GapMind for Amino acid biosynthesis

 

L-tyrosine biosynthesis

Analysis of pathway tyr in 35 genomes

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

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