GapMind for catabolism of small carbon sources

 

Protein WP_013706564.1 in Desulfobacca acetoxidans DSM 11109

Annotation: NCBI__GCF_000195295.1:WP_013706564.1

Length: 234 amino acids

Source: GCF_000195295.1 in NCBI

Candidate for 36 steps in catabolism of small carbon sources

Pathway Step Score Similar to Id. Cov. Bits Other hit Other id. Other bits
L-glutamate catabolism gltL med GluA aka CGL1950, component of Glutamate porter (characterized) 43% 88% 144.8 lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- 42% 182.6
L-histidine catabolism aapP med ABC transporter for L-Glutamine, L-Histidine, and other L-amino acids, ATPase component (characterized) 41% 78% 137.1 lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- 42% 182.6
putrescine catabolism potA lo spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31 (characterized) 40% 60% 145.6 lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- 42% 182.6
D-glucosamine (chitosamine) catabolism AO353_21725 lo ABC transporter for D-Glucosamine, putative ATPase component (characterized) 38% 89% 145.2 lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- 42% 182.6
D-sorbitol (glucitol) catabolism mtlK lo ABC transporter for D-Sorbitol, ATPase component (characterized) 39% 57% 144.1 lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- 42% 182.6
D-mannitol catabolism mtlK lo ABC transporter for D-mannitol and D-mannose, ATPase component (characterized) 37% 56% 142.1 lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- 42% 182.6
L-fucose catabolism SM_b21106 lo ABC transporter for L-Fucose, ATPase component (characterized) 36% 58% 141 lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- 42% 182.6
N-acetyl-D-glucosamine catabolism SMc02869 lo N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized) 39% 60% 140.6 lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- 42% 182.6
D-glucosamine (chitosamine) catabolism SMc02869 lo N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized) 39% 60% 140.6 lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- 42% 182.6
D-cellobiose catabolism gtsD lo ABC transporter for D-Galactose and D-Glucose, ATPase component (characterized) 37% 54% 139.4 lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- 42% 182.6
D-galactose catabolism PfGW456L13_1897 lo ABC transporter for D-Galactose and D-Glucose, ATPase component (characterized) 37% 54% 139.4 lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- 42% 182.6
D-glucose catabolism gtsD lo ABC transporter for D-Galactose and D-Glucose, ATPase component (characterized) 37% 54% 139.4 lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- 42% 182.6
lactose catabolism gtsD lo ABC transporter for D-Galactose and D-Glucose, ATPase component (characterized) 37% 54% 139.4 lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- 42% 182.6
D-maltose catabolism gtsD lo ABC transporter for D-Galactose and D-Glucose, ATPase component (characterized) 37% 54% 139.4 lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- 42% 182.6
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) 35% 57% 139.4 lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- 42% 182.6
sucrose catabolism gtsD lo ABC transporter for D-Galactose and D-Glucose, ATPase component (characterized) 37% 54% 139.4 lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- 42% 182.6
trehalose catabolism gtsD lo ABC transporter for D-Galactose and D-Glucose, ATPase component (characterized) 37% 54% 139.4 lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- 42% 182.6
trehalose catabolism thuK 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) 35% 57% 139.4 lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- 42% 182.6
D-alanine catabolism Pf6N2E2_5405 lo ABC transporter for D-Alanine, ATPase component (characterized) 38% 87% 139 lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- 42% 182.6
L-asparagine catabolism aapP lo AapP, component of General L-amino acid porter; transports basic and acidic amino acids preferentially, but also transports aliphatic amino acids (catalyzes both uptake and efflux) (characterized) 40% 79% 136.7 lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- 42% 182.6
L-aspartate catabolism aapP lo AapP, component of General L-amino acid porter; transports basic and acidic amino acids preferentially, but also transports aliphatic amino acids (catalyzes both uptake and efflux) (characterized) 40% 79% 136.7 lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- 42% 182.6
L-glutamate catabolism aapP lo AapP, component of General L-amino acid porter; transports basic and acidic amino acids preferentially, but also transports aliphatic amino acids (catalyzes both uptake and efflux) (characterized) 40% 79% 136.7 lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- 42% 182.6
L-leucine catabolism aapP lo AapP, component of General L-amino acid porter; transports basic and acidic amino acids preferentially, but also transports aliphatic amino acids (catalyzes both uptake and efflux) (characterized) 40% 79% 136.7 lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- 42% 182.6
L-proline catabolism aapP lo AapP, component of General L-amino acid porter; transports basic and acidic amino acids preferentially, but also transports aliphatic amino acids (catalyzes both uptake and efflux) (characterized) 40% 79% 136.7 lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- 42% 182.6
xylitol catabolism Dshi_0546 lo ABC transporter for Xylitol, ATPase component (characterized) 40% 59% 136 lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- 42% 182.6
D-xylose catabolism gtsD lo ABC transporter for D-Glucose-6-Phosphate, ATPase component (characterized) 36% 54% 135.6 lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- 42% 182.6
lactose catabolism lacK lo ABC transporter for Lactose, ATPase component (characterized) 40% 59% 133.7 lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- 42% 182.6
L-histidine catabolism Ac3H11_2560 lo ABC transporter for L-Histidine, ATPase component (characterized) 36% 83% 132.1 lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- 42% 182.6
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) 36% 55% 130.6 lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- 42% 182.6
D-maltose catabolism malK lo Maltose/maltodextrin import ATP-binding protein MalK; EC 7.5.2.1 (characterized) 37% 57% 130.6 lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- 42% 182.6
D-maltose 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) 37% 53% 129.8 lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- 42% 182.6
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) 37% 53% 129.8 lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- 42% 182.6
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) 37% 53% 129.8 lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- 42% 182.6
D-maltose catabolism malK_Aa lo ABC-type maltose transporter (EC 7.5.2.1) (characterized) 35% 54% 128.3 lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- 42% 182.6
D-maltose catabolism musK lo ABC-type maltose transporter (EC 7.5.2.1) (characterized) 35% 55% 124 lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- 42% 182.6
glycerol catabolism glpT lo GlpT, component of Glycerol uptake porter, GlpSTPQV (characterized) 33% 55% 94.4 lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- 42% 182.6

Sequence Analysis Tools

View WP_013706564.1 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

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Sequence

MQKNKDVPVQPQSLIILRGVTKIYHQGLEEVKALRDVDLKIADGEFVAVTGKSGCGKSTL
LHVIGGLENVSAGSIQFQGRDLSRFDDVQLTRYRRDQVGIVFQSFNLMPLLTIVENVALP
QILRGTPSHEALRLAGEWLRRVNLTHRRNHKPHQVSGGEMQRAAIARALINRPALLLADE
PTGNLDSTHAAQVLQLFAELHRQERLTVVMVTHALEAAQFADRTLKMQDGRLHP

This GapMind analysis is from Apr 09 2024. 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