GapMind for catabolism of small carbon sources

 

Protein Dsui_3464 in Dechlorosoma suillum PS

Annotation: FitnessBrowser__PS:Dsui_3464

Length: 263 amino acids

Source: PS in FitnessBrowser

Candidate for 39 steps in catabolism of small carbon sources

Pathway Step Score Similar to Id. Cov. Bits Other hit Other id. Other bits
L-histidine catabolism Ac3H11_2560 med ABC transporter for L-Histidine, ATPase component (characterized) 47% 99% 226.9 Nitrate import ATP-binding protein NrtC; EC 7.3.2.4 45% 225.3
putrescine catabolism potA lo PotG aka B0855, component of Putrescine porter (characterized) 42% 66% 182.2 ABC transporter for L-Histidine, ATPase component 47% 226.9
D-maltose catabolism malK lo ABC-type maltose transporter (subunit 3/3) (EC 7.5.2.1) (characterized) 44% 56% 177.2 ABC transporter for L-Histidine, ATPase component 47% 226.9
D-maltose catabolism malK_Bb lo ABC-type maltose transport, ATP binding protein (characterized, see rationale) 44% 62% 177.2 ABC transporter for L-Histidine, ATPase component 47% 226.9
D-maltose catabolism aglK lo ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized) 44% 58% 175.6 ABC transporter for L-Histidine, ATPase component 47% 226.9
D-maltose catabolism thuK lo ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized) 44% 58% 175.6 ABC transporter for L-Histidine, ATPase component 47% 226.9
sucrose catabolism aglK lo ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized) 44% 58% 175.6 ABC transporter for L-Histidine, ATPase component 47% 226.9
trehalose catabolism aglK lo ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized) 44% 58% 175.6 ABC transporter for L-Histidine, ATPase component 47% 226.9
trehalose catabolism thuK lo Trehalose/maltose import ATP-binding protein MalK; EC 7.5.2.1 (characterized) 45% 58% 175.3 ABC transporter for L-Histidine, ATPase component 47% 226.9
D-maltose catabolism malK1 lo 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% 58% 174.9 ABC transporter for L-Histidine, ATPase component 47% 226.9
N-acetyl-D-glucosamine catabolism SMc02869 lo N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized) 45% 65% 174.5 ABC transporter for L-Histidine, ATPase component 47% 226.9
D-glucosamine (chitosamine) catabolism SMc02869 lo N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized) 45% 65% 174.5 ABC transporter for L-Histidine, ATPase component 47% 226.9
D-glucosamine (chitosamine) catabolism SM_b21216 lo ABC transporter for D-Glucosamine, ATPase component (characterized) 44% 59% 173.7 ABC transporter for L-Histidine, ATPase component 47% 226.9
D-cellobiose catabolism SMc04256 lo ABC transporter for D-Cellobiose and D-Salicin, ATPase component (characterized) 44% 59% 172.6 ABC transporter for L-Histidine, ATPase component 47% 226.9
D-sorbitol (glucitol) catabolism mtlK lo ABC transporter for D-Sorbitol, ATPase component (characterized) 42% 56% 171 ABC transporter for L-Histidine, ATPase component 47% 226.9
D-maltose catabolism malK_Aa lo ABC-type maltose transporter (EC 7.5.2.1) (characterized) 41% 56% 170.6 ABC transporter for L-Histidine, ATPase component 47% 226.9
lactose catabolism lacK lo LacK, component of Lactose porter (characterized) 43% 59% 170.2 ABC transporter for L-Histidine, ATPase component 47% 226.9
D-cellobiose catabolism aglK' lo Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 44% 56% 168.3 ABC transporter for L-Histidine, ATPase component 47% 226.9
D-glucose catabolism aglK' lo Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 44% 56% 168.3 ABC transporter for L-Histidine, ATPase component 47% 226.9
lactose catabolism aglK' lo Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 44% 56% 168.3 ABC transporter for L-Histidine, ATPase component 47% 226.9
D-maltose catabolism aglK' lo Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 44% 56% 168.3 ABC transporter for L-Histidine, ATPase component 47% 226.9
sucrose catabolism aglK' lo Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 44% 56% 168.3 ABC transporter for L-Histidine, ATPase component 47% 226.9
trehalose catabolism aglK' lo Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 44% 56% 168.3 ABC transporter for L-Histidine, ATPase component 47% 226.9
D-mannitol catabolism mtlK lo SmoK aka POLK, component of Hexitol (glucitol; mannitol) porter (characterized) 43% 63% 167.9 ABC transporter for L-Histidine, ATPase component 47% 226.9
sucrose catabolism thuK lo ABC transporter (characterized, see rationale) 42% 55% 164.1 ABC transporter for L-Histidine, ATPase component 47% 226.9
L-arabinose catabolism xacJ lo Xylose/arabinose import ATP-binding protein XacJ; EC 7.5.2.13 (characterized, see rationale) 43% 54% 161.8 ABC transporter for L-Histidine, ATPase component 47% 226.9
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) 39% 55% 161 ABC transporter for L-Histidine, ATPase component 47% 226.9
D-cellobiose catabolism gtsD 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) 41% 57% 160.6 ABC transporter for L-Histidine, ATPase component 47% 226.9
D-glucose catabolism gtsD 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) 41% 57% 160.6 ABC transporter for L-Histidine, ATPase component 47% 226.9
lactose catabolism gtsD 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) 41% 57% 160.6 ABC transporter for L-Histidine, ATPase component 47% 226.9
D-maltose catabolism gtsD 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) 41% 57% 160.6 ABC transporter for L-Histidine, ATPase component 47% 226.9
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) 41% 57% 160.6 ABC transporter for L-Histidine, ATPase component 47% 226.9
sucrose catabolism gtsD 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) 41% 57% 160.6 ABC transporter for L-Histidine, ATPase component 47% 226.9
trehalose catabolism gtsD 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) 41% 57% 160.6 ABC transporter for L-Histidine, ATPase component 47% 226.9
xylitol catabolism Dshi_0546 lo ABC transporter for Xylitol, ATPase component (characterized) 42% 62% 159.5 ABC transporter for L-Histidine, ATPase component 47% 226.9
xylitol catabolism HSERO_RS17020 lo ABC-type sugar transport system, ATPase component protein (characterized, see rationale) 42% 51% 154.8 ABC transporter for L-Histidine, ATPase component 47% 226.9
D-maltose catabolism musK lo ABC-type maltose transporter (EC 7.5.2.1) (characterized) 40% 59% 154.1 ABC transporter for L-Histidine, ATPase component 47% 226.9
trehalose catabolism treV lo TreV, component of Trehalose porter (characterized) 39% 62% 138.7 ABC transporter for L-Histidine, ATPase component 47% 226.9
L-arabinose catabolism xylGsa lo Xylose/arabinose import ATP-binding protein XylG; EC 7.5.2.13 (characterized, see rationale) 32% 100% 125.6 ABC transporter for L-Histidine, ATPase component 47% 226.9

Sequence Analysis Tools

View Dsui_3464 at FitnessBrowser

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

Find homologs in fast.genomics

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Sequence

MSDILIKDVQKVFKTPGGDVTALKDINLTVKQGEFVCLLGPSGCGKSTLLNAVAGFQPPS
AGEIVIEGKKILTPGPDRGMVFQEYALFPWMTVAQNIAFGLQIQKKEKAEIDLTVNQLLD
LLHLKDFRDRFPKDLSGGMRQRVAIARVLALDSPIMLMDEPFGALDALTRRNLQDELLRI
WEKLNKTILFVTHSIEESIYLADRIVVMTYRPGTIKRDQYVTMPRPRDPSSHEFNELKRE
LGRLVMEEQQRHAADELKLAAVD

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