GapMind for catabolism of small carbon sources

 

Protein WP_011906830.1 in Novosphingobium aromaticivorans DSM 12444

Annotation: NCBI__GCF_000013325.1:WP_011906830.1

Length: 241 amino acids

Source: GCF_000013325.1 in NCBI

Candidate for 53 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) 45% 84% 155.2 Macrolide export ATP-binding/permease protein MacB; EC 7.6.2.- 44% 182.2
L-asparagine catabolism bgtA med ATPase (characterized, see rationale) 40% 80% 141.4 Macrolide export ATP-binding/permease protein MacB; EC 7.6.2.- 44% 182.2
L-aspartate catabolism bgtA med ATPase (characterized, see rationale) 40% 80% 141.4 Macrolide export ATP-binding/permease protein MacB; EC 7.6.2.- 44% 182.2
L-arginine catabolism artP med Arginine transport ATP-binding protein ArtP; EC 7.4.2.- (characterized) 43% 85% 136.7 Macrolide export ATP-binding/permease protein MacB; EC 7.6.2.- 44% 182.2
L-histidine catabolism PA5503 lo Methionine import ATP-binding protein MetN 2, component of L-Histidine uptake porter, MetIQN (characterized) 43% 63% 162.2 Macrolide export ATP-binding/permease protein MacB; EC 7.6.2.- 44% 182.2
L-asparagine catabolism bztD lo BztD, component of Glutamate/glutamine/aspartate/asparagine porter (characterized) 38% 83% 139.8 Macrolide export ATP-binding/permease protein MacB; EC 7.6.2.- 44% 182.2
L-aspartate catabolism bztD lo BztD, component of Glutamate/glutamine/aspartate/asparagine porter (characterized) 38% 83% 139.8 Macrolide export ATP-binding/permease protein MacB; EC 7.6.2.- 44% 182.2
L-histidine catabolism aapP lo ABC transporter for L-Glutamine, L-Histidine, and other L-amino acids, ATPase component (characterized) 38% 88% 139.4 Macrolide export ATP-binding/permease protein MacB; EC 7.6.2.- 44% 182.2
L-arabinose catabolism araV lo AraV, component of Arabinose, fructose, xylose porter (characterized) 35% 58% 137.5 Macrolide export ATP-binding/permease protein MacB; EC 7.6.2.- 44% 182.2
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) 37% 87% 137.5 Macrolide export ATP-binding/permease protein MacB; EC 7.6.2.- 44% 182.2
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) 37% 87% 137.5 Macrolide export ATP-binding/permease protein MacB; EC 7.6.2.- 44% 182.2
D-fructose catabolism araV lo AraV, component of Arabinose, fructose, xylose porter (characterized) 35% 58% 137.5 Macrolide export ATP-binding/permease protein MacB; EC 7.6.2.- 44% 182.2
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) 37% 87% 137.5 Macrolide export ATP-binding/permease protein MacB; EC 7.6.2.- 44% 182.2
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) 37% 87% 137.5 Macrolide export ATP-binding/permease protein MacB; EC 7.6.2.- 44% 182.2
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) 37% 87% 137.5 Macrolide export ATP-binding/permease protein MacB; EC 7.6.2.- 44% 182.2
sucrose catabolism araV lo AraV, component of Arabinose, fructose, xylose porter (characterized) 35% 58% 137.5 Macrolide export ATP-binding/permease protein MacB; EC 7.6.2.- 44% 182.2
D-xylose catabolism araV lo AraV, component of Arabinose, fructose, xylose porter (characterized) 35% 58% 137.5 Macrolide export ATP-binding/permease protein MacB; EC 7.6.2.- 44% 182.2
L-asparagine catabolism peb1C lo PEB1C, component of Uptake system for glutamate and aspartate (characterized) 37% 87% 135.2 Macrolide export ATP-binding/permease protein MacB; EC 7.6.2.- 44% 182.2
L-aspartate catabolism peb1C lo PEB1C, component of Uptake system for glutamate and aspartate (characterized) 37% 87% 135.2 Macrolide export ATP-binding/permease protein MacB; EC 7.6.2.- 44% 182.2
D-cellobiose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 36% 65% 133.3 Macrolide export ATP-binding/permease protein MacB; EC 7.6.2.- 44% 182.2
D-galactose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 36% 65% 133.3 Macrolide export ATP-binding/permease protein MacB; EC 7.6.2.- 44% 182.2
D-glucose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 36% 65% 133.3 Macrolide export ATP-binding/permease protein MacB; EC 7.6.2.- 44% 182.2
L-histidine catabolism Ac3H11_2560 lo ABC transporter for L-Histidine, ATPase component (characterized) 40% 83% 133.3 Macrolide export ATP-binding/permease protein MacB; EC 7.6.2.- 44% 182.2
lactose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 36% 65% 133.3 Macrolide export ATP-binding/permease protein MacB; EC 7.6.2.- 44% 182.2
D-maltose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 36% 65% 133.3 Macrolide export ATP-binding/permease protein MacB; EC 7.6.2.- 44% 182.2
D-mannose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 36% 65% 133.3 Macrolide export ATP-binding/permease protein MacB; EC 7.6.2.- 44% 182.2
sucrose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 36% 65% 133.3 Macrolide export ATP-binding/permease protein MacB; EC 7.6.2.- 44% 182.2
trehalose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 36% 65% 133.3 Macrolide export ATP-binding/permease protein MacB; EC 7.6.2.- 44% 182.2
D-alanine catabolism Pf6N2E2_5405 lo ABC transporter for D-Alanine, ATPase component (characterized) 39% 85% 131.7 Macrolide export ATP-binding/permease protein MacB; EC 7.6.2.- 44% 182.2
L-asparagine catabolism aatP lo Glutamate/aspartate transport ATP-binding protein GltL aka B0652, component of Glutamate/aspartate porter (characterized) 39% 84% 129.4 Macrolide export ATP-binding/permease protein MacB; EC 7.6.2.- 44% 182.2
L-aspartate catabolism aatP lo Glutamate/aspartate transport ATP-binding protein GltL aka B0652, component of Glutamate/aspartate porter (characterized) 39% 84% 129.4 Macrolide export ATP-binding/permease protein MacB; EC 7.6.2.- 44% 182.2
D-cellobiose catabolism gtsD lo Sugar ABC transporter ATP-binding protein (characterized, see rationale) 36% 57% 125.9 Macrolide export ATP-binding/permease protein MacB; EC 7.6.2.- 44% 182.2
D-glucose catabolism gtsD lo Sugar ABC transporter ATP-binding protein (characterized, see rationale) 36% 57% 125.9 Macrolide export ATP-binding/permease protein MacB; EC 7.6.2.- 44% 182.2
lactose catabolism gtsD lo Sugar ABC transporter ATP-binding protein (characterized, see rationale) 36% 57% 125.9 Macrolide export ATP-binding/permease protein MacB; EC 7.6.2.- 44% 182.2
D-maltose catabolism gtsD lo Sugar ABC transporter ATP-binding protein (characterized, see rationale) 36% 57% 125.9 Macrolide export ATP-binding/permease protein MacB; EC 7.6.2.- 44% 182.2
sucrose catabolism gtsD lo Sugar ABC transporter ATP-binding protein (characterized, see rationale) 36% 57% 125.9 Macrolide export ATP-binding/permease protein MacB; EC 7.6.2.- 44% 182.2
trehalose catabolism gtsD lo Sugar ABC transporter ATP-binding protein (characterized, see rationale) 36% 57% 125.9 Macrolide export ATP-binding/permease protein MacB; EC 7.6.2.- 44% 182.2
trehalose catabolism thuK lo Trehalose import ATP-binding protein SugC; EC 7.5.2.- (characterized) 35% 56% 123.6 Macrolide export ATP-binding/permease protein MacB; EC 7.6.2.- 44% 182.2
L-arabinose catabolism xacJ lo Xylose/arabinose import ATP-binding protein XacJ; EC 7.5.2.13 (characterized, see rationale) 37% 55% 123.2 Macrolide export ATP-binding/permease protein MacB; EC 7.6.2.- 44% 182.2
D-glucosamine (chitosamine) catabolism SM_b21216 lo ABC transporter for D-Glucosamine, ATPase component (characterized) 35% 59% 121.7 Macrolide export ATP-binding/permease protein MacB; EC 7.6.2.- 44% 182.2
D-xylose catabolism gtsD lo ABC transporter for D-Glucose-6-Phosphate, ATPase component (characterized) 35% 54% 121.7 Macrolide export ATP-binding/permease protein MacB; EC 7.6.2.- 44% 182.2
N-acetyl-D-glucosamine catabolism SMc02869 lo N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized) 32% 65% 120.9 Macrolide export ATP-binding/permease protein MacB; EC 7.6.2.- 44% 182.2
D-glucosamine (chitosamine) catabolism SMc02869 lo N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized) 32% 65% 120.9 Macrolide export ATP-binding/permease protein MacB; EC 7.6.2.- 44% 182.2
D-galactose catabolism PfGW456L13_1897 lo ABC transporter for D-Galactose and D-Glucose, ATPase component (characterized) 34% 54% 114.4 Macrolide export ATP-binding/permease protein MacB; EC 7.6.2.- 44% 182.2
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) 33% 57% 113.2 Macrolide export ATP-binding/permease protein MacB; EC 7.6.2.- 44% 182.2
xylitol catabolism HSERO_RS17020 lo ABC-type sugar transport system, ATPase component protein (characterized, see rationale) 35% 56% 111.3 Macrolide export ATP-binding/permease protein MacB; EC 7.6.2.- 44% 182.2
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) 32% 56% 107.5 Macrolide export ATP-binding/permease protein MacB; EC 7.6.2.- 44% 182.2
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) 32% 56% 107.5 Macrolide export ATP-binding/permease protein MacB; EC 7.6.2.- 44% 182.2
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) 32% 56% 107.5 Macrolide export ATP-binding/permease protein MacB; EC 7.6.2.- 44% 182.2
D-maltose catabolism malK_Aa lo ABC-type maltose transporter (EC 7.5.2.1) (characterized) 33% 55% 106.7 Macrolide export ATP-binding/permease protein MacB; EC 7.6.2.- 44% 182.2
D-cellobiose catabolism cbtF lo CbtF, component of Cellobiose and cellooligosaccharide porter (characterized) 31% 65% 104 Macrolide export ATP-binding/permease protein MacB; EC 7.6.2.- 44% 182.2
D-cellobiose catabolism TM0027 lo TM0027, component of β-glucoside porter (Conners et al., 2005). Binds cellobiose, laminaribiose (Nanavati et al. 2006). Regulated by cellobiose-responsive repressor BglR (characterized) 30% 85% 102.8 Macrolide export ATP-binding/permease protein MacB; EC 7.6.2.- 44% 182.2
myo-inositol catabolism PGA1_c07320 lo Inositol transport system ATP-binding protein (characterized) 31% 73% 80.1 Macrolide export ATP-binding/permease protein MacB; EC 7.6.2.- 44% 182.2

Sequence Analysis Tools

View WP_011906830.1 at NCBI

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

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Sequence

MESPDSASPAAFTGTRLNKIYRTGETEVHALRDVDLSIPQGEVLVLLGPSGSGKSTLLNI
LGGLDRPTSGNLSWFDHDLVAADEAALTRFRRAHVGFIFQFYNLIPSLTAEENVRLVTDI
AESPMPPGEALERVGLADRRNHYPAQLSGGEQQRVAVARAIAKRPAVLLCDEPTGALDSR
TGVRVLETLASANRELATTVVIITHNAGIAAMAHRVFHFLDGRIARIVRNERPVDPAGIT
W

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