L-tryptophan biosynthesis

GapMind for Amino acid biosynthesis

L-tryptophan biosynthesis

Analysis of pathway trp in 35 genomes

Genome	Best path
Acidovorax sp. GW101-3H11	trpE, trpD_1, trpD_2, PRAI, IGPS, trpA, trpB
Azospirillum brasilense Sp245	trpE, trpD_1, trpD_2, PRAI, IGPS, trpA, trpB
Bacteroides thetaiotaomicron VPI-5482	trpE, trpD_1, trpD_2, PRAI, IGPS, trpA, trpB
Burkholderia phytofirmans PsJN	trpE, trpD_1, trpD_2, PRAI, IGPS, trpA, trpB
Caulobacter crescentus NA1000	trpE, trpD_1, trpD_2, PRAI, IGPS, trpA, trpB
Cupriavidus basilensis 4G11	trpE, trpD_1, trpD_2, PRAI, IGPS, trpA, trpB
Dechlorosoma suillum PS	trpE, trpD_1, trpD_2, PRAI, IGPS, trpA, trpB
Desulfovibrio vulgaris Hildenborough	trpE, trpD_1, trpD_2, PRAI, IGPS, trpA, trpB
Desulfovibrio vulgaris Miyazaki F	trpE, trpD_1, trpD_2, PRAI, IGPS, trpA, trpB
Dinoroseobacter shibae DFL-12	trpE, trpD_1, trpD_2, PRAI, IGPS, trpA, trpB
Dyella japonica UNC79MFTsu3.2	trpE, trpD_1, trpD_2, PRAI, IGPS, trpA, trpB
Echinicola vietnamensis KMM 6221, DSM 17526	trpE, trpD_1, trpD_2, PRAI, IGPS, trpA, trpB
Escherichia coli BW25113	trpE, trpD_1, trpD_2, PRAI, IGPS, trpA, trpB
Herbaspirillum seropedicae SmR1	trpE, trpD_1, trpD_2, PRAI, IGPS, trpA, trpB
Klebsiella michiganensis M5al	trpE, trpD_1, trpD_2, PRAI, IGPS, trpA, trpB
Magnetospirillum magneticum AMB-1	trpE, trpD_1, trpD_2, PRAI, IGPS, trpA, trpB
Marinobacter adhaerens HP15	trpE, trpD_1, trpD_2, PRAI, IGPS, trpA, trpB
Paraburkholderia bryophila 376MFSha3.1	trpE, trpD_1, trpD_2, PRAI, IGPS, trpA, trpB
Pedobacter sp. GW460-11-11-14-LB5	trpE, trpD_1, trpD_2, PRAI, IGPS, trpA, trpB
Phaeobacter inhibens BS107	trpE, trpD_1, trpD_2, PRAI, IGPS, trpA, trpB
Pseudomonas fluorescens FW300-N1B4	trpE, trpD_1, trpD_2, PRAI *, IGPS, trpA, trpB
Pseudomonas fluorescens FW300-N2C3	trpE, trpD_1, trpD_2, PRAI, IGPS, trpA, trpB
Pseudomonas fluorescens FW300-N2E2	trpE, trpD_1, trpD_2, PRAI, IGPS, trpA, trpB
Pseudomonas fluorescens FW300-N2E3	trpE, trpD_1, trpD_2, PRAI, IGPS, trpA, trpB
Pseudomonas fluorescens GW456-L13	trpE, trpD_1, trpD_2, PRAI, IGPS, trpA, trpB
Pseudomonas putida KT2440	trpE, trpD_1, trpD_2, PRAI, IGPS, trpA, trpB
Pseudomonas simiae WCS417	trpE, trpD_1, trpD_2, PRAI, IGPS, trpA, trpB
Pseudomonas stutzeri RCH2	trpE, trpD_1, trpD_2, PRAI, IGPS, trpA, trpB
Shewanella amazonensis SB2B	trpE, trpD_1, trpD_2, PRAI, IGPS, trpA, trpB
Shewanella loihica PV-4	trpE, trpD_1, trpD_2, PRAI, IGPS, trpA, trpB
Shewanella oneidensis MR-1	trpE, trpD_1, trpD_2, PRAI, IGPS, trpA, trpB
Shewanella sp. ANA-3	trpE, trpD_1, trpD_2, PRAI, IGPS, trpA, trpB
Sinorhizobium meliloti 1021	trpED, trpD_2, PRAI, IGPS, trpA, trpB
Sphingomonas koreensis DSMZ 15582	trpE, trpD_1, trpD_2, PRAI, IGPS, trpA, trpB
Synechococcus elongatus PCC 7942	trpE, trpD_1, trpD_2, PRAI, IGPS, trpA, trpB

Confidence: high confidence medium confidence low confidence
? – known gap: despite the lack of a good candidate for this step, this organism (or a related organism) performs the pathway

This GapMind analysis is from Apr 09 2024. The underlying query database was built on Apr 09 2024.

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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
changes to Amino acid biosynthesis since the publication.

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 Amino acid biosynthesis