Table 2 Generated bacterial pathway models. Bacterial models generated with GEM System from the complete genomes containing more than 500 enzymes is listed here (complete list of 90 models is available at our web site [29]). Here the KEGG coverage is calculated as the percentage of correctly extracted enzyme in the corresponding organism specific pathways in the KEGG database.
From: GEM System: automatic prototyping of cell-wide metabolic pathway models from genomes
species | genes | metabolites | reactions | enzymes | KEGG coverage |
|---|---|---|---|---|---|
Bacillus anthracis Ames | 5311 | 1007 | 776 | 675 | 423/ 457(92.56%) |
Bordetella bronchiseptica RB50 | 4994 | 1038 | 788 | 669 | 429/ 460(93.26%) |
Bacillus halodurans C-125 | 4066 | 1056 | 812 | 693 | 422/ 435(97.01%) |
Bradyrhizobium japonicum USDA110 | 8317 | 1257 | 995 | 863 | 521/ 555(93.87%) |
Bordetella parapertussis 12822 | 4185 | 1011 | 763 | 644 | 404/ 433(93.30%) |
Bordetella pertussis Tohama I | 3447 | 957 | 717 | 602 | 394/ 422(93.36%) |
Bacillus subtilis 168 | 4106 | 1060 | 818 | 699 | 464/ 476(97.48%) |
Bacteroides thetaiotaomicron VPI-5482 | 4778 | 912 | 696 | 583 | 361/ 379(95.25%) |
Caulobacter crescentus CB15 | 3737 | 1068 | 807 | 689 | 405/ 420(96.43%) |
Corynebacterium efficiens YS-314 | 2950 | 944 | 674 | 574 | 352/ 383(91.91%) |
Chromobacterium violaceum ATCC 12472 | 4407 | 1047 | 834 | 729 | 484/ 523(92.54%) |
Escherichia coli CFT073 | 5379 | 1120 | 906 | 780 | 525/ 554(94.77%) |
Escherichia coli O157:H7 EDL933 | 5349 | 1197 | 972 | 842 | 545/ 566(96.29%) |
Escherichia coli K-12 MG1655 | 4289 | 1195 | 968 | 835 | 579/ 579(100.00%) |
Escherichia coli O157:H7 Sakai | 5361 | 1206 | 972 | 842 | 548/ 568(96.48%) |
Fusobacterium nucleatum ATCC 25586 | 2067 | 804 | 608 | 514 | 302/ 326(92.64%) |
Gloeobacter violaceus PCC7421 | 4430 | 945 | 689 | 587 | 347/ 375(92.53%) |
Haemophilus influenzae Rd KW20 | 1709 | 907 | 664 | 551 | 358/ 359(99.72%) |
Lactococcus lactis subsp. lactis IL1403 | 2266 | 925 | 683 | 567 | 312/ 328(95.12%) |
Mycobacterium bovis subsp. bovis AF2122/97 | 3920 | 943 | 690 | 592 | 414/ 456(90.79%) |
Mycobacterium leprae TN | 1605 | 851 | 605 | 501 | 285/ 315(90.48%) |
Mycobacterium tuberculosis CDC1551 | 4187 | 1064 | 780 | 678 | 403/ 424(95.05%) |
Mycobacterium tuberculosis H37Rv | 3869 | 1070 | 806 | 684 | 405/ 431(93.97%) |
Nitrosomonas europaea ATCC 19718 | 2461 | 832 | 621 | 514 | 334/ 360(92.78%) |
Neisseria meningitidis Z2491 (serogroup A) | 2065 | 895 | 663 | 562 | 334/ 346(96.53%) |
Neisseria meningitidis MC58 (serogroup B) | 2025 | 867 | 635 | 532 | 329/ 339(97.05%) |
Oceanobacillus iheyensis HTE831 | 3496 | 967 | 731 | 617 | 398/ 435(91.49%) |
Pseudomonas aeruginosa PA01 | 5565 | 1218 | 944 | 826 | 499/ 517(96.52%) |
Photorhabdus luminescens | 4683 | 1026 | 785 | 672 | 458/ 501(91.42%) |
Pasteurella multocida PM70 | 2014 | 913 | 671 | 561 | 372/ 391(95.14%) |
Pseudomonas putida KT2440 | 5350 | 1087 | 840 | 722 | 456/ 492(92.68%) |
Pseudomonas syringae pv. tomato DC3000 | 5471 | 1077 | 841 | 719 | 446/ 483(92.34%) |
Rhodopirellula baltica (Pirellula sp. strain 1) | 7325 | 971 | 748 | 639 | 412/ 432(95.37%) |
Staphylococcus aureus MW2 | 2632 | 866 | 634 | 541 | 343/ 360(95.28%) |
Staphylococcus epidermidis ATCC 12228 | 2419 | 843 | 612 | 514 | 328/ 350(93.71%) |
Shigella flexneri 301 (serotype 2a) | 4180 | 1084 | 858 | 736 | 493/ 532(92.67%) |
Shigella flexneri 2457T (serotype 2a) | 4068 | 1044 | 817 | 701 | 486/ 533(91.18%) |
Salmonella typhi Ty2 | 4323 | 1100 | 887 | 764 | 527/ 563(93.61%) |
Synechococcus sp. WH 8102 | 2517 | 804 | 575 | 508 | 347/ 375(92.53%) |
Thermosynechococcus elongatus BP-1 | 2475 | 851 | 628 | 512 | 318/ 350(90.86%) |
Thermotoga maritima MSB8 | 1846 | 862 | 622 | 515 | 292/ 305(95.74%) |
Xanthomonas axonopodis pv. citri 306 | 4312 | 1054 | 804 | 679 | 424/ 451(94.01%) |
Xanthomonas campestris pv. ATCC 33913 | 4181 | 1051 | 809 | 685 | 437/ 462(94.59%) |
Yersinia pestis KIM | 4090 | 1075 | 846 | 723 | 472/498(94.78%) |