GapMind for Amino acid biosynthesis

 

L-methionine biosynthesis in Desulfovibrio vulgaris Miyazaki F

Best path

asp-kinase, asd, asd-S-transferase, asd-S-ferredoxin, asd-S-perS, metH, ramA

Also see fitness data for the top candidates

Rules

Overview: Methionine biosynthesis in GapMind is based on MetaCyc pathways L-methionine biosynthesis I via O-succinylhomoserine and cystathionine (link), II via O-phosphohomoserine and cystathionine (link), III via O-acetylhomoserine (link), or IV with reductive sulfhydrylation of aspartate semialdehyde (link). These pathways vary in how aspartate semialdehyde is reduced and sulfhydrylated to homocysteine. GapMind does not represent the formation of the methyl donors for methionine synthase, such as 5-methyltetrahydrofolate or methyl corrinoid proteins.

24 steps (14 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
asp-kinase aspartate kinase DvMF_0276
asd aspartate semi-aldehyde dehydrogenase DvMF_2382
asd-S-transferase sulfuration of L-aspartate semialdehyde, persulfide component DvMF_1464
asd-S-ferredoxin reductive sulfuration of L-aspartate semialdehyde, ferredoxin component DvMF_0262
asd-S-perS putative persulfide forming protein DvMF_0044
metH vitamin B12-dependent methionine synthase DvMF_0476
ramA ATP-dependent reduction of co(II)balamin DvMF_1398
Alternative steps:
B12-reactivation-domain MetH reactivation domain
hom homoserine dehydrogenase DvMF_1412
hom_kinase homoserine kinase DvMF_0971 DvMF_1410
mesA Methylcobalamin:homocysteine methyltransferase MesA
mesB Methylcobalamin:homocysteine methyltransferase MesB
mesD oxygen-dependent methionine synthase, methyltransferase component MesD
mesX oxygen-dependent methionine synthase, putative oxygenase component MesX
metA homoserine O-succinyltransferase
metB cystathionine gamma-synthase
metC cystathionine beta-lyase DvMF_1822
metE vitamin B12-independent methionine synthase DvMF_2035
metX homoserine O-acetyltransferase
metY O-acetylhomoserine sulfhydrylase
metZ O-succinylhomoserine sulfhydrylase
split_metH_1 Methionine synthase component, B12 binding and B12-binding cap domains DvMF_0476
split_metH_2 Methionine synthase component, methyltransferase domain DvMF_0476
split_metH_3 Methionine synthase component, pterin-binding domain DvMF_0476

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