Protein 7024901 in Shewanella sp. ANA-3
Annotation: FitnessBrowser__ANA3:7024901
Length: 405 amino acids
Source: ANA3 in FitnessBrowser
Candidate for 22 steps in catabolism of small carbon sources
| Pathway | Step | Score | Similar to | Id. | Cov. | Bits | Other hit | Other id. | Other bits |
|---|
| L-arabinose catabolism | araWsh | hi | Inner-membrane translocator (characterized, see rationale) | 100% | 100% | 762.3 | Galactofuranose transporter permease protein YtfT | 56% | 337.4 |
| D-galactose catabolism | ytfT | hi | Galactofuranose transporter permease protein YtfT (characterized) | 56% | 97% | 337.4 | Fructose import permease protein FruF | 41% | 223.4 |
| D-fructose catabolism | fruF | med | Fructose import permease protein FruF (characterized) | 42% | 94% | 223.4 | Galactofuranose transporter permease protein YtfT | 56% | 337.4 |
| sucrose catabolism | fruF | med | Fructose import permease protein FruF (characterized) | 42% | 94% | 223.4 | Galactofuranose transporter permease protein YtfT | 56% | 337.4 |
| D-fructose catabolism | frcC | lo | Ribose ABC transport system, permease protein RbsC (characterized, see rationale) | 37% | 93% | 189.5 | Galactofuranose transporter permease protein YtfT | 56% | 337.4 |
| sucrose catabolism | frcC | lo | Ribose ABC transport system, permease protein RbsC (characterized, see rationale) | 37% | 93% | 189.5 | Galactofuranose transporter permease protein YtfT | 56% | 337.4 |
| D-ribose catabolism | rbsC | lo | ABC-type transporter, integral membrane subunit, component of D-ribose porter (Nanavati et al., 2006). Induced by ribose (characterized) | 36% | 98% | 188.3 | Galactofuranose transporter permease protein YtfT | 56% | 337.4 |
| xylitol catabolism | PS417_12060 | lo | ABC transporter permease; SubName: Full=Monosaccharide ABC transporter membrane protein, CUT2 family; SubName: Full=Sugar ABC transporter permease (characterized, see rationale) | 32% | 97% | 169.9 | Galactofuranose transporter permease protein YtfT | 56% | 337.4 |
| D-mannose catabolism | HSERO_RS03645 | lo | ABC-type sugar transport system, permease component protein (characterized, see rationale) | 37% | 81% | 169.1 | Galactofuranose transporter permease protein YtfT | 56% | 337.4 |
| myo-inositol catabolism | PS417_11895 | lo | Inositol transport system permease protein (characterized) | 35% | 92% | 167.9 | Galactofuranose transporter permease protein YtfT | 56% | 337.4 |
| 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% | 97% | 142.5 | Galactofuranose transporter permease protein YtfT | 56% | 337.4 |
| D-cellobiose catabolism | mglC | lo | 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) | 34% | 87% | 141.7 | Galactofuranose transporter permease protein YtfT | 56% | 337.4 |
| D-glucose catabolism | mglC | lo | 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) | 34% | 87% | 141.7 | Galactofuranose transporter permease protein YtfT | 56% | 337.4 |
| lactose catabolism | mglC | lo | 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) | 34% | 87% | 141.7 | Galactofuranose transporter permease protein YtfT | 56% | 337.4 |
| D-maltose catabolism | mglC | lo | 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) | 34% | 87% | 141.7 | Galactofuranose transporter permease protein YtfT | 56% | 337.4 |
| sucrose catabolism | mglC | lo | 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) | 34% | 87% | 141.7 | Galactofuranose transporter permease protein YtfT | 56% | 337.4 |
| trehalose catabolism | mglC | lo | 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) | 34% | 87% | 141.7 | Galactofuranose transporter permease protein YtfT | 56% | 337.4 |
| D-xylose catabolism | xylH | lo | 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) | 34% | 87% | 141.7 | Galactofuranose transporter permease protein YtfT | 56% | 337.4 |
| L-fucose catabolism | HSERO_RS05255 | lo | ABC-type sugar transport system, permease component protein (characterized, see rationale) | 30% | 89% | 137.9 | Galactofuranose transporter permease protein YtfT | 56% | 337.4 |
| D-fructose catabolism | fruG | lo | Fructose import permease protein FruG (characterized) | 31% | 94% | 136.3 | Galactofuranose transporter permease protein YtfT | 56% | 337.4 |
| sucrose catabolism | fruG | lo | Fructose import permease protein FruG (characterized) | 31% | 94% | 136.3 | Galactofuranose transporter permease protein YtfT | 56% | 337.4 |
| 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) | 31% | 82% | 129.4 | Galactofuranose transporter permease protein YtfT | 56% | 337.4 |
Sequence Analysis Tools
View 7024901 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
MKSSAETLSSTRMSADLISPQMNASEAHSSERQPRMQESHKTMVQEKNARYQAGKSTSMG
RYLWPLLALSILLLANLFIDSSFFNISYQDDRLYGSLIDILNRSAPVALLSIGMSLVIAT
GGIDLSVGAVMAIAGAVCANLLLVPDISLVTVIAAGLIVGLLAGCINGGLVSFLGIQPIV
ATLLLMVAGRGVAQLINQGQIITFQHPGFAAIGVGQFLGLPMPVWIVIGMLTFSQLLLRK
TALGLFIEAVGCNAKASRYLGINDKSIKLFAYGIAGLCAALAGMISTADIQGSDANNAGL
WLELDAVLAVVIGGAALTGGRFSLILSVVGALIIQTLATTIIVSGLPAKFNLLIKAIVIL
TVLLLQSAKFRRQLSALFKSKRHADAKPAEKATSAKASAATGEKL
This GapMind analysis is from Sep 17 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