GapMind for catabolism of small carbon sources

 

Protein 8500849 in Desulfovibrio vulgaris Miyazaki F

Annotation: DvMF_1587 ABC transporter related (RefSeq)

Length: 366 amino acids

Source: Miya in FitnessBrowser

Candidate for 47 steps in catabolism of small carbon sources

Pathway Step Score Similar to Id. Cov. Bits Other hit Other id. Other bits
putrescine catabolism potA med spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31 (characterized) 43% 85% 242.3 CP4-6 prophage; ABC transporter ATP-binding protein AfuC 42% 258.8
trehalose catabolism thuK med Trehalose import ATP-binding protein SugC; EC 7.5.2.- (characterized) 41% 88% 236.5 CP4-6 prophage; ABC transporter ATP-binding protein AfuC 42% 258.8
L-fucose catabolism SM_b21106 med ABC transporter for L-Fucose, ATPase component (characterized) 40% 100% 235.7 CP4-6 prophage; ABC transporter ATP-binding protein AfuC 42% 258.8
D-maltose catabolism malK_Bb med ABC-type maltose transport, ATP binding protein (characterized, see rationale) 43% 84% 233 CP4-6 prophage; ABC transporter ATP-binding protein AfuC 42% 258.8
D-sorbitol (glucitol) catabolism mtlK med ABC transporter for D-Sorbitol, ATPase component (characterized) 41% 88% 226.1 CP4-6 prophage; ABC transporter ATP-binding protein AfuC 42% 258.8
D-maltose catabolism aglK med ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized) 42% 88% 225.3 CP4-6 prophage; ABC transporter ATP-binding protein AfuC 42% 258.8
D-maltose catabolism thuK med ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized) 42% 88% 225.3 CP4-6 prophage; ABC transporter ATP-binding protein AfuC 42% 258.8
sucrose catabolism aglK med ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized) 42% 88% 225.3 CP4-6 prophage; ABC transporter ATP-binding protein AfuC 42% 258.8
trehalose catabolism aglK med ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized) 42% 88% 225.3 CP4-6 prophage; ABC transporter ATP-binding protein AfuC 42% 258.8
L-arabinose catabolism xacJ med Xylose/arabinose import ATP-binding protein XacJ; EC 7.5.2.13 (characterized, see rationale) 41% 75% 221.1 CP4-6 prophage; ABC transporter ATP-binding protein AfuC 42% 258.8
N-acetyl-D-glucosamine catabolism SMc02869 med N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized) 40% 91% 219.2 CP4-6 prophage; ABC transporter ATP-binding protein AfuC 42% 258.8
D-glucosamine (chitosamine) catabolism SMc02869 med N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized) 40% 91% 219.2 CP4-6 prophage; ABC transporter ATP-binding protein AfuC 42% 258.8
lactose catabolism lacK med LacK, component of Lactose porter (characterized) 41% 82% 217.2 CP4-6 prophage; ABC transporter ATP-binding protein AfuC 42% 258.8
D-glucosamine (chitosamine) catabolism SM_b21216 med ABC transporter for D-Glucosamine, ATPase component (characterized) 41% 83% 214.2 CP4-6 prophage; ABC transporter ATP-binding protein AfuC 42% 258.8
D-cellobiose catabolism gtsD med ABC transporter for D-Galactose and D-Glucose, ATPase component (characterized) 41% 79% 213.8 CP4-6 prophage; ABC transporter ATP-binding protein AfuC 42% 258.8
D-galactose catabolism PfGW456L13_1897 med ABC transporter for D-Galactose and D-Glucose, ATPase component (characterized) 41% 79% 213.8 CP4-6 prophage; ABC transporter ATP-binding protein AfuC 42% 258.8
D-glucose catabolism gtsD med ABC transporter for D-Galactose and D-Glucose, ATPase component (characterized) 41% 79% 213.8 CP4-6 prophage; ABC transporter ATP-binding protein AfuC 42% 258.8
lactose catabolism gtsD med ABC transporter for D-Galactose and D-Glucose, ATPase component (characterized) 41% 79% 213.8 CP4-6 prophage; ABC transporter ATP-binding protein AfuC 42% 258.8
D-maltose catabolism gtsD med ABC transporter for D-Galactose and D-Glucose, ATPase component (characterized) 41% 79% 213.8 CP4-6 prophage; ABC transporter ATP-binding protein AfuC 42% 258.8
sucrose catabolism gtsD med ABC transporter for D-Galactose and D-Glucose, ATPase component (characterized) 41% 79% 213.8 CP4-6 prophage; ABC transporter ATP-binding protein AfuC 42% 258.8
trehalose catabolism gtsD med ABC transporter for D-Galactose and D-Glucose, ATPase component (characterized) 41% 79% 213.8 CP4-6 prophage; ABC transporter ATP-binding protein AfuC 42% 258.8
D-maltose catabolism malK1 med MalK; aka Sugar ABC transporter, ATP-binding protein, component of The maltose, maltotriose, mannotetraose (MalE1)/maltose, maltotriose, trehalose (MalE2) porter (Nanavati et al., 2005). For MalG1 (823aas) and MalG2 (833aas), the C-terminal transmembrane domain with 6 putative TMSs is preceded by a single N-terminal TMS and a large (600 residue) hydrophilic region showing sequence similarity to MLP1 and 2 (9.A.14; e-12 & e-7) as well as other proteins (characterized) 43% 79% 213 CP4-6 prophage; ABC transporter ATP-binding protein AfuC 42% 258.8
D-cellobiose catabolism aglK' med Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 40% 84% 209.5 CP4-6 prophage; ABC transporter ATP-binding protein AfuC 42% 258.8
D-glucose catabolism aglK' med Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 40% 84% 209.5 CP4-6 prophage; ABC transporter ATP-binding protein AfuC 42% 258.8
lactose catabolism aglK' med Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 40% 84% 209.5 CP4-6 prophage; ABC transporter ATP-binding protein AfuC 42% 258.8
D-maltose catabolism aglK' med Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 40% 84% 209.5 CP4-6 prophage; ABC transporter ATP-binding protein AfuC 42% 258.8
sucrose catabolism aglK' med Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 40% 84% 209.5 CP4-6 prophage; ABC transporter ATP-binding protein AfuC 42% 258.8
trehalose catabolism aglK' med Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 40% 84% 209.5 CP4-6 prophage; ABC transporter ATP-binding protein AfuC 42% 258.8
trehalose catabolism treV med TreV, component of Trehalose porter (characterized) 43% 75% 206.5 CP4-6 prophage; ABC transporter ATP-binding protein AfuC 42% 258.8
L-histidine catabolism hutV med ABC transporter for L-Histidine, ATPase component (characterized) 40% 85% 161 CP4-6 prophage; ABC transporter ATP-binding protein AfuC 42% 258.8
D-maltose catabolism malK lo ABC-type maltose transporter (subunit 3/3) (EC 7.5.2.1) (characterized) 40% 94% 228.4 CP4-6 prophage; ABC transporter ATP-binding protein AfuC 42% 258.8
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) 37% 96% 220.7 CP4-6 prophage; ABC transporter ATP-binding protein AfuC 42% 258.8
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) 37% 96% 220.7 CP4-6 prophage; ABC transporter ATP-binding protein AfuC 42% 258.8
D-xylose catabolism gtsD lo ABC transporter for D-Glucose-6-Phosphate, ATPase component (characterized) 37% 97% 218.8 CP4-6 prophage; ABC transporter ATP-binding protein AfuC 42% 258.8
D-mannitol catabolism mtlK lo ABC transporter for D-mannitol and D-mannose, ATPase component (characterized) 37% 99% 218 CP4-6 prophage; ABC transporter ATP-binding protein AfuC 42% 258.8
xylitol catabolism HSERO_RS17020 lo ABC-type sugar transport system, ATPase component protein (characterized, see rationale) 38% 88% 214.5 CP4-6 prophage; ABC transporter ATP-binding protein AfuC 42% 258.8
xylitol catabolism Dshi_0546 lo ABC transporter for Xylitol, ATPase component (characterized) 37% 99% 211.5 CP4-6 prophage; ABC transporter ATP-binding protein AfuC 42% 258.8
D-cellobiose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 35% 92% 189.9 CP4-6 prophage; ABC transporter ATP-binding protein AfuC 42% 258.8
D-galactose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 35% 92% 189.9 CP4-6 prophage; ABC transporter ATP-binding protein AfuC 42% 258.8
D-glucose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 35% 92% 189.9 CP4-6 prophage; ABC transporter ATP-binding protein AfuC 42% 258.8
lactose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 35% 92% 189.9 CP4-6 prophage; ABC transporter ATP-binding protein AfuC 42% 258.8
D-maltose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 35% 92% 189.9 CP4-6 prophage; ABC transporter ATP-binding protein AfuC 42% 258.8
D-mannose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 35% 92% 189.9 CP4-6 prophage; ABC transporter ATP-binding protein AfuC 42% 258.8
sucrose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 35% 92% 189.9 CP4-6 prophage; ABC transporter ATP-binding protein AfuC 42% 258.8
trehalose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 35% 92% 189.9 CP4-6 prophage; ABC transporter ATP-binding protein AfuC 42% 258.8
glycerol catabolism glpT lo ABC transporter for Glycerol, ATPase component 2 (characterized) 34% 80% 163.7 CP4-6 prophage; ABC transporter ATP-binding protein AfuC 42% 258.8
glycerol catabolism glpS lo ABC transporter for Glycerol, ATPase component 1 (characterized) 34% 96% 157.5 CP4-6 prophage; ABC transporter ATP-binding protein AfuC 42% 258.8

Sequence Analysis Tools

View 8500849 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

MADITLAGIGKAYGAHAVLDGLSLTVNHGECFTLLGPSGCGKTVLLRLIAGFETPDAGTI
SIGGEPVSDAVTGDCVPPDARDLGVVFQDYAVWPHMSVADNIGYPLKLAGLPAAERTRQV
LETVEMVNLTGLENRMPSQLSGGQQQRVALARALVGRPSLMLLDEPLCNLDANLREEMRF
EIKELQRTLGITILYVTHDQEIALAISDRLAIMDHAGAIRQVGTPWEIFERPADEFVFRF
MGVANFLPARRRGMAMLAAGGEQPVPWGLPDGDAEHWMAGFRPSDVRLARQGDGLRGTVR
RASFLGAMTDYLIEVDGASFRTQLDTHEALARGLMFAEGEPCVVGFHDLHWFDAATVAAQ
APQGGE

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 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