Protein GFF3853 in Phaeobacter inhibens BS107
Annotation: PGA1_78p00170 putative sn-glycerol-3-phosphate transport system permease protein UgpA
Length: 310 amino acids
Source: Phaeo in FitnessBrowser
Candidate for 10 steps in catabolism of small carbon sources
| Pathway | Step | Score | Similar to | Id. | Cov. | Bits | Other hit | Other id. | Other bits |
|---|
| D-cellobiose catabolism | SMc04258 | hi | ABC transporter for D-Cellobiose and D-Salicin, permease component 2 (characterized) | 74% | 97% | 454.9 | GtsB (GLcF), component of Glucose porter, GtsABCD | 44% | 270.4 |
| D-cellobiose catabolism | gtsB | med | GtsB (GLcF), component of Glucose porter, GtsABCD (characterized) | 44% | 97% | 270.4 | ABC transporter for D-Cellobiose and D-Salicin, permease component 2 | 74% | 454.9 |
| D-glucose catabolism | gtsB | med | GtsB (GLcF), component of Glucose porter, GtsABCD (characterized) | 44% | 97% | 270.4 | ABC transporter for D-Cellobiose and D-Salicin, permease component 2 | 74% | 454.9 |
| lactose catabolism | gtsB | med | GtsB (GLcF), component of Glucose porter, GtsABCD (characterized) | 44% | 97% | 270.4 | ABC transporter for D-Cellobiose and D-Salicin, permease component 2 | 74% | 454.9 |
| D-maltose catabolism | gtsB | med | GtsB (GLcF), component of Glucose porter, GtsABCD (characterized) | 44% | 97% | 270.4 | ABC transporter for D-Cellobiose and D-Salicin, permease component 2 | 74% | 454.9 |
| sucrose catabolism | gtsB | med | GtsB (GLcF), component of Glucose porter, GtsABCD (characterized) | 44% | 97% | 270.4 | ABC transporter for D-Cellobiose and D-Salicin, permease component 2 | 74% | 454.9 |
| trehalose catabolism | gtsB | med | GtsB (GLcF), component of Glucose porter, GtsABCD (characterized) | 44% | 97% | 270.4 | ABC transporter for D-Cellobiose and D-Salicin, permease component 2 | 74% | 454.9 |
| D-xylose catabolism | gtsB | med | ABC transporter for D-Glucose-6-Phosphate, permease component 2 (characterized) | 43% | 97% | 268.9 | ABC transporter for D-Cellobiose and D-Salicin, permease component 2 | 74% | 454.9 |
| D-galactose catabolism | PfGW456L13_1895 | med | ABC transporter for D-Galactose and D-Glucose, permease component 1 (characterized) | 43% | 97% | 267.7 | ABC transporter for D-Cellobiose and D-Salicin, permease component 2 | 74% | 454.9 |
| L-arabinose catabolism | xacH | lo | Xylose/arabinose import permease protein XacH (characterized, see rationale) | 32% | 89% | 160.2 | ABC transporter for D-Cellobiose and D-Salicin, permease component 2 | 74% | 454.9 |
Sequence Analysis Tools
View GFF3853 at FitnessBrowser
PaperBLAST (search for papers about homologs of this protein)
Search CDD (the Conserved Domains Database, which includes COG and superfam)
Predict protein localization: PSORTb (Gram negative bacteria)
Predict transmembrane helices and signal peptides: Phobius
Check the SEED with FIGfam search
Fitness BLAST: loading...
Sequence
MTPAPPTGRSGRSPTARPRPPRVLRNLNAKIASVPMILTALVVFMGGTAWTVAHSFTKSR
LLPKWKFVGFDQYERLWSSNRWLISVENLLIYGLCSLVLTMAIGFTLAALLDRKIRFEGA
FRTIFLYPFALSFVVTGLAWQWILNPDFGIQNVVRSWGWESFAFDPLNNPETVIFGVLIA
GLWQGSGFVMVIMLAGLRGIDEDIWKAARVDGIGVTKTYVRVIIPMMRPVFVTALVIIAS
GIIKLYDLVVAQTNGGPGISSEVPAKYVINYMFEAQNLGQGFAASTMMLLSVIIILVPWA
YLEFGGKKRG
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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, or view the source code.
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