GapMind for catabolism of small carbon sources

 

Protein WP_104913074.1 in Pontimonas salivibrio CL-TW6

Annotation: NCBI__GCF_002950575.1:WP_104913074.1

Length: 261 amino acids

Source: GCF_002950575.1 in NCBI

Candidate for 20 steps in catabolism of small carbon sources

Pathway Step Score Similar to Id. Cov. Bits Other hit Other id. Other bits
L-fucose catabolism SM_b21105 med ABC transporter for L-Fucose, permease component 2 (characterized) 35% 93% 174.1 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 34% 172.6
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% 90% 172.6 ABC transporter for L-Fucose, permease component 2 35% 174.1
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% 90% 172.6 ABC transporter for L-Fucose, permease component 2 35% 174.1
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) 34% 90% 172.6 ABC transporter for L-Fucose, permease component 2 35% 174.1
D-cellobiose catabolism msdB2 lo Binding-protein-dependent transport systems inner membrane component (characterized, see rationale) 30% 91% 157.9 ABC transporter for L-Fucose, permease component 2 35% 174.1
D-maltose catabolism malG_Bb lo ABC-type Maltose/ Maltodextrin permease (characterized, see rationale) 34% 82% 153.3 ABC transporter for L-Fucose, permease component 2 35% 174.1
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% 95% 147.5 ABC transporter for L-Fucose, permease component 2 35% 174.1
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% 95% 147.5 ABC transporter for L-Fucose, permease component 2 35% 174.1
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% 95% 147.5 ABC transporter for L-Fucose, permease component 2 35% 174.1
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% 95% 147.5 ABC transporter for L-Fucose, permease component 2 35% 174.1
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% 95% 147.5 ABC transporter for L-Fucose, permease component 2 35% 174.1
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% 95% 147.5 ABC transporter for L-Fucose, permease component 2 35% 174.1
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% 95% 147.5 ABC transporter for L-Fucose, permease component 2 35% 174.1
D-glucosamine (chitosamine) catabolism SM_b21219 lo ABC transporter for D-Glucosamine, permease component 1 (characterized) 31% 93% 142.5 ABC transporter for L-Fucose, permease component 2 35% 174.1
xylitol catabolism Dshi_0549 lo ABC transporter for Xylitol, permease component 2 (characterized) 31% 94% 135.6 ABC transporter for L-Fucose, permease component 2 35% 174.1
N-acetyl-D-glucosamine catabolism SMc02871 lo N-Acetyl-D-glucosamine ABC transport system, permease component 2 (characterized) 30% 92% 134.8 ABC transporter for L-Fucose, permease component 2 35% 174.1
D-glucosamine (chitosamine) catabolism SMc02871 lo N-Acetyl-D-glucosamine ABC transport system, permease component 2 (characterized) 30% 92% 134.8 ABC transporter for L-Fucose, permease component 2 35% 174.1
D-maltose catabolism malG_Aa lo Binding-protein-dependent transport systems inner membrane component (characterized, see rationale) 31% 85% 131.7 ABC transporter for L-Fucose, permease component 2 35% 174.1
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% 93% 122.1 ABC transporter for L-Fucose, permease component 2 35% 174.1
D-maltose catabolism malG lo ABC-type maltose transporter (subunit 2/3) (EC 7.5.2.1) (characterized) 32% 75% 108.6 ABC transporter for L-Fucose, permease component 2 35% 174.1

Sequence Analysis Tools

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Predict protein localization: PSORTb

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Sequence

MAGLTIVVLGPLYWVTMSAFKNREEIIRREPTLFPETPTLDNFRRLFTATDYPTYLANSA
SVAVATMVVTIIVSMAAAYALYRLRVPGSGRLAGIILLSYMIPGTLLIVPLYGTLFRLGL
IDTHLGLVLVNVAFTAPFCTWLLRGFLLSIPDDLDAAAALDGAGPIRTMTQVVFPLLAPG
VATVAVFSFVYAWKEFVFASQFVLSDSLDTLPIGLKAIIGQYTVDWGLVMAGAVFTLLPT
VLLFAVVGRFFVGGLMSGANK

This GapMind analysis is from Sep 24 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:

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