Protein WP_054254652.1 in Acidovorax caeni R-24608
Annotation: NCBI__GCF_001298675.1:WP_054254652.1
Length: 293 amino acids
Source: GCF_001298675.1 in NCBI
Candidate for 15 steps in catabolism of small carbon sources
| Pathway | Step | Score | Similar to | Id. | Cov. | Bits | Other hit | Other id. | Other bits |
|---|
| D-maltose catabolism | thuF | lo | Trehalose/maltose transport system permease protein MalF (characterized) | 33% | 96% | 144.1 | ABC-type glycerol 3-phosphate transporter (EC 7.6.2.10) | 60% | 361.3 |
| trehalose catabolism | thuF | lo | Trehalose/maltose transport system permease protein MalF (characterized) | 33% | 96% | 144.1 | ABC-type glycerol 3-phosphate transporter (EC 7.6.2.10) | 60% | 361.3 |
| sucrose catabolism | thuF | lo | Maltose transport system permease protein malF aka TT_C1628, component of The trehalose/maltose/sucrose/palatinose porter (TTC1627-9) plus MalK1 (ABC protein, shared with 3.A.1.1.24) (Silva et al. 2005; Chevance et al., 2006). The receptor (TTC1627) binds disaccharide alpha-glycosides, namely trehalose (alpha-1,1), sucrose (alpha-1,2), maltose (alpha-1,4), palatinose (alpha-1,6) and glucose (characterized) | 32% | 97% | 141.7 | ABC-type glycerol 3-phosphate transporter (EC 7.6.2.10) | 60% | 361.3 |
| lactose catabolism | lacF | lo | ABC transporter for Lactose, permease component 1 (characterized) | 32% | 92% | 136 | ABC-type glycerol 3-phosphate transporter (EC 7.6.2.10) | 60% | 361.3 |
| D-cellobiose catabolism | gtsB | lo | ABC transporter for D-Galactose and D-Glucose, permease component 1 (characterized) | 30% | 93% | 128.6 | ABC-type glycerol 3-phosphate transporter (EC 7.6.2.10) | 60% | 361.3 |
| D-galactose catabolism | PfGW456L13_1895 | lo | ABC transporter for D-Galactose and D-Glucose, permease component 1 (characterized) | 30% | 93% | 128.6 | ABC-type glycerol 3-phosphate transporter (EC 7.6.2.10) | 60% | 361.3 |
| D-glucose catabolism | gtsB | lo | ABC transporter for D-Galactose and D-Glucose, permease component 1 (characterized) | 30% | 93% | 128.6 | ABC-type glycerol 3-phosphate transporter (EC 7.6.2.10) | 60% | 361.3 |
| lactose catabolism | gtsB | lo | ABC transporter for D-Galactose and D-Glucose, permease component 1 (characterized) | 30% | 93% | 128.6 | ABC-type glycerol 3-phosphate transporter (EC 7.6.2.10) | 60% | 361.3 |
| D-maltose catabolism | gtsB | lo | ABC transporter for D-Galactose and D-Glucose, permease component 1 (characterized) | 30% | 93% | 128.6 | ABC-type glycerol 3-phosphate transporter (EC 7.6.2.10) | 60% | 361.3 |
| sucrose catabolism | gtsB | lo | ABC transporter for D-Galactose and D-Glucose, permease component 1 (characterized) | 30% | 93% | 128.6 | ABC-type glycerol 3-phosphate transporter (EC 7.6.2.10) | 60% | 361.3 |
| trehalose catabolism | gtsB | lo | ABC transporter for D-Galactose and D-Glucose, permease component 1 (characterized) | 30% | 93% | 128.6 | ABC-type glycerol 3-phosphate transporter (EC 7.6.2.10) | 60% | 361.3 |
| D-cellobiose catabolism | msdC1 | lo | Binding-protein-dependent transport systems inner membrane component (characterized, see rationale) | 35% | 72% | 123.2 | ABC-type glycerol 3-phosphate transporter (EC 7.6.2.10) | 60% | 361.3 |
| N-acetyl-D-glucosamine catabolism | SMc02872 | lo | ABC transporter for N-Acetyl-D-glucosamine, permease protein 1 (characterized) | 31% | 94% | 118.6 | ABC-type glycerol 3-phosphate transporter (EC 7.6.2.10) | 60% | 361.3 |
| D-glucosamine (chitosamine) catabolism | SMc02872 | lo | ABC transporter for N-Acetyl-D-glucosamine, permease protein 1 (characterized) | 31% | 94% | 118.6 | ABC-type glycerol 3-phosphate transporter (EC 7.6.2.10) | 60% | 361.3 |
| trehalose catabolism | treT | lo | TreT, component of Trehalose porter (characterized) | 30% | 96% | 98.6 | ABC-type glycerol 3-phosphate transporter (EC 7.6.2.10) | 60% | 361.3 |
Sequence Analysis Tools
View WP_054254652.1 at NCBI
Find papers: PaperBLAST
Find functional residues: SitesBLAST
Search for conserved domains
Find the best match in UniProt
Compare to protein structures
Predict transmenbrane helices: Phobius
Predict protein localization: PSORTb
Find homologs in fast.genomics
Fitness BLAST: loading...
Sequence
MEKRVLFRSRWLPWVLLLPQLAIVGVFFFWPASQAILQSVQMEDAFGMSREFVGLENFER
LWNDSSYLASFQVTALFSVLVAGIGIVLALVLAVFADRITRGALVYRTLLIMPYAVAPVI
AGVLWMFIFSPSIGVLAYGLEKMGYTWNHLMNDNQAMALVVIASVWKQISYNFLFFLAGL
QSIPKSLIEAAAIDGAGPWRRFWSIQLPLLSPTTFFLLVINIVYAFFDTFGIIDATTHGG
PGQSTSILVYKVYLDGFKALDLGGSAAQSVVLMVMVIALTVVQFRYVEKKVQY
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