Protein WP_011317344.1 in Trichormus variabilis ATCC 29413
Annotation: NCBI__GCF_000204075.1:WP_011317344.1
Length: 301 amino acids
Source: GCF_000204075.1 in NCBI
Candidate for 9 steps in catabolism of small carbon sources
| Pathway | Step | Score | Similar to | Id. | Cov. | Bits | Other hit | Other id. | Other bits |
|---|
| lactose catabolism | lacF | lo | LacF, component of Lactose porter (characterized) | 38% | 92% | 198 | transmembrane permease MsmF | 37% | 199.9 |
| D-cellobiose catabolism | cebF | lo | CBP protein aka CebF, component of The cellobiose/cellotriose (and possibly higher cellooligosaccharides), CebEFGMsiK [MsiK functions to energize several ABC transporters including those for maltose/maltotriose and trehalose] (characterized) | 37% | 92% | 181 | transmembrane permease MsmF | 37% | 199.9 |
| D-maltose catabolism | thuF | lo | Trehalose/maltose transport system permease protein MalF (characterized) | 33% | 97% | 166.4 | transmembrane permease MsmF | 37% | 199.9 |
| trehalose catabolism | thuF | lo | Trehalose/maltose transport system permease protein MalF (characterized) | 33% | 97% | 166.4 | transmembrane permease MsmF | 37% | 199.9 |
| N-acetyl-D-glucosamine catabolism | ngcF | lo | NgcF, component of N-Acetylglucosamine/N,N'-diacetyl chitobiose porter (NgcK (C) not identified) (characterized) | 34% | 96% | 158.3 | transmembrane permease MsmF | 37% | 199.9 |
| D-glucosamine (chitosamine) catabolism | ngcF | lo | NgcF, component of N-Acetylglucosamine/N,N'-diacetyl chitobiose porter (NgcK (C) not identified) (characterized) | 34% | 96% | 158.3 | transmembrane permease MsmF | 37% | 199.9 |
| xylitol catabolism | Dshi_0548 | lo | ABC transporter for Xylitol, permease component 1 (characterized) | 31% | 96% | 133.7 | transmembrane permease MsmF | 37% | 199.9 |
| xylitol catabolism | HSERO_RS17005 | lo | ABC-type sugar transport system, permease component protein (characterized, see rationale) | 31% | 96% | 129.4 | transmembrane permease MsmF | 37% | 199.9 |
| D-maltose catabolism | musF | lo | ABC-type sugar transport system, permease component, component of Maltose transporter, MusEFGKI (characterized) | 30% | 91% | 124.8 | transmembrane permease MsmF | 37% | 199.9 |
Sequence Analysis Tools
View WP_011317344.1 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
MVLRIRRWRNNHRRNITDSLFGYVFMMPTLLVLGTFVVLPILYSVFLSLNKVQLLGGVAY
QFIGLRNFQRLVDDQLVWIALRNTAEYVVIVVPSQTILALILAVTLNAGIRGKNWWRILY
FLPTVTSSAVLTLIFMWIYNTDGLLNDFLAFVGLPTYNWLGDPAVALKGIMLMNIWSTAP
FYMVIYLAALQDIPAKLYEAAELDGANWWQKFIYITIPLLKPVTFFVIAVGVIGTFQLFD
QSYIFSGGTGGPNNATLTVVLLIYQMVFRYLQMGYAAAIAFLLAVVIIAITLIQRRVFAG
E
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