GapMind for catabolism of small carbon sources

 

Protein WP_066600434.1 in Sphingobium czechense LL01

Annotation: NCBI__GCF_001046645.1:WP_066600434.1

Length: 206 amino acids

Source: GCF_001046645.1 in NCBI

Candidate for 31 steps in catabolism of small carbon sources

Pathway Step Score Similar to Id. Cov. Bits Other hit Other id. Other bits
D-maltose catabolism thuK lo Trehalose/maltose import ATP-binding protein MalK; EC 7.5.2.1 (characterized) 39% 56% 134 ABC-type molybdate transporter (EC 7.3.2.5) 47% 183.0
trehalose catabolism thuK lo Trehalose/maltose import ATP-binding protein MalK; EC 7.5.2.1 (characterized) 39% 56% 134 ABC-type molybdate transporter (EC 7.3.2.5) 47% 183.0
lactose catabolism lacK lo LacK, component of Lactose porter (characterized) 40% 55% 127.5 ABC-type molybdate transporter (EC 7.3.2.5) 47% 183.0
D-cellobiose catabolism gtsD lo Sugar-binding transport ATP-binding protein aka MalK1 aka TT_C0211, 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% 52% 124.8 ABC-type molybdate transporter (EC 7.3.2.5) 47% 183.0
D-glucose catabolism gtsD lo Sugar-binding transport ATP-binding protein aka MalK1 aka TT_C0211, 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% 52% 124.8 ABC-type molybdate transporter (EC 7.3.2.5) 47% 183.0
lactose catabolism gtsD lo Sugar-binding transport ATP-binding protein aka MalK1 aka TT_C0211, 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% 52% 124.8 ABC-type molybdate transporter (EC 7.3.2.5) 47% 183.0
D-maltose catabolism gtsD lo Sugar-binding transport ATP-binding protein aka MalK1 aka TT_C0211, 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% 52% 124.8 ABC-type molybdate transporter (EC 7.3.2.5) 47% 183.0
D-mannose catabolism TT_C0211 lo Sugar-binding transport ATP-binding protein aka MalK1 aka TT_C0211, 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% 52% 124.8 ABC-type molybdate transporter (EC 7.3.2.5) 47% 183.0
sucrose catabolism gtsD lo Sugar-binding transport ATP-binding protein aka MalK1 aka TT_C0211, 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% 52% 124.8 ABC-type molybdate transporter (EC 7.3.2.5) 47% 183.0
sucrose catabolism thuK lo Sugar-binding transport ATP-binding protein aka MalK1 aka TT_C0211, 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% 52% 124.8 ABC-type molybdate transporter (EC 7.3.2.5) 47% 183.0
trehalose catabolism gtsD lo Sugar-binding transport ATP-binding protein aka MalK1 aka TT_C0211, 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% 52% 124.8 ABC-type molybdate transporter (EC 7.3.2.5) 47% 183.0
L-arabinose catabolism araV lo AraV, component of Arabinose, fructose, xylose porter (characterized) 37% 52% 121.7 ABC-type molybdate transporter (EC 7.3.2.5) 47% 183.0
D-fructose catabolism araV lo AraV, component of Arabinose, fructose, xylose porter (characterized) 37% 52% 121.7 ABC-type molybdate transporter (EC 7.3.2.5) 47% 183.0
sucrose catabolism araV lo AraV, component of Arabinose, fructose, xylose porter (characterized) 37% 52% 121.7 ABC-type molybdate transporter (EC 7.3.2.5) 47% 183.0
D-xylose catabolism araV lo AraV, component of Arabinose, fructose, xylose porter (characterized) 37% 52% 121.7 ABC-type molybdate transporter (EC 7.3.2.5) 47% 183.0
L-arabinose catabolism xacJ lo Xylose/arabinose import ATP-binding protein XacJ; EC 7.5.2.13 (characterized, see rationale) 38% 53% 121.3 ABC-type molybdate transporter (EC 7.3.2.5) 47% 183.0
L-arabinose catabolism xacK lo Xylose/arabinose import ATP-binding protein XacK; EC 7.5.2.13 (characterized, see rationale) 37% 51% 119.4 ABC-type molybdate transporter (EC 7.3.2.5) 47% 183.0
D-sorbitol (glucitol) catabolism mtlK lo ABC transporter for D-Sorbitol, ATPase component (characterized) 40% 54% 119 ABC-type molybdate transporter (EC 7.3.2.5) 47% 183.0
D-mannitol catabolism mtlK lo SmoK aka POLK, component of Hexitol (glucitol; mannitol) porter (characterized) 37% 61% 118.6 ABC-type molybdate transporter (EC 7.3.2.5) 47% 183.0
D-glucosamine (chitosamine) catabolism SM_b21216 lo ABC transporter for D-Glucosamine, ATPase component (characterized) 37% 56% 118.2 ABC-type molybdate transporter (EC 7.3.2.5) 47% 183.0
D-maltose catabolism aglK lo ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized) 39% 56% 118.2 ABC-type molybdate transporter (EC 7.3.2.5) 47% 183.0
sucrose catabolism aglK lo ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized) 39% 56% 118.2 ABC-type molybdate transporter (EC 7.3.2.5) 47% 183.0
trehalose catabolism aglK lo ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized) 39% 56% 118.2 ABC-type molybdate transporter (EC 7.3.2.5) 47% 183.0
D-maltose catabolism malK lo Maltose-transporting ATPase (EC 3.6.3.19) (characterized) 38% 50% 117.1 ABC-type molybdate transporter (EC 7.3.2.5) 47% 183.0
trehalose catabolism treV lo TreV, component of Trehalose porter (characterized) 34% 62% 115.5 ABC-type molybdate transporter (EC 7.3.2.5) 47% 183.0
L-arginine catabolism braF lo ATP-binding component of a broad range amino acid ABC transporter (characterized, see rationale) 31% 66% 76.6 ABC-type molybdate transporter (EC 7.3.2.5) 47% 183.0
L-glutamate catabolism braF lo ATP-binding component of a broad range amino acid ABC transporter (characterized, see rationale) 31% 66% 76.6 ABC-type molybdate transporter (EC 7.3.2.5) 47% 183.0
L-histidine catabolism braF lo ATP-binding component of a broad range amino acid ABC transporter (characterized, see rationale) 31% 66% 76.6 ABC-type molybdate transporter (EC 7.3.2.5) 47% 183.0
L-isoleucine catabolism livG lo ATP-binding component of a broad range amino acid ABC transporter (characterized, see rationale) 31% 66% 76.6 ABC-type molybdate transporter (EC 7.3.2.5) 47% 183.0
L-leucine catabolism livG lo ATP-binding component of a broad range amino acid ABC transporter (characterized, see rationale) 31% 66% 76.6 ABC-type molybdate transporter (EC 7.3.2.5) 47% 183.0
L-valine catabolism livG lo ATP-binding component of a broad range amino acid ABC transporter (characterized, see rationale) 31% 66% 76.6 ABC-type molybdate transporter (EC 7.3.2.5) 47% 183.0

Sequence Analysis Tools

View WP_066600434.1 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

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Sequence

MLIDIDVRRRVGGRIIGVTMRTDTGISALFGPSGIGKTTILHMVAGLIRPDEGHIRIDGT
LLFDHRQAIDIPSKLRGCGYVFQDTRLFPHLRVRANLLYGRRGEGPASLSTVIDLLGLDG
LLDRWPITLSGGEAQRVAIGRALLSGPQILLMDEPLSSLDDRRKAGLLGLIRDIPRRTGI
PILYVTHDAAEIDALDATRIDVLNPA

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