GapMind for Amino acid biosynthesis

 

L-methionine biosynthesis in Ammonifex degensii KC4

Best path

asp-kinase, asd, asd-S-transferase, asd-S-ferredoxin, asd-S-perS, metE

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 (13 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
asp-kinase aspartate kinase ADEG_RS04495 ADEG_RS04485
asd aspartate semi-aldehyde dehydrogenase ADEG_RS01750
asd-S-transferase L-aspartate semialdehyde sulfurtransferase, persulfide component ADEG_RS07235
asd-S-ferredoxin L-aspartate semialdehyde sulfurtransferase, NIL/ferredoxin component ADEG_RS07230 ADEG_RS01660
asd-S-perS L-aspartate semialdehyde sulfurtransferase, persulfide-forming component ADEG_RS07225
metE vitamin B12-independent methionine synthase ADEG_RS05675
Alternative steps:
B12-reactivation-domain MetH reactivation domain
hom homoserine dehydrogenase ADEG_RS04485 ADEG_RS04495
hom_kinase homoserine kinase ADEG_RS04490 ADEG_RS03365
mesA Methylcobalamin:homocysteine methyltransferase MesA
mesB Methylcobalamin:homocysteine methyltransferase MesB ADEG_RS01025
mesC Methylcobalamin:homocysteine methyltransferase MesC
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 ADEG_RS06970 ADEG_RS00220
metH vitamin B12-dependent methionine synthase
metX homoserine O-acetyltransferase
metY O-acetylhomoserine sulfhydrylase
metZ O-succinylhomoserine sulfhydrylase
ramA ATP-dependent reduction of co(II)balamin ADEG_RS01690 ADEG_RS05765
split_metE_1 vitamin B12-independent methionine synthase, folate-binding component
split_metE_2 vitamin B12-independent methionine synthase, catalytic component ADEG_RS05675
split_metH_1 Methionine synthase component, B12 binding and B12-binding cap domains
split_metH_2 Methionine synthase component, methyltransferase domain
split_metH_3 Methionine synthase component, pterin-binding domain ADEG_RS01705

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 Jul 25 2024. The underlying query database was built on Jul 25 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