GapMind for catabolism of small carbon sources

 

Protein WP_061534086.1 in Collimonas arenae Ter10

Annotation: NCBI__GCF_001584165.1:WP_061534086.1

Length: 359 amino acids

Source: GCF_001584165.1 in NCBI

Candidate for 56 steps in catabolism of small carbon sources

Pathway Step Score Similar to Id. Cov. Bits Other hit Other id. Other bits
D-maltose catabolism malK_Aa med ABC-type maltose transporter (EC 7.5.2.1) (characterized) 52% 97% 365.5 sn-glycerol-3-phosphate import ATP-binding protein UgpC; EC 7.6.2.10 62% 418.3
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) 53% 97% 359.8 sn-glycerol-3-phosphate import ATP-binding protein UgpC; EC 7.6.2.10 62% 418.3
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) 53% 97% 359.8 sn-glycerol-3-phosphate import ATP-binding protein UgpC; EC 7.6.2.10 62% 418.3
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) 53% 97% 359.8 sn-glycerol-3-phosphate import ATP-binding protein UgpC; EC 7.6.2.10 62% 418.3
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) 53% 97% 359.8 sn-glycerol-3-phosphate import ATP-binding protein UgpC; EC 7.6.2.10 62% 418.3
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) 53% 97% 359.8 sn-glycerol-3-phosphate import ATP-binding protein UgpC; EC 7.6.2.10 62% 418.3
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) 53% 97% 359.8 sn-glycerol-3-phosphate import ATP-binding protein UgpC; EC 7.6.2.10 62% 418.3
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) 53% 97% 359.8 sn-glycerol-3-phosphate import ATP-binding protein UgpC; EC 7.6.2.10 62% 418.3
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) 53% 97% 359.8 sn-glycerol-3-phosphate import ATP-binding protein UgpC; EC 7.6.2.10 62% 418.3
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) 53% 97% 359.8 sn-glycerol-3-phosphate import ATP-binding protein UgpC; EC 7.6.2.10 62% 418.3
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) 53% 97% 359.8 sn-glycerol-3-phosphate import ATP-binding protein UgpC; EC 7.6.2.10 62% 418.3
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) 52% 99% 355.1 sn-glycerol-3-phosphate import ATP-binding protein UgpC; EC 7.6.2.10 62% 418.3
lactose catabolism lacK med ABC transporter for Lactose, ATPase component (characterized) 50% 98% 342.8 sn-glycerol-3-phosphate import ATP-binding protein UgpC; EC 7.6.2.10 62% 418.3
D-mannitol catabolism mtlK med ABC transporter for D-mannitol and D-mannose, ATPase component (characterized) 49% 97% 340.9 sn-glycerol-3-phosphate import ATP-binding protein UgpC; EC 7.6.2.10 62% 418.3
D-xylose catabolism gtsD med ABC transporter for D-Glucose-6-Phosphate, ATPase component (characterized) 49% 95% 336.3 sn-glycerol-3-phosphate import ATP-binding protein UgpC; EC 7.6.2.10 62% 418.3
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) 49% 100% 335.1 sn-glycerol-3-phosphate import ATP-binding protein UgpC; EC 7.6.2.10 62% 418.3
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) 49% 100% 335.1 sn-glycerol-3-phosphate import ATP-binding protein UgpC; EC 7.6.2.10 62% 418.3
L-fucose catabolism SM_b21106 med ABC transporter for L-Fucose, ATPase component (characterized) 49% 99% 333.6 sn-glycerol-3-phosphate import ATP-binding protein UgpC; EC 7.6.2.10 62% 418.3
D-sorbitol (glucitol) catabolism mtlK med MtlK, component of The polyol (mannitol, glucitol (sorbitol), arabitol (arabinitol; lyxitol)) uptake porter, MtlEFGK (characterized) 49% 97% 333.2 sn-glycerol-3-phosphate import ATP-binding protein UgpC; EC 7.6.2.10 62% 418.3
D-maltose catabolism malK med ABC-type maltose transporter (subunit 3/3) (EC 7.5.2.1) (characterized) 50% 97% 327 sn-glycerol-3-phosphate import ATP-binding protein UgpC; EC 7.6.2.10 62% 418.3
D-glucosamine (chitosamine) catabolism SM_b21216 med ABC transporter for D-Glucosamine, ATPase component (characterized) 47% 100% 326.6 sn-glycerol-3-phosphate import ATP-binding protein UgpC; EC 7.6.2.10 62% 418.3
D-galactose catabolism PfGW456L13_1897 med ABC transporter for D-Galactose and D-Glucose, ATPase component (characterized) 46% 95% 326.2 sn-glycerol-3-phosphate import ATP-binding protein UgpC; EC 7.6.2.10 62% 418.3
xylitol catabolism HSERO_RS17020 med ABC-type sugar transport system, ATPase component protein (characterized, see rationale) 47% 90% 321.6 sn-glycerol-3-phosphate import ATP-binding protein UgpC; EC 7.6.2.10 62% 418.3
D-maltose catabolism aglK med ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized) 49% 98% 318.2 sn-glycerol-3-phosphate import ATP-binding protein UgpC; EC 7.6.2.10 62% 418.3
sucrose catabolism aglK med ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized) 49% 98% 318.2 sn-glycerol-3-phosphate import ATP-binding protein UgpC; EC 7.6.2.10 62% 418.3
trehalose catabolism aglK med ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized) 49% 98% 318.2 sn-glycerol-3-phosphate import ATP-binding protein UgpC; EC 7.6.2.10 62% 418.3
xylitol catabolism Dshi_0546 med ABC transporter for Xylitol, ATPase component (characterized) 48% 99% 317.8 sn-glycerol-3-phosphate import ATP-binding protein UgpC; EC 7.6.2.10 62% 418.3
D-maltose catabolism malK_Bb med ABC-type maltose transport, ATP binding protein (characterized, see rationale) 46% 100% 314.7 sn-glycerol-3-phosphate import ATP-binding protein UgpC; EC 7.6.2.10 62% 418.3
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) 48% 100% 314.3 sn-glycerol-3-phosphate import ATP-binding protein UgpC; EC 7.6.2.10 62% 418.3
L-arabinose catabolism xacK med Xylose/arabinose import ATP-binding protein XacK; EC 7.5.2.13 (characterized, see rationale) 47% 96% 305.4 sn-glycerol-3-phosphate import ATP-binding protein UgpC; EC 7.6.2.10 62% 418.3
D-maltose catabolism musK med ABC-type maltose transporter (EC 7.5.2.1) (characterized) 47% 100% 301.6 sn-glycerol-3-phosphate import ATP-binding protein UgpC; EC 7.6.2.10 62% 418.3
D-cellobiose catabolism SMc04256 med ABC transporter for D-Cellobiose and D-Salicin, ATPase component (characterized) 44% 100% 293.5 sn-glycerol-3-phosphate import ATP-binding protein UgpC; EC 7.6.2.10 62% 418.3
D-cellobiose catabolism aglK' med Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 47% 95% 293.1 sn-glycerol-3-phosphate import ATP-binding protein UgpC; EC 7.6.2.10 62% 418.3
D-glucose catabolism aglK' med Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 47% 95% 293.1 sn-glycerol-3-phosphate import ATP-binding protein UgpC; EC 7.6.2.10 62% 418.3
lactose catabolism aglK' med Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 47% 95% 293.1 sn-glycerol-3-phosphate import ATP-binding protein UgpC; EC 7.6.2.10 62% 418.3
D-maltose catabolism aglK' med Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 47% 95% 293.1 sn-glycerol-3-phosphate import ATP-binding protein UgpC; EC 7.6.2.10 62% 418.3
sucrose catabolism aglK' med Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 47% 95% 293.1 sn-glycerol-3-phosphate import ATP-binding protein UgpC; EC 7.6.2.10 62% 418.3
trehalose catabolism aglK' med Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 47% 95% 293.1 sn-glycerol-3-phosphate import ATP-binding protein UgpC; EC 7.6.2.10 62% 418.3
N-acetyl-D-glucosamine catabolism SMc02869 med N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized) 56% 72% 288.5 sn-glycerol-3-phosphate import ATP-binding protein UgpC; EC 7.6.2.10 62% 418.3
D-glucosamine (chitosamine) catabolism SMc02869 med N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized) 56% 72% 288.5 sn-glycerol-3-phosphate import ATP-binding protein UgpC; EC 7.6.2.10 62% 418.3
L-arabinose catabolism xacJ med Xylose/arabinose import ATP-binding protein XacJ; EC 7.5.2.13 (characterized, see rationale) 43% 95% 270.8 sn-glycerol-3-phosphate import ATP-binding protein UgpC; EC 7.6.2.10 62% 418.3
trehalose catabolism treV med TreV, component of Trehalose porter (characterized) 48% 76% 235 sn-glycerol-3-phosphate import ATP-binding protein UgpC; EC 7.6.2.10 62% 418.3
glycerol catabolism glpT lo GlpT, component of Glycerol uptake porter, GlpSTPQV (characterized) 33% 96% 221.5 sn-glycerol-3-phosphate import ATP-binding protein UgpC; EC 7.6.2.10 62% 418.3
L-arabinose catabolism araV lo AraV, component of Arabinose, fructose, xylose porter (characterized) 37% 92% 218.4 sn-glycerol-3-phosphate import ATP-binding protein UgpC; EC 7.6.2.10 62% 418.3
D-fructose catabolism araV lo AraV, component of Arabinose, fructose, xylose porter (characterized) 37% 92% 218.4 sn-glycerol-3-phosphate import ATP-binding protein UgpC; EC 7.6.2.10 62% 418.3
sucrose catabolism araV lo AraV, component of Arabinose, fructose, xylose porter (characterized) 37% 92% 218.4 sn-glycerol-3-phosphate import ATP-binding protein UgpC; EC 7.6.2.10 62% 418.3
D-xylose catabolism araV lo AraV, component of Arabinose, fructose, xylose porter (characterized) 37% 92% 218.4 sn-glycerol-3-phosphate import ATP-binding protein UgpC; EC 7.6.2.10 62% 418.3
D-cellobiose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 38% 80% 207.2 sn-glycerol-3-phosphate import ATP-binding protein UgpC; EC 7.6.2.10 62% 418.3
D-galactose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 38% 80% 207.2 sn-glycerol-3-phosphate import ATP-binding protein UgpC; EC 7.6.2.10 62% 418.3
D-glucose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 38% 80% 207.2 sn-glycerol-3-phosphate import ATP-binding protein UgpC; EC 7.6.2.10 62% 418.3
lactose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 38% 80% 207.2 sn-glycerol-3-phosphate import ATP-binding protein UgpC; EC 7.6.2.10 62% 418.3
D-maltose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 38% 80% 207.2 sn-glycerol-3-phosphate import ATP-binding protein UgpC; EC 7.6.2.10 62% 418.3
D-mannose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 38% 80% 207.2 sn-glycerol-3-phosphate import ATP-binding protein UgpC; EC 7.6.2.10 62% 418.3
sucrose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 38% 80% 207.2 sn-glycerol-3-phosphate import ATP-binding protein UgpC; EC 7.6.2.10 62% 418.3
trehalose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 38% 80% 207.2 sn-glycerol-3-phosphate import ATP-binding protein UgpC; EC 7.6.2.10 62% 418.3
glycerol catabolism glpS lo GlpS, component of Glycerol uptake porter, GlpSTPQV (characterized) 34% 97% 187.2 sn-glycerol-3-phosphate import ATP-binding protein UgpC; EC 7.6.2.10 62% 418.3

Sequence Analysis Tools

View WP_061534086.1 at NCBI

Find papers: PaperBLAST

Find functional residues: SitesBLAST

Search for conserved domains

Find the best match in UniProt

Compare to protein structures

Predict transmenbrane helices: Phobius

Predict protein localization: PSORTb

Find homologs in fast.genomics

Fitness BLAST: loading...

Sequence

MAKVHLENVKKTYGKAPKTVDVIHGISIDIADGEFIVMVGPSGCGKSTLLRMVAGLEEIT
SGDIVIGDRVVNKLEPKDRDIAMVFQNYALYPHMSVYENMAYGLKIRGLSKDDIEVRVQK
AAKILELGALLQRTPRQLSGGQRQRVAMGRAIVREPAVFLFDEPLSNLDAKLRVQMRLEI
QKLHRTLGTTSLYVTHDQVEAMTLGQRMIVMNGGRAEQIGTPAEVYAKPATTFVASFIGS
PPMNLLNGRVATDGNSFVVDNAAPIPLPFTHNAIAGHDCILGLRPEHLLFGQPGLSMRAE
LVEALGADLLVHASIGDQTLVMRVPAATAVETGQQITAGFETNSLHWFNSQTTQRIEFS

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