Finding step gtsC for trehalose catabolism in Lactobacillus shenzhenensis LY-73
4 candidates for gtsC: glucose ABC transporter, permease component 2 (GtsC)
| Score | Gene | Description | Similar to | Id. | Cov. | Bits | Other hit | Other id. | Other bits |
|---|
| lo | L248_RS12535 | carbohydrate ABC transporter permease | ABC transporter for D-Glucose-6-Phosphate, permease component 1 (characterized) | 32% | 99% | 144.8 | L-arabinose transport system permease protein AraQ | 35% | 176.0 |
| lo | L248_RS14290 | carbohydrate ABC transporter permease | Sugar ABC transporter permease (characterized, see rationale) | 31% | 94% | 136.7 | L-arabinose transport system permease protein AraQ | 35% | 179.1 |
| lo | L248_RS09265 | carbohydrate ABC transporter permease | GtsC (GLcG), component of Glucose porter, GtsABCD (characterized) | 32% | 94% | 134.4 | MsmG aka SMU.880, component of The raffinose/stachyose transporter, MsmEFGK (MalK (3.A.1.1.27) can probably substitute for MsmK; Webb et al., 2008). This system may also transport melibiose, isomaltotriose and sucrose as well as isomaltosaccharides | 80% | 452.2 |
| lo | L248_RS05350 | carbohydrate ABC transporter permease | Sugar transport system permease protein aka TT_C0326, component of The glucose/mannose porter TTC0326-8 plus MalK1 (ABC protein, shared with 3.A.1.1.25) (characterized) | 30% | 76% | 98.6 | Sugar ABC transporter, permease protein, component of Probable glycerophosphocholine (GPC) uptake porter (Chandravanshi et al. 2016). The system may include a receptor and three membrane proteins (of 378 aas and 6 TMSs, 299 aas and 7 TMSs, and 113 aas and 3 TMSs (?). The ATPase has not been identified | 37% | 161.0 |
Confidence: high confidence medium confidence low confidence
transporter – transporters and PTS systems are shaded because predicting their specificity is particularly challenging.
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 gtsC
- Curated sequence Q72KX4: Sugar transport system permease protein aka TT_C0326, component of The glucose/mannose porter TTC0326-8 plus MalK1 (ABC protein, shared with 3.A.1.1.25)
- Curated sequence Q88P36: GtsC (GLcG), component of Glucose porter, GtsABCD
- Curated sequence PfGW456L13_1896: ABC transporter for D-Galactose and D-Glucose, permease component 2
- Curated sequence GFF4322: ABC transporter for D-Glucose-6-Phosphate, permease component 1
- UniProt sequence A0A165KQ00: SubName: Full=Sugar ABC transporter permease {ECO:0000313|EMBL:KZT15784.1};
Or cluster all characterized gtsC proteins
This GapMind analysis is from Sep 24 2021. The underlying query database was built on Sep 17 2021.
Links
Downloads
Related tools
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