 1 15 -0.215
4-7 413 867 Plastidic aldolase [Medicago sativa]  16224244 8.14E-04 21.1 8.9 44.18 5.69 20.14 12.89 2 0 0 -0.022
4-7 429 892 Putative plastidic aldolase [Oryza sativa] 34895322 2.17E-07 42.0 8.8 43.04 6.24 40.23 9.79 4 0 0 -0.198
4-7 432 900 Fructose-bisphosphate aldolase [Arabidopsis thaliana]  79322643 3.76E-05 33.3 5.6 42.55 6.39 20.18 9.00 2 0 0 0.022
3-10 135 2444 Fructose-bisphosphate aldolase, class-I [Medicago truncatula] 92898537 9.63E-08 26.6 4.7 41.49 7.32 20.19 5.95 2 0 0 -0.141
3-10 141 2480 Fructose-bisphosphate aldolase, class-I [Medicago truncatula] 92898536 9.78E-08 13.9 9.1 40.61 7.68 40.20 12.98 4 0 0 -0.31
4-7 559 1112 Triosephosphate isomerase [Glycine max]  77540216 9.19E-08 27.2 5.8 29.71 6.31 120.28 53.36 12 0 0 0.04
3-10 147 2471 NAD-dependent glyceraldehyde-3-phosphate dehydrogenase [Arabidopsis thaliana] 4966351 3.11E-11 43.5 7.4 36.88 7.30 30.21 5.16 3 0 0 -0.074
3-10 153 2490 Glyceraldehyde-3-phosphate dehydrogenase [Glycine max]  85720768 4.45E-13 36.8 6.8 36.00 7.44 120.34 49.11 12 0 0 -0.102
4-7 360 765 Phosphoglycerate kinase [Medicago truncatula]  92872325 1.19E-06 50.0 6.7 46.91 6.07 30.22 8.14 3 0 0 0.157
4-7 169 405 putative 2,3-bisphosphoglycerate-independent phosphoglycerate mutase [Oryza sativa] 57863824 6.15E-08 60.8 5.1 81.96 5.87 36.20 8.80 4 0 0 -0.274
4-7 251 557 Enolase [Glycine max]  42521309 3.74E-12 47.7 5.2 58.41 5.47 100.35 35.59 10 1 9 -0.155
3-10 67 2270 Pyruvate kinase [Glycine max]  22296818 2.61E-09 55.3 7.6 54.48 7.72 80.30 23.48 8 0 0 -0.02
3-10 75   Pyruvate kinase [Medicago truncatula]  92868232 9.77E-04 54.2 7.4 52.93 7.85 28.14 6.00 3 0 0 0.025
02.02 Gluconeogenesis                              
4-7 420 897 Malate dehydrogenase, cytosolic [Medicago truncatula] 92877283 7.88E-08 35.6 6.1 43.61 6.31 50.23 12.65 5 0 0 0.052
02.07 Pentose phosphate                              
02.10 TCA pathway                              
4-7 330 718 Isocitrate dehydrogenase NADP-dependent [Medicago truncatula] 92875135 1.67E-07 46.0 6 52.70 6.56 48.30 12.38 5 0 0 -0.223
4-7 427 890 Malate dehydrogenase/ oxidoreductase [Arabidopsis thaliana] 15232820 2.73E-09 42.4 8.7 43.28 5.65 26.29 11.91 3 0 0 0.078
4-7 421 877 Malate dehydrogenase precursor, mitochondrion [Medicago sativa] 2827080 3.47E-11 35.9 9 43.61 6.31 20.20 10.20 2 0 0 0.124
4-7 157 381 Succinate dehydrogenase (ubiquinone) flavoprotein subunit [Arabidopsis thaliana] 15240075 5.49E-10 69.7 5.8 79.50 5.95 40.28 10.41 4 0 0 -0.355
02.13 Respiration                              
4-7 260 579 Mitochondrial F1 ATP synthase beta subunit [Arabidopsis thaliana]  17939849 6.94E-10 63.4 6.6 57.28 5.09 60.26 14.43 6 0 0 -0.185
4-7 262 568 ATPase subunit 1 [Zea mays] 40795005 1.42E-06 55.2 5.8 57.28 6.56 30.17 6.50 3 0 0 -0.085
4-7 231 531 ATP synthase CF1 alpha subunit [Glycine max] 91214148 6.74E-09 55.7 5 61.26 5.21 100.25 25.29 10 0 0 -0.045
02.16 Fermentation                              
4-7 390 830 Alcohol dehydrogenase 1 [Glycine max]  22597178 1.01E-06 40.0 6.2 45.95 6.69 20.17 5.72 2 0 0 -0.126
4-7 214 485 Aldehyde dehydrogenase [Medicago truncatula] 92893594 2.03E-06 54.4 5.2 63.91 5.38 30.15 7.95 3 0 0 -0.007
4-7 253 548 Aldehyde dehydrogenase [Arabidopsis thaliana] 15228319 4.37E-07 58.6 7.2 58.41 6.44 28.20 7.06 3 1 6 -0.072
4-7 277 599 Aldehyde dehydrogenase [Arabidopsis thaliana] 4835765 2.82E-05 54.9 6.1 55.19 6.32 30.17 6.09 3 0 0 -0.042
3-10 60 2273 Aldehyde dehydrogenase [Medicago truncatula] 92877332 6.78E-06 61.3 6.4 55.57 7.03 26.20 5.24 3 0 0 -0.097
02.20 Electron transport                              
02.30 Photosynthesis                              
02.30.01 Light reactions
02.30.02 Calvin cycle                              
4-7 317 707 Ribulose-1,5-bisphosphate carboxylase/oxygenase activase precursor [Zea mays] 19855034 7.52E-10 47.9 6.3 49.92 4.13 18.24 7.85 2 0 0 -0.401
4-7 387 822 Phosphoribulokinase [Arabidopsis thaliana] 15222551 6.87E-07 44.5 5.7 46.43 5.03 38.21 11.65 4 0 0 -0.313
02.99 Others                              
3-10 99 2387 Formate dehydrogenase, mitochondrial precursor (NAD-dependent formate dehydrogenase) [Oryza sativa] 21263611 1.17E-09 41.2 7 48.28 6.85 20.24 9.57 2 0 0 -0.213
4-7 485 997 Putative lactoylglutathione lyase [Brassica oleracea] 1469219 3.23E-04 28.9 4.8 36.66 5.81 20.21 10.04 2 0 0 -0.311
03 Cell growth/division                              
03.01 Cell growth                              
03.13 Meiosis                              
03.16 DNA synth/replication                              
03.19 Recombination/repair                              
03.22 Cell cycle                              
4-7 479 986 Proliferating cell nuclear antigen [Glycine max] 18726 2.48E-08 26.1 4.5 37.64 4.51 70.25 47.03 7 0 0 -0.174
03.25 Cytokinesis                              
03.26 Growth regulators                              
03.30 Seed maturation                              
4-7 144 354 Lea protein [Glycine max]  1389897 8.36E-12 67.9 6.1 83.59 6.46 220.30 47.28 22 0 0 -0.816
4-7 274 593 Lea protein [Glycine max]  22324932 2.17E-05 12.9 9.2 55.38 6.40 20.17 14.17 2 0 0 -1.287
3-10 76 2523 Lea protein [Glycine max]  311698 2.18E-07 49.4 7.4 52.85 7.08 40.21 8.30 4 0 0 -1.223
4-7 423 883 35 kDa seed maturation protein [Glycine max]  4102190 4.56E-06 35.3 5.9 43.53 6.13 40.22 18.04 4 0 0 -1.178
4-7 477 981 seed maturation protein PM34 [Glycine max]  9622153 2.04E-08 31.8 6.7 37.96 6.52 40.22 18.77 4 0 0 -0.286
4-7 538 1089 Seed maturation protein PM25 [Glycine max]  6648966 7.20E-11 25.7 4.8 31.61 4.57 70.33 49.41 7 0 0 -0.242
3-10 3 1980 Seed maturation protein PM39 [Glycine max]  5802248 3.76E-08 46.7 5.6 144.50 6.83 70.25 20.63 7 0 0 -0.793
3-10 271   Seed maturation protein PM30 [Glycine max]  4838147 7.42E-06 15.1 9.4 19.53 9.40 30.29 28.57 3 0 0 -1.456
03.99 Other                              
04 Transcription                              
04.01 rRNA synthesis                              
04.10 tRNA synthesis                              
04.19 mRNA synthesis                              
4-7 282 608 Helicase, C-terminal [Medicago truncatula]  92886790 1.72E-07 52.5 5.2 54.68 5.64 50.22 13.15 5 0 0 -0.238
4-7 293 648 Putative nuclear RNA binding protein [Oryza sativa] 53793416 2.76E-05 40.9 6.2 50.16 6.70 20.18 4.23 2 0 0 -1.175
4-7 309 696 Helicase, C-terminal [Medicago truncatula] 92873011 2.61E-08 46.7 5.5 50.00 5.53 38.22 12.83 4 0 0 -0.173
04.19.01  General TFs                              
04.19.04  Specific TFs                              
04.19.07  Chromatin modification                              
04.22 mRNA processing                              
04.31  RNA transport                              
04.99  Others                              
4-7 621   HMG-Y related protein variant A [Glycine max] 18647 1.92E-06 18.8 10.9 22.90 5.84 30.17 27.27 3 0 0 -1.039
05 Protein synthesis                              
05.01 Ribosomal proteins                              
4-7 445 932 60S acidic ribosomal protein P0 [Glycine max] 1710587 7.20E-09 34.2 5 40.91 5.23 30.26 17.81 3 0 0 -0.003
3-10 109 2390 Ribosomal protein L3 [Medicago truncatula] 92881046 1.53E-06 44.3 10.6 46.90 7.32 40.14 12.85 4 0 0 -0.665
3-10 189   Ribosomal protein S6 [Glycine max]  44662864 2.94E-06 28.1 11.2 31.59 7.31 18.16 12.55 2 0 0 -0.77
3-10 198 2624 Ribosomal protein S6e [Medicago truncatula] 92886960 2.49E-06 28.2 11.2 30.83 8.70 18.23 14.52 2 0 0 -0.842
05.04 Translation factors                              
4-7 39 174 Elongation factor 2 [Medicago sativa]  71535003 1.05E-03 19.6 5 113.63 6.26 20.17 7.39 2 0 0 -0.384
4-7 283 616 Elongation factor 1, gamma chain [Medicago truncatula] 92893885 6.27E-07 47.7 6.5 54.68 6.03 20.27 7.42 2 0 0 -0.375
4-7 336 743 ATP binding / GTP binding / translation elongation factor [Arabidopsis thaliana] 15237059 5.37E-10 51.6 5.8 46.98 5.08 20.25 5.88 2 0 0 -0.12
4-7 347 759 GTP binding / translation elongation factor [Arabidopsis thaliana] 15236220 5.68E-07 49.4 6.3 51.83 5.11 40.24 10.13 4 0 0 -0.117
4-7 453 940 Eukaryotic initiation factor 3I1 subunit [Arabidopsis thaliana]  12407664 1.85E-03 36.5 7 40.09 6.62 20.11 6.40 2 0 0 -0.383
4-7 645 1246 Translation initiation factor eIF-5A [Oryza sativa] 77555893 1.30E-07 17.6 5.6 20.54 5.81 20.24 18.75 2 0 0 -0.497
3-10 196 2626 Translation protein SH3-like [Medicago truncatula] 87241572 5.31E-07 17.2 10.5 30.99 8.98 20.15 15.48 2 0 0 -0.257
05.07 Translation control                              
05.10 tRNA synthases                              
4-7 130 327 Glycyl tRNA synthetase, putative [Arabidopsis thaliana]  21592545 4.61E-07 77.2 6 89.78 6.59 50.23 8.55 5 0 0 -0.338
4-7 176 416 Aspartyl-tRNA synthetase, class IIb; tRNA synthetase, class II (D, K and N) [Medicago truncatula] 92897799 1.42E-08 60.6 6 73.77 5.90 20.19 4.25 2 0 0 -0.205
3-10 27 2163 Threonyl-tRNA synthetase [Arabidopsis thaliana] 15081626 4.95E-06 77.3 6.1 66.82 6.93 40.21 6.07 4 0 0 -0.44
3-10 57 2245 tRNA synthetase, class II (G, H, P and S) [Medicago truncatula]  92873428 3.56E-05 56.4 6.1 56.60 6.78 30.19 5.94 3 0 0 -0.497
05.99 Others                              
4-7 494 1024 Nascent polypeptide-associated complex (NAC); UBA-like [Medicago truncatula] 92878642 4.31E-07 24.7 4.1 35.11 3.99 50.28 25.99 5 0 0 -0.793
4-7 563 1124 Nascent polypeptide-associated complex (NAC); UBA-like [Medicago truncatula] 87241023 1.56E-06 22.1 4.2 29.48 4.15 20.22 13.30 2 0 0 -0.749
3-10 250 2806 Nascent polypeptide-associated complex (NAC) [Medicago truncatula]  92886523 1.40E-10 16.5 5.7 21.34 6.90 30.32 15.13 3 0 0 -0.577
06 Protein destination and storage                              
06.01 Folding and stability                              
4-7 154 363 DnaK-type molecular chaperone hsp70 [Oryza sativa] 77552704 3.94E-08 59.9 4.9 81.14 5.08 90.24 18.20 9 0 0 -0.428
4-7 194 453 JT0901 chaperonin 60 beta precursor [Arabidopsis thaliana] 81601 3.13E-11 63.8 6.2 67.23 5.31 100.23 19.83 10 0 0 -0.114
4-7 224 520 Putative  TCP-1/cpn60 chaperonin family protein [Oryza sativa] 50919217 2.43E-07 58.8 5.2 62.40 5.28 20.23 4.58 2 0 0 -0.041
4-7 91   Heat shock protein 90 [Arabidopsis thaliana]  15215642 7.91E-06 60.8 5 100.05 4.81 40.18 6.26 4 0 0 -0.582
4-7 146 368 Heat shock protein Hsp70 [Medicago truncatula]  92895891 7.15E-11 72.4 5.8 81.96 5.31 90.27 17.33 9 0 0 -0.318
3-10 277   Heat shock protein Hsp20 [Medicago truncatula]  87240494 5.14E-06 18.2 5.7 18.70 6.94 20.23 16.98 2 0 0 -0.676
4-7 220 511 Rubisco subunit binding-protein alpha subunit, chloroplast precursor [Oryza sativa] 77554291 1.00E-06 61.1 5 62.78 4.7 20.24 5.02 2 0 0 -0.032
4-7 659 1269 Peptidyl-prolyl cis-trans isomerase [Arabidopsis thaliana] 15239019 2.06E-09 17.7 5.1 19.14 6.58 20.22 9.20 2 0 0 -0.358
3-10 267 2832 Cyclophilin; peptidyl-prolyl cis-trans isomerase [Glycine max]  17981611 2.34E-05 18.2 8.6 19.72 8.86 30.20 20.35 3 0 0 -0.241
4-7 200   Protein disulfide isomerase [Medicago sativa] 19654 4.89E-07 57.1 4.8 65.62 4.58 20.19 4.69 2 0 0 -0.357
4-7 196 466 Protein kinase; GroEL-like chaperone, ATPase [Medicago truncatula]  92891163 5.69E-07 56.9 5.3 66.00 5.71 110.27 23.15 11 0 0 -0.033
4-7 207 472 Chaperonin, t-complex protein alpha subunit [Arabidopsis thaliana]  9293959 9.08E-08 59.9 6.4 64.67 6.34 82.22 17.09 9 0 0 -0.091
4-7 211 473 Putative t-complex protein 1 theta chain [Oryza sativa] 52076692 7.96E-07 60.3 6.1 64.29 6.46 50.22 7.50 5 0 0 -0.105
4-7 221 505 Similar to chaperonin [Arabidopsis thaliana] 15229866 1.35E-06 59.8 6 62.78 6.49 18.21 3.77 2 0 0 -0.094
06.04 Targeting                              
06.07 Modification                              
06.10 Complex assembly                              
06.13 Proteolysis                              
4-7 51   Clp amino terminal domain, putative [Oryza sativa] 77553513 8.93E-05 156.2 6.7 111.59 5.50 20.18 1.42 2 0 0 -0.402
4-7 183 413 Putative subtilisin precursor [Glycine max] 7543936 8.78E-13 82.7 6.9 70.09 6.59 100.36 20.13 10 1 12 -0.084
4-7 111 298 Peptidase M, neutral zinc metallopeptidases, zinc-binding site [Medicago truncatula] 92876896 2.04E-08 88.9 5.7 94.83 5.42 98.29 12.56 10 0 0 -0.35
4-7 242 555 Peptidase M17, leucyl aminopeptidase, N-terminal [Medicago truncatula] 92895784 8.24E-08 59.6 7.7 59.55 5.68 30.18 6.53 3 1 7 0.07
4-7 268 586 Ubiquitin interacting motif, Von Willebrand factor, type A [Medicago truncatula] 92894545 7.32E-10 42.0 4.5 56.33 4.24 20.28 6.53 2 0 0 -0.357
4-7 667 1350 Ubiquitin-like protein [Oryza sativa] 1668773 2.75E-06 10.9 4.8 18.36 4.84 20.14 12.00 2 0 0 -0.681
4-7 233 522 26S proteasome AAA ATPase subunit P45 [Medicago truncatula]  87241031 2.12E-08 49.5 5.8 61.26 6.14 130.30 37.30 13 0 0 -0.439
4-7 288 634 26S proteasome AAA ATPase subunit P45 [Medicago truncatula] 92867387 1.57E-08 46.4 5.3 53.81 5.47 80.22 28.19 8 0 0 -0.374
3-10 120 2411 26S proteasome AAA ATPase subunit P45 [Medicago truncatula] 92870338 2.32E-08 45.1 8.9 45.35 8.61 98.29 28.36 10 0 0 -0.347
4-7 296   26S proteasome AAA-ATPase subunit RPT1a [Arabidopsis thaliana]  6652878 1.45E-09 47.8 6.3 47.22 5.22 118.31 34.27 12 0 0 -0.398
4-7 322 710 26S protease regulatory subunit 6A homolog (TAT-binding protein homolog 1) (TBP-1) [Brassica rapa] 3024434 2.81E-05 47.5 4.8 52.70 4.55 40.22 12.50 4 0 0 -0.43
4-7 422 1341 26S proteasome regulatory particle non-ATPase subunit8 [Oryza sativa] 17297979 1.69E-09 34.9 6.3 43.53 6.09 30.26 12.58 3 1 8 -0.129
4-7 555 1115 26S proteasome regulatory particle non-ATPase subunit12 [Oryza sativa] 50936535 3.07E-08 30.8 4.8 29.83 4.81 30.28 14.98 3 0 0 -0.243
3-10 178 2583 Similar to 26S proteasome [Oryza sativa] 34903124 2.70E-08 34.3 6.1 33.25 6.71 20.26 11.40 2 0 0 -0.211
4-7 314 689 Proteasome component region PCI [Medicago truncatula]  92896846 2.07E-07 30.5 5.3 52.86 5.88 30.25 14.91 3 0 0 0.029
3-10 200 2647 Proteasome subunit alpha type 7 (20S proteasome alpha subunit D) [Oryza sativa] 12644044 2.86E-10 27.1 8.1 30.35 7.49 20.28 13.31 2 0 0 -0.371
3-10 205 2661 Proteasome subunit alpha type 7 (ec 3.4.25.1) (20s proteasome alphasubunit d) (20s proteasome subunit alpha-4) [Medicago truncatula] 92886169 2.11E-10 27.1 7.3 29.59 7.30 58.29 24.90 6 0 0 -0.265
4-7 589 1162 Proteasome subunit alpha type 5 [Oryza sativa] 77551900 1.36E-09 20.5 5.1 25.94 4.42 30.29 25.54 3 1 7 -0.143
4-7 604 1184 Proteasome subunit PRGB); peptidase/ threonine endopeptidase [Arabidopsis thaliana] 15228805 2.17E-08 22.5 5.9 23.88 5.98 20.18 12.75 2 0 0 -0.034
3-10 225 2723 Peptidase T1A, proteasome beta-subunit [Medicago truncatula]  92868982 3.57E-07 29.1 6.1 23.34 7.50 40.24 12.18 4 0 0 -0.15
3-10 228 2726 Peptidase T1A, proteasome beta-subunit [Medicago truncatula]  92888792 1.19E-09 26.1 8.9 23.09 8.35 48.26 15.15 5 0 0 -0.358
4-7 505 1029 34 kDa maturing seed vacuolar thiol protease precursor [Glycine max] 1199563 9.87E-09 42.8 5.6 34.34 4.61 20.34 11.87 2 0 0 -0.555
4-7 349 753 Peptidase aspartic, catalytic; UBA-like [Medicago truncatula]  92874926 1.93E-07 45.0 4.8 49.52 5.10 40.23 12.86 4 0 0 -0.27
4-7 609 1190 Endopeptidase/ peptidase/ threonine endopeptidase [Arabidopsis thaliana] 79325892 5.00E-06 25.3 5.2 23.70 5.29 20.17 11.54 2 0 0 -0.141
06.20 Storage proteins                              
4-7 443 921 Glycinin [Glycine microphylla]  90186615 1.21E-12 63.1 5.6 41.32 5.61 30.36 6.62 3 1 12 -0.899
4-7 402 847 Glycinin [Glycine max]  4249566 4.11E-06 58.2 5.4 44.92 6.30 20.27 7.93 2 1 13 -0.815
4-7 76 244 Beta-conglycinin alpha prime subunit [Glycine max] 74271741 1.93E-06 72.2 5.4 52.85 7.08 56.21 13.00 6 2 13 -1.075
4-7 122 342 Beta-conglycinin alpha subunit [Glycine max]  68264915 1.93E-08 70.1 4.9 91.94 5.18 140.30 25.00 14 1 6 -0.983
4-7 286 638 Beta- Conglycinin Beta Homotrimers [Glycine max] 21465633 2.49E-11 48.0 5.6 54.13 5.86 106.30 34.13 11 1 7 -0.648
3-10 98 2332 Glycinin G1 subunit [soybeans, Peptide, 495 aa] [Glycine max] 255221 1.67E-09 55.7 5.8 49.05 8.61 20.18 5.05 2 0 0 -0.7
3-10 159   Glycinin G2 precursor [Glycine max] 18609 6.79E-09 54.3 5.5 34.60 6.89 38.29 13.40 4 0 0 -0.648
4-7 433 913 Glycinin [Glycine max]  6015515 2.51E-07 24.2 4.3 42.06 5.78 30.28 31.40 3 0 0 -1.988
3-10 2   Glycinin A5A4B3 [Glycine max] 56201482 4.06E-05 63.8 5 154.59 9.14 20.35 7.46 2 1 10 -0.952
4-7 500 1343 A Chain A, Crystal Structure Of The Soybean Agglutinin In A Complex With A Biantennary Blood Group Antigen Analog [Glycine max] 14719778 4.23E-06 27.6 5 34.64 5.53 60.22 24.51 6 0 0 -0.107
4-7 655 1261 Napin-type 2S albumin 3 [Glycine max] 4097896 3.21E-09 18.5 5.1 19.58 5.25 38.30 31.65 4 0 0 -0.956
3-10 126   Basic 7S globulin [Glycine max] 434061 2.12E-10 46.4 8.2 43.57 9.17 20.21 6.09 2 0 0 -0.03
3-10 284   Basic 7S globulin 2 precursor [Contains: Basic 7S globulin 2 high kDa subunit; Basic 7S globulin] [Glycine max] 51316037 1.35E-07 47.2 8.1 17.87 8.00 50.34 18.94 5 0 0 -0.078
06.21 Allergens                              
4-7 208 482 Allergen Gly m Bd 28K [Glycine max]  12697782 4.08E-10 52.6 5.7 64.48 5.82 50.24 14.80 5 0 0 -0.265
06.99 Other
07 Transporters                              
07.01 Ions                              
4-7 565 1126 Ferritin-2, chloroplast precursor (SFerH-2) [Glycine max] 29839388 3.09E-06 28.7 5.7 29.06 5.50 40.16 14.40 4 0 0 -0.271
07.07 Sugars                          
4-7 149 405 Sucrose binding protein homolog S-64 [Glycine max] 6179947 1.57E-06 55.8 6.3 81.96 5.87 20.22 3.68 2 1 12 -0.553
07.10 Amino Acids                              
07.13 Lipids                              
07.16 Purine/pyrimides                              
07.22 Transport ATPases                              
4-7 258 573 Similar to vacuolar ATP synthase subunit B isoform [Arabidopsis thaliana] 6721109 2.42E-10 58.2 4.9 57.85 4.87 130.35 28.46 13 1 9 -0.185
4-7 486 993 Similar to vacuolar proton ATPase subunit E [Zea mays]  5565981 4.81E-06 15.2 6.4 36.66 6.27 20.21 10.16 2 0 0 -0.823
4-7 167 404 VHA-A; ATP binding / hydrogen-transporting ATP synthase, rotational mechanism / hydrogen-transporting ATPase, rotational mechanism [Arabidopsis thaliana] 79321468 1.41E-08 68.8 5 77.46 5.66 50.27 13.00 5 0 0 -0.172
3-10 68 2287 Hydrogen-transporting ATP synthase [Glycine max] 22739 1.89E-06 55.3 6.2 53.88 6.85 20.15 5.31 2 0 0 -0.037
07.25 ABC-type                              
07.99 Others                              
08 Intracellular traffic                              
08.01 Nuclear                              
08.02 Chloroplast                              
3-10 43 2195 Dynamin central region; Dynamin; Dynamin GTPase effector [Medicago truncatula] 92891191 6.47E-09 69.1 8 61.07 8.05 88.22 17.37 9 0 0 -0.394
3-10 50   Putative dynamin [Oryza sativa] 50932725 2.26E-08 60.7 7 59.35 8.30 30.24 9.44 3 0 0 -0.32
08.04 Mitochondrial                              
08.07 Vesicular                              
08.10 Perixosomal                              
08.13 Vacuolar                              
08.16 Extracellular                              
08.19 Import                              
08.99 Others                              
4-7 619 1200 ADP-ribosylation factor family [Oryza sativa] 77556132 3.50E-05 22.0 7.4 23.18 6.68 18.17 12.44 2 0 0 -0.163
3-10 173 2574 Annexin, putative [Medicago truncatula]  92891289 8.55E-08 38.4 9 33.95 8.15 30.22 7.16 3 0 0 -0.513
3-10 177 2585 Annexin, putative [Medicago truncatula]  92891291 2.00E-05 35.5 9 33.63 7.29 30.18 7.40 3 0 0 -0.551
09 Cell structure                              
09.01 Cell wall                              
4-7 329 717 AXS2 (UDP-D-APIOSE/UDP-D-XYLOSE SYNTHASE 2) [Arabidopsis thaliana] 18390863 1.02E-08 43.8 5.5 53.57 5.52 20.22 8.74 2 0 0 -0.268
09.04 Cytoskeleton                              
4-7 252 550 Tubulin B4 [Glycine max]  62546343 4.97E-07 50.4 4.6 58.41 6.06 70.24 18.04 7 1 6 -0.364
3-10 83 2325 Tubulin A [Glycine max]  62546341 1.95E-08 49.7 4.9 52.24 6.73 20.20 5.56 2 0 0 -0.14
4-7 346 754 Actin 3, putative [Oryza sativa]  77553072 1.30E-11 28.5 5.2 52.46 5.83 36.38 23.85 4 0 0 0.024
4-7 354 773 Actin [Oryza sativa]  77556832 1.38E-04 41.7 5.4 52.38 5.30 16.17 7.43 2 1 9 -0.131
09.07 ER/Golgi                              
4-7 120 311 Luminal binding protein [Arabidopsis thaliana]  1695717 1.05E-07 73.6 4.9 92.31 5.75 48.25 7.92 5 1 15 -0.459
09.10 Nucleus                              
09.13 Chromosomes                              
09.16 Mitochondria                              
09.19 Perixosome                              
09.25 Vacuole                              
09.26 Chloroplast                              
09.99 Others                              
10 Signal transduction                              
10.01 Receptors                              
10.04 Mediators                              
3-10 207 2687 Ras small GTPase, Rab type [Medicago truncatula] 92869041 1.11E-07 25.3 6.4 27.07 6.93 58.30 31.22 6 0 0 -0.496
4-7 587 1158 Ras-like GTP-binding protein [Arabidopsis thaliana]  91806311 1.50E-05 24.3 5.2 26.04 5.46 20.18 10.09 2 0 0 -0.347
4-7 644 1245 GTP-binding ADP-ribosylation factor Arf1 [Aspergillus oryzae]  83773942 5.39E-09 21.0 5.4 20.62 6.56 46.25 39.34 5 0 0 -0.262
3-10 112 2404 Putative GTP-binding protein [Oryza sativa] 50942045 7.92E-08 44.3 6.3 46.81 7.12 20.26 6.35 2 1 6 -0.32
3-10 241   Putative GTP-binding protein yptm3 [Oryza sativa] 50909885 1.36E-04 23.0 7.2 22.17 7.33 18.14 10.00 2 0 0 -0.203
4-7 501 1036 14-3-3-like protein D (SGF14D) [Glycine max] 3023197 1.96E-08 29.5 4.6 34.58 4.51 48.28 34.87 5 0 0 -0.57
4-7 525 1067 14-3-3 protein [Medicago truncatula] 92869249 1.22E-11 29.4 4.7 32.92 4.58 30.27 11.58 3 0 0 -0.556
4-7 536 1087 GF14 chi chain [Arabidopsis thaliana] 1256534 1.17E-10 29.9 4.5 31.73 4.44 20.30 10.86 2 0 0 -0.431
4-7 540 1094 14-3-3-like protein A (SGF14A) [Glycine max] 3023194 4.87E-06 29.0 4.5 31.25 4.35 20.17 8.95 2 0 0 -0.432
4-7 548 1111 14-3-3-like protein B (SGF14B) [Glycine max] 3023195 1.71E-06 27.9 4.6 30.13 4.59 40.17 11.34 4 0 0 -0.375
10.04.04 Kinases                              
10.04.07 Phosphatases                              
10.04.10 G proteins                              
3-10 179 2580 G beta-like protein [Glycine max] 1256608 5.31E-12 35.6 7.6 33.04 7.86 20.24 8.62 2 0 0 -0.153
3-10 184   G protein beta subunit-like [Medicago sativa] 2385376 1.39E-05 35.7 7.2 32.29 7.92 18.35 11.08 2 0 0 -0.153
10.99 Others                              
11 Disease/defense                              
11.01 Resistance genes                              
11.02 Defense-related                              
3-10 270 2834 Major latex protein homolog [Glycine max]  6318194 1.32E-07 17.7 6.3 19.53 6.76 30.18 22.88 3 0 0 -0.603
11.03 Cell death                              
11.04 Cell rescue                              
11.05 Stress responses                              
4-7 171 367 Stress inducible protein [Glycine max] 872116 1.06E-07 63.6 5.8 77.05 6.41 30.24 6.33 3 0 0 -0.963
4-7 550 1105 Dehydrin [Glycine max]  37495451 2.22E-14 23.8 6 30.13 6.46 40.34 30.09 4 0 0 -1.346
4-7 670 1294 Glycine-rich RNA-binding protein [Glycine max]  5726567 6.95E-10 15.8 7.1 18.04 6.50 70.26 49.38 7 0 0 -0.803
3-10 229 2747 Cysteine proteinase inhibitor [Glycine max] 1944319 4.46E-10 27.6 7.7 23.06 7.06 20.29 15.92 2 0 0 -0.563
4-7 624 1219 Kunitz trypsin inhibitor [Glycine max]  15216344 7.45E-09 24.0 4.8 22.10 4.77 20.24 7.37 2 2 12 -0.159
4-7 642 1241 Kunitz trypsin inhibitor KTi1 [Glycine max] 256635 2.37E-05 22.5 4.8 20.76 4.51 40.23 32.02 4 1 12 0.039
11.06 Detoxification