Protein WP_068000560.1 in Pseudovibrio axinellae Ad2
Annotation: NCBI__GCF_001623255.1:WP_068000560.1
Length: 332 amino acids
Source: GCF_001623255.1 in NCBI
Candidate for 30 steps in catabolism of small carbon sources
| Pathway | Step | Score | Similar to | Id. | Cov. | Bits | Other hit | Other id. | Other bits |
|---|
| D-ribose catabolism | rbsC | hi | ABC transporter permease (characterized, see rationale) | 47% | 99% | 273.9 | Putative beta-xyloside ABC transporter, permease component, component of Glucose porter. Also bind xylose (Boucher and Noll 2011). Induced by glucose (Frock et al. 2012). Directly regulated by glucose-responsive regulator GluR | 43% | 236.5 |
| D-fructose catabolism | frcC | hi | Ribose ABC transport system, permease protein RbsC (characterized, see rationale) | 43% | 95% | 247.7 | Putative beta-xyloside ABC transporter, permease component, component of Glucose porter. Also bind xylose (Boucher and Noll 2011). Induced by glucose (Frock et al. 2012). Directly regulated by glucose-responsive regulator GluR | 43% | 236.5 |
| sucrose catabolism | frcC | hi | Ribose ABC transport system, permease protein RbsC (characterized, see rationale) | 43% | 95% | 247.7 | Putative beta-xyloside ABC transporter, permease component, component of Glucose porter. Also bind xylose (Boucher and Noll 2011). Induced by glucose (Frock et al. 2012). Directly regulated by glucose-responsive regulator GluR | 43% | 236.5 |
| xylitol catabolism | PS417_12060 | hi | ABC transporter permease; SubName: Full=Monosaccharide ABC transporter membrane protein, CUT2 family; SubName: Full=Sugar ABC transporter permease (characterized, see rationale) | 41% | 99% | 246.9 | Putative beta-xyloside ABC transporter, permease component, component of Glucose porter. Also bind xylose (Boucher and Noll 2011). Induced by glucose (Frock et al. 2012). Directly regulated by glucose-responsive regulator GluR | 43% | 236.5 |
| D-cellobiose catabolism | mglC | med | Putative beta-xyloside ABC transporter, permease component, component of Glucose porter. Also bind xylose (Boucher and Noll 2011). Induced by glucose (Frock et al. 2012). Directly regulated by glucose-responsive regulator GluR (characterized) | 43% | 97% | 236.5 | Ribose import permease protein RbsC | 43% | 235.0 |
| D-glucose catabolism | mglC | med | Putative beta-xyloside ABC transporter, permease component, component of Glucose porter. Also bind xylose (Boucher and Noll 2011). Induced by glucose (Frock et al. 2012). Directly regulated by glucose-responsive regulator GluR (characterized) | 43% | 97% | 236.5 | Ribose import permease protein RbsC | 43% | 235.0 |
| lactose catabolism | mglC | med | Putative beta-xyloside ABC transporter, permease component, component of Glucose porter. Also bind xylose (Boucher and Noll 2011). Induced by glucose (Frock et al. 2012). Directly regulated by glucose-responsive regulator GluR (characterized) | 43% | 97% | 236.5 | Ribose import permease protein RbsC | 43% | 235.0 |
| D-maltose catabolism | mglC | med | Putative beta-xyloside ABC transporter, permease component, component of Glucose porter. Also bind xylose (Boucher and Noll 2011). Induced by glucose (Frock et al. 2012). Directly regulated by glucose-responsive regulator GluR (characterized) | 43% | 97% | 236.5 | Ribose import permease protein RbsC | 43% | 235.0 |
| sucrose catabolism | mglC | med | Putative beta-xyloside ABC transporter, permease component, component of Glucose porter. Also bind xylose (Boucher and Noll 2011). Induced by glucose (Frock et al. 2012). Directly regulated by glucose-responsive regulator GluR (characterized) | 43% | 97% | 236.5 | Ribose import permease protein RbsC | 43% | 235.0 |
| trehalose catabolism | mglC | med | Putative beta-xyloside ABC transporter, permease component, component of Glucose porter. Also bind xylose (Boucher and Noll 2011). Induced by glucose (Frock et al. 2012). Directly regulated by glucose-responsive regulator GluR (characterized) | 43% | 97% | 236.5 | Ribose import permease protein RbsC | 43% | 235.0 |
| D-xylose catabolism | xylH | med | Putative beta-xyloside ABC transporter, permease component, component of Glucose porter. Also bind xylose (Boucher and Noll 2011). Induced by glucose (Frock et al. 2012). Directly regulated by glucose-responsive regulator GluR (characterized) | 43% | 97% | 236.5 | Ribose import permease protein RbsC | 43% | 235.0 |
| D-mannose catabolism | HSERO_RS03645 | med | ABC-type sugar transport system, permease component protein (characterized, see rationale) | 42% | 97% | 229.9 | Putative beta-xyloside ABC transporter, permease component, component of Glucose porter. Also bind xylose (Boucher and Noll 2011). Induced by glucose (Frock et al. 2012). Directly regulated by glucose-responsive regulator GluR | 43% | 236.5 |
| myo-inositol catabolism | iatP | med | 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) | 42% | 89% | 227.3 | Putative beta-xyloside ABC transporter, permease component, component of Glucose porter. Also bind xylose (Boucher and Noll 2011). Induced by glucose (Frock et al. 2012). Directly regulated by glucose-responsive regulator GluR | 43% | 236.5 |
| L-fucose catabolism | HSERO_RS05255 | med | ABC-type sugar transport system, permease component protein (characterized, see rationale) | 40% | 87% | 226.9 | Putative beta-xyloside ABC transporter, permease component, component of Glucose porter. Also bind xylose (Boucher and Noll 2011). Induced by glucose (Frock et al. 2012). Directly regulated by glucose-responsive regulator GluR | 43% | 236.5 |
| 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) | 37% | 100% | 202.6 | Putative beta-xyloside ABC transporter, permease component, component of Glucose porter. Also bind xylose (Boucher and Noll 2011). Induced by glucose (Frock et al. 2012). Directly regulated by glucose-responsive regulator GluR | 43% | 236.5 |
| D-mannose catabolism | frcC | lo | Fructose import permease protein FrcC (characterized) | 39% | 89% | 199.1 | Putative beta-xyloside ABC transporter, permease component, component of Glucose porter. Also bind xylose (Boucher and Noll 2011). Induced by glucose (Frock et al. 2012). Directly regulated by glucose-responsive regulator GluR | 43% | 236.5 |
| D-ribose catabolism | frcC | lo | Fructose import permease protein FrcC (characterized) | 39% | 89% | 199.1 | Putative beta-xyloside ABC transporter, permease component, component of Glucose porter. Also bind xylose (Boucher and Noll 2011). Induced by glucose (Frock et al. 2012). Directly regulated by glucose-responsive regulator GluR | 43% | 236.5 |
| myo-inositol catabolism | PS417_11895 | lo | m-Inositol ABC transporter, permease component (iatP) (characterized) | 38% | 94% | 198 | Putative beta-xyloside ABC transporter, permease component, component of Glucose porter. Also bind xylose (Boucher and Noll 2011). Induced by glucose (Frock et al. 2012). Directly regulated by glucose-responsive regulator GluR | 43% | 236.5 |
| L-arabinose catabolism | araH | lo | L-arabinose ABC transporter, permease protein AraH (characterized) | 33% | 99% | 186.4 | Putative beta-xyloside ABC transporter, permease component, component of Glucose porter. Also bind xylose (Boucher and Noll 2011). Induced by glucose (Frock et al. 2012). Directly regulated by glucose-responsive regulator GluR | 43% | 236.5 |
| D-galactose catabolism | BPHYT_RS16925 | lo | Arabinose ABC transporter permease (characterized, see rationale) | 31% | 100% | 174.1 | Putative beta-xyloside ABC transporter, permease component, component of Glucose porter. Also bind xylose (Boucher and Noll 2011). Induced by glucose (Frock et al. 2012). Directly regulated by glucose-responsive regulator GluR | 43% | 236.5 |
| 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) | 34% | 91% | 172.9 | Putative beta-xyloside ABC transporter, permease component, component of Glucose porter. Also bind xylose (Boucher and Noll 2011). Induced by glucose (Frock et al. 2012). Directly regulated by glucose-responsive regulator GluR | 43% | 236.5 |
| D-galactose catabolism | mglC | lo | MglC aka B2148, component of Galactose/glucose (methyl galactoside) porter (characterized) | 32% | 98% | 156 | Putative beta-xyloside ABC transporter, permease component, component of Glucose porter. Also bind xylose (Boucher and Noll 2011). Induced by glucose (Frock et al. 2012). Directly regulated by glucose-responsive regulator GluR | 43% | 236.5 |
| L-arabinose catabolism | araZsh | lo | Inner-membrane translocator (characterized, see rationale) | 33% | 92% | 154.8 | Putative beta-xyloside ABC transporter, permease component, component of Glucose porter. Also bind xylose (Boucher and Noll 2011). Induced by glucose (Frock et al. 2012). Directly regulated by glucose-responsive regulator GluR | 43% | 236.5 |
| L-rhamnose catabolism | rhaQ | lo | RhaQ (characterized, see rationale) | 31% | 87% | 154.8 | Putative beta-xyloside ABC transporter, permease component, component of Glucose porter. Also bind xylose (Boucher and Noll 2011). Induced by glucose (Frock et al. 2012). Directly regulated by glucose-responsive regulator GluR | 43% | 236.5 |
| D-galactose catabolism | yjtF | lo | Inner membrane ABC transporter permease protein YjfF (characterized) | 35% | 90% | 153.3 | Putative beta-xyloside ABC transporter, permease component, component of Glucose porter. Also bind xylose (Boucher and Noll 2011). Induced by glucose (Frock et al. 2012). Directly regulated by glucose-responsive regulator GluR | 43% | 236.5 |
| L-fucose catabolism | BPHYT_RS34240 | lo | Monosaccharide-transporting ATPase; EC 3.6.3.17; Flags: Precursor (characterized, see rationale) | 31% | 84% | 150.6 | Putative beta-xyloside ABC transporter, permease component, component of Glucose porter. Also bind xylose (Boucher and Noll 2011). Induced by glucose (Frock et al. 2012). Directly regulated by glucose-responsive regulator GluR | 43% | 236.5 |
| L-rhamnose catabolism | BPHYT_RS34240 | lo | Monosaccharide-transporting ATPase; EC 3.6.3.17; Flags: Precursor (characterized, see rationale) | 31% | 84% | 150.6 | Putative beta-xyloside ABC transporter, permease component, component of Glucose porter. Also bind xylose (Boucher and Noll 2011). Induced by glucose (Frock et al. 2012). Directly regulated by glucose-responsive regulator GluR | 43% | 236.5 |
| D-galactose catabolism | ytfT | lo | Galactofuranose transporter permease protein YtfT (characterized) | 32% | 89% | 146.7 | Putative beta-xyloside ABC transporter, permease component, component of Glucose porter. Also bind xylose (Boucher and Noll 2011). Induced by glucose (Frock et al. 2012). Directly regulated by glucose-responsive regulator GluR | 43% | 236.5 |
| L-arabinose catabolism | araWsh | lo | Inner-membrane translocator (characterized, see rationale) | 32% | 76% | 144.4 | Putative beta-xyloside ABC transporter, permease component, component of Glucose porter. Also bind xylose (Boucher and Noll 2011). Induced by glucose (Frock et al. 2012). Directly regulated by glucose-responsive regulator GluR | 43% | 236.5 |
| L-arabinose catabolism | xylHsa | lo | Xylose/arabinose import permease protein XylH (characterized, see rationale) | 31% | 85% | 131.7 | Putative beta-xyloside ABC transporter, permease component, component of Glucose porter. Also bind xylose (Boucher and Noll 2011). Induced by glucose (Frock et al. 2012). Directly regulated by glucose-responsive regulator GluR | 43% | 236.5 |
Sequence Analysis Tools
View WP_068000560.1 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
MTIQTGDEVAQASGNFSIRTVLHNAGIGLALLALILFFSIFTEHFLTANNITNILTQVTI
NLILAVGMTFVILIGGIDLSVGSVMAFASVIAGKAITLAGLGPFEAIVLAVIAATAVGVV
CGAINGTITARWSLPSFIITLGMLNIARGAALQASNAQTIYSFPLAFEDFGSAMFYGVPV
VFMVALALVFIAWFILNFTVFGRLLYGIGNNEEAVRLAGHSVYRYKIAAFTICGLTAGIA
AVVYMARLNISSPIAGIGFELNAIAAVIIGGTSLNGGRGSVIGTLIGAFIIGVLANGLIL
IGLSDFMRQMITGVVIIIAVILDYYRAKYTRR
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