Finding step metY for L-methionine biosynthesis in Methanococcus aeolicus Nankai-3
No candidates for metY: O-acetylhomoserine sulfhydrylase
GapMind classifies a step as low confidence even if it does not find any candidates. You can still try to find candidates by using Curated BLAST (which searches the 6-frame translation) or by text search of the annotations (which may indicate weak homology, under 30% identity or 50% coverage, that GapMind does not consider). See the links below.
Definition of step metY
- Curated proteins or TIGRFams with EC 2.5.1.49 (search)
- Curated sequence O31631: Cystathionine gamma-synthase/O-acetylhomoserine (thiol)-lyase; CGS/OAH thiolyase; O-acetylhomoserine sulfhydrylase; OAH sulfhydrylase; EC 2.5.1.-
- Ignore hits to items matching O-succinylhomoserine sulfhydrylase when looking for 'other' hits
- Curated sequence CH_123612: O-acetylhomoserine O-acetylserine sulphydrylase
- Curated sequence Q9WZY4: O-acetyl-L-homoserine sulfhydrylase; OAH sulfhydrylase; O-acetylhomoserine thiolase; EC 2.5.1.-
- Curated sequence Q5SK88: O-acetyl-L-homoserine sulfhydrylase 1; OAH-sulfhydrylase 1; EC 2.5.1.-
- UniProt sequence A0A2T5J8K7: SubName: Full=O-acetylhomoserine (Thiol)-lyase {ECO:0000313|EMBL:PTQ95791.1};
- Comment: METI_BACSU (O31631) has activity as OAS but is given a more vague EC number. CH_123612, Q9WZY4, and Q5SK88 are annotated as this but without the EC number. In Mucilaginibacter yixingensis YX-36, C8P68_RS15690 is important for fitness in minimal media; it is usually annotated as O-succinylhomoserine sulfhydrylase, but the acylating enzmye (C8P68_RS13005) is similar to O-acetyltransferases and has the correct functional residues (i.e., similar to H1YC36 in supplementary data set 3 of PMID:28581482); so it must be an o-acetylhomoserine sulfhydrylase.
Or cluster all characterized metY proteins
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:
- ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
- HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.
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:
- ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
- ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
- HMMer finds a hit (regardless of coverage or other bits).
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:
- our ignorance of proteins' functions,
- omissions in the gene models,
- frame-shift errors in the genome sequence, or
- the organism lacks the pathway.
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