GapMind for catabolism of small carbon sources

 

Protein PfGW456L13_3910 in Pseudomonas fluorescens GW456-L13

Annotation: FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_3910

Length: 325 amino acids

Source: pseudo13_GW456_L13 in FitnessBrowser

Candidate for 22 steps in catabolism of small carbon sources

Pathway Step Score Similar to Id. Cov. Bits Other hit Other id. Other bits
D-ribose catabolism rbsC hi ABC transporter permease (characterized, see rationale) 97% 100% 601.3 Erythritol permease, component of ABC transporter, component of The erythritol uptake permease, EryEFG (Yost et al., 2006) (probably orthologous to 3.A.1.2.11) 38% 194.1
D-fructose catabolism frcC hi Ribose ABC transport system, permease protein RbsC (characterized, see rationale) 41% 91% 205.7 Ribose import permease protein RbsC 36% 195.7
sucrose catabolism frcC hi Ribose ABC transport system, permease protein RbsC (characterized, see rationale) 41% 91% 205.7 Ribose import permease protein RbsC 36% 195.7
L-fucose catabolism HSERO_RS05255 med ABC-type sugar transport system, permease component protein (characterized, see rationale) 39% 95% 210.7 Ribose import permease protein RbsC 36% 195.7
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) 37% 92% 188 Ribose import permease protein RbsC 36% 195.7
D-mannose catabolism HSERO_RS03645 lo ABC-type sugar transport system, permease component protein (characterized, see rationale) 37% 87% 186.8 Ribose import permease protein RbsC 36% 195.7
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) 37% 91% 177.9 Ribose import permease protein RbsC 36% 195.7
myo-inositol catabolism PS417_11895 lo Inositol transport system permease protein (characterized) 36% 94% 175.6 Ribose import permease protein RbsC 36% 195.7
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) 34% 96% 172.2 Ribose import permease protein RbsC 36% 195.7
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) 34% 96% 172.2 Ribose import permease protein RbsC 36% 195.7
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) 34% 96% 172.2 Ribose import permease protein RbsC 36% 195.7
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) 34% 96% 172.2 Ribose import permease protein RbsC 36% 195.7
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) 34% 96% 172.2 Ribose import permease protein RbsC 36% 195.7
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) 34% 96% 172.2 Ribose import permease protein RbsC 36% 195.7
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) 34% 96% 172.2 Ribose import permease protein RbsC 36% 195.7
D-xylose catabolism xylF_Tm lo ABC-type transporter, integral membrane subunit, component of Xylose porter (Nanavati et al. 2006). Regulated by xylose-responsive regulator XylR (characterized) 37% 96% 165.2 Ribose import permease protein RbsC 36% 195.7
D-galactose catabolism BPHYT_RS16925 lo Monosaccharide-transporting ATPase; EC 3.6.3.17 (characterized, see rationale) 31% 88% 153.7 Ribose import permease protein RbsC 36% 195.7
D-fructose catabolism fruF lo Fructose import permease protein FruF (characterized) 31% 85% 147.1 Ribose import permease protein RbsC 36% 195.7
sucrose catabolism fruF lo Fructose import permease protein FruF (characterized) 31% 85% 147.1 Ribose import permease protein RbsC 36% 195.7
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) 32% 90% 142.1 Ribose import permease protein RbsC 36% 195.7
L-arabinose catabolism araWsh lo Inner-membrane translocator (characterized, see rationale) 31% 80% 136.3 Ribose import permease protein RbsC 36% 195.7
D-galactose catabolism yjtF lo Inner membrane ABC transporter permease protein YjfF (characterized) 31% 86% 120.9 Ribose import permease protein RbsC 36% 195.7

Sequence Analysis Tools

View PfGW456L13_3910 at FitnessBrowser

Find papers: PaperBLAST

Find functional residues: SitesBLAST

Search for conserved domains

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Predict transmenbrane helices: Phobius

Predict protein localization: PSORTb

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Sequence

MNTASYAGKRSGNFYGLGTYLGLAGALLAMIVLFSVLSSHFLSYDTFSTLANQIPDLMVL
AVGMTFVLIIGGIDLSVGSVLALAASTVSVAILGWGWGVLPAALLGMAVAALAGTITGSI
TVAWRIPSFIVSLGVLEMARGVAYQMTGSRTAYIGDAFAWLSNPIAFGISPSFIIALLII
FVAQAVLTRTVFGRYLIGIGTNEEAVRLAGINPKPYKVLVFSLMGLLAGVAALFQISRLE
AADPNAGSGLELQVIAAVVIGGTSLMGGRGSVISTFFGVLIISVLAAGLAQIGATEPTKR
IITGAVIVVAVVLDTYRSQRASRRT

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:

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