GapMind for catabolism of small carbon sources

 

Protein WP_058930800.1 in Pseudarthrobacter sulfonivorans Ar51

Annotation: NCBI__GCF_001484605.1:WP_058930800.1

Length: 373 amino acids

Source: GCF_001484605.1 in NCBI

Candidate for 58 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% 91% 265 Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD 42% 277.7
D-maltose catabolism thuK med Trehalose/maltose import ATP-binding protein MalK; EC 7.5.2.1 (characterized) 40% 98% 250 Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD 42% 277.7
trehalose catabolism thuK med Trehalose/maltose import ATP-binding protein MalK; EC 7.5.2.1 (characterized) 40% 98% 250 Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD 42% 277.7
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) 44% 87% 247.7 Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD 42% 277.7
D-cellobiose catabolism gtsD med GtsD (GLcK), component of Glucose porter, GtsABCD (characterized) 43% 77% 236.5 Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD 42% 277.7
D-glucose catabolism gtsD med GtsD (GLcK), component of Glucose porter, GtsABCD (characterized) 43% 77% 236.5 Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD 42% 277.7
lactose catabolism gtsD med GtsD (GLcK), component of Glucose porter, GtsABCD (characterized) 43% 77% 236.5 Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD 42% 277.7
D-maltose catabolism gtsD med GtsD (GLcK), component of Glucose porter, GtsABCD (characterized) 43% 77% 236.5 Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD 42% 277.7
sucrose catabolism gtsD med GtsD (GLcK), component of Glucose porter, GtsABCD (characterized) 43% 77% 236.5 Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD 42% 277.7
trehalose catabolism gtsD med GtsD (GLcK), component of Glucose porter, GtsABCD (characterized) 43% 77% 236.5 Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD 42% 277.7
D-mannitol catabolism mtlK med SmoK aka POLK, component of Hexitol (glucitol; mannitol) porter (characterized) 41% 90% 230.7 Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD 42% 277.7
D-maltose catabolism malK_Aa med ABC-type maltose transporter (EC 7.5.2.1) (characterized) 41% 76% 227.3 Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD 42% 277.7
D-sorbitol (glucitol) catabolism mtlK med ABC transporter for D-Sorbitol, ATPase component (characterized) 47% 72% 226.5 Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD 42% 277.7
L-fucose catabolism SM_b21106 med ABC transporter for L-Fucose, ATPase component (characterized) 40% 86% 225.7 Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD 42% 277.7
L-arabinose catabolism xacJ med Xylose/arabinose import ATP-binding protein XacJ; EC 7.5.2.13 (characterized, see rationale) 41% 77% 224.6 Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD 42% 277.7
D-glucosamine (chitosamine) catabolism SM_b21216 med ABC transporter for D-Glucosamine, ATPase component (characterized) 40% 82% 224.2 Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD 42% 277.7
xylitol catabolism HSERO_RS17020 med ABC-type sugar transport system, ATPase component protein (characterized, see rationale) 40% 72% 223.4 Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD 42% 277.7
trehalose catabolism treV med TreV, component of Trehalose porter (characterized) 42% 77% 219.9 Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD 42% 277.7
N-acetyl-D-glucosamine catabolism SMc02869 med N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized) 43% 76% 215.7 Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD 42% 277.7
D-glucosamine (chitosamine) catabolism SMc02869 med N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized) 43% 76% 215.7 Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD 42% 277.7
D-cellobiose catabolism aglK' med Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 40% 77% 213.4 Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD 42% 277.7
D-glucose catabolism aglK' med Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 40% 77% 213.4 Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD 42% 277.7
lactose catabolism aglK' med Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 40% 77% 213.4 Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD 42% 277.7
D-maltose catabolism aglK med Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 40% 77% 213.4 Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD 42% 277.7
D-maltose catabolism aglK' med Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 40% 77% 213.4 Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD 42% 277.7
sucrose catabolism aglK med Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 40% 77% 213.4 Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD 42% 277.7
sucrose catabolism aglK' med Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 40% 77% 213.4 Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD 42% 277.7
trehalose catabolism aglK med Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 40% 77% 213.4 Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD 42% 277.7
trehalose catabolism aglK' med Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 40% 77% 213.4 Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD 42% 277.7
D-maltose catabolism malK_Bb med ABC-type maltose transport, ATP binding protein (characterized, see rationale) 41% 72% 211.1 Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD 42% 277.7
L-histidine catabolism Ac3H11_2560 med ABC transporter for L-Histidine, ATPase component (characterized) 42% 83% 168.3 Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD 42% 277.7
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% 93% 237.3 Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD 42% 277.7
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% 93% 237.3 Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD 42% 277.7
D-cellobiose catabolism msiK lo 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) 39% 93% 235 Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD 42% 277.7
D-galactose catabolism PfGW456L13_1897 lo ABC transporter for D-Galactose and D-Glucose, ATPase component (characterized) 38% 92% 233 Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD 42% 277.7
D-xylose catabolism gtsD lo ABC transporter for D-Glucose-6-Phosphate, ATPase component (characterized) 37% 92% 231.5 Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD 42% 277.7
lactose catabolism lacK lo ABC transporter for Lactose, ATPase component (characterized) 38% 98% 230.7 Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD 42% 277.7
D-maltose catabolism malK lo Maltose/maltodextrin import ATP-binding protein MalK; EC 7.5.2.1 (characterized) 40% 85% 230.3 Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD 42% 277.7
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) 36% 98% 223.4 Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD 42% 277.7
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) 36% 98% 223.4 Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD 42% 277.7
D-maltose catabolism musK lo ABC-type maltose transporter (EC 7.5.2.1) (characterized) 38% 88% 221.5 Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD 42% 277.7
L-arabinose catabolism xacK lo Xylose/arabinose import ATP-binding protein XacK; EC 7.5.2.13 (characterized, see rationale) 37% 93% 219.5 Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD 42% 277.7
D-cellobiose catabolism SMc04256 lo ABC transporter for D-Cellobiose and D-Salicin, ATPase component (characterized) 37% 90% 212.6 Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD 42% 277.7
xylitol catabolism Dshi_0546 lo ABC transporter for Xylitol, ATPase component (characterized) 38% 86% 212.6 Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD 42% 277.7
D-cellobiose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 36% 98% 209.9 Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD 42% 277.7
D-galactose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 36% 98% 209.9 Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD 42% 277.7
D-glucose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 36% 98% 209.9 Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD 42% 277.7
lactose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 36% 98% 209.9 Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD 42% 277.7
D-maltose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 36% 98% 209.9 Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD 42% 277.7
D-mannose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 36% 98% 209.9 Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD 42% 277.7
sucrose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 36% 98% 209.9 Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD 42% 277.7
trehalose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 36% 98% 209.9 Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD 42% 277.7
L-proline catabolism opuBA lo BusAA, component of Uptake system for glycine-betaine (high affinity) and proline (low affinity) (OpuAA-OpuABC) or BusAA-ABC of Lactococcus lactis). BusAA, the ATPase subunit, has a C-terminal tandem cystathionine β-synthase (CBS) domain which is the cytoplasmic K+ sensor for osmotic stress (osmotic strength)while the BusABC subunit has the membrane and receptor domains fused to each other (Biemans-Oldehinkel et al., 2006; Mahmood et al., 2006; Gul et al. 2012). An N-terminal amphipathic α-helix of OpuA is necessary for high activity but is not critical for biogenesis or the ionic regulation of transport (characterized) 35% 82% 200.3 Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD 42% 277.7
L-arabinose catabolism araV lo AraV, component of Arabinose, fructose, xylose porter (characterized) 34% 78% 189.9 Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD 42% 277.7
D-fructose catabolism araV lo AraV, component of Arabinose, fructose, xylose porter (characterized) 34% 78% 189.9 Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD 42% 277.7
sucrose catabolism araV lo AraV, component of Arabinose, fructose, xylose porter (characterized) 34% 78% 189.9 Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD 42% 277.7
D-xylose catabolism araV lo AraV, component of Arabinose, fructose, xylose porter (characterized) 34% 78% 189.9 Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD 42% 277.7
L-proline catabolism proV lo glycine betaine/l-proline transport atp-binding protein prov (characterized) 33% 86% 179.9 Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD 42% 277.7

Sequence Analysis Tools

View WP_058930800.1 at NCBI

Find papers: PaperBLAST

Find functional residues: SitesBLAST

Search for conserved domains

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Compare to protein structures

Predict transmenbrane helices: Phobius

Predict protein localization: PSORTb

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Sequence

MTTSVISAAASTRTTASAQGSIELRQVRKTYGDVVAVDELDLVVEPGEFVTLLGPSGSGK
TTTMMMVAGFEEHTSGSVLIDGKPVDSLPPRDRNLGVVFQNYALFPHMSARENVEFALRM
RKIPKAERRQRADSALERVGLGKMGDRKPRQLSGGQQQRVALARSLVFNPAALLLDEPMA
ALDKRLREHMQEEIKTLQKSLGISVLFVTHDQDEAMAMSDRIVVMKDGRIVQSGPPEEVY
NHPLTDWVASFLGDTNLIPCTVLERKDGEALVDLGGLGLGRVRDRGVTGEKYAVSIRPEN
LKFSSEASTDNCGKASLVSSTNLGATVRHRLTAGGHELQVRELSSDASGRPASGAELFVT
WEPDKAQLLVLEQ

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