GapMind for Amino acid biosynthesis

 

L-methionine biosynthesis in Phaeobacter inhibens BS107

Best path

asp-kinase, asd, hom, metX, metY, split_metH_1, split_metH_2, split_metH_3, 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 (15 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
asp-kinase aspartate kinase PGA1_c23510
asd aspartate semi-aldehyde dehydrogenase PGA1_c31480
hom homoserine dehydrogenase PGA1_c08650
metX homoserine O-acetyltransferase PGA1_c14560
metY O-acetylhomoserine sulfhydrylase PGA1_c07640 PGA1_c23540
split_metH_1 Methionine synthase component, B12 binding and B12-binding cap domains PGA1_c13350
split_metH_2 Methionine synthase component, methyltransferase domain PGA1_c13370
split_metH_3 Methionine synthase component, pterin-binding domain PGA1_c16040
ramA ATP-dependent reduction of co(II)balamin PGA1_c15200
Alternative steps:
asd-S-ferredoxin reductive sulfuration of L-aspartate semialdehyde, ferredoxin component
asd-S-perS putative persulfide forming protein
asd-S-transferase sulfuration of L-aspartate semialdehyde, persulfide component
B12-reactivation-domain MetH reactivation domain
hom_kinase homoserine kinase PGA1_c14090
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 PGA1_c14560
metB cystathionine gamma-synthase PGA1_c16600 PGA1_c23540
metC cystathionine beta-lyase PGA1_c00860 PGA1_c15810
metE vitamin B12-independent methionine synthase
metH* vitamin B12-dependent methionine synthase PGA1_c13370 with PGA1_c16040
metZ O-succinylhomoserine sulfhydrylase PGA1_c23540 PGA1_c16600

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.

Links

Downloads

Related tools

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 (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). 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. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. 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, the paper from 2022 on GapMind for carbon sources, 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