Protein YP_004139518.1 in Mesorhizobium ciceri WSM1271
Annotation: NCBI__GCF_000185905.1:YP_004139518.1
Length: 500 amino acids
Source: GCF_000185905.1 in NCBI
Candidate for 23 steps in catabolism of small carbon sources
| Pathway | Step | Score | Similar to | Id. | Cov. | Bits | Other hit | Other id. | Other bits |
|---|
| myo-inositol catabolism | PS417_11890 | med | Inositol transport system ATP-binding protein (characterized) | 46% | 96% | 434.5 | Monosaccharide-transporting ATPase, 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 | 46% | 427.2 |
| D-cellobiose catabolism | mglA | med | Monosaccharide-transporting ATPase, 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) | 46% | 99% | 427.2 | Inositol transport system ATP-binding protein | 46% | 434.5 |
| D-glucose catabolism | mglA | med | Monosaccharide-transporting ATPase, 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) | 46% | 99% | 427.2 | Inositol transport system ATP-binding protein | 46% | 434.5 |
| lactose catabolism | mglA | med | Monosaccharide-transporting ATPase, 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) | 46% | 99% | 427.2 | Inositol transport system ATP-binding protein | 46% | 434.5 |
| D-maltose catabolism | mglA | med | Monosaccharide-transporting ATPase, 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) | 46% | 99% | 427.2 | Inositol transport system ATP-binding protein | 46% | 434.5 |
| sucrose catabolism | mglA | med | Monosaccharide-transporting ATPase, 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) | 46% | 99% | 427.2 | Inositol transport system ATP-binding protein | 46% | 434.5 |
| trehalose catabolism | mglA | med | Monosaccharide-transporting ATPase, 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) | 46% | 99% | 427.2 | Inositol transport system ATP-binding protein | 46% | 434.5 |
| D-xylose catabolism | xylG | med | Monosaccharide-transporting ATPase, 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) | 46% | 99% | 427.2 | Inositol transport system ATP-binding protein | 46% | 434.5 |
| D-ribose catabolism | rbsA | med | Ribose import ATP-binding protein RbsA 2, component of D-ribose porter (Nanavati et al., 2006). Induced by ribose (characterized) | 46% | 96% | 426 | Inositol transport system ATP-binding protein | 46% | 434.5 |
| D-fructose catabolism | frcA | med | ABC-type sugar transport system, ATP-binding protein; EC 3.6.3.17 (characterized, see rationale) | 46% | 94% | 420.6 | Inositol transport system ATP-binding protein | 46% | 434.5 |
| sucrose catabolism | frcA | med | ABC-type sugar transport system, ATP-binding protein; EC 3.6.3.17 (characterized, see rationale) | 46% | 94% | 420.6 | Inositol transport system ATP-binding protein | 46% | 434.5 |
| L-fucose catabolism | HSERO_RS05250 | med | Ribose import ATP-binding protein RbsA; EC 7.5.2.7 (characterized, see rationale) | 46% | 95% | 420.2 | Inositol transport system ATP-binding protein | 46% | 434.5 |
| 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) | 45% | 97% | 418.3 | Inositol transport system ATP-binding protein | 46% | 434.5 |
| D-mannose catabolism | HSERO_RS03640 | med | Ribose import ATP-binding protein RbsA; EC 7.5.2.7 (characterized, see rationale) | 44% | 94% | 417.5 | Inositol transport system ATP-binding protein | 46% | 434.5 |
| D-galactose catabolism | BPHYT_RS16930 | med | Arabinose import ATP-binding protein AraG; EC 7.5.2.12 (characterized, see rationale) | 45% | 96% | 414.8 | Inositol transport system ATP-binding protein | 46% | 434.5 |
| D-galactose catabolism | mglA | med | Galactose/methyl galactoside import ATP-binding protein MglA; EC 7.5.2.11 (characterized) | 41% | 98% | 405.2 | Inositol transport system ATP-binding protein | 46% | 434.5 |
| L-arabinose catabolism | araG | med | L-arabinose ABC transporter, ATP-binding protein AraG; EC 3.6.3.17 (characterized) | 43% | 97% | 403.3 | Inositol transport system ATP-binding protein | 46% | 434.5 |
| D-xylose catabolism | xylK_Tm | med | Ribose import ATP-binding protein RbsA 1; EC 7.5.2.7 (characterized, see rationale) | 45% | 96% | 401.7 | Inositol transport system ATP-binding protein | 46% | 434.5 |
| D-galactose catabolism | ytfR | med | galactofuranose ABC transporter putative ATP binding subunit (EC 7.5.2.9) (characterized) | 41% | 98% | 380.9 | Inositol transport system ATP-binding protein | 46% | 434.5 |
| L-arabinose catabolism | gguA | med | GguA aka ATU2347 aka AGR_C_4264, component of Multiple sugar (arabinose, xylose, galactose, glucose, fucose) putative porter (characterized) | 42% | 99% | 373.6 | Inositol transport system ATP-binding protein | 46% | 434.5 |
| D-galactose catabolism | gguA | med | GguA aka ATU2347 aka AGR_C_4264, component of Multiple sugar (arabinose, xylose, galactose, glucose, fucose) putative porter (characterized) | 42% | 99% | 373.6 | Inositol transport system ATP-binding protein | 46% | 434.5 |
| L-arabinose catabolism | araVsh | lo | ABC transporter related (characterized, see rationale) | 39% | 99% | 358.2 | Inositol transport system ATP-binding protein | 46% | 434.5 |
| xylitol catabolism | PS417_12065 | lo | D-ribose transporter ATP-binding protein; SubName: Full=Putative xylitol transport system ATP-binding protein; SubName: Full=Sugar ABC transporter ATP-binding protein (characterized, see rationale) | 38% | 100% | 354 | Inositol transport system ATP-binding protein | 46% | 434.5 |
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
MTVAADCALDMRGISKNFPGVKALSNVNFAVKFGTVHAVVGENGAGKSTLMKILNGSYAP
TSGTIKVGDAEVRMRRPADAQALGIRMVHQEINLVPDLTVAENVYLGRMPGKWTFLRKRE
MVRAAAAVLDELGAAINPRERLGNLSISQQQLVEIAKAYAAQPRIIVLDEPTSSLSEHET
AALFRILRKMRDDGIAIVYISHRLKEVLEIADEVTVLRDGSMIQTRPIKGIKAADMIRLM
VGREVSNVFPKSPAAIGKSVLRVEHISDGQRFRDVSFEVRAGEILGLTGLVGAGRTEVAR
AIFGLSRLVEGTVSVNGREVSINSPSQAVRAGIAYVPEDRKGDGVVPGMSVRENISLPIL
RRLTRFGRISRSADRALARDSVKQFSISPPDGERRISLLSGGNQQKAVIAKWLAAKPSAL
ILDEPTRGVDVGAKAEIHHIIGQLVAGGMAVVMISSELPEILGVCDRVVVMRDGYASEPL
LRSELSEERIMALATGEEMA
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