asp-kinase, asd, hom, metX, metY, metH*, B12-reactivation-domain
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.
Or see definitions of steps
Step | Description | Best candidate | 2nd candidate |
---|---|---|---|
asp-kinase | aspartate kinase | SARO_RS16780 | |
asd | aspartate semi-aldehyde dehydrogenase | SARO_RS07070 | |
hom | homoserine dehydrogenase | SARO_RS00095 | SARO_RS16780 |
metX | homoserine O-acetyltransferase | SARO_RS03415 | |
metY | O-acetylhomoserine sulfhydrylase | SARO_RS13530 | SARO_RS04055 |
metH* | vitamin B12-dependent methionine synthase | SARO_RS16275 with SARO_RS16280 | |
B12-reactivation-domain | MetH reactivation domain | SARO_RS16275 | |
Alternative steps: | |||
asd-S-ferredoxin | L-aspartate semialdehyde sulfurtransferase, NIL/ferredoxin component | ||
asd-S-perS | L-aspartate semialdehyde sulfurtransferase, persulfide-forming component | ||
asd-S-transferase | L-aspartate semialdehyde sulfurtransferase, persulfide component | ||
hom_kinase | homoserine kinase | SARO_RS05420 | SARO_RS09515 |
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 | ||
metA | homoserine O-succinyltransferase | SARO_RS03415 | |
metB | cystathionine gamma-synthase | SARO_RS13530 | SARO_RS04055 |
metC | cystathionine beta-lyase | SARO_RS12875 | SARO_RS13530 |
metE | vitamin B12-independent methionine synthase | ||
metZ | O-succinylhomoserine sulfhydrylase | SARO_RS13530 | SARO_RS04055 |
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 | ||
split_metH_1 | Methionine synthase component, B12 binding and B12-binding cap domains | SARO_RS16275 | |
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 Jul 25 2024. The underlying query database was built on Jul 25 2024.
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:
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