GapMind for Amino acid biosynthesis

 

L-methionine biosynthesis in Pseudomonas fluorescens GW456-L13

Best path

asp-kinase, asd, hom, metA, metZ, metH, B12-reactivation-domain

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 PfGW456L13_1981
asd aspartate semi-aldehyde dehydrogenase PfGW456L13_3944 PfGW456L13_3943
hom homoserine dehydrogenase PfGW456L13_1723
metA homoserine O-succinyltransferase PfGW456L13_1007
metZ O-succinylhomoserine sulfhydrylase PfGW456L13_3934
metH vitamin B12-dependent methionine synthase PfGW456L13_2847
B12-reactivation-domain MetH reactivation domain PfGW456L13_2847
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
hom_kinase homoserine kinase PfGW456L13_596
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
metB cystathionine gamma-synthase PfGW456L13_3934
metC cystathionine beta-lyase PfGW456L13_3090 PfGW456L13_3934
metE vitamin B12-independent methionine synthase PfGW456L13_3767
metX homoserine O-acetyltransferase PfGW456L13_1007
metY O-acetylhomoserine sulfhydrylase PfGW456L13_3934
ramA ATP-dependent reduction of co(II)balamin
split_metH_1 Methionine synthase component, B12 binding and B12-binding cap domains PfGW456L13_2847
split_metH_2 Methionine synthase component, methyltransferase domain
split_metH_3 Methionine synthase component, pterin-binding 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 (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:

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