Protein WP_104914308.1 in Pontimonas salivibrio CL-TW6
Annotation: NCBI__GCF_002950575.1:WP_104914308.1
Length: 343 amino acids
Source: GCF_002950575.1 in NCBI
Candidate for 24 steps in catabolism of small carbon sources
| Pathway | Step | Score | Similar to | Id. | Cov. | Bits | Other hit | Other id. | Other bits |
|---|
| 2'-deoxyinosine catabolism | H281DRAFT_01112 | med | deoxynucleoside transporter, permease component 2 (characterized) | 39% | 91% | 238.8 | RhaP, 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!) | 33% | 168.7 |
| L-rhamnose catabolism | rhaP | lo | RhaP, 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) | 33% | 93% | 168.7 | deoxynucleoside transporter, permease component 2 | 39% | 238.8 |
| D-ribose catabolism | rbsC | lo | ABC-type transporter, integral membrane subunit, component of D-ribose porter (Nanavati et al., 2006). Induced by ribose (characterized) | 31% | 92% | 168.3 | deoxynucleoside transporter, permease component 2 | 39% | 238.8 |
| D-mannose catabolism | HSERO_RS03645 | lo | ABC-type sugar transport system, permease component protein (characterized, see rationale) | 33% | 85% | 167.5 | deoxynucleoside transporter, permease component 2 | 39% | 238.8 |
| L-fucose catabolism | HSERO_RS05255 | lo | ABC-type sugar transport system, permease component protein (characterized, see rationale) | 34% | 90% | 161 | deoxynucleoside transporter, permease component 2 | 39% | 238.8 |
| L-fucose catabolism | BPHYT_RS34240 | lo | Monosaccharide-transporting ATPase; EC 3.6.3.17; Flags: Precursor (characterized, see rationale) | 32% | 87% | 154.5 | deoxynucleoside transporter, permease component 2 | 39% | 238.8 |
| L-rhamnose catabolism | BPHYT_RS34240 | lo | Monosaccharide-transporting ATPase; EC 3.6.3.17; Flags: Precursor (characterized, see rationale) | 32% | 87% | 154.5 | deoxynucleoside transporter, permease component 2 | 39% | 238.8 |
| D-fructose catabolism | frcC | lo | Fructose import permease protein FrcC (characterized) | 31% | 89% | 149.4 | deoxynucleoside transporter, permease component 2 | 39% | 238.8 |
| D-mannose catabolism | frcC | lo | Fructose import permease protein FrcC (characterized) | 31% | 89% | 149.4 | deoxynucleoside transporter, permease component 2 | 39% | 238.8 |
| D-ribose catabolism | frcC | lo | Fructose import permease protein FrcC (characterized) | 31% | 89% | 149.4 | deoxynucleoside transporter, permease component 2 | 39% | 238.8 |
| sucrose catabolism | frcC | lo | Fructose import permease protein FrcC (characterized) | 31% | 89% | 149.4 | deoxynucleoside transporter, permease component 2 | 39% | 238.8 |
| myo-inositol catabolism | iatP | lo | Inositol ABC transport system, permease protein IatP, 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) | 33% | 89% | 148.3 | deoxynucleoside transporter, permease component 2 | 39% | 238.8 |
| D-xylose catabolism | xylF_Tm | lo | ABC-type transporter, integral membrane subunit, component of Xylose porter (Nanavati et al. 2006). Regulated by xylose-responsive regulator XylR (characterized) | 32% | 95% | 143.7 | deoxynucleoside transporter, permease component 2 | 39% | 238.8 |
| L-arabinose catabolism | araZsh | lo | Inner-membrane translocator (characterized, see rationale) | 32% | 98% | 142.5 | deoxynucleoside transporter, permease component 2 | 39% | 238.8 |
| D-fructose catabolism | fruG | lo | Fructose import permease protein FruG (characterized) | 31% | 89% | 142.1 | deoxynucleoside transporter, permease component 2 | 39% | 238.8 |
| L-rhamnose catabolism | rhaQ | lo | RhaQ (characterized, see rationale) | 31% | 91% | 142.1 | deoxynucleoside transporter, permease component 2 | 39% | 238.8 |
| sucrose catabolism | fruG | lo | Fructose import permease protein FruG (characterized) | 31% | 89% | 142.1 | deoxynucleoside transporter, permease component 2 | 39% | 238.8 |
| D-cellobiose catabolism | mglC | lo | MglC aka B2148, component of Galactose/glucose (methyl galactoside) porter (characterized) | 31% | 96% | 137.9 | deoxynucleoside transporter, permease component 2 | 39% | 238.8 |
| D-galactose catabolism | mglC | lo | MglC aka B2148, component of Galactose/glucose (methyl galactoside) porter (characterized) | 31% | 96% | 137.9 | deoxynucleoside transporter, permease component 2 | 39% | 238.8 |
| D-glucose catabolism | mglC | lo | MglC aka B2148, component of Galactose/glucose (methyl galactoside) porter (characterized) | 31% | 96% | 137.9 | deoxynucleoside transporter, permease component 2 | 39% | 238.8 |
| lactose catabolism | mglC | lo | MglC aka B2148, component of Galactose/glucose (methyl galactoside) porter (characterized) | 31% | 96% | 137.9 | deoxynucleoside transporter, permease component 2 | 39% | 238.8 |
| D-maltose catabolism | mglC | lo | MglC aka B2148, component of Galactose/glucose (methyl galactoside) porter (characterized) | 31% | 96% | 137.9 | deoxynucleoside transporter, permease component 2 | 39% | 238.8 |
| sucrose catabolism | mglC | lo | MglC aka B2148, component of Galactose/glucose (methyl galactoside) porter (characterized) | 31% | 96% | 137.9 | deoxynucleoside transporter, permease component 2 | 39% | 238.8 |
| trehalose catabolism | mglC | lo | MglC aka B2148, component of Galactose/glucose (methyl galactoside) porter (characterized) | 31% | 96% | 137.9 | deoxynucleoside transporter, permease component 2 | 39% | 238.8 |
Sequence Analysis Tools
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
MSTVAQFVERFRGANNEGILLLVLAALVLVIGTLNPVFFSVSTLFSILRGVLVPLILALA
VLIIMISGGIDVSFVAIAIFAGYTSVVIAQSGGGDPGLIVIILIALFFGLLLGAFNGFVI
SLFRLPTLIVSLGTQSLFKGILLAYVGSKYIANLPPSMDSVATTNILSIPQDQGVANLHV
LVIPVAIILILVAWVLKKTMFGRAVYAIGGDMEAARRAGFPVVRTQFYIYMLAGALAAIG
GFLHVTLGRAANPQDLVGNELDVLAAVVLGGASVFGGRGSVFGTVLGVLLIQVINNSLIL
AGVPTSWQRTAVGVLLLVGVGIQALSARRQSMKSHVTEDTEKE
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