GapMind for catabolism of small carbon sources

 

Protein WP_084164874.1 in Skermanella stibiiresistens SB22

Annotation: NCBI__GCF_000576635.1:WP_084164874.1

Length: 288 amino acids

Source: GCF_000576635.1 in NCBI

Candidate for 27 steps in catabolism of small carbon sources

Pathway Step Score Similar to Id. Cov. Bits Other hit Other id. Other bits
xylitol catabolism Dshi_0549 hi ABC transporter for Xylitol, permease component 2 (characterized) 71% 95% 377.5 MtlG, component of The polyol (mannitol, glucitol (sorbitol), arabitol (arabinitol; lyxitol)) uptake porter, MtlEFGK 40% 210.3
L-fucose catabolism SM_b21105 lo ABC transporter for L-Fucose, permease component 2 (characterized) 37% 98% 210.3 ABC transporter for Xylitol, permease component 2 71% 377.5
D-mannitol catabolism mtlG lo MtlG, component of The polyol (mannitol, glucitol (sorbitol), arabitol (arabinitol; lyxitol)) uptake porter, MtlEFGK (characterized) 40% 99% 210.3 ABC transporter for Xylitol, permease component 2 71% 377.5
D-sorbitol (glucitol) catabolism mtlG lo MtlG, component of The polyol (mannitol, glucitol (sorbitol), arabitol (arabinitol; lyxitol)) uptake porter, MtlEFGK (characterized) 40% 99% 210.3 ABC transporter for Xylitol, permease component 2 71% 377.5
xylitol catabolism HSERO_RS17010 lo ABC-type sugar transport system, permease component protein (characterized, see rationale) 36% 99% 189.9 ABC transporter for Xylitol, permease component 2 71% 377.5
D-maltose catabolism thuG lo 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) 39% 95% 189.1 ABC transporter for Xylitol, permease component 2 71% 377.5
sucrose catabolism thuG lo 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) 39% 95% 189.1 ABC transporter for Xylitol, permease component 2 71% 377.5
trehalose catabolism thuG lo 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) 39% 95% 189.1 ABC transporter for Xylitol, permease component 2 71% 377.5
glycerol catabolism glpQ lo GlpQ, component of Glycerol uptake porter, GlpSTPQV (characterized) 36% 98% 185.3 ABC transporter for Xylitol, permease component 2 71% 377.5
N-acetyl-D-glucosamine catabolism ngcG lo NgcG, component of N-Acetylglucosamine/N,N'-diacetyl chitobiose porter (NgcK (C) not identified) (characterized) 32% 96% 144.8 ABC transporter for Xylitol, permease component 2 71% 377.5
D-glucosamine (chitosamine) catabolism ngcG lo NgcG, component of N-Acetylglucosamine/N,N'-diacetyl chitobiose porter (NgcK (C) not identified) (characterized) 32% 96% 144.8 ABC transporter for Xylitol, permease component 2 71% 377.5
N-acetyl-D-glucosamine catabolism SMc02871 lo ABC transporter for N-Acetyl-D-glucosamine, permease protein 2 (characterized) 32% 95% 136.7 ABC transporter for Xylitol, permease component 2 71% 377.5
D-glucosamine (chitosamine) catabolism SMc02871 lo ABC transporter for N-Acetyl-D-glucosamine, permease protein 2 (characterized) 32% 95% 136.7 ABC transporter for Xylitol, permease component 2 71% 377.5
L-arabinose catabolism araU lo AraU, component of Arabinose, fructose, xylose porter (characterized) 30% 90% 111.3 ABC transporter for Xylitol, permease component 2 71% 377.5
D-fructose catabolism araU lo AraU, component of Arabinose, fructose, xylose porter (characterized) 30% 90% 111.3 ABC transporter for Xylitol, permease component 2 71% 377.5
sucrose catabolism araU lo AraU, component of Arabinose, fructose, xylose porter (characterized) 30% 90% 111.3 ABC transporter for Xylitol, permease component 2 71% 377.5
D-xylose catabolism araU lo AraU, component of Arabinose, fructose, xylose porter (characterized) 30% 90% 111.3 ABC transporter for Xylitol, permease component 2 71% 377.5
D-maltose catabolism aglG lo ABC transporter for D-Maltose and D-Trehalose, permease component 2 (characterized) 31% 62% 110.2 ABC transporter for Xylitol, permease component 2 71% 377.5
sucrose catabolism aglG lo ABC transporter for D-Maltose and D-Trehalose, permease component 2 (characterized) 31% 62% 110.2 ABC transporter for Xylitol, permease component 2 71% 377.5
trehalose catabolism aglG lo ABC transporter for D-Maltose and D-Trehalose, permease component 2 (characterized) 31% 62% 110.2 ABC transporter for Xylitol, permease component 2 71% 377.5
D-cellobiose catabolism gtsC lo Sugar ABC transporter permease (characterized, see rationale) 30% 71% 97.8 ABC transporter for Xylitol, permease component 2 71% 377.5
D-glucose catabolism gtsC lo Sugar ABC transporter permease (characterized, see rationale) 30% 71% 97.8 ABC transporter for Xylitol, permease component 2 71% 377.5
lactose catabolism gtsC lo Sugar ABC transporter permease (characterized, see rationale) 30% 71% 97.8 ABC transporter for Xylitol, permease component 2 71% 377.5
D-maltose catabolism gtsC lo Sugar ABC transporter permease (characterized, see rationale) 30% 71% 97.8 ABC transporter for Xylitol, permease component 2 71% 377.5
sucrose catabolism gtsC lo Sugar ABC transporter permease (characterized, see rationale) 30% 71% 97.8 ABC transporter for Xylitol, permease component 2 71% 377.5
trehalose catabolism gtsC lo Sugar ABC transporter permease (characterized, see rationale) 30% 71% 97.8 ABC transporter for Xylitol, permease component 2 71% 377.5
D-maltose catabolism malG lo Maltose-transporting ATPase (EC 3.6.3.19) (characterized) 32% 73% 97.1 ABC transporter for Xylitol, permease component 2 71% 377.5

Sequence Analysis Tools

View WP_084164874.1 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

MAVATAGGTVPAASHTKPKRLVSAWHLVGLLAIFLFAVFPFYWMVATSLKTQAEALASPP
IWVFTPRLDNYFEVLFNRDVLSSLTNSIIIAVSTTILAVGLGTPAAYALARFEFKSKEEL
WFWFITNRMLSPIVVALPIFLMARTLNLIDTHIVLILVYLTFNLPIVVWICTDQFRGVPK
DLDEAARLAGASRFTIFWRIALPLAMPGVAVSAIFSFIFSWNELLYALVLTRNVARTAPV
AATSFMSGYDLPWGEIMATGTLIVLPVIVFALIVSKHLVQGLTMGAVK

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