GapMind for catabolism of small carbon sources

 

Protein AO353_20825 in Pseudomonas fluorescens FW300-N2E3

Annotation: AO353_20825 ABC transporter permease

Length: 325 amino acids

Source: pseudo3_N2E3 in FitnessBrowser

Candidate for 26 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) 96% 100% 589.3 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) 37% 198.7
L-fucose catabolism HSERO_RS05255 med ABC-type sugar transport system, permease component protein (characterized, see rationale) 37% 95% 206.1 Ribose import permease protein RbsC 39% 199.9
D-fructose catabolism frcC med Ribose ABC transport system, permease protein RbsC (characterized, see rationale) 39% 90% 201.4 Ribose import permease protein RbsC 39% 199.9
sucrose catabolism frcC med Ribose ABC transport system, permease protein RbsC (characterized, see rationale) 39% 90% 201.4 Ribose import permease protein RbsC 39% 199.9
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) 38% 98% 190.3 Ribose import permease protein RbsC 39% 199.9
D-mannose catabolism HSERO_RS03645 lo ABC-type sugar transport system, permease component protein (characterized, see rationale) 37% 87% 188.7 Ribose import permease protein RbsC 39% 199.9
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% 177.6 Ribose import permease protein RbsC 39% 199.9
myo-inositol catabolism PS417_11895 lo Inositol transport system permease protein (characterized) 37% 93% 172.6 Ribose import permease protein RbsC 39% 199.9
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) 35% 96% 172.2 Ribose import permease protein RbsC 39% 199.9
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) 35% 96% 172.2 Ribose import permease protein RbsC 39% 199.9
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) 35% 96% 172.2 Ribose import permease protein RbsC 39% 199.9
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) 35% 96% 172.2 Ribose import permease protein RbsC 39% 199.9
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) 35% 96% 172.2 Ribose import permease protein RbsC 39% 199.9
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) 35% 96% 172.2 Ribose import permease protein RbsC 39% 199.9
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) 35% 96% 172.2 Ribose import permease protein RbsC 39% 199.9
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% 166 Ribose import permease protein RbsC 39% 199.9
D-galactose catabolism BPHYT_RS16925 lo Monosaccharide-transporting ATPase; EC 3.6.3.17 (characterized, see rationale) 32% 90% 158.7 Ribose import permease protein RbsC 39% 199.9
D-fructose catabolism fruF lo Fructose import permease protein FruF (characterized) 31% 85% 147.9 Ribose import permease protein RbsC 39% 199.9
sucrose catabolism fruF lo Fructose import permease protein FruF (characterized) 31% 85% 147.9 Ribose import permease protein RbsC 39% 199.9
D-galactose catabolism ytfT lo Galactofuranose transporter permease protein YtfT (characterized) 31% 88% 144.1 Ribose import permease protein RbsC 39% 199.9
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% 142.9 Ribose import permease protein RbsC 39% 199.9
L-arabinose catabolism araWsh lo Inner-membrane translocator (characterized, see rationale) 31% 79% 139 Ribose import permease protein RbsC 39% 199.9
D-fructose catabolism fruG lo Fructose import permease protein FruG (characterized) 30% 88% 126.3 Ribose import permease protein RbsC 39% 199.9
sucrose catabolism fruG lo Fructose import permease protein FruG (characterized) 30% 88% 126.3 Ribose import permease protein RbsC 39% 199.9
D-galactose catabolism yjtF lo Inner membrane ABC transporter permease protein YjfF (characterized) 33% 86% 125.9 Ribose import permease protein RbsC 39% 199.9
myo-inositol catabolism PGA1_c07310 lo Inositol transport system permease protein (characterized) 30% 90% 122.9 Ribose import permease protein RbsC 39% 199.9

Sequence Analysis Tools

View AO353_20825 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

MITALSAGKRSSNFYGLGTYLGLAGALLAMIALFSVLSSHFLSYDTFSTLANQIPDLMVL
AVGMTFVLIIGGIDLSVGSVLALAGSTVSVAILGWGWSVLPAALLGMAAAAVAGTITGSI
TVAWRIPSFIVSLGVLEMARGVAYQMTGSRTAYIGDAFAWLSNPITFGISPSFIIALLVI
FIAQAVLTRTVFGRYLIGIGTNEEAVRLAGINPKPYKILVFSLMGLLAGIAALFQISRLE
AADPNAGSGLELQVIAAVVIGGTSLMGGRGSVISTFFGVLIISVLAAGLAQIGATEPTKR
IITGAVIVVAVVLDTYRSQRASRRS

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 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