GapMind for catabolism of small carbon sources

 

Protein HSERO_RS03645 in Herbaspirillum seropedicae SmR1

Annotation: HSERO_RS03645 ribose ABC transporter permease

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

PaperBLAST (search for papers about homologs of this protein)

Search CDD (the Conserved Domains Database, which includes COG and superfam)

Search PFam (including for weak hits, up to E = 1)

Predict protein localization: PSORTb (Gram negative bacteria)

Predict transmembrane helices and signal peptides: Phobius

Check the SEED with FIGfam search

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:

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:

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:

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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, or view the source code.

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