GapMind for catabolism of small carbon sources

 

Protein Ac3H11_1610 in Acidovorax sp. GW101-3H11

Annotation: FitnessBrowser__acidovorax_3H11:Ac3H11_1610

Length: 362 amino acids

Source: acidovorax_3H11 in FitnessBrowser

Candidate for 36 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) 40% 100% 258.8 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 43% 258.5
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) 43% 92% 258.5 ABC transporter for Xylitol, ATPase component 40% 258.8
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) 43% 92% 258.5 ABC transporter for Xylitol, ATPase component 40% 258.8
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) 43% 92% 258.5 ABC transporter for Xylitol, ATPase component 40% 258.8
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) 43% 92% 258.5 ABC transporter for Xylitol, ATPase component 40% 258.8
D-maltose catabolism thuK 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) 43% 92% 258.5 ABC transporter for Xylitol, ATPase component 40% 258.8
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) 43% 92% 258.5 ABC transporter for Xylitol, ATPase component 40% 258.8
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) 43% 92% 258.5 ABC transporter for Xylitol, ATPase component 40% 258.8
sucrose catabolism thuK 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) 43% 92% 258.5 ABC transporter for Xylitol, ATPase component 40% 258.8
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) 43% 92% 258.5 ABC transporter for Xylitol, ATPase component 40% 258.8
trehalose catabolism thuK 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) 43% 92% 258.5 ABC transporter for Xylitol, ATPase component 40% 258.8
putrescine catabolism potA med PotG aka B0855, component of Putrescine porter (characterized) 41% 95% 258.1 ABC transporter for Xylitol, ATPase component 40% 258.8
D-sorbitol (glucitol) catabolism mtlK med ABC transporter for D-Sorbitol, ATPase component (characterized) 40% 100% 251.5 ABC transporter for Xylitol, ATPase component 40% 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) 42% 93% 249.2 ABC transporter for Xylitol, ATPase component 40% 258.8
D-mannitol catabolism mtlK med ABC transporter for D-mannitol and D-mannose, ATPase component (characterized) 41% 98% 246.1 ABC transporter for Xylitol, ATPase component 40% 258.8
lactose catabolism lacK med ABC transporter for Lactose, ATPase component (characterized) 40% 94% 244.2 ABC transporter for Xylitol, ATPase component 40% 258.8
N-acetyl-D-glucosamine catabolism SMc02869 med N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized) 42% 86% 236.5 ABC transporter for Xylitol, ATPase component 40% 258.8
D-glucosamine (chitosamine) catabolism SMc02869 med N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized) 42% 86% 236.5 ABC transporter for Xylitol, ATPase component 40% 258.8
L-arabinose catabolism xacJ med Xylose/arabinose import ATP-binding protein XacJ; EC 7.5.2.13 (characterized, see rationale) 45% 75% 235.7 ABC transporter for Xylitol, ATPase component 40% 258.8
D-cellobiose catabolism SMc04256 med ABC transporter for D-Cellobiose and D-Salicin, ATPase component (characterized) 40% 85% 228.4 ABC transporter for Xylitol, ATPase component 40% 258.8
D-cellobiose catabolism aglK' med Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 41% 84% 226.1 ABC transporter for Xylitol, ATPase component 40% 258.8
D-glucose catabolism aglK' med Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 41% 84% 226.1 ABC transporter for Xylitol, ATPase component 40% 258.8
lactose catabolism aglK' med Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 41% 84% 226.1 ABC transporter for Xylitol, ATPase component 40% 258.8
D-maltose catabolism aglK med Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 41% 84% 226.1 ABC transporter for Xylitol, ATPase component 40% 258.8
D-maltose catabolism aglK' med Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 41% 84% 226.1 ABC transporter for Xylitol, ATPase component 40% 258.8
sucrose catabolism aglK med Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 41% 84% 226.1 ABC transporter for Xylitol, ATPase component 40% 258.8
sucrose catabolism aglK' med Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 41% 84% 226.1 ABC transporter for Xylitol, ATPase component 40% 258.8
trehalose catabolism aglK med Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 41% 84% 226.1 ABC transporter for Xylitol, ATPase component 40% 258.8
trehalose catabolism aglK' med Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 41% 84% 226.1 ABC transporter for Xylitol, ATPase component 40% 258.8
D-xylose catabolism gtsD med ABC transporter for D-Glucose-6-Phosphate, ATPase component (characterized) 40% 76% 222.2 ABC transporter for Xylitol, ATPase component 40% 258.8
D-maltose catabolism malK lo ABC-type maltose transporter (subunit 3/3) (EC 7.5.2.1) (characterized) 39% 99% 249.2 ABC transporter for Xylitol, ATPase component 40% 258.8
L-arabinose catabolism xacK lo Xylose/arabinose import ATP-binding protein XacK; EC 7.5.2.13 (characterized, see rationale) 39% 97% 238.4 ABC transporter for Xylitol, ATPase component 40% 258.8
trehalose catabolism malK lo MsmK aka SMU.882, component of The raffinose/stachyose transporter, MsmEFGK (MalK (3.A.1.1.27) can probably substitute for MsmK; Webb et al., 2008). This system may also transport melibiose, isomaltotriose and sucrose as well as isomaltosaccharides (characterized) 36% 95% 225.7 ABC transporter for Xylitol, ATPase component 40% 258.8
xylitol catabolism HSERO_RS17020 lo ABC-type sugar transport system, ATPase component protein (characterized, see rationale) 38% 82% 221.9 ABC transporter for Xylitol, ATPase component 40% 258.8
L-proline catabolism proV lo glycine betaine/l-proline transport atp-binding protein prov (characterized) 40% 56% 174.5 ABC transporter for Xylitol, ATPase component 40% 258.8
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% 64% 172.9 ABC transporter for Xylitol, ATPase component 40% 258.8

Sequence Analysis Tools

View Ac3H11_1610 at FitnessBrowser

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Find functional residues: SitesBLAST

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Predict transmenbrane helices: Phobius

Predict protein localization: PSORTb

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Sequence

MSFLQLTDVTKFYGSTCAVQSMNLSVEKGEFVSLLGPSGCGKTTTLQMVAGFEAVTSGRI
ELAGRDITHAKANTRGLGIVFQSYALFPHMTVADNVSFGLEMRKVPKAERKDRVAQALGL
VHLEKHAGRYPRELSGGQRQRVALARALVIEPPVLLLDEPLSNLDAKLREEMQFELRQIQ
RKVGTTTVMVTHDQSEAMSISDRVVVMEAGRATQIDHPHRVYEHPRTRFISTFVGKANLV
PGQVTTASATHTHVGAGPIEVRVEGAQFRPGAAVLLSVRPEKLQLVPTVQGRIDGEVCER
FFLGSQWLYRVGTGMGDLMVLAPNDGRGALEEGERTGLDWPDHCMRLLPADEAALADTEA
TP

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:

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