GapMind for catabolism of small carbon sources

 

L-phenylalanine catabolism

Analysis of pathway phenylalanine in 276 genomes

Genome Best path
Acidovorax caeni R-24608 livF, livG, livH, livM, livJ, PAH, PCBD, QDPR, HPD, hmgA, maiA, fahA, atoA, atoD, atoB
Actinokineospora bangkokensis 44EHW livF, livG, livH, livM, livJ, ARO8, PPDCalpha, PPDCbeta, pad-dh, paaK, paaA, paaB, paaC, paaE, paaG, paaZ1, paaZ2, paaJ1, paaF, paaH, paaJ2
Actinomyces timonensis 7400942 aroP, PAH, PCBD, QDPR, HPD, hmgA, maiA, fahA, aacS, atoB
Algiphilus aromaticivorans DG1253 aroP, PAH, PCBD, QDPR, HPD, hmgA, maiA, fahA, aacS, atoB
Algoriphagus aquaeductus T4 aroP, PAH, PCBD, QDPR, HPD, hmgA, maiA, fahA, atoA, atoD, atoB
Algoriphagus machipongonensis PR1 aroP, PAH, PCBD, QDPR, HPD, hmgA, maiA, fahA, atoA, atoD, atoB
Alicyclobacillus ferrooxydans TC-34 aroP, ARO8, PPDCalpha, PPDCbeta, pad-dh, paaK, paaA, paaB, paaC, paaE, paaG, paaZ1, paaZ2, paaJ1, paaF, paaH, paaJ2
Alishewanella agri BL06 aroP, PAH, PCBD, QDPR, HPD, hmgA, maiA, fahA, atoA, atoD, atoB
Alistipes indistinctus YIT 12060 aroP, PAH, PCBD, QDPR, HPD, hmgA, maiA, fahA, aacS, atoB
Alistipes shahii WAL 8301 aroP, PAH, PCBD, QDPR, HPD, hmgA, maiA, fahA, aacS, atoB
Alkalitalea saponilacus SC/BZ-SP2 aroP, PAH, PCBD, QDPR, HPD, hmgA, maiA, fahA, aacS, atoB
Amantichitinum ursilacus IGB-41 livF, livG, livH, livM, livJ, PAH, PCBD, QDPR, HPD, hmgA, maiA, fahA, aacS, atoB
Amphibacillus jilinensis Y1 aroP, PAH, PCBD, QDPR, HPD, hmgA, maiA, fahA, aacS, atoB
Amphritea japonica JAMM 1866 livF, livG, livH, livM, livJ, ARO8, iorAB, paaA, paaB, paaC, paaE, paaG, paaZ1, paaZ2, paaJ1, paaF, paaH, paaJ2
Amycolatopsis halophila YIM 93223 aroP, ARO8, PPDCalpha, PPDCbeta, pad-dh, paaK, paaA, paaB, paaC, paaE, paaG, paaZ1, paaZ2, paaJ1, paaF, paaH, paaJ2
Amycolatopsis xylanica CPCC 202699 livF, livG, livH, livM, livJ, ARO8, PPDCalpha, PPDCbeta, pad-dh, paaK, paaA, paaB, paaC, paaE, paaG, paaZ1, paaZ2, paaJ1, paaF, paaH, paaJ2
Aquimarina agarilytica ZC1 aroP, PAH, PCBD, QDPR, HPD, hmgA, maiA, fahA, atoA, atoD, atoB
Aquimarina longa SW024 aroP, ARO8, iorAB, paaA, paaB, paaC, paaE, paaG, paaZ1, paaZ2, paaJ1, paaF, paaH, paaJ2
Aquimarina macrocephali JAMB N27 aroP, ARO8, iorAB, paaA, paaB, paaC, paaE, paaG, paaZ1, paaZ2, paaJ1, paaF, paaH, paaJ2
Archaeoglobus sulfaticallidus PM70-1 aroP, ARO8, iorA, iorB, paaA, paaB, paaC, paaE, paaG, paaZ1, paaZ2, paaJ1, paaF, paaH, paaJ2
Arcticibacter svalbardensis MN12-7 aroP, PAH, PCBD, QDPR, HPD, hmgA, maiA, fahA, aacS, atoB
Ardenticatena maritima 110S livF, livG, livH, livM, livJ, ARO8, PPDCalpha, PPDCbeta, pfor, paaK, paaA, paaB, paaC, paaE, paaG, paaZ1, paaZ2, paaJ1, paaF, paaH, paaJ2
Arenimonas metalli CF5-1 aroP, PAH, PCBD, QDPR, HPD, hmgA, maiA, fahA, atoA, atoD, atoB
Arenitalea lutea P7-3-5 aroP, PAH, PCBD, QDPR, HPD, hmgA, maiA, fahA, atoA, atoD, atoB
Azospirillum humicireducens SgZ-5 livF, livG, livH, livM, livJ, ARO8, iorAB, paaA, paaB, paaC, paaE, paaG, paaZ1, paaZ2, paaJ1, paaF, paaH, paaJ2
Azospirillum thiophilum BV-S livF, livG, livH, livM, livJ, ARO8, iorAB, paaA, paaB, paaC, paaE, paaG, paaZ1, paaZ2, paaJ1, paaF, paaH, paaJ2
Bacillus altitudinis 41KF2b aroP, PAH, PCBD, QDPR, HPD, hmgA, maiA, fahA, atoA, atoD, atoB
Bacillus coahuilensis m4-4 aroP, ARO8, iorAB, paaA, paaB, paaC, paaE, paaG, paaZ1, paaZ2, paaJ1, paaF, paaH, paaJ2
Bacillus cytotoxicus NVH 391-98 aroP, PAH, PCBD, QDPR, HPD, hmgA, maiA, fahA, atoA, atoD, atoB
Bacillus horneckiae 1P01SC livF, livG, livH, livM, livJ, PAH, PCBD, QDPR, HPD, hmgA, maiA, fahA, atoA, atoD, atoB
Bacillus okhensis Kh10-101 aroP, PAH, PCBD, QDPR, HPD, hmgA, maiA, fahA, atoA, atoD, atoB
Bacillus safensis FO-36b aroP, ARO8, iorAB, paaA, paaB, paaC, paaE, paaG, paaZ1, paaZ2, paaJ1, paaF, paaH, paaJ2
Bacillus velezensis CBMB205 aroP, PAH, PCBD, QDPR, HPD, hmgA, maiA, fahA, atoA, atoD, atoB
Bacteroides clarus YIT 12056 aroP, PAH, PCBD, QDPR, HPD, hmgA, maiA, fahA, aacS, atoB
Bacteroides faecis MAJ27 aroP, PAH, PCBD, QDPR, HPD, hmgA, maiA, fahA, aacS, atoB
Bacteroides fluxus YIT 12057 aroP, PAH, PCBD, QDPR, HPD, hmgA, maiA, fahA, aacS, atoB
Bacteroides oleiciplenus YIT 12058 aroP, PAH, PCBD, QDPR, HPD, hmgA, maiA, fahA, aacS, atoB
Barnesiella intestinihominis YIT 11860 aroP, PAH, PCBD, QDPR, HPD, hmgA, maiA, fahA, aacS, atoB
Belnapia rosea CPCC 100156 livF, livG, livH, livM, livJ, PAH, PCBD, QDPR, HPD, hmgA, maiA, fahA, atoA, atoD, atoB
Bizionia argentinensis JUB59 aroP, ARO8, iorAB, paaA, paaB, paaC, paaE, paaG, paaZ1, paaZ2, paaJ1, paaF, paaH, paaJ2
Bradyrhizobium diazoefficiens USDA110 livF, livG, livH, livM, livJ, ARO8, iorAB, paaA, paaB, paaC, paaE, paaG, paaZ1, paaZ2, paaJ1, paaF, paaH, paaJ2
Brevibacterium jeotgali SJ5-8 aroP, PAH, PCBD, QDPR, HPD, hmgA, maiA, fahA, atoA, atoD, atoB
Brucella inopinata BO1 livF, livG, livH, livM, livJ, PAH, PCBD, QDPR, HPD, hmgA, maiA, fahA, aacS, atoB
Brucella microti CCM 4915 livF, livG, livH, livM, livJ, PAH, PCBD, QDPR, HPD, hmgA, maiA, fahA, aacS, atoB
Bryobacter aggregatus MPL3 aroP, PAH, PCBD, QDPR, HPD, hmgA, maiA, fahA, aacS, atoB
Caldicellulosiruptor hydrothermalis 108 aroP, PAH, PCBD, QDPR, HPD, hmgA, maiA, fahA, aacS, atoB
Caldicellulosiruptor kronotskyensis 2002 aroP, PAH, PCBD, QDPR, HPD, hmgA, maiA, fahA, aacS, atoB
Carboxydothermus pertinax Ug1 aroP, ARO8, iorA, iorB, paaA, paaB, paaC, paaE, paaG, paaZ1, paaZ2, paaJ1, paaF, paaH, paaJ2
Catellicoccus marimammalium M35/04/3 aroP, PAH, PCBD, QDPR, HPD, hmgA, maiA, fahA, aacS, atoB
Chromobacterium vaccinii MWU205 livF, livG, livH, livM, livJ, PAH, PCBD, QDPR, HPD, hmgA, maiA, fahA, aacS, atoB
Chryseobacterium angstadtii KM aroP, ARO8, ARO10, pad-dh, paaK, paaA, paaB, paaC, paaE, paaG, paaZ1, paaZ2, paaJ1, paaF, paaH, paaJ2
Chryseobacterium arthrosphaerae CC-VM-7 aroP, ARO8, ARO10, pad-dh, paaK, paaA, paaB, paaC, paaE, paaG, paaZ1, paaZ2, paaJ1, paaF, paaH, paaJ2
Chryseobacterium viscerum 687B-08 aroP, ARO8, ARO10, pad-dh, paaK, paaA, paaB, paaC, paaE, paaG, paaZ1, paaZ2, paaJ1, paaF, paaH, paaJ2
Cloacibacillus porcorum CL-84 livF, livG, livH, livM, livJ, PAH, PCBD, QDPR, HPD, hmgA, maiA, fahA, atoA, atoD, atoB
Cobetia crustatorum JO1 livF, livG, livH, livM, livJ, PAH, PCBD, QDPR, HPD, hmgA, maiA, fahA, atoA, atoD, atoB
Collimonas arenae Ter10 livF, livG, livH, livM, livJ, PAH, PCBD, QDPR, HPD, hmgA, maiA, fahA, atoA, atoD, atoB
Collimonas pratensis Ter91 livF, livG, livH, livM, livJ, PAH, PCBD, QDPR, HPD, hmgA, maiA, fahA, atoA, atoD, atoB
Collinsella tanakaei YIT 12063 aroP, PAH, PCBD, QDPR, HPD, hmgA, maiA, fahA, aacS, atoB
Coprobacter fastidiosus NSB1 aroP, PAH, PCBD, QDPR, HPD, hmgA, maiA, fahA, aacS, atoB
Corynebacterium deserti GIMN1.010 aroP, PAH, PCBD, QDPR, HPD, hmgA, maiA, fahA, atoA, atoD, atoB
Corynebacterium frankenforstense ST18 aroP, ARO8, iorAB, paaA, paaB, paaC, paaE, paaG, paaZ1, paaZ2, paaJ1, paaF, paaH, paaJ2
Corynebacterium lactis RW2-5 aroP, PAH, PCBD, QDPR, HPD, hmgA, maiA, fahA, atoA, atoD, atoB
Croceitalea dokdonensis DOKDO 023 aroP, PAH, PCBD, QDPR, HPD, hmgA, maiA, fahA, atoA, atoD, atoB
Cronobacter condimenti 1330 aroP, PAH, PCBD, QDPR, HPD, hmgA, maiA, fahA, aacS, atoB
Cronobacter muytjensii ATCC 51329 livF, livG, livH, livM, livJ, PAH, PCBD, QDPR, HPD, hmgA, maiA, fahA, aacS, atoB
Cronobacter universalis NCTC 9529 livF, livG, livH, livM, livJ, PAH, PCBD, QDPR, HPD, hmgA, maiA, fahA, aacS, atoB
Desulfatitalea tepidiphila S28bF aroP, ARO8, iorA, iorB, paaA, paaB, paaC, paaE, paaG, paaZ1, paaZ2, paaJ1, paaF, paaH, paaJ2
Desulfotomaculum hydrothermale Lam5 aroP, PAH, PCBD, QDPR, HPD, hmgA, maiA, fahA, aacS, atoB
Dethiosulfovibrio salsuginis USBA 82 aroP, PAH, PCBD, QDPR, HPD, hmgA, maiA, fahA, atoA, atoD, atoB
Devosia chinhatensis IPL18 aroP, PAH, PCBD, QDPR, HPD, hmgA, maiA, fahA, aacS, atoB
Devriesea agamarum IMP2 aroP, PAH, PCBD, QDPR, HPD, hmgA, maiA, fahA, aacS, atoB
Dialister succinatiphilus YIT 11850 aroP, PAH, PCBD, QDPR, HPD, hmgA, maiA, fahA, aacS, atoB
Dietzia timorensis ID05-A0528 aroP, PAH, PCBD, QDPR, HPD, hmgA, maiA, fahA, atoA, atoD, atoB
Dokdonella koreensis DS-123 aroP, PAH, PCBD, QDPR, HPD, hmgA, maiA, fahA, atoA, atoD, atoB
Domibacillus robiginosus WS 4628 aroP, ARO8, iorAB, paaA, paaB, paaC, paaE, paaG, paaZ1, paaZ2, paaJ1, paaF, paaH, paaJ2
Duganella sacchari Sac-22 livF, livG, livH, livM, livJ, ARO8, iorAB, paaA, paaB, paaC, paaE, paaG, paaZ1, paaZ2, paaJ1, paaF, paaH, paaJ2
Dyadobacter tibetensis Y620-1 aroP, PAH, PCBD, QDPR, HPD, hmgA, maiA, fahA, aacS, atoB
Dyella jiangningensis SBZ3-12 aroP, PAH, PCBD, QDPR, HPD, hmgA, maiA, fahA, atoA, atoD, atoB
Endozoicomonas montiporae CL-33 livF, livG, livH, livM, livJ, PAH, PCBD, QDPR, HPD, hmgA, maiA, fahA, aacS, atoB
Enterococcus termitis LMG 8895 aroP, PAH, PCBD, QDPR, HPD, hmgA, maiA, fahA, aacS, atoB
Enterorhabdus caecimuris B7 aroP, PAH, PCBD, QDPR, HPD, hmgA, maiA, fahA, aacS, atoB
Epibacterium ulvae U95 aroP, PAH, PCBD, QDPR, HPD, hmgA, maiA, fahA, atoA, atoD, atoB
Erythrobacter gangjinensis K7-2 aroP, PAH, PCBD, QDPR, HPD, hmgA, maiA, fahA, atoA, atoD, atoB
Erythrobacter marinus HWDM-33 aroP, PAH, PCBD, QDPR, HPD, hmgA, maiA, fahA, atoA, atoD, atoB
Ethanoligenens harbinense YUAN-3 aroP, PAH, PCBD, QDPR, HPD, hmgA, maiA, fahA, aacS, atoB
Fervidicella metallireducens AeB aroP, PAH, PCBD, QDPR, HPD, hmgA, maiA, fahA, atoA, atoD, atoB
Fibrella aestuarina BUZ 2 aroP, PAH, PCBD, QDPR, HPD, hmgA, maiA, fahA, aacS, atoB
Flammeovirga pacifica WPAGA1 aroP, PAH, PCBD, QDPR, HPD, hmgA, maiA, fahA, aacS, atoB
Flaviramulus ichthyoenteri Th78 aroP, PAH, PCBD, QDPR, HPD, hmgA, maiA, fahA, atoA, atoD, atoB
Flavobacterium beibuense F44-8 aroP, PAH, PCBD, QDPR, HPD, hmgA, maiA, fahA, atoA, atoD, atoB
Flavobacterium glycines Gm-149 aroP, PAH, PCBD, QDPR, HPD, hmgA, maiA, fahA, atoA, atoD, atoB
Flavobacterium sp. LM5 aroP, PAH, PCBD, QDPR, HPD, hmgA, maiA, fahA, atoA, atoD, atoB
Flavobacterium ummariense DS-12 aroP, PAH, PCBD, QDPR, HPD, hmgA, maiA, fahA, atoA, atoD, atoB
Frischella perrara PEB0191 aroP, PAH, PCBD, QDPR, HPD, hmgA, maiA, fahA, aacS, atoB
Galbibacter marinus ck-I2-15 aroP, PAH, PCBD, QDPR, HPD, hmgA, maiA, fahA, atoA, atoD, atoB
Gallaecimonas xiamenensis 3-C-1 aroP, PAH, PCBD, QDPR, HPD, hmgA, maiA, fahA, aacS, atoB
Geobacter daltonii FRC-32 aroP, ARO8, iorA, iorB, padB, padC, padD, padG, padI, padE, padF, padH, bamB, bamC, bamD, bamE, bamF, bamG, bamH, bamI, dch, had, oah, pimB, gcdH, ech, fadB, atoB
Gillisia marina CBA3202 aroP, PAH, PCBD, QDPR, HPD, hmgA, maiA, fahA, atoA, atoD, atoB
Gracilibacillus halophilus YIM-C55.5 aroP, PAH, PCBD, QDPR, HPD, hmgA, maiA, fahA, aacS, atoB
Granulicella mallensis MP5ACTX8 aroP, PAH, PCBD, QDPR, HPD, hmgA, maiA, fahA, atoA, atoD, atoB
Granulicella tundricola MP5ACTX9 aroP, PAH, PCBD, QDPR, HPD, hmgA, maiA, fahA, atoA, atoD, atoB
Hafnia paralvei ATCC 29927 livF, livG, livH, livM, livJ, ARO8, ARO10, pad-dh, paaK, paaA, paaB, paaC, paaE, paaG, paaZ1, paaZ2, paaJ1, paaF, paaH, paaJ2
Haladaptatus cibarius D43 livF, livG, livH, livM, livJ, ARO8, PPDCalpha, PPDCbeta, pfor, paaK, paaA, paaB, paaC, paaE, paaG, paaZ1, paaZ2, paaJ1, paaF, paaH, paaJ2
Halioglobus japonicus S1-36 aroP, PAH, PCBD, QDPR, HPD, hmgA, maiA, fahA, atoA, atoD, atoB
Halobacillus alkaliphilus FP5 aroP, PAH, PCBD, QDPR, HPD, hmgA, maiA, fahA, atoA, atoD, atoB
Halococcus hamelinensis 100A6 aroP, ARO8, iorAB, paaA, paaB, paaC, paaE, paaG, paaZ1, paaZ2, paaJ1, paaF, paaH, paaJ2
Halomonas salina B6 aroP, PAH, PCBD, QDPR, HPD, hmgA, maiA, fahA, atoA, atoD, atoB
Halomonas smyrnensis AAD6 aroP, PAH, PCBD, QDPR, HPD, hmgA, maiA, fahA, atoA, atoD, atoB
Halomonas stevensii S18214 aroP, PAH, PCBD, QDPR, HPD, hmgA, maiA, fahA, atoA, atoD, atoB
Halomonas titanicae BH1 aroP, ARO8, iorAB, paaA, paaB, paaC, paaE, paaG, paaZ1, paaZ2, paaJ1, paaF, paaH, paaJ2
Halomonas xinjiangensis TRM 0175 aroP, PAH, PCBD, QDPR, HPD, hmgA, maiA, fahA, aacS, atoB
Halopiger salifodinae KCY07-B2 aroP, ARO8, PPDCalpha, PPDCbeta, pfor, paaK, paaA, paaB, paaC, paaE, paaG, paaZ1, paaZ2, paaJ1, paaF, paaH, paaJ2
Halostagnicola larsenii XH-48 aroP, ARO8, PPDCalpha, PPDCbeta, pfor, paaK, paaA, paaB, paaC, paaE, paaG, paaZ1, paaZ2, paaJ1, paaF, paaH, paaJ2
Haloterrigena daqingensis JX313 aroP, PAH, PCBD, QDPR, HPD, hmgA, maiA, fahA, aacS, atoB
Herbaspirillum aquaticum IEH 4430 livF, livG, livH, livM, livJ, ARO8, iorAB, paaA, paaB, paaC, paaE, paaG, paaZ1, paaZ2, paaJ1, paaF, paaH, paaJ2
Hippea alviniae EP5-r livF, livG, livH, livM, livJ, PAH, PCBD, QDPR, HPD, hmgA, maiA, fahA, aacS, atoB
Hippea jasoniae Mar08-272r livF, livG, livH, livM, livJ, ARO8, iorA, iorB, paaA, paaB, paaC, paaE, paaG, paaZ1, paaZ2, paaJ1, paaF, paaH, paaJ2
Hoeflea phototrophica DFL-43 livF, livG, livH, livM, livJ, ARO8, iorAB, paaA, paaB, paaC, paaE, paaG, paaZ1, paaZ2, paaJ1, paaF, paaH, paaJ2
Hyphomicrobium nitrativorans NL23 livF, livG, livH, livM, livJ, PAH, PCBD, QDPR, HPD, hmgA, maiA, fahA, aacS, atoB
Imtechella halotolerans K1 aroP, PAH, PCBD, QDPR, HPD, hmgA, maiA, fahA, atoA, atoD, atoB
Indibacter alkaliphilus LW1 aroP, PAH, PCBD, QDPR, HPD, hmgA, maiA, fahA, atoA, atoD, atoB
Jannaschia aquimarina GSW-M26 aroP, ARO8, iorAB, paaA, paaB, paaC, paaE, paaG, paaZ1, paaZ2, paaJ1, paaF, paaH, paaJ2
Jeotgalibacillus soli P9 aroP, PAH, PCBD, QDPR, HPD, hmgA, maiA, fahA, atoA, atoD, atoB
Kangiella geojedonensis YCS-5 aroP, PAH, PCBD, QDPR, HPD, hmgA, maiA, fahA, atoA, atoD, atoB
Knoellia flava TL1 livF, livG, livH, livM, livJ, PAH, PCBD, QDPR, HPD, hmgA, maiA, fahA, atoA, atoD, atoB
Kocuria flava HO-9041 aroP, ARO8, PPDCalpha, PPDCbeta, pad-dh, paaK, paaA, paaB, paaC, paaE, paaG, paaZ1, paaZ2, paaJ1, paaF, paaH, paaJ2
Kocuria turfanensis HO-9042 aroP, ARO8, PPDCalpha, PPDCbeta, pad-dh, paaK, paaA, paaB, paaC, paaE, paaG, paaZ1, paaZ2, paaJ1, paaF, paaH, paaJ2
Laceyella sediminis RHA1 aroP, ARO8, PPDCalpha, PPDCbeta, pad-dh, paaK, paaA, paaB, paaC, paaE, paaG, paaZ1, paaZ2, paaJ1, paaF, paaH, paaJ2
Lacinutrix algicola AKS293 aroP, ARO8, iorAB, paaA, paaB, paaC, paaE, paaG, paaZ1, paaZ2, paaJ1, paaF, paaH, paaJ2
Lacinutrix himadriensis E4-9a aroP, ARO8, iorAB, paaA, paaB, paaC, paaE, paaG, paaZ1, paaZ2, paaJ1, paaF, paaH, paaJ2
Lacinutrix mariniflava AKS432 aroP, ARO8, iorAB, paaA, paaB, paaC, paaE, paaG, paaZ1, paaZ2, paaJ1, paaF, paaH, paaJ2
Lactobacillus curieae CCTCC M 2011381 aroP, PAH, PCBD, QDPR, HPD, hmgA, maiA, fahA, aacS, atoB
Lactobacillus delbrueckii ZN7a-9 aroP, PAH, PCBD, QDPR, HPD, hmgA, maiA, fahA, aacS, atoB
Lactobacillus hokkaidonensis LOOC260 aroP, PAH, PCBD, QDPR, HPD, hmgA, maiA, fahA, aacS, atoB
Lactobacillus oryzae SG293 aroP, PAH, PCBD, QDPR, HPD, hmgA, maiA, fahA, aacS, atoB
Lactobacillus pobuzihii E100301 aroP, PAH, PCBD, QDPR, HPD, hmgA, maiA, fahA, aacS, atoB
Lactobacillus shenzhenensis LY-73 aroP, PAH, PCBD, QDPR, HPD, hmgA, maiA, fahA, aacS, atoB
Lactobacillus silagei IWT126 aroP, PAH, PCBD, QDPR, HPD, hmgA, maiA, fahA, aacS, atoB
Leeuwenhoekiella blandensis MED217 aroP, PAH, PCBD, QDPR, HPD, hmgA, maiA, fahA, atoA, atoD, atoB
Lentibacillus jeotgali Grbi aroP, PAH, PCBD, QDPR, HPD, hmgA, maiA, fahA, atoA, atoD, atoB
Limnohabitans curvus MWH-C5 livF, livG, livH, livM, livJ, PAH, PCBD, QDPR, HPD, hmgA, maiA, fahA, atoA, atoD, atoB
Limnohabitans parvus II-B4 livF, livG, livH, livM, livJ, ARO8, iorAB, paaA, paaB, paaC, paaE, paaG, paaZ1, paaZ2, paaJ1, paaF, paaH, paaJ2
Listeria fleischmannii LU2006-1 aroP, PAH, PCBD, QDPR, HPD, hmgA, maiA, fahA, aacS, atoB
Luteimonas huabeiensis HB2 aroP, PAH, PCBD, QDPR, HPD, hmgA, maiA, fahA, atoA, atoD, atoB
Luteipulveratus mongoliensis MN07-A0370 livF, livG, livH, livM, livJ, ARO8, PPDCalpha, PPDCbeta, pad-dh, paaK, paaA, paaB, paaC, paaE, paaG, paaZ1, paaZ2, paaJ1, paaF, paaH, paaJ2
Lutibaculum baratangense AMV1 livF, livG, livH, livM, livJ, PAH, PCBD, QDPR, HPD, hmgA, maiA, fahA, aacS, atoB
Lysobacter daejeonensis GH1-9 aroP, PAH, PCBD, QDPR, HPD, hmgA, maiA, fahA, atoA, atoD, atoB
Magnetovibrio blakemorei MV-1 aroP, PAH, PCBD, QDPR, HPD, hmgA, maiA, fahA, aacS, atoB
Marinicella litoralis KMM 3900 aroP, ARO8, iorAB, paaA, paaB, paaC, paaE, paaG, paaZ1, paaZ2, paaJ1, paaF, paaH, paaJ2
Mariniradius saccharolyticus AK6 aroP, PAH, PCBD, QDPR, HPD, hmgA, maiA, fahA, atoA, atoD, atoB
Marinobacter algicola DG893 livF, livG, livH, livM, livJ, ARO8, iorAB, paaA, paaB, paaC, paaE, paaG, paaZ1, paaZ2, paaJ1, paaF, paaH, paaJ2
Marinobacter guineae M3B livF, livG, livH, livM, livJ, ARO8, iorAB, paaA, paaB, paaC, paaE, paaG, paaZ1, paaZ2, paaJ1, paaF, paaH, paaJ2
Marinobacter psychrophilus 20041 livF, livG, livH, livM, livJ, ARO8, ARO10, pad-dh, paaK, paaA, paaB, paaC, paaE, paaG, paaZ1, paaZ2, paaJ1, paaF, paaH, paaJ2
Marinomonas arctica 328 livF, livG, livH, livM, livJ, ARO8, ARO10, pad-dh, paaK, paaA, paaB, paaC, paaE, paaG, paaZ1, paaZ2, paaJ1, paaF, paaH, paaJ2
Marivita geojedonensis DPG-138 aroP, ARO8, iorAB, paaA, paaB, paaC, paaE, paaG, paaZ1, paaZ2, paaJ1, paaF, paaH, paaJ2
Martelella endophytica YC6887 aroP, PAH, PCBD, QDPR, HPD, hmgA, maiA, fahA, aacS, atoB
Megamonas funiformis YIT 11815 aroP, PAH, PCBD, QDPR, HPD, hmgA, maiA, fahA, aacS, atoB
Mesorhizobium ciceri WSM1271 livF, livG, livH, livM, livJ, PAH, PCBD, QDPR, HPD, hmgA, maiA, fahA, aacS, atoB
Methanobacterium arcticum M2 aroP, PAH, PCBD, QDPR, HPD, hmgA, maiA, fahA, aacS, atoB
Methanobacterium veterum MK4 aroP, PAH, PCBD, QDPR, HPD, hmgA, maiA, fahA, aacS, atoB
Methanocella arvoryzae MRE50 aroP, PAH, PCBD, QDPR, HPD, hmgA, maiA, fahA, aacS, atoB
Methanococcus aeolicus Nankai-3 aroP, PAH, PCBD, QDPR, HPD, hmgA, maiA, fahA, aacS, atoB
Methanoculleus horonobensis T10 aroP, PAH, PCBD, QDPR, HPD, hmgA, maiA, fahA, aacS, atoB
Methanolinea tarda NOBI-1 aroP, PAH, PCBD, QDPR, HPD, hmgA, maiA, fahA, aacS, atoB
Methanosarcina soligelidi SMA-21 aroP, PAH, PCBD, QDPR, HPD, hmgA, maiA, fahA, aacS, atoB
Methanospirillum lacunae Ki8-1 aroP, PAH, PCBD, QDPR, HPD, hmgA, maiA, fahA, aacS, atoB
Methanospirillum stamsii Pt1 aroP, PAH, PCBD, QDPR, HPD, hmgA, maiA, fahA, aacS, atoB
Methylibium petroleiphilum PM1 livF, livG, livH, livM, livJ, ARO8, ARO10, pfor, paaK, paaA, paaB, paaC, paaE, paaG, paaZ1, paaZ2, paaJ1, paaF, paaH, paaJ2
Methylobacterium gossipiicola Gh-105 livF, livG, livH, livM, livJ, PAH, PCBD, QDPR, HPD, hmgA, maiA, fahA, atoA, atoD, atoB
Methylocapsa aurea KYG livF, livG, livH, livM, livJ, PAH, PCBD, QDPR, HPD, hmgA, maiA, fahA, atoA, atoD, atoB
Methylotenera versatilis 301 aroP, PAH, PCBD, QDPR, HPD, hmgA, maiA, fahA, aacS, atoB
Microbacterium profundi Shh49 aroP, ARO8, PPDCalpha, PPDCbeta, pad-dh, paaK, paaA, paaB, paaC, paaE, paaG, paaZ1, paaZ2, paaJ1, paaF, paaH, paaJ2
Microvirga lotononidis WSM3557 livF, livG, livH, livM, livJ, ARO8, iorAB, paaA, paaB, paaC, paaE, paaG, paaZ1, paaZ2, paaJ1, paaF, paaH, paaJ2
Moritella dasanensis ArB 0140 aroP, PAH, PCBD, QDPR, HPD, hmgA, maiA, fahA, aacS, atoB
Mucilaginibacter gossypii Gh-67 aroP, PAH, PCBD, QDPR, HPD, hmgA, maiA, fahA, atoA, atoD, atoB
Mucilaginibacter gossypiicola Gh-48 aroP, PAH, PCBD, QDPR, HPD, hmgA, maiA, fahA, atoA, atoD, atoB
Mucilaginibacter mallensis MP1X4 aroP, PAH, PCBD, QDPR, HPD, hmgA, maiA, fahA, atoA, atoD, atoB
Nafulsella turpanensis ZLM-10 aroP, PAH, PCBD, QDPR, HPD, hmgA, maiA, fahA, atoA, atoD, atoB
Natronomonas moolapensis 8.8.11 aroP, PAH, PCBD, QDPR, HPD, hmgA, maiA, fahA, aacS, atoB
Nautilia profundicola AmH aroP, PAH, PCBD, QDPR, HPD, hmgA, maiA, fahA, aacS, atoB
Neiella marina J221 aroP, PAH, PCBD, QDPR, HPD, hmgA, maiA, fahA, aacS, atoB
Neptunomonas antarctica S3-22 livF, livG, livH, livM, livJ, ARO8, iorAB, paaA, paaB, paaC, paaE, paaG, paaZ1, paaZ2*, paaJ1, paaF, paaH, paaJ2
Nocardioides daejeonensis MJ31 aroP, ARO8, PPDCalpha, PPDCbeta, pad-dh, paaK, paaA, paaB, paaC, paaE, paaG, paaZ1, paaZ2, paaJ1, paaF, paaH, paaJ2
Nocardioides dokdonensis FR1436 livF, livG, livH, livM, livJ, ARO8, PPDCalpha, PPDCbeta, pad-dh, paaK, paaA, paaB, paaC, paaE, paaG, paaZ1, paaZ2, paaJ1, paaF, paaH, paaJ2
Nocardiopsis baichengensis YIM 90130 aroP, ARO8, PPDCalpha, PPDCbeta, pad-dh, paaK, paaA, paaB, paaC, paaE, paaG, paaZ1, paaZ2, paaJ1, paaF, paaH, paaJ2
Nocardiopsis gilva YIM 90087 aroP, ARO8, PPDCalpha, PPDCbeta, pad-dh, paaK, paaA, paaB, paaC, paaE, paaG, paaZ1, paaZ2, paaJ1, paaF, paaH, paaJ2
Novosphingobium barchaimii LL02 aroP, PAH, PCBD, QDPR, HPD, hmgA, maiA, fahA, atoA, atoD, atoB
Novosphingobium fuchskuhlense FNE08-7 aroP, PAH, PCBD, QDPR, HPD, hmgA, maiA, fahA, atoA, atoD, atoB
Novosphingobium lindaniclasticum LE124 aroP, PAH, PCBD, QDPR, HPD, hmgA, maiA, fahA, atoA, atoD, atoB
Oceanisphaera arctica V1-41 livF, livG, livH, livM, livJ, PAH, PCBD, QDPR, HPD, hmgA, maiA, fahA, atoA, atoD, atoB
Ochrobactrum rhizosphaerae PR17 livF, livG, livH, livM, livJ, PAH, PCBD, QDPR, HPD, hmgA, maiA, fahA, aacS, atoB
Ochrobactrum thiophenivorans DSM 7216 livF, livG, livH, livM, livJ, PAH, PCBD, QDPR, HPD, hmgA, maiA, fahA, aacS, atoB
Oscillibacter ruminantium GH1 aroP, ARO8, iorAB, paaA, paaB, paaC, paaE, paaG, paaZ1, paaZ2, paaJ1, paaF, paaH, paaJ2
Paenisporosarcina indica PN2 aroP, ARO8, iorAB, paaA, paaB, paaC, paaE, paaG, paaZ1, paaZ2, paaJ1, paaF, paaH, paaJ2
Palaeococcus pacificus DY20341 aroP, PAH, PCBD, QDPR, HPD, hmgA, maiA, fahA, aacS, atoB
Paludibacter propionicigenes WB4 aroP, PAH, PCBD, QDPR, HPD, hmgA, maiA, fahA, aacS, atoB
Pandoraea thiooxydans ATSB16 livF, livG, livH, livM, livJ, ARO8, iorAB, paaA, paaB, paaC, paaE, paaG, paaZ1, paaZ2, paaJ1, paaF, paaH, paaJ2
Pantoea rwandensis LMG 26275 livF, livG, livH, livM, livJ, PAH, PCBD, QDPR, HPD, hmgA, maiA, fahA, atoA, atoD, atoB
Pedobacter arcticus A12 aroP, PAH, PCBD, QDPR, HPD, hmgA, maiA, fahA, aacS, atoB
Photobacterium gaetbulicola Gung47 aroP, PAH, PCBD, QDPR, HPD, hmgA, maiA, fahA, atoA, atoD, atoB
Photobacterium jeanii R-40508 aroP, PAH, PCBD, QDPR, HPD, hmgA, maiA, fahA, aacS, atoB
Phyllobacterium brassicacearum STM 196 livF, livG, livH, livM, livJ, PAH, PCBD, QDPR, HPD, hmgA, maiA, fahA, atoA, atoD, atoB
Phyllobacterium endophyticum PEPV15 livF, livG, livH, livM, livJ, PAH, PCBD, QDPR, HPD, hmgA, maiA, fahA, atoA, atoD, atoB
Phyllobacterium leguminum ORS 1419 livF, livG, livH, livM, livJ, PAH, PCBD, QDPR, HPD, hmgA, maiA, fahA, aacS, atoB
Planktomarina temperata RCA23 livF, livG, livH, livM, livJ, ARO8, iorAB, paaA, paaB, paaC, paaE, paaG, paaZ1, paaZ2, paaJ1, paaF, paaH, paaJ2
Planococcus halocryophilus Or1 aroP, PAH, PCBD, QDPR, HPD, hmgA, maiA, fahA, atoA, atoD, atoB
Pleomorphomonas diazotrophica R5-392 aroP, PAH, PCBD, QDPR, HPD, hmgA, maiA, fahA, aacS, atoB
Polaribacter dokdonensis DSW-5 aroP, PAH, PCBD, QDPR, HPD, hmgA, maiA, fahA, atoA, atoD, atoB
Pontibacillus litoralis JSM 072002 aroP, ARO8, PPDCalpha, PPDCbeta, pad-dh, paaK, paaA, paaB, paaC, paaE, paaG, paaZ1, paaZ2, paaJ1, paaF, paaH, paaJ2
Pontibacter lucknowensis DM9 aroP, ARO8, iorAB, paaA, paaB, paaC, paaE, paaG, paaZ1, paaZ2, paaJ1, paaF, paaH, paaJ2
Pontibacter ramchanderi LP43 aroP, PAH, PCBD, QDPR, HPD, hmgA, maiA, fahA, atoA, atoD, atoB
Pontimonas salivibrio CL-TW6 aroP, PAH, PCBD, QDPR, HPD, hmgA, maiA, fahA, atoA, atoD, atoB
Porphyrobacter dokdonensis DSW-74 aroP, PAH, PCBD, QDPR, HPD, hmgA, maiA, fahA, atoA, atoD, atoB
Pseudoalteromonas arctica A 37-1-2 aroP, PAH, PCBD, QDPR, HPD, hmgA, maiA, fahA, atoA, atoD, atoB
Pseudomonas baetica a390 livF, livG, livH, livM, livJ, PAH, PCBD, QDPR, HPD, hmgA, maiA, fahA, atoA, atoD, atoB
Pseudomonas litoralis 2SM5 livF, livG, livH, livM, livJ, PAH, PCBD, QDPR, HPD, hmgA, maiA, fahA, atoA, atoD, atoB
Pseudomonas taeanensis MS-3 livF, livG, livH, livM, livJ, PAH, PCBD, QDPR, HPD, hmgA, maiA, fahA, atoA, atoD, atoB
Pseudovibrio axinellae Ad2 livF, livG, livH, livM, livJ, ARO8, iorAB, paaA, paaB, paaC, paaE, paaG, paaZ1, paaZ2, paaJ1, paaF, paaH, paaJ2
Psychrobacter arcticus 273-4 aroP, PAH, PCBD, QDPR, HPD, hmgA, maiA, fahA, atoA, atoD, atoB
Psychrobacter cryohalolentis K5 aroP, PAH, PCBD, QDPR, HPD, hmgA, maiA, fahA, atoA, atoD, atoB
Psychromonas ingrahamii 37 aroP, ARO8, ARO10, pad-dh, paaK, paaA, paaB, paaC, paaE, paaG, paaZ1, paaZ2, paaJ1, paaF, paaH, paaJ2
Psychromonas ossibalaenae JAMM 0738 aroP, PAH, PCBD, QDPR, HPD, hmgA, maiA, fahA, aacS, atoB
Rhizobium freirei PRF 81 livF, livG, livH, livM, livJ, ARO8, iorAB, paaA, paaB, paaC, paaE, paaG, paaZ1, paaZ2, paaJ1, paaF, paaH, paaJ2
Rhizobium grahamii CCGE 502 livF, livG, livH, livM, livJ, ARO8, ARO10, pad-dh, paaK, paaA, paaB, paaC, paaE, paaG, paaZ1, paaZ2, paaJ1, paaF, paaH, paaJ2
Rhizobium subbaraonis JC85 livF, livG, livH, livM, livJ, PAH, PCBD, QDPR, HPD, hmgA, maiA, fahA, aacS, atoB
Rhodanobacter denitrificans 2APBS1 aroP, PAH, PCBD, QDPR, HPD, hmgA, maiA, fahA, atoA, atoD, atoB
Rhodobacter johrii JA192 aroP, PAH, PCBD, QDPR, HPD, hmgA, maiA, fahA, atoA, atoD, atoB
Rhodobacter maris JA276 aroP, PAH, PCBD, QDPR, HPD, hmgA, maiA, fahA, atoA, atoD, atoB
Rhodobacter ovatus JA234 aroP, PAH, PCBD, QDPR, HPD, hmgA, maiA, fahA, atoA, atoD, atoB
Rhodobacter viridis JA737 aroP, PAH, PCBD, QDPR, HPD, hmgA, maiA, fahA, atoA, atoD, atoB
Rhodococcus qingshengii djl-6-2 aroP, ARO8, PPDCalpha, PPDCbeta, pad-dh, paaK, paaA, paaB, paaC, paaE, paaG, paaZ1, paaZ2, paaJ1, paaF, paaH, paaJ2
Rhodopseudomonas pseudopalustris DSM 123 livF, livG, livH, livM, livJ, ARO8, ARO10, pad-dh, paaK, padB, padC, padD, padG, padI, padE, padF, padH, bcrA, bcrB, bcrC, bcrD, Ch1CoA, badK, badH, badI, pimD, pimC, pimF, gcdH, ech, fadB, atoB
Roseateles aquatilis CCUG 48205 livF, livG, livH, livM, livJ, ARO8, iorAB, paaA, paaB, paaC, paaE, paaG, paaZ1, paaZ2, paaJ1, paaF, paaH, paaJ2
Roseivirga spongicola UST030701-084 aroP, ARO8, iorAB, paaA, paaB, paaC, paaE, paaG, paaZ1, paaZ2, paaJ1, paaF, paaH, paaJ2
Rubrivirga marina SAORIC-28 aroP, PAH, PCBD, QDPR, HPD, hmgA, maiA, fahA, aacS, atoB
Ruegeria conchae TW15 livF, livG, livH, livM, livJ, ARO8, iorAB, paaA, paaB, paaC, paaE, paaG, paaZ1, paaZ2, paaJ1, paaF, paaH, paaJ2
Saccharomonospora marina XMU15 aroP, ARO8, PPDCalpha, PPDCbeta, pad-dh, paaK, paaA, paaB, paaC, paaE, paaG, paaZ1, paaZ2, paaJ1, paaF, paaH, paaJ2
Salinicoccus carnicancri Crm aroP, PAH, PCBD, QDPR, HPD, hmgA, maiA, fahA, atoA, atoD, atoB
Serinicoccus profundi MCCC 1A05965 aroP, ARO8, PPDCalpha, PPDCbeta, pad-dh, paaK, paaA, paaB, paaC, paaE, paaG, paaZ1, paaZ2, paaJ1, paaF, paaH, paaJ2
Shewanella halifaxensis HAW-EB4 aroP, PAH, PCBD, QDPR, HPD, hmgA, maiA, fahA, atoA, atoD, atoB
Skermanella stibiiresistens SB22 livF, livG, livH, livM, livJ, PAH, PCBD, QDPR, HPD, hmgA, maiA, fahA, atoA, atoD, atoB
Snodgrassella alvi wkB2 aroP, PAH, PCBD, QDPR, HPD, hmgA, maiA, fahA, atoA, atoD, atoB
Sphaerochaeta globosa Buddy livF, livG, livH, livM, livJ, PAH, PCBD, QDPR, HPD, hmgA, maiA, fahA, aacS, atoB
Sphaerochaeta pleomorpha Grapes aroP, PAH, PCBD, QDPR, HPD, hmgA, maiA, fahA, aacS, atoB
Sphingobium baderi LL03 aroP, PAH, PCBD, QDPR, HPD, hmgA, maiA, fahA, atoA, atoD, atoB
Sphingobium czechense LL01 aroP, PAH, PCBD, QDPR, HPD, hmgA, maiA, fahA, atoA, atoD, atoB
Sphingobium quisquiliarum P25 aroP, PAH, PCBD, QDPR, HPD, hmgA, maiA, fahA, atoA, atoD, atoB
Sphingomonas histidinilytica UM2 aroP, ARO8, ARO10, pad-dh, paaK, paaA, paaB, paaC, paaE, paaG, paaZ1, paaZ2, paaJ1, paaF, paaH, paaJ2
Sphingomonas indica Dd16 aroP, ARO8, iorAB, paaA, paaB, paaC, paaE, paaG, paaZ1, paaZ2, paaJ1, paaF, paaH, paaJ2
Sphingomonas laterariae LNB2 aroP, PAH, PCBD, QDPR, HPD, hmgA, maiA, fahA, atoA, atoD, atoB
Sphingopyxis indica DS15 aroP, PAH, PCBD, QDPR, HPD, hmgA, maiA, fahA, atoA, atoD, atoB
Sphingopyxis terrae UI2 aroP, PAH, PCBD, QDPR, HPD, hmgA, maiA, fahA, atoA, atoD, atoB
Sporolactobacillus vineae SL153 aroP, PAH, PCBD, QDPR, HPD, hmgA, maiA, fahA, atoA, atoD, atoB
Streptacidiphilus oryzae TH49 aroP, ARO8, PPDCalpha, PPDCbeta, pad-dh, paaK, paaA, paaB, paaC, paaE, paaG, paaZ1, paaZ2, paaJ1, paaF, paaH, paaJ2
Streptococcus anginosus CCUG 39159 aroP, PAH, PCBD, QDPR, HPD, hmgA, maiA, fahA, atoA, atoD, atoB
Streptococcus massiliensis 4401825 aroP, PAH, PCBD, QDPR, HPD, hmgA, maiA, fahA, aacS, atoB
Streptococcus oralis 7747 aroP, PAH, PCBD, QDPR, HPD, hmgA, maiA, fahA, aacS, atoB
Streptococcus oralis AZ_3a aroP, PAH, PCBD, QDPR, HPD, hmgA, maiA, fahA, aacS, atoB
Streptomyces kebangsaanensis SUK12 livF, livG, livH, livM, livJ, ARO8, PPDCalpha, PPDCbeta, pad-dh, paaK, paaA, paaB, paaC, paaE, paaG, paaZ1, paaZ2, paaJ1, paaF, paaH, paaJ2
Succinatimonas hippei YIT 12066 aroP, PAH, PCBD, QDPR, HPD, hmgA, maiA, fahA, aacS, atoB
Sulfurimonas gotlandica GD1 aroP, PAH, PCBD, QDPR, HPD, hmgA, maiA, fahA, aacS, atoB
Tatumella morbirosei LMG 23360 aroP, PAH, PCBD, QDPR, HPD, hmgA, maiA, fahA, aacS, atoB
Thauera humireducens SgZ-1 livF, livG, livH, livM, livJ, ARO8, iorAB, paaA, paaB, paaC, paaE, paaG, paaZ1, paaZ2, paaJ1, paaF, paaH, paaJ2
Thermoactinomyces daqus H-18 aroP, ARO8, ARO10, pad-dh, paaK, paaA, paaB, paaC, paaE, paaG, paaZ1, paaZ2, paaJ1, paaF, paaH, paaJ2
Thermobifida halotolerans YIM 90462 aroP, ARO8, PPDCalpha, PPDCbeta, pad-dh, paaK, paaA, paaB, paaC, paaE, paaG, paaZ1, paaZ2, paaJ1, paaF, paaH, paaJ2
Thermodesulfovibrio aggregans TGE-P1 aroP, PAH, PCBD, QDPR, HPD, hmgA, maiA, fahA, aacS, atoB
Thermophagus xiamenensis HS1 aroP, PAH, PCBD, QDPR, HPD, hmgA, maiA, fahA, aacS, atoB
Thermovenabulum gondwanense R270 aroP, ARO8, iorA, iorB, paaA, paaB, paaC, paaE, paaG, paaZ1, paaZ2, paaJ1, paaF, paaH, paaJ2
Thioclava dalianensis DLFJ1-1 livF, livG, livH, livM, livJ, ARO8, ARO10, pad-dh, paaK, paaA, paaB, paaC, paaE, paaG, paaZ1, paaZ2, paaJ1, paaF, paaH, paaJ2
Thiohalospira halophila HL 3 aroP, PAH, PCBD, QDPR, HPD, hmgA, maiA, fahA, aacS, atoB
Tistlia consotensis USBA 355 livF, livG, livH, livM, livJ, PAH, PCBD, QDPR, HPD, hmgA, maiA, fahA, aacS, atoB
Vagococcus penaei CD276 aroP, PAH, PCBD, QDPR, HPD, hmgA, maiA, fahA, atoA, atoD, atoB
Verminephrobacter eiseniae EF01-2 livF, livG, livH, livM, livJ, ARO8, iorAB, paaA, paaB, paaC, paaE, paaG, paaZ1, paaZ2, paaJ1, paaF, paaH, paaJ2
Weissella oryzae SG25 aroP, PAH, PCBD, QDPR, HPD, hmgA, maiA, fahA, aacS, atoB
Williamsia sterculiae CPCC 203464 aroP, PAH, PCBD, QDPR, HPD, hmgA, maiA, fahA, aacS, atoB
Yersinia intermedia Y228 livF, livG, livH, livM, livJ, PAH, PCBD, QDPR, HPD, hmgA, maiA, fahA, atoA, atoD, atoB

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