GapMind for Amino acid biosynthesis

 

L-methionine biosynthesis

Analysis of pathway met in 35 genomes

Genome Best path
Acidovorax sp. GW101-3H11 asp-kinase, asd, hom, metA, metZ, metH*, B12-reactivation-domain
Azospirillum brasilense Sp245 asp-kinase, asd, hom, metX, metY, metE
Bacteroides thetaiotaomicron VPI-5482 asp-kinase, asd, hom, metX, metY, metH*, B12-reactivation-domain
Burkholderia phytofirmans PsJN asp-kinase, asd, hom, metA, metZ, metH*, B12-reactivation-domain
Caulobacter crescentus NA1000 asp-kinase, asd, hom, metX, metY, metH*, B12-reactivation-domain
Cupriavidus basilensis 4G11 asp-kinase, asd, hom, metA, metZ, metH*, B12-reactivation-domain
Dechlorosoma suillum PS asp-kinase, asd, hom, metA, metZ, metH, B12-reactivation-domain
Desulfovibrio vulgaris Hildenborough asp-kinase, asd, asd-S-transferase, asd-S-ferredoxin, asd-S-perS, metH, ramA
Desulfovibrio vulgaris Miyazaki F asp-kinase, asd, asd-S-transferase, asd-S-ferredoxin, asd-S-perS, metH, ramA
Dinoroseobacter shibae DFL-12 asp-kinase, asd, hom, metX, metY, split_metH_1, split_metH_2, split_metH_3, ramA
Dyella japonica UNC79MFTsu3.2 asp-kinase, asd, hom, metA, metB, metC?, metH*, B12-reactivation-domain
Echinicola vietnamensis KMM 6221, DSM 17526 asp-kinase, asd, hom, metX, metY, metH*, B12-reactivation-domain
Escherichia coli BW25113 asp-kinase, asd, hom, metA, metB, metC, metH, B12-reactivation-domain
Herbaspirillum seropedicae SmR1 asp-kinase, asd, hom, metA, metZ, metH, B12-reactivation-domain
Klebsiella michiganensis M5al asp-kinase, asd, hom, metA, metB, metC, metH, B12-reactivation-domain
Magnetospirillum magneticum AMB-1 asp-kinase, asd, hom, metX, metY, metH, B12-reactivation-domain
Marinobacter adhaerens HP15 asp-kinase, asd, hom, metA, metZ, metH, B12-reactivation-domain
Paraburkholderia bryophila 376MFSha3.1 asp-kinase, asd, hom, metA, metZ, metH*, B12-reactivation-domain
Pedobacter sp. GW460-11-11-14-LB5 asp-kinase, asd, hom, metX, metY, metH, B12-reactivation-domain
Phaeobacter inhibens BS107 asp-kinase, asd, hom, metX, metY, split_metH_1, split_metH_2, split_metH_3, ramA
Pseudomonas fluorescens FW300-N1B4 asp-kinase, asd, hom, metA, metB?, metC, metH, B12-reactivation-domain
Pseudomonas fluorescens FW300-N2C3 asp-kinase, asd, hom, metA, metZ, metH, B12-reactivation-domain
Pseudomonas fluorescens FW300-N2E2 asp-kinase, asd, hom, metA, metZ, metH, B12-reactivation-domain
Pseudomonas fluorescens FW300-N2E3 asp-kinase, asd, hom, metA, metZ, metH, B12-reactivation-domain
Pseudomonas fluorescens GW456-L13 asp-kinase, asd, hom, metA, metZ, metH, B12-reactivation-domain
Pseudomonas putida KT2440 asp-kinase, asd, hom, metA, metZ, metH, B12-reactivation-domain
Pseudomonas simiae WCS417 asp-kinase, asd, hom, metA, metZ, metH, B12-reactivation-domain
Pseudomonas stutzeri RCH2 asp-kinase, asd, hom, metA, metZ, metH, B12-reactivation-domain
Shewanella amazonensis SB2B asp-kinase, asd, hom, metA, metB, metC, metH, B12-reactivation-domain
Shewanella loihica PV-4 asp-kinase, asd, hom, metA, metB, metC, metH, B12-reactivation-domain
Shewanella oneidensis MR-1 asp-kinase, asd, hom, metA, metB, metC, metH, B12-reactivation-domain
Shewanella sp. ANA-3 asp-kinase, asd, hom, metA, metB, metC, metH, B12-reactivation-domain
Sinorhizobium meliloti 1021 asp-kinase, asd, hom, metX, metB, metC, split_metH_1, split_metH_2, split_metH_3, B12-reactivation-domain
Sphingomonas koreensis DSMZ 15582 asp-kinase, asd, hom, metX, metY, metH*, B12-reactivation-domain
Synechococcus elongatus PCC 7942 asp-kinase, asd, hom, metX, metY, metH, B12-reactivation-domain

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