GapMind for catabolism of small carbon sources

 

Protein H281DRAFT_03232 in Paraburkholderia bryophila 376MFSha3.1

Annotation: H281DRAFT_03232 carbohydrate ABC transporter membrane protein 2, CUT1 family

Length: 283 amino acids

Source: Burk376 in FitnessBrowser

Candidate for 25 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) 37% 99% 192.6 ABC transporter for D-Cellobiose and D-Salicin, permease component 1 35% 170.2
D-glucose catabolism gtsC med GtsC (GLcG), component of Glucose porter, GtsABCD (characterized) 37% 99% 192.6 ABC transporter for D-Cellobiose and D-Salicin, permease component 1 35% 170.2
lactose catabolism gtsC med GtsC (GLcG), component of Glucose porter, GtsABCD (characterized) 37% 99% 192.6 ABC transporter for D-Cellobiose and D-Salicin, permease component 1 35% 170.2
D-maltose catabolism gtsC med GtsC (GLcG), component of Glucose porter, GtsABCD (characterized) 37% 99% 192.6 ABC transporter for D-Cellobiose and D-Salicin, permease component 1 35% 170.2
sucrose catabolism gtsC med GtsC (GLcG), component of Glucose porter, GtsABCD (characterized) 37% 99% 192.6 ABC transporter for D-Cellobiose and D-Salicin, permease component 1 35% 170.2
trehalose catabolism gtsC med GtsC (GLcG), component of Glucose porter, GtsABCD (characterized) 37% 99% 192.6 ABC transporter for D-Cellobiose and D-Salicin, permease component 1 35% 170.2
D-galactose catabolism PfGW456L13_1896 med ABC transporter for D-Galactose and D-Glucose, permease component 2 (characterized) 37% 93% 183.7 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) 35% 174.1
D-xylose catabolism gtsC lo ABC transporter for D-Glucose-6-Phosphate, permease component 1 (characterized) 35% 98% 181.4 ABC transporter for D-Galactose and D-Glucose, permease component 2 37% 183.7
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) 36% 94% 174.1 GtsC (GLcG), component of Glucose porter, GtsABCD 37% 192.6
D-cellobiose catabolism SMc04257 lo ABC transporter for D-Cellobiose and D-Salicin, permease component 1 (characterized) 35% 89% 170.2 GtsC (GLcG), component of Glucose porter, GtsABCD 37% 192.6
N-acetyl-D-glucosamine catabolism SMc02871 lo N-Acetyl-D-glucosamine ABC transport system, permease component 2 (characterized) 33% 92% 158.3 GtsC (GLcG), component of Glucose porter, GtsABCD 37% 192.6
D-glucosamine (chitosamine) catabolism SMc02871 lo N-Acetyl-D-glucosamine ABC transport system, permease component 2 (characterized) 33% 92% 158.3 GtsC (GLcG), component of Glucose porter, GtsABCD 37% 192.6
N-acetyl-D-glucosamine catabolism ngcG lo NgcG, component of N-Acetylglucosamine/N,N'-diacetyl chitobiose porter (NgcK (C) not identified) (characterized) 32% 85% 151.4 GtsC (GLcG), component of Glucose porter, GtsABCD 37% 192.6
D-glucosamine (chitosamine) catabolism ngcG lo NgcG, component of N-Acetylglucosamine/N,N'-diacetyl chitobiose porter (NgcK (C) not identified) (characterized) 32% 85% 151.4 GtsC (GLcG), component of Glucose porter, GtsABCD 37% 192.6
lactose catabolism lacG lo LacG, component of Lactose porter (characterized) 31% 94% 144.1 GtsC (GLcG), component of Glucose porter, GtsABCD 37% 192.6
D-maltose catabolism aglG lo ABC transporter for D-Maltose and D-Trehalose, permease component 2 (characterized) 36% 62% 143.3 GtsC (GLcG), component of Glucose porter, GtsABCD 37% 192.6
sucrose catabolism aglG lo ABC transporter for D-Maltose and D-Trehalose, permease component 2 (characterized) 36% 62% 143.3 GtsC (GLcG), component of Glucose porter, GtsABCD 37% 192.6
trehalose catabolism aglG lo ABC transporter for D-Maltose and D-Trehalose, permease component 2 (characterized) 36% 62% 143.3 GtsC (GLcG), component of Glucose porter, GtsABCD 37% 192.6
D-cellobiose catabolism aglG' lo Inner membrane ABC transporter permease protein (characterized, see rationale) 32% 61% 120.6 GtsC (GLcG), component of Glucose porter, GtsABCD 37% 192.6
D-glucose catabolism aglG' lo Inner membrane ABC transporter permease protein (characterized, see rationale) 32% 61% 120.6 GtsC (GLcG), component of Glucose porter, GtsABCD 37% 192.6
lactose catabolism aglG' lo Inner membrane ABC transporter permease protein (characterized, see rationale) 32% 61% 120.6 GtsC (GLcG), component of Glucose porter, GtsABCD 37% 192.6
D-maltose catabolism aglG' lo Inner membrane ABC transporter permease protein (characterized, see rationale) 32% 61% 120.6 GtsC (GLcG), component of Glucose porter, GtsABCD 37% 192.6
sucrose catabolism aglG' lo Inner membrane ABC transporter permease protein (characterized, see rationale) 32% 61% 120.6 GtsC (GLcG), component of Glucose porter, GtsABCD 37% 192.6
trehalose catabolism aglG' lo Inner membrane ABC transporter permease protein (characterized, see rationale) 32% 61% 120.6 GtsC (GLcG), component of Glucose porter, GtsABCD 37% 192.6
trehalose catabolism thuG lo Trehalose/maltose transport system permease protein MalG (characterized) 31% 94% 119 GtsC (GLcG), component of Glucose porter, GtsABCD 37% 192.6

Sequence Analysis Tools

View H281DRAFT_03232 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

MFPIPIDKWKPATRRVYKLTLPIALLIWLLPMIAVLVTSIRSSEELSEGNYWGWPKHFAL
FDNYREALTTSPMLHYFWNSVLITVPAVIGSIALAAMAGFALAIYRFRGNSSLFATFVAG
NFVPVQVLMIPVRDLSLQLGVFNTVSALILFHVSFQTGFCALFLRNFIKQLPFELVEAAR
IEGANEWTVFFRIVLPLIRPALAALAILVFTFVWNDYFWALCLTQGDDAAPITVGVAALK
GQWTTAWNLVSAGSILAALPSVAMFFAMQKHFVAGLTFGATKG

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