chorismate biosynthesis

GapMind for Amino acid biosynthesis

chorismate biosynthesis

Analysis of pathway chorismate in 35 genomes

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

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