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 Aug 03 2021. The underlying query database was built on Aug 03 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, or see 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