Finding step metC for L-methionine biosynthesis in Novosphingobium aromaticivorans DSM 12444
4 candidates for metC: cystathionine beta-lyase
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
GapMind searches the predicted proteins for candidates by using ublast (a fast alternative to protein BLAST) to find similarities to characterized proteins or by using HMMer to find similarities to enzyme models (usually from TIGRFams). For alignments to characterized proteins (from ublast), scores of 44 bits correspond to an expectation value (E) of about 0.001.
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