GapMind for catabolism of small carbon sources

 

Protein GFF2674 in Pseudomonas simiae WCS417

Annotation: PS417_13640 ribose ABC transporter permease

Length: 325 amino acids

Source: WCS417 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-fructose catabolism frcC hi Ribose ABC transport system, permease protein RbsC (characterized, see rationale) 74% 93% 456.4 EryF aka RB0338, component of The erythritol permease, EryEFG (Geddes et al., 2010) (probably orthologous to 3.A.1.2.16) 41% 229.6
sucrose catabolism frcC hi Ribose ABC transport system, permease protein RbsC (characterized, see rationale) 74% 93% 456.4 EryF aka RB0338, component of The erythritol permease, EryEFG (Geddes et al., 2010) (probably orthologous to 3.A.1.2.16) 41% 229.6
D-mannose catabolism HSERO_RS03645 hi ABC-type sugar transport system, permease component protein (characterized, see rationale) 54% 94% 328.2 EryF aka RB0338, component of The erythritol permease, EryEFG (Geddes et al., 2010) (probably orthologous to 3.A.1.2.16) 41% 229.6
xylitol catabolism PS417_12060 hi ABC transporter permease; SubName: Full=Monosaccharide ABC transporter membrane protein, CUT2 family; SubName: Full=Sugar ABC transporter permease (characterized, see rationale) 47% 97% 249.2 EryF aka RB0338, component of The erythritol permease, EryEFG (Geddes et al., 2010) (probably orthologous to 3.A.1.2.16) 41% 229.6
L-fucose catabolism HSERO_RS05255 med ABC-type sugar transport system, permease component protein (characterized, see rationale) 45% 87% 231.9 EryF aka RB0338, component of The erythritol permease, EryEFG (Geddes et al., 2010) (probably orthologous to 3.A.1.2.16) 41% 229.6
D-ribose catabolism rbsC med ABC-type transporter, integral membrane subunit, component of D-ribose porter (Nanavati et al., 2006). Induced by ribose (characterized) 44% 91% 229.2 EryF aka RB0338, component of The erythritol permease, EryEFG (Geddes et al., 2010) (probably orthologous to 3.A.1.2.16) 41% 229.6
D-cellobiose catabolism mglC med 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) 41% 99% 216.5 EryF aka RB0338, component of The erythritol permease, EryEFG (Geddes et al., 2010) (probably orthologous to 3.A.1.2.16) 41% 229.6
D-glucose catabolism mglC med 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) 41% 99% 216.5 EryF aka RB0338, component of The erythritol permease, EryEFG (Geddes et al., 2010) (probably orthologous to 3.A.1.2.16) 41% 229.6
lactose catabolism mglC med 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) 41% 99% 216.5 EryF aka RB0338, component of The erythritol permease, EryEFG (Geddes et al., 2010) (probably orthologous to 3.A.1.2.16) 41% 229.6
D-maltose catabolism mglC med 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) 41% 99% 216.5 EryF aka RB0338, component of The erythritol permease, EryEFG (Geddes et al., 2010) (probably orthologous to 3.A.1.2.16) 41% 229.6
sucrose catabolism mglC med 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) 41% 99% 216.5 EryF aka RB0338, component of The erythritol permease, EryEFG (Geddes et al., 2010) (probably orthologous to 3.A.1.2.16) 41% 229.6
trehalose catabolism mglC med 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) 41% 99% 216.5 EryF aka RB0338, component of The erythritol permease, EryEFG (Geddes et al., 2010) (probably orthologous to 3.A.1.2.16) 41% 229.6
D-xylose catabolism xylH med 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) 41% 99% 216.5 EryF aka RB0338, component of The erythritol permease, EryEFG (Geddes et al., 2010) (probably orthologous to 3.A.1.2.16) 41% 229.6
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% 90% 212.2 EryF aka RB0338, component of The erythritol permease, EryEFG (Geddes et al., 2010) (probably orthologous to 3.A.1.2.16) 41% 229.6
myo-inositol catabolism PS417_11895 lo Inositol transport system permease protein (characterized) 40% 99% 215.7 EryF aka RB0338, component of The erythritol permease, EryEFG (Geddes et al., 2010) (probably orthologous to 3.A.1.2.16) 41% 229.6
D-galactose catabolism mglC lo MglC aka B2148, component of Galactose/glucose (methyl galactoside) porter (characterized) 38% 96% 201.8 EryF aka RB0338, component of The erythritol permease, EryEFG (Geddes et al., 2010) (probably orthologous to 3.A.1.2.16) 41% 229.6
D-mannose catabolism frcC lo Fructose import permease protein FrcC (characterized) 37% 84% 192.2 EryF aka RB0338, component of The erythritol permease, EryEFG (Geddes et al., 2010) (probably orthologous to 3.A.1.2.16) 41% 229.6
D-ribose catabolism frcC lo Fructose import permease protein FrcC (characterized) 37% 84% 192.2 EryF aka RB0338, component of The erythritol permease, EryEFG (Geddes et al., 2010) (probably orthologous to 3.A.1.2.16) 41% 229.6
D-fructose catabolism fruF lo Fructose import permease protein FruF (characterized) 35% 81% 176.8 EryF aka RB0338, component of The erythritol permease, EryEFG (Geddes et al., 2010) (probably orthologous to 3.A.1.2.16) 41% 229.6
sucrose catabolism fruF lo Fructose import permease protein FruF (characterized) 35% 81% 176.8 EryF aka RB0338, component of The erythritol permease, EryEFG (Geddes et al., 2010) (probably orthologous to 3.A.1.2.16) 41% 229.6
L-fucose catabolism BPHYT_RS34240 lo Monosaccharide-transporting ATPase; EC 3.6.3.17; Flags: Precursor (characterized, see rationale) 35% 91% 166.4 EryF aka RB0338, component of The erythritol permease, EryEFG (Geddes et al., 2010) (probably orthologous to 3.A.1.2.16) 41% 229.6
L-rhamnose catabolism BPHYT_RS34240 lo Monosaccharide-transporting ATPase; EC 3.6.3.17; Flags: Precursor (characterized, see rationale) 35% 91% 166.4 EryF aka RB0338, component of The erythritol permease, EryEFG (Geddes et al., 2010) (probably orthologous to 3.A.1.2.16) 41% 229.6
2'-deoxyinosine catabolism H281DRAFT_01115 lo deoxynucleoside transporter, permease component 1 (characterized) 31% 87% 120.6 EryF aka RB0338, component of The erythritol permease, EryEFG (Geddes et al., 2010) (probably orthologous to 3.A.1.2.16) 41% 229.6

Sequence Analysis Tools

View GFF2674 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

MAELNIATTNKAERARELMRTVGMLPVLILLLVGFALASENFLTMQNLSIISQQASVNVV
LAAGMTFVILTAGIDLSVGAILAASAVVALQASMSPQFGMFGIAAGIGFGLLLGLVNGGL
IAFMRLPPFIVTLGALTAMRGLARLLADDKTVFNPDLPFAFIGNDSLLGVPWLVIIAVAV
VALSWFILRRTVMGVQIYSVGGNPEAARLSGIKVWKVLLFVYAMSGALAGLGAVMSASRL
FAANGLQLGQSYELDAIAAVILGGTSFTGGVGTIGGTLIGALIIAVLTNGLVLLGVSDIW
QYIIKGIVIIGAVALDRYRQSGART

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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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 preprint 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