L-tryptophan catabolism

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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Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

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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:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

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:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

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:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

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:

the paper from 2019 on GapMind for amino acid biosynthesis
the 2024 update on GapMind for amino acid biosynthesis
the paper from 2022 on GapMind for carbon sources
the source code
instructions for running GapMind on your computer

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

GapMind for catabolism of small carbon sources