GapMind for Amino acid biosynthesis

 

L-phenylalanine biosynthesis

Analysis of pathway phe in 35 genomes

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

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