GapMind for catabolism of small carbon sources

 

L-tryptophan catabolism

Analysis of pathway tryptophan in 201 genomes

Genome Best path
Acidimicrobium ferrooxidans DSM 10331 aroP, tnaA
Acidithiobacillus ferrooxidans ATCC 23270 aroP, tnaA
Acidovorax sp. GW101-3H11 aroP, kynA, kynB, kyn, andAa, andAb, andAc, andAd, xylE, praB, praC, praD, mhpD, mhpE, adh, acs
Algiphilus aromaticivorans DG1253 aroP, tnaA
Alicycliphilus denitrificans K601 aroP, tnaA
Alkalihalobacterium alkalinitrilicum DSM 22532 tnaT, kynA, kynB, kyn, antA, antB, antC, xylE, praB, praC, praD, mhpD, mhpE, adh, ackA, pta
Allochromatium vinosum DSM 180 aroP, tnaA
Ammonifex degensii KC4 aroP, tnaA
Anaerobutyricum hallii DSM 3353 trpP, ecfA1, ecfA2, ecfT, tnaA
Aquimarina longa SW024 aroP, tnaA
Archaeoglobus veneficus SNP6 aroP, tnaA
Arcobacter nitrofigilis DSM 7299 aroP, tnaA
Azoarcus olearius 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 brasilense Sp245 aroP, tnaA
Azospirillum sp. B510 aroP, kynA, kynB, kyn, andAa, andAb, andAc, andAd, catA, catB, catC, pcaD, catI, catJ, pcaF
Bacteroides thetaiotaomicron VPI-5482 aroP, tnaA
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
Billgrantia desiderata SP1 aroP, kynA, kynB, kyn, antA, antB, antC, catA*, catB, catC, pcaD, catI, catJ, pcaF
Bradyrhizobium sp. BTAi1 aroP, tnaA
Brevundimonas sp. GW460-12-10-14-LB2 aroP, tnaA
Burkholderia phytofirmans PsJN aroP, kynA, kynB, kyn, hpaH, nbaC, nbaD, nbaE, nbaF, nbaG, mhpD, mhpE, adh, ackA, pta
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
Carboxydothermus pertinax Ug1 aroP, tnaA
Caulobacter crescentus NA1000 aroP, tnaA
Cereibacter sphaeroides ATCC 17029 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
Clostridium tyrobutyricum FAM22553 trpP, ecfA1, ecfA2, ecfT, tnaA
Crocosphaera subtropica ATCC 51142 aroP, tnaA
Cupriavidus basilensis FW507-4G11 aroP, kynA, kynB, kyn, antA, antB, antC, xylE, praB, praC, praD, mhpD, mhpE, adh, ackA, pta
Dechloromonas agitata is5 aroP, tnaA
Dechlorosoma suillum PS 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
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
Desulfogranum mediterraneum DSM 13871 aroP, tnaA
Desulforamulus ruminis DSM 2154 aroP, tnaA
Desulfoscipio geothermicus DSM 3669 tnaT, tnaA
Desulfotalea psychrophila LSv54 aroP, tnaA
Desulfovibrio oxyclinae DSM 11498 tnaT, tnaA
Desulfovibrio vulgaris Hildenborough JW710 tnaB, tnaA
Desulfovibrio vulgaris Miyazaki F aroP, tnaA
Desulfurobacterium atlanticum DSM 15668 aroP, tnaA
Desulfuromonas acetexigens aroP, tnaA
Desulfuromusa kysingii DSM 7343 aroP, tnaA
Dinoroseobacter shibae DFL-12 aroP, tnaA
Dyella japonica UNC79MFTsu3.2 aroP, tnaA
Echinicola vietnamensis KMM 6221, DSM 17526 aroP, tnaA
Escherichia coli BW25113 aroP, tnaA
Ferroglobus placidus DSM 10642 aroP, tnaA
Frankia alni ACN14a aroP, tnaA
Geobacter metallireducens GS-15 aroP, tnaA
Geotalea uraniireducens Rf4 aroP, tnaA
Halococcus hamelinensis 100A6 aroP, tnaA
Haloechinothrix alba DSM 45207 tnaT, tnaA
Haloferax volcanii DS2 aroP, tnaA
Haloglycomyces albus DSM 45210 aroP, tnaA
Halorhodospira halophila SL1 aroP, tnaA
Heliomicrobium 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
Herbaspirillum seropedicae SmR1 aroP, kynA, kynB, kyn, antA, antB, antC, catA, catB, catC, pcaD, pcaI, pcaJ, pcaF
Hippea alviniae EP5-r aroP, tnaA
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 michiganensis M5al 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
Magnetospirillum magneticum AMB-1 aroP, tnaA
Malonomonas rubra DSM 5091 aroP, tnaA
Maridesulfovibrio bastinii DSM 16055 tnaT, tnaA
Maridesulfovibrio zosterae DSM 11974 tnaT, tnaA
Marinobacter adhaerens HP15 aroP, kynA, kynB, kyn, antA, antB, antC, xylE, praB, praC, praD, mhpD, mhpE, adh, ackA, pta
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 mazei Go1 aroP, tnaA
Methanospirillum lacunae Ki8-1 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 Apr-46 aroP, kynA, kynB, kyn, antA, antB, antC, catA, catB, catC, pcaD, pcaI, pcaJ, pcaF
Methylocapsa acidiphila B2 aroP, tnaA
Methylocapsa aurea KYG 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
Methylomonas methanica MC09 aroP, tnaA
Methylosarcina fibrata AML-C10 aroP, tnaA
Methylotuvimicrobium alcaliphilum 20Z tnaT, 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
Nocardioides dokdonensis FR1436 aroP, 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 atlantica CCGE1002 aroP, tnaA
Paraburkholderia bryophila 376MFSha3.1 aroP, kynA, kynB, kyn, antA, antB, antC, catA, catB, catC, pcaD, pcaI, pcaJ, pcaF
Paraburkholderia phymatum STM815 aroP, kynA, kynB, kyn, antA, antB, antC, catA, catB, catC, pcaD, pcaI, pcaJ, pcaF
Paucidesulfovibrio gracilis DSM 16080 tnaT, tnaA
Pedobacter sp. GW460-11-11-14-LB5 aroP, tnaA
Pelobacter propionicus DSM 2379 aroP, tnaA
Persephonella marina EX-H1 aroP, tnaA
Phaeacidiphilus oryzae TH49 aroP, kynA, kynB, kyn, andAa, andAb, andAc, andAd, xylE, praB, praC, praD, mhpD, mhpE, adh, acs
Phaeobacter inhibens BS107 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 fluorescens FW300-N1B4 aroP, kynA, kynB, kyn, antA, antB, antC, catA, catB, catC, pcaD, catI, catJ, pcaF
Pseudomonas fluorescens FW300-N2C3 aroP, tnaA
Pseudomonas fluorescens FW300-N2E2 aroP, tnaA
Pseudomonas fluorescens FW300-N2E3 aroP, kynA, kynB, kyn, antA, antB, antC, catA, catB, catC, pcaD, catI, catJ, pcaF
Pseudomonas fluorescens GW456-L13 aroP, kynA, kynB, kyn, antA, antB, antC, catA, catB, catC, pcaD, catI, catJ, pcaF
Pseudomonas putida KT2440 aroP, kynA, kynB, kyn, antA, antB, antC, catA, catB, catC, pcaD, pcaI, pcaJ, pcaF
Pseudomonas simiae WCS417 aroP, kynA, kynB, kyn, antA, antB, antC, catA, catB, catC, pcaD, catI, catJ, pcaF
Pseudomonas stutzeri RCH2 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 johnstonii 3841 aroP, tnaA
Rhizobium leguminosarum WSM1325 aroP, tnaA
Rhizorhabdus wittichii RW1 aroP, kynA, kynB, kyn, hpaH, nbaC, nbaD, nbaE, nbaF, nbaG, mhpD, mhpE, adh, acs
Rhodanobacter denitrificans FW104-10B01 aroP, kynA, kynB, sibC, kyn, nbaC, nbaD, nbaE, nbaF, nbaG, mhpD, mhpE, adh, acs
Rhodomicrobium vannielii ATCC 17100 aroP, tnaA
Rhodopseudomonas palustris CGA009 aroP, tnaA
Rhodospirillum centenum SW; ATCC 51521 aroP, tnaA
Rhodospirillum rubrum ATCC 11170 aroP, tnaA
Roseburia faecis M72 trpP, ecfA1, ecfA2, ecfT, tnaA
Saccharomonospora cyanea NA-134 aroP, tnaA
Sedimenticola selenatireducens DSM 17993 aroP, tnaA
Shewanella amazonensis SB2B tnaB, tnaA
Shewanella loihica PV-4 tnaB, tnaA
Shewanella oneidensis MR-1 tnaB, tnaA
Shewanella sp. ANA-3 tnaB, tnaA
Sinorhizobium fredii NGR234 aroP, tnaA
Sinorhizobium medicae WSM419 aroP, tnaA
Sinorhizobium meliloti 1021 aroP, tnaA
Sphingomonas koreensis DSMZ 15582 aroP, tnaA
Stenotrophomonas chelatiphaga DSM 21508 aroP, tnaA
Steroidobacter denitrificans DSM 18526 aroP, tnaA
Stutzerimonas stutzeri A1501 aroP, kynA, kynB, kyn, antA, antB, antC, catA, catB, catC, pcaD, catI, catJ, pcaF
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
Synechococcus elongatus PCC 7942 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
Thermus aquaticus YT-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
Thiohalospira halophila HL 3 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
Tistlia consotensis USBA 355 aroP, tnaA
Trichlorobacter lovleyi SZ aroP, tnaA
Trichodesmium erythraeum IMS101 Annotated Metagenome-Assembled Genome 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 Apr 09 2024. 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