Finding step gtsB for sucrose catabolism in Phaeobacter inhibens BS107
4 candidates for gtsB: glucose ABC transporter, permease component 1 (GtsB)
| Score | Gene | Description | Similar to | Id. | Cov. | Bits | Other hit | Other id. | Other bits |
|---|
| med | PGA1_c19490 | ABC transporter, inner-membrane protein | ABC transporter for D-Galactose and D-Glucose, permease component 1 (characterized) | 47% | 95% | 279.6 | ABC transporter for D-Cellobiose and D-Salicin, permease component 2 | 52% | 316.6 |
| med | PGA1_78p00170 | putative sn-glycerol-3-phosphate transport system permease protein UgpA | GtsB (GLcF), component of Glucose porter, GtsABCD (characterized) | 44% | 97% | 270.4 | ABC transporter for D-Cellobiose and D-Salicin, permease component 2 | 74% | 454.9 |
| lo | PGA1_c07410 | binding protein dependent transport system permease | ABC transporter for D-Glucose-6-Phosphate, permease component 2 (characterized) | 30% | 95% | 144.1 | TogM, component of Saturated and unsaturated oligogalacturonide transporter, TogMNAB (transports di- to tetrasaccharide pectin degradation products which consist of D-galacuronate, sometimes with 4-deoxy-L-threo-5-hexosulose uronate at the reducing end of the oligosaccharide) (Hugouvieux-Cotte-Pattat et al. 2001). Regulated by pectin utilization regulator KdgR | 33% | 157.9 |
| lo | PGA1_c27940 | ABC transporter permease protein | ABC transporter permease (characterized, see rationale) | 31% | 96% | 117.5 | N-Acetyl-D-glucosamine ABC transport system, permease component 1 | 100% | 625.2 |
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.
Also see fitness data for the candidates
Definition of step gtsB
- Curated sequence Q88P37: GtsB (GLcF), component of Glucose porter, GtsABCD
- Curated sequence PfGW456L13_1895: ABC transporter for D-Galactose and D-Glucose, permease component 1
- Curated sequence Q72KX3: Glucose transport system permease protein aka TT_C0327, component of The glucose/mannose porter TTC0326-8 plus MalK1 (ABC protein, shared with 3.A.1.1.25)
- Curated sequence GFF4323: ABC transporter for D-Glucose-6-Phosphate, permease component 2
- UniProt sequence A0A165KPZ4: SubName: Full=ABC transporter permease {ECO:0000313|EMBL:KZT15783.1};
Or cluster all characterized gtsB proteins
This GapMind analysis is from Apr 09 2024. 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