GapMind for catabolism of small carbon sources

 

Protein WP_010529572.1 in Lentibacillus jeotgali Grbi

Annotation: NCBI__GCF_000224785.1:WP_010529572.1

Length: 384 amino acids

Source: GCF_000224785.1 in NCBI

Candidate for 55 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 med 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) 57% 73% 277.7 Carnitine transport ATP-binding protein OpuCA; EC 7.6.2.9 67% 521.5
L-histidine catabolism hutV med ABC transporter for L-Histidine, ATPase component (characterized) 45% 82% 196.8 Carnitine transport ATP-binding protein OpuCA; EC 7.6.2.9 67% 521.5
L-proline catabolism hutV med HutV aka HISV aka R02702 aka SMC00670, component of Uptake system for hisitidine, proline, proline-betaine and glycine-betaine (characterized) 42% 84% 188 Carnitine transport ATP-binding protein OpuCA; EC 7.6.2.9 67% 521.5
L-proline catabolism proV lo Glycine betaine/proline betaine transport system ATP-binding protein ProV (characterized) 36% 87% 226.9 Carnitine transport ATP-binding protein OpuCA; EC 7.6.2.9 67% 521.5
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% 83% 201.4 Carnitine transport ATP-binding protein OpuCA; EC 7.6.2.9 67% 521.5
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) 37% 83% 201.4 Carnitine transport ATP-binding protein OpuCA; EC 7.6.2.9 67% 521.5
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) 36% 87% 196.1 Carnitine transport ATP-binding protein OpuCA; EC 7.6.2.9 67% 521.5
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) 36% 87% 196.1 Carnitine transport ATP-binding protein OpuCA; EC 7.6.2.9 67% 521.5
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) 36% 87% 196.1 Carnitine transport ATP-binding protein OpuCA; EC 7.6.2.9 67% 521.5
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) 36% 87% 196.1 Carnitine transport ATP-binding protein OpuCA; EC 7.6.2.9 67% 521.5
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) 36% 87% 196.1 Carnitine transport ATP-binding protein OpuCA; EC 7.6.2.9 67% 521.5
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) 36% 87% 196.1 Carnitine transport ATP-binding protein OpuCA; EC 7.6.2.9 67% 521.5
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) 36% 87% 196.1 Carnitine transport ATP-binding protein OpuCA; EC 7.6.2.9 67% 521.5
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) 36% 87% 196.1 Carnitine transport ATP-binding protein OpuCA; EC 7.6.2.9 67% 521.5
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) 36% 87% 196.1 Carnitine transport ATP-binding protein OpuCA; EC 7.6.2.9 67% 521.5
D-maltose catabolism malK_Aa lo ABC-type maltose transporter (EC 7.5.2.1) (characterized) 41% 63% 193.4 Carnitine transport ATP-binding protein OpuCA; EC 7.6.2.9 67% 521.5
D-sorbitol (glucitol) catabolism mtlK lo ABC transporter for D-Sorbitol, ATPase component (characterized) 38% 75% 186.8 Carnitine transport ATP-binding protein OpuCA; EC 7.6.2.9 67% 521.5
N-acetyl-D-glucosamine catabolism SMc02869 lo N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized) 40% 70% 186.4 Carnitine transport ATP-binding protein OpuCA; EC 7.6.2.9 67% 521.5
D-glucosamine (chitosamine) catabolism SMc02869 lo N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized) 40% 70% 186.4 Carnitine transport ATP-binding protein OpuCA; EC 7.6.2.9 67% 521.5
putrescine catabolism potA lo spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31 (characterized) 40% 62% 184.9 Carnitine transport ATP-binding protein OpuCA; EC 7.6.2.9 67% 521.5
trehalose catabolism malK lo MsmK aka SMU.882, component of The raffinose/stachyose transporter, MsmEFGK (MalK (3.A.1.1.27) can probably substitute for MsmK; Webb et al., 2008). This system may also transport melibiose, isomaltotriose and sucrose as well as isomaltosaccharides (characterized) 35% 81% 183.3 Carnitine transport ATP-binding protein OpuCA; EC 7.6.2.9 67% 521.5
D-mannitol catabolism mtlK lo SmoK aka POLK, component of Hexitol (glucitol; mannitol) porter (characterized) 35% 80% 180.6 Carnitine transport ATP-binding protein OpuCA; EC 7.6.2.9 67% 521.5
D-maltose catabolism malK lo ABC-type maltose transporter (subunit 3/3) (EC 7.5.2.1) (characterized) 33% 89% 179.1 Carnitine transport ATP-binding protein OpuCA; EC 7.6.2.9 67% 521.5
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) 37% 65% 176.8 Carnitine transport ATP-binding protein OpuCA; EC 7.6.2.9 67% 521.5
D-galactose catabolism PfGW456L13_1897 lo ABC transporter for D-Galactose and D-Glucose, ATPase component (characterized) 41% 61% 174.9 Carnitine transport ATP-binding protein OpuCA; EC 7.6.2.9 67% 521.5
lactose catabolism lacK lo ABC transporter for Lactose, ATPase component (characterized) 36% 80% 174.5 Carnitine transport ATP-binding protein OpuCA; EC 7.6.2.9 67% 521.5
xylitol catabolism HSERO_RS17020 lo ABC-type sugar transport system, ATPase component protein (characterized, see rationale) 40% 56% 174.5 Carnitine transport ATP-binding protein OpuCA; EC 7.6.2.9 67% 521.5
D-xylose catabolism gtsD lo ABC transporter for D-Glucose-6-Phosphate, ATPase component (characterized) 39% 61% 172.9 Carnitine transport ATP-binding protein OpuCA; EC 7.6.2.9 67% 521.5
xylitol catabolism Dshi_0546 lo ABC transporter for Xylitol, ATPase component (characterized) 36% 72% 170.2 Carnitine transport ATP-binding protein OpuCA; EC 7.6.2.9 67% 521.5
D-maltose catabolism aglK lo ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized) 35% 73% 168.7 Carnitine transport ATP-binding protein OpuCA; EC 7.6.2.9 67% 521.5
sucrose catabolism aglK lo ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized) 35% 73% 168.7 Carnitine transport ATP-binding protein OpuCA; EC 7.6.2.9 67% 521.5
trehalose catabolism aglK lo ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized) 35% 73% 168.7 Carnitine transport ATP-binding protein OpuCA; EC 7.6.2.9 67% 521.5
L-glutamate catabolism gltL lo GluA aka CGL1950, component of Glutamate porter (characterized) 39% 98% 167.9 Carnitine transport ATP-binding protein OpuCA; EC 7.6.2.9 67% 521.5
L-asparagine catabolism peb1C lo PEB1C, component of Uptake system for glutamate and aspartate (characterized) 38% 98% 166.4 Carnitine transport ATP-binding protein OpuCA; EC 7.6.2.9 67% 521.5
L-aspartate catabolism peb1C lo PEB1C, component of Uptake system for glutamate and aspartate (characterized) 38% 98% 166.4 Carnitine transport ATP-binding protein OpuCA; EC 7.6.2.9 67% 521.5
D-cellobiose catabolism aglK' lo Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 36% 65% 161.4 Carnitine transport ATP-binding protein OpuCA; EC 7.6.2.9 67% 521.5
D-glucose catabolism aglK' lo Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 36% 65% 161.4 Carnitine transport ATP-binding protein OpuCA; EC 7.6.2.9 67% 521.5
lactose catabolism aglK' lo Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 36% 65% 161.4 Carnitine transport ATP-binding protein OpuCA; EC 7.6.2.9 67% 521.5
D-maltose catabolism aglK' lo Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 36% 65% 161.4 Carnitine transport ATP-binding protein OpuCA; EC 7.6.2.9 67% 521.5
sucrose catabolism aglK' lo Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 36% 65% 161.4 Carnitine transport ATP-binding protein OpuCA; EC 7.6.2.9 67% 521.5
trehalose catabolism aglK' lo Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 36% 65% 161.4 Carnitine transport ATP-binding protein OpuCA; EC 7.6.2.9 67% 521.5
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) 38% 89% 158.3 Carnitine transport ATP-binding protein OpuCA; EC 7.6.2.9 67% 521.5
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) 38% 89% 158.3 Carnitine transport ATP-binding protein OpuCA; EC 7.6.2.9 67% 521.5
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) 38% 89% 158.3 Carnitine transport ATP-binding protein OpuCA; EC 7.6.2.9 67% 521.5
L-histidine 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) 38% 89% 158.3 Carnitine transport ATP-binding protein OpuCA; EC 7.6.2.9 67% 521.5
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) 38% 89% 158.3 Carnitine transport ATP-binding protein OpuCA; EC 7.6.2.9 67% 521.5
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) 38% 89% 158.3 Carnitine transport ATP-binding protein OpuCA; EC 7.6.2.9 67% 521.5
L-asparagine catabolism bztD lo BztD, component of Glutamate/glutamine/aspartate/asparagine porter (characterized) 36% 90% 156.8 Carnitine transport ATP-binding protein OpuCA; EC 7.6.2.9 67% 521.5
L-aspartate catabolism bztD lo BztD, component of Glutamate/glutamine/aspartate/asparagine porter (characterized) 36% 90% 156.8 Carnitine transport ATP-binding protein OpuCA; EC 7.6.2.9 67% 521.5
D-alanine catabolism Pf6N2E2_5405 lo ABC transporter for D-Alanine, ATPase component (characterized) 37% 94% 154.1 Carnitine transport ATP-binding protein OpuCA; EC 7.6.2.9 67% 521.5
L-asparagine catabolism bgtA lo ATPase (characterized, see rationale) 34% 92% 153.3 Carnitine transport ATP-binding protein OpuCA; EC 7.6.2.9 67% 521.5
L-aspartate catabolism bgtA lo ATPase (characterized, see rationale) 34% 92% 153.3 Carnitine transport ATP-binding protein OpuCA; EC 7.6.2.9 67% 521.5
L-lysine catabolism hisP lo ABC transporter for L-Lysine, ATPase component (characterized) 36% 97% 147.1 Carnitine transport ATP-binding protein OpuCA; EC 7.6.2.9 67% 521.5
D-glucosamine (chitosamine) catabolism AO353_21725 lo ABC transporter for D-glucosamine, ATPase component (characterized) 35% 95% 141 Carnitine transport ATP-binding protein OpuCA; EC 7.6.2.9 67% 521.5
L-proline catabolism HSERO_RS00900 lo ABC-type branched-chain amino acid transport system, ATPase component protein (characterized, see rationale) 30% 89% 94 Carnitine transport ATP-binding protein OpuCA; EC 7.6.2.9 67% 521.5

Sequence Analysis Tools

View WP_010529572.1 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

MLQFNHVFKTYSDGTSAVKDLNLKINKGEFVCFIGPSGCGKTTTMKMVNRLIDITEGSIL
VDDKDIKDQDAVELRRSMGYVIQQIGLMPHMTIKENIVLVGTLLKWSKERKDERARELLK
LVNMPEEYLDKYPHELSGGQQQRIGVLRALAVNPPLILMDEPFGALDPITRDSLQEEFKK
LQKELNKTIIFVTHDMDEALKLADKVVIMRDGEVVQADTPEEILRHPANEFVEEFLGRDR
LIQGKPDVTTVGQIMESSPVTAQTGATLKSAISTMRDRHVDSLLVVDSNNVLQGYIDIEA
MNLNYKKANIVDDLMETDVFSVSGESLLRDTVHKILRRGAAYVPVVDEAYHLEGIVTRAT
LANLVYDTIWGDGKELEEKVAAAE

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