Protein WP_075662939.1 in Corynebacterium frankenforstense ST18
Annotation: NCBI__GCF_001941485.1:WP_075662939.1
Length: 254 amino acids
Source: GCF_001941485.1 in NCBI
Candidate for 14 steps in catabolism of small carbon sources
| Pathway | Step | Score | Similar to | Id. | Cov. | Bits | Other hit | Other id. | Other bits |
|---|
| myo-inositol catabolism | PGA1_c07320 | hi | Inositol transport system ATP-binding protein (characterized) | 48% | 98% | 229.2 | Probable ABC-transport system ATP binding protein, component of XylFGH downstream of characterized transcriptional regulator, ROK7B7 (Sco6008); XylF (Sco6009); XylG (Sco6010); XylH (Sco6011)) | 44% | 187.6 |
| L-arabinose catabolism | xylGsa | med | Xylose/arabinose import ATP-binding protein XylG; EC 7.5.2.13 (characterized, see rationale) | 43% | 95% | 203 | Inositol transport system ATP-binding protein | 48% | 229.2 |
| D-fructose catabolism | frcA | med | Fructose import ATP-binding protein FrcA; EC 7.5.2.- (characterized) | 41% | 96% | 177.6 | Inositol transport system ATP-binding protein | 48% | 229.2 |
| D-mannose catabolism | frcA | med | Fructose import ATP-binding protein FrcA; EC 7.5.2.- (characterized) | 41% | 96% | 177.6 | Inositol transport system ATP-binding protein | 48% | 229.2 |
| D-ribose catabolism | frcA | med | Fructose import ATP-binding protein FrcA; EC 7.5.2.- (characterized) | 41% | 96% | 177.6 | Inositol transport system ATP-binding protein | 48% | 229.2 |
| sucrose catabolism | frcA | med | Fructose import ATP-binding protein FrcA; EC 7.5.2.- (characterized) | 41% | 96% | 177.6 | Inositol transport system ATP-binding protein | 48% | 229.2 |
| D-cellobiose catabolism | mglA | lo | glucose transporter, ATPase component (characterized) | 38% | 90% | 164.9 | Inositol transport system ATP-binding protein | 48% | 229.2 |
| D-glucose catabolism | mglA | lo | glucose transporter, ATPase component (characterized) | 38% | 90% | 164.9 | Inositol transport system ATP-binding protein | 48% | 229.2 |
| lactose catabolism | mglA | lo | glucose transporter, ATPase component (characterized) | 38% | 90% | 164.9 | Inositol transport system ATP-binding protein | 48% | 229.2 |
| D-maltose catabolism | mglA | lo | glucose transporter, ATPase component (characterized) | 38% | 90% | 164.9 | Inositol transport system ATP-binding protein | 48% | 229.2 |
| sucrose catabolism | mglA | lo | glucose transporter, ATPase component (characterized) | 38% | 90% | 164.9 | Inositol transport system ATP-binding protein | 48% | 229.2 |
| trehalose catabolism | mglA | lo | glucose transporter, ATPase component (characterized) | 38% | 90% | 164.9 | Inositol transport system ATP-binding protein | 48% | 229.2 |
| L-arabinose catabolism | araVsh | lo | ABC transporter related (characterized, see rationale) | 36% | 50% | 148.7 | Inositol transport system ATP-binding protein | 48% | 229.2 |
| xylitol catabolism | PS417_12065 | lo | D-ribose transporter ATP-binding protein; SubName: Full=Putative xylitol transport system ATP-binding protein; SubName: Full=Sugar ABC transporter ATP-binding protein (characterized, see rationale) | 31% | 51% | 123.6 | Inositol transport system ATP-binding protein | 48% | 229.2 |
Sequence Analysis Tools
View WP_075662939.1 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
MSEPLVELRDVTKSYGPFDALRGVGFAVRAGSVTCVLGDNGAGKSTLIKVLAGLHRQTSG
QLLIDGEEVRFSGPRDALDHGIATVYQDLAVVGQMSVWRNFFLGQELRGRLGWLRVDEMR
ETTARALAEMGIDIPDVDVPVDSLSGGQRQVLAIARAVHFGARLLILDEPTAALGVKQSG
MVLRLIAAARDRGLGVVFITHNPHHAWLVGDRFVLLNLGRQTMDAAHDETSLDELTLEMS
GGGELEEISEQLRA
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