GapMind for catabolism of small carbon sources

 

Protein WP_040662387.1 in Oscillibacter ruminantium GH1

Annotation: NCBI__GCF_000307265.1:WP_040662387.1

Length: 332 amino acids

Source: GCF_000307265.1 in NCBI

Candidate for 28 steps in catabolism of small carbon sources

Pathway Step Score Similar to Id. Cov. Bits Other hit Other id. Other bits
D-xylose catabolism xylF_Tm med ABC-type transporter, integral membrane subunit, component of Xylose porter (Nanavati et al. 2006). Regulated by xylose-responsive regulator XylR (characterized) 37% 95% 196.1 EryF aka RB0338, component of The erythritol permease, EryEFG (Geddes et al., 2010) (probably orthologous to 3.A.1.2.16) 34% 194.9
D-ribose catabolism rbsC lo ABC-type transporter, integral membrane subunit, component of D-ribose porter (Nanavati et al., 2006). Induced by ribose (characterized) 37% 94% 191.8 ABC-type transporter, integral membrane subunit, component of Xylose porter (Nanavati et al. 2006). Regulated by xylose-responsive regulator XylR 37% 196.1
D-fructose catabolism frcC lo Ribose ABC transport system, permease protein RbsC (characterized, see rationale) 36% 92% 180.6 ABC-type transporter, integral membrane subunit, component of Xylose porter (Nanavati et al. 2006). Regulated by xylose-responsive regulator XylR 37% 196.1
sucrose catabolism frcC lo Ribose ABC transport system, permease protein RbsC (characterized, see rationale) 36% 92% 180.6 ABC-type transporter, integral membrane subunit, component of Xylose porter (Nanavati et al. 2006). Regulated by xylose-responsive regulator XylR 37% 196.1
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) 33% 95% 180.6 ABC-type transporter, integral membrane subunit, component of Xylose porter (Nanavati et al. 2006). Regulated by xylose-responsive regulator XylR 37% 196.1
D-mannose catabolism HSERO_RS03645 lo ABC-type sugar transport system, permease component protein (characterized, see rationale) 34% 86% 177.2 ABC-type transporter, integral membrane subunit, component of Xylose porter (Nanavati et al. 2006). Regulated by xylose-responsive regulator XylR 37% 196.1
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) 33% 96% 175.6 ABC-type transporter, integral membrane subunit, component of Xylose porter (Nanavati et al. 2006). Regulated by xylose-responsive regulator XylR 37% 196.1
L-fucose catabolism HSERO_RS05255 lo ABC-type sugar transport system, permease component protein (characterized, see rationale) 33% 94% 175.6 ABC-type transporter, integral membrane subunit, component of Xylose porter (Nanavati et al. 2006). Regulated by xylose-responsive regulator XylR 37% 196.1
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) 33% 96% 175.6 ABC-type transporter, integral membrane subunit, component of Xylose porter (Nanavati et al. 2006). Regulated by xylose-responsive regulator XylR 37% 196.1
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) 33% 96% 175.6 ABC-type transporter, integral membrane subunit, component of Xylose porter (Nanavati et al. 2006). Regulated by xylose-responsive regulator XylR 37% 196.1
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) 33% 96% 175.6 ABC-type transporter, integral membrane subunit, component of Xylose porter (Nanavati et al. 2006). Regulated by xylose-responsive regulator XylR 37% 196.1
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) 33% 96% 175.6 ABC-type transporter, integral membrane subunit, component of Xylose porter (Nanavati et al. 2006). Regulated by xylose-responsive regulator XylR 37% 196.1
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) 33% 96% 175.6 ABC-type transporter, integral membrane subunit, component of Xylose porter (Nanavati et al. 2006). Regulated by xylose-responsive regulator XylR 37% 196.1
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) 33% 96% 175.6 ABC-type transporter, integral membrane subunit, component of Xylose porter (Nanavati et al. 2006). Regulated by xylose-responsive regulator XylR 37% 196.1
myo-inositol catabolism PS417_11895 lo Inositol transport system permease protein (characterized) 35% 93% 171.8 ABC-type transporter, integral membrane subunit, component of Xylose porter (Nanavati et al. 2006). Regulated by xylose-responsive regulator XylR 37% 196.1
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) 33% 92% 168.3 ABC-type transporter, integral membrane subunit, component of Xylose porter (Nanavati et al. 2006). Regulated by xylose-responsive regulator XylR 37% 196.1
D-galactose catabolism mglC lo MglC aka B2148, component of Galactose/glucose (methyl galactoside) porter (characterized) 31% 100% 162.2 ABC-type transporter, integral membrane subunit, component of Xylose porter (Nanavati et al. 2006). Regulated by xylose-responsive regulator XylR 37% 196.1
D-mannose catabolism frcC lo Fructose import permease protein FrcC (characterized) 32% 85% 157.5 ABC-type transporter, integral membrane subunit, component of Xylose porter (Nanavati et al. 2006). Regulated by xylose-responsive regulator XylR 37% 196.1
D-ribose catabolism frcC lo Fructose import permease protein FrcC (characterized) 32% 85% 157.5 ABC-type transporter, integral membrane subunit, component of Xylose porter (Nanavati et al. 2006). Regulated by xylose-responsive regulator XylR 37% 196.1
D-galactose catabolism BPHYT_RS16925 lo Arabinose ABC transporter permease (characterized, see rationale) 31% 91% 152.5 ABC-type transporter, integral membrane subunit, component of Xylose porter (Nanavati et al. 2006). Regulated by xylose-responsive regulator XylR 37% 196.1
D-fructose catabolism fruF lo Fructose import permease protein FruF (characterized) 30% 98% 147.5 ABC-type transporter, integral membrane subunit, component of Xylose porter (Nanavati et al. 2006). Regulated by xylose-responsive regulator XylR 37% 196.1
sucrose catabolism fruF lo Fructose import permease protein FruF (characterized) 30% 98% 147.5 ABC-type transporter, integral membrane subunit, component of Xylose porter (Nanavati et al. 2006). Regulated by xylose-responsive regulator XylR 37% 196.1
D-fructose catabolism fruG lo Fructose import permease protein FruG (characterized) 30% 98% 146 ABC-type transporter, integral membrane subunit, component of Xylose porter (Nanavati et al. 2006). Regulated by xylose-responsive regulator XylR 37% 196.1
sucrose catabolism fruG lo Fructose import permease protein FruG (characterized) 30% 98% 146 ABC-type transporter, integral membrane subunit, component of Xylose porter (Nanavati et al. 2006). Regulated by xylose-responsive regulator XylR 37% 196.1
D-galactose catabolism ytfT lo Galactofuranose transporter permease protein YtfT (characterized) 32% 89% 144.1 ABC-type transporter, integral membrane subunit, component of Xylose porter (Nanavati et al. 2006). Regulated by xylose-responsive regulator XylR 37% 196.1
L-arabinose catabolism araZsh lo Inner-membrane translocator (characterized, see rationale) 32% 96% 142.5 ABC-type transporter, integral membrane subunit, component of Xylose porter (Nanavati et al. 2006). Regulated by xylose-responsive regulator XylR 37% 196.1
L-arabinose catabolism araWsh lo Inner-membrane translocator (characterized, see rationale) 32% 73% 131 ABC-type transporter, integral membrane subunit, component of Xylose porter (Nanavati et al. 2006). Regulated by xylose-responsive regulator XylR 37% 196.1
D-galactose catabolism yjtF lo Inner membrane ABC transporter permease protein YjfF (characterized) 31% 89% 129 ABC-type transporter, integral membrane subunit, component of Xylose porter (Nanavati et al. 2006). Regulated by xylose-responsive regulator XylR 37% 196.1

Sequence Analysis Tools

View WP_040662387.1 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

MNEKKSNRLNQALSARGVRSVVTAVIGFLILFVVFAVASPSFRSGNNIQNLLRQIAPTLI
IGIGQGYVLITGNIDLSIGSVVGMSCMTAGTMMTKGVNPVLACLLTVLLALLVGFVNGTL
VAKMKLPSFIATLGTMTLARGLAQLVNNNHNTDFIGNDAQAFRDLFYYGEFAKLYSAVWI
AVILWVVFNFLLSKTRTGRHIYAVGSNLDAARLSGINEYRTILITYVVSAFCACVTGLIL
LASAGMGTMDAGGTYEMYAVAACVIGGISTLGGTGILAGVIAGAGIWGILQNGLQFVGAP
VALRNIIIGIIVILAVMMDVVARSSRKKIKKA

This GapMind analysis is from Sep 24 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:

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