GapMind for catabolism of small carbon sources

 

L-tryptophan catabolism

Analysis of pathway tryptophan in 35 genomes

Genome Best path
Acidovorax sp. GW101-3H11 aroP, kynA, kynB, kyn, andAa, andAb, andAc, andAd, xylE, praB, praC, praD, mhpD, mhpE, adh, acs
Azospirillum brasilense Sp245 aroP, tnaA
Bacteroides thetaiotaomicron VPI-5482 aroP, tnaA
Burkholderia phytofirmans PsJN aroP, kynA, kynB, kyn, hpaH, nbaC, nbaD, nbaE, nbaF, nbaG, mhpD, mhpE, adh, ackA, pta
Caulobacter crescentus NA1000 aroP, tnaA
Cupriavidus basilensis 4G11 aroP, kynA, kynB, kyn, antA, antB, antC, xylE, praB, praC, praD, mhpD, mhpE, adh, ackA, pta
Dechlorosoma suillum PS aroP, tnaA
Desulfovibrio vulgaris Hildenborough tnaB, tnaA
Desulfovibrio vulgaris Miyazaki F aroP, tnaA
Dinoroseobacter shibae DFL-12 aroP, tnaA
Dyella japonica UNC79MFTsu3.2 aroP, kynA, kynB, sibC, kyn, nbaC, nbaD, nbaE, nbaF, nbaG, mhpD, mhpE, adh, acs
Echinicola vietnamensis KMM 6221, DSM 17526 aroP, tnaA
Escherichia coli BW25113 aroP, tnaA
Herbaspirillum seropedicae SmR1 aroP, kynA, kynB, kyn, antA, antB, antC, catA, catB, catC, pcaD, pcaI, pcaJ, pcaF
Klebsiella michiganensis M5al aroP, tnaA
Magnetospirillum magneticum AMB-1 aroP, tnaA
Marinobacter adhaerens HP15 aroP, kynA, kynB, kyn, antA, antB, antC, xylE, praB, praC, praD, mhpD, mhpE, adh, ackA, pta
Paraburkholderia bryophila 376MFSha3.1 aroP, kynA, kynB, kyn, antA, antB, antC, catA, catB, catC, pcaD, pcaI, pcaJ, pcaF
Pedobacter sp. GW460-11-11-14-LB5 aroP, tnaA
Phaeobacter inhibens BS107 aroP, tnaA
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
Shewanella amazonensis SB2B tnaB, tnaA
Shewanella loihica PV-4 tnaB, tnaA
Shewanella oneidensis MR-1 tnaB, tnaA
Shewanella sp. ANA-3 tnaB, tnaA
Sinorhizobium meliloti 1021 aroP, tnaA
Sphingomonas koreensis DSMZ 15582 aroP, tnaA
Synechococcus elongatus PCC 7942 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 17 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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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 the paper from 2019 on GapMind for amino acid biosynthesis, or view the source code.

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