Protein HSERO_RS03645 in Herbaspirillum seropedicae SmR1
Annotation: FitnessBrowser__HerbieS:HSERO_RS03645
Length: 339 amino acids
Source: HerbieS in FitnessBrowser
Candidate for 23 steps in catabolism of small carbon sources
| Pathway | Step | Score | Similar to | Id. | Cov. | Bits | Other hit | Other id. | Other bits |
|---|
| D-mannose catabolism | HSERO_RS03645 | hi | ABC-type sugar transport system, permease component protein (characterized, see rationale) | 100% | 99% | 662.1 | ABC-type transporter, integral membrane subunit, component of D-ribose porter (Nanavati et al., 2006). Induced by ribose | 45% | 243.4 |
| D-fructose catabolism | frcC | hi | Ribose ABC transport system, permease protein RbsC (characterized, see rationale) | 55% | 99% | 342 | ABC-type transporter, integral membrane subunit, component of D-ribose porter (Nanavati et al., 2006). Induced by ribose | 45% | 243.4 |
| sucrose catabolism | frcC | hi | Ribose ABC transport system, permease protein RbsC (characterized, see rationale) | 55% | 99% | 342 | ABC-type transporter, integral membrane subunit, component of D-ribose porter (Nanavati et al., 2006). Induced by ribose | 45% | 243.4 |
| xylitol catabolism | PS417_12060 | med | ABC transporter permease; SubName: Full=Monosaccharide ABC transporter membrane protein, CUT2 family; SubName: Full=Sugar ABC transporter permease (characterized, see rationale) | 46% | 93% | 250.4 | ABC-type transporter, integral membrane subunit, component of D-ribose porter (Nanavati et al., 2006). Induced by ribose | 45% | 243.4 |
| D-ribose catabolism | rbsC | med | ABC-type transporter, integral membrane subunit, component of D-ribose porter (Nanavati et al., 2006). Induced by ribose (characterized) | 45% | 96% | 243.4 | RbsC, component of The probable autoinducer-2 (AI-2;, a furanosyl borate diester: 3aS,6S,6aR)-2,2,6,6a-tetrahydroxy-3a-methyltetrahydrofuro[3,2-d][1,3,2]dioxaborolan-2-uide) uptake porter (Shao et al., 2007) (50-70% identical to RbsABC of E. coli; TC# 3.A.1.2.1) | 42% | 242.3 |
| 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% | 92% | 222.2 | ABC-type transporter, integral membrane subunit, component of D-ribose porter (Nanavati et al., 2006). Induced by ribose | 45% | 243.4 |
| myo-inositol catabolism | PS417_11895 | med | Inositol transport system permease protein (characterized) | 41% | 93% | 216.1 | ABC-type transporter, integral membrane subunit, component of D-ribose porter (Nanavati et al., 2006). Induced by ribose | 45% | 243.4 |
| D-galactose catabolism | ytfT | med | Galactofuranose transporter permease protein YtfT (characterized) | 41% | 79% | 188.3 | ABC-type transporter, integral membrane subunit, component of D-ribose porter (Nanavati et al., 2006). Induced by ribose | 45% | 243.4 |
| 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) | 39% | 95% | 211.5 | ABC-type transporter, integral membrane subunit, component of D-ribose porter (Nanavati et al., 2006). Induced by ribose | 45% | 243.4 |
| 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) | 39% | 95% | 211.5 | ABC-type transporter, integral membrane subunit, component of D-ribose porter (Nanavati et al., 2006). Induced by ribose | 45% | 243.4 |
| 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) | 39% | 95% | 211.5 | ABC-type transporter, integral membrane subunit, component of D-ribose porter (Nanavati et al., 2006). Induced by ribose | 45% | 243.4 |
| 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) | 39% | 95% | 211.5 | ABC-type transporter, integral membrane subunit, component of D-ribose porter (Nanavati et al., 2006). Induced by ribose | 45% | 243.4 |
| 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) | 39% | 95% | 211.5 | ABC-type transporter, integral membrane subunit, component of D-ribose porter (Nanavati et al., 2006). Induced by ribose | 45% | 243.4 |
| 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) | 39% | 95% | 211.5 | ABC-type transporter, integral membrane subunit, component of D-ribose porter (Nanavati et al., 2006). Induced by ribose | 45% | 243.4 |
| 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) | 39% | 95% | 211.5 | ABC-type transporter, integral membrane subunit, component of D-ribose porter (Nanavati et al., 2006). Induced by ribose | 45% | 243.4 |
| D-galactose catabolism | mglC | lo | MglC aka B2148, component of Galactose/glucose (methyl galactoside) porter (characterized) | 36% | 95% | 198 | ABC-type transporter, integral membrane subunit, component of D-ribose porter (Nanavati et al., 2006). Induced by ribose | 45% | 243.4 |
| L-arabinose catabolism | araH | lo | L-arabinose ABC transporter, permease protein AraH (characterized) | 37% | 96% | 196.1 | ABC-type transporter, integral membrane subunit, component of D-ribose porter (Nanavati et al., 2006). Induced by ribose | 45% | 243.4 |
| 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) | 37% | 92% | 184.9 | ABC-type transporter, integral membrane subunit, component of D-ribose porter (Nanavati et al., 2006). Induced by ribose | 45% | 243.4 |
| D-fructose catabolism | fruF | lo | Fructose import permease protein FruF (characterized) | 38% | 84% | 171.4 | ABC-type transporter, integral membrane subunit, component of D-ribose porter (Nanavati et al., 2006). Induced by ribose | 45% | 243.4 |
| sucrose catabolism | fruF | lo | Fructose import permease protein FruF (characterized) | 38% | 84% | 171.4 | ABC-type transporter, integral membrane subunit, component of D-ribose porter (Nanavati et al., 2006). Induced by ribose | 45% | 243.4 |
| L-arabinose catabolism | araWsh | lo | Inner-membrane translocator (characterized, see rationale) | 37% | 69% | 169.1 | ABC-type transporter, integral membrane subunit, component of D-ribose porter (Nanavati et al., 2006). Induced by ribose | 45% | 243.4 |
| D-galactose catabolism | yjtF | lo | Inner membrane ABC transporter permease protein YjfF (characterized) | 34% | 95% | 162.9 | ABC-type transporter, integral membrane subunit, component of D-ribose porter (Nanavati et al., 2006). Induced by ribose | 45% | 243.4 |
| L-arabinose catabolism | araZsh | lo | Inner-membrane translocator (characterized, see rationale) | 34% | 95% | 157.9 | ABC-type transporter, integral membrane subunit, component of D-ribose porter (Nanavati et al., 2006). Induced by ribose | 45% | 243.4 |
Sequence Analysis Tools
View HSERO_RS03645 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
MTHTHDAVPPGARRSSSTTAQWLLHRLGMLPVLVVLYLLFYGLTLYLSGDGTSNFASAEN
TMNILRQVAINLVLAAGMTFVILTAGIDLSVGSVLAVSAVLGMQVSLGAAPGWAIPMFIF
SGLVMGMVNGAMVALLNINAFVVTLGTMTAFRGAAYLLADGTTVLNNDIPSFEWIGNGDF
LHVPWLIWVAVAVVLLSWVILRKTVLGMHIYAIGGNLQAARLTGIRVGLVLLFVYSISGL
FSGLAGAMSASRLYGANGNWGSGYELDAIAAVVLGGTSLMGGVGSIWGTVVGALIIGVMN
NGLTILGLSSFWQYVAKGAVIVLAVILDKWRQKDAAQSA
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:
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