GapMind for Amino acid biosynthesis

 

L-methionine biosynthesis in Rhodanobacter denitrificans FW104-10B01

Best path

asp-kinase, asd, hom, metA, metB, metC, metH*, B12-reactivation-domain

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.

27 steps (16 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
asp-kinase aspartate kinase LRK54_RS12625
asd aspartate semi-aldehyde dehydrogenase LRK54_RS01715
hom homoserine dehydrogenase LRK54_RS10365 LRK54_RS05300
metA homoserine O-succinyltransferase LRK54_RS16045 LRK54_RS05310
metB cystathionine gamma-synthase LRK54_RS05305 LRK54_RS05660
metC cystathionine beta-lyase LRK54_RS05660 LRK54_RS05305
metH* vitamin B12-dependent methionine synthase LRK54_RS02120 with LRK54_RS02115
B12-reactivation-domain MetH reactivation domain LRK54_RS02120
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 LRK54_RS10360
mesA Methylcobalamin:homocysteine methyltransferase MesA
mesB Methylcobalamin:homocysteine methyltransferase MesB
mesC Methylcobalamin:homocysteine methyltransferase MesC
mesD oxygen-dependent methionine synthase, methyltransferase component MesD
mesX oxygen-dependent methionine synthase, putative oxygenase component MesX
metE vitamin B12-independent methionine synthase LRK54_RS12135
metX homoserine O-acetyltransferase LRK54_RS16045 LRK54_RS05310
metY O-acetylhomoserine sulfhydrylase LRK54_RS05660 LRK54_RS05305
metZ O-succinylhomoserine sulfhydrylase LRK54_RS05660 LRK54_RS05305
ramA ATP-dependent reduction of co(II)balamin
split_metE_1 vitamin B12-independent methionine synthase, folate-binding component
split_metE_2 vitamin B12-independent methionine synthase, catalytic component LRK54_RS12135
split_metH_1 Methionine synthase component, B12 binding and B12-binding cap domains LRK54_RS02120
split_metH_2 Methionine synthase component, methyltransferase domain LRK54_RS02115
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 Apr 09 2024. The underlying query database was built on Apr 09 2024.

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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