GapMind for catabolism of small carbon sources

 

Protein WP_108358583.1 in Limnohabitans curvus MWH-C5

Annotation: NCBI__GCF_003063475.1:WP_108358583.1

Length: 289 amino acids

Source: GCF_003063475.1 in NCBI

Candidate for 17 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 Sugar ABC transporter permease (characterized, see rationale) 74% 100% 441.4 ABC transporter for D-Cellobiose and D-Salicin, permease component 1 49% 294.7
D-glucose catabolism gtsC hi Sugar ABC transporter permease (characterized, see rationale) 74% 100% 441.4 ABC transporter for D-Cellobiose and D-Salicin, permease component 1 49% 294.7
lactose catabolism gtsC hi Sugar ABC transporter permease (characterized, see rationale) 74% 100% 441.4 ABC transporter for D-Cellobiose and D-Salicin, permease component 1 49% 294.7
D-maltose catabolism gtsC hi Sugar ABC transporter permease (characterized, see rationale) 74% 100% 441.4 ABC transporter for D-Cellobiose and D-Salicin, permease component 1 49% 294.7
sucrose catabolism gtsC hi Sugar ABC transporter permease (characterized, see rationale) 74% 100% 441.4 ABC transporter for D-Cellobiose and D-Salicin, permease component 1 49% 294.7
trehalose catabolism gtsC hi Sugar ABC transporter permease (characterized, see rationale) 74% 100% 441.4 ABC transporter for D-Cellobiose and D-Salicin, permease component 1 49% 294.7
D-galactose catabolism PfGW456L13_1896 hi ABC transporter for D-Galactose and D-Glucose, permease component 2 (characterized) 59% 96% 336.7 ABC transporter for D-Cellobiose and D-Salicin, permease component 1 49% 294.7
D-xylose catabolism gtsC med ABC transporter for D-Glucose-6-Phosphate, permease component 1 (characterized) 60% 96% 339.7 ABC transporter for D-Galactose and D-Glucose, permease component 2 59% 336.7
D-cellobiose catabolism SMc04257 med ABC transporter for D-Cellobiose and D-Salicin, permease component 1 (characterized) 49% 92% 294.7 GtsC (GLcG), component of Glucose porter, GtsABCD 62% 344.0
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) 47% 100% 263.1 GtsC (GLcG), component of Glucose porter, GtsABCD 62% 344.0
L-arabinose catabolism araU lo AraU, component of Arabinose, fructose, xylose porter (characterized) 32% 96% 146.4 GtsC (GLcG), component of Glucose porter, GtsABCD 62% 344.0
D-fructose catabolism araU lo AraU, component of Arabinose, fructose, xylose porter (characterized) 32% 96% 146.4 GtsC (GLcG), component of Glucose porter, GtsABCD 62% 344.0
sucrose catabolism araU lo AraU, component of Arabinose, fructose, xylose porter (characterized) 32% 96% 146.4 GtsC (GLcG), component of Glucose porter, GtsABCD 62% 344.0
D-xylose catabolism araU lo AraU, component of Arabinose, fructose, xylose porter (characterized) 32% 96% 146.4 GtsC (GLcG), component of Glucose porter, GtsABCD 62% 344.0
D-maltose catabolism aglG lo ABC transporter for D-Maltose and D-Trehalose, permease component 2 (characterized) 33% 61% 122.9 GtsC (GLcG), component of Glucose porter, GtsABCD 62% 344.0
sucrose catabolism aglG lo ABC transporter for D-Maltose and D-Trehalose, permease component 2 (characterized) 33% 61% 122.9 GtsC (GLcG), component of Glucose porter, GtsABCD 62% 344.0
trehalose catabolism aglG lo ABC transporter for D-Maltose and D-Trehalose, permease component 2 (characterized) 33% 61% 122.9 GtsC (GLcG), component of Glucose porter, GtsABCD 62% 344.0

Sequence Analysis Tools

View WP_108358583.1 at NCBI

Find papers: PaperBLAST

Find functional residues: SitesBLAST

Search for conserved domains

Find the best match in UniProt

Compare to protein structures

Predict transmenbrane helices: Phobius

Predict protein localization: PSORTb

Find homologs in fast.genomics

Fitness BLAST: loading...

Sequence

MSTKFFSIHILSRAVLYATLLIGAVFFLAPLYVMVVTSLKDADEIRQNSLVSLPGGVNLD
AWRLAWDSACTGAQCSGLEPFFWNSVWMTIPAVLISTTWGALNGYVLSLWKFRGSETLFA
FLLFGVFMPFQVVLLPMSQVLGWLGLSSSIMGLILVHLLAGLPSTSLFFRNYYAAVPKDL
LNAARMDGAGFWMIFFRIIVPMSTPIVMVTLIWQFTQIWNDFLFGVAFSGADSKPITVGL
NNLANTTSSVKAYNVDMAAALIAGLPTMLVYVVAGRYFVRGLTAGAVKG

This GapMind analysis is from Sep 24 2021. The underlying query database was built on Sep 17 2021.

Links

Downloads

Related tools

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