GapMind for catabolism of small carbon sources

 

L-tryptophan catabolism

Analysis of pathway tryptophan in 276 genomes

Genome Best path
Acidovorax caeni R-24608 aroP, tnaA
Actinokineospora bangkokensis 44EHW aroP, tnaA
Actinomyces timonensis 7400942 aroP, tnaA
Algiphilus aromaticivorans DG1253 aroP, tnaA
Algoriphagus aquaeductus T4 aroP, tnaA
Algoriphagus machipongonensis PR1 aroP, tnaA
Alicyclobacillus ferrooxydans TC-34 aroP, tnaA
Alishewanella agri BL06 aroP, kynA, kynB, kyn, antA, antB, antC, catA, catB, catC, pcaD, pcaI, pcaJ, pcaF
Alistipes indistinctus YIT 12060 aroP, tnaA
Alistipes shahii WAL 8301 aroP, tnaA
Alkalitalea saponilacus SC/BZ-SP2 aroP, tnaA
Amantichitinum ursilacus IGB-41 aroP, tnaA
Amphibacillus jilinensis Y1 trpP, ecfA1, ecfA2, ecfT, tnaA
Amphritea japonica JAMM 1866 aroP, tnaA
Amycolatopsis halophila YIM 93223 aroP, tnaA
Amycolatopsis xylanica CPCC 202699 aroP, tnaA
Aquimarina agarilytica ZC1 aroP, tnaA
Aquimarina longa SW024 aroP, tnaA
Aquimarina macrocephali JAMB N27 aroP, tnaA
Archaeoglobus sulfaticallidus PM70-1 aroP, tnaA
Arcticibacter svalbardensis MN12-7 aroP, tnaA
Ardenticatena maritima 110S aroP, tnaA
Arenimonas metalli CF5-1 aroP, tnaA
Arenitalea lutea P7-3-5 aroP, tnaA
Azospirillum humicireducens SgZ-5 aroP, kynA, kynB, kyn, andAa, andAb, andAc, andAd, catA, catB, catC, pcaD, catI, catJ, pcaF
Azospirillum thiophilum BV-S aroP, tnaA
Bacillus altitudinis 41KF2b trpP, ecfA1, ecfA2, ecfT, tnaA
Bacillus coahuilensis m4-4 tnaT, tnaA
Bacillus cytotoxicus NVH 391-98 aroP, tnaA
Bacillus horneckiae 1P01SC trpP, ecfA1, ecfA2, ecfT, kynA, kynB, kyn, hpaH, nbaC, nbaD, nbaE, nbaF, nbaG, mhpD, mhpE, adh, ackA, pta
Bacillus okhensis Kh10-101 tnaT, kynA, kynB, kyn, antA, antB, antC, xylE, praB, praC, praD, mhpD, mhpE, adh, ackA, pta
Bacillus safensis FO-36b trpP, ecfA1, ecfA2, ecfT, tnaA
Bacillus velezensis CBMB205 trpP, ecfA1, ecfA2, ecfT, tnaA
Bacteroides clarus YIT 12056 aroP, tnaA
Bacteroides faecis MAJ27 aroP, tnaA
Bacteroides fluxus YIT 12057 aroP, tnaA
Bacteroides oleiciplenus YIT 12058 aroP, tnaA
Barnesiella intestinihominis YIT 11860 aroP, tnaA
Belnapia rosea CPCC 100156 aroP, tnaA
Bizionia argentinensis JUB59 aroP, tnaA
Bradyrhizobium diazoefficiens USDA110 aroP, tnaA
Brevibacterium jeotgali SJ5-8 aroP, tnaA
Brucella inopinata BO1 aroP, tnaA
Brucella microti CCM 4915 aroP, tnaA
Bryobacter aggregatus MPL3 aroP, tnaA
Caldicellulosiruptor hydrothermalis 108 trpP, ecfA1, ecfA2, ecfT, tnaA
Caldicellulosiruptor kronotskyensis 2002 trpP, ecfA1, ecfA2, ecfT, tnaA
Carboxydothermus pertinax Ug1 aroP, tnaA
Catellicoccus marimammalium M35/04/3 aroP, tnaA
Chromobacterium vaccinii MWU205 aroP, tnaA
Chryseobacterium angstadtii KM aroP, tnaA
Chryseobacterium arthrosphaerae CC-VM-7 aroP, tnaA
Chryseobacterium viscerum 687B-08 aroP, tnaA
Cloacibacillus porcorum CL-84 trpP, ecfA1, ecfA2, ecfT, tnaA
Cobetia crustatorum JO1 aroP, tnaA
Collimonas arenae Ter10 aroP, tnaA
Collimonas pratensis Ter91 aroP, kynA, kynB, kyn, andAa, andAb, andAc, andAd, catA, catB, catC, pcaD, pcaI, pcaJ, pcaF
Collinsella tanakaei YIT 12063 aroP, tnaA
Coprobacter fastidiosus NSB1 aroP, tnaA
Corynebacterium deserti GIMN1.010 aroP, tnaA
Corynebacterium frankenforstense ST18 aroP, tnaA
Corynebacterium lactis RW2-5 aroP, tnaA
Croceitalea dokdonensis DOKDO 023 aroP, tnaA
Cronobacter condimenti 1330 aroP, tnaA
Cronobacter muytjensii ATCC 51329 aroP, tnaA
Cronobacter universalis NCTC 9529 aroP, tnaA
Desulfatitalea tepidiphila S28bF aroP, tnaA
Desulfotomaculum hydrothermale Lam5 trpP, ecfA1, ecfA2, ecfT, tnaA
Dethiosulfovibrio salsuginis USBA 82 trpP, ecfA1, ecfA2, ecfT, tnaA
Devosia chinhatensis IPL18 aroP, tnaA
Devriesea agamarum IMP2 aroP, tnaA
Dialister succinatiphilus YIT 11850 aroP, tnaA
Dietzia timorensis ID05-A0528 aroP, kynA, kynB, kyn, antA, antB, antC, catA, catB, catC, pcaD, pcaI, pcaJ, pcaF
Dokdonella koreensis DS-123 aroP, tnaA
Domibacillus robiginosus WS 4628 aroP, tnaA
Duganella sacchari Sac-22 aroP, kynA, kynB, kyn, hpaH, nbaC, nbaD, nbaE, nbaF, nbaG, mhpD, mhpE, adh, acs
Dyadobacter tibetensis Y620-1 aroP, tnaA
Dyella jiangningensis SBZ3-12 aroP, kynA, kynB, sibC, kyn, nbaC, nbaD, nbaE, nbaF, nbaG, mhpD, mhpE, adh, acs
Endozoicomonas montiporae CL-33 tnaB, tnaA
Enterococcus termitis LMG 8895 trpP, ecfA1, ecfA2, ecfT, tnaA
Enterorhabdus caecimuris B7 trpP, ecfA1, ecfA2, ecfT, tnaA
Epibacterium ulvae U95 aroP, tnaA
Erythrobacter gangjinensis K7-2 aroP, tnaA
Erythrobacter marinus HWDM-33 aroP, tnaA
Ethanoligenens harbinense YUAN-3 trpP, ecfA1, ecfA2, ecfT, tnaA
Fervidicella metallireducens AeB trpP, ecfA1, ecfA2, ecfT, tnaA
Fibrella aestuarina BUZ 2 aroP, tnaA
Flammeovirga pacifica WPAGA1 aroP, tnaA
Flaviramulus ichthyoenteri Th78 aroP, tnaA
Flavobacterium beibuense F44-8 aroP, tnaA
Flavobacterium glycines Gm-149 aroP, tnaA
Flavobacterium sp. LM5 aroP, tnaA
Flavobacterium ummariense DS-12 aroP, tnaA
Frischella perrara PEB0191 aroP, tnaA
Galbibacter marinus ck-I2-15 aroP, tnaA
Gallaecimonas xiamenensis 3-C-1 aroP, tnaA
Geobacter daltonii FRC-32 aroP, tnaA
Gillisia marina CBA3202 aroP, tnaA
Gracilibacillus halophilus YIM-C55.5 tnaT, tnaA
Granulicella mallensis MP5ACTX8 aroP, tnaA
Granulicella tundricola MP5ACTX9 aroP, tnaA
Hafnia paralvei ATCC 29927 aroP, tnaA
Haladaptatus cibarius D43 aroP, tnaA
Halioglobus japonicus S1-36 aroP, tnaA
Halobacillus alkaliphilus FP5 trpP, ecfA1, ecfA2, ecfT, tnaA
Halococcus hamelinensis 100A6 aroP, tnaA
Halomonas salina B6 aroP, tnaA
Halomonas smyrnensis AAD6 aroP, tnaA
Halomonas stevensii S18214 aroP, tnaA
Halomonas titanicae BH1 aroP, kynA, kynB, kyn, antA, antB, antC, catA, catB, catC, pcaD, catI, catJ, pcaF
Halomonas xinjiangensis TRM 0175 aroP, tnaA
Halopiger salifodinae KCY07-B2 aroP, tnaA
Halostagnicola larsenii XH-48 aroP, tnaA
Haloterrigena daqingensis JX313 aroP, tnaA
Herbaspirillum aquaticum IEH 4430 aroP, kynA, kynB, kyn, antA, antB, antC, catA, catB, catC, pcaD, pcaI, pcaJ, pcaF
Hippea alviniae EP5-r aroP, tnaA
Hippea jasoniae Mar08-272r aroP, tnaA
Hoeflea phototrophica DFL-43 aroP, tnaA
Hyphomicrobium nitrativorans NL23 aroP, tnaA
Imtechella halotolerans K1 aroP, tnaA
Indibacter alkaliphilus LW1 aroP, tnaA
Jannaschia aquimarina GSW-M26 aroP, tnaA
Jeotgalibacillus soli P9 trpP, ecfA1, ecfA2, ecfT, tnaA
Kangiella geojedonensis YCS-5 aroP, kynA, kynB, sibC, kyn, nbaC, nbaD, nbaE, nbaF, nbaG, mhpD, mhpE, adh, acs
Knoellia flava TL1 aroP, tnaA
Kocuria flava HO-9041 aroP, tnaA
Kocuria turfanensis HO-9042 aroP, tnaA
Laceyella sediminis RHA1 aroP, tnaA
Lacinutrix algicola AKS293 aroP, tnaA
Lacinutrix himadriensis E4-9a aroP, tnaA
Lacinutrix mariniflava AKS432 aroP, tnaA
Lactobacillus curieae CCTCC M 2011381 aroP, tnaA
Lactobacillus delbrueckii ZN7a-9 trpP, ecfA1, ecfA2, ecfT, tnaA
Lactobacillus hokkaidonensis LOOC260 aroP, tnaA
Lactobacillus oryzae SG293 aroP, tnaA
Lactobacillus pobuzihii E100301 aroP, tnaA
Lactobacillus shenzhenensis LY-73 trpP, ecfA1, ecfA2, ecfT, tnaA
Lactobacillus silagei IWT126 aroP, tnaA
Leeuwenhoekiella blandensis MED217 aroP, tnaA
Lentibacillus jeotgali Grbi trpP, ecfA1, ecfA2, ecfT, tnaA
Limnohabitans curvus MWH-C5 aroP, tnaA
Limnohabitans parvus II-B4 aroP, tnaA
Listeria fleischmannii LU2006-1 aroP, tnaA
Luteimonas huabeiensis HB2 aroP, kynA, kynB, kyn, antA, antB, antC, catA, catB, catC, pcaD, pcaI, pcaJ, pcaF
Luteipulveratus mongoliensis MN07-A0370 aroP, tnaA
Lutibaculum baratangense AMV1 aroP, tnaA
Lysobacter daejeonensis GH1-9 aroP, tnaA
Magnetovibrio blakemorei MV-1 aroP, tnaA
Marinicella litoralis KMM 3900 aroP, kynA, kynB, sibC, kyn, nbaC, nbaD, nbaE, nbaF, nbaG, mhpD, mhpE, adh, acs
Mariniradius saccharolyticus AK6 aroP, tnaA
Marinobacter algicola DG893 aroP, kynA, kynB, kyn, antA, antB, antC, xylE, praB, praC, praD, mhpD, mhpE, adh, acs
Marinobacter guineae M3B aroP, tnaA
Marinobacter psychrophilus 20041 aroP, kynA, kynB, kyn, antA, antB, antC, catA, catB, catC, pcaD, pcaI, pcaJ, pcaF
Marinomonas arctica 328 aroP, tnaA
Marivita geojedonensis DPG-138 aroP, kynA, kynB, kyn, antA, antB, antC, catA, catB, catC, pcaD, pcaI, pcaJ, pcaF
Martelella endophytica YC6887 aroP, tnaA
Megamonas funiformis YIT 11815 aroP, tnaA
Mesorhizobium ciceri WSM1271 aroP, kynA, kynB, kyn, andAa, andAb, andAc, andAd, xylE, xylF, mhpD, mhpE, adh, acs
Methanobacterium arcticum M2 aroP, tnaA
Methanobacterium veterum MK4 aroP, tnaA
Methanocella arvoryzae MRE50 aroP, tnaA
Methanococcus aeolicus Nankai-3 tnaT, tnaA
Methanoculleus horonobensis T10 aroP, tnaA
Methanolinea tarda NOBI-1 aroP, tnaA
Methanosarcina soligelidi SMA-21 aroP, tnaA
Methanospirillum lacunae Ki8-1 aroP, tnaA
Methanospirillum stamsii Pt1 aroP, tnaA
Methylibium petroleiphilum PM1 aroP, tnaA
Methylobacterium gossipiicola Gh-105 aroP, tnaA
Methylocapsa aurea KYG aroP, tnaA
Methylotenera versatilis 301 aroP, tnaA
Microbacterium profundi Shh49 tnaT, tnaA
Microvirga lotononidis WSM3557 aroP, tnaA
Moritella dasanensis ArB 0140 tnaB, tnaA
Mucilaginibacter gossypii Gh-67 aroP, tnaA
Mucilaginibacter gossypiicola Gh-48 aroP, tnaA
Mucilaginibacter mallensis MP1X4 aroP, tnaA
Nafulsella turpanensis ZLM-10 aroP, tnaA
Natronomonas moolapensis 8.8.11 aroP, tnaA
Nautilia profundicola AmH aroP, tnaA
Neiella marina J221 aroP, tnaA
Neptunomonas antarctica S3-22 aroP, tnaA
Nocardioides daejeonensis MJ31 aroP, kynA, kynB, kyn, andAa, andAb, andAc, andAd, catA, catB, catC, pcaD, pcaI, pcaJ, pcaF
Nocardioides dokdonensis FR1436 aroP, tnaA
Nocardiopsis baichengensis YIM 90130 tnaT, tnaA
Nocardiopsis gilva YIM 90087 aroP, tnaA
Novosphingobium barchaimii LL02 aroP, tnaA
Novosphingobium fuchskuhlense FNE08-7 aroP, tnaA
Novosphingobium lindaniclasticum LE124 aroP, tnaA
Oceanisphaera arctica V1-41 tnaT, kynA, kynB, kyn, antA, antB, antC, catA, catB, catC, pcaD, catI, catJ, pcaF
Ochrobactrum rhizosphaerae PR17 aroP, tnaA
Ochrobactrum thiophenivorans DSM 7216 aroP, tnaA
Oscillibacter ruminantium GH1 trpP, ecfA1, ecfA2, ecfT, tnaA
Paenisporosarcina indica PN2 trpP, ecfA1, ecfA2, ecfT, tnaA
Palaeococcus pacificus DY20341 aroP, tnaA
Paludibacter propionicigenes WB4 aroP, tnaA
Pandoraea thiooxydans ATSB16 aroP, tnaA
Pantoea rwandensis LMG 26275 aroP, tnaA
Pedobacter arcticus A12 aroP, tnaA
Photobacterium gaetbulicola Gung47 tnaB, tnaA
Photobacterium jeanii R-40508 tnaB, tnaA
Phyllobacterium brassicacearum STM 196 aroP, kynA, kynB, kyn, antA, antB, antC, catA, catB, catC, pcaD, catI, catJ, pcaF
Phyllobacterium endophyticum PEPV15 aroP, tnaA
Phyllobacterium leguminum ORS 1419 aroP, tnaA
Planktomarina temperata RCA23 aroP, tnaA
Planococcus halocryophilus Or1 trpP, ecfA1, ecfA2, ecfT, tnaA
Pleomorphomonas diazotrophica R5-392 aroP, tnaA
Polaribacter dokdonensis DSW-5 aroP, tnaA
Pontibacillus litoralis JSM 072002 trpP, ecfA1, ecfA2, ecfT, tnaA
Pontibacter lucknowensis DM9 aroP, kynA, kynB, kyn, antA, antB, antC, catA, catB, catC, pcaD, pcaI, pcaJ, pcaF
Pontibacter ramchanderi LP43 aroP, kynA, kynB, kyn, antA, antB, antC, catA, catB, catC, pcaD, pcaI, pcaJ, pcaF
Pontimonas salivibrio CL-TW6 aroP, tnaA
Porphyrobacter dokdonensis DSW-74 aroP, tnaA
Pseudoalteromonas arctica A 37-1-2 aroP, tnaA
Pseudomonas baetica a390 aroP, tnaA
Pseudomonas litoralis 2SM5 aroP, kynA, kynB, kyn, antA, antB, antC, catA, catB, catC, pcaD, catI, catJ, pcaF
Pseudomonas taeanensis MS-3 aroP, kynA, kynB, kyn, antA, antB, antC, xylE, praB, praC, praD, mhpD, mhpE, adh, ackA, pta
Pseudovibrio axinellae Ad2 tnaB, tnaA
Psychrobacter arcticus 273-4 aroP, tnaA
Psychrobacter cryohalolentis K5 aroP, tnaA
Psychromonas ingrahamii 37 aroP, tnaA
Psychromonas ossibalaenae JAMM 0738 tnaB, tnaA
Rhizobium freirei PRF 81 aroP, tnaA
Rhizobium grahamii CCGE 502 aroP, tnaA
Rhizobium subbaraonis JC85 aroP, tnaA
Rhodanobacter denitrificans 2APBS1 aroP, kynA, kynB, sibC, kyn, nbaC, nbaD, nbaE, nbaF, nbaG, mhpD, mhpE, adh, acs
Rhodobacter johrii JA192 aroP, tnaA
Rhodobacter maris JA276 aroP, tnaA
Rhodobacter ovatus JA234 aroP, tnaA
Rhodobacter viridis JA737 aroP, tnaA
Rhodococcus qingshengii djl-6-2 aroP, kynA, kynB, kyn, hpaH, nbaC, nbaD, nbaE, nbaF, nbaG, mhpD, mhpE, adh, ackA, pta
Rhodopseudomonas pseudopalustris DSM 123 aroP, tnaA
Roseateles aquatilis CCUG 48205 aroP, tnaA
Roseivirga spongicola UST030701-084 aroP, tnaA
Rubrivirga marina SAORIC-28 aroP, tnaA
Ruegeria conchae TW15 aroP, kynA, kynB, sibC, kyn, nbaC, nbaD, nbaE, nbaF, nbaG, mhpD, mhpE, adh, ackA, pta
Saccharomonospora marina XMU15 aroP, tnaA
Salinicoccus carnicancri Crm trpP, ecfA1, ecfA2, ecfT, kynA, kynB, kyn, antA, antB, antC, xylE, xylF, mhpD, mhpE, adh, ackA, pta
Serinicoccus profundi MCCC 1A05965 aroP, tnaA
Shewanella halifaxensis HAW-EB4 tnaB, tnaA
Skermanella stibiiresistens SB22 aroP, kynA, kynB, kyn, antA, antB, antC, catA, catB, catC, pcaD, pcaI, pcaJ, pcaF
Snodgrassella alvi wkB2 aroP, tnaA
Sphaerochaeta globosa Buddy aroP, tnaA
Sphaerochaeta pleomorpha Grapes aroP, tnaA
Sphingobium baderi LL03 aroP, tnaA
Sphingobium czechense LL01 aroP, kynA, kynB, kyn, antA, antB, antC, catA, catB, catC, pcaD, pcaI, pcaJ, pcaF
Sphingobium quisquiliarum P25 aroP, tnaA
Sphingomonas histidinilytica UM2 aroP, kynA, kynB, kyn, hpaH, nbaC, nbaD, nbaE, nbaF, nbaG, mhpD, mhpE, ald-dh-CoA
Sphingomonas indica Dd16 aroP, tnaA
Sphingomonas laterariae LNB2 aroP, kynA, kynB, kyn, hpaH, nbaC, nbaD, nbaE, nbaF, nbaG, mhpD, mhpE, ald-dh-CoA
Sphingopyxis indica DS15 aroP, tnaA
Sphingopyxis terrae UI2 aroP, kynA, kynB, kyn, hpaH, nbaC, nbaD, nbaE, nbaF, nbaG, mhpD, mhpE, ald-dh-CoA
Sporolactobacillus vineae SL153 trpP, ecfA1, ecfA2, ecfT, tnaA
Streptacidiphilus oryzae TH49 aroP, kynA, kynB, kyn, andAa, andAb, andAc, andAd, xylE, praB, praC, praD, mhpD, mhpE, adh, acs
Streptococcus anginosus CCUG 39159 trpP, ecfA1, ecfA2, ecfT, tnaA
Streptococcus massiliensis 4401825 trpP, ecfA1, ecfA2, ecfT, tnaA
Streptococcus oralis 7747 trpP, ecfA1, ecfA2, ecfT, tnaA
Streptococcus oralis AZ_3a trpP, ecfA1, ecfA2, ecfT, tnaA
Streptomyces kebangsaanensis SUK12 aroP, tnaA
Succinatimonas hippei YIT 12066 aroP, tnaA
Sulfurimonas gotlandica GD1 aroP, tnaA
Tatumella morbirosei LMG 23360 aroP, tnaA
Thauera humireducens SgZ-1 aroP, tnaA
Thermoactinomyces daqus H-18 aroP, tnaA
Thermobifida halotolerans YIM 90462 aroP, tnaA
Thermodesulfovibrio aggregans TGE-P1 aroP, tnaA
Thermophagus xiamenensis HS1 aroP, tnaA
Thermovenabulum gondwanense R270 tnaT, tnaA
Thioclava dalianensis DLFJ1-1 aroP, tnaA
Thiohalospira halophila HL 3 aroP, tnaA
Tistlia consotensis USBA 355 aroP, tnaA
Vagococcus penaei CD276 trpP, ecfA1, ecfA2, ecfT, tnaA
Verminephrobacter eiseniae EF01-2 aroP, tnaA
Weissella oryzae SG25 aroP, tnaA
Williamsia sterculiae CPCC 203464 aroP, tnaA
Yersinia intermedia Y228 aroP, tnaA

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