GapMind for catabolism of small carbon sources

 

Protein 209225 in Desulfovibrio vulgaris Hildenborough

Annotation: DVU0291 ABC transporter, ATP-binding protein

Length: 354 amino acids

Source: 882 in MicrobesOnline

Candidate for 26 steps in catabolism of small carbon sources

Pathway Step Score Similar to Id. Cov. Bits Other hit Other id. Other bits
sucrose catabolism thuK lo ABC transporter (characterized, see rationale) 36% 83% 182.2 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 37% 203.0
putrescine catabolism potA lo PotG aka B0855, component of Putrescine porter (characterized) 38% 78% 179.5 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 37% 203.0
D-maltose catabolism malK lo Maltose/maltodextrin import ATP-binding protein MalK; EC 7.5.2.1 (characterized) 36% 81% 179.1 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 37% 203.0
D-cellobiose catabolism gtsD lo Sugar ABC transporter ATP-binding protein (characterized, see rationale) 36% 90% 178.7 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 37% 203.0
D-glucose catabolism gtsD lo Sugar ABC transporter ATP-binding protein (characterized, see rationale) 36% 90% 178.7 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 37% 203.0
lactose catabolism gtsD lo Sugar ABC transporter ATP-binding protein (characterized, see rationale) 36% 90% 178.7 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 37% 203.0
D-maltose catabolism gtsD lo Sugar ABC transporter ATP-binding protein (characterized, see rationale) 36% 90% 178.7 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 37% 203.0
sucrose catabolism gtsD lo Sugar ABC transporter ATP-binding protein (characterized, see rationale) 36% 90% 178.7 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 37% 203.0
trehalose catabolism gtsD lo Sugar ABC transporter ATP-binding protein (characterized, see rationale) 36% 90% 178.7 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 37% 203.0
trehalose catabolism thuK lo Trehalose import ATP-binding protein SugC; EC 7.5.2.- (characterized) 35% 84% 178.7 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 37% 203.0
D-maltose 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) 43% 59% 176.8 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 37% 203.0
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) 43% 59% 176.8 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 37% 203.0
D-sorbitol (glucitol) catabolism mtlK lo ABC transporter for D-Sorbitol, ATPase component (characterized) 35% 85% 174.1 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 37% 203.0
xylitol catabolism Dshi_0546 lo ABC transporter for Xylitol, ATPase component (characterized) 34% 94% 170.2 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 37% 203.0
L-arabinose catabolism xacK lo Xylose/arabinose import ATP-binding protein XacK; EC 7.5.2.13 (characterized, see rationale) 37% 80% 167.2 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 37% 203.0
D-maltose catabolism malK_Bb lo ABC-type maltose transport, ATP binding protein (characterized, see rationale) 32% 87% 165.6 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 37% 203.0
D-maltose catabolism malK_Aa lo ABC-type maltose transporter (EC 7.5.2.1) (characterized) 40% 61% 164.5 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 37% 203.0
xylitol catabolism HSERO_RS17020 lo ABC-type sugar transport system, ATPase component protein (characterized, see rationale) 33% 89% 164.5 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 37% 203.0
L-fucose catabolism SM_b21106 lo ABC transporter for L-Fucose, ATPase component (characterized) 37% 66% 161 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 37% 203.0
D-galactose catabolism PfGW456L13_1897 lo ABC transporter for D-Galactose and D-Glucose, ATPase component (characterized) 40% 57% 160.2 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 37% 203.0
D-maltose catabolism musK lo ABC-type maltose transporter (EC 7.5.2.1) (characterized) 35% 87% 160.2 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 37% 203.0
D-glucosamine (chitosamine) catabolism SM_b21216 lo ABC transporter for D-Glucosamine, ATPase component (characterized) 34% 93% 158.3 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 37% 203.0
L-arabinose catabolism xacJ lo Xylose/arabinose import ATP-binding protein XacJ; EC 7.5.2.13 (characterized, see rationale) 40% 61% 156.8 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 37% 203.0
lactose catabolism lacK lo LacK, component of Lactose porter (characterized) 36% 74% 156 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 37% 203.0
D-maltose catabolism malK_Sm lo MalK, component of Maltose/Maltotriose/maltodextrin (up to 7 glucose units) transporters MalXFGK (MsmK (3.A.1.1.28) can probably substitute for MalK; Webb et al., 2008) (characterized) 38% 63% 153.3 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 37% 203.0
trehalose catabolism malK lo MalK, component of Maltose/Maltotriose/maltodextrin (up to 7 glucose units) transporters MalXFGK (MsmK (3.A.1.1.28) can probably substitute for MalK; Webb et al., 2008) (characterized) 38% 63% 153.3 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 37% 203.0

Sequence Analysis Tools

View 209225 at MicrobesOnline

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

MVLAVEGLGRTLAGREVLHDVNLTAAAGEVVCLVGPSGVGKTTLLRCIAGLDAPDEGTIR
VTPPQGHGGGVVLVFQDYLLFPHLSVFENVAFGPRARGVRGAALKERVHTMLRAFRLDTD
DLAHMASRYPAQLSAGQRQRVALARALVCDPAVLLLDEPFANLDRGLRGEMAAFVRDVVR
RFGVATVTVTHDLEEAFAIGDRLGVMLGGTLAQLAPPLDVYRHPADEATARFLGPVTVLD
ETTRRTLGIDTPPAAATACADTMQGLRLYRPEALAVRPWADGPAVLVSARFTGQVMQLLL
DVEGQELLVHTLDDAPPTGTRLCVSLREIPGMTSAPTDAAASPSADTEHPGLVP

This GapMind analysis is from Sep 17 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 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