GapMind for catabolism of small carbon sources

 

4-hydroxybenzoate catabolism

Analysis of pathway 4-hydroxybenzoate in 201 genomes

Genome Best path
Acidimicrobium ferrooxidans DSM 10331 pcaK, pobA, praA, xylF, mhpD, mhpE, adh, acs
Acidithiobacillus ferrooxidans ATCC 23270 pcaK, pobA, praA, xylF, mhpD, mhpE, adh, acs
Acidovorax sp. GW101-3H11 pcaK, pobA, ligA, ligB, ligC, ligI, ligU, ligJ, ligK
Algiphilus aromaticivorans DG1253 pcaK, pobA, praA, xylF, mhpD, mhpE, adh, acs
Alicycliphilus denitrificans K601 pcaK, pobA, praA, praB, praC, praD, mhpD, mhpE, adh, acs
Alkalihalobacterium alkalinitrilicum DSM 22532 pcaK, pobA, praA, praB, praC, praD, mhpD, mhpE, adh, ackA, pta
Allochromatium vinosum DSM 180 pcaK, pobA, praA, xylF, mhpD, mhpE, adh, ackA, pta
Ammonifex degensii KC4 pcaK, pobA, praA, xylF, mhpD, mhpE, adh, acs
Anaerobutyricum hallii DSM 3353 pcaK, pobA, praA, xylF, mhpD, mhpE, adh, ackA, pta
Aquimarina longa SW024 pcaK, pobA, praA, praB, praC, praD, mhpD, mhpE, adh, ackA, pta
Archaeoglobus veneficus SNP6 pcaK, pobA, praA, xylF, mhpD, mhpE, adh, acs
Arcobacter nitrofigilis DSM 7299 pcaK, pobA, praA, xylF, mhpD, mhpE, adh, ackA, pta
Azoarcus olearius BH72 pcaK, pobA, ligA, ligB, ligC, ligI, ligU, ligJ, ligK
Azohydromonas australica DSM 1124 pcaK, pobA, ligA, ligB, ligC, ligI, ligU, ligJ, ligK
Azorhizobium caulinodans ORS 571 pcaK, pobA, pcaH, pcaG, pcaB, pcaC, pcaD, pcaI, pcaJ, pcaF
Azospirillum brasilense Sp245 pcaK, pobA, ligA, ligB, ligC, ligI, ligU, ligJ, ligK
Azospirillum sp. B510 pcaK, pobA, pcaH, pcaG, pcaB, pcaC, pcaD, catI, catJ, pcaF
Bacteroides thetaiotaomicron VPI-5482 pcaK, pobA, praA, xylF, mhpD, mhpE, adh, ackA, pta
Beijerinckia indica ATCC 9039 pcaK, pobA, praA, xylF, mhpD, mhpE, adh, acs
Beijerinckia mobilis UQM 1969 pcaK, pobA, pcaH, pcaG, pcaB, pcaC, pcaD, pcaI, pcaJ, pcaF
Billgrantia desiderata SP1 fcbT1, fcbT2, fcbT3, pobA, pcaH, pcaG, pcaB, pcaC, pcaD, catI, catJ, pcaF
Bradyrhizobium sp. BTAi1 pcaK, pobA, ligA, ligB, ligC, ligI, ligU, ligJ, ligK
Brevundimonas sp. GW460-12-10-14-LB2 pcaK, pobA, praA, xylF, mhpD, mhpE, adh, acs
Burkholderia phytofirmans PsJN pcaK, pobA, pcaH, pcaG, pcaB, pcaC, pcaD, pcaI, pcaJ, pcaF
Burkholderia vietnamiensis G4 pcaK, pobA, pcaH, pcaG, pcaB, pcaC, pcaD, pcaI, pcaJ, pcaF
Calditerrivibrio nitroreducens DSM 19672 pcaK, pobA, praA, xylF, mhpD, mhpE, adh, ackA, pta
Caminibacter mediatlanticus TB-2 pcaK, pobA, praA, xylF, mhpD, mhpE, adh, acs
Carboxydothermus pertinax Ug1 pcaK, pobA, praA, praB, praC, praD, mhpD, mhpE, ald-dh-CoA
Caulobacter crescentus NA1000 pcaK, pobA, pcaH, pcaG, pcaB, pcaC, pcaD, pcaI, pcaJ, pcaF
Cereibacter sphaeroides ATCC 17029 pcaK, pobA, praA, xylF, mhpD, mhpE, adh, acs
Chlorobaculum parvum NCIB 8327 pcaK, pobA, praA, xylF, mhpD, mhpE, adh, acs
Chlorobaculum tepidum TLS pcaK, pobA, praA, xylF, mhpD, mhpE, adh, acs
Chlorobium limicola DSM 245 pcaK, pobA, praA, xylF, mhpD, mhpE, adh, acs
Chlorobium phaeobacteroides BS1 pcaK, pobA, praA, xylF, mhpD, mhpE, adh, acs
Clostridium acetobutylicum ATCC 824 pcaK, pobA, praA, xylF, mhpD, mhpE, adh, ackA, pta
Clostridium kluyveri DSM 555 pcaK, pobA, praA, xylF, mhpD, mhpE, adh, ackA, pta
Clostridium tyrobutyricum FAM22553 pcaK, pobA, praA, xylF, mhpD, mhpE, adh, ackA, pta
Crocosphaera subtropica ATCC 51142 pcaK, pobA, praA, xylF, mhpD, mhpE, adh, ackA, pta
Cupriavidus basilensis FW507-4G11 pcaK, pobA, pcaH, pcaG, pcaB, pcaC, pcaD, pcaI, pcaJ, pcaF
Dechloromonas agitata is5 pcaK, pobA, praA, xylF, mhpD, mhpE, adh, ackA, pta
Dechlorosoma suillum PS pcaK, pobA, praA, xylF, mhpD, mhpE, adh, acs
Dehalococcoides mccartyi 195 pcaK, pobA, praA, xylF, mhpD, mhpE, ald-dh-CoA
Denitrovibrio acetiphilus DSM 12809 pcaK, pobA, praA, xylF, mhpD, mhpE, adh, ackA, pta
Derxia gummosa DSM 723 pcaK, pobA, ligA, ligB, ligC, ligI, ligU, ligJ, ligK
Desulfacinum hydrothermale DSM 13146 pcaK, pobA, praA, xylF, mhpD, mhpE, ald-dh-CoA
Desulfacinum infernum DSM 9756 pcaK, pobA, praA, xylF, mhpD, mhpE, ald-dh-CoA
Desulfarculus baarsii DSM 2075 pcaK, pobA, praA, xylF, mhpD, mhpE, adh, ackA, pta
Desulfatibacillum aliphaticivorans DSM 15576 pcaK, pobA, praA, xylF, mhpD, mhpE, adh, acs
Desulfatiglans anilini DSM 4660 fcbT1, fcbT2, fcbT3, hcl, hcrA, hcrB, hcrC, bamB, bamC, bamD, bamE, bamF, bamG, bamH, bamI, dch, had, oah, pimB, gcdH, ech, fadB, atoB
Desulfitobacterium hafniense DCB-2 pcaK, pobA, praA, xylF, mhpD, mhpE, ald-dh-CoA
Desulfobacca acetoxidans DSM 11109 pcaK, pobA, praA, xylF, mhpD, mhpE, ald-dh-CoA
Desulfobacter vibrioformis DSM 8776 pcaK, pobA, praA, xylF, mhpD, mhpE, adh, ackA, pta
Desulfogranum mediterraneum DSM 13871 pcaK, pobA, praA, xylF, mhpD, mhpE, adh, ackA, pta
Desulforamulus ruminis DSM 2154 pcaK, pobA, praA, xylF, mhpD, mhpE, ald-dh-CoA
Desulfoscipio geothermicus DSM 3669 pcaK, pobA, praA, xylF, mhpD, mhpE, ald-dh-CoA
Desulfotalea psychrophila LSv54 pcaK, pobA, praA, xylF, mhpD, mhpE, adh, ackA, pta
Desulfovibrio oxyclinae DSM 11498 pcaK, pobA, praA, xylF, mhpD, mhpE, adh, ackA, pta
Desulfovibrio vulgaris Hildenborough JW710 pcaK, pobA, praA, xylF, mhpD, mhpE, adh, ackA, pta
Desulfovibrio vulgaris Miyazaki F pcaK, pobA, praA, xylF, mhpD, mhpE, ald-dh-CoA
Desulfurobacterium atlanticum DSM 15668 pcaK, pobA, praA, xylF, mhpD, mhpE, adh, acs
Desulfuromonas acetexigens pcaK, pobA, praA, xylF, mhpD, mhpE, adh, ackA, pta
Desulfuromusa kysingii DSM 7343 pcaK, pobA, praA, xylF, mhpD, mhpE, adh, ackA, pta
Dinoroseobacter shibae DFL-12 pcaK, pobA, pcaH, pcaG, pcaB, pcaC, pcaD, pcaI, pcaJ, pcaF
Dyella japonica UNC79MFTsu3.2 pcaK, pobA, praA, xylF, mhpD, mhpE, adh, acs
Echinicola vietnamensis KMM 6221, DSM 17526 pcaK, pobA, praA, xylF, mhpD, mhpE, adh, acs
Escherichia coli BW25113 pcaK, pobA, praA, xylF, mhpD, mhpE, adh, ackA, pta
Ferroglobus placidus DSM 10642 pcaK, hcl, hcrA, hcrB, hcrC, bcrA, bcrB, bcrC, bcrD, dch, had, oah, pimB, gcdH, ech, fadB, atoB
Frankia alni ACN14a pcaK, pobA, praA, xylF, mhpD, mhpE, adh, acs
Geobacter metallireducens GS-15 pcaK, hcl, hcrA, hcrB, hcrC, bamB, bamC, bamD, bamE, bamF, bamG, bamH, bamI, dch, had, oah, pimB, gcdH, ech, fadB, atoB
Geotalea uraniireducens Rf4 pcaK, pobA, praA, xylF, mhpD, mhpE, adh, ackA, pta
Halococcus hamelinensis 100A6 pcaK, pobA, praA, xylF, mhpD, mhpE, adh, acs
Haloechinothrix alba DSM 45207 pcaK, pobA, pcaH, pcaG, pcaB, pcaC, pcaD, catI, catJ, pcaF
Haloferax volcanii DS2 pcaK, pobA, praA, xylF, mhpD, mhpE, adh, acs
Haloglycomyces albus DSM 45210 pcaK, pobA, praA, xylF, mhpD, mhpE, adh, ackA, pta
Halorhodospira halophila SL1 pcaK, pobA, praA, xylF, mhpD, mhpE, adh, acs
Heliomicrobium modesticaldum Ice1; ATCC 51547 pcaK, pobA, praA, xylF, mhpD, mhpE, ald-dh-CoA
Herbaspirillum autotrophicum IAM 14942 pcaK, pobA, pcaH, pcaG, pcaB, pcaC, pcaD, pcaI, pcaJ, pcaF
Herbaspirillum seropedicae SmR1 pcaK, pobA, pcaH, pcaG, pcaB, pcaC, pcaD, pcaI, pcaJ, pcaF
Hippea alviniae EP5-r pcaK, pobA, praA, xylF, mhpD, mhpE, adh, acs
Hydrogenophaga taeniospiralis NBRC 102512 pcaK, pobA, ligA, ligB, ligC, ligI, ligU, ligJ, ligK
Hydrogenovibrio halophilus DSM 15072 pcaK, pobA, praA, xylF, mhpD, mhpE, adh, ackA, pta
Hydrogenovibrio kuenenii DSM 12350 pcaK, pobA, praA, xylF, mhpD, mhpE, adh, ackA, pta
Hydrogenovibrio marinus DSM 11271 pcaK, pobA, praA, xylF, mhpD, mhpE, adh, ackA, pta
Hyphomicrobium sulfonivorans WDL6 pcaK, pobA, praA, xylF, mhpD, mhpE, adh, acs
Klebsiella michiganensis M5al pcaK, pobA, pcaH, pcaG, pcaB, pcaC, pcaD, pcaI, pcaJ, pcaF
Klebsiella variicola At-22 pcaK, pobA, pcaH, pcaG, pcaB, pcaC, pcaD, pcaI, pcaJ, pcaF
Kyrpidia tusciae DSM 2912 pcaK, pobA, praA, praB, praC, praD, mhpD, mhpE, adh, acs
Leptospirillum ferrooxidans C2-3 pcaK, pobA, praA, xylF, mhpD, mhpE, adh, acs
Magnetospirillum magneticum AMB-1 pcaK, hcl, hcrA, hcrB, hcrC, bcrA, bcrB, bcrC, bcrD, dch, had, oah, pimB, gcdH, ech, fadB, atoB
Malonomonas rubra DSM 5091 pcaK, pobA, praA, xylF, mhpD, mhpE, adh, ackA, pta
Maridesulfovibrio bastinii DSM 16055 pcaK, pobA, praA, xylF, mhpD, mhpE, adh, ackA, pta
Maridesulfovibrio zosterae DSM 11974 pcaK, pobA, praA, xylF, mhpD, mhpE, ald-dh-CoA*
Marinobacter adhaerens HP15 pcaK, pobA, praA, praB, praC, praD, mhpD, mhpE, adh, ackA, pta
Mesorhizobium ciceri WSM1271 pcaK, pobA, pcaH, pcaG, pcaB, pcaC, pcaD, catI, catJ, pcaF
Methanobacterium lacus AL-21 pcaK, pobA, praA, xylF, mhpD, mhpE, adh, acs
Methanococcus aeolicus Nankai-3 pcaK, pobA, praA, xylF, mhpD, mhpE, ald-dh-CoA
Methanococcus maripaludis C5 pcaK, pobA, praA, xylF, mhpD, mhpE, ald-dh-CoA
Methanosarcina acetivorans C2A pcaK, pobA, praA, xylF, mhpD, mhpE, adh, ackA, pta
Methanosarcina mazei Go1 pcaK, pobA, praA, xylF, mhpD, mhpE, adh, ackA, pta
Methanospirillum lacunae Ki8-1 pcaK, pobA, praA, xylF, mhpD, mhpE, adh, acs
Methanothermobacter thermautotrophicus Delta H pcaK, pobA, praA, xylF, mhpD, mhpE, ald-dh-CoA
Methylobacterium nodulans ORS 2060 pcaK, pobA, pcaH, pcaG, pcaB, pcaC, pcaD, pcaI, pcaJ, pcaF
Methylobacterium sp. 4-46 Apr-46 pcaK, pobA, pcaH, pcaG, pcaB, pcaC, pcaD, pcaI, pcaJ, pcaF
Methylocapsa acidiphila B2 pcaK, pobA, praA, xylF, mhpD, mhpE, adh, acs
Methylocapsa aurea KYG pcaK, pobA, praA, xylF, mhpD, mhpE, adh, acs
Methylocella silvestris BL2 pcaK, pobA, praA, praB, praC, praD, mhpD, mhpE, adh, acs
Methylococcus capsulatus Bath pcaK, pobA, praA, xylF, mhpD, mhpE, adh, acs
Methylocystis bryophila S285 pcaK, pobA, praA, xylF, mhpD, mhpE, adh, acs
Methyloferula stellata AR4T pcaK, pobA, praA, xylF, mhpD, mhpE, adh, acs
Methylohalobius crimeensis 10Ki pcaK, pobA, praA, xylF, mhpD, mhpE, adh, acs
Methylomonas methanica MC09 pcaK, pobA, praA, xylF, mhpD, mhpE, adh, ackA, pta
Methylosarcina fibrata AML-C10 pcaK, pobA, praA, xylF, mhpD, mhpE, adh, acs
Methylotuvimicrobium alcaliphilum 20Z pcaK, pobA, praA, xylF, mhpD, mhpE, adh, ackA, pta
Methylovulum miyakonense HT12 pcaK, pobA, praA, xylF, mhpD, mhpE, adh, acs
Mycolicibacterium vanbaalenii PYR-1 pcaK, pobA, pcaH, pcaG, pcaB, pcaC, pcaD, pcaI, pcaJ, pcaF
Nitratifractor salsuginis DSM 16511 pcaK, pobA, praA, xylF, mhpD, mhpE, adh, ackA, pta
Nitratiruptor tergarcus DSM 16512 pcaK, pobA, praA, xylF, mhpD, mhpE, adh, acs
Nitriliruptor alkaliphilus DSM 45188 pcaK, pobA, pcaH, pcaG, pcaB, pcaC, pcaD, catI, catJ, pcaF
Nocardioides dokdonensis FR1436 pcaK, pobA, praA, xylF, mhpD, mhpE, adh, acs
Nocardiopsis lucentensis DSM 44048 pcaK, pobA, pcaH, pcaG, pcaB, pcaC, pcaD, pcaI, pcaJ, pcaF
Nostoc punctiforme ATCC 29133; PCC 73102 pcaK, pobA, praA, xylF, mhpD, mhpE, adh, acs
Novosphingobium aromaticivorans DSM 12444 pcaK, pobA, ligA, ligB, ligC, ligI, ligU, ligJ, ligK
Oleispira antarctica pcaK, pobA, praA, xylF, mhpD, mhpE, ald-dh-CoA
Paraburkholderia atlantica CCGE1002 pcaK, pobA, pcaH, pcaG, pcaB, pcaC, pcaD, pcaI, pcaJ, pcaF
Paraburkholderia bryophila 376MFSha3.1 pcaK, pobA, pcaH, pcaG, pcaB, pcaC, pcaD, pcaI, pcaJ, pcaF
Paraburkholderia phymatum STM815 pcaK, pobA, ligA, ligB, ligC, ligI, ligU, ligJ, ligK
Paucidesulfovibrio gracilis DSM 16080 pcaK, pobA, praA, xylF, mhpD, mhpE, adh, ackA, pta
Pedobacter sp. GW460-11-11-14-LB5 pcaK, pobA, praA, xylF, mhpD, mhpE, adh, ackA, pta
Pelobacter propionicus DSM 2379 pcaK, pobA, praA, xylF, mhpD, mhpE, adh, ackA, pta
Persephonella marina EX-H1 pcaK, pobA, praA, xylF, mhpD, mhpE, adh, acs
Phaeacidiphilus oryzae TH49 pcaK, pobA, pcaH, pcaG, pcaB, pcaC, pcaD, pcaI, pcaJ, pcaF
Phaeobacter inhibens BS107 pcaK, pobA, pcaH, pcaG, pcaB, pcaC, pcaD, pcaI, pcaJ, pcaF
Polaromonas naphthalenivorans CJ2 pcaK, pobA, ligA, ligB, ligC, ligI, ligU, ligJ, ligK
Prosthecochloris aestuarii DSM 271 pcaK, pobA, praA, xylF, mhpD, mhpE, adh, acs
Pseudarthrobacter sulfonivorans Ar51 pcaK, pobA, pcaH, pcaG, pcaB, pcaC, pcaD, pcaI, pcaJ, pcaF
Pseudomonas benzenivorans DSM 8628 pcaK, pobA, pcaH, pcaG, pcaB, pcaC, pcaD, catI, catJ, pcaF
Pseudomonas fluorescens FW300-N1B4 pcaK, pobA, pcaH, pcaG, pcaB, pcaC, pcaD, catI, catJ, pcaF
Pseudomonas fluorescens FW300-N2C3 pcaK, pobA, pcaH, pcaG, pcaB, pcaC, pcaD, catI, catJ, pcaF
Pseudomonas fluorescens FW300-N2E2 pcaK, pobA, pcaH, pcaG, pcaB, pcaC, pcaD, catI, catJ, pcaF
Pseudomonas fluorescens FW300-N2E3 pcaK, pobA, pcaH, pcaG, pcaB, pcaC, pcaD, catI, catJ, pcaF
Pseudomonas fluorescens GW456-L13 pcaK, pobA, pcaH, pcaG, pcaB, pcaC, pcaD, catI, catJ, pcaF
Pseudomonas putida KT2440 pcaK, pobA, pcaH, pcaG, pcaB, pcaC, pcaD, pcaI, pcaJ, pcaF
Pseudomonas simiae WCS417 pcaK, pobA, pcaH, pcaG, pcaB, pcaC, pcaD, catI, catJ, pcaF
Pseudomonas stutzeri RCH2 pcaK, pobA, pcaH, pcaG, pcaB, pcaC, pcaD, catI, catJ, pcaF
Pyrolobus fumarii 1A pcaK, pobA, praA, xylF, mhpD, mhpE, ald-dh-CoA
Rhizobium etli CFN 42 pcaK, pobA, pcaH, pcaG, pcaB, pcaC, pcaD, pcaI, pcaJ, pcaF
Rhizobium johnstonii 3841 pcaK, pobA, pcaH, pcaG, pcaB, pcaC, pcaD, pcaI, pcaJ, pcaF
Rhizobium leguminosarum WSM1325 pcaK, pobA, pcaH, pcaG, pcaB, pcaC, pcaD, pcaI, pcaJ, pcaF
Rhizorhabdus wittichii RW1 pcaK, pobA, pcaH, pcaG, pcaB, pcaC, pcaD, pcaI, pcaJ, pcaF
Rhodanobacter denitrificans FW104-10B01 pcaK, pobA, praA, xylF, mhpD, mhpE, adh, acs
Rhodomicrobium vannielii ATCC 17100 pcaK, hcl, hcrA, hcrB, hcrC, bcrA, bcrB, bcrC, bcrD, dch, had, oah, pimB, gcdH, ech, fadB, atoB
Rhodopseudomonas palustris CGA009 pcaK, hcl, hcrA, hcrB, hcrC, bcrA, bcrB, bcrC, bcrD, Ch1CoA, badK, badH, badI, pimD, pimC, pimF, gcdH, ech, fadB, atoB
Rhodospirillum centenum SW; ATCC 51521 pcaK, pobA, praA, xylF, mhpD, mhpE, adh, acs
Rhodospirillum rubrum ATCC 11170 pcaK, pobA, praA, xylF, mhpD, mhpE, adh, ackA, pta
Roseburia faecis M72 pcaK, pobA, praA, xylF, mhpD, mhpE, adh, ackA, pta
Saccharomonospora cyanea NA-134 pcaK, pobA, pcaH, pcaG, pcaB, pcaC, pcaD, catI, catJ, pcaF
Sedimenticola selenatireducens DSM 17993 pcaK, hcl, hcrA, hcrB, hcrC, boxA, boxB, boxC, boxD, paaF, paaH, paaJ2
Shewanella amazonensis SB2B pcaK, pobA, praA, xylF, mhpD, mhpE, adh, ackA, pta
Shewanella loihica PV-4 pcaK, pobA, praA, xylF, mhpD, mhpE, adh, ackA, pta
Shewanella oneidensis MR-1 pcaK, pobA, praA, xylF, mhpD, mhpE, adh, ackA, pta
Shewanella sp. ANA-3 pcaK, pobA, praA, xylF, mhpD, mhpE, adh, ackA, pta
Sinorhizobium fredii NGR234 pcaK, pobA, pcaH, pcaG, pcaB, pcaC, pcaD, catI, catJ, pcaF
Sinorhizobium medicae WSM419 pcaK, pobA, pcaH, pcaG, pcaB, pcaC, pcaD, pcaI, pcaJ, pcaF
Sinorhizobium meliloti 1021 pcaK, pobA, pcaH, pcaG, pcaB, pcaC, pcaD, catI, catJ, pcaF
Sphingomonas koreensis DSMZ 15582 pcaK, pobA, ligA, ligB, ligC, ligI, ligU, ligJ, ligK
Stenotrophomonas chelatiphaga DSM 21508 pcaK, pobA, pcaH, pcaG, pcaB, pcaC, pcaD, pcaI, pcaJ, pcaF
Steroidobacter denitrificans DSM 18526 pcaK, pobA, praA, xylF, mhpD, mhpE, adh, ackA, pta
Stutzerimonas stutzeri A1501 pcaK, pobA, pcaH, pcaG, pcaB, pcaC, pcaD, catI, catJ, pcaF
Sulfuricurvum kujiense DSM 16994 pcaK, pobA, praA, xylF, mhpD, mhpE, adh, ackA, pta
Sulfurihydrogenibium azorense Az-Fu1 pcaK, pobA, praA, xylF, mhpD, mhpE, adh, acs
Sulfurihydrogenibium subterraneum DSM 15120 pcaK, pobA, praA, xylF, mhpD, mhpE, adh, acs
Sulfurimonas denitrificans DSM 1251 pcaK, pobA, praA, xylF, mhpD, mhpE, adh, ackA, pta
Sulfuritalea hydrogenivorans DSM 22779 pcaK, hcl, hcrA, hcrB, hcrC, bcrA, bcrB, bcrC, bcrD, dch, had, oah, pimB, gcdH, ech, fadB, atoB
Sulfurivirga caldicuralii DSM 17737 pcaK, pobA, praA, xylF, mhpD, mhpE, adh, acs
Synechococcus elongatus PCC 7942 pcaK, pobA, praA, xylF, mhpD, mhpE, adh, acs
Teredinibacter turnerae T7901 pcaK, pobA, praA, xylF, mhpD, mhpE, adh, ackA, pta
Thauera aminoaromatica S2 pcaK, hcl, hcrA, hcrB, hcrC, bcrA, bcrB, bcrC, bcrD, dch, had, oah, pimB, gcdH, ech, fadB, atoB
Thermithiobacillus tepidarius DSM 3134 pcaK, pobA, praA, xylF, mhpD, mhpE, adh, acs
Thermocrinis albus DSM 14484 pcaK, pobA, praA, xylF, mhpD, mhpE, adh, acs
Thermodesulforhabdus norvegica DSM 9990 pcaK, pobA, praA, xylF, mhpD, mhpE, adh, acs
Thermomonospora curvata DSM 43183 pcaK, pobA, pcaH, pcaG, pcaB, pcaC, pcaD, pcaI, pcaJ, pcaF
Thermovibrio ammonificans HB-1 pcaK, pobA, praA, xylF, mhpD, mhpE, adh, acs
Thermus aquaticus YT-1 pcaK, pobA, praA, xylF, mhpD, mhpE, adh, acs
Thioalkalivibrio denitrificans ALJD pcaK, pobA, praA, xylF, mhpD, mhpE, adh, ackA, pta
Thioalkalivibrio halophilus HL17 pcaK, pobA, praA, xylF, mhpD, mhpE, adh, acs
Thioalkalivibrio paradoxus ARh 1 pcaK, pobA, praA, xylF, mhpD, mhpE, adh, acs
Thioalkalivibrio thiocyanodenitrificans ARhD 1 pcaK, pobA, praA, xylF, mhpD, mhpE, adh, ackA, pta
Thiohalomonas denitrificans HLD2 pcaK, pobA, praA, xylF, mhpD, mhpE, adh, acs
Thiohalospira halophila HL 3 pcaK, pobA, praA, xylF, mhpD, mhpE, adh, acs
Thiomicrorhabdus arctica DSM 13458 pcaK, pobA, praA, xylF, mhpD, mhpE, ald-dh-CoA
Thiomicrorhabdus chilensis DSM 12352 pcaK, pobA, praA, xylF, mhpD, mhpE, adh, acs
Thiomicrospira cyclica ALM1 pcaK, pobA, praA, xylF, mhpD, mhpE, adh, acs
Thiomicrospira microaerophila ASL8-2 pcaK, pobA, praA, xylF, mhpD, mhpE, adh, acs
Thiomicrospira pelophila DSM 1534 pcaK, pobA, praA, xylF, mhpD, mhpE, adh, acs
Thiothrix lacustris DSM 21227 pcaK, pobA, praA, praB, praC, praD, mhpD, mhpE, adh, ackA, pta
Tistlia consotensis USBA 355 pcaK, pobA, pcaH, pcaG, pcaB, pcaC, pcaD, pcaI, pcaJ, pcaF
Trichlorobacter lovleyi SZ pcaK, pobA, praA, xylF, mhpD, mhpE, adh, ackA, pta
Trichodesmium erythraeum IMS101 Annotated Metagenome-Assembled Genome pcaK, pobA, praA, xylF, mhpD, mhpE, adh, acs
Trichormus variabilis ATCC 29413 pcaK, pobA, praA, xylF, mhpD, mhpE, adh, acs
Xanthobacter autotrophicus Py2 pcaK, pobA, pcaH, pcaG, pcaB, pcaC, pcaD, pcaI, pcaJ, pcaF
Xenophilus azovorans DSM 13620 pcaK, pobA, praA, praB, praC, praD, mhpD, mhpE, adh, acs

Confidence: high confidence medium confidence low confidence
transporter – transporters and PTS systems are shaded because predicting their specificity is particularly challenging.

This GapMind analysis is from Apr 09 2024. The underlying query database was built on Sep 17 2021.

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About GapMind

Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.

A candidate for a step is "high confidence" if either:

where "other" refers to the best ublast hit to a sequence that is not annotated as performing this step (and is not "ignored").

Otherwise, a candidate is "medium confidence" if either:

Other blast hits with at least 50% coverage are "low confidence."

Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:

GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).

For more information, see:

If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know

by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory