JSim Kegg Models Page
This page allows users to run about 72,000 biochemical models from the Kegg Pathways Database under JSim. Each model consists of a single pathway for a single organism. 126 pathways and 825 organisms are represented, although no single organism has all possible pathways.
To run these models online, you must have a Java plugin installed in your WWW browser. To run them in JSim on your own computer, download the model code and the JSim application. Either way, see Running JSim for instructions on how to use JSim. The SBML models do not define the forward and backward reaction rate constants, so these must be specified by the user before running the models.
The models presented here were released by KEGG on Aug 9, 2008. See here for details.
Return to complete JSim model archives.
Organisms
- aae: Aquifex aeolicus
- aau: Arthrobacter aurescens
- aav: Acidovorax avenae
- aba: Acidobacteria bacterium
- abc: Acinetobacter baumannii ACICU
- abm: Acinetobacter baumannii SDF
- abo: Alcanivorax borkumensis
- abu: Arcobacter butzleri
- aby: Acinetobacter baumannii AYE
- acb: Acinetobacter baumannii ATCC 17978
- ace: Acidothermus cellulolyticus
- aci: Acinetobacter sp. ADP1
- acl: Acholeplasma laidlawii
- acr: Acidiphilium cryptum JF-5
- ade: Anaeromyxobacter dehalogenans 2CP-C
- aeh: Alkalilimnicola ehrlichei
- afm: Aspergillus fumigatus
- afu: Archaeoglobus fulgidus
- afw: Anaeromyxobacter sp. Fw109-5
- aga: Anopheles gambiae (mosquito)
- ago: Ashbya gossypii (Eremothecium gossypii)
- aha: Aeromonas hydrophila
- ajs: Acidovorax sp. JS42
- ama: Anaplasma marginale St. Maries
- amr: Acaryochloris marina
- amt: Alkaliphilus metalliredigens
- ana: Anabaena sp. PCC7120
- ang: Aspergillus niger
- ani: Aspergillus nidulans
- aoe: Alkaliphilus oremlandii
- aor: Aspergillus oryzae
- apa: Actinobacillus pleuropneumoniae AP76 (serotype 7)
- ape: Aeropyrum pernix
- aph: Anaplasma phagocytophilum
- apj: Actinobacillus pleuropneumoniae JL03 (serotype 3)
- apl: Actinobacillus pleuropneumoniae L20 (serotype 5b)
- art: Arthrobacter sp. FB24
- asa: Aeromonas salmonicida
- asu: Actinobacillus succinogenes
- atc: Agrobacterium tumefaciens C58 (Cereon)
- ath: Arabidopsis thaliana (thale cress)
- atu: Agrobacterium tumefaciens C58
- ava: Anabaena variabilis
- ayw: Phytoplasma AYWB
- azc: Azorhizobium caulinodans
- azo: Azoarcus sp. BH72
- baa: Bacillus anthracis A2012
- bab: Buchnera aphidicola Bp
- bac: Burkholderia ambifaria MC40-6
- bad: Bifidobacterium adolescentis
- baf: Borrelia afzelii
- bam: Burkholderia cepacia
- ban: Bacillus anthracis Ames
- bar: Bacillus anthracis Ames 0581
- bas: Buchnera aphidicola Sg
- bat: Bacillus anthracis Sterne
- bav: Bordetella avium
- bay: Bacillus amyloliquefaciens
- bba: Bdellovibrio bacteriovorus
- bbk: Bartonella bacilliformis
- bbr: Bordetella bronchiseptica
- bbt: Bradyrhizobium sp. BTAi1
- bbu: Borrelia burgdorferi
- bca: Bacillus cereus ATCC 10987
- bcc: Buchnera aphidicola Cc
- bce: Bacillus cereus ATCC 14579
- bch: Burkholderia cenocepacia HI2424
- bci: Baumannia cicadellinicola
- bcl: Bacillus clausii
- bcm: Burkholderia cenocepacia MC0-3
- bcn: Burkholderia cenocepacia AU1054
- bcs: Brucella canis
- bcy: Bacillus cytotoxis NVH 391-98
- bcz: Bacillus cereus ZK
- bfl: Candidatus Blochmannia floridanus
- bfr: Bacteroides fragilis YCH46
- bfs: Bacteroides fragilis NCTC9343
- bga: Borrelia garinii
- bha: Bacillus halodurans
- bhe: Bartonella henselae
- bid: Beijerinckia indica
- bja: Bradyrhizobium japonicum
- bld: Bacillus licheniformis DSM13
- bli: Bacillus licheniformis ATCC 14580
- blj: Bifidobacterium longum DJO10A
- blo: Bifidobacterium longum NCC2705
- bma: Burkholderia mallei ATCC 23344
- bmb: Brucella abortus 9-941
- bmc: Brucella abortus S19
- bme: Brucella melitensis 16M
- bmf: Brucella melitensis biovar Abortus
- bml: Burkholderia mallei NCTC 10229
- bmn: Burkholderia mallei NCTC 10247
- bms: Brucella suis 1330
- bmt: Brucella suis ATCC 23445
- bmu: Burkholderia multivorans ATCC 17616 (JGI)
- bmv: Burkholderia mallei SAVP1
- bmy: Brugia malayi (filaria)
- bov: Brucella ovis
- bpa: Bordetella parapertussis
- bpd: Burkholderia pseudomallei 668
- bpe: Bordetella pertussis
- bph: Burkholderia phymatum
- bpl: Burkholderia pseudomallei 1106a
- bpm: Burkholderia pseudomallei 1710b
- bpn: Candidatus Blochmannia pennsylvanicus
- bps: Burkholderia pseudomallei K96243
- bpt: Bordetella petrii
- bpu: Bacillus pumilus
- bqu: Bartonella quintana
- bra: Bradyrhizobium sp. ORS278
- bsu: Bacillus subtilis
- bta: Bos taurus (cow)
- bte: Burkholderia thailandensis
- bth: Bacteroides thetaiotaomicron
- btk: Bacillus thuringiensis 97-27
- btl: Bacillus thuringiensis Al Hakam
- btr: Bartonella tribocorum
- buc: Buchnera aphidicola APS
- bur: Burkholderia sp. 383
- bvi: Burkholderia vietnamiensis
- bvu: Bacteroides vulgatus
- bwe: Bacillus weihenstephanensis
- bxe: Burkholderia xenovorans
- cab: Chlamydophila abortus
- cac: Clostridium acetobutylicum
- cak: Caulobacter sp. K31
- cal: Candida albicans
- cau: Chloroflexus aurantiacus
- cba: Clostridium botulinum A ATCC 19397
- cbb: Clostridium botulinum B1 Okra
- cbd: Coxiella burnetii Dugway 5J108-111
- cbe: Clostridium beijerinckii
- cbf: Clostridium botulinum F Langeland
- cbh: Clostridium botulinum A Hall
- cbk: Clostridium botulinum B Eklund 17B
- cbl: Clostridium botulinum A3 Loch Maree
- cbo: Clostridium botulinum A ATCC 3502
- cbs: Coxiella burnetii RSA 331
- cbu: Coxiella burnetii RSA 493
- cca: Chlamydophila caviae
- cch: Chlorobium chlorochromatii
- cco: Campylobacter concisus 13826
- ccr: Caulobacter crescentus CB15
- ccv: Campylobacter curvus
- cdf: Clostridium difficile
- cdi: Corynebacterium diphtheriae
- cef: Corynebacterium efficiens
- cel: Caenorhabditis elegans (nematode)
- cfa: Canis familiaris (dog)
- cfe: Chlamydophila felis
- cff: Campylobacter fetus
- cgb: Corynebacterium glutamicum ATCC 13032 (Bielefeld)
- cgl: Corynebacterium glutamicum ATCC 13032 (Kyowa Hakko)
- cgr: Candida glabrata
- cgt: Corynebacterium glutamicum R
- cha: Campylobacter hominis ATCC BAA-381
- cho: Cryptosporidium hominis
- chu: Cytophaga hutchinsonii
- chy: Carboxydothermus hydrogenoformans
- cja: Cellvibrio japonicus
- cjd: Campylobacter jejuni subsp. doylei 269.97
- cje: Campylobacter jejuni NCTC11168
- cjj: Campylobacter jejuni 81-176
- cjk: Corynebacterium jeikeium
- cjr: Campylobacter jejuni RM1221
- cju: Campylobacter jejuni 81116
- ckl: Clostridium kluyveri DSM 555
- cko: Citrobacter koseri ATCC BAA-895
- cma: Caldivirga maquilingensis
- cme: Cyanidioschyzon merolae
- cmi: Clavibacter michiganensis subsp. michiganensis
- cms: Clavibacter michiganensis subsp. sepedonicus
- cmu: Chlamydia muridarum
- cnb: Cryptococcus neoformans B-3501A
- cne: Cryptococcus neoformans JEC21
- cno: Clostridium novyi
- cpa: Chlamydophila pneumoniae AR39
- cpb: Chlorobium phaeobacteroides BS1
- cpe: Clostridium perfringens 13
- cpf: Clostridium perfringens ATCC 13124
- cph: Chlorobium phaeobacteroides DSM 266
- cpj: Chlamydophila pneumoniae J138
- cpn: Chlamydophila pneumoniae CWL029
- cpr: Clostridium perfringens SM101
- cps: Colwellia psychrerythraea
- cpt: Chlamydophila pneumoniae TW183
- cpv: Cryptosporidium parvum
- cpy: Clostridium phytofermentans
- cre: Chlamydomonas reinhardtii
- crp: Candidatus Carsonella ruddii
- csa: Chromohalobacter salexigens
- csc: Caldicellulosiruptor saccharolyticus
- cta: Chlamydia trachomatis A/HAR-13 (serovar A)
- ctb: Chlamydia trachomatis 434/Bu
- ctc: Clostridium tetani E88
- cte: Chlorobaculum tepidum
- cth: Clostridium thermocellum
- cti: Cupriavidus taiwanensis
- ctl: Chlamydia trachomatis L2b/UCH-1/proctitis
- ctr: Chlamydia trachomatis D/UW-3/CX (serovar D)
- cur: Corynebacterium urealyticum
- cvi: Chromobacterium violaceum
- cya: Cyanobacteria Yellowstone A-Prime
- cyb: Cyanobacteria Yellowstone B-Prime
- cyt: Cyanothece sp. ATCC 51142
- daag: (Undocumented)
- dac: Delftia acidovorans
- dame: (Undocumented)
- dar: Dechloromonas aromatica
- dau: Candidatus Desulforudis audaxviator
- dbmo: Bombyx mori (silkmoth)
- dcbr: (Undocumented)
- dcin: (Undocumented)
- dde: Desulfovibrio desulfuricans G20
- ddi: Dictyostelium discoideum
- deb: Dehalococcoides sp. BAV1
- decb: (Undocumented)
- deh: Dehalococcoides sp. CBDB1
- det: Dehalococcoides ethenogenes
- dfru: Fugu rubripes (Japanese puffer fish)
- dge: Deinococcus geothermalis
- dha: Debaryomyces hansenii
- dkwa: Kluyveromyces waltii
- dme: Drosophila melanogaster (fruit fly)
- dno: Dichelobacter nodosus
- dol: Candidatus Desulfococcus oleovorans
- dola: Oryzias latipes (Japanese medaka)
- dota: Ostreococcus tauri
- dpkn: (Undocumented)
- dpo: Drosophila pseudoobscura pseudoobscura
- dpop: (Undocumented)
- dps: Desulfotalea psychrophila
- dptm: (Undocumented)
- dra: Deinococcus radiodurans
- dre: Danio rerio (zebrafish)
- drm: Desulfotomaculum reducens
- dsba: Saccharomyces bayanus
- dsh: Dinoroseobacter shibae
- dsmi: Saccharomyces mikatae
- dspd: (Undocumented)
- dsy: Desulfitobacterium hafniense Y51
- dtni: Tetraodon nigroviridis (green spotted puffer)
- dtps: (Undocumented)
- dvl: Desulfovibrio vulgaris DP4
- dvu: Desulfovibrio vulgaris Hildenborough
- dvvi: (Undocumented)
- eacp: (Undocumented)
- eath: Arabidopsis thaliana (thale cress) (EST)
- eba: Aromatoleum aromaticum EbN1
- ebna: Brassica napus (rape) (EST)
- ebvl: Beta vulgaris (beet) (EST)
- eca: Erwinia carotovora
- ecan: Capsicum annuum (chile pepper) (EST)
- ecc: Escherichia coli CFT073 (UPEC)
- ecd: Escherichia coli K-12 DH10B
- ece: Escherichia coli O157 EDL933 (EHEC)
- ech: Ehrlichia chaffeensis
- eci: Escherichia coli UTI89 (UPEC)
- ecj: Escherichia coli K-12 W3110
- ecl: Escherichia coli ATCC 8739
- ecm: Escherichia coli SECEC
- ecn: Ehrlichia canis
- eco: Escherichia coli K-12 MG1655
- ecp: Escherichia coli 536 (UPEC)
- ecs: Escherichia coli O157 Sakai (EHEC)
- ecsi: Citrus sinensis (Valencia orange) (EST)
- ecsv: Ciona savignyi (EST)
- ecu: Encephalitozoon cuniculi
- ecv: Escherichia coli APEC O1
- ecw: Escherichia coli E24377A
- ecx: Escherichia coli HS
- eees: Euphorbia esula (leafy spurge) (EST)
- efa: Enterococcus faecalis
- efar: Festuca arundinacea (tall fescue) (EST)
- egar: Gossypium arboreum (tree cotton) (EST)
- eghi: Gossypium hirsutum (upland cotton) (EST)
- egma: Glycine max (soybean) (EST)
- egra: Gossypium raimondii (EST)
- ehan: Helianthus annuus (sunflower) (EST)
- ehi: Entamoeba histolytica
- ehvu: Hordeum vulgare (barley) (EST)
- eini: Ipomoea nil (Japanese morning glory) (EST)
- eli: Erythrobacter litoralis
- elja: Lotus japonicus (lotus) (EST)
- elpe: Lactuca perennis (blue lettuce) (EST)
- elsi: Lactuca saligna (willow-leaf lettuce) (EST)
- elst: Lactuca sativa (lettuce) (EST)
- elvi: Lactuca virosa (wild lettuce) (EST)
- emec: Manihot esculenta (cassava) (EST)
- emte: Molgula tectiformis (EST)
- emtr: Medicago truncatula (barrel medic) (EST)
- enbe: Nicotiana benthamiana (EST)
- ent: Enterobacter sp. 638
- enta: Nicotiana tabacum (tobacco) (EST)
- eosa: Oryza sativa (rice) (EST)
- eosi: Oryza sativa indica (Indian rice) (EST)
- eosj: Oryza sativa japonica (Japanese rice) (EST)
- epgl: Picea glauca (white spruce) (EST)
- epop: Populus trichocarpa (black cottonwood) (EST)
- eppa: (Undocumented)
- eppi: Pinus pinaster (maritime pine) (EST)
- eppp: Physcomitrella patens subsp. patens (EST)
- epps: Prunus persica (peach) (EST)
- epsi: Picea sitchensis (sitka spruce) (EST)
- epta: Pinus taeda (loblolly pine) (EST)
- eptp: Populus tremula (European aspen) (EST)
- erg: Ehrlichia ruminantium Gardel
- eru: Ehrlichia ruminantium Welgevonden (South Africa)
- erw: Ehrlichia ruminantium Welgevonden (France)
- esa: Enterobacter sakazakii
- esbi: Sorghum bicolor (sorghum) (EST)
- esi: Exiguobacterium sibiricum
- esja: Schistosoma japonicum (fluke) (EST)
- esly: Solanum lycopersicum (tomato) (EST)
- esof: Saccharum officinarum (sugarcane) (EST)
- espp: (Undocumented)
- espu: Strongylocentrotus purpuratus (purple sea urchin) (EST)
- estu: Solanum tuberosum (potato) (EST)
- eta: Erwinia tasmaniensis
- etae: Triticum aestivum (wheat) (EST)
- evvi: Vitis vinifera (wine grape) (EST)
- ezel: (Undocumented)
- ezma: Zea mays (maize) (EST)
- fal: Frankia alni
- fgr: Fusarium graminearum
- fjo: Flavobacterium johnsoniae
- fma: Finegoldia magna
- fno: Fervidobacterium nodosum
- fnu: Fusobacterium nucleatum
- fph: Francisella philomiragia
- fps: Flavobacterium psychrophilum
- fra: Frankia sp. CcI3
- fre: Frankia sp. EAN1pec
- fta: Francisella tularensis subsp. holarctica FTNF002-00
- ftf: Francisella tularensis subsp. tularensis FSC 198
- fth: Francisella tularensis subsp. holarctica OSU18
- ftl: Francisella tularensis subsp. holarctica LVS
- ftm: Francisella tularensis subsp. mediasiatica FSC147
- ftn: Francisella tularensis subsp. novicida U112
- ftu: Francisella tularensis subsp. tularensis SCHU S4
- ftw: Francisella tularensis subsp. tularensis WY96-3418
- gbe: Granulobacter bethesdensis
- gdi: Gluconacetobacter diazotrophicus PAl 5 (Brazil)
- gfo: Gramella forsetii
- gga: Gallus gallus (chicken)
- gka: Geobacillus kaustophilus
- gla: Giardia lamblia
- glo: Geobacter lovleyi
- gme: Geobacter metallireducens
- gox: Gluconobacter oxydans
- gsu: Geobacter sulfurreducens
- gtn: Geobacillus thermodenitrificans
- gur: Geobacter uraniumreducens
- gvi: Gloeobacter violaceus
- hac: Helicobacter acinonychis
- hal: Halobacterium sp. NRC-1
- har: Herminiimonas arsenicoxydans
- hau: Herpetosiphon aurantiacus
- hbu: Hyperthermus butylicus
- hch: Hahella chejuensis
- hdu: Haemophilus ducreyi
- hha: Halorhodospira halophila
- hhe: Helicobacter hepaticus
- hin: Haemophilus influenzae Rd KW20 (serotype d)
- hip: Haemophilus influenzae PittEE
- hiq: Haemophilus influenzae PittGG
- hit: Haemophilus influenzae 86-028NP (nontypeable)
- hma: Haloarcula marismortui
- hmo: Heliobacterium modesticaldum
- hne: Hyphomonas neptunium
- hpa: Helicobacter pylori HPAG1
- hpj: Helicobacter pylori J99
- hpy: Helicobacter pylori 26695
- hsa: Homo sapiens (human)
- hsl: Halobacterium salinarum R1
- hsm: Haemophilus somnus 2336
- hso: Haemophilus somnus 129PT
- hwa: Haloquadratum walsbyi
- iho: Ignicoccus hospitalis
- ilo: Idiomarina loihiensis
- jan: Jannaschia sp. CCS1
- kcr: Candidatus Korarchaeum cryptofilum
- kla: Kluyveromyces lactis
- kpn: Klebsiella pneumoniae
- kra: Kineococcus radiotolerans
- krh: Kocuria rhizophila
- lac: Lactobacillus acidophilus
- lbc: Laccaria bicolor
- lbf: Leptospira biflexa serovar Patoc Patoc 1 (Ames)
- lbi: Leptospira biflexa serovar Patoc Patoc 1 (Paris)
- lbj: Leptospira borgpetersenii JB197
- lbl: Leptospira borgpetersenii L550
- lbr: Lactobacillus brevis
- lbu: Lactobacillus delbrueckii ATCC BAA-365
- lca: Lactobacillus casei ATCC 334
- lch: Leptothrix cholodnii
- lci: Leuconostoc citreum
- ldb: Lactobacillus delbrueckii ATCC 11842
- lfe: Lactobacillus fermentum
- lga: Lactobacillus gasseri
- lhe: Lactobacillus helveticus
- lic: Leptospira interrogans serovar Copenhageni
- lil: Leptospira interrogans serovar lai
- lin: Listeria innocua
- lip: Lawsonia intracellularis
- ljo: Lactobacillus johnsonii
- lla: Lactococcus lactis subsp. lactis IL1403
- llc: Lactococcus lactis subsp. cremoris SK11
- llm: Lactococcus lactis subsp. cremoris MG1363
- lma: Leishmania major
- lme: Leuconostoc mesenteroides
- lmf: Listeria monocytogenes F2365
- lmo: Listeria monocytogenes EGD-e
- lpc: Legionella pneumophila Corby
- lpf: Legionella pneumophila Lens
- lpl: Lactobacillus plantarum WCFS1
- lpn: Legionella pneumophila Philadelphia 1
- lpp: Legionella pneumophila Paris
- lre: Lactobacillus reuteri DSM 20016
- lsa: Lactobacillus sakei
- lsl: Lactobacillus salivarius
- lsp: Lysinibacillus sphaericus
- lwe: Listeria welshimeri SLCC5334
- lxx: Leifsonia xyli xyli CTCB07
- maa: Mycoplasma agalactiae
- mab: Mycobacterium abscessus ATCC 19977T
- mac: Methanosarcina acetivorans
- mae: Methanococcus aeolicus
- mag: Magnetospirillum magneticum
- maq: Marinobacter aquaeolei
- mar: Microcystis aeruginosa
- mav: Mycobacterium avium 104
- mba: Methanosarcina barkeri
- mbb: Mycobacterium bovis BCG Pasteur 1173P2
- mbn: Candidatus Methanoregula boonei
- mbo: Mycobacterium bovis AF2122/97
- mbr: Monosiga brevicollis
- mbu: Methanococcoides burtonii
- mca: Methylococcus capsulatus
- mcc: Macaca mulatta (rhesus monkey)
- mcp: Mycoplasma capricolum
- mdo: Monodelphis domestica (opossum)
- mem: Methanoculleus marisnigri
- mes: Mesorhizobium sp. BNC1
- met: Methylobacterium sp. 4-46
- mex: Methylobacterium extorquens
- mfa: Methylobacillus flagellatus
- mfl: Mesoplasma florum
- mga: Mycoplasma gallisepticum
- mge: Mycoplasma genitalium
- mgi: Mycobacterium gilvum
- mgl: Malassezia globosa
- mgm: Magnetococcus sp. MC-1
- mgr: Magnaporthe grisea
- mhj: Mycoplasma hyopneumoniae J
- mhp: Mycoplasma hyopneumoniae 7448
- mhu: Methanospirillum hungatei
- mhy: Mycoplasma hyopneumoniae 232
- mja: Methanococcus jannaschii
- mjl: Mycobacterium sp. JLS
- mka: Methanopyrus kandleri
- mkm: Mycobacterium sp. KMS
- mla: Methanocorpusculum labreanum
- mle: Mycobacterium leprae TN
- mlo: Mesorhizobium loti
- mma: Methanosarcina mazei
- mmc: Mycobacterium sp. MCS
- mmi: Mycobacterium marinum M
- mmo: Mycoplasma mobile
- mmp: Methanococcus maripaludis S2
- mmq: Methanococcus maripaludis C5
- mmr: Maricaulis maris
- mms: Minibacterium massiliensis
- mmu: Mus musculus (mouse)
- mmw: Marinomonas sp. MWYL1
- mmx: Methanococcus maripaludis C6
- mmy: Mycoplasma mycoides
- mmz: Methanococcus maripaludis C7
- mpa: Mycobacterium avium paratuberculosis
- mpe: Mycoplasma penetrans
- mpn: Mycoplasma pneumoniae
- mpt: Methylibium petroleiphilum
- mpu: Mycoplasma pulmonis
- mra: Mycobacterium tuberculosis H37Ra
- mrd: Methylobacterium radiotolerans
- mse: Metallosphaera sedula
- msi: Methanobrevibacter smithii ATCC 35061
- msm: Mycobacterium smegmatis
- mst: Methanosphaera stadtmanae
- msu: Mannheimia succiniciproducens
- msy: Mycoplasma synoviae
- mta: Moorella thermoacetica
- mtc: Mycobacterium tuberculosis CDC1551
- mtf: Mycobacterium tuberculosis F11
- mth: Methanobacterium thermoautotrophicum
- mtp: Methanosaeta thermophila
- mtu: Mycobacterium tuberculosis H37Rv
- mul: Mycobacterium ulcerans
- mva: Mycobacterium vanbaalenii
- mvn: Methanococcus vannielii
- mxa: Myxococcus xanthus
- nar: Novosphingobium aromaticivorans
- nca: Nocardioides sp. JS614
- ncr: Neurospora crassa
- neq: Nanoarchaeum equitans
- net: Nitrosomonas eutropha
- neu: Nitrosomonas europaea
- nfa: Nocardia farcinica
- ngo: Neisseria gonorrhoeae
- nha: Nitrobacter hamburgensis
- nis: Nitratiruptor sp. SB155-2
- nma: Neisseria meningitidis Z2491 (serogroup A)
- nmc: Neisseria meningitidis FAM18 (serogroup C)
- nme: Neisseria meningitidis MC58 (serogroup B)
- nmn: Neisseria meningitidis 053442 (serogroup C)
- nmr: Nitrosopumilus maritimus
- nmu: Nitrosospira multiformis
- noc: Nitrosococcus oceani
- nph: Natronomonas pharaonis
- npu: Nostoc punctiforme
- nse: Neorickettsia sennetsu
- nve: Nematostella vectensis (sea anemone)
- nwi: Nitrobacter winogradskyi
- oaa: Ornithorhynchus anatinus (platypus)
- oan: Ochrobactrum anthropi
- oih: Oceanobacillus iheyensis
- olu: Ostreococcus lucimarinus
- ooe: Oenococcus oeni
- osa: Oryza sativa japonica (Japanese rice)
- ote: Opitutus terrae
- ots: Orientia tsutsugamushi Boryong
- ott: Orientia tsutsugamushi Ikeda
- pab: Pyrococcus abyssi
- pac: Propionibacterium acnes
- pae: Pseudomonas aeruginosa PAO1
- pai: Pyrobaculum aerophilum
- pan: Podospora anserina
- pap: Pseudomonas aeruginosa PA7
- par: Psychrobacter arcticum
- pas: Pyrobaculum arsenaticum
- pat: Pseudoalteromonas atlantica
- pau: Pseudomonas aeruginosa UCBPP-PA14
- pca: Pelobacter carbinolicus
- pcl: Pyrobaculum calidifontis
- pcr: Psychrobacter cryohalolentis
- pcu: Candidatus Protochlamydia amoebophila
- pde: Paracoccus denitrificans
- pdi: Parabacteroides distasonis
- pen: Pseudomonas entomophila
- pfa: Plasmodium falciparum 3D7
- pfl: Pseudomonas fluorescens Pf-5
- pfo: Pseudomonas fluorescens Pf0-1
- pfu: Pyrococcus furiosus
- pgi: Porphyromonas gingivalis W83
- pgn: Porphyromonas gingivalis ATCC 33277
- pha: Pseudoalteromonas haloplanktis
- pho: Pyrococcus horikoshii
- pic: Pichia stipitis
- pin: Psychromonas ingrahamii
- pis: Pyrobaculum islandicum
- pla: Parvibaculum lavamentivorans
- plt: Pelodictyon luteolum
- plu: Photorhabdus luminescens
- pma: Prochlorococcus marinus SS120
- pmb: Prochlorococcus marinus AS9601
- pmc: Prochlorococcus marinus MIT 9515
- pme: Prochlorococcus marinus NATL1A
- pmf: Prochlorococcus marinus MIT 9303
- pmg: Prochlorococcus marinus MIT 9301
- pmh: Prochlorococcus marinus MIT 9215
- pmi: Prochlorococcus marinus MIT9312
- pmj: Prochlorococcus marinus MIT 9211
- pmm: Prochlorococcus marinus MED4
- pmn: Prochlorococcus marinus NATL2A
- pmo: Petrotoga mobilis
- pmt: Prochlorococcus marinus MIT9313
- pmu: Pasteurella multocida
- pmy: Pseudomonas mendocina
- pna: Polaromonas naphthalenivorans
- pne: Polynucleobacter necessarius
- pnu: Polynucleobacter sp. QLW-P1DMWA-1
- pol: Polaromonas sp. JS666
- poy: Phytoplasma OY
- ppd: Pelobacter propionicus
- ppe: Pediococcus pentosaceus
- ppf: Pseudomonas putida F1
- ppg: Pseudomonas putida GB-1
- ppp: Physcomitrella patens subsp. patens
- ppr: Photobacterium profundum
- ppu: Pseudomonas putida KT2440
- ppw: Pseudomonas putida W619
- prw: Psychrobacter sp. PRwf-1
- psa: Pseudomonas stutzeri
- psb: Pseudomonas syringae pv. syringae B728a
- psp: Pseudomonas syringae pv. phaseolicola 1448A
- pst: Pseudomonas syringae pv. tomato DC3000
- pth: Pelotomaculum thermopropionicum
- pto: Picrophilus torridus
- ptr: Pan troglodytes (chimpanzee)
- pub: Candidatus Pelagibacter ubique
- pvi: Prosthecochloris vibrioformis
- pyo: Plasmodium yoelii
- rak: Rickettsia akari
- rba: Rhodopirellula baltica
- rbe: Rickettsia bellii RML369-C
- rbo: Rickettsia bellii OSU 85-389
- rca: Roseiflexus castenholzii DSM13941
- rci: Uncultured methanogenic archaeon RC-I
- rcm: Rickettsia canadensis
- rco: Rickettsia conorii
- rde: Roseobacter denitrificans
- rec: Rhizobium etli CIAT 652
- reh: Ralstonia eutropha H16
- ret: Rhizobium etli CFN 42
- reu: Ralstonia eutropha JMP134
- rfe: Rickettsia felis
- rfr: Rhodoferax ferrireducens
- rha: Rhodococcus sp. RHA1
- rle: Rhizobium leguminosarum
- rma: Candidatus Ruthia magnifica
- rme: Ralstonia metallidurans
- rms: Rickettsia massiliae
- rno: Rattus norvegicus (rat)
- rpa: Rhodopseudomonas palustris CGA009
- rpb: Rhodopseudomonas palustris HaA2
- rpc: Rhodopseudomonas palustris BisB18
- rpd: Rhodopseudomonas palustris BisB5
- rpe: Rhodopseudomonas palustris BisA53
- rpr: Rickettsia prowazekii
- rpt: Rhodopseudomonas palustris TIE-1
- rri: Rickettsia rickettsii Sheila Smith
- rrj: Rickettsia rickettsii Iowa
- rrs: Roseiflexus sp. RS-1
- rru: Rhodospirillum rubrum
- rsa: Renibacterium salmoninarum
- rsh: Rhodobacter sphaeroides ATCC 17029
- rso: Ralstonia solanacearum
- rsp: Rhodobacter sphaeroides 2.4.1
- rsq: Rhodobacter sphaeroides ATCC 17025
- rty: Rickettsia typhi
- rxy: Rubrobacter xylanophilus
- saa: Staphylococcus aureus USA300
- sab: Staphylococcus aureus RF122
- sac: Staphylococcus aureus COL
- sae: Staphylococcus aureus Newman
- sag: Streptococcus agalactiae 2603 (serotype V)
- sah: Staphylococcus aureus JH1
- sai: Sulfolobus acidocaldarius
- saj: Staphylococcus aureus JH9
- sak: Streptococcus agalactiae A909 (serotype Ia)
- sal: Sphingopyxis alaskensis
- sam: Staphylococcus aureus MW2
- san: Streptococcus agalactiae NEM316 (serotype III)
- sao: Staphylococcus aureus NCTC8325
- saq: Salinispora arenicola
- sar: Staphylococcus aureus MRSA252
- sas: Staphylococcus aureus MSSA476
- sat: Syntrophus aciditrophicus
- sau: Staphylococcus aureus N315
- sav: Staphylococcus aureus Mu50
- saw: Staphylococcus aureus Mu3
- sax: Staphylococcus aureus USA300 TCH1516
- saz: Shewanella amazonensis
- sbc: Shigella boydii CDC 3083-94
- sbl: Shewanella baltica OS155
- sbm: Shewanella baltica OS185
- sbn: Shewanella baltica OS195
- sbo: Shigella boydii Sb227
- sce: Saccharomyces cerevisiae
- scl: Sorangium cellulosum
- sco: Streptomyces coelicolor
- sde: Saccharophagus degradans
- sdn: Shewanella denitrificans
- sdy: Shigella dysenteriae
- sec: Salmonella enterica subsp. enterica serovar Choleraesuis
- sen: Saccharopolyspora erythraea
- sep: Staphylococcus epidermidis ATCC 12228
- ser: Staphylococcus epidermidis RP62A
- ses: Salmonella enterica subsp. arizonae
- sfl: Shigella flexneri 301 (serotype 2a)
- sfr: Shewanella frigidimarina
- sfu: Syntrophobacter fumaroxidans
- sfv: Shigella flexneri 8401 (serotype 5b)
- sfx: Shigella flexneri 2457T (serotype 2a)
- sgl: Sodalis glossinidius
- sgo: Streptococcus gordonii
- sgr: Streptomyces griseus
- sha: Staphylococcus haemolyticus
- she: Shewanella sp. MR-4
- shl: Shewanella halifaxensis
- shm: Shewanella sp. MR-7
- shn: Shewanella sp. ANA-3
- shw: Shewanella sp. W3-18-1
- sil: Ruegeria pomeroyi
- sit: Silicibacter sp. TM1040
- slo: Shewanella loihica
- sma: Streptomyces avermitilis
- smd: Sinorhizobium medicae
- sme: Sinorhizobium meliloti
- smg: Candidatus Sulcia muelleri GWSS
- sml: Stenotrophomonas maltophilia
- smr: Staphylothermus marinus
- smu: Streptococcus mutans
- son: Shewanella oneidensis
- spa: Streptococcus pyogenes MGAS10394 (serotype M6)
- spb: Streptococcus pyogenes MGAS6180 (serotype M28)
- spc: Shewanella putrefaciens
- spd: Streptococcus pneumoniae D39
- spe: Serratia proteamaculans
- spf: Streptococcus pyogenes Manfredo (serotype M5)
- spg: Streptococcus pyogenes MGAS315 (serotype M3)
- sph: Streptococcus pyogenes MGAS10270 (serotype M2)
- spi: Streptococcus pyogenes MGAS10750 (serotype M4)
- spj: Streptococcus pyogenes MGAS2096 (serotype M12)
- spk: Streptococcus pyogenes MGAS9429 (serotype M12)
- spl: Shewanella pealeana
- spm: Streptococcus pyogenes MGAS8232 (serotype M18)
- spn: Streptococcus pneumoniae TIGR4
- spo: Schizosaccharomyces pombe
- spq: Salmonella enterica subsp. enterica serovar Paratyphi B
- spr: Streptococcus pneumoniae R6
- sps: Streptococcus pyogenes SSI-1 (serotype M3)
- spt: Salmonella enterica subsp. enterica serovar Paratyphi A
- spu: Strongylocentrotus purpuratus (purple sea urchin)
- spv: Streptococcus pneumoniae Hungary19A 6
- spw: Streptococcus pneumoniae CGSP14 (serotype 14)
- spy: Streptococcus pyogenes SF370 (serotype M1)
- spz: Streptococcus pyogenes MGAS5005 (serotype M1)
- sru: Salinibacter ruber
- ssa: Streptococcus sanguinis
- ssc: Sus scrofa (pig)
- sse: Shewanella sediminis
- ssn: Shigella sonnei
- sso: Sulfolobus solfataricus
- ssp: Staphylococcus saprophyticus
- ssu: Streptococcus suis 05ZYH33
- ssv: Streptococcus suis 98HAH33
- stc: Streptococcus thermophilus CNRZ1066
- ste: Streptococcus thermophilus LMD-9
- sth: Symbiobacterium thermophilum
- stl: Streptococcus thermophilus LMG18311
- stm: Salmonella typhimurium LT2
- sto: Sulfolobus tokodaii
- stp: Salinispora tropica
- stt: Salmonella enterica subsp. enterica serovar Typhi Ty2
- sty: Salmonella enterica subsp. enterica serovar Typhi CT18
- sul: Sulfurihydrogenibium sp. YO3AOP1
- sun: Sulfurovum sp. NBC37-1
- sus: Solibacter usitatus
- swd: Shewanella woodyi ATCC 51908
- swi: Sphingomonas wittichii
- swo: Syntrophomonas wolfei
- syc: Synechococcus elongatus PCC6301
- syd: Synechococcus sp. CC9605
- sye: Synechococcus sp. CC9902
- syf: Synechococcus elongatus PCC7942
- syg: Synechococcus sp. CC9311
- syn: Synechocystis sp. PCC6803
- syp: Synechococcus sp. PCC7002
- syr: Synechococcus sp. RCC307
- syw: Synechococcus sp. WH8102
- syx: Synechococcus sp. WH7803
- tac: Thermoplasma acidophilum
- tan: Theileria annulata
- tbd: Thiobacillus denitrificans
- tbr: Trypanosoma brucei
- tca: Tribolium castaneum (red flour beetle)
- tcr: Trypanosoma cruzi
- tcx: Thiomicrospira crunogena
- tde: Treponema denticola
- tdn: Thiomicrospira denitrificans
- tel: Thermosynechococcus elongatus
- ter: Trichodesmium erythraeum
- tet: Tetrahymena thermophila
- tex: Thermoanaerobacter sp. X514
- tfu: Thermobifida fusca
- tko: Thermococcus kodakaraensis
- tle: Thermotoga lettingae
- tma: Thermotoga maritima
- tme: Thermosipho melanesiensis
- tne: Thermoproteus neutrophilus
- tpa: Treponema pallidum subsp. pallidum Nichols
- tpd: Thermoanaerobacter pseudethanolicus
- tpe: Thermofilum pendens
- tpp: Treponema pallidum subsp. pallidum SS14
- tpt: Thermotoga petrophila
- tpv: Theileria parva
- trq: Thermotoga sp. RQ2
- tte: Thermoanaerobacter tengcongensis
- tth: Thermus thermophilus HB27
- ttj: Thermus thermophilus HB8
- tva: Trichomonas vaginalis
- tvo: Thermoplasma volcanium
- twh: Tropheryma whipplei Twist
- tws: Tropheryma whipplei TW08/27
- uma: Ustilago maydis
- upa: Ureaplasma parvum serovar 3 ATCC 27815
- uur: Ureaplasma parvum serovar 3 ATCC 700970
- vch: Vibrio cholerae O1
- vco: Vibrio cholerae O395
- vei: Verminephrobacter eiseniae
- vfi: Vibrio fischeri
- vha: Vibrio harveyi
- vok: Candidatus Vesicomyosocius okutanii
- vpa: Vibrio parahaemolyticus
- vpo: Vanderwaltozyma polyspora
- vvu: Vibrio vulnificus CMCP6
- vvy: Vibrio vulnificus YJ016
- wbm: Wolbachia wBm
- wbr: Wigglesworthia glossinidia
- wol: Wolbachia wMel
- wpi: Wolbachia pipientis
- wsu: Wolinella succinogenes
- xac: Xanthomonas axonopodis
- xau: Xanthobacter autotrophicus
- xcb: Xanthomonas campestris pv. campestris 8004
- xcc: Xanthomonas campestris pv. campestris ATCC 33913
- xcv: Xanthomonas campestris pv. vesicatoria
- xfa: Xylella fastidiosa 9a5c
- xfm: Xylella fastidiosa M12
- xfn: Xylella fastidiosa M23
- xft: Xylella fastidiosa Temecula1
- xla: Xenopus laevis (African clawed frog)
- xom: Xanthomonas oryzae MAFF311018
- xoo: Xanthomonas oryzae KACC10331
- xtr: Xenopus tropicalis (western clawed frog)
- yen: Yersinia enterocolitica
- yli: Yarrowia lipolytica
- ypa: Yersinia pestis Antiqua
- ype: Yersinia pestis CO92
- ypg: Yersinia pestis Angola
- ypi: Yersinia pseudotuberculosis IP31758
- ypk: Yersinia pestis KIM
- ypm: Yersinia pestis Mediaevails
- ypn: Yersinia pestis Nepal516
- ypp: Yersinia pestis Pestoides
- yps: Yersinia pseudotuberculosis IP32953
- ypy: Yersinia pseudotuberculosis YPIII
- zmo: Zymomonas mobilis
Pathways
- 00010: Glycolysis / Gluconeogenesis
- 00020: Citrate cycle (TCA cycle)
- 00030: Pentose phosphate pathway
- 00031: (Undocumented)
- 00040: Pentose and glucuronate interconversions
- 00051: Fructose and mannose metabolism
- 00052: Galactose metabolism
- 00053: Ascorbate and aldarate metabolism
- 00061: Fatty acid biosynthesis
- 00062: Fatty acid elongation in mitochondria
- 00071: Fatty acid metabolism
- 00072: Synthesis and degradation of ketone bodies
- 00100: (Undocumented)
- 00120: (Undocumented)
- 00130: Ubiquinone and other terpenoid-quinone biosynthesis
- 00140: (Undocumented)
- 00150: Androgen and estrogen metabolism
- 00220: (Undocumented)
- 00230: Purine metabolism
- 00232: Caffeine metabolism
- 00240: Pyrimidine metabolism
- 00251: (Undocumented)
- 00252: (Undocumented)
- 00260: Glycine, serine and threonine metabolism
- 00271: (Undocumented)
- 00272: (Undocumented)
- 00280: Valine, leucine and isoleucine degradation
- 00281: Geraniol degradation
- 00290: Valine, leucine and isoleucine biosynthesis
- 00300: Lysine biosynthesis
- 00310: Lysine degradation
- 00311: Penicillin and cephalosporin biosynthesis
- 00330: Arginine and proline metabolism
- 00331: Clavulanic acid biosynthesis
- 00340: Histidine metabolism
- 00350: Tyrosine metabolism
- 00351: 1,1,1-Trichloro-2,2-bis(4-chlorophenyl)ethane (DDT) degradation
- 00360: Phenylalanine metabolism
- 00361: gamma-Hexachlorocyclohexane degradation
- 00362: (Undocumented)
- 00363: Bisphenol A degradation
- 00364: Fluorobenzoate degradation
- 00380: Tryptophan metabolism
- 00400: Phenylalanine, tyrosine and tryptophan biosynthesis
- 00401: Novobiocin biosynthesis
- 00410: beta-Alanine metabolism
- 00430: Taurine and hypotaurine metabolism
- 00440: Phosphonate and phosphinate metabolism
- 00450: Selenoamino acid metabolism
- 00460: (Undocumented)
- 00471: D-Glutamine and D-glutamate metabolism
- 00472: D-Arginine and D-ornithine metabolism
- 00473: D-Alanine metabolism
- 00480: Glutathione metabolism
- 00500: Starch and sucrose metabolism
- 00510: (Undocumented)
- 00520: Amino sugar and nucleotide sugar metabolism
- 00521: Streptomycin biosynthesis
- 00523: Polyketide sugar unit biosynthesis
- 00530: (Undocumented)
- 00540: Lipopolysaccharide biosynthesis
- 00550: Peptidoglycan biosynthesis
- 00561: Glycerolipid metabolism
- 00562: Inositol phosphate metabolism
- 00564: Glycerophospholipid metabolism
- 00565: Ether lipid metabolism
- 00590: Arachidonic acid metabolism
- 00591: Linoleic acid metabolism
- 00592: alpha-Linolenic acid metabolism
- 00600: Sphingolipid metabolism
- 00620: Pyruvate metabolism
- 00621: (Undocumented)
- 00622: Toluene and xylene degradation
- 00623: 2,4-Dichlorobenzoate degradation
- 00624: 1- and 2-Methylnaphthalene degradation
- 00625: (Undocumented)
- 00626: Naphthalene and anthracene degradation
- 00627: 1,4-Dichlorobenzene degradation
- 00628: Fluorene degradation
- 00629: Carbazole degradation
- 00630: Glyoxylate and dicarboxylate metabolism
- 00631: 1,2-Dichloroethane degradation
- 00632: (Undocumented)
- 00633: Trinitrotoluene degradation
- 00640: Propanoate metabolism
- 00641: 3-Chloroacrylic acid degradation
- 00642: Ethylbenzene degradation
- 00643: Styrene degradation
- 00650: Butanoate metabolism
- 00660: C5-Branched dibasic acid metabolism
- 00670: One carbon pool by folate
- 00680: Methane metabolism
- 00710: (Undocumented)
- 00720: (Undocumented)
- 00730: Thiamine metabolism
- 00740: Riboflavin metabolism
- 00750: Vitamin B6 metabolism
- 00760: Nicotinate and nicotinamide metabolism
- 00770: Pantothenate and CoA biosynthesis
- 00780: Biotin metabolism
- 00785: Lipoic acid metabolism
- 00790: Folate biosynthesis
- 00791: Atrazine degradation
- 00830: Retinol metabolism
- 00860: Porphyrin and chlorophyll metabolism
- 00900: Terpenoid backbone biosynthesis
- 00901: (Undocumented)
- 00902: Monoterpenoid biosynthesis
- 00903: (Undocumented)
- 00904: (Undocumented)
- 00905: Brassinosteroid biosynthesis
- 00906: Carotenoid biosynthesis
- 00908: (Undocumented)
- 00910: Nitrogen metabolism
- 00920: Sulfur metabolism
- 00930: Caprolactam degradation
- 00940: (Undocumented)
- 00941: (Undocumented)
- 00944: (Undocumented)
- 00950: (Undocumented)
- 00960: (Undocumented)
- 00970: Aminoacyl-tRNA biosynthesis
- 00980: Metabolism of xenobiotics by cytochrome P450
- 00981: (Undocumented)
- 00982: (Undocumented)
- 00983: (Undocumented)
[This page was last modified 02Nov09, 10:38 am.]
Model development and archiving support at physiome.org provided by the following grants: NIH U01HL122199 Analyzing the Cardiac Power Grid, 09/15/2015 - 05/31/2020, NIH/NIBIB BE08407 Software Integration, JSim and SBW 6/1/09-5/31/13; NIH/NHLBI T15 HL88516-01 Modeling for Heart, Lung and Blood: From Cell to Organ, 4/1/07-3/31/11; NSF BES-0506477 Adaptive Multi-Scale Model Simulation, 8/15/05-7/31/08; NIH/NHLBI R01 HL073598 Core 3: 3D Imaging and Computer Modeling of the Respiratory Tract, 9/1/04-8/31/09; as well as prior support from NIH/NCRR P41 RR01243 Simulation Resource in Circulatory Mass Transport and Exchange, 12/1/1980-11/30/01 and NIH/NIBIB R01 EB001973 JSim: A Simulation Analysis Platform, 3/1/02-2/28/07.