Finding step metC for L-methionine biosynthesis in Methanococcus aeolicus Nankai-3
No candidates for metC: cystathionine beta-lyase
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 metC
- Curated proteins or TIGRFams with EC 4.4.1.13 (search)
- Ignore hits to Q84UD0 when looking for 'other' hits (cysteine-S-conjugate beta-lyase (EC 4.4.1.13); L-cystine beta-lyase (EC 4.4.1.35))
- Ignore hits to Q9EYM7 when looking for 'other' hits (cysteine-S-conjugate beta-lyase (EC 4.4.1.13))
- Ignore hits to Q9SIV0 when looking for 'other' hits (S-alkyl-thiohydroximate lyase SUR1; Protein ABERRANT LATERAL ROOT FORMATION 1; Protein HOOKLESS 3; Protein ROOTY; Protein ROOTY 1; Protein SUPERROOT 1; EC 4.4.1.-. alkyl-thiohydroximate C-S lyase (EC 4.4.1.13))
- Ignore hits to CH_088676 when looking for 'other' hits (cystathionine beta-lyase; EC 4.4.1.8)
- Ignore hits to Q46061 when looking for 'other' hits (L-cysteine desulfidase (EC 4.4.1.28))
- Curated sequence Q5H4T8: cystathionine gamma-lyase (EC 4.4.1.1)
- Comment: BRENDA annotates Q84UD0 with this EC number but it may be a cystine lyase only (PMID:12525491). BRENDA annotates Q9EYM7 with this EC but it appears to be a cystathionine beta synthase (PMID:12101301). Q9SIV0 appears to be specific to glucosinolate biosynthesis. CH_088676 is annotated as this but with a different EC number, so it is ignored. Q4606 is annotated as cysteine desulfidase but is nearly identical to Q93QC6, which is a cystathionine beta-lyase, so it is ignored. XoMetC (Q5H4T8) is annotated as a gamma-lyase by BRENDA, but it also has beta-lyase activity (PMID:24531493).
Or cluster all characterized metC 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