GapMind for catabolism of small carbon sources

 

Protein WP_019557545.1 in Thiomicrorhabdus arctica DSM 13458

Annotation: NCBI__GCF_000381085.1:WP_019557545.1

Length: 397 amino acids

Source: GCF_000381085.1 in NCBI

Candidate for 89 steps in catabolism of small carbon sources

Pathway Step Score Similar to Id. Cov. Bits Other hit Other id. Other bits
L-proline catabolism proV hi Glycine betaine/proline betaine transport system ATP-binding protein ProV (characterized) 56% 98% 443.7 ABC-type quaternary amine transporter (EC 7.6.2.9) 52% 386.0
L-proline catabolism opuBA med BusAA, component of Uptake system for glycine-betaine (high affinity) and proline (low affinity) (OpuAA-OpuABC) or BusAA-ABC of Lactococcus lactis). BusAA, the ATPase subunit, has a C-terminal tandem cystathionine β-synthase (CBS) domain which is the cytoplasmic K+ sensor for osmotic stress (osmotic strength)while the BusABC subunit has the membrane and receptor domains fused to each other (Biemans-Oldehinkel et al., 2006; Mahmood et al., 2006; Gul et al. 2012). An N-terminal amphipathic α-helix of OpuA is necessary for high activity but is not critical for biogenesis or the ionic regulation of transport (characterized) 47% 95% 345.9 Glycine betaine/proline betaine transport system ATP-binding protein ProV 56% 443.7
L-histidine catabolism hutV med ABC transporter for L-Histidine, ATPase component (characterized) 56% 95% 301.6 Glycine betaine/proline betaine transport system ATP-binding protein ProV 56% 443.7
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) 53% 95% 290 Glycine betaine/proline betaine transport system ATP-binding protein ProV 56% 443.7
L-asparagine catabolism aatP med ABC transporter for L-aspartate, L-asparagine, L-glutamate, and L-glutamine, ATPase component (characterized) 40% 87% 155.2 Glycine betaine/proline betaine transport system ATP-binding protein ProV 56% 443.7
L-aspartate catabolism aatP med ABC transporter for L-aspartate, L-asparagine, L-glutamate, and L-glutamine, ATPase component (characterized) 40% 87% 155.2 Glycine betaine/proline betaine transport system ATP-binding protein ProV 56% 443.7
L-glutamate catabolism gltL med ABC transporter for L-aspartate, L-asparagine, L-glutamate, and L-glutamine, ATPase component (characterized) 40% 87% 155.2 Glycine betaine/proline betaine transport system ATP-binding protein ProV 56% 443.7
putrescine catabolism potA lo PotG aka B0855, component of Putrescine porter (characterized) 42% 59% 173.7 Glycine betaine/proline betaine transport system ATP-binding protein ProV 56% 443.7
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) 31% 92% 173.3 Glycine betaine/proline betaine transport system ATP-binding protein ProV 56% 443.7
D-maltose catabolism thuK lo ThuK aka RB0314 aka SMB20328, component of Trehalose/maltose/sucrose porter (trehalose inducible) (characterized) 35% 85% 173.3 Glycine betaine/proline betaine transport system ATP-binding protein ProV 56% 443.7
sucrose catabolism thuK lo ThuK aka RB0314 aka SMB20328, component of Trehalose/maltose/sucrose porter (trehalose inducible) (characterized) 35% 85% 173.3 Glycine betaine/proline betaine transport system ATP-binding protein ProV 56% 443.7
trehalose catabolism thuK lo ThuK aka RB0314 aka SMB20328, component of Trehalose/maltose/sucrose porter (trehalose inducible) (characterized) 35% 85% 173.3 Glycine betaine/proline betaine transport system ATP-binding protein ProV 56% 443.7
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) 32% 94% 168.7 Glycine betaine/proline betaine transport system ATP-binding protein ProV 56% 443.7
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) 32% 94% 168.7 Glycine betaine/proline betaine transport system ATP-binding protein ProV 56% 443.7
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) 32% 94% 168.7 Glycine betaine/proline betaine transport system ATP-binding protein ProV 56% 443.7
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) 32% 94% 168.7 Glycine betaine/proline betaine transport system ATP-binding protein ProV 56% 443.7
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) 32% 94% 168.7 Glycine betaine/proline betaine transport system ATP-binding protein ProV 56% 443.7
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) 32% 94% 168.7 Glycine betaine/proline betaine transport system ATP-binding protein ProV 56% 443.7
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) 32% 94% 168.7 Glycine betaine/proline betaine transport system ATP-binding protein ProV 56% 443.7
L-histidine catabolism PA5503 lo Methionine import ATP-binding protein MetN 2, component of L-Histidine uptake porter, MetIQN (characterized) 40% 67% 166.4 Glycine betaine/proline betaine transport system ATP-binding protein ProV 56% 443.7
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) 31% 81% 165.2 Glycine betaine/proline betaine transport system ATP-binding protein ProV 56% 443.7
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) 31% 81% 165.2 Glycine betaine/proline betaine transport system ATP-binding protein ProV 56% 443.7
D-mannitol catabolism mtlK lo ABC transporter for D-mannitol and D-mannose, ATPase component (characterized) 38% 63% 164.1 Glycine betaine/proline betaine transport system ATP-binding protein ProV 56% 443.7
L-arabinose catabolism xacJ lo Xylose/arabinose import ATP-binding protein XacJ; EC 7.5.2.13 (characterized, see rationale) 38% 58% 162.9 Glycine betaine/proline betaine transport system ATP-binding protein ProV 56% 443.7
L-lysine catabolism hisP lo ABC transporter for L-Lysine, ATPase component (characterized) 36% 98% 159.8 Glycine betaine/proline betaine transport system ATP-binding protein ProV 56% 443.7
D-sorbitol (glucitol) catabolism mtlK lo ABC transporter for D-Mannitol, D-Mannose, and D-Sorbitol, ATPase component (characterized) 36% 63% 159.8 Glycine betaine/proline betaine transport system ATP-binding protein ProV 56% 443.7
L-arginine catabolism artP lo Arginine transport ATP-binding protein ArtM (characterized) 39% 98% 159.5 Glycine betaine/proline betaine transport system ATP-binding protein ProV 56% 443.7
L-fucose catabolism SM_b21106 lo ABC transporter for L-Fucose, ATPase component (characterized) 39% 63% 159.1 Glycine betaine/proline betaine transport system ATP-binding protein ProV 56% 443.7
D-maltose catabolism aglK lo ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized) 33% 81% 159.1 Glycine betaine/proline betaine transport system ATP-binding protein ProV 56% 443.7
sucrose catabolism aglK lo ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized) 33% 81% 159.1 Glycine betaine/proline betaine transport system ATP-binding protein ProV 56% 443.7
trehalose catabolism aglK lo ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized) 33% 81% 159.1 Glycine betaine/proline betaine transport system ATP-binding protein ProV 56% 443.7
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) 38% 87% 158.7 Glycine betaine/proline betaine transport system ATP-binding protein ProV 56% 443.7
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) 38% 87% 158.7 Glycine betaine/proline betaine transport system ATP-binding protein ProV 56% 443.7
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) 38% 87% 158.7 Glycine betaine/proline betaine transport system ATP-binding protein ProV 56% 443.7
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% 87% 158.7 Glycine betaine/proline betaine transport system ATP-binding protein ProV 56% 443.7
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) 38% 87% 158.7 Glycine betaine/proline betaine transport system ATP-binding protein ProV 56% 443.7
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) 38% 87% 158.7 Glycine betaine/proline betaine transport system ATP-binding protein ProV 56% 443.7
L-arabinose catabolism araV lo AraV, component of Arabinose, fructose, xylose porter (characterized) 31% 96% 158.3 Glycine betaine/proline betaine transport system ATP-binding protein ProV 56% 443.7
D-fructose catabolism araV lo AraV, component of Arabinose, fructose, xylose porter (characterized) 31% 96% 158.3 Glycine betaine/proline betaine transport system ATP-binding protein ProV 56% 443.7
sucrose catabolism araV lo AraV, component of Arabinose, fructose, xylose porter (characterized) 31% 96% 158.3 Glycine betaine/proline betaine transport system ATP-binding protein ProV 56% 443.7
D-xylose catabolism araV lo AraV, component of Arabinose, fructose, xylose porter (characterized) 31% 96% 158.3 Glycine betaine/proline betaine transport system ATP-binding protein ProV 56% 443.7
L-histidine catabolism hisP lo Histidine transport ATP-binding protein HisP (characterized) 38% 92% 157.1 Glycine betaine/proline betaine transport system ATP-binding protein ProV 56% 443.7
D-maltose catabolism malK_Bb lo ABC-type maltose transport, ATP binding protein (characterized, see rationale) 35% 69% 157.1 Glycine betaine/proline betaine transport system ATP-binding protein ProV 56% 443.7
D-maltose catabolism musK lo ABC-type maltose transporter (EC 7.5.2.1) (characterized) 36% 59% 155.6 Glycine betaine/proline betaine transport system ATP-binding protein ProV 56% 443.7
L-asparagine catabolism bztD lo BztD, component of Glutamate/glutamine/aspartate/asparagine porter (characterized) 37% 85% 154.8 Glycine betaine/proline betaine transport system ATP-binding protein ProV 56% 443.7
L-aspartate catabolism bztD lo BztD, component of Glutamate/glutamine/aspartate/asparagine porter (characterized) 37% 85% 154.8 Glycine betaine/proline betaine transport system ATP-binding protein ProV 56% 443.7
D-maltose catabolism malK lo Maltose-transporting ATPase (EC 3.6.3.19) (characterized) 36% 60% 154.8 Glycine betaine/proline betaine transport system ATP-binding protein ProV 56% 443.7
L-arabinose catabolism xacK lo Xylose/arabinose import ATP-binding protein XacK; EC 7.5.2.13 (characterized, see rationale) 36% 60% 154.5 Glycine betaine/proline betaine transport system ATP-binding protein ProV 56% 443.7
D-alanine catabolism Pf6N2E2_5405 lo ABC transporter for D-Alanine, ATPase component (characterized) 37% 88% 154.1 Glycine betaine/proline betaine transport system ATP-binding protein ProV 56% 443.7
trehalose catabolism treV lo TreV, component of Trehalose porter (characterized) 35% 69% 153.3 Glycine betaine/proline betaine transport system ATP-binding protein ProV 56% 443.7
xylitol catabolism Dshi_0546 lo ABC transporter for Xylitol, ATPase component (characterized) 34% 70% 152.5 Glycine betaine/proline betaine transport system ATP-binding protein ProV 56% 443.7
D-maltose catabolism malK_Aa lo ABC-type maltose transporter (EC 7.5.2.1) (characterized) 35% 58% 151.8 Glycine betaine/proline betaine transport system ATP-binding protein ProV 56% 443.7
D-xylose catabolism gtsD lo ABC transporter for D-Glucose-6-Phosphate, ATPase component (characterized) 37% 58% 151.4 Glycine betaine/proline betaine transport system ATP-binding protein ProV 56% 443.7
D-cellobiose catabolism aglK' lo Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 34% 82% 150.6 Glycine betaine/proline betaine transport system ATP-binding protein ProV 56% 443.7
D-glucose catabolism aglK' lo Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 34% 82% 150.6 Glycine betaine/proline betaine transport system ATP-binding protein ProV 56% 443.7
lactose catabolism aglK' lo Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 34% 82% 150.6 Glycine betaine/proline betaine transport system ATP-binding protein ProV 56% 443.7
D-maltose catabolism aglK' lo Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 34% 82% 150.6 Glycine betaine/proline betaine transport system ATP-binding protein ProV 56% 443.7
sucrose catabolism aglK' lo Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 34% 82% 150.6 Glycine betaine/proline betaine transport system ATP-binding protein ProV 56% 443.7
trehalose catabolism aglK' lo Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 34% 82% 150.6 Glycine betaine/proline betaine transport system ATP-binding protein ProV 56% 443.7
L-asparagine catabolism glnQ lo Glutamine ABC transporter ATP-binding protein, component of Glutamine transporter, GlnQP. Takes up glutamine, asparagine and glutamate which compete for each other for binding both substrate and the transmembrane protein constituent of the system (Fulyani et al. 2015). Tandem substrate binding domains (SBDs) differ in substrate specificity and affinity, allowing cells to efficiently accumulate different amino acids via a single ABC transporter. Analysis revealed the roles of individual residues in determining the substrate affinity (characterized) 35% 99% 150.2 Glycine betaine/proline betaine transport system ATP-binding protein ProV 56% 443.7
L-histidine catabolism bgtA lo BgtA aka SLR1735, component of Arginine/lysine/histidine/glutamine porter (characterized) 37% 88% 149.8 Glycine betaine/proline betaine transport system ATP-binding protein ProV 56% 443.7
D-glucosamine (chitosamine) catabolism SM_b21216 lo ABC transporter for D-Glucosamine, ATPase component (characterized) 34% 69% 149.1 Glycine betaine/proline betaine transport system ATP-binding protein ProV 56% 443.7
L-citrulline catabolism AO353_03040 lo ABC transporter for L-Arginine and L-Citrulline, ATPase component (characterized) 33% 98% 148.7 Glycine betaine/proline betaine transport system ATP-binding protein ProV 56% 443.7
N-acetyl-D-glucosamine catabolism SMc02869 lo N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized) 32% 69% 148.3 Glycine betaine/proline betaine transport system ATP-binding protein ProV 56% 443.7
D-glucosamine (chitosamine) catabolism SMc02869 lo N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized) 32% 69% 148.3 Glycine betaine/proline betaine transport system ATP-binding protein ProV 56% 443.7
lactose catabolism lacK lo ABC transporter for Lactose, ATPase component (characterized) 36% 63% 148.3 Glycine betaine/proline betaine transport system ATP-binding protein ProV 56% 443.7
D-cellobiose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 33% 70% 147.9 Glycine betaine/proline betaine transport system ATP-binding protein ProV 56% 443.7
D-galactose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 33% 70% 147.9 Glycine betaine/proline betaine transport system ATP-binding protein ProV 56% 443.7
D-glucose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 33% 70% 147.9 Glycine betaine/proline betaine transport system ATP-binding protein ProV 56% 443.7
lactose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 33% 70% 147.9 Glycine betaine/proline betaine transport system ATP-binding protein ProV 56% 443.7
D-maltose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 33% 70% 147.9 Glycine betaine/proline betaine transport system ATP-binding protein ProV 56% 443.7
D-mannose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 33% 70% 147.9 Glycine betaine/proline betaine transport system ATP-binding protein ProV 56% 443.7
sucrose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 33% 70% 147.9 Glycine betaine/proline betaine transport system ATP-binding protein ProV 56% 443.7
trehalose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 33% 70% 147.9 Glycine betaine/proline betaine transport system ATP-binding protein ProV 56% 443.7
D-cellobiose catabolism SMc04256 lo ABC transporter for D-Cellobiose and D-Salicin, ATPase component (characterized) 36% 63% 147.5 Glycine betaine/proline betaine transport system ATP-binding protein ProV 56% 443.7
L-histidine catabolism BPHYT_RS24015 lo ABC transporter related (characterized, see rationale) 34% 94% 147.5 Glycine betaine/proline betaine transport system ATP-binding protein ProV 56% 443.7
L-asparagine catabolism bgtA lo ATPase (characterized, see rationale) 37% 85% 146.4 Glycine betaine/proline betaine transport system ATP-binding protein ProV 56% 443.7
L-aspartate catabolism bgtA lo ATPase (characterized, see rationale) 37% 85% 146.4 Glycine betaine/proline betaine transport system ATP-binding protein ProV 56% 443.7
D-mannose catabolism TM1750 lo TM1750, component of Probable mannose/mannoside porter. Induced by beta-mannan (Conners et al., 2005). Regulated by mannose-responsive regulator manR (characterized) 38% 70% 145.6 Glycine betaine/proline betaine transport system ATP-binding protein ProV 56% 443.7
D-glucosamine (chitosamine) catabolism AO353_21725 lo ABC transporter for D-glucosamine, ATPase component (characterized) 34% 94% 141.4 Glycine betaine/proline betaine transport system ATP-binding protein ProV 56% 443.7
L-histidine catabolism Ac3H11_2560 lo ABC transporter for L-Histidine, ATPase component (characterized) 39% 75% 138.3 Glycine betaine/proline betaine transport system ATP-binding protein ProV 56% 443.7
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) 36% 89% 136.3 Glycine betaine/proline betaine transport system ATP-binding protein ProV 56% 443.7
L-tryptophan catabolism ecfA1 lo Energy-coupling factor transporter ATP-binding protein EcfA1; Short=ECF transporter A component EcfA; EC 7.-.-.- (characterized, see rationale) 39% 78% 136 Glycine betaine/proline betaine transport system ATP-binding protein ProV 56% 443.7
xylitol catabolism HSERO_RS17020 lo ABC-type sugar transport system, ATPase component protein (characterized, see rationale) 33% 52% 135.6 Glycine betaine/proline betaine transport system ATP-binding protein ProV 56% 443.7
glycerol catabolism glpS lo ABC transporter for Glycerol, ATPase component 1 (characterized) 31% 65% 131 Glycine betaine/proline betaine transport system ATP-binding protein ProV 56% 443.7
D-mannose catabolism TM1749 lo TM1749, component of Probable mannose/mannoside porter. Induced by beta-mannan (Conners et al., 2005). Regulated by mannose-responsive regulator manR (characterized) 34% 74% 123.6 Glycine betaine/proline betaine transport system ATP-binding protein ProV 56% 443.7
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) 32% 93% 122.9 Glycine betaine/proline betaine transport system ATP-binding protein ProV 56% 443.7
L-tryptophan catabolism ecfA2 lo Energy-coupling factor transporter ATP-binding protein EcfA2; Short=ECF transporter A component EcfA2; EC 7.-.-.- (characterized, see rationale) 34% 78% 122.5 Glycine betaine/proline betaine transport system ATP-binding protein ProV 56% 443.7
D-cellobiose catabolism cbtF lo CbtF, component of Cellobiose and cellooligosaccharide porter (characterized) 30% 78% 113.6 Glycine betaine/proline betaine transport system ATP-binding protein ProV 56% 443.7

Sequence Analysis Tools

View WP_019557545.1 at NCBI

Find papers: PaperBLAST

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

MTIKNVKLKVENLYKVFGDHPKKTISLIHKGLDKEAIFAKTGNTVGVNNASFEVYAGEIF
VVMGLSGSGKSTLVRLLNRLIEPTEGNIWIDGQNITQMSDKELRQARRKKISMVFQSFAL
LPHMTVIENAAFGLTLDGFNKNQAQKEALDALEQVGLGTHANSYPSELSGGMQQRVGIAR
ALATGSEIMLMDEAFSALDPLIRTEMQDELVKLQEKNHRTIIFISHDLDEAMRIGDRIAI
MEQGNIVQVGTPEEILRNPETEYVEAFFKGVSMSEVLTAKNIINHKFFSVPKKGSQGLKT
LSRLLDDSDFDYAYITTSDKRFIGVSTVESMQAAAKTTDKVEDSYLTGVTTIDADTPLNE
VIGLMAEAPCPLPITNEKNEIIGILTRTKLLKALDPN

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