Finding step srlB for D-sorbitol (glucitol) catabolism in Methanobacterium veterum MK4
No candidates for srlB: PTS system for sorbitol SrlABE, EII-A component SrlB
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 srlB
- Curated sequence CH_090883: PTS system, glucitol/sorbitol-specific, IIA component. PTS system glucitol/sorbitol-specific EIIA component; EIIA-Gut; EIII-Gut; Glucitol/sorbitol-specific phosphotransferase enzyme IIA component. PTHA aka SRLB aka GUTB aka B2704, component of Glucitol porter. sorbitol-specific PTS enzyme IIA component (EC 2.7.1.198; EC 2.7.1.197). sorbitol-specific PTS enzyme IIA component (EC 2.7.1.198; EC 2.7.1.197)
- Curated sequence O32334: GutB, component of The Glucitol Enzyme II complex, IICBC (GutA1A2) IIA (GutB)
- UniProt sequence O32523: SubName: Full=Sorbitol phosphotransferase enzyme II {ECO:0000313|EMBL:CAA74943.1};
- Comment: A complication in Erwinia -- srlB is present in Erwinia amylovora (O32523_ERWAM, 50% identical) but is not curated, probably because PMID:9435786 do not report a mutant in it. Since it is in a characterized cluster, decided to include it. PMID:9435786 also suggests that EII-BC1 is split into srlA/srlE but I think this is not correct.
Or cluster all characterized srlB proteins
This GapMind analysis is from Sep 24 2021. The underlying query database was built on Sep 17 2021.
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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