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| phylum | order | species | KEGG | COG |
| Actinobacteria | Actinobacteridae | Bifidobacterium longum NCC2705<\i> | blo | |
| Corynebacterium glutamicum ATCC 13032 | cgl | Cgl | ||
| Corynebacterium efficiens YS-314 | cef | |||
| Mycobacterium leprae TN | mle | Mle | ||
| Mycobacterium tuberculosis CDC1551, clinical strain | mtc | MtC | ||
| Mycobacterium tuberculosis H37Rv, laboratory strain | mtu | Mtu | ||
| Streptomyces coelicolor A3(2) | sco | |||
| Streptomyces avermitilis | sma | |||
| Tropheryma | Tropheryma whipplei Twist | twh | ||
| Tropheryma whipplei TW08/27 | tws | |||
| Aquificae | Aquificales | Aquifex aeolicus VF5 | aae | Aae |
| Bacteroidetes | Bacteroides (class) | Bacteroides thetaiotaomicron VPI-5482 | bth | |
| Chlamydiae | Chlamydiales | Chlamydia muridarum (Chlamydia trachomatis MoPn) | cmu | |
| Chlamydia trachomatis serovar D | ctr | Ctr | ||
| Chlamydophila caviae GPIC | cca | |||
| Chlamydophila pneumoniae AR39 | cpa | |||
| Chlamydophila pneumoniae CWL029 | cpn | Cpn | ||
| Chlamydophila pneumoniae J138 | cpj | |||
| Chlorobi | Chlorobia | Chlorobium tepidum TLS | cte | |
| Cyanobacteria | Chroococcales | Synechocystis sp. PCC 6803 | syn | Syn |
| Thermosynechococcus elongatus BP-1 | tel | |||
| Nostocales | Anabaena sp. PCC 7120 (Nostoc sp. PCC 7120) | ana | Nos | |
| Deinococcus-Thermus | Deinococci | Deinococcus radiodurans R1 | dra | Dra |
| Firmicutes | Bacillales | Bacillus anthracis Ames | ban | |
| Bacillus cereus ATCC 14579 | bce | |||
| Bacillus halodurans C-125 | bha | Bha | ||
| Bacillus subtilis 168 | bsu | Bsu | ||
| Listeria innocua CLIP 11262 | lin | Lin | ||
| Listeria monocytogenes EGD-e | lmo | |||
| Oceanobacillus iheyensis HTE831 | oih | |||
| Staphylococcus aureus MW2 | sam | Sau | ||
| Staphylococcus aureus Mu50, MRSA strain with vancomycin resistance | sav | |||
| Staphylococcus aureus N315, meticillin-resistant (MRSA) | sau | |||
| Staphylococcus epidermidis ATCC 12228 | sep | |||
| Clostridia | Clostridium acetobutylicum ATCC 824 | cac | Cac | |
| Clostridium perfringens 13 | cpe | |||
| Clostridium tetani E88 | ctc | |||
| Thermoanaerobacter tengcongensis MB4T | tte | |||
| Lactobacillales | Enterococcus faecalis V583 (vancomycin-resistant clinical isolate) | efa | ||
| Lactobacillus plantarum WCFS1 | lpl | |||
| Lactococcus lactis subsp. lactis IL1403 | lla | Lla | ||
| Streptococcus agalactiae 2603 (serotype V) | sag | |||
| Streptococcus agalactiae NEM316 | san | |||
| Streptococcus mutans UA159 (serotypeC) | smu | |||
| Streptococcus pneumoniae R6 | spr | |||
| Streptococcus pneumoniae TIGR4 | spn | Spn | ||
| Streptococcus pyogenes SF370 (serotyp M1) | spy | Spy | ||
| Streptococcus pyogenes MGAS315 (serotype M3) | spg | |||
| Streptococcus pyogenes MGAS8232 (serotype M18) | spm | |||
| Streptococcus pyogenes SSI-1 | sps | |||
| Mollicutes | Mycoplasma genitalium G-37 | mge | Mge | |
| Mycoplasma penetrans HF-2 | mpe | |||
| Mycoplasma pneumoniae M129 | mpn | Mpn | ||
| Mycoplasma pulmonis UAB CTIP | mpu | Mpu | ||
| Ureaplasma urealyticum serovar 3 | uur | Uur | ||
| Fusobacteria | Fusobacterales | Fusobacterium nucleatum ATCC 25586 | fnu | Fnu |
| Proteobacteria | Alphaproteobacteria | Agrobacterium tumefaciens C58 (Cereon) | atc | Atu |
| Agrobacterium tumefaciens C58 (U.Washington/Dupont) | atu | |||
| Bradyrhizobium japonicum USDA110 | bja | |||
| Brucella melitensis 16M | bme | Bme | ||
| Brucella suis 1330 | bms | |||
| Caulobacter crescentus CB15 | ccr | Ccr | ||
| Mesorhizobium loti MAFF303099 | mlo | Mlo | ||
| Rickettsia conorii Malish 7 | rco | Rco | ||
| Rickettsia prowazekii Madrid E | rpr | Rpr | ||
| Sinorhizobium meliloti 1021 | sme | Sme | ||
| Betaproteobacteria | Neisseria meningitidis MC58 (serogroup B) | nme | Nme | |
| Neisseria meningitidis Z2491 (serogroup A) | nma | NmA | ||
| Nitrosomonas europaea ATCC 19718 | neu | |||
| Ralstonia solanacearum GMI1000 | rso | Rso | ||
| Epsilonproteobacteria | Campylobacter jejuni NCTC11168 | cje | Cje | |
| Helicobacter pylori 26695 | hpy | Hpy | ||
| Helicobacter pylori J99 | hpj | jHp | ||
| Gammaproteobacteria | Escherichia coli K-12 W3110 | ecj | ||
| Buchnera aphidicola Bp (symbiont of Baizongia pistaciae) | bab | |||
| Buchnera aphidicola Sg (symbiont of Schizaphis graminum) | bas | |||
| Buchnera sp. APS (symbiont of Acyrthosiphon pisum) | buc | Buc | ||
| Coxiella burnetii RSA 493 | cbu | |||
| Escherichia coli CFT073 | ecc | |||
| Escherichia coli K-12 MG1655 | eco | Eco | ||
| Escherichia coli O157:H7 Sakai | ecs | Ecs | ||
| Escherichia coli O157:H7 EDL933 | ece | EcZ | ||
| Haemophilus influenzae Rd KW20 | hin | Hin | ||
| Pasteurella multocida PM70 | pmu | Pmu | ||
| Pseudomonas aeruginosa PA01 | pae | Pae | ||
| Pseudomonas putida KT2440 | ppu | |||
| Pseudomonas syringae pv. tomato DC3000 | pst | |||
| Salmonella typhi CT18 | sty | Sty | ||
| Salmonella typhi Ty2 | stt | |||
| Salmonella typhimurium LT2 | stm | |||
| Shewanella oneidensis MR-1 | son | |||
| Shigella flexneri 301 (serotype 2a) | sfl | |||
| Shigella flexneri 2457T (serotype 2a) | sfx | |||
| Vibrio cholerae El Tor N16961 | vch | Vch | ||
| Vibrio parahaemolyticus RIMD 2210633 | vpa | |||
| Vibrio vulnificus CMCP6 | vvu | |||
| Wigglesworthia brevipalpis | wbr | |||
| Xanthomonas campestris pv. campestris ATCC 33913 | xcc | |||
| Xanthomonas axonopodis pv. citri 306 | xac | |||
| Xylella fastidiosa 9a5c | xfa | Xfa | ||
| Xylella fastidiosa Temecula1 | xft | |||
| Yersinia pestis CO92 | ype | Ype | ||
| Yersinia pestis KIM | ypk | |||
| Spirochaetes | Spirochaetales | Borrelia burgdorferi B31 | bbu | Bbu |
| Leptospira interrogans 56601 (serovarlai) | lil | |||
| Treponema pallidum Nichols | tpa | Tpa | ||
| Thermotogae | Thermotogales | Thermotoga maritima MSB8 | tma | Tma |
