Annotation: NCBI__GCF_000359745.1:WP_004112707.1
Length: 309 amino acids
Source: GCF_000359745.1 in NCBI
| Pathway | Step | Score | Similar to | Id. | Cov. | Bits | Other hit | Other id. | Other bits |
|---|---|---|---|---|---|---|---|---|---|
| xylitol catabolism | Dshi_0548 | med | ABC transporter for Xylitol, permease component 1 (characterized) | 38% | 97% | 174.1 | Predicted arabinoside porter. Regulated by arabinose-responsive regulator AraR | 33% | 169.9 |
| trehalose catabolism | thuF | lo | Trehalose transport system permease protein SugA (characterized) | 34% | 93% | 157.1 | ABC transporter for Xylitol, permease component 1 | 38% | 174.1 |
| D-mannitol catabolism | mtlF | lo | SmoF, component of Hexitol (glucitol; mannitol) porter (characterized) | 34% | 93% | 153.7 | ABC transporter for Xylitol, permease component 1 | 38% | 174.1 |
| D-sorbitol (glucitol) catabolism | mtlF | lo | SmoF, component of Hexitol (glucitol; mannitol) porter (characterized) | 34% | 93% | 153.7 | ABC transporter for Xylitol, permease component 1 | 38% | 174.1 |
| glycerol catabolism | glpP | lo | GlpP, component of Glycerol uptake porter, GlpSTPQV (characterized) | 31% | 92% | 140.2 | ABC transporter for Xylitol, permease component 1 | 38% | 174.1 |
View WP_004112707.1 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...
MHTTAIRSLPTLTPVRRGFVRRNLPYLLIAPSVIMLLALIAYPLLFALKSSFYFWNLQVG PQPLAFVGIDNYVQALDAFDFRAALTNTLILSVLGTAIEFSLGLAIALVLLKALPGMNVV RALLILPTTIAPIVVGFLFRYLYDPGGGLVTWVLQSLWLPVPAEGILGSPTTALAAILFV DIWQWTPFFAIVLYASLLSVPDEIIEAARLDRASAWTILMRIKLPLIRRTATIIVMLRFM QIFNTFDTVLVLTRGGPGTSTRTLGYSLYEQGLVNFNVGLVSAQTWITVLIVNVIIALYV FFAFRNEEW
This GapMind analysis is from Sep 24 2021. The underlying query database was built on Sep 17 2021.
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:
Otherwise, a candidate is "medium confidence" if either:
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:
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