L-tryptophan catabolism

GapMind for catabolism of small carbon sources

L-tryptophan catabolism

Analysis of pathway tryptophan in 150 genomes

Genome	Best path
Acidimicrobium ferrooxidans DSM 10331	aroP, tnaA
Acidithiobacillus ferrooxidans ATCC 23270	aroP, tnaA
Alicycliphilus denitrificans K601	aroP, tnaA
Allochromatium vinosum DSM 180	aroP, tnaA
Ammonifex degensii KC4	aroP, tnaA
Archaeoglobus veneficus SNP6	aroP, tnaA
Arcobacter nitrofigilis DSM 7299	aroP, tnaA
Azoarcus sp. BH72	aroP, tnaA
Azohydromonas australica DSM 1124	aroP, kynA, kynB, kyn, antA, antB, antC, catA, catB, catC, pcaD, pcaI, pcaJ, pcaF
Azorhizobium caulinodans ORS 571	aroP, tnaA
Azospirillum lipoferum B510	aroP, kynA, kynB, kyn, andAa, andAb, andAc, andAd, catA, catB, catC, pcaD, catI, catJ, pcaF
Bacillus alkalinitrilicus DSM 22532	tnaT, kynA, kynB, kyn, antA, antB, antC, xylE, praB, praC, praD, mhpD, mhpE, adh, ackA, pta
Beijerinckia indica ATCC 9039	aroP, tnaA
Beijerinckia mobilis UQM 1969	aroP, kynA, kynB, kyn, antA, antB, antC, xylE, praB, praC, praD, mhpD, mhpE, adh, acs
Bradyrhizobium sp. BTAi1	aroP, tnaA
Burkholderia vietnamiensis G4	aroP, kynA, kynB, kyn, andAa, andAb, andAc, andAd, xylE, praB, praC, praD, mhpD, mhpE, adh, acs
Calditerrivibrio nitroreducens DSM 19672	aroP, tnaA
Caminibacter mediatlanticus TB-2	aroP, tnaA
Chlorobaculum parvum NCIB 8327	tnaT, tnaA
Chlorobaculum tepidum TLS	aroP, tnaA
Chlorobium limicola DSM 245	aroP, tnaA
Chlorobium phaeobacteroides BS1	tnaT, tnaA
Clostridium acetobutylicum ATCC 824	trpP, ecfA1, ecfA2, ecfT, tnaA
Clostridium kluyveri DSM 555	trpP, ecfA1, ecfA2, ecfT, tnaA
Crocosphaera subtropica ATCC 51142	aroP, tnaA
Dechloromonas agitata is5	aroP, tnaA
Dehalococcoides mccartyi 195	aroP, tnaA
Denitrovibrio acetiphilus DSM 12809	aroP, tnaA
Derxia gummosa DSM 723	aroP, tnaA
Desulfacinum hydrothermale DSM 13146	aroP, tnaA
Desulfacinum infernum DSM 9756	aroP, tnaA
Desulfallas geothermicus DSM 3669	tnaT, tnaA
Desulfarculus baarsii DSM 2075	tnaT, tnaA
Desulfatibacillum aliphaticivorans DSM 15576	aroP, tnaA
Desulfatiglans anilini DSM 4660	aroP, tnaA
Desulfitobacterium hafniense DCB-2	aroP, tnaA
Desulfobacca acetoxidans DSM 11109	aroP, tnaA
Desulfobacter vibrioformis DSM 8776	tnaT, tnaA
Desulfobulbus mediterraneus DSM 13871	aroP, tnaA
Desulfotalea psychrophila LSv54	aroP, tnaA
Desulfotomaculum ruminis DSM 2154	aroP, tnaA
Desulfovibrio bastinii DSM 16055	tnaT, tnaA
Desulfovibrio gracilis DSM 16080	tnaT, tnaA
Desulfovibrio oxyclinae DSM 11498	tnaT, tnaA
Desulfovibrio zosterae DSM 11974	tnaT, tnaA
Desulfurobacterium atlanticum DSM 15668	aroP, tnaA
Desulfuromonas acetexigens	aroP, tnaA
Desulfuromusa kysingii DSM 7343	aroP, tnaA
Ferroglobus placidus DSM 10642	aroP, tnaA
Frankia alni ACN14A	aroP, tnaA
Geobacter lovleyi SZ	aroP, tnaA
Geobacter metallireducens GS-15	aroP, tnaA
Geobacter uraniireducens Rf4	aroP, tnaA
Haloechinothrix alba DSM 45207	tnaT, tnaA
Haloglycomyces albus DSM 45210	aroP, tnaA
Halomonas desiderata SP1	aroP, kynA, kynB, kyn, antA, antB, antC, catA, catB, catC, pcaD, catI, catJ, pcaF
Halorhodospira halophila SL1	aroP, tnaA
Heliobacterium modesticaldum Ice1; ATCC 51547	trpP, ecfA1, ecfA2, ecfT, tnaA
Herbaspirillum autotrophicum IAM 14942	aroP, kynA, kynB, kyn, hpaH, nbaC, nbaD, nbaE, nbaF, nbaG, mhpD, mhpE, adh, acs
Hydrogenophaga taeniospiralis NBRC 102512	aroP, tnaA
Hydrogenovibrio halophilus DSM 15072	aroP, tnaA
Hydrogenovibrio kuenenii DSM 12350	aroP, tnaA
Hydrogenovibrio marinus DSM 11271	aroP, tnaA
Hyphomicrobium sulfonivorans WDL6	aroP, tnaA
Klebsiella variicola At-22	aroP, kynA, kynB, kyn, antA, antB, antC, catA, catB, catC, pcaD, pcaI, pcaJ, pcaF
Kyrpidia tusciae DSM 2912	aroP, tnaA
Leptospirillum ferrooxidans C2-3	aroP, tnaA
Malonomonas rubra DSM 5091	aroP, tnaA
Mesorhizobium ciceri WSM1271	aroP, kynA, kynB, kyn, andAa, andAb, andAc, andAd, xylE, xylF, mhpD, mhpE, adh, acs
Methanobacterium lacus AL-21	aroP, tnaA
Methanococcus aeolicus Nankai-3	tnaT, tnaA
Methanococcus maripaludis C5	tnaT, tnaA
Methanosarcina acetivorans C2A	tnaT, tnaA
Methanosarcina barkeri Fusaro	trpP, ecfA1, ecfA2, ecfT, tnaA
Methanosarcina mazei Go1	aroP, tnaA
Methanothermobacter thermautotrophicus Delta H	aroP, tnaA
Methylobacterium nodulans ORS 2060	aroP, kynA, kynB, kyn, antA, antB, antC, catA, catB, catC, pcaD, pcaI, pcaJ, pcaF
Methylobacterium sp. 4-46	aroP, kynA, kynB, kyn, antA, antB, antC, catA, catB, catC, pcaD, pcaI, pcaJ, pcaF
Methylocapsa acidiphila B2	aroP, tnaA
Methylocapsa aurea KYG T	aroP, tnaA
Methylocella silvestris BL2	aroP, kynA, kynB, kyn, andAa, andAb, andAc, andAd, xylE, praB, praC, praD, mhpD, mhpE, adh, acs
Methylococcus capsulatus Bath	aroP, tnaA
Methylocystis bryophila S285	aroP, tnaA
Methyloferula stellata AR4T	aroP, tnaA
Methylohalobius crimeensis 10Ki	tnaT, tnaA
Methylomicrobium alcaliphilum 20Z	tnaT, tnaA
Methylomonas methanica MC09	aroP, tnaA
Methylosarcina fibrata AML-C10	aroP, tnaA
Methylovulum miyakonense HT12	aroP, tnaA
Mycolicibacterium vanbaalenii PYR-1	aroP, tnaA
Nitratifractor salsuginis DSM 16511	aroP, tnaA
Nitratiruptor tergarcus DSM 16512	aroP, tnaA
Nitriliruptor alkaliphilus DSM 45188	tnaT, tnaA
Nocardiopsis lucentensis DSM 44048	tnaT, tnaA
Nostoc punctiforme ATCC 29133; PCC 73102	aroP, tnaA
Novosphingobium aromaticivorans DSM 12444	aroP, kynA, kynB, kyn, andAa, andAb, andAc, andAd, xylE, xylF, mhpD, mhpE, adh, acs
Oleispira antarctica	aroP, tnaA
Paraburkholderia phymatum STM815	aroP, kynA, kynB, kyn, antA, antB, antC, catA, catB, catC, pcaD, pcaI, pcaJ, pcaF
Paraburkholderia sp. CCGE1002	aroP, tnaA
Pelobacter propionicus DSM 2379	aroP, tnaA
Persephonella marina EX-H1	aroP, tnaA
Polaromonas naphthalenivorans CJ2	aroP, kynA, kynB, kyn, antA, antB, antC, catA, catB, catC, pcaD, pcaI, pcaJ, pcaF
Prosthecochloris aestuarii DSM 271	aroP, tnaA
Pseudarthrobacter sulfonivorans Ar51	aroP, kynA, kynB, kyn, antA, antB, antC, xylE, xylF, mhpD, mhpE, adh, ackA, pta
Pseudomonas benzenivorans DSM 8628	aroP, kynA, kynB, kyn, antA, antB, antC, xylE, praB, praC, praD, mhpD, mhpE, adh, ackA, pta
Pseudomonas stutzeri A1501	aroP, kynA, kynB, kyn, antA, antB, antC, catA, catB, catC, pcaD, catI, catJ, pcaF
Pyrolobus fumarii 1A	aroP, tnaA
Rhizobium etli CFN 42	aroP, tnaA
Rhizobium leguminosarum 3841	aroP, tnaA
Rhizobium leguminosarum WSM1325	aroP, tnaA
Rhodobacter sphaeroides ATCC 17029	aroP, tnaA
Rhodomicrobium vannielii ATCC 17100	aroP, tnaA
Rhodopseudomonas palustris CGA009	aroP, tnaA
Rhodospirillum centenum SW; ATCC 51521	aroP, tnaA
Rhodospirillum rubrum ATCC 11170	aroP, tnaA
Saccharomonospora cyanea NA-134	aroP, tnaA
Sedimenticola selenatireducens DSM 17993	aroP, tnaA
Sinorhizobium fredii NGR234	aroP, tnaA
Sinorhizobium medicae WSM419	aroP, tnaA
Sphingomonas wittichii RW1	aroP, kynA, kynB, kyn, hpaH, nbaC, nbaD, nbaE, nbaF, nbaG, mhpD, mhpE, adh, acs
Stenotrophomonas chelatiphaga DSM 21508	aroP, tnaA
Steroidobacter denitrificans DSM 18526	aroP, tnaA
Sulfuricurvum kujiense DSM 16994	aroP, tnaA
Sulfurihydrogenibium azorense Az-Fu1	aroP, tnaA
Sulfurihydrogenibium subterraneum DSM 15120	aroP, tnaA
Sulfurimonas denitrificans DSM 1251	aroP, tnaA
Sulfuritalea hydrogenivorans DSM 22779	aroP, tnaA
Sulfurivirga caldicuralii DSM 17737	aroP, tnaA
Teredinibacter turnerae T7901	aroP, tnaA
Thauera aminoaromatica S2	aroP, tnaA
Thermithiobacillus tepidarius DSM 3134	aroP, tnaA
Thermocrinis albus DSM 14484	aroP, tnaA
Thermodesulforhabdus norvegica DSM 9990	aroP, tnaA
Thermomonospora curvata DSM 43183	aroP, tnaA
Thermovibrio ammonificans HB-1	aroP, tnaA
Thioalkalivibrio denitrificans ALJD	aroP, tnaA
Thioalkalivibrio halophilus HL17	aroP, tnaA
Thioalkalivibrio paradoxus ARh 1	aroP, tnaA
Thioalkalivibrio thiocyanodenitrificans ARhD 1	aroP, tnaA
Thiohalomonas denitrificans HLD2	aroP, tnaA
Thiomicrorhabdus arctica DSM 13458	aroP, tnaA
Thiomicrorhabdus chilensis DSM 12352	aroP, tnaA
Thiomicrospira cyclica ALM1	aroP, tnaA
Thiomicrospira microaerophila ASL8-2	aroP, tnaA
Thiomicrospira pelophila DSM 1534	aroP, tnaA
Thiothrix lacustris DSM 21227	aroP, tnaA
Trichodesmium erythraeum IMS101	aroP, tnaA
Trichormus variabilis ATCC 29413	aroP, tnaA
Xanthobacter autotrophicus Py2	aroP, kynA, kynB, kyn, antA, antB, antC, catA, catB, catC, pcaD, pcaI, pcaJ, pcaF
Xenophilus azovorans DSM 13620	aroP, kynA, kynB, kyn, andAa, andAb, andAc, andAd, xylE, 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 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

Related tools

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 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