GapMind for catabolism of small carbon sources

 

Protein 208681 in Desulfovibrio vulgaris Hildenborough

Annotation: DVU3161 ABC transporter, ATP-binding protein

Length: 349 amino acids

Source: 882 in MicrobesOnline

Candidate for 59 steps in catabolism of small carbon sources

Pathway Step Score Similar to Id. Cov. Bits Other hit Other id. Other bits
xylitol catabolism Dshi_0546 med ABC transporter for Xylitol, ATPase component (characterized) 47% 100% 302.4 AlgS, component of Alginate (MW 27,000 Da) (and Alginate oligosaccharides) uptake porter. Sphingomonas species A1 is a 'pit-forming' bacterium that directly incorporates alginate into its cytoplasm through a pit-dependent transport system, termed a 'superchannel' (Murata et al., 2008). The pit is a novel organ acquired through the fluidity and reconstitution of cell surface molecules, and through cooperation with the transport machinery in the cells. It confers upon bacterial cells a more efficient way to secure and assimilate macromolecules 46% 298.5
D-maltose catabolism thuK med Trehalose/maltose import ATP-binding protein MalK; EC 7.5.2.1 (characterized) 46% 99% 293.9 ABC transporter for Xylitol, ATPase component 47% 302.4
trehalose catabolism thuK med Trehalose/maltose import ATP-binding protein MalK; EC 7.5.2.1 (characterized) 46% 99% 293.9 ABC transporter for Xylitol, ATPase component 47% 302.4
D-sorbitol (glucitol) catabolism mtlK med ABC transporter for D-Sorbitol, ATPase component (characterized) 46% 99% 291.6 ABC transporter for Xylitol, ATPase component 47% 302.4
D-cellobiose catabolism msiK med MsiK protein, 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) 44% 99% 291.2 ABC transporter for Xylitol, ATPase component 47% 302.4
sucrose catabolism thuK med ABC transporter (characterized, see rationale) 46% 92% 291.2 ABC transporter for Xylitol, ATPase component 47% 302.4
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) 45% 96% 289.7 ABC transporter for Xylitol, ATPase component 47% 302.4
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) 45% 96% 289.7 ABC transporter for Xylitol, ATPase component 47% 302.4
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) 45% 96% 289.7 ABC transporter for Xylitol, ATPase component 47% 302.4
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) 45% 96% 289.7 ABC transporter for Xylitol, ATPase component 47% 302.4
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) 45% 96% 289.7 ABC transporter for Xylitol, ATPase component 47% 302.4
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) 45% 96% 289.7 ABC transporter for Xylitol, ATPase component 47% 302.4
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) 45% 96% 289.7 ABC transporter for Xylitol, ATPase component 47% 302.4
D-mannitol catabolism mtlK med SmoK aka POLK, component of Hexitol (glucitol; mannitol) porter (characterized) 46% 98% 288.5 ABC transporter for Xylitol, ATPase component 47% 302.4
D-maltose catabolism malK_Aa med ABC-type maltose transporter (EC 7.5.2.1) (characterized) 44% 95% 286.6 ABC transporter for Xylitol, ATPase component 47% 302.4
xylitol catabolism HSERO_RS17020 med ABC-type sugar transport system, ATPase component protein (characterized, see rationale) 45% 89% 283.1 ABC transporter for Xylitol, ATPase component 47% 302.4
L-arabinose catabolism xacJ med Xylose/arabinose import ATP-binding protein XacJ; EC 7.5.2.13 (characterized, see rationale) 45% 95% 282 ABC transporter for Xylitol, ATPase component 47% 302.4
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% 98% 281.6 ABC transporter for Xylitol, ATPase component 47% 302.4
L-arabinose catabolism xacK med Xylose/arabinose import ATP-binding protein XacK; EC 7.5.2.13 (characterized, see rationale) 44% 95% 280.4 ABC transporter for Xylitol, ATPase component 47% 302.4
D-glucosamine (chitosamine) catabolism SM_b21216 med ABC transporter for D-Glucosamine, ATPase component (characterized) 44% 98% 280.4 ABC transporter for Xylitol, ATPase component 47% 302.4
D-xylose catabolism gtsD med ABC transporter for D-Glucose-6-Phosphate, ATPase component (characterized) 43% 95% 279.3 ABC transporter for Xylitol, ATPase component 47% 302.4
D-maltose catabolism malK med ABC-type maltose transporter (subunit 3/3) (EC 7.5.2.1) (characterized) 42% 98% 278.5 ABC transporter for Xylitol, ATPase component 47% 302.4
D-galactose catabolism PfGW456L13_1897 med ABC transporter for D-Galactose and D-Glucose, ATPase component (characterized) 43% 94% 274.6 ABC transporter for Xylitol, ATPase component 47% 302.4
D-cellobiose catabolism SMc04256 med ABC transporter for D-Cellobiose and D-Salicin, ATPase component (characterized) 45% 100% 273.1 ABC transporter for Xylitol, ATPase component 47% 302.4
D-maltose catabolism malK_Sm med 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) 42% 99% 271.2 ABC transporter for Xylitol, ATPase component 47% 302.4
trehalose catabolism malK med 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) 42% 99% 271.2 ABC transporter for Xylitol, ATPase component 47% 302.4
D-maltose catabolism musK med ABC-type maltose transporter (EC 7.5.2.1) (characterized) 43% 99% 269.2 ABC transporter for Xylitol, ATPase component 47% 302.4
L-fucose catabolism SM_b21106 med ABC transporter for L-Fucose, ATPase component (characterized) 41% 100% 265.8 ABC transporter for Xylitol, ATPase component 47% 302.4
N-acetyl-D-glucosamine catabolism SMc02869 med N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized) 45% 100% 264.6 ABC transporter for Xylitol, ATPase component 47% 302.4
D-glucosamine (chitosamine) catabolism SMc02869 med N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized) 45% 100% 264.6 ABC transporter for Xylitol, ATPase component 47% 302.4
lactose catabolism lacK med ABC transporter for Lactose, ATPase component (characterized) 44% 90% 258.5 ABC transporter for Xylitol, ATPase component 47% 302.4
D-cellobiose catabolism aglK' med Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 42% 95% 257.3 ABC transporter for Xylitol, ATPase component 47% 302.4
D-glucose catabolism aglK' med Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 42% 95% 257.3 ABC transporter for Xylitol, ATPase component 47% 302.4
lactose catabolism aglK' med Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 42% 95% 257.3 ABC transporter for Xylitol, ATPase component 47% 302.4
D-maltose catabolism aglK med Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 42% 95% 257.3 ABC transporter for Xylitol, ATPase component 47% 302.4
D-maltose catabolism aglK' med Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 42% 95% 257.3 ABC transporter for Xylitol, ATPase component 47% 302.4
sucrose catabolism aglK med Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 42% 95% 257.3 ABC transporter for Xylitol, ATPase component 47% 302.4
sucrose catabolism aglK' med Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 42% 95% 257.3 ABC transporter for Xylitol, ATPase component 47% 302.4
trehalose catabolism aglK med Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 42% 95% 257.3 ABC transporter for Xylitol, ATPase component 47% 302.4
trehalose catabolism aglK' med Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 42% 95% 257.3 ABC transporter for Xylitol, ATPase component 47% 302.4
D-maltose catabolism malK_Bb med ABC-type maltose transport, ATP binding protein (characterized, see rationale) 41% 99% 251.9 ABC transporter for Xylitol, ATPase component 47% 302.4
putrescine catabolism potA med spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31 (characterized) 46% 72% 236.5 ABC transporter for Xylitol, ATPase component 47% 302.4
L-proline catabolism opuBA med BilEA aka OpuBA protein, component of A proline/glycine betaine uptake system. Also reported to be a bile exclusion system that exports oxgall and other bile compounds, BilEA/EB or OpuBA/BB (required for normal virulence) (characterized) 41% 73% 177.9 ABC transporter for Xylitol, ATPase component 47% 302.4
L-histidine catabolism Ac3H11_2560 med ABC transporter for L-Histidine, ATPase component (characterized) 42% 83% 159.5 ABC transporter for Xylitol, ATPase component 47% 302.4
trehalose catabolism treV lo TreV, component of Trehalose porter (characterized) 37% 94% 225.3 ABC transporter for Xylitol, ATPase component 47% 302.4
glycerol catabolism glpT lo GlpT, component of Glycerol uptake porter, GlpSTPQV (characterized) 36% 94% 209.9 ABC transporter for Xylitol, ATPase component 47% 302.4
D-cellobiose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 34% 99% 201.8 ABC transporter for Xylitol, ATPase component 47% 302.4
D-galactose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 34% 99% 201.8 ABC transporter for Xylitol, ATPase component 47% 302.4
D-glucose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 34% 99% 201.8 ABC transporter for Xylitol, ATPase component 47% 302.4
lactose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 34% 99% 201.8 ABC transporter for Xylitol, ATPase component 47% 302.4
D-maltose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 34% 99% 201.8 ABC transporter for Xylitol, ATPase component 47% 302.4
D-mannose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 34% 99% 201.8 ABC transporter for Xylitol, ATPase component 47% 302.4
sucrose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 34% 99% 201.8 ABC transporter for Xylitol, ATPase component 47% 302.4
trehalose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 34% 99% 201.8 ABC transporter for Xylitol, ATPase component 47% 302.4
L-arabinose catabolism araV lo AraV, component of Arabinose, fructose, xylose porter (characterized) 34% 96% 197.6 ABC transporter for Xylitol, ATPase component 47% 302.4
D-fructose catabolism araV lo AraV, component of Arabinose, fructose, xylose porter (characterized) 34% 96% 197.6 ABC transporter for Xylitol, ATPase component 47% 302.4
sucrose catabolism araV lo AraV, component of Arabinose, fructose, xylose porter (characterized) 34% 96% 197.6 ABC transporter for Xylitol, ATPase component 47% 302.4
D-xylose catabolism araV lo AraV, component of Arabinose, fructose, xylose porter (characterized) 34% 96% 197.6 ABC transporter for Xylitol, ATPase component 47% 302.4
glycerol catabolism glpS lo ABC transporter for Glycerol, ATPase component 1 (characterized) 33% 94% 177.9 ABC transporter for Xylitol, ATPase component 47% 302.4

Sequence Analysis Tools

View 208681 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

MSTIVLDKVSRHWGDVRAVDDVSFEVEQGDMLVLLGPSGCGKSTTLRLIAGLESVTSGRI
LIGGRDVTNLPPAQRQLAMVFQSYALFPHLTVRDNILFGLVVRKVPAAERQKRLDRAVEI
LGLGKLLERKPGELSGGQQQRVALGRALVAEAAVCLMDEPLSNLDAKLRQEMRREIRALQ
QTLGMTMVYVTHDQTEAMSMADRIILMQGGRIVQNATPTEMYSRPATAFAGSFIGTPPMN
LVRLQGNDDGIRVAGSRSGRVTCHAGADCMLGIRPEHIRIVDDGWRAVVESVEYLGSNSV
LSCRVGSEELSVVVHGVTDTVVGAEIYLHCPEEHVHIFDAATGARHATT

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