Protein WP_004127647.1 in Rhizobium freirei PRF 81
Annotation: NCBI__GCF_000359745.1:WP_004127647.1
Length: 294 amino acids
Source: GCF_000359745.1 in NCBI
Candidate for 7 steps in catabolism of small carbon sources
| Pathway | Step | Score | Similar to | Id. | Cov. | Bits | Other hit | Other id. | Other bits |
|---|
| D-glucosamine (chitosamine) catabolism | SM_b21220 | hi | ABC transporter for D-Glucosamine, permease component 2 (characterized) | 88% | 100% | 505.4 | PalF, component of Platinose (isomaltulose) (6-O-α-D-glucopyranosyl-D-fructofuranose) porter | 38% | 221.1 |
| D-maltose catabolism | thuF | med | MalF, component of Maltose/trehalose porter (characterized) | 41% | 92% | 217.2 | ABC transporter for D-Glucosamine, permease component 2 | 88% | 505.4 |
| trehalose catabolism | thuF | med | MalF, component of Maltose/trehalose porter (characterized) | 41% | 92% | 217.2 | ABC transporter for D-Glucosamine, permease component 2 | 88% | 505.4 |
| sucrose catabolism | thuF | lo | ABC transporter permease (characterized, see rationale) | 40% | 90% | 219.5 | ABC transporter for D-Glucosamine, permease component 2 | 88% | 505.4 |
| L-fucose catabolism | SM_b21104 | lo | ABC transporter for L-Fucose, permease component 1 (characterized) | 33% | 94% | 153.7 | ABC transporter for D-Glucosamine, permease component 2 | 88% | 505.4 |
| D-sorbitol (glucitol) catabolism | mtlF | lo | ABC transporter for D-Sorbitol, permease component 2 (characterized) | 30% | 91% | 139 | ABC transporter for D-Glucosamine, permease component 2 | 88% | 505.4 |
| trehalose catabolism | treT | lo | TreT, component of Trehalose porter (characterized) | 30% | 96% | 128.6 | ABC transporter for D-Glucosamine, permease component 2 | 88% | 505.4 |
Sequence Analysis Tools
View WP_004127647.1 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
MSGTSMTTRAWLLMLPLLVVMIAVIGWPLVDTVGLSFTDAKLVGTGGNFVGIDNYAKMLA
NPSFQRTLITTAWFAIVSVAAEMVLGVLAALLLNQDFKGRGVLRALMILPWALPTVVNAT
LWRLIYNPEYGALNAALTQLGLLDAYRSWLGEPGTALTALIVADCWKNFPLVALIALAAL
QAVPRDITAASLVDGAGPFTRFRFVILPYLAGPLMVALVLRTIEAFKVFDIIWVMTRGGP
ANSTRTLSILVYQEAFSFQRAGSGASLALIVTLLVTVLAATYAALVRKTAESAT
This GapMind analysis is from Sep 24 2021. 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