Protein GFF2162 in Pseudomonas simiae WCS417
Annotation: FitnessBrowser__WCS417:GFF2162
Length: 500 amino acids
Source: WCS417 in FitnessBrowser
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-galactose catabolism | BPHYT_RS16930 | hi | Arabinose import ATP-binding protein AraG; EC 7.5.2.12 (characterized, see rationale) | 86% | 96% | 825.1 | L-arabinose ABC transporter, ATP-binding protein AraG; EC 3.6.3.17 | 60% | 582.8 |
| L-arabinose catabolism | araG | hi | L-arabinose ABC transporter, ATP-binding protein AraG; EC 3.6.3.17 (characterized) | 60% | 97% | 582.8 | ribose transport, ATP-binding protein RbsA; EC 3.6.3.17 | 44% | 411.0 |
| D-ribose catabolism | rbsA | med | ribose transport, ATP-binding protein RbsA; EC 3.6.3.17 (characterized) | 44% | 98% | 411 | L-arabinose ABC transporter, ATP-binding protein AraG; EC 3.6.3.17 | 60% | 582.8 |
| D-mannose catabolism | HSERO_RS03640 | med | Ribose import ATP-binding protein RbsA; EC 7.5.2.7 (characterized, see rationale) | 42% | 95% | 392.5 | L-arabinose ABC transporter, ATP-binding protein AraG; EC 3.6.3.17 | 60% | 582.8 |
| D-galactose catabolism | mglA | med | Galactose/methyl galactoside import ATP-binding protein MglA aka B2149, component of Galactose/glucose (methyl galactoside) porter (characterized) | 43% | 97% | 389.4 | L-arabinose ABC transporter, ATP-binding protein AraG; EC 3.6.3.17 | 60% | 582.8 |
| myo-inositol catabolism | iatA | med | Inositol transport ATP-binding protein IatA, component of The myoinositol (high affinity)/ D-ribose (low affinity) transporter IatP/IatA/IbpA. The structure of IbpA with myoinositol bound has been solved (characterized) | 45% | 95% | 387.1 | L-arabinose ABC transporter, ATP-binding protein AraG; EC 3.6.3.17 | 60% | 582.8 |
| D-fructose catabolism | frcA | med | ABC-type sugar transport system, ATP-binding protein; EC 3.6.3.17 (characterized, see rationale) | 43% | 94% | 365.9 | L-arabinose ABC transporter, ATP-binding protein AraG; EC 3.6.3.17 | 60% | 582.8 |
| sucrose catabolism | frcA | med | ABC-type sugar transport system, ATP-binding protein; EC 3.6.3.17 (characterized, see rationale) | 43% | 94% | 365.9 | L-arabinose ABC transporter, ATP-binding protein AraG; EC 3.6.3.17 | 60% | 582.8 |
| L-rhamnose catabolism | rhaT' | med | RhaT, component of Rhamnose porter (Richardson et al., 2004) (Transport activity is dependent on rhamnokinase (RhaK; AAQ92412) activity (Richardson and Oresnik, 2007) This could be an example of group translocation!) (characterized) | 41% | 96% | 361.7 | L-arabinose ABC transporter, ATP-binding protein AraG; EC 3.6.3.17 | 60% | 582.8 |
| D-xylose catabolism | xylG | med | Xylose import ATP-binding protein XylG; EC 7.5.2.10 (characterized) | 40% | 97% | 353.6 | L-arabinose ABC transporter, ATP-binding protein AraG; EC 3.6.3.17 | 60% | 582.8 |
| D-galactose catabolism | ytfR | lo | galactofuranose ABC transporter putative ATP binding subunit (EC 7.5.2.9) (characterized) | 38% | 97% | 349.7 | L-arabinose ABC transporter, ATP-binding protein AraG; EC 3.6.3.17 | 60% | 582.8 |
Sequence Analysis Tools
View GFF2162 at FitnessBrowser
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
MTAAALRFDGIGKTFPGVKALDGISFSAHPGQVHALMGENGAGKSTLLKILGGAYIPNSG
TLHIGEQVMAFKSAADSIASGVAVIHQELHLVPEMSVAENLFLGHLPSRFGVVNRGLLRK
QALACLKGLADEIDPAEKLGRLSLGQRQLVEIAKALSRGAHVIAFDEPTSSLSAREIDRL
MAIIARLRDEGKVVLYVSHRMEEVFRICNAVTVFKDGRYVRTFEDMSALTHDQLVTCMVG
RDIQDIYDYRPREHGEVALKVDGLLGPGLREPVSFNVRKGEILGLFGLVGAGRTELFRLL
SGLERASAGQLELCGEPLHLQSPRDAIAAGVLLCPEDRKKEGIIPLSSVAENINISARGA
HSTFGWLLREGWEKGNADQQINAMKVKTPNAAQKIMYLSGGNQQKSILGRWLSMPMKVLL
LDEPTRGIDIGAKAEIYQIIHNLAAQGIAVIVVSSDLMEVMGIADRILVLCEGALRGEQT
REHATESNLLQLALPRSVAN
This GapMind analysis is from Sep 17 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