Table 1.
Number of ORFs and those with modeled 3D structures in 276 genomes
| Species | ORF | Model | % |
|---|---|---|---|
| Archaea | |||
| Archaeoglobus fulgidus DSM4304 | 2,407 | 1,233 | 51.2 |
| Aeropyrum pernix K1 | 2,694 | 789 | 29.3 |
| Halobacterium sp. NRC-1 | 2,605 | 1,195 | 45.9 |
| Methanosarcina acetivorans C2A | 4,544 | 2,124 | 46.7 |
| Methanocaldococcus jannaschii DSM2661 | 1,770 | 875 | 49.4 |
| Methanopyrus kandleri AV19 | 1,687 | 784 | 46.5 |
| Methanosarcina mazei Goe1 | 3,371 | 1,634 | 48.5 |
| Methanothermobacter thermautotrophicus | 1,869 | 998 | 53.4 |
| Nanoarchaeum equitans Kin4-M | 536 | 264 | 49.3 |
| Pyrococcus abyssi Orsay | 1,784 | 942 | 52.8 |
| Pyrobaculum aerophilum IM2 | 2,605 | 1,047 | 40.2 |
| Pyrococcus furiosus DSM 3638 | 2,065 | 1,035 | 50.1 |
| Pyrococcus horikoshii OT3 | 2,061 | 879 | 42.6 |
| Sulfolobus solfataricus P2 | 2,994 | 1,365 | 45.6 |
| Sulfolobus tokodaii 7 | 2,826 | 1,228 | 43.5 |
| Thermoplasma acidophilum DSM1728 | 1,478 | 844 | 57.1 |
| Thermoplasma volcaniumGSS1 | 1,526 | 839 | 55.0 |
| sum | 38,822 | 18,075 | 46.6 |
| Eubacteria | |||
| Aquifex aeolicus VF5 | 1,553 | 929 | 59.8 |
| Nostoc sp. PCC 7120 | 6,132 | 2,765 | 45.1 |
| Agrobacterium tumefaciens C58 | 5,301 | 3,017 | 56.9 |
| A. tumefaciens C58 (Dupont) | 5,402 | 3,028 | 56.1 |
| Bacillus anthracis str. Ames | 5,311 | 2,463 | 46.4 |
| Buchnera aphidicola Sg | 552 | 410 | 74.3 |
| B. aphidicola | 507 | 385 | 75.9 |
| Bordetella bronchiseptica RB50 | 4,994 | 2,934 | 58.8 |
| Borrelia burgdorferi | 1,639 | 535 | 32.6 |
| Bacillus cereus ATCC 14579 | 5,255 | 2,534 | 48.2 |
| Candidatus Blochmannia floridanus | 583 | 447 | 76.7 |
| Bacillus halodurans C-125 | 4,066 | 2,127 | 52.3 |
| Bradyrhizobium japonicum | 8,317 | 4,449 | 53.5 |
| Bifidobacterium longum NCC2705 | 1,731 | 985 | 56.9 |
| Brucella melitensis 16M | 3,198 | 1,801 | 56.3 |
| Bordetella parapertussis | 4,185 | 2,525 | 60.3 |
| B. pertussis Tohama I | 3,447 | 2,179 | 63.2 |
| Bacillus subtilis 168 | 4,106 | 2,153 | 52.4 |
| Brucella suis 1330 | 3,264 | 1,677 | 51.4 |
| Bacteroides thetaiotaomicron VPI-5482 | 4,816 | 2,462 | 51.1 |
| Buchnera sp. APS | 574 | 436 | 76.0 |
| Clostridium acetobutylicum ATCC824 | 3,848 | 2,053 | 53.4 |
| Coxiella burnetii RSA 493 | 2,045 | 925 | 45.2 |
| Chlamydophila caviae GPIC | 1,005 | 505 | 50.2 |
| Caulobacter crescentus | 3,737 | 2,084 | 55.8 |
| Corynebacterium diphtheriae NCTC13129 | 2,272 | 1,165 | 51.3 |
| Corynebacterium efficiens YS-314 | 2,998 | 1,513 | 50.5 |
| Corynebacterium glutamicum ATCC 13032 | 3,099 | 1,554 | 50.1 |
| Campylobacter jejuni | 1,634 | 893 | 54.7 |
| Chlamydia muridarum Nigg | 911 | 483 | 53.0 |
| Clostridium perfringens 13 | 2,723 | 1,470 | 54.0 |
| Chlamydophila pneumoniae AR39 | 1,116 | 495 | 44.4 |
| Chlamydophila pneumoniae CWL029 | 1,052 | 496 | 47.1 |
| Chlamydophila pneumoniae J138 | 1,069 | 501 | 46.9 |
| Chlamydophila pneumoniae TW-183 | 1,113 | 501 | 45.0 |
| Chlorobium tepidum TLS | 2,252 | 1,166 | 51.8 |
| Clostridium tetani E88 | 2,432 | 1,306 | 53.7 |
| Chlamydia trachomatis D/UW-3/CX | 894 | 485 | 54.3 |
| Chromobacterium violaceum ATCC 12472 | 4,385 | 2,343 | 53.4 |
| Deinococcus radiodurans R1 | 3,102 | 1,579 | 50.9 |
| Escherichia coli K-12 MG1655 | 4,284 | 2,398 | 56.0 |
| E. coli O157:H7 | 5,447 | 2,607 | 47.9 |
| E. coli O157:H7 EDL933 | 5,449 | 2,629 | 48.2 |
| E. coli CFT073 | 5,379 | 2,558 | 47.6 |
| Enterococcus faecalis V583 | 3,265 | 1,568 | 48.0 |
| Fusobacterium nucleatum ATCC 25586 | 2,067 | 1,011 | 48.9 |
| Geobacter sulfurreducens PCA | 3,445 | 1,902 | 55.2 |
| Gloeobacter violaceus PCC 7421 | 4,430 | 2,208 | 49.8 |
| Haemophilus ducreyi 35000HP | 1,717 | 865 | 50.4 |
| Helicobacter hepaticus ATCC 51449 | 1,875 | 902 | 48.1 |
| Haemophilus influenzae Rd | 1,709 | 1,038 | 60.7 |
| Helicobacter pylori 26695 | 1,566 | 741 | 47.3 |
| Helicobacter pylori J99 | 1,491 | 747 | 50.1 |
| Listeria innocua Clip11262 | 3,043 | 1,641 | 53.9 |
| Leptospira interrogans serovar | 4,725 | 1,719 | 36.4 |
| Lactococcus lactis IL1403 | 2,266 | 1,254 | 55.3 |
| Listeria monocytogenes EGD-e | 2,846 | 1,653 | 58.1 |
| Lactobacillus plantarum WCFS1 | 3,009 | 1,647 | 54.7 |
| Mycobacterium bovis subsp. | 3,920 | 2,018 | 51.5 |
| Mycoplasma gallisepticum R | 726 | 371 | 51.1 |
| Mycoplasma genitalium G37 | 480 | 305 | 63.5 |
| Mycobacterium leprae TN | 1,605 | 918 | 57.2 |
| Mesorhizobium loti MAFF303099 | 7,281 | 3,829 | 52.6 |
| Mycoplasma penetrans | 1,037 | 472 | 45.5 |
| Mycoplasma pneumoniae M129 | 688 | 333 | 48.4 |
| Mycoplasma pulmonis UAB CTIP | 782 | 398 | 50.9 |
| Mycobacterium tuberculosis H37Rv | 3,918 | 2,036 | 52.0 |
| Mycobacterium tuberculosis CDC1551 | 4,187 | 1,990 | 47.5 |
| Nitrosomonas europaea ATCC 19718 | 2,461 | 1,366 | 55.5 |
| Neisseria meningitidis MC58 | 2,025 | 1,016 | 50.2 |
| Neisseria meningitidis Z2491 | 2,065 | 1,025 | 49.6 |
| Oceanobacillus iheyensis HTE831 | 3,496 | 1,892 | 54.1 |
| Phytoplasma asteris, OY strain | 754 | 423 | 56.1 |
| Pseudomonas aeruginosa PAO1 | 5,566 | 3,206 | 57.6 |
| Porphyromonas gingivalis W83 | 1,909 | 944 | 49.4 |
| Photorhabdus luminescens laumondii | 4,683 | 2,286 | 48.8 |
| Prochlorococcus marinus MED4 | 1,712 | 933 | 54.5 |
| Prochlorococcus marinus MIT9313 | 2,265 | 1,122 | 49.5 |
| Prochlorococcus marinus marinus | 1,882 | 939 | 49.9 |
| Pasteurella multocida PM70 | 2,014 | 1,237 | 61.4 |
| Pseudomonas putida KT2440 | 5,350 | 2,968 | 55.5 |
| Pseudomonas syringae pv. tomato str. | 5,608 | 2,938 | 52.4 |
| Pirellula sp. 1 | 7,325 | 2,588 | 35.3 |
| Rickettsia conorii Malish 7 | 1,374 | 572 | 41.6 |
| Rhodopseudomonas palustris | 4,814 | 2,739 | 56.9 |
| Rickettsia prowazekii Madrid E | 834 | 498 | 59.7 |
| Ralstonia solanacearum GMI1000 | 5,116 | 2,698 | 52.7 |
| Streptococcus agalactiae | 2,124 | 1,159 | 54.6 |
| Streptococcus agalactiae NEM316 | 2,094 | 1,174 | 56.1 |
| Staphylococcus aureus Mu50 | 2,748 | 1,451 | 52.8 |
| Staphylococcus aureus N315 | 2,624 | 1,447 | 55.1 |
| Staphylococcus aureus MW2 | 2,659 | 1,410 | 53.0 |
| Streptomyces avermitilis | 7,671 | 4,001 | 52.2 |
| Streptomyces coelicolor A3(2) | 8,154 | 4,195 | 51.4 |
| Staphylococcus epidermidis ATCC 12228 | 2,485 | 1,303 | 52.4 |
| Shigella flexneri 2a 301 | 4,452 | 2,306 | 51.8 |
| Shigella flexneri 2a str. 2457T | 4,068 | 2,159 | 53.1 |
| Sinorhizobium meliloti 1021 | 6,205 | 3,499 | 56.4 |
| Streptococcus mutans UA159 | 1,960 | 1,136 | 58.0 |
| Shewanella oneidensis MR-1 | 4,778 | 2,291 | 47.9 |
| Streptococcus pneumoniae R6 | 2,094 | 1,101 | 52.6 |
| Streptococcus pneumoniae TIGR4 | 2,043 | 1,135 | 55.6 |
| Streptococcus pyogenes SF370 | 1,696 | 956 | 56.4 |
| Streptococcus pyogenes MGAS8232 | 1,845 | 996 | 54.0 |
| Streptococcus pyogenes MGAS315 | 1,865 | 986 | 52.9 |
| Streptococcus pyogenes SSI-1 | 1,861 | 976 | 52.4 |
| Salmonella typhi CT18 | 4,767 | 2,347 | 49.2 |
| Salmonella typhimurium LT2 | 4,554 | 2,457 | 54.0 |
| Salmonella enterica subsp. enterica | 4,323 | 2,263 | 52.3 |
| Synechocystis sp. PCC 6803 | 3,167 | 1,679 | 53.0 |
| Synechococcus sp. WH 8102 | 2,517 | 1,243 | 49.4 |
| Thermosynechococcus elongatus BP-1 | 2,475 | 1,303 | 52.6 |
| Thermotoga maritima MSB8 | 1,846 | 1,051 | 56.9 |
| Treponema pallidum subsp. | 1,031 | 517 | 50.1 |
| Thermoanaerobacter tengcongensis MB4T | 2,588 | 1,403 | 54.2 |
| Tropheryma whipplei TW08/27 | 783 | 494 | 63.1 |
| Tropheryma whipplei str. Twist | 808 | 499 | 61.8 |
| Ureaplasma urealyticum | 611 | 303 | 49.6 |
| Vibrio cholerae N16961 | 3,828 | 1,971 | 51.5 |
| Vibrio parahaemolyticus RIMD 2210633 | 4,832 | 2,461 | 50.9 |
| Vibrio vulnificus CMCP6 | 4,537 | 2,461 | 54.2 |
| Vibrio vulnificus YJ016 | 5,028 | 2,499 | 49.7 |
| Wigglesworthia brevipalpis | 611 | 441 | 72.2 |
| Wolinella succinogenes DSMZ 1740 | 2,044 | 1,208 | 59.1 |
| Xanthomonas axonopodis pv. citri 306 | 4,427 | 2,374 | 53.6 |
| Xanthomonas campestris pv. campestris | 4,181 | 2,287 | 54.7 |
| Xylella fastidiosa 9a5c | 2,832 | 1,158 | 40.9 |
| Xylella fastidiosa Temecula1 | 2,036 | 1,066 | 52.4 |
| Yersinia pestis CO92 | 4,083 | 2,116 | 51.8 |
| Yersinia pestis KIM | 4,281 | 2,123 | 49.6 |
| sum | 396,126 | 206,311 | 52.1 |
| Eukaryotes | |||
| Arabidopsis thaliana | 28,723 | 14,394 | 50.1 |
| Caenorhabditis briggsae | 14,713 | 7,063 | 48.0 |
| Caenorhabditis elegans | 22,220 | 8,841 | 39.8 |
| Ciona intestinalis | 15,865 | 7,994 | 50.4 |
| Drosophila melanogaster | 18,302 | 9,541 | 52.1 |
| Danio rerio | 26,587 | 16,443 | 61.8 |
| Encephalitozoon cuniculi | 1,996 | 887 | 44.4 |
| Guillardia theta Nucleomorph | 632 | 307 | 48.6 |
| Homo sapiens (ENSEMBLE) | 28,063 | 15,467 | 55.1 |
| Leishmania major Friedlin | 173 | 62 | 35.8 |
| Mus musculus | 24,928 | 14,382 | 57.7 |
| Neurospora crassa | 10,088 | 3,800 | 37.7 |
| Oryza sativa | 16,724 | 4,517 | 27.0 |
| Plasmodium falciparum 3D7 | 5,268 | 1,905 | 36.2 |
| Rattus norvegicus | 28,682 | 16,740 | 58.4 |
| Saccharomyces cerevisiae | 5,869 | 2,913 | 49.6 |
| Schizosaccharomyces pombe | 5,261 | 2,807 | 53.4 |
| Takifugu rubripes rubripes | 37,452 | 15,202 | 40.6 |
| sum | 291,546 | 143,265 | 49.1 |
| Phages/Viruses | |||
| 186 | 46 | 8 | 17.4 |
| 44AHJD | 21 | 1 | 4.8 |
| 44RR2.8t | 252 | 51 | 20.2 |
| 933W | 80 | 9 | 11.3 |
| A118 | 72 | 9 | 12.5 |
| A511 | 11 | 0 | 0.0 |
| Aeh1 | 331 | 51 | 15.4 |
| APSE-1 | 54 | 6 | 11.1 |
| B1 | 11 | 1 | 9.1 |
| B103 | 17 | 4 | 23.5 |
| Bcep781 | 61 | 5 | 8.2 |
| BF23 | 8 | 1 | 12.5 |
| bIL170 | 64 | 2 | 3.1 |
| bIL285 | 62 | 5 | 8.1 |
| bIL286 | 61 | 7 | 11.5 |
| bIL309 | 56 | 6 | 10.7 |
| bIL310 | 29 | 4 | 13.8 |
| bIL311 | 22 | 6 | 27.3 |
| bIL312 | 27 | 3 | 11.1 |
| BK5-T | 63 | 6 | 9.5 |
| Bxb1 | 86 | 12 | 14.0 |
| C2 | 39 | 2 | 5.1 |
| Cp-1 | 28 | 2 | 7.1 |
| ϕCTX | 47 | 4 | 8.5 |
| D29 | 79 | 15 | 19.0 |
| D3 | 94 | 11 | 11.7 |
| Rb15 | 49 | 6 | 12.2 |
| ϕg1e | 49 | 6 | 12.2 |
| GA-1 | 35 | 3 | 8.6 |
| Gh-1 | 42 | 12 | 28.6 |
| H-19B | 22 | 4 | 18.2 |
| HF2 | 114 | 11 | 9.6 |
| HK022 | 57 | 8 | 14.0 |
| HK620 | 58 | 6 | 10.3 |
| HK97 | 61 | 10 | 16.4 |
| HP1 | 41 | 3 | 7.3 |
| HP2 | 36 | 3 | 8.3 |
| K139 | 44 | 4 | 9.1 |
| KVP40 | 381 | 57 | 15.0 |
| 2,389 | 57 | 7 | 12.3 |
| L-413C | 40 | 4 | 10.0 |
| L5 | 85 | 12 | 14.1 |
| λ | 66 | 18 | 27.3 |
| A2 | 61 | 8 | 13.1 |
| Mu | 53 | 6 | 11.3 |
| N15 | 60 | 13 | 21.7 |
| Mycoplasma virus P1 | 11 | 0 | 0.0 |
| Enterobacteria phage P1 | 11 | 0 | 0.0 |
| P2 | 42 | 5 | 11.9 |
| P22 | 36 | 9 | 25.0 |
| P27 | 58 | 9 | 15.5 |
| P335 | 49 | 6 | 12.2 |
| P4 | 12 | 2 | 16.7 |
| P60 | 80 | 13 | 16.3 |
| PA01 | 34 | 5 | 14.7 |
| PaP3 | 69 | 8 | 11.6 |
| ϕKZ | 306 | 25 | 8.2 |
| ϕCh1 | 98 | 9 | 9.2 |
| ϕYeO3-12 | 59 | 13 | 22.0 |
| ϕ105 | 51 | 8 | 15.7 |
| ϕC31 | 55 | 8 | 14.5 |
| ϕ3626 | 50 | 10 | 20.0 |
| ϕE125 | 71 | 12 | 16.9 |
| ϕETA | 66 | 8 | 12.1 |
| ϕNIH1.1 | 55 | 6 | 10.9 |
| ϕPV83 | 65 | 9 | 13.8 |
| ϕSLT | 62 | 12 | 19.4 |
| ϕadh | 63 | 8 | 12.7 |
| ϕBT1 | 55 | 9 | 16.4 |
| ϕA1122 | 50 | 10 | 20.0 |
| P68 | 22 | 2 | 9.1 |
| ϕKMV | 48 | 11 | 22.9 |
| PM2 | 22 | 1 | 4.5 |
| PRD1 | 22 | 4 | 18.2 |
| ΨM2 | 31 | 1 | 3.2 |
| ΨM100 | 37 | 4 | 10.8 |
| PY54 | 67 | 10 | 14.9 |
| PZA | 27 | 4 | 14.8 |
| R1t | 50 | 6 | 12.0 |
| RB69 | 256 | 56 | 21.9 |
| RB49 | 272 | 49 | 18.0 |
| Rd | 47 | 6 | 12.8 |
| RM378 | 146 | 17 | 11.6 |
| PVL | 62 | 8 | 12.9 |
| Sfi11 | 25 | 1 | 4.0 |
| V | 53 | 7 | 13.2 |
| SIO1 | 34 | 6 | 17.6 |
| Sk1 | 54 | 1 | 1.9 |
| SP6 | 20 | 6 | 30.0 |
| SP βc2 | 185 | 33 | 17.8 |
| SPP1 | 106 | 7 | 6.6 |
| MM1 | 53 | 6 | 11.3 |
| ST64B | 56 | 8 | 14.3 |
| ST64T | 65 | 9 | 13.8 |
| 7201 | 46 | 8 | 17.4 |
| DT1 | 47 | 7 | 14.9 |
| O1205 | 57 | 4 | 7.0 |
| Sfi19 | 45 | 6 | 13.3 |
| Sfi21 | 50 | 9 | 18.0 |
| Stx2 | 165 | 11 | 6.7 |
| T3 | 44 | 10 | 22.7 |
| T4 | 278 | 58 | 20.9 |
| T7 | 58 | 10 | 17.2 |
| TM4 | 89 | 5 | 5.6 |
| TP901-1 | 56 | 7 | 12.5 |
| Tuc2009 | 56 | 7 | 12.5 |
| Ul36 | 58 | 5 | 8.6 |
| VHML | 57 | 8 | 14.0 |
| VpV262 | 67 | 4 | 6.0 |
| VT2-Sa | 82 | 11 | 13.4 |
| Wϕ | 44 | 4 | 9.1 |
| Sum | 7,699 | 1073 | 13.9 |
| Total | 734,193 | 368,724 | 50.2 |