GapMind for catabolism of small carbon sources

 

Protein 3608624 in Dinoroseobacter shibae DFL-12

Annotation: Dshi_2017 ABC transporter related (RefSeq)

Length: 333 amino acids

Source: Dino in FitnessBrowser

Candidate for 35 steps in catabolism of small carbon sources

Pathway Step Score Similar to Id. Cov. Bits Other hit Other id. Other bits
N-acetyl-D-glucosamine catabolism SMc02869 med N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized) 52% 100% 342 sn-glycerol-3-phosphate import ATP-binding protein UgpC; EC 7.6.2.10 56% 342.4
D-glucosamine (chitosamine) catabolism SMc02869 med N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized) 52% 100% 342 sn-glycerol-3-phosphate import ATP-binding protein UgpC; EC 7.6.2.10 56% 342.4
sucrose catabolism thuK med ThuK aka RB0314 aka SMB20328, component of Trehalose/maltose/sucrose porter (trehalose inducible) (characterized) 53% 97% 329.7 sn-glycerol-3-phosphate import ATP-binding protein UgpC; EC 7.6.2.10 56% 342.4
trehalose catabolism thuK med ThuK aka RB0314 aka SMB20328, component of Trehalose/maltose/sucrose porter (trehalose inducible) (characterized) 53% 97% 329.7 sn-glycerol-3-phosphate import ATP-binding protein UgpC; EC 7.6.2.10 56% 342.4
D-cellobiose catabolism gtsD med ABC transporter for D-Galactose and D-Glucose, ATPase component (characterized) 47% 95% 315.1 sn-glycerol-3-phosphate import ATP-binding protein UgpC; EC 7.6.2.10 56% 342.4
D-galactose catabolism PfGW456L13_1897 med ABC transporter for D-Galactose and D-Glucose, ATPase component (characterized) 47% 95% 315.1 sn-glycerol-3-phosphate import ATP-binding protein UgpC; EC 7.6.2.10 56% 342.4
D-glucose catabolism gtsD med ABC transporter for D-Galactose and D-Glucose, ATPase component (characterized) 47% 95% 315.1 sn-glycerol-3-phosphate import ATP-binding protein UgpC; EC 7.6.2.10 56% 342.4
lactose catabolism gtsD med ABC transporter for D-Galactose and D-Glucose, ATPase component (characterized) 47% 95% 315.1 sn-glycerol-3-phosphate import ATP-binding protein UgpC; EC 7.6.2.10 56% 342.4
D-maltose catabolism gtsD med ABC transporter for D-Galactose and D-Glucose, ATPase component (characterized) 47% 95% 315.1 sn-glycerol-3-phosphate import ATP-binding protein UgpC; EC 7.6.2.10 56% 342.4
sucrose catabolism gtsD med ABC transporter for D-Galactose and D-Glucose, ATPase component (characterized) 47% 95% 315.1 sn-glycerol-3-phosphate import ATP-binding protein UgpC; EC 7.6.2.10 56% 342.4
trehalose catabolism gtsD med ABC transporter for D-Galactose and D-Glucose, ATPase component (characterized) 47% 95% 315.1 sn-glycerol-3-phosphate import ATP-binding protein UgpC; EC 7.6.2.10 56% 342.4
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) 53% 86% 312.4 sn-glycerol-3-phosphate import ATP-binding protein UgpC; EC 7.6.2.10 56% 342.4
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) 57% 76% 311.6 sn-glycerol-3-phosphate import ATP-binding protein UgpC; EC 7.6.2.10 56% 342.4
D-maltose catabolism malK_Bb med ABC-type maltose transport, ATP binding protein (characterized, see rationale) 54% 87% 309.7 sn-glycerol-3-phosphate import ATP-binding protein UgpC; EC 7.6.2.10 56% 342.4
D-xylose catabolism gtsD med ABC transporter for D-Glucose-6-Phosphate, ATPase component (characterized) 49% 85% 299.7 sn-glycerol-3-phosphate import ATP-binding protein UgpC; EC 7.6.2.10 56% 342.4
L-arabinose catabolism xacK med Xylose/arabinose import ATP-binding protein XacK; EC 7.5.2.13 (characterized, see rationale) 47% 95% 294.3 sn-glycerol-3-phosphate import ATP-binding protein UgpC; EC 7.6.2.10 56% 342.4
D-glucosamine (chitosamine) catabolism SM_b21216 med ABC transporter for D-Glucosamine, ATPase component (characterized) 47% 99% 289.3 sn-glycerol-3-phosphate import ATP-binding protein UgpC; EC 7.6.2.10 56% 342.4
trehalose catabolism treV med TreV, component of Trehalose porter (characterized) 47% 87% 258.1 sn-glycerol-3-phosphate import ATP-binding protein UgpC; EC 7.6.2.10 56% 342.4
putrescine catabolism potA med spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31 (characterized) 46% 75% 250 sn-glycerol-3-phosphate import ATP-binding protein UgpC; EC 7.6.2.10 56% 342.4
L-arabinose catabolism araV med AraV, component of Arabinose, fructose, xylose porter (characterized) 40% 78% 205.7 sn-glycerol-3-phosphate import ATP-binding protein UgpC; EC 7.6.2.10 56% 342.4
D-fructose catabolism araV med AraV, component of Arabinose, fructose, xylose porter (characterized) 40% 78% 205.7 sn-glycerol-3-phosphate import ATP-binding protein UgpC; EC 7.6.2.10 56% 342.4
sucrose catabolism araV med AraV, component of Arabinose, fructose, xylose porter (characterized) 40% 78% 205.7 sn-glycerol-3-phosphate import ATP-binding protein UgpC; EC 7.6.2.10 56% 342.4
D-xylose catabolism araV med AraV, component of Arabinose, fructose, xylose porter (characterized) 40% 78% 205.7 sn-glycerol-3-phosphate import ATP-binding protein UgpC; EC 7.6.2.10 56% 342.4
D-cellobiose catabolism glcV med monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 40% 80% 200.3 sn-glycerol-3-phosphate import ATP-binding protein UgpC; EC 7.6.2.10 56% 342.4
D-galactose catabolism glcV med monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 40% 80% 200.3 sn-glycerol-3-phosphate import ATP-binding protein UgpC; EC 7.6.2.10 56% 342.4
D-glucose catabolism glcV med monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 40% 80% 200.3 sn-glycerol-3-phosphate import ATP-binding protein UgpC; EC 7.6.2.10 56% 342.4
lactose catabolism glcV med monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 40% 80% 200.3 sn-glycerol-3-phosphate import ATP-binding protein UgpC; EC 7.6.2.10 56% 342.4
D-maltose catabolism glcV med monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 40% 80% 200.3 sn-glycerol-3-phosphate import ATP-binding protein UgpC; EC 7.6.2.10 56% 342.4
D-mannose catabolism glcV med monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 40% 80% 200.3 sn-glycerol-3-phosphate import ATP-binding protein UgpC; EC 7.6.2.10 56% 342.4
sucrose catabolism glcV med monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 40% 80% 200.3 sn-glycerol-3-phosphate import ATP-binding protein UgpC; EC 7.6.2.10 56% 342.4
trehalose catabolism glcV med monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 40% 80% 200.3 sn-glycerol-3-phosphate import ATP-binding protein UgpC; EC 7.6.2.10 56% 342.4
glycerol catabolism glpT lo GlpT, component of Glycerol uptake porter, GlpSTPQV (characterized) 34% 99% 208.8 sn-glycerol-3-phosphate import ATP-binding protein UgpC; EC 7.6.2.10 56% 342.4
L-asparagine catabolism glnQ lo Glutamine ABC transporter ATP-binding protein, component of Glutamine transporter, GlnQP. Takes up glutamine, asparagine and glutamate which compete for each other for binding both substrate and the transmembrane protein constituent of the system (Fulyani et al. 2015). Tandem substrate binding domains (SBDs) differ in substrate specificity and affinity, allowing cells to efficiently accumulate different amino acids via a single ABC transporter. Analysis revealed the roles of individual residues in determining the substrate affinity (characterized) 38% 96% 154.8 sn-glycerol-3-phosphate import ATP-binding protein UgpC; EC 7.6.2.10 56% 342.4
L-asparagine catabolism peb1C lo PEB1C, component of Uptake system for glutamate and aspartate (characterized) 39% 98% 153.3 sn-glycerol-3-phosphate import ATP-binding protein UgpC; EC 7.6.2.10 56% 342.4
L-aspartate catabolism peb1C lo PEB1C, component of Uptake system for glutamate and aspartate (characterized) 39% 98% 153.3 sn-glycerol-3-phosphate import ATP-binding protein UgpC; EC 7.6.2.10 56% 342.4

Sequence Analysis Tools

View 3608624 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

MATLTLDNVKKSFGKTDVIHGVSIDVTEGEFIVIVGPSGCGKSTLLRMVAGLETVSSGEV
RIDGRVVNTLEPMDRDIAMVFQNYALYPHMSVFDNMAYGLKIAKVPKAEIADRVAVAAKL
LQLEPYLGRKPKELSGGQRQRVAMGRAIVRKPAVFLFDEPLSNLDAKLRVQMRLEIKALQ
RELGVTSLYVTHDQVEAMTLADRMIVMNGGVADQIGAPLEVYANPQTAFVAGFIGSPPTN
FLPADMVRAGPAGQQVGIRPEHLRVAPQGRLEAHVAYAEALGAETLLHLRASQGTTLTVR
QDAAAPMPAEGATVQLDWDDSDTMLFADNGRRV

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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 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