List of protein families currently covered by SVMProt, statistics of datasets and prediction results.
(May/11/2003)(Sep/25/2003) (Mar/31/2004) (Dec/18/2004) (Apr/05/2005)

Predicted results are given in TP (true positive), FN (false negative), TN (true negative), FP (false positive), Sensitivity(TP/(TP+FN)), and Specificity(TN/(TN+FP)). Number of positive or negative samples in testing and independent evaluation sets is TP+FN or TN+FP respectively.

Protein family

 Training set Testing set Independent evaluation set
positive negative positive negative positive negative
TP FN TN FP TP FN Sensitivity TN FP Specificity
EC1.1 Oxidoreductases acting on the CH-OH group of donors
 1164 2324 1795 10 7594 14 494 105 82.5% 4760 192 96.1%
EC1.2 Oxidoreductases acting on the aldehyde or oxo group of donors
 665 1920 705 14 8051 25 259 69 79.0% 4908 77 98.5%
EC1.3 Oxidoreductases acting on the CH-CH group of donors
 491 1917 131 3 8090 17 73 37 66.4% 4941 57 98.9%
EC1.4 Oxidoreductases acting on the CH-NH2 group of donors
 307 1869 92 2 8179 8 50 26 65.8% 4990 26 99.5%
EC1.5 Oxidoreductases acting on the CH-NH group of donors
 276 1755 56 3 8278 5 41 29 58.6% 4985 21 99.6%
EC1.6 Oxidoreductases acting on NADH or NADPH
 1333 2132 2189 21 7857 19 1118 65 94.5% 4901 88 98.2%
EC1.7 Oxidoreductases acting on other nitrogenous compounds as donors
 170 1356 86 0 8703 2 29 15 65.9% 5005 13 99.7%
EC1.8 Oxidoreductases acting on a sulfur group of donors
 299 1531 114 2 8500 13 40 28 58.8% 4989 20 99.6%
EC1.9 Oxidoreductases acting on a heme group of donors
 561 807 9493 22 9246 24 4805 36 99.3% 4978 48 99.0%
EC1.10 Oxidoreductases acting on diphenols and related substances as donors
 219 1348 88 0 8728 4 65 20 76.5% 4996 30 99.4%
EC1.11 Oxidoreductases acting on a peroxide as acceptor
 344 1416 343 2 8664 5 146 22 86.9% 5009 22 99.6%
EC1.13 Oxidoreductases acting on single donors with incorporation of molecular oxygen (oxygenases)
 152 1232 90 7 8832 4 29 23 55.8% 5009 13 99.7%
EC1.14 Oxidoreductases acting on paired donors with incorporation reduction of molecular oxygen
 566 1896 786 0 8120 8 93 38 71.0% 4941 57 98.9%
EC1.15 Oxidoreductases acting on superoxide as acceptor
 259 881 416 2 9214 7 222 18 92.5% 5019 20 99.6%
EC1.17 Oxidoreductases acting on CH2 groups
 100 1308 109 4 8779 8 43 12 78.2% 5026 9 99.8%
EC1.18 Oxidoreductases acting on iron-sulfur proteins as donors
 244 1229 232 1 8842 8 78 7 91.8% 5005 22 99.6%
EC2.1 Transferases transferring one-carbon groups
 1509 2991 800 0 6903 2 190 89 68.1% 4194 740 85.0%
EC2.2 Transferases transferring aldehyde or ketone residues
 35 1197 30 2 1121 0 26 5 83.9% 1005 3 99.7%
EC2.3 Acyltransferases
302 1001 246 0 1284 4 196 44 81.7% 966 27 97.3%
EC2.4 Glycosyltransferases
 945 1896 1211 25 7940 41 203 85 70.5% 4640 286 94.2%
EC2.5 Transferases transferring alkyl or aryl groups, other than methyl groups
 764 2174 519 24 7832 33 137 58 70.3% 4915 93 98.1%
EC2.6 Transferases transferring nitrogenous groups
 343 1684 301 5 8395 6 75 32 70.1% 4982 49 99.0%
EC2.7 Transferases transferring phosphorus-containing groups
 3892 5324 3761 4 6140 6 2463 553 81.7% 5082 625 89.0%
EC2.8 Transferases transferring sulfur-containing groups
 203 1549 43 0 8531 7 20 10 66.7% 5021 11 99.8%
EC3.1 Hydrolases acting on ester bonds
 2482 3859 1504 53 5677 100 379 154 71.1% 4355 452 90.6%
EC3.2 Glycosylases
337 867 379 2 1397 13 268 49 84.5% 939 51 94.8%
EC3.3 Hydrolases acting on ether bonds
 97 1999 44 22 8053 49 32 22 59.3% 5007 32 99.4%
EC3.4 Hydrolases acting on peptide bonds (Peptidases)
 2011 3402 1522 35 6207 29 264 90 74.6% 4528 279 94.2%
EC3.5 Hydrolases acting on carbon-nitrogen bonds, other than peptide bonds
 1020 2498 440 2 7447 3 130 85 60.5% 4849 110 97.8%
EC3.6 Hydrolases acting on acid anhydrides
 2195 2504 1449 1 7435 4 687 63 91.6% 4742 220 95.6%
EC4.1 Carbon-carbon lyases
546 1145 776 5 1113 17 547 62 89.8% 881 105 89.4%
EC4.2 Carbon-oxygen lyases
505 1231 382 1 1047 2 324 79 80.4% 915 77 92.2%
EC4.3 Carbon-nitrogen lyases
218 1068 194 2 9009 8 29 10 74.4% 4994 37 99.3%
EC4.4 Carbon-sulfur lyases
182 1999 53 23 8072 14 35 23 60.3% 5024 7 99.9%
EC4.6 Phosphorus-oxygen lyases
200 1789 63 14 8250 7 55 27 67.1% 4112 899 82.1%
EC5.1 Racemases and Epimerases
379 1796 91 4 8249 19 35 31 53.0% 4990 30 99.4%
EC5.2 Cis-trans-Isomerases
35 1404 113 2 8671 11 72 36 66.7% 5008 24 99.5%
EC5.3 Intramolecular oxidoreductases
461 1122 92 3 1062 0 135 43 75.8% 4910 99 98.0%
EC5.4 Intramolecular transferases
329 1714 143 4 8337 16 42 35 54.5% 4991 31 99.4%
EC5.5 Intramolecular lyases
47 909 24 0 9196 0 75 32 70.1% 4982 49 99.0%
EC5.99 Other Isomerases
163 1038 393 8 9036 9 153 13 92.2% 5007 22 99.6%
EC6.1 Ligases forming carbon-oxygen bonds
 281 1115 381 1 1185 13 286 29 90.8% 980 27 97.3%
EC6.2 Ligases forming carbon-sulfur bonds
 149 1233 154 4 8858 4 51 13 79.7% 5203 13 99.8%
EC6.3 Ligases forming carbon-nitrogen bonds
 381 1133 358 2 1148 3 294 57 83.8% 946 45 95.5%
EC6.4 Ligases forming carbon-carbon bonds
 99 1543 45 0 8548 8 28 16 63.6% 5033 4 99.9%
EC6.5 Ligases forming phosphoric ester bonds
 94 1679 36 2 8408 3 22 9 71.0% 5027 6 99.9%
TC1.A alpha-type channels
 381
 1786
 272
 8
 10425
 7
 164
 25 86.8%
 6037
 44
 99.3%
TC1.B beta-barrel porins
 221 2008 58 0 12452 2 65 27 70.7% 7178 29 99.6%
TC1.C Pore-forming toxins (proteins and peptides)
 357 2007 33 14 12371 0 100 27 78.7% 6452 15 99.8%
TC1.E Holins
100 513 55 5 11837 14 55 15 78.6% 6151 4 99.9%
TC2.A porters (symporters, uniporters, antiporters)
 629 1175 781 4 10938 13 370 54 87.3% 5945 90 98.5%
TC2.C Ion-gradient-driven energizers
 166 1014 86 2 11325 10 91 28 76.5% 6140 13 99.8%
TC3.A P-P-bond-hydrolysis-driven transporters
 1220 2549 1301 20 9568 15 897 243 78.7% 5895 143 97.6%
TC3.D Oxidoreduction-driven transporters
 435 1529 981 1 12980 5 617 60 91.1% 7197 36 99.5%
TC3.E Light absorption-driven transporters
 139 954 696 5 13648 2 395 16 96.1% 7267 11 99.8%
TC4.A Phosphotransfer-driven group translocators
197 887 212 8 11429 5 153 32 82.7% 6120 21 99.7%
TC8.A Auxiliary transport proteins
 223 1388 169 5 10925 13 124 43 74.3% 6120 15 99.8%
TC9.A Recognized transporters of unknown biochemical mechanism
203 1034 188 1 11247 29 130 35 78.8% 6085 43 99.3%
TC9.B Putative uncharacterized transport proteins
869 2079 581 5 10153 5 469 116 80.2% 6002 98 98.4%
TC 1A.1 Voltage-gated ion channel (VIC) family
 50 7299 18 0 7280 0 15 7 68.2% 7188 48 99.3%
TC 2A.1 Major facilitator family (MFS)
 248 7260 53 1 7232 4 62 19 76.5% 7040 154 97.9%
TC 2A.3 Amino acid-polyamine-organocation (APC) family
 91 7284 32 0 7264 0 31 2 93.9% 7171 46 99.4%
TC 2A.6 Resistance-nodulation-cell division (RND) family
 65 7296 22 0 7281 0 23 9 71.9% 7191 43 99.4%
TC 3A.1 ATP-binding cassette (ABC) family
 641 2008 150 0 12554 0 351 22 94.1% 6644 613 91.6%
TC 3A.3 P-type ATPase (P-ATPase) family
 123 1999 44 0 12585 0 66 2 97.1% 6954 314 95.7%
TC 3A.5 Type II (general) secretory pathway (IISP) family
 254 1997 29 0 12587 0 110 18 85.9% 6653 615 91.5%
TC 3A.15 The Outer Membrane Protein Secreting Main Terminal Branch (MTB) family
 84 1997 9 0 12604 1 20 13 60.6% 7135 142 98.0%
G protein coupled receptors
 927 1320 4993 5 13212 4 2421 111 95.6% 7104 140 98.1%
7 transmembrane receptor (rhodopsin family & chemoreceptor )
 729 1061 4604 7 13535 3 2223 71 96.9% 7214 61 99.2%
7 transmembrane receptor (secretin family)
 218 2007 71 0 12580 1 117 12 90.7% 6900 370 94.9%
7 transmembrane receptor (metabotropic glutamate family)
 116 2001 40 0 12613 0 62 7 89.9% 6975 308 95.8%
7 transmembrane receptor (odorant receptor)
 130 1999 11 0 12631 0 38 1 97.4% 7113 178 97.6%
RNA-binding proteins
 2161 2965 1844 6 6802 14 437 10 97.8% 4685 196 96.0%
mRNA-binding proteins
 277 2106 129 0 10164 0 130 34 79.3% 5833 213 96.5%
rRNA-binding proteins
 708 972 1243 2 9031 13 95 6 94.1% 4931 66 98.7%
tRNA-binding proteins
 94 792 114 0 9295 2 48 3 94.1% 5028 5 99.9%
snRNA-binding proteins*
 33 1988 7 0 10373 1 9 11 45.0% 6133 18 99.7%
Structural proteins (Matrix protein,Core protein,Viral occlusion body,Keratin)
 858 1353 4977 4 8512 12 2615 41 98.5% 4884 40 99.2%
Transmembrane
 2105 2563 11135 1722 8237 1368 3054 335 90.1% 5254 809 86.7%
Outer membrane
 602 1539 547 0 8384 1 318 25 92.7% 4276 672 86.4%
Cell adhesion
 513 1678 322 1 8208 15 232 38 85.9% 4897 44 99.1%
Coat proteins
 346 1474 297 8 8344 26 167 30 84.8% 4885 29 99.4%
Envelope proteins
 177 1999 112 11 7904 28 135 15 90.0% 4927 25 99.5%
Nuclear receptors
 334 538 601 7 1755 6 221 26 89.5% 962 24 97.6%
Tyrosine kinase receptors
 14 1197 3 0 1121 0 5 2 71.4% 1006 2 99.8%
Growth factor
 329 1320 205 5 8695 4 142 21 87.1% 4970 28 99.4%
Antigen
 836 1867 1200 2 7786 8 720 29 96.1% 4747 74 98.5%
Chlorophyll
 189 603 945 3 14630 10 515 14 97.4% 6965 11 99.8%
Chlorophyll biosynthesis
 309 1742 109 0 13424 0 153 24 86.4% 6158 777 88.8%
Herbicide resistance
 227 1999 205 7 13196 2 199 10 95.2% 6948 10 99.9%
Photoreceptor
 354 1537 893 3 13611 11 548 42 92.9% 6896 26 99.6%
Photorespiration
 368 1672 8197 4 13504 76 4257 13 99.7% 6955 24 99.7%
Photosynthesis
 1054 1914 544 0 12950 47 613 44 93.3% 6664 132 98.1%
Photosystem I
 264 1491 392 70 13726 1 326 8 97.6% 5900 1061 84.8%
Photosystem II
 506 986 2018 4 14120 46 1192 31 97.5% 6890 36 99.5%
Plant defense
 559 1830 456 5 13302 14 289 37 88.7% 6857 60 99.1%
DNA condensation
 50 2360 31 20 12591 0 37 2 94.9% 6779 119 98.3%
DNA integration
 134 1173 148 2 13724 4 87 12 87.9% 6867 6 99.9%
DNA recombination
 889 2468 766 4 12129 15 600 83 87.8% 6646 72 98.9%
DNA repair
 2142 3643 1174 5 10590 56 1275 163 88.7% 6335 209 96.8%
DNA replication
 1131 2603 925 8 11550 302 737 124 85.6% 6413 223 96.6%
DNA-directed DNA polymerase
 273 2075 188 7 12742 20 140 52 72.9% 6814 23 99.7%
DNA-directed RNA polymerase
 484 2110 760 2 12717 11 504 51 90.8% 6799 41 99.4%
Repressor
 1337 2347 723 0 11218 430 529 38 93.3% 6113 280 95.6%
All DNA-binding
3569 4426 5630 155 7645 1040 3012 320 90.4% 5101 861 85.6%
Lipid degradation
403 1775 232 1 13629 6 187 50 78.9% 7696 5 99.9%
Lipid metabolism
293 1969 155 50 13276 124 128 33 79.5% 7632 64 99.2%
Lipid synthesis
891 2607 722 67 12615 55 578 125 82.2% 7605 30 99.6%
Lipid transport
153 2109 87 23 13436 26 62 16 79.5% 7712 15 99.8%
Lipid-binding
274 1530 165 1 13918 8 141 26 84.4% 7714 10 99.9%
Lipopolysaccharide biosynthesis
285 10837 134 9 4590 0 105 32 76.6% 7710 13 99.8%
Lipoprotein
1648 5065 1724 68 8634 199 1501 156 90.6% 5459 81 98.5%
Lipoyl
72 1987 58 12 13529 17 49 13 79.0% 7758 11 99.9%
All lipid-binding proteins
3232 3701 3966 51 7763 36 3205 361 89.9% 5086 160 97.0%
Calcium-binding
1816 4389 2055 245 8039 1906 1130 180 86.3% 6373 851 88.2%
Cobalt-binding
568 2151 456 2 13407 10 360 81 81.6% 7809 7 99.9%
Copper-binding
652 1999 417 109 13115 270 390 77 83.5% 7587 146 98.1%
Iron-binding
3128 3428 4869 290 3992 675 1104 71 94.0% 6328 598 91.4%
Magnesium-binding
2583 4023 2307 594 7267 115 3412 792 81.2% 5848 805 87.9%
Manganese-binding
1608 3099 1146 217 10841 1086 1061 182 85.4% 7148 415 94.5%
Nickel-binding
407 2001 95 2 13576 138 156 45 77.6% 7816 65 99.2%
Potassium-binding
408 1845 489 10 13789 8 301 32 90.4% 7847 4 99.9%
Sodium-binding
777 2010 338 1 13591 30 410 41 90.9% 7831 11 99.9%
Zinc-binding
2731 6416 6610 569 5931 360 4616 1546 74.9% 6289 127 98.0%
Metal-binding
5013 3101 11806 1015 4217 522 12070 3391 78.1% 4529 617 88.0%
Antioxidant
145 3450 81 4 12429 5 83 10 89.2% 7937 23 99.7%
Hormone
584 3371 309 2 12389 1 285 25 91.9% 7840 64 99.2%
Immune response
447 2998 268 1 12561 2 132 20 86.8% 7815 4 99.9%
Inflammatory response
134 3320 83 15 12425 7 56 8 87.5% 7882 20 99.7%
Innate immunity
193 3382 69 16 12276 9 52 6 89.7% 7860 8 99.9%
Motor protein
212 1656 198 8 13630 425 85 8 91.4% 7666 217 97.2%
Virulence
 544 2983 268 2 12278 17 165 8 95.4% 7665 6 99.9%
Actin binding
584 3312 282 0 13327 2 169 9 94.9% 6180 34 99.5%
Actin capping
81 0 28 4 12597 7 17 3 85.0% 7379 2 99.9%
mRNA capping
60 1085 101 0 14816 1 42 10 80.8% 7312 11 99.8%
mRNA slicing
621 2570 288 1 13044 2 170 50 77.3% 7111 50 99.3%
Last update: 17 January 2008

*temporary results,still under development.