GapMind for catabolism of small carbon sources

 

Protein SM_b20972 in Sinorhizobium meliloti 1021

Annotation: SM_b20972 sugar uptake ABC transporter ATP-binding protein

Length: 391 amino acids

Source: Smeli in FitnessBrowser

Candidate for 15 steps in catabolism of small carbon sources

Pathway Step Score Similar to Id. Cov. Bits Other hit Other id. Other bits
D-mannitol catabolism mtlK hi ABC transporter for D-Mannitol, D-Mannose, and D-Sorbitol, ATPase component (characterized) 56% 99% 395.2 ABC-type maltose transporter (subunit 3/3) (EC 7.5.2.1) 51% 361.3
D-sorbitol (glucitol) catabolism mtlK hi ABC transporter for D-Mannitol, D-Mannose, and D-Sorbitol, ATPase component (characterized) 56% 99% 395.2 ABC-type maltose transporter (subunit 3/3) (EC 7.5.2.1) 51% 361.3
D-maltose catabolism malK med ABC-type maltose transporter (subunit 3/3) (EC 7.5.2.1) (characterized) 51% 99% 361.3 ABC transporter for D-Mannitol, D-Mannose, and D-Sorbitol, ATPase component 56% 395.2
D-cellobiose catabolism gtsD med 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) 55% 96% 357.5 ABC transporter for D-Mannitol, D-Mannose, and D-Sorbitol, ATPase component 56% 395.2
D-glucose catabolism gtsD med 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) 55% 96% 357.5 ABC transporter for D-Mannitol, D-Mannose, and D-Sorbitol, ATPase component 56% 395.2
lactose catabolism gtsD med 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) 55% 96% 357.5 ABC transporter for D-Mannitol, D-Mannose, and D-Sorbitol, ATPase component 56% 395.2
D-maltose catabolism gtsD med 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) 55% 96% 357.5 ABC transporter for D-Mannitol, D-Mannose, and D-Sorbitol, ATPase component 56% 395.2
D-mannose catabolism TT_C0211 med 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) 55% 96% 357.5 ABC transporter for D-Mannitol, D-Mannose, and D-Sorbitol, ATPase component 56% 395.2
sucrose catabolism gtsD med 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) 55% 96% 357.5 ABC transporter for D-Mannitol, D-Mannose, and D-Sorbitol, ATPase component 56% 395.2
trehalose catabolism gtsD med 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) 55% 96% 357.5 ABC transporter for D-Mannitol, D-Mannose, and D-Sorbitol, ATPase component 56% 395.2
xylitol catabolism Dshi_0546 med ABC transporter for Xylitol, ATPase component (characterized) 50% 100% 344.7 ABC transporter for D-Mannitol, D-Mannose, and D-Sorbitol, ATPase component 56% 395.2
L-arabinose catabolism xacK med Xylose/arabinose import ATP-binding protein XacK; EC 7.5.2.13 (characterized, see rationale) 48% 98% 316.6 ABC transporter for D-Mannitol, D-Mannose, and D-Sorbitol, ATPase component 56% 395.2
L-arabinose catabolism xacJ med Xylose/arabinose import ATP-binding protein XacJ; EC 7.5.2.13 (characterized, see rationale) 46% 98% 297.4 ABC transporter for D-Mannitol, D-Mannose, and D-Sorbitol, ATPase component 56% 395.2
trehalose catabolism treV med TreV, component of Trehalose porter (characterized) 45% 95% 251.5 ABC transporter for D-Mannitol, D-Mannose, and D-Sorbitol, ATPase component 56% 395.2
glycerol catabolism glpS lo GlpS, component of Glycerol uptake porter, GlpSTPQV (characterized) 35% 98% 213.8 ABC transporter for D-Mannitol, D-Mannose, and D-Sorbitol, ATPase component 56% 395.2

Sequence Analysis Tools

View SM_b20972 at FitnessBrowser

PaperBLAST (search for papers about homologs of this protein)

Search CDD (the Conserved Domains Database, which includes COG and superfam)

Search PFam (including for weak hits, up to E = 1)

Predict protein localization: PSORTb (Gram negative bacteria)

Predict transmembrane helices and signal peptides: Phobius

Check the SEED with FIGfam search

Fitness BLAST: loading...

Sequence

MATIRIDNLRKSFGSHEILRGIDLEIADGEFVCFLGPSGCGKSTLLRSIAGLENLDGGSI
RLGDRDITDLPSARRDIAMVFQNYALYPHMNVRKNLSFGLALNGMKRNEIDRRVNNAAEI
LRITELLDRKPRQLSGGQRQRVAIGRAIVREPKLFLLDEPLSNLDAGLRVTMRVELAALH
ERLGVTMIYVTHDQVEAMTLSDRVVVLDKGRVSQFGTPLELFYRPANLFVAGFIGSPRMN
FLPAGVAEQAATRVTLAGGGLSRPVTLDTRSSESLNRDRPVTLGIRPDKLELTSPEEAHL
AGTVRLVERLGTESHVHIRVEGGGDLTAVVRGTHPVASRDQVHLRLPPEHCHLFDAEGTA
IARRLDPETKALIDNEKARGARAPVLEERHA

This GapMind analysis is from Sep 17 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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint on GapMind for carbon sources, or view the source code.

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