GapMind for catabolism of small carbon sources

 

Protein PfGW456L13_1896 in Pseudomonas fluorescens GW456-L13

Annotation: Glucose ABC transport system, inner membrane component 2

Length: 281 amino acids

Source: pseudo13_GW456_L13 in FitnessBrowser

Candidate for 24 steps in catabolism of small carbon sources

Pathway Step Score Similar to Id. Cov. Bits Other hit Other id. Other bits
D-cellobiose catabolism gtsC hi ABC transporter for D-Galactose and D-Glucose, permease component 2 (characterized) 100% 100% 560.1 ABC transporter for D-Cellobiose and D-Salicin, permease component 1 49% 289.7
D-galactose catabolism PfGW456L13_1896 hi ABC transporter for D-Galactose and D-Glucose, permease component 2 (characterized) 100% 100% 560.1 ABC transporter for D-Cellobiose and D-Salicin, permease component 1 49% 289.7
D-glucose catabolism gtsC hi ABC transporter for D-Galactose and D-Glucose, permease component 2 (characterized) 100% 100% 560.1 ABC transporter for D-Cellobiose and D-Salicin, permease component 1 49% 289.7
lactose catabolism gtsC hi ABC transporter for D-Galactose and D-Glucose, permease component 2 (characterized) 100% 100% 560.1 ABC transporter for D-Cellobiose and D-Salicin, permease component 1 49% 289.7
D-maltose catabolism gtsC hi ABC transporter for D-Galactose and D-Glucose, permease component 2 (characterized) 100% 100% 560.1 ABC transporter for D-Cellobiose and D-Salicin, permease component 1 49% 289.7
sucrose catabolism gtsC hi ABC transporter for D-Galactose and D-Glucose, permease component 2 (characterized) 100% 100% 560.1 ABC transporter for D-Cellobiose and D-Salicin, permease component 1 49% 289.7
trehalose catabolism gtsC hi ABC transporter for D-Galactose and D-Glucose, permease component 2 (characterized) 100% 100% 560.1 ABC transporter for D-Cellobiose and D-Salicin, permease component 1 49% 289.7
D-xylose catabolism gtsC med ABC transporter for D-Glucose-6-Phosphate, permease component 1 (characterized) 85% 100% 493 ABC transporter for D-Galactose and D-Glucose, permease component 2 100% 560.1
D-cellobiose catabolism SMc04257 med ABC transporter for D-Cellobiose and D-Salicin, permease component 1 (characterized) 49% 92% 289.7 ABC transporter for D-Galactose and D-Glucose, permease component 2 100% 560.1
D-mannose catabolism TT_C0326 med Sugar transport system permease protein aka TT_C0326, component of The glucose/mannose porter TTC0326-8 plus MalK1 (ABC protein, shared with 3.A.1.1.25) (characterized) 49% 100% 264.6 ABC transporter for D-Galactose and D-Glucose, permease component 2 100% 560.1
L-arabinose catabolism xacI lo Xylose/arabinose import permease protein XacI (characterized, see rationale) 33% 94% 161.4 ABC transporter for D-Galactose and D-Glucose, permease component 2 100% 560.1
N-acetyl-D-glucosamine catabolism SMc02871 lo ABC transporter for N-Acetyl-D-glucosamine, permease protein 2 (characterized) 30% 100% 139.4 ABC transporter for D-Galactose and D-Glucose, permease component 2 100% 560.1
D-glucosamine (chitosamine) catabolism SMc02871 lo ABC transporter for N-Acetyl-D-glucosamine, permease protein 2 (characterized) 30% 100% 139.4 ABC transporter for D-Galactose and D-Glucose, permease component 2 100% 560.1
D-cellobiose catabolism msdB2 lo Binding-protein-dependent transport systems inner membrane component (characterized, see rationale) 31% 93% 127.9 ABC transporter for D-Galactose and D-Glucose, permease component 2 100% 560.1
D-maltose catabolism aglG lo ABC transporter for D-Maltose and D-Trehalose, permease component 2 (characterized) 33% 57% 119 ABC transporter for D-Galactose and D-Glucose, permease component 2 100% 560.1
sucrose catabolism aglG lo ABC transporter for D-Maltose and D-Trehalose, permease component 2 (characterized) 33% 57% 119 ABC transporter for D-Galactose and D-Glucose, permease component 2 100% 560.1
trehalose catabolism aglG lo ABC transporter for D-Maltose and D-Trehalose, permease component 2 (characterized) 33% 57% 119 ABC transporter for D-Galactose and D-Glucose, permease component 2 100% 560.1
D-cellobiose catabolism aglG' lo Inner membrane ABC transporter permease protein (characterized, see rationale) 31% 54% 115.5 ABC transporter for D-Galactose and D-Glucose, permease component 2 100% 560.1
D-glucose catabolism aglG' lo Inner membrane ABC transporter permease protein (characterized, see rationale) 31% 54% 115.5 ABC transporter for D-Galactose and D-Glucose, permease component 2 100% 560.1
lactose catabolism aglG' lo Inner membrane ABC transporter permease protein (characterized, see rationale) 31% 54% 115.5 ABC transporter for D-Galactose and D-Glucose, permease component 2 100% 560.1
D-maltose catabolism aglG' lo Inner membrane ABC transporter permease protein (characterized, see rationale) 31% 54% 115.5 ABC transporter for D-Galactose and D-Glucose, permease component 2 100% 560.1
sucrose catabolism aglG' lo Inner membrane ABC transporter permease protein (characterized, see rationale) 31% 54% 115.5 ABC transporter for D-Galactose and D-Glucose, permease component 2 100% 560.1
trehalose catabolism aglG' lo Inner membrane ABC transporter permease protein (characterized, see rationale) 31% 54% 115.5 ABC transporter for D-Galactose and D-Glucose, permease component 2 100% 560.1
D-cellobiose catabolism cebG lo CBP protein aka CebG, component of The cellobiose/cellotriose (and possibly higher cellooligosaccharides), CebEFGMsiK [MsiK functions to energize several ABC transporters including those for maltose/maltotriose and trehalose] (characterized) 30% 95% 97.1 ABC transporter for D-Galactose and D-Glucose, permease component 2 100% 560.1

Sequence Analysis Tools

View PfGW456L13_1896 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

MTNQLGKSGISFSRIAIYATLLLAAAVYLIPLVVMLLTSFKSPEDIRTGNLLSWPTVIDG
IGWIKAWDVVGGYFWNSVKITVPAVLISTFIGAMNGYVLSMWRFRGSQLFFGLLLFGCFL
PFQTVLLPASFTLGKFGLANTTTGLVLVHVVYGLAFTTLFFRNYYVSIPDALVKAARLDG
AGFFTIFLKILLPMSIPIVMVCLIWQFTQIWNDFLFGVVFASGDAQPITVALNNLVNTST
GAKEYNVDMAAAMIAGLPTLLVYIFAGKYFLRGLTSGAVKG

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