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 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