Protein WP_011882562.1 in Burkholderia vietnamiensis G4
Annotation: NCBI__GCF_000016205.1:WP_011882562.1
Length: 286 amino acids
Source: GCF_000016205.1 in NCBI
Candidate for 11 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 | 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) | 40% | 96% | 178.3 | Predicted arabinoside porter. Regulated by arabinose-responsive regulator AraR | 39% | 185.3 |
| 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) | 40% | 96% | 178.3 | Predicted arabinoside porter. Regulated by arabinose-responsive regulator AraR | 39% | 185.3 |
| trehalose 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) | 40% | 96% | 178.3 | Predicted arabinoside porter. Regulated by arabinose-responsive regulator AraR | 39% | 185.3 |
| xylitol catabolism | Dshi_0548 | lo | ABC transporter for Xylitol, permease component 1 (characterized) | 38% | 94% | 168.3 | Predicted arabinoside porter. Regulated by arabinose-responsive regulator AraR | 39% | 185.3 |
| D-glucosamine (chitosamine) catabolism | SM_b21220 | lo | ABC transporter for D-Glucosamine, permease component 2 (characterized) | 34% | 92% | 156.8 | Predicted arabinoside porter. Regulated by arabinose-responsive regulator AraR | 39% | 185.3 |
| D-sorbitol (glucitol) catabolism | mtlF | lo | ABC transporter for D-Sorbitol, permease component 2 (characterized) | 34% | 88% | 151.4 | Predicted arabinoside porter. Regulated by arabinose-responsive regulator AraR | 39% | 185.3 |
| xylitol catabolism | HSERO_RS17005 | lo | ABC-type sugar transport system, permease component protein (characterized, see rationale) | 34% | 97% | 142.1 | Predicted arabinoside porter. Regulated by arabinose-responsive regulator AraR | 39% | 185.3 |
| glycerol catabolism | glpP | lo | GlpP, component of Glycerol uptake porter, GlpSTPQV (characterized) | 33% | 93% | 137.9 | Predicted arabinoside porter. Regulated by arabinose-responsive regulator AraR | 39% | 185.3 |
| lactose catabolism | lacF | lo | LacF, component of Lactose porter (characterized) | 32% | 91% | 129 | Predicted arabinoside porter. Regulated by arabinose-responsive regulator AraR | 39% | 185.3 |
| trehalose catabolism | treT | lo | TreT, component of Trehalose porter (characterized) | 34% | 96% | 114.8 | Predicted arabinoside porter. Regulated by arabinose-responsive regulator AraR | 39% | 185.3 |
| L-arabinose catabolism | xacH | lo | Xylose/arabinose import permease protein XacH (characterized, see rationale) | 30% | 89% | 108.2 | Predicted arabinoside porter. Regulated by arabinose-responsive regulator AraR | 39% | 185.3 |
Sequence Analysis Tools
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
MVRSLPFVALLGPALLVLAALALYPVAQVLVDSFCRVDYAAGRRAFAGLANYRAVLGDDA
FSAGFGNTLRFTIVASLAEVALGFGLALLFVRAFPGRRIALPLAILPMMLSTLVCSAIWR
NWLNFDGFLNALLAVFGIEGVRWLSDPHLALWSLALVDVWQWTPMAFLIVLAGLQSIPHE
LYEAARTDGASEWQCLRDITLPLAAPQIGLALLLRSIDTFKLFDKVYALTGGGPGNATQT
LSTYIYDTGFRFFDVGTASAASVLMLAASALLVSGYVWQTVRKRRA
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