GapMind for catabolism of small carbon sources

 

Protein AO356_05190 in Pseudomonas fluorescens FW300-N2C3

Annotation: AO356_05190 sugar ABC transporter permease

Length: 302 amino acids

Source: pseudo5_N2C3_1 in FitnessBrowser

Candidate for 12 steps in catabolism of small carbon sources

Pathway Step Score Similar to Id. Cov. Bits Other hit Other id. Other bits
D-cellobiose catabolism gtsB hi ABC transporter for D-Glucose-6-Phosphate, permease component 2 (characterized) 96% 100% 591.3 ABC transporter for D-Cellobiose and D-Salicin, permease component 2 42% 245.4
D-glucose catabolism gtsB hi ABC transporter for D-Glucose-6-Phosphate, permease component 2 (characterized) 96% 100% 591.3 ABC transporter for D-Cellobiose and D-Salicin, permease component 2 42% 245.4
lactose catabolism gtsB hi ABC transporter for D-Glucose-6-Phosphate, permease component 2 (characterized) 96% 100% 591.3 ABC transporter for D-Cellobiose and D-Salicin, permease component 2 42% 245.4
D-maltose catabolism gtsB hi ABC transporter for D-Glucose-6-Phosphate, permease component 2 (characterized) 96% 100% 591.3 ABC transporter for D-Cellobiose and D-Salicin, permease component 2 42% 245.4
sucrose catabolism gtsB hi ABC transporter for D-Glucose-6-Phosphate, permease component 2 (characterized) 96% 100% 591.3 ABC transporter for D-Cellobiose and D-Salicin, permease component 2 42% 245.4
trehalose catabolism gtsB hi ABC transporter for D-Glucose-6-Phosphate, permease component 2 (characterized) 96% 100% 591.3 ABC transporter for D-Cellobiose and D-Salicin, permease component 2 42% 245.4
D-xylose catabolism gtsB hi ABC transporter for D-Glucose-6-Phosphate, permease component 2 (characterized) 96% 100% 591.3 ABC transporter for D-Galactose and D-Glucose, permease component 1 88% 557.0
D-galactose catabolism PfGW456L13_1895 hi ABC transporter for D-Galactose and D-Glucose, permease component 1 (characterized) 88% 100% 557 ABC transporter for D-Cellobiose and D-Salicin, permease component 2 42% 245.4
D-cellobiose catabolism SMc04258 med ABC transporter for D-Cellobiose and D-Salicin, permease component 2 (characterized) 42% 96% 245.4 ABC transporter for D-Glucose-6-Phosphate, permease component 2 96% 591.3
L-arabinose catabolism xacH lo Xylose/arabinose import permease protein XacH (characterized, see rationale) 34% 89% 156.4 ABC transporter for D-Glucose-6-Phosphate, permease component 2 96% 591.3
D-mannose catabolism TT_C0327 lo Glucose transport system permease protein aka TT_C0327, component of The glucose/mannose porter TTC0326-8 plus MalK1 (ABC protein, shared with 3.A.1.1.25) (characterized) 36% 57% 127.1 ABC transporter for D-Glucose-6-Phosphate, permease component 2 96% 591.3
trehalose catabolism thuF lo Trehalose transport system permease protein SugA (characterized) 30% 94% 120.6 ABC transporter for D-Glucose-6-Phosphate, permease component 2 96% 591.3

Sequence Analysis Tools

View AO356_05190 at FitnessBrowser

PaperBLAST (search for papers about homologs of this protein)

Search CDD (the Conserved Domains Database, which includes COG and superfam)

Predict protein localization: PSORTb (Gram negative bacteria)

Predict transmembrane helices and signal peptides: Phobius

Check the SEED with FIGfam search

Fitness BLAST: loading...

Sequence

MSSVAVFSKASPFDALQRWLPKLVLAPSMFIVLVGFYGYILWTFVLSFTTSTFLPNYKWA
GLAQYARLMDNDRWWVASKNLVLFGGMFIGITLVIGVLLAVFLDQRIRREGFIRTIYLYP
MALSMIVTGTAWKWLLNPGMGLDKLLRDWGWEGFRLDWLIDPDRVVYCLVIAAVWQASGF
IMAMFLAGLRGVDQSIIRAAQIDGASMPRIYWKVVLPSLRPVFFSAVMILAHIAIKSFDL
VAAMTAGGPGYSSDLPAMFMYSFTFSRGQMGMGSASAILMLGAILAIIVPYLYSELRTKR
HD

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 paper from 2022 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