GapMind for catabolism of small carbon sources

 

Protein WP_232422354.1 in Methylosarcina fibrata AML-C10

Annotation: NCBI__GCF_000372865.1:WP_232422354.1

Length: 271 amino acids

Source: GCF_000372865.1 in NCBI

Candidate for 28 steps in catabolism of small carbon sources

Pathway Step Score Similar to Id. Cov. Bits Other hit Other id. Other bits
trehalose catabolism thuG hi Trehalose transport system permease protein SugB (characterized) 59% 97% 330.9 PalG, component of Palatinose (isomaltulose; 6-O-α-D-glucopyranosyl-D-fructose) uptake porter 40% 204.1
D-maltose catabolism thuG med Maltose transport system permease protein malG aka TT_C1629, component of The trehalose/maltose/sucrose/palatinose porter (TTC1627-9) plus MalK1 (ABC protein, shared with 3.A.1.1.24) (Silva et al. 2005; Chevance et al., 2006). The receptor (TTC1627) binds disaccharide alpha-glycosides, namely trehalose (alpha-1,1), sucrose (alpha-1,2), maltose (alpha-1,4), palatinose (alpha-1,6) and glucose (characterized) 47% 98% 238 Trehalose transport system permease protein SugB 59% 330.9
sucrose catabolism thuG med Maltose transport system permease protein malG aka TT_C1629, component of The trehalose/maltose/sucrose/palatinose porter (TTC1627-9) plus MalK1 (ABC protein, shared with 3.A.1.1.24) (Silva et al. 2005; Chevance et al., 2006). The receptor (TTC1627) binds disaccharide alpha-glycosides, namely trehalose (alpha-1,1), sucrose (alpha-1,2), maltose (alpha-1,4), palatinose (alpha-1,6) and glucose (characterized) 47% 98% 238 Trehalose transport system permease protein SugB 59% 330.9
xylitol catabolism Dshi_0549 lo ABC transporter for Xylitol, permease component 2 (characterized) 38% 98% 161.8 Trehalose transport system permease protein SugB 59% 330.9
L-fucose catabolism SM_b21105 lo ABC transporter for L-Fucose, permease component 2 (characterized) 33% 97% 158.7 Trehalose transport system permease protein SugB 59% 330.9
D-glucosamine (chitosamine) catabolism SM_b21219 lo ABC transporter for D-Glucosamine, permease component 1 (characterized) 36% 95% 158.3 Trehalose transport system permease protein SugB 59% 330.9
D-maltose catabolism malG lo Maltose-transporting ATPase (EC 3.6.3.19) (characterized) 35% 93% 154.1 Trehalose transport system permease protein SugB 59% 330.9
D-cellobiose catabolism msdB2 lo Binding-protein-dependent transport systems inner membrane component (characterized, see rationale) 31% 92% 141.7 Trehalose transport system permease protein SugB 59% 330.9
D-sorbitol (glucitol) catabolism mtlG lo ABC transporter for D-Sorbitol, permease component 1 (characterized) 32% 89% 138.3 Trehalose transport system permease protein SugB 59% 330.9
glycerol catabolism glpQ lo ABC transporter for Glycerol, permease component 2 (characterized) 30% 95% 137.1 Trehalose transport system permease protein SugB 59% 330.9
D-cellobiose catabolism gtsC 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) 33% 99% 134.8 Trehalose transport system permease protein SugB 59% 330.9
D-glucose catabolism gtsC 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) 33% 99% 134.8 Trehalose transport system permease protein SugB 59% 330.9
lactose catabolism gtsC 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) 33% 99% 134.8 Trehalose transport system permease protein SugB 59% 330.9
D-maltose catabolism gtsC 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) 33% 99% 134.8 Trehalose transport system permease protein SugB 59% 330.9
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) 33% 99% 134.8 Trehalose transport system permease protein SugB 59% 330.9
sucrose catabolism gtsC 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) 33% 99% 134.8 Trehalose transport system permease protein SugB 59% 330.9
trehalose catabolism gtsC 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) 33% 99% 134.8 Trehalose transport system permease protein SugB 59% 330.9
xylitol catabolism HSERO_RS17010 lo ABC-type sugar transport system, permease component protein (characterized, see rationale) 33% 95% 133.3 Trehalose transport system permease protein SugB 59% 330.9
D-mannitol catabolism mtlG lo SmoG, component of Hexitol (glucitol; mannitol) porter (characterized) 32% 96% 129 Trehalose transport system permease protein SugB 59% 330.9
D-maltose catabolism aglG lo ABC transporter for D-Maltose and D-Trehalose, permease component 2 (characterized) 32% 67% 124 Trehalose transport system permease protein SugB 59% 330.9
sucrose catabolism aglG lo ABC transporter for D-Maltose and D-Trehalose, permease component 2 (characterized) 32% 67% 124 Trehalose transport system permease protein SugB 59% 330.9
trehalose catabolism aglG lo ABC transporter for D-Maltose and D-Trehalose, permease component 2 (characterized) 32% 67% 124 Trehalose transport system permease protein SugB 59% 330.9
D-cellobiose catabolism aglG' lo Inner membrane ABC transporter permease protein (characterized, see rationale) 33% 61% 121.3 Trehalose transport system permease protein SugB 59% 330.9
D-glucose catabolism aglG' lo Inner membrane ABC transporter permease protein (characterized, see rationale) 33% 61% 121.3 Trehalose transport system permease protein SugB 59% 330.9
lactose catabolism aglG' lo Inner membrane ABC transporter permease protein (characterized, see rationale) 33% 61% 121.3 Trehalose transport system permease protein SugB 59% 330.9
D-maltose catabolism aglG' lo Inner membrane ABC transporter permease protein (characterized, see rationale) 33% 61% 121.3 Trehalose transport system permease protein SugB 59% 330.9
sucrose catabolism aglG' lo Inner membrane ABC transporter permease protein (characterized, see rationale) 33% 61% 121.3 Trehalose transport system permease protein SugB 59% 330.9
trehalose catabolism aglG' lo Inner membrane ABC transporter permease protein (characterized, see rationale) 33% 61% 121.3 Trehalose transport system permease protein SugB 59% 330.9

Sequence Analysis Tools

View WP_232422354.1 at NCBI

Find papers: PaperBLAST

Find functional residues: SitesBLAST

Search for conserved domains

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Predict transmenbrane helices: Phobius

Predict protein localization: PSORTb

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Sequence

MERLFWGVASLAALSYTLLPVLWIFSLSLKKPEHLADRRLFPDEIYWGHYRAVFNDPQFP
AALWNSVGIALMATSLSVTLAAFAAYAIARLQFPGKNAVLAAALAIAMFPPVAIIGPLFD
LWRSLGFFDTWAGLILPYMTFALPLSIWTLAAFFRELPGDLEKAARVDGATPFQVFRLII
APLAAPGVFTSAILVFIFAWNDFLFAAALTSTDAARTVPAAIAFFTGPSQFEQPTGAIAA
ASVVVTVPVAMVVLLFQRRLVSGLTAGAVKG

This GapMind analysis is from Apr 09 2024. 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:

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