Finding step metH for L-methionine biosynthesis in Halococcus hamelinensis 100A6
No candidates for metH: vitamin B12-dependent methionine synthase
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 metH
- Curated proteins or TIGRFams with EC 2.1.1.13 (search)
- Ignore hits to GFF1501 when looking for 'other' hits (ATP-dependent reduction of co(II)balamin (RamA-like) (EC:2.1.1.13))
- Ignore hits to GFF1318 when looking for 'other' hits (Accessory protein for co(II)balamin reduction (DUF1638) (EC:2.1.1.13))
- Ignore hits to GFF1321 when looking for 'other' hits (Methionine synthase component, methyltransferase domain (EC:2.1.1.13))
- Ignore hits to GFF1319 when looking for 'other' hits (Methionine synthase component, B12 binding and B12-binding cap domains (EC:2.1.1.13))
- Ignore hits to GFF1582 when looking for 'other' hits (Methionine synthase component, pterin-binding domain (EC:2.1.1.13))
- UniProt sequence Q72BP9_DESVH: RecName: Full=Methionine synthase {ECO:0000256|ARBA:ARBA00013998}; EC=2.1.1.13 {ECO:0000256|ARBA:ARBA00012032}; AltName: Full=5-methyltetrahydrofolate--homocysteine methyltransferase {ECO:0000256|ARBA:ARBA00031040};
- UniProt sequence B8DKK4_DESVM: RecName: Full=Methionine synthase {ECO:0000256|ARBA:ARBA00013998}; EC=2.1.1.13 {ECO:0000256|ARBA:ARBA00012032}; AltName: Full=5-methyltetrahydrofolate--homocysteine methyltransferase {ECO:0000256|ARBA:ARBA00031040};
- Comment: Desulfovibrio have a somewhat diverged MetH, without the activation domain, but confirmed by cofitness (DVU1585 = Q72BP9_DESVH is cofit with MetF; DvMF_0476 = B8DKK4_DESVM is cofit with a RamA- like activation protein). 3-part split MetH proteins from Phaeobacter are ignored.
Or cluster all characterized metH 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