GapMind for catabolism of small carbon sources

 

4-hydroxybenzoate catabolism

Analysis of pathway 4-hydroxybenzoate in 276 genomes

Genome Best path
Acidovorax caeni R-24608 pcaK, pobA, praA, praB, praC, praD, mhpD, mhpE, adh, acs
Actinokineospora bangkokensis 44EHW pcaK, pobA, praA, xylF, mhpD, mhpE, adh, acs
Actinomyces timonensis 7400942 pcaK, pobA, praA, xylF, mhpD, mhpE, adh, ackA, pta
Algiphilus aromaticivorans DG1253 pcaK, pobA, praA, xylF, mhpD, mhpE, adh, acs
Algoriphagus aquaeductus T4 pcaK, pobA, praA, xylF, mhpD, mhpE, adh, ackA, pta
Algoriphagus machipongonensis PR1 pcaK, pobA, praA, xylF, mhpD, mhpE, adh, acs
Alicyclobacillus ferrooxydans TC-34 pcaK, pobA, praA, xylF, mhpD, mhpE, adh, acs
Alishewanella agri BL06 pcaK, pobA, pcaH, pcaG, pcaB, pcaC, pcaD, pcaI, pcaJ, pcaF
Alistipes indistinctus YIT 12060 pcaK, pobA, praA, xylF, mhpD, mhpE, adh, ackA, pta
Alistipes shahii WAL 8301 pcaK, pobA, praA, xylF, mhpD, mhpE, adh, ackA, pta
Alkalitalea saponilacus SC/BZ-SP2 pcaK, pobA, praA, xylF, mhpD, mhpE, adh, ackA, pta
Amantichitinum ursilacus IGB-41 pcaK, pobA, praA, xylF, mhpD, mhpE, ald-dh-CoA
Amphibacillus jilinensis Y1 pcaK, pobA, praA, praB, praC, praD, mhpD, mhpE, ald-dh-CoA
Amphritea japonica JAMM 1866 pcaK, pobA, ligA, ligB, ligC, ligI, ligU, ligJ, ligK
Amycolatopsis halophila YIM 93223 pcaK, pobA, pcaH, pcaG, pcaB, pcaC*, pcaD, catI, catJ, pcaF
Amycolatopsis xylanica CPCC 202699 pcaK, pobA, pcaH, pcaG, pcaB, pcaC, pcaD, catI, catJ, pcaF
Aquimarina agarilytica ZC1 pcaK, pobA, praA, xylF, mhpD, mhpE, adh, ackA, pta
Aquimarina longa SW024 pcaK, pobA, praA, praB, praC, praD, mhpD, mhpE, adh, ackA, pta
Aquimarina macrocephali JAMB N27 pcaK, pobA, praA, praB, praC, praD, mhpD, mhpE, adh, ackA, pta
Archaeoglobus sulfaticallidus PM70-1 pcaK, pobA, praA, xylF, mhpD, mhpE, adh, acs
Arcticibacter svalbardensis MN12-7 pcaK, pobA, praA, xylF, mhpD, mhpE, adh, ackA, pta
Ardenticatena maritima 110S pcaK, pobA, praA, xylF, mhpD, mhpE, adh, acs
Arenimonas metalli CF5-1 pcaK, pobA, praA, xylF, mhpD, mhpE, adh, acs
Arenitalea lutea P7-3-5 pcaK, pobA, praA, xylF, mhpD, mhpE, adh, ackA, pta
Azospirillum humicireducens SgZ-5 pcaK, pobA, pcaH, pcaG, pcaB, pcaC, pcaD, catI, catJ, pcaF
Azospirillum thiophilum BV-S pcaK, pobA, pcaH, pcaG, pcaB, pcaC, pcaD, catI, catJ, pcaF
Bacillus altitudinis 41KF2b pcaK, pobA, praA, praB, praC, praD, mhpD, mhpE, adh, ackA, pta
Bacillus coahuilensis m4-4 pcaK, pobA, praA, praB, praC, praD, mhpD, mhpE, adh, ackA, pta
Bacillus cytotoxicus NVH 391-98 pcaK, pobA, praA, praB, praC, praD, mhpD, mhpE, adh, ackA, pta
Bacillus horneckiae 1P01SC pcaK, pobA, praA, praB, praC, praD, mhpD, mhpE, adh, ackA, pta
Bacillus okhensis Kh10-101 pcaK, pobA, praA, praB, praC, praD, mhpD, mhpE, adh, ackA, pta
Bacillus safensis FO-36b pcaK, pobA, praA, praB, praC, praD, mhpD, mhpE, adh, ackA, pta
Bacillus velezensis CBMB205 pcaK, pobA, praA, praB, praC, praD, mhpD, mhpE, adh, ackA, pta
Bacteroides clarus YIT 12056 pcaK, pobA, praA, xylF, mhpD, mhpE, adh, ackA, pta
Bacteroides faecis MAJ27 pcaK, pobA, praA, xylF, mhpD, mhpE, adh, ackA, pta
Bacteroides fluxus YIT 12057 pcaK, pobA, praA, xylF, mhpD, mhpE, adh, ackA, pta
Bacteroides oleiciplenus YIT 12058 pcaK, pobA, praA, xylF, mhpD, mhpE, adh, ackA, pta
Barnesiella intestinihominis YIT 11860 pcaK, pobA, praA, xylF, mhpD, mhpE, adh, ackA, pta
Belnapia rosea CPCC 100156 pcaK, pobA, pcaH, pcaG, pcaB, pcaC, pcaD, pcaI, pcaJ, pcaF
Bizionia argentinensis JUB59 pcaK, pobA, praA, xylF, mhpD, mhpE, adh, acs
Bradyrhizobium diazoefficiens USDA110 pcaK, pobA, pcaH, pcaG, pcaB, pcaC, pcaD, pcaI, pcaJ, pcaF
Brevibacterium jeotgali SJ5-8 pcaK, pobA, praA, xylF, mhpD, mhpE, adh, acs
Brucella inopinata BO1 pcaK, pobA, pcaH, pcaG, pcaB, pcaC, pcaD, pcaI, pcaJ, pcaF
Brucella microti CCM 4915 pcaK, pobA, pcaH, pcaG, pcaB, pcaC, pcaD, pcaI, pcaJ, pcaF
Bryobacter aggregatus MPL3 pcaK, pobA, praA, xylF, mhpD, mhpE, adh, acs
Caldicellulosiruptor hydrothermalis 108 pcaK, pobA, praA, xylF, mhpD, mhpE, adh, ackA, pta
Caldicellulosiruptor kronotskyensis 2002 pcaK, pobA, praA, xylF, mhpD, mhpE, adh, ackA, pta
Carboxydothermus pertinax Ug1 pcaK, pobA, praA, praB, praC, praD, mhpD, mhpE, ald-dh-CoA
Catellicoccus marimammalium M35/04/3 pcaK, pobA, praA, xylF, mhpD, mhpE, adh, ackA, pta
Chromobacterium vaccinii MWU205 pcaK, pobA, praA, xylF, mhpD, mhpE, adh, ackA, pta
Chryseobacterium angstadtii KM pcaK, pobA, praA, xylF, mhpD, mhpE, adh, acs
Chryseobacterium arthrosphaerae CC-VM-7 pcaK, pobA, praA, xylF, mhpD, mhpE, adh, acs
Chryseobacterium viscerum 687B-08 pcaK, pobA, praA, xylF, mhpD, mhpE, adh, acs
Cloacibacillus porcorum CL-84 pcaK, pobA, praA, praB, praC, praD, mhpD, mhpE, ald-dh-CoA
Cobetia crustatorum JO1 pcaK, pobA, praA, xylF, mhpD, mhpE, adh, acs
Collimonas arenae Ter10 pcaK, pobA, pcaH, pcaG, pcaB, pcaC, pcaD, pcaI, pcaJ, pcaF
Collimonas pratensis Ter91 pcaK, pobA, pcaH, pcaG, pcaB, pcaC, pcaD, pcaI, pcaJ, pcaF
Collinsella tanakaei YIT 12063 pcaK, pobA, praA, xylF, mhpD, mhpE, ald-dh-CoA
Coprobacter fastidiosus NSB1 pcaK, pobA, praA, xylF, mhpD, mhpE, adh, ackA, pta
Corynebacterium deserti GIMN1.010 pcaK, pobA, pcaH, pcaG, pcaB, pcaC, pcaD, pcaI, pcaJ, pcaF
Corynebacterium frankenforstense ST18 pcaK, pobA, praA, xylF, mhpD, mhpE, adh, ackA, pta
Corynebacterium lactis RW2-5 pcaK, pobA, praA, xylF, mhpD, mhpE, adh, ackA, pta
Croceitalea dokdonensis DOKDO 023 pcaK, pobA, praA, xylF, mhpD, mhpE, adh, acs
Cronobacter condimenti 1330 pcaK, pobA, praA, xylF, mhpD, mhpE, adh, ackA, pta
Cronobacter muytjensii ATCC 51329 pcaK, pobA, praA, xylF, mhpD, mhpE, adh, ackA, pta
Cronobacter universalis NCTC 9529 pcaK, pobA, praA, xylF, mhpD, mhpE, adh, ackA, pta
Desulfatitalea tepidiphila S28bF pcaK, pobA, praA, xylF, mhpD, mhpE, adh, acs
Desulfotomaculum hydrothermale Lam5 pcaK, pobA, praA, xylF, mhpD, mhpE, ald-dh-CoA
Dethiosulfovibrio salsuginis USBA 82 pcaK, pobA, praA, xylF, mhpD, mhpE, ald-dh-CoA
Devosia chinhatensis IPL18 pcaK, pobA, praA, xylF, mhpD, mhpE, adh, acs
Devriesea agamarum IMP2 pcaK, pobA, praA, xylF, mhpD, mhpE, ald-dh-CoA
Dialister succinatiphilus YIT 11850 pcaK, pobA, praA, xylF, mhpD, mhpE, adh, acs
Dietzia timorensis ID05-A0528 pcaK, pobA, pcaH, pcaG, pcaB, pcaC, pcaD, pcaI, pcaJ, pcaF
Dokdonella koreensis DS-123 pcaK, pobA, praA, xylF, mhpD, mhpE, adh, acs
Domibacillus robiginosus WS 4628 pcaK, pobA, praA, praB, praC, praD, mhpD, mhpE, adh, ackA, pta
Duganella sacchari Sac-22 pcaK, pobA, praA, praB, praC, praD, mhpD, mhpE, adh, acs
Dyadobacter tibetensis Y620-1 pcaK, pobA, praA, xylF, mhpD, mhpE, adh, acs
Dyella jiangningensis SBZ3-12 pcaK, pobA, pcaH, pcaG, pcaB, pcaC, pcaD, pcaI, pcaJ, pcaF
Endozoicomonas montiporae CL-33 pcaK, pobA, praA, xylF, mhpD, mhpE, adh, ackA, pta
Enterococcus termitis LMG 8895 pcaK, pobA, praA, xylF, mhpD, mhpE, ald-dh-CoA
Enterorhabdus caecimuris B7 pcaK, pobA, praA, xylF, mhpD, mhpE, adh, ackA, pta
Epibacterium ulvae U95 pcaK, pobA, pcaH, pcaG, pcaB, pcaC, pcaD, pcaI, pcaJ, pcaF
Erythrobacter gangjinensis K7-2 pcaK, pobA, praA, xylF, mhpD, mhpE, adh, acs
Erythrobacter marinus HWDM-33 pcaK, pobA, praA, xylF, mhpD, mhpE, adh, acs
Ethanoligenens harbinense YUAN-3 pcaK, pobA, praA, xylF, mhpD, mhpE, ald-dh-CoA
Fervidicella metallireducens AeB pcaK, pobA, praA, xylF, mhpD, mhpE, ald-dh-CoA
Fibrella aestuarina BUZ 2 pcaK, pobA, praA, xylF, mhpD, mhpE, adh, acs
Flammeovirga pacifica WPAGA1 pcaK, pobA, praA, xylF, mhpD, mhpE, adh, ackA, pta
Flaviramulus ichthyoenteri Th78 pcaK, pobA, praA, xylF, mhpD, mhpE, adh, ackA, pta
Flavobacterium beibuense F44-8 pcaK, pobA, praA, xylF, mhpD, mhpE, adh, acs
Flavobacterium glycines Gm-149 pcaK, pobA, pcaH, pcaG, pcaB, pcaC, pcaD, pcaI, pcaJ, pcaF
Flavobacterium sp. LM5 pcaK, pobA, praA, xylF, mhpD, mhpE, adh, ackA, pta
Flavobacterium ummariense DS-12 pcaK, pobA, praA, xylF, mhpD, mhpE, adh, acs
Frischella perrara PEB0191 pcaK, pobA, praA, xylF, mhpD, mhpE, ald-dh-CoA
Galbibacter marinus ck-I2-15 pcaK, pobA, praA, xylF, mhpD, mhpE, adh, ackA, pta
Gallaecimonas xiamenensis 3-C-1 pcaK, pobA, praA, xylF, mhpD, mhpE, adh, ackA, pta
Geobacter daltonii FRC-32 pcaK, hcl, hcrA, hcrB, hcrC, bamB, bamC, bamD, bamE, bamF, bamG, bamH, bamI, dch, had, oah, pimB, gcdH, ech, fadB, atoB
Gillisia marina CBA3202 pcaK, pobA, praA, xylF, mhpD, mhpE, adh, acs
Gracilibacillus halophilus YIM-C55.5 pcaK, pobA, praA, xylF, mhpD, mhpE, adh, ackA, pta
Granulicella mallensis MP5ACTX8 pcaK, pobA, praA, xylF, mhpD, mhpE, adh, acs
Granulicella tundricola MP5ACTX9 pcaK, pobA, praA, xylF, mhpD, mhpE, adh, acs
Hafnia paralvei ATCC 29927 pcaK, pobA, praA, xylF, mhpD, mhpE, ald-dh-CoA
Haladaptatus cibarius D43 pcaK, pobA, praA, xylF, mhpD, mhpE, adh, acs
Halioglobus japonicus S1-36 pcaK, pobA, praA, xylF, mhpD, mhpE, adh, acs
Halobacillus alkaliphilus FP5 pcaK, pobA, praA, xylF, mhpD, mhpE, adh, ackA, pta
Halococcus hamelinensis 100A6 pcaK, pobA, praA, xylF, mhpD, mhpE, adh, acs
Halomonas salina B6 pcaK, pobA, praA, xylF, mhpD, mhpE, adh, ackA, pta
Halomonas smyrnensis AAD6 pcaK, pobA, praA, xylF, mhpD, mhpE, adh, acs
Halomonas stevensii S18214 pcaK, pobA, praA, xylF, mhpD, mhpE, adh, ackA, pta
Halomonas titanicae BH1 pcaK, pobA, pcaH, pcaG, pcaB, pcaC, pcaD, catI, catJ, pcaF
Halomonas xinjiangensis TRM 0175 pcaK, pobA, pcaH, pcaG, pcaB, pcaC, pcaD, catI, catJ, pcaF
Halopiger salifodinae KCY07-B2 pcaK, pobA, praA, xylF, mhpD, mhpE, adh, acs
Halostagnicola larsenii XH-48 pcaK, pobA, praA, xylF, mhpD, mhpE, adh, acs
Haloterrigena daqingensis JX313 pcaK, pobA, praA, xylF, mhpD, mhpE, adh, acs
Herbaspirillum aquaticum IEH 4430 pcaK, pobA, pcaH, pcaG, pcaB, pcaC, pcaD, pcaI, pcaJ, pcaF
Hippea alviniae EP5-r pcaK, pobA, praA, xylF, mhpD, mhpE, adh, acs
Hippea jasoniae Mar08-272r pcaK, pobA, praA, xylF, mhpD, mhpE, adh, acs
Hoeflea phototrophica DFL-43 pcaK, pobA, pcaH, pcaG, pcaB, pcaC, pcaD, catI, catJ, pcaF
Hyphomicrobium nitrativorans NL23 pcaK, pobA, praA, xylF, mhpD, mhpE, adh, acs
Imtechella halotolerans K1 pcaK, pobA, praA, xylF, mhpD, mhpE, adh, ackA, pta
Indibacter alkaliphilus LW1 pcaK, pobA, praA, xylF, mhpD, mhpE, adh, ackA, pta
Jannaschia aquimarina GSW-M26 pcaK, pobA, pcaH, pcaG, pcaB, pcaC, pcaD, pcaI, pcaJ, pcaF
Jeotgalibacillus soli P9 pcaK, pobA, praA, praB, praC, praD, mhpD, mhpE, adh, ackA, pta
Kangiella geojedonensis YCS-5 pcaK, pobA, praA, xylF, mhpD, mhpE, adh, acs
Knoellia flava TL1 pcaK, pobA, praA, xylF, mhpD, mhpE, adh, ackA, pta
Kocuria flava HO-9041 pcaK, pobA, pcaH, pcaG, pcaB, pcaC, pcaD*, pcaI, pcaJ, pcaF
Kocuria turfanensis HO-9042 pcaK, pobA, pcaH, pcaG, pcaB, pcaC, pcaD*, pcaI, pcaJ, pcaF
Laceyella sediminis RHA1 pcaK, pobA, praA, xylF, mhpD, mhpE, adh, acs
Lacinutrix algicola AKS293 pcaK, pobA, praA, xylF, mhpD, mhpE, adh, acs
Lacinutrix himadriensis E4-9a pcaK, pobA, praA, xylF, mhpD, mhpE, adh, acs
Lacinutrix mariniflava AKS432 pcaK, pobA, praA, xylF, mhpD, mhpE, adh, acs
Lactobacillus curieae CCTCC M 2011381 pcaK, pobA, praA, xylF, mhpD, mhpE, ald-dh-CoA
Lactobacillus delbrueckii ZN7a-9 pcaK, pobA, praA, xylF, mhpD, mhpE, ald-dh-CoA
Lactobacillus hokkaidonensis LOOC260 pcaK, pobA, praA, xylF, mhpD, mhpE, ald-dh-CoA
Lactobacillus oryzae SG293 pcaK, pobA, praA, xylF, mhpD, mhpE, ald-dh-CoA
Lactobacillus pobuzihii E100301 pcaK, pobA, praA, xylF, mhpD, mhpE, ald-dh-CoA
Lactobacillus shenzhenensis LY-73 pcaK, pobA, praA, xylF, mhpD, mhpE, ald-dh-CoA
Lactobacillus silagei IWT126 pcaK, pobA, praA, xylF, mhpD, mhpE, ald-dh-CoA
Leeuwenhoekiella blandensis MED217 pcaK, pobA, praA, xylF, mhpD, mhpE, adh, ackA, pta
Lentibacillus jeotgali Grbi pcaK, pobA, praA, xylF, mhpD, mhpE, adh, ackA, pta
Limnohabitans curvus MWH-C5 pcaK, pobA, ligA, ligB, ligC, ligI, ligU, ligJ, ligK
Limnohabitans parvus II-B4 pcaK, pobA, ligA, ligB, ligC, ligI, ligU, ligJ, ligK
Listeria fleischmannii LU2006-1 pcaK, pobA, praA, xylF, mhpD, mhpE, ald-dh-CoA
Luteimonas huabeiensis HB2 pcaK, pobA, ligA, ligB, ligC, ligI, ligU, ligJ, ligK
Luteipulveratus mongoliensis MN07-A0370 pcaK, pobA, praA, xylF, mhpD, mhpE, adh, ackA, pta
Lutibaculum baratangense AMV1 pcaK, pobA, pcaH, pcaG, pcaB, pcaC, pcaD, pcaI, pcaJ, pcaF
Lysobacter daejeonensis GH1-9 pcaK, pobA, praA, xylF, mhpD, mhpE, adh, acs
Magnetovibrio blakemorei MV-1 pcaK, pobA, praA, xylF, mhpD, mhpE, adh, acs
Marinicella litoralis KMM 3900 pcaK, pobA, praA, xylF, mhpD, mhpE, adh, acs
Mariniradius saccharolyticus AK6 pcaK, pobA, praA, xylF, mhpD, mhpE, adh, ackA, pta
Marinobacter algicola DG893 pcaK, pobA, pcaH, pcaG, pcaB, pcaC, pcaD, catI, catJ, pcaF
Marinobacter guineae M3B pcaK, pobA, praA, praB, praC, praD, mhpD, mhpE, adh, ackA, pta
Marinobacter psychrophilus 20041 pcaK, pobA, praA, xylF, mhpD, mhpE, adh, ackA, pta
Marinomonas arctica 328 pcaK, pobA, ligA, ligB, ligC, ligI, ligU, ligJ, ligK
Marivita geojedonensis DPG-138 pcaK, pobA, pcaH, pcaG, pcaB, pcaC, pcaD, pcaI, pcaJ, pcaF
Martelella endophytica YC6887 pcaK, pobA, praA, xylF, mhpD, mhpE, adh, acs
Megamonas funiformis YIT 11815 pcaK, pobA, praA, xylF, mhpD, mhpE, ald-dh-CoA
Mesorhizobium ciceri WSM1271 pcaK, pobA, pcaH, pcaG, pcaB, pcaC, pcaD, catI, catJ, pcaF
Methanobacterium arcticum M2 pcaK, pobA, praA, xylF, mhpD, mhpE, adh, acs
Methanobacterium veterum MK4 pcaK, pobA, praA, xylF, mhpD, mhpE, adh, acs
Methanocella arvoryzae MRE50 pcaK, pobA, praA, xylF, mhpD, mhpE, adh, acs
Methanococcus aeolicus Nankai-3 pcaK, pobA, praA, xylF, mhpD, mhpE, ald-dh-CoA
Methanoculleus horonobensis T10 pcaK, pobA, praA, xylF, mhpD, mhpE, adh, acs
Methanolinea tarda NOBI-1 pcaK, pobA, praA, xylF, mhpD, mhpE, adh, acs
Methanosarcina soligelidi SMA-21 pcaK, pobA, praA, xylF, mhpD, mhpE, adh, ackA, pta
Methanospirillum lacunae Ki8-1 pcaK, pobA, praA, xylF, mhpD, mhpE, adh, acs
Methanospirillum stamsii Pt1 pcaK, pobA, praA, xylF, mhpD, mhpE, adh, acs
Methylibium petroleiphilum PM1 pcaK, pobA, praA, praB, praC, praD, mhpD, mhpE, adh, acs
Methylobacterium gossipiicola Gh-105 pcaK, pobA, praA, xylF, mhpD, mhpE, adh, acs
Methylocapsa aurea KYG pcaK, pobA, praA, xylF, mhpD, mhpE, adh, acs
Methylotenera versatilis 301 pcaK, pobA, praA, xylF, mhpD, mhpE, adh, acs
Microbacterium profundi Shh49 pcaK, pobA, ligA, ligB, ligC, ligI, ligU, ligJ, ligK
Microvirga lotononidis WSM3557 pcaK, pobA, pcaH, pcaG, pcaB, pcaC, pcaD, catI, catJ, pcaF
Moritella dasanensis ArB 0140 pcaK, pobA, praA, xylF, mhpD, mhpE, adh, ackA, pta
Mucilaginibacter gossypii Gh-67 pcaK, pobA, praA, xylF, mhpD, mhpE, adh, ackA, pta
Mucilaginibacter gossypiicola Gh-48 pcaK, pobA, praA, xylF, mhpD, mhpE, adh, acs
Mucilaginibacter mallensis MP1X4 pcaK, pobA, praA, xylF, mhpD, mhpE, adh, acs
Nafulsella turpanensis ZLM-10 pcaK, pobA, praA, xylF, mhpD, mhpE, adh, ackA, pta
Natronomonas moolapensis 8.8.11 pcaK, pobA, praA, xylF, mhpD, mhpE, adh, acs
Nautilia profundicola AmH pcaK, pobA, praA, xylF, mhpD, mhpE, adh, acs
Neiella marina J221 pcaK, pobA, praA, xylF, mhpD, mhpE, ald-dh-CoA
Neptunomonas antarctica S3-22 pcaK, pobA, ligA, ligB, ligC, ligI, ligU, ligJ, ligK
Nocardioides daejeonensis MJ31 pcaK, pobA, praA, xylF, mhpD, mhpE, adh, acs
Nocardioides dokdonensis FR1436 pcaK, pobA, praA, xylF, mhpD, mhpE, adh, acs
Nocardiopsis baichengensis YIM 90130 pcaK, pobA, pcaH, pcaG, pcaB, pcaC, pcaD, catI, catJ, pcaF
Nocardiopsis gilva YIM 90087 pcaK, pobA, pcaH, pcaG, pcaB, pcaC, pcaD*, catI, catJ, pcaF
Novosphingobium barchaimii LL02 pcaK, pobA, ligA, ligB, ligC, ligI, ligU, ligJ, ligK
Novosphingobium fuchskuhlense FNE08-7 pcaK, pobA, ligA, ligB, ligC, ligI, ligU, ligJ, ligK
Novosphingobium lindaniclasticum LE124 pcaK, pobA, ligA, ligB, ligC, ligI, ligU, ligJ, ligK
Oceanisphaera arctica V1-41 pcaK, pobA, pcaH, pcaG, pcaB, pcaC, pcaD, catI, catJ, pcaF
Ochrobactrum rhizosphaerae PR17 pcaK, pobA, praA, xylF, mhpD, mhpE, adh, acs
Ochrobactrum thiophenivorans DSM 7216 pcaK, pobA, praA, xylF, mhpD, mhpE, adh, acs
Oscillibacter ruminantium GH1 pcaK, pobA, praA, xylF, mhpD, mhpE, adh, ackA, pta
Paenisporosarcina indica PN2 pcaK, pobA, praA, praB, praC, praD, mhpD, mhpE, adh, acs
Palaeococcus pacificus DY20341 pcaK, pobA, praA, xylF, mhpD, mhpE, ald-dh-CoA
Paludibacter propionicigenes WB4 pcaK, pobA, praA, xylF, mhpD, mhpE, adh, ackA, pta
Pandoraea thiooxydans ATSB16 pcaK, hcl, hcrA, hcrB, hcrC, boxA, boxB, boxC, boxD, paaF, paaH, paaJ2
Pantoea rwandensis LMG 26275 pcaK, pobA, praA, praB, praC, praD, mhpD, mhpE, adh, ackA, pta
Pedobacter arcticus A12 pcaK, pobA, praA, xylF, mhpD, mhpE, adh, acs
Photobacterium gaetbulicola Gung47 pcaK, pobA, praA, xylF, mhpD, mhpE, ald-dh-CoA
Photobacterium jeanii R-40508 pcaK, pobA, praA, xylF, mhpD, mhpE, adh, ackA, pta
Phyllobacterium brassicacearum STM 196 pcaK, pobA, pcaH, pcaG, pcaB, pcaC, pcaD, catI, catJ, pcaF
Phyllobacterium endophyticum PEPV15 pcaK, pobA, praA, xylF, mhpD, mhpE, adh, acs
Phyllobacterium leguminum ORS 1419 pcaK, pobA, praA, xylF, mhpD, mhpE, adh, acs
Planktomarina temperata RCA23 pcaK, pobA, pcaH, pcaG, pcaB, pcaC, pcaD, pcaI, pcaJ, pcaF
Planococcus halocryophilus Or1 pcaK, pobA, praA, praB, praC, praD, mhpD, mhpE, adh, acs
Pleomorphomonas diazotrophica R5-392 pcaK, pobA, praA, xylF, mhpD, mhpE, adh, ackA, pta
Polaribacter dokdonensis DSW-5 pcaK, pobA, praA, xylF, mhpD, mhpE, adh, ackA, pta
Pontibacillus litoralis JSM 072002 pcaK, pobA, praA, praB, praC, praD, mhpD, mhpE, ald-dh-CoA
Pontibacter lucknowensis DM9 pcaK, pobA, pcaH, pcaG, pcaB, pcaC, pcaD, pcaI, pcaJ, pcaF
Pontibacter ramchanderi LP43 pcaK, pobA, pcaH, pcaG, pcaB, pcaC, pcaD, pcaI, pcaJ, pcaF
Pontimonas salivibrio CL-TW6 pcaK, pobA, praA, xylF, mhpD, mhpE, adh, ackA, pta
Porphyrobacter dokdonensis DSW-74 pcaK, pobA, praA, xylF, mhpD, mhpE, adh, acs
Pseudoalteromonas arctica A 37-1-2 pcaK, pobA, praA, xylF, mhpD, mhpE, adh, ackA, pta
Pseudomonas baetica a390 pcaK, pobA, pcaH, pcaG, pcaB, pcaC, pcaD, pcaI, pcaJ, pcaF
Pseudomonas litoralis 2SM5 pcaK, pobA, praA, xylF, mhpD, mhpE, adh, ackA, pta
Pseudomonas taeanensis MS-3 pcaK, pobA, pcaH, pcaG, pcaB, pcaC, pcaD, catI, catJ, pcaF
Pseudovibrio axinellae Ad2 pcaK, pobA, pcaH, pcaG, pcaB, pcaC, pcaD, pcaI, pcaJ, pcaF
Psychrobacter arcticus 273-4 pcaK, pobA, praA, xylF, mhpD, mhpE, adh, ackA, pta
Psychrobacter cryohalolentis K5 pcaK, pobA, pcaH, pcaG, pcaB, pcaC, pcaD, pcaI, pcaJ, pcaF
Psychromonas ingrahamii 37 pcaK, pobA, praA, xylF, mhpD, mhpE, adh, ackA, pta
Psychromonas ossibalaenae JAMM 0738 pcaK, pobA, praA, xylF, mhpD, mhpE, adh, ackA, pta
Rhizobium freirei PRF 81 pcaK, pobA, pcaH, pcaG, pcaB, pcaC, pcaD, catI, catJ, pcaF
Rhizobium grahamii CCGE 502 pcaK, pobA, pcaH, pcaG, pcaB, pcaC, pcaD, catI, catJ, pcaF
Rhizobium subbaraonis JC85 pcaK, pobA, pcaH, pcaG, pcaB, pcaC, pcaD, pcaI, pcaJ, pcaF
Rhodanobacter denitrificans 2APBS1 pcaK, pobA, praA, xylF, mhpD, mhpE, adh, acs
Rhodobacter johrii JA192 pcaK, pobA, praA, xylF, mhpD, mhpE, adh, ackA, pta
Rhodobacter maris JA276 pcaK, pobA, praA, xylF, mhpD, mhpE, adh, ackA, pta
Rhodobacter ovatus JA234 pcaK, pobA, praA, xylF, mhpD, mhpE, adh, acs
Rhodobacter viridis JA737 pcaK, pobA, praA, xylF, mhpD, mhpE, adh, acs
Rhodococcus qingshengii djl-6-2 pcaK, pobA, pcaH, pcaG, pcaB, pcaC, pcaD, catI, catJ, pcaF
Rhodopseudomonas pseudopalustris DSM 123 pcaK, hcl, hcrA, hcrB, hcrC, bcrA, bcrB, bcrC, bcrD, Ch1CoA, badK, badH, badI, pimD, pimC, pimF, gcdH, ech, fadB, atoB
Roseateles aquatilis CCUG 48205 pcaK, pobA, praA, xylF, mhpD, mhpE, adh, acs
Roseivirga spongicola UST030701-084 pcaK, pobA, praA, xylF, mhpD, mhpE, adh, acs
Rubrivirga marina SAORIC-28 pcaK, pobA, praA, xylF, mhpD, mhpE, adh, ackA, pta
Ruegeria conchae TW15 pcaK, pobA, praA, xylF, mhpD, mhpE, adh, ackA, pta
Saccharomonospora marina XMU15 pcaK, pobA, pcaH, pcaG, pcaB, pcaC, pcaD, catI, catJ, pcaF
Salinicoccus carnicancri Crm pcaK, pobA, praA, xylF, mhpD, mhpE, adh, ackA, pta
Serinicoccus profundi MCCC 1A05965 pcaK, pobA, praA, xylF, mhpD, mhpE, adh, ackA, pta
Shewanella halifaxensis HAW-EB4 pcaK, pobA, praA, xylF, mhpD, mhpE, adh, ackA, pta
Skermanella stibiiresistens SB22 pcaK, pobA, pcaH, pcaG, pcaB, pcaC, pcaD, pcaI, pcaJ, pcaF
Snodgrassella alvi wkB2 pcaK, pobA, praA, xylF, mhpD, mhpE, adh, ackA, pta
Sphaerochaeta globosa Buddy pcaK, pobA, praA, xylF, mhpD, mhpE, ald-dh-CoA
Sphaerochaeta pleomorpha Grapes pcaK, pobA, praA, xylF, mhpD, mhpE, ald-dh-CoA
Sphingobium baderi LL03 pcaK, pobA, praA, xylF, mhpD, mhpE, ald-dh-CoA
Sphingobium czechense LL01 pcaK, pobA, ligA, ligB, ligC, ligI, ligU, ligJ, ligK
Sphingobium quisquiliarum P25 pcaK, pobA, ligA, ligB, ligC, ligI, ligU, ligJ, ligK
Sphingomonas histidinilytica UM2 pcaK, pobA, praA, praB, praC, praD, mhpD, mhpE, ald-dh-CoA
Sphingomonas indica Dd16 pcaK, pobA, praA, xylF, mhpD, mhpE, adh, acs
Sphingomonas laterariae LNB2 pcaK, pobA, praA, praB, praC, praD, mhpD, mhpE, ald-dh-CoA
Sphingopyxis indica DS15 pcaK, pobA, praA, xylF, mhpD, mhpE, adh, acs
Sphingopyxis terrae UI2 pcaK, pobA, praA, praB, praC, praD, mhpD, mhpE, ald-dh-CoA
Sporolactobacillus vineae SL153 pcaK, pobA, praA, xylF, mhpD, mhpE, ald-dh-CoA
Streptacidiphilus oryzae TH49 pcaK, pobA, pcaH, pcaG, pcaB, pcaC, pcaD, pcaI, pcaJ, pcaF
Streptococcus anginosus CCUG 39159 pcaK, pobA, praA, xylF, mhpD, mhpE, ald-dh-CoA
Streptococcus massiliensis 4401825 pcaK, pobA, praA, xylF, mhpD, mhpE, ald-dh-CoA
Streptococcus oralis 7747 pcaK, pobA, praA, xylF, mhpD, mhpE, ald-dh-CoA
Streptococcus oralis AZ_3a pcaK, pobA, praA, xylF, mhpD, mhpE, ald-dh-CoA
Streptomyces kebangsaanensis SUK12 pcaK, pobA, pcaH, pcaG, pcaB, pcaC, pcaD, pcaI, pcaJ, pcaF
Succinatimonas hippei YIT 12066 pcaK, pobA, praA, xylF, mhpD, mhpE, adh, ackA, pta
Sulfurimonas gotlandica GD1 pcaK, pobA, praA, xylF, mhpD, mhpE, adh, ackA, pta
Tatumella morbirosei LMG 23360 pcaK, pobA, praA, praB, praC, praD, mhpD, mhpE, adh, ackA, pta
Thauera humireducens SgZ-1 pcaK, pobA, ligA, ligB, ligC, ligI, ligU, ligJ, ligK
Thermoactinomyces daqus H-18 pcaK, pobA, praA, xylF, mhpD, mhpE, adh, acs
Thermobifida halotolerans YIM 90462 pcaK, pobA, pcaH, pcaG, pcaB, pcaC, pcaD, catI, catJ, pcaF
Thermodesulfovibrio aggregans TGE-P1 pcaK, pobA, praA, xylF, mhpD, mhpE, adh, acs
Thermophagus xiamenensis HS1 pcaK, pobA, praA, xylF, mhpD, mhpE, adh, ackA, pta
Thermovenabulum gondwanense R270 pcaK, pobA, praA, xylF, mhpD, mhpE, ald-dh-CoA
Thioclava dalianensis DLFJ1-1 pcaK, pobA, pcaH, pcaG, pcaB, pcaC, pcaD, pcaI, pcaJ, pcaF
Thiohalospira halophila HL 3 pcaK, pobA, praA, xylF, mhpD, mhpE, adh, acs
Tistlia consotensis USBA 355 pcaK, pobA, pcaH, pcaG, pcaB, pcaC, pcaD, pcaI, pcaJ, pcaF
Vagococcus penaei CD276 pcaK, pobA, praA, praB, praC, praD, mhpD, mhpE, ald-dh-CoA
Verminephrobacter eiseniae EF01-2 pcaK, pobA, ligA, ligB, ligC, ligI, ligU, ligJ, ligK
Weissella oryzae SG25 pcaK, pobA, praA, xylF, mhpD, mhpE, ald-dh-CoA
Williamsia sterculiae CPCC 203464 pcaK, pobA, praA, praB, praC, praD, mhpD, mhpE, ald-dh-CoA
Yersinia intermedia Y228 pcaK, pobA, praA, xylF, mhpD, mhpE, ald-dh-CoA

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 Sep 24 2021. 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