Finding step gtsA for lactose catabolism in Snodgrassella alvi wkB2
No candidates for gtsA: glucose ABC transporter, substrate-binding component (GtsA)
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 gtsA
- Curated sequence Q88P38: GtsA (GLcE), component of Glucose porter, GtsABCD
- Curated sequence Q72KX2: Glucose-binding protein aka TT_C0328, component of The glucose/mannose porter TTC0326-8 plus MalK1 (ABC protein, shared with 3.A.1.1.25)
- Curated sequence PfGW456L13_1894: ABC transporter for D-Galactose and D-Glucose, periplasmic substrate-binding component
- Curated sequence GFF4324: ABC transporter for D-Glucose-6-Phosphate, periplasmic substrate-binding component
- UniProt sequence A0A165KPY4: SubName: Full=Sugar ABC transporter substrate-binding protein {ECO:0000313|EMBL:KZT15782.1};
- Comment: gtsABCD-like ABC transporters, from Thermus, Pseudomonas putida, and Pseudomonas fluorescens GW456-L13. (Some components cluster with glcSTUV from Saccharolobus, which is described separately; those are marked ignore here.) The system in P. fluorescens is very similar (~90% a.a. identity) to PS417_22145:PS417_22130 (GFF4324:GFF4321), which is involved in glucose-6-phosphate utilization, probably as a glucose transporter. Fitness data also identified a gtsABCD-like glucose transporter in Acidovorax sp. GW101-3H11 (Ac3H11_2062:Ac3H11_2064:Ac3H11_2065:Ac3H11_2066; A0A165KPY4, A0A165KPZ4, A0A165KQ00, A0A165KQ08).
Or cluster all characterized gtsA 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