GapMind for catabolism of small carbon sources

 

Protein WP_025761778.1 in Dyadobacter tibetensis Y620-1

Annotation: NCBI__GCF_000566685.1:WP_025761778.1

Length: 321 amino acids

Source: GCF_000566685.1 in NCBI

Candidate for 48 steps in catabolism of small carbon sources

Pathway Step Score Similar to Id. Cov. Bits Other hit Other id. Other bits
L-proline catabolism opuBA lo BilEA aka OpuBA protein, component of A proline/glycine betaine uptake system. Also reported to be a bile exclusion system that exports oxgall and other bile compounds, BilEA/EB or OpuBA/BB (required for normal virulence) (characterized) 39% 86% 201.8 Choline transport ATP-binding protein OpuBA 44% 237.7
L-proline catabolism proV lo glycine betaine/l-proline transport atp-binding protein prov (characterized) 39% 59% 175.6 Choline transport ATP-binding protein OpuBA 44% 237.7
D-alanine catabolism Pf6N2E2_5405 lo ABC transporter for D-Alanine, ATPase component (characterized) 36% 93% 164.1 Choline transport ATP-binding protein OpuBA 44% 237.7
D-maltose catabolism thuK lo Trehalose/maltose import ATP-binding protein MalK; EC 7.5.2.1 (characterized) 38% 68% 157.1 Choline transport ATP-binding protein OpuBA 44% 237.7
trehalose catabolism thuK lo Trehalose/maltose import ATP-binding protein MalK; EC 7.5.2.1 (characterized) 38% 68% 157.1 Choline transport ATP-binding protein OpuBA 44% 237.7
L-histidine catabolism hutV lo ABC transporter for L-Histidine, ATPase component (characterized) 37% 84% 154.8 Choline transport ATP-binding protein OpuBA 44% 237.7
xylitol catabolism Dshi_0546 lo ABC transporter for Xylitol, ATPase component (characterized) 36% 73% 151.8 Choline transport ATP-binding protein OpuBA 44% 237.7
L-fucose catabolism SM_b21106 lo ABC transporter for L-Fucose, ATPase component (characterized) 36% 67% 151.4 Choline transport ATP-binding protein OpuBA 44% 237.7
L-arginine catabolism artP lo Probable ATP-binding component of ABC transporter, component of Amino acid transporter, PA5152-PA5155. Probably transports numerous amino acids including lysine, arginine, histidine, D-alanine and D-valine (Johnson et al. 2008). Regulated by ArgR (characterized) 32% 97% 150.6 Choline transport ATP-binding protein OpuBA 44% 237.7
L-histidine catabolism hisP lo Probable ATP-binding component of ABC transporter, component of Amino acid transporter, PA5152-PA5155. Probably transports numerous amino acids including lysine, arginine, histidine, D-alanine and D-valine (Johnson et al. 2008). Regulated by ArgR (characterized) 32% 97% 150.6 Choline transport ATP-binding protein OpuBA 44% 237.7
L-lysine catabolism hisP lo Probable ATP-binding component of ABC transporter, component of Amino acid transporter, PA5152-PA5155. Probably transports numerous amino acids including lysine, arginine, histidine, D-alanine and D-valine (Johnson et al. 2008). Regulated by ArgR (characterized) 32% 97% 150.6 Choline transport ATP-binding protein OpuBA 44% 237.7
L-histidine catabolism aapP lo ABC transporter for L-Glutamine, L-Histidine, and other L-amino acids, ATPase component (characterized) 34% 91% 149.8 Choline transport ATP-binding protein OpuBA 44% 237.7
L-proline catabolism hutV lo HutV aka HISV aka R02702 aka SMC00670, component of Uptake system for hisitidine, proline, proline-betaine and glycine-betaine (characterized) 37% 82% 149.4 Choline transport ATP-binding protein OpuBA 44% 237.7
putrescine catabolism potA lo PotG aka B0855, component of Putrescine porter (characterized) 37% 62% 148.3 Choline transport ATP-binding protein OpuBA 44% 237.7
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) 33% 93% 147.9 Choline transport ATP-binding protein OpuBA 44% 237.7
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) 33% 93% 147.9 Choline transport ATP-binding protein OpuBA 44% 237.7
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) 33% 93% 147.9 Choline transport ATP-binding protein OpuBA 44% 237.7
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) 33% 93% 147.9 Choline transport ATP-binding protein OpuBA 44% 237.7
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) 33% 93% 147.9 Choline transport ATP-binding protein OpuBA 44% 237.7
L-asparagine catabolism aatP lo ABC transporter for L-Asparagine and possibly other L-amino acids, putative ATPase component (characterized) 37% 89% 147.5 Choline transport ATP-binding protein OpuBA 44% 237.7
L-aspartate catabolism aatP lo ABC transporter for L-Asparagine and possibly other L-amino acids, putative ATPase component (characterized) 37% 89% 147.5 Choline transport ATP-binding protein OpuBA 44% 237.7
D-mannitol catabolism mtlK lo ABC transporter for D-Mannitol, D-Mannose, and D-Mannose, ATPase component (characterized) 33% 78% 145.2 Choline transport ATP-binding protein OpuBA 44% 237.7
L-arabinose catabolism xacJ lo Xylose/arabinose import ATP-binding protein XacJ; EC 7.5.2.13 (characterized, see rationale) 37% 63% 143.7 Choline transport ATP-binding protein OpuBA 44% 237.7
D-sorbitol (glucitol) catabolism mtlK lo ABC transporter for D-Mannitol, D-Mannose, and D-Sorbitol, ATPase component (characterized) 34% 66% 143.7 Choline transport ATP-binding protein OpuBA 44% 237.7
L-asparagine catabolism bgtA lo ATPase (characterized, see rationale) 34% 91% 143.3 Choline transport ATP-binding protein OpuBA 44% 237.7
L-aspartate catabolism bgtA lo ATPase (characterized, see rationale) 34% 91% 143.3 Choline transport ATP-binding protein OpuBA 44% 237.7
sucrose catabolism thuK lo ABC transporter (characterized, see rationale) 35% 63% 142.9 Choline transport ATP-binding protein OpuBA 44% 237.7
lactose catabolism lacK lo ABC transporter for Lactose, ATPase component (characterized) 35% 70% 141.4 Choline transport ATP-binding protein OpuBA 44% 237.7
D-glucosamine (chitosamine) catabolism AO353_21725 lo ABC transporter for D-Glucosamine, putative ATPase component (characterized) 33% 95% 139.4 Choline transport ATP-binding protein OpuBA 44% 237.7
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) 37% 64% 139 Choline transport ATP-binding protein OpuBA 44% 237.7
D-cellobiose catabolism SMc04256 lo ABC transporter for D-Cellobiose and D-Salicin, ATPase component (characterized) 35% 65% 137.5 Choline transport ATP-binding protein OpuBA 44% 237.7
D-maltose catabolism musK lo ABC-type maltose transporter (EC 7.5.2.1) (characterized) 32% 77% 136.7 Choline transport ATP-binding protein OpuBA 44% 237.7
L-arabinose catabolism xacK lo Xylose/arabinose import ATP-binding protein XacK; EC 7.5.2.13 (characterized, see rationale) 35% 70% 136.3 Choline transport ATP-binding protein OpuBA 44% 237.7
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) 35% 67% 136 Choline transport ATP-binding protein OpuBA 44% 237.7
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) 35% 67% 136 Choline transport ATP-binding protein OpuBA 44% 237.7
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) 35% 67% 136 Choline transport ATP-binding protein OpuBA 44% 237.7
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) 35% 67% 136 Choline transport ATP-binding protein OpuBA 44% 237.7
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) 35% 67% 136 Choline transport ATP-binding protein OpuBA 44% 237.7
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) 35% 67% 136 Choline transport ATP-binding protein OpuBA 44% 237.7
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) 35% 67% 136 Choline transport ATP-binding protein OpuBA 44% 237.7
D-maltose catabolism malK lo Maltose-transporting ATPase (EC 3.6.3.19) (characterized) 33% 66% 135.2 Choline transport ATP-binding protein OpuBA 44% 237.7
L-citrulline catabolism PS417_17605 lo ATP-binding cassette domain-containing protein; SubName: Full=Amino acid transporter; SubName: Full=Histidine ABC transporter ATP-binding protein; SubName: Full=Histidine transport system ATP-binding protein (characterized, see rationale) 32% 90% 132.9 Choline transport ATP-binding protein OpuBA 44% 237.7
glycerol catabolism glpS lo ABC transporter for Glycerol, ATPase component 1 (characterized) 33% 67% 126.3 Choline transport ATP-binding protein OpuBA 44% 237.7
L-tryptophan catabolism ecfA1 lo Energy-coupling factor transporter ATP-binding protein EcfA1; Short=ECF transporter A component EcfA; EC 7.-.-.- (characterized, see rationale) 31% 92% 123.6 Choline transport ATP-binding protein OpuBA 44% 237.7
D-maltose catabolism malK_Sm lo 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) 30% 89% 123.2 Choline transport ATP-binding protein OpuBA 44% 237.7
trehalose catabolism malK lo 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) 30% 89% 123.2 Choline transport ATP-binding protein OpuBA 44% 237.7
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) 35% 86% 119.4 Choline transport ATP-binding protein OpuBA 44% 237.7
glycerol catabolism glpT lo ABC transporter for Glycerol, ATPase component 2 (characterized) 32% 61% 114 Choline transport ATP-binding protein OpuBA 44% 237.7

Sequence Analysis Tools

View WP_025761778.1 at NCBI

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Find functional residues: SitesBLAST

Search for conserved domains

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Predict transmenbrane helices: Phobius

Predict protein localization: PSORTb

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Sequence

MIQVNRVSKHYGSIKAVNRISFEAKLGSTTVLVGTSGSGKTTTLKTINRLIEPSEGQILI
DGKDISLQKPQLLRRQIGYVSQNNGLFPHYTVRQNVAIVPSLIGWSAEKTLQRSEEILEQ
LLIPMAQFGHKFPKELSGGQYQRVALARALVTRPPVLLMDEPFGALDPVTRQQIRQELKS
LPGHPERSIVLVTHDLAEAIELGDQIVVMDRGKCLQQGPASDLLFKPRDSFIKSFFDTQR
FQLELSAVTLEQAIHYLHSNQHSTSTKIETRNLTLWETITLMEKENLTSLYYQSSSGQIF
QLTIPILLSCISQIKAKYGIT

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