GapMind for catabolism of small carbon sources

 

Protein WP_084012489.1 in Thermobifida halotolerans YIM 90462

Annotation: NCBI__GCF_001660385.1:WP_084012489.1

Length: 309 amino acids

Source: GCF_001660385.1 in NCBI

Candidate for 23 steps in catabolism of small carbon sources

Pathway Step Score Similar to Id. Cov. Bits Other hit Other id. Other bits
D-sorbitol (glucitol) catabolism mtlG hi ABC transporter for D-Sorbitol, permease component 1 (characterized) 43% 91% 246.9
D-mannitol catabolism mtlG med ABC transporter for D-Mannitol, D-Mannose, and D-Mannose, permease component 1 (characterized) 42% 97% 245 ABC transporter for D-Sorbitol, permease component 1 43% 246.9
xylitol catabolism Dshi_0549 lo ABC transporter for Xylitol, permease component 2 (characterized) 38% 94% 191.4 ABC transporter for D-Sorbitol, permease component 1 43% 246.9
trehalose catabolism thuG lo Trehalose transport system permease protein SugB (characterized) 36% 97% 153.3 ABC transporter for D-Sorbitol, permease component 1 43% 246.9
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) 34% 97% 152.5 ABC transporter for D-Sorbitol, permease component 1 43% 246.9
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) 34% 97% 152.5 ABC transporter for D-Sorbitol, permease component 1 43% 246.9
D-glucosamine (chitosamine) catabolism SM_b21219 lo ABC transporter for D-Glucosamine, permease component 1 (characterized) 35% 93% 150.6 ABC transporter for D-Sorbitol, permease component 1 43% 246.9
L-fucose catabolism SM_b21105 lo ABC transporter for L-Fucose, permease component 2 (characterized) 32% 99% 145.2 ABC transporter for D-Sorbitol, permease component 1 43% 246.9
D-cellobiose catabolism msdB2 lo Binding-protein-dependent transport systems inner membrane component (characterized, see rationale) 31% 88% 129 ABC transporter for D-Sorbitol, permease component 1 43% 246.9
xylitol catabolism HSERO_RS17010 lo ABC-type sugar transport system, permease component protein (characterized, see rationale) 32% 96% 127.5 ABC transporter for D-Sorbitol, permease component 1 43% 246.9
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) 31% 100% 118.6 ABC transporter for D-Sorbitol, permease component 1 43% 246.9
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) 31% 100% 118.6 ABC transporter for D-Sorbitol, permease component 1 43% 246.9
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) 31% 100% 118.6 ABC transporter for D-Sorbitol, permease component 1 43% 246.9
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) 31% 100% 118.6 ABC transporter for D-Sorbitol, permease component 1 43% 246.9
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) 31% 100% 118.6 ABC transporter for D-Sorbitol, permease component 1 43% 246.9
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) 31% 100% 118.6 ABC transporter for D-Sorbitol, permease component 1 43% 246.9
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) 31% 100% 118.6 ABC transporter for D-Sorbitol, permease component 1 43% 246.9
D-maltose catabolism aglG lo ABC transporter for D-Maltose and D-Trehalose, permease component 2 (characterized) 31% 62% 110.5 ABC transporter for D-Sorbitol, permease component 1 43% 246.9
sucrose catabolism aglG lo ABC transporter for D-Maltose and D-Trehalose, permease component 2 (characterized) 31% 62% 110.5 ABC transporter for D-Sorbitol, permease component 1 43% 246.9
trehalose catabolism aglG lo ABC transporter for D-Maltose and D-Trehalose, permease component 2 (characterized) 31% 62% 110.5 ABC transporter for D-Sorbitol, permease component 1 43% 246.9
trehalose catabolism treU lo TreU, component of Trehalose porter (characterized) 30% 99% 103.6 ABC transporter for D-Sorbitol, permease component 1 43% 246.9
D-xylose catabolism gtsC lo ABC transporter for D-Glucose-6-Phosphate, permease component 1 (characterized) 32% 74% 97.8 ABC transporter for D-Sorbitol, permease component 1 43% 246.9
L-arabinose catabolism xacI lo Xylose/arabinose import permease protein XacI (characterized, see rationale) 31% 62% 71.6 ABC transporter for D-Sorbitol, permease component 1 43% 246.9

Sequence Analysis Tools

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

MTKLLPASSSHEAPTSGDEATRVPTADTAARHRGRWPLLWSRLGRAGIGLLGWTIAFVLF
FPVLWMFLSGLKQEAQASTDPPTFLFTPTLDQFEAIFDRDFAPYLLNSLMASVGSTFLVI
VLATPAAYALSLAPVPKWRDSLFFFISTRMMPMVAIILPLYVIANDIGVLDNITMLSLVY
TVMNLPIAVWMIRSFLLELPKGVLEAAKVDGATFGVELRRIILPMIAPGLAATALICFIF
AWNEFFFAVSLTSTRAATVPVFLTGFVTSEGLFLARLSAAATMAALPVILAGWIAQKWLV
RGLTLGAVK

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