GapMind for catabolism of small carbon sources

 

Protein H281DRAFT_02632 in Paraburkholderia bryophila 376MFSha3.1

Annotation: H281DRAFT_02632 carbohydrate ABC transporter membrane protein 2, CUT1 family

Length: 283 amino acids

Source: Burk376 in FitnessBrowser

Candidate for 21 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 med GtsC (GLcG), component of Glucose porter, GtsABCD (characterized) 35% 99% 177.6 N-Acetyl-D-glucosamine ABC transport system, permease component 2 32% 161.4
D-glucose catabolism gtsC med GtsC (GLcG), component of Glucose porter, GtsABCD (characterized) 35% 99% 177.6 N-Acetyl-D-glucosamine ABC transport system, permease component 2 32% 161.4
lactose catabolism gtsC med GtsC (GLcG), component of Glucose porter, GtsABCD (characterized) 35% 99% 177.6 N-Acetyl-D-glucosamine ABC transport system, permease component 2 32% 161.4
D-maltose catabolism gtsC med GtsC (GLcG), component of Glucose porter, GtsABCD (characterized) 35% 99% 177.6 N-Acetyl-D-glucosamine ABC transport system, permease component 2 32% 161.4
sucrose catabolism gtsC med GtsC (GLcG), component of Glucose porter, GtsABCD (characterized) 35% 99% 177.6 N-Acetyl-D-glucosamine ABC transport system, permease component 2 32% 161.4
trehalose catabolism gtsC med GtsC (GLcG), component of Glucose porter, GtsABCD (characterized) 35% 99% 177.6 N-Acetyl-D-glucosamine ABC transport system, permease component 2 32% 161.4
D-galactose catabolism PfGW456L13_1896 med ABC transporter for D-Galactose and D-Glucose, permease component 2 (characterized) 36% 96% 174.5 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) 34% 169.5
D-mannose catabolism TT_C0326 lo 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) 34% 98% 169.5 GtsC (GLcG), component of Glucose porter, GtsABCD 35% 177.6
D-xylose catabolism gtsC lo ABC transporter for D-Glucose-6-Phosphate, permease component 1 (characterized) 34% 96% 169.5 ABC transporter for D-Galactose and D-Glucose, permease component 2 36% 174.5
N-acetyl-D-glucosamine catabolism SMc02871 lo N-Acetyl-D-glucosamine ABC transport system, permease component 2 (characterized) 32% 98% 161.4 GtsC (GLcG), component of Glucose porter, GtsABCD 35% 177.6
D-glucosamine (chitosamine) catabolism SMc02871 lo N-Acetyl-D-glucosamine ABC transport system, permease component 2 (characterized) 32% 98% 161.4 GtsC (GLcG), component of Glucose porter, GtsABCD 35% 177.6
D-maltose catabolism thuG lo ABC transporter for D-Trehalose, permease component 2 (characterized) 33% 98% 161 GtsC (GLcG), component of Glucose porter, GtsABCD 35% 177.6
sucrose catabolism thuG lo ABC transporter for D-Trehalose, permease component 2 (characterized) 33% 98% 161 GtsC (GLcG), component of Glucose porter, GtsABCD 35% 177.6
trehalose catabolism thuG lo ABC transporter for D-Trehalose, permease component 2 (characterized) 33% 98% 161 GtsC (GLcG), component of Glucose porter, GtsABCD 35% 177.6
D-cellobiose catabolism SMc04257 lo ABC transporter for D-Cellobiose and D-Salicin, permease component 1 (characterized) 33% 90% 153.7 GtsC (GLcG), component of Glucose porter, GtsABCD 35% 177.6
N-acetyl-D-glucosamine catabolism ngcG lo NgcG, component of N-Acetylglucosamine/N,N'-diacetyl chitobiose porter (NgcK (C) not identified) (characterized) 33% 84% 152.1 GtsC (GLcG), component of Glucose porter, GtsABCD 35% 177.6
D-glucosamine (chitosamine) catabolism ngcG lo NgcG, component of N-Acetylglucosamine/N,N'-diacetyl chitobiose porter (NgcK (C) not identified) (characterized) 33% 84% 152.1 GtsC (GLcG), component of Glucose porter, GtsABCD 35% 177.6
D-maltose catabolism aglG lo ABC transporter for D-Maltose and D-Trehalose, permease component 2 (characterized) 35% 62% 139.4 GtsC (GLcG), component of Glucose porter, GtsABCD 35% 177.6
sucrose catabolism aglG lo ABC transporter for D-Maltose and D-Trehalose, permease component 2 (characterized) 35% 62% 139.4 GtsC (GLcG), component of Glucose porter, GtsABCD 35% 177.6
trehalose catabolism aglG lo ABC transporter for D-Maltose and D-Trehalose, permease component 2 (characterized) 35% 62% 139.4 GtsC (GLcG), component of Glucose porter, GtsABCD 35% 177.6
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) 31% 94% 127.5 GtsC (GLcG), component of Glucose porter, GtsABCD 35% 177.6

Sequence Analysis Tools

View H281DRAFT_02632 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

MYPLPVEHWKPWSRTLYKASLPVALFVWLLPMLAVLITSIRSSDELSQGDYWAWPKHFAL
IDNYGAALTQTPMLHYFANSMLITVPSVLGAILLASMAGFALATYRFRGNIVVLFTFVAG
NFVPVQILMIPVRDMALKVGLFNTVWALIIFHVAFQTGFCTLFLRNFIKQLPFELIEAAR
VEGASEWTIYARIVLPLIRPALAALGILVFTFVWNDYFWALCLTQGDDAAPITVGVAALK
GQWTTAWNLVAAGSVLAALPSVLMFFAMQKHFVAGLTFGASKG

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