GapMind for catabolism of small carbon sources

 

Protein WP_081673849.1 in Novosphingobium lindaniclasticum LE124

Annotation: NCBI__GCF_000445125.1:WP_081673849.1

Length: 331 amino acids

Source: GCF_000445125.1 in NCBI

Candidate for 122 steps in catabolism of small carbon sources

Pathway Step Score Similar to Id. Cov. Bits Other hit Other id. Other bits
putrescine catabolism potA med spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31 (characterized) 45% 81% 244.2 CysA aka B2422, component of Sulfate/thiosulfate porter 64% 318.2
D-mannitol catabolism mtlK med SmoK aka POLK, component of Hexitol (glucitol; mannitol) porter (characterized) 42% 87% 226.1 CysA aka B2422, component of Sulfate/thiosulfate porter 64% 318.2
D-maltose catabolism malK_Bb med ABC-type maltose transport, ATP binding protein (characterized, see rationale) 42% 90% 222.2 CysA aka B2422, component of Sulfate/thiosulfate porter 64% 318.2
N-acetyl-D-glucosamine catabolism SMc02869 med N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized) 41% 94% 220.7 CysA aka B2422, component of Sulfate/thiosulfate porter 64% 318.2
D-glucosamine (chitosamine) catabolism SMc02869 med N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized) 41% 94% 220.7 CysA aka B2422, component of Sulfate/thiosulfate porter 64% 318.2
D-maltose catabolism malK med ABC-type maltose transporter (subunit 3/3) (EC 7.5.2.1) (characterized) 41% 80% 217.2 CysA aka B2422, component of Sulfate/thiosulfate porter 64% 318.2
D-sorbitol (glucitol) catabolism mtlK med ABC transporter for D-Sorbitol, ATPase component (characterized) 46% 71% 216.1 CysA aka B2422, component of Sulfate/thiosulfate porter 64% 318.2
trehalose catabolism treV med TreV, component of Trehalose porter (characterized) 45% 74% 205.3 CysA aka B2422, component of Sulfate/thiosulfate porter 64% 318.2
L-asparagine catabolism bgtA med ATPase (characterized, see rationale) 40% 92% 175.3 CysA aka B2422, component of Sulfate/thiosulfate porter 64% 318.2
L-aspartate catabolism bgtA med ATPase (characterized, see rationale) 40% 92% 175.3 CysA aka B2422, component of Sulfate/thiosulfate porter 64% 318.2
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) 40% 73% 173.7 CysA aka B2422, component of Sulfate/thiosulfate porter 64% 318.2
L-histidine catabolism Ac3H11_2560 med ABC transporter for L-Histidine, ATPase component (characterized) 44% 75% 151.8 CysA aka B2422, component of Sulfate/thiosulfate porter 64% 318.2
L-fucose catabolism SM_b21106 lo ABC transporter for L-Fucose, ATPase component (characterized) 49% 68% 233.4 CysA aka B2422, component of Sulfate/thiosulfate porter 64% 318.2
xylitol catabolism Dshi_0546 lo ABC transporter for Xylitol, ATPase component (characterized) 48% 69% 223 CysA aka B2422, component of Sulfate/thiosulfate porter 64% 318.2
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) 47% 63% 218.8 CysA aka B2422, component of Sulfate/thiosulfate porter 64% 318.2
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) 47% 63% 218.8 CysA aka B2422, component of Sulfate/thiosulfate porter 64% 318.2
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) 47% 63% 218.8 CysA aka B2422, component of Sulfate/thiosulfate porter 64% 318.2
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) 47% 63% 218.8 CysA aka B2422, component of Sulfate/thiosulfate porter 64% 318.2
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) 47% 63% 218.8 CysA aka B2422, component of Sulfate/thiosulfate porter 64% 318.2
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) 47% 63% 218.8 CysA aka B2422, component of Sulfate/thiosulfate porter 64% 318.2
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) 47% 63% 218.8 CysA aka B2422, component of Sulfate/thiosulfate porter 64% 318.2
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) 47% 63% 218.8 CysA aka B2422, component of Sulfate/thiosulfate porter 64% 318.2
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) 47% 63% 218.8 CysA aka B2422, component of Sulfate/thiosulfate porter 64% 318.2
trehalose 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) 47% 63% 218.8 CysA aka B2422, component of Sulfate/thiosulfate porter 64% 318.2
xylitol catabolism HSERO_RS17020 lo ABC-type sugar transport system, ATPase component protein (characterized, see rationale) 49% 57% 217.6 CysA aka B2422, component of Sulfate/thiosulfate porter 64% 318.2
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) 48% 63% 217.2 CysA aka B2422, component of Sulfate/thiosulfate porter 64% 318.2
D-maltose catabolism aglK lo ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized) 46% 67% 211.1 CysA aka B2422, component of Sulfate/thiosulfate porter 64% 318.2
sucrose catabolism aglK lo ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized) 46% 67% 211.1 CysA aka B2422, component of Sulfate/thiosulfate porter 64% 318.2
trehalose catabolism aglK lo ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized) 46% 67% 211.1 CysA aka B2422, component of Sulfate/thiosulfate porter 64% 318.2
D-maltose catabolism malK_Aa lo ABC-type maltose transporter (EC 7.5.2.1) (characterized) 47% 61% 209.9 CysA aka B2422, component of Sulfate/thiosulfate porter 64% 318.2
lactose catabolism lacK lo LacK, component of Lactose porter (characterized) 39% 81% 209.5 CysA aka B2422, component of Sulfate/thiosulfate porter 64% 318.2
D-glucosamine (chitosamine) catabolism SM_b21216 lo ABC transporter for D-Glucosamine, ATPase component (characterized) 46% 65% 207.2 CysA aka B2422, component of Sulfate/thiosulfate porter 64% 318.2
D-xylose catabolism gtsD lo ABC transporter for D-Glucose-6-Phosphate, ATPase component (characterized) 44% 66% 203.4 CysA aka B2422, component of Sulfate/thiosulfate porter 64% 318.2
L-arabinose catabolism xacJ lo Xylose/arabinose import ATP-binding protein XacJ; EC 7.5.2.13 (characterized, see rationale) 43% 61% 203 CysA aka B2422, component of Sulfate/thiosulfate porter 64% 318.2
D-galactose catabolism PfGW456L13_1897 lo ABC transporter for D-Galactose and D-Glucose, ATPase component (characterized) 44% 65% 203 CysA aka B2422, component of Sulfate/thiosulfate porter 64% 318.2
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) 43% 66% 202.2 CysA aka B2422, component of Sulfate/thiosulfate porter 64% 318.2
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) 43% 66% 202.2 CysA aka B2422, component of Sulfate/thiosulfate porter 64% 318.2
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) 44% 58% 199.9 CysA aka B2422, component of Sulfate/thiosulfate porter 64% 318.2
L-arabinose catabolism xacK lo Xylose/arabinose import ATP-binding protein XacK; EC 7.5.2.13 (characterized, see rationale) 39% 76% 196.8 CysA aka B2422, component of Sulfate/thiosulfate porter 64% 318.2
D-cellobiose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 41% 70% 193.4 CysA aka B2422, component of Sulfate/thiosulfate porter 64% 318.2
D-galactose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 41% 70% 193.4 CysA aka B2422, component of Sulfate/thiosulfate porter 64% 318.2
D-glucose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 41% 70% 193.4 CysA aka B2422, component of Sulfate/thiosulfate porter 64% 318.2
lactose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 41% 70% 193.4 CysA aka B2422, component of Sulfate/thiosulfate porter 64% 318.2
D-maltose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 41% 70% 193.4 CysA aka B2422, component of Sulfate/thiosulfate porter 64% 318.2
D-mannose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 41% 70% 193.4 CysA aka B2422, component of Sulfate/thiosulfate porter 64% 318.2
sucrose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 41% 70% 193.4 CysA aka B2422, component of Sulfate/thiosulfate porter 64% 318.2
trehalose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 41% 70% 193.4 CysA aka B2422, component of Sulfate/thiosulfate porter 64% 318.2
D-cellobiose catabolism aglK' lo Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 37% 87% 193 CysA aka B2422, component of Sulfate/thiosulfate porter 64% 318.2
D-glucose catabolism aglK' lo Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 37% 87% 193 CysA aka B2422, component of Sulfate/thiosulfate porter 64% 318.2
lactose catabolism aglK' lo Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 37% 87% 193 CysA aka B2422, component of Sulfate/thiosulfate porter 64% 318.2
D-maltose catabolism aglK' lo Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 37% 87% 193 CysA aka B2422, component of Sulfate/thiosulfate porter 64% 318.2
sucrose catabolism aglK' lo Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 37% 87% 193 CysA aka B2422, component of Sulfate/thiosulfate porter 64% 318.2
trehalose catabolism aglK' lo Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 37% 87% 193 CysA aka B2422, component of Sulfate/thiosulfate porter 64% 318.2
L-arabinose catabolism araV lo AraV, component of Arabinose, fructose, xylose porter (characterized) 38% 80% 189.1 CysA aka B2422, component of Sulfate/thiosulfate porter 64% 318.2
D-fructose catabolism araV lo AraV, component of Arabinose, fructose, xylose porter (characterized) 38% 80% 189.1 CysA aka B2422, component of Sulfate/thiosulfate porter 64% 318.2
sucrose catabolism araV lo AraV, component of Arabinose, fructose, xylose porter (characterized) 38% 80% 189.1 CysA aka B2422, component of Sulfate/thiosulfate porter 64% 318.2
D-xylose catabolism araV lo AraV, component of Arabinose, fructose, xylose porter (characterized) 38% 80% 189.1 CysA aka B2422, component of Sulfate/thiosulfate porter 64% 318.2
D-maltose catabolism musK lo ABC-type maltose transporter (EC 7.5.2.1) (characterized) 42% 59% 186.8 CysA aka B2422, component of Sulfate/thiosulfate porter 64% 318.2
D-cellobiose catabolism SMc04256 lo ABC transporter for D-Cellobiose and D-Salicin, ATPase component (characterized) 38% 80% 186 CysA aka B2422, component of Sulfate/thiosulfate porter 64% 318.2
L-arginine catabolism artP lo Arginine transport ATP-binding protein ArtM (characterized) 39% 98% 168.7 CysA aka B2422, component of Sulfate/thiosulfate porter 64% 318.2
L-proline catabolism proV lo Glycine betaine/proline betaine transport system ATP-binding protein ProV (characterized) 38% 58% 166.4 CysA aka B2422, component of Sulfate/thiosulfate porter 64% 318.2
glycerol catabolism glpT lo GlpT, component of Glycerol uptake porter, GlpSTPQV (characterized) 38% 73% 166 CysA aka B2422, component of Sulfate/thiosulfate porter 64% 318.2
L-glutamate catabolism gltL lo GluA aka CGL1950, component of Glutamate porter (characterized) 40% 98% 164.5 CysA aka B2422, component of Sulfate/thiosulfate porter 64% 318.2
D-glucosamine (chitosamine) catabolism AO353_21725 lo ABC transporter for D-Glucosamine, putative ATPase component (characterized) 37% 97% 162.2 CysA aka B2422, component of Sulfate/thiosulfate porter 64% 318.2
L-histidine catabolism hutV lo HutV aka HISV aka R02702 aka SMC00670, component of Uptake system for hisitidine, proline, proline-betaine and glycine-betaine (characterized) 36% 94% 160.6 CysA aka B2422, component of Sulfate/thiosulfate porter 64% 318.2
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) 36% 94% 160.6 CysA aka B2422, component of Sulfate/thiosulfate porter 64% 318.2
L-lysine catabolism hisP lo Amino-acid ABC transporter, ATP-binding protein (characterized, see rationale) 38% 92% 159.8 CysA aka B2422, component of Sulfate/thiosulfate porter 64% 318.2
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) 37% 99% 157.5 CysA aka B2422, component of Sulfate/thiosulfate porter 64% 318.2
L-histidine catabolism PA5503 lo Methionine import ATP-binding protein MetN 2, component of L-Histidine uptake porter, MetIQN (characterized) 39% 70% 157.5 CysA aka B2422, component of Sulfate/thiosulfate porter 64% 318.2
D-alanine catabolism Pf6N2E2_5405 lo ABC transporter for D-Alanine, ATPase component (characterized) 36% 98% 154.5 CysA aka B2422, component of Sulfate/thiosulfate porter 64% 318.2
L-histidine catabolism BPHYT_RS24015 lo ABC transporter related (characterized, see rationale) 38% 94% 154.1 CysA aka B2422, component of Sulfate/thiosulfate porter 64% 318.2
L-histidine catabolism aapP lo ABC transporter for L-Glutamine, L-Histidine, and other L-amino acids, ATPase component (characterized) 37% 93% 154.1 CysA aka B2422, component of Sulfate/thiosulfate porter 64% 318.2
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) 38% 90% 153.3 CysA aka B2422, component of Sulfate/thiosulfate porter 64% 318.2
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) 38% 90% 153.3 CysA aka B2422, component of Sulfate/thiosulfate porter 64% 318.2
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) 38% 90% 153.3 CysA aka B2422, component of Sulfate/thiosulfate porter 64% 318.2
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) 38% 90% 153.3 CysA aka B2422, component of Sulfate/thiosulfate porter 64% 318.2
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) 38% 90% 153.3 CysA aka B2422, component of Sulfate/thiosulfate porter 64% 318.2
L-histidine catabolism bgtA lo BgtA aka SLR1735, component of Arginine/lysine/histidine/glutamine porter (characterized) 38% 96% 152.5 CysA aka B2422, component of Sulfate/thiosulfate porter 64% 318.2
L-asparagine catabolism aatP lo ABC transporter for L-asparagine and L-glutamate, ATPase component (characterized) 37% 92% 151.8 CysA aka B2422, component of Sulfate/thiosulfate porter 64% 318.2
L-aspartate catabolism aatP lo ABC transporter for L-asparagine and L-glutamate, ATPase component (characterized) 37% 92% 151.8 CysA aka B2422, component of Sulfate/thiosulfate porter 64% 318.2
glycerol catabolism glpS lo GlpS, component of Glycerol uptake porter, GlpSTPQV (characterized) 38% 65% 151.8 CysA aka B2422, component of Sulfate/thiosulfate porter 64% 318.2
L-asparagine catabolism bztD lo BztD, component of Glutamate/glutamine/aspartate/asparagine porter (characterized) 34% 93% 149.1 CysA aka B2422, component of Sulfate/thiosulfate porter 64% 318.2
L-aspartate catabolism bztD lo BztD, component of Glutamate/glutamine/aspartate/asparagine porter (characterized) 34% 93% 149.1 CysA aka B2422, component of Sulfate/thiosulfate porter 64% 318.2
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) 35% 96% 149.1 CysA aka B2422, component of Sulfate/thiosulfate porter 64% 318.2
L-asparagine catabolism peb1C lo PEB1C, component of Uptake system for glutamate and aspartate (characterized) 34% 98% 146 CysA aka B2422, component of Sulfate/thiosulfate porter 64% 318.2
L-aspartate catabolism peb1C lo PEB1C, component of Uptake system for glutamate and aspartate (characterized) 34% 98% 146 CysA aka B2422, component of Sulfate/thiosulfate porter 64% 318.2
L-isoleucine catabolism livG lo ABC transporter ATP-binding protein-branched chain amino acid transport, component of The branched chain hydrophobic amino acid transporter, LivJFGHM (characterized) 34% 94% 144.1 CysA aka B2422, component of Sulfate/thiosulfate porter 64% 318.2
L-leucine catabolism livG lo ABC transporter ATP-binding protein-branched chain amino acid transport, component of The branched chain hydrophobic amino acid transporter, LivJFGHM (characterized) 34% 94% 144.1 CysA aka B2422, component of Sulfate/thiosulfate porter 64% 318.2
L-valine catabolism livG lo ABC transporter ATP-binding protein-branched chain amino acid transport, component of The branched chain hydrophobic amino acid transporter, LivJFGHM (characterized) 34% 94% 144.1 CysA aka B2422, component of Sulfate/thiosulfate porter 64% 318.2
L-proline catabolism HSERO_RS00895 lo ABC-type branched-chain amino acid transport system, ATPase component protein (characterized, see rationale) 33% 98% 139.8 CysA aka B2422, component of Sulfate/thiosulfate porter 64% 318.2
L-citrulline catabolism AO353_03040 lo ABC transporter for L-Arginine and L-Citrulline, ATPase component (characterized) 32% 97% 138.3 CysA aka B2422, component of Sulfate/thiosulfate porter 64% 318.2
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) 34% 90% 137.9 CysA aka B2422, component of Sulfate/thiosulfate porter 64% 318.2
L-tryptophan catabolism ecfA2 lo Energy-coupling factor transporter ATP-binding protein EcfA2; Short=ECF transporter A component EcfA2; EC 7.-.-.- (characterized, see rationale) 40% 78% 135.2 CysA aka B2422, component of Sulfate/thiosulfate porter 64% 318.2
L-tryptophan catabolism ecfA1 lo Energy-coupling factor transporter ATP-binding protein EcfA1; Short=ECF transporter A component EcfA; EC 7.-.-.- (characterized, see rationale) 35% 82% 128.3 CysA aka B2422, component of Sulfate/thiosulfate porter 64% 318.2
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) 31% 80% 125.2 CysA aka B2422, component of Sulfate/thiosulfate porter 64% 318.2
L-phenylalanine catabolism livG lo ABC transporter ATP-binding protein (characterized, see rationale) 33% 92% 125.2 CysA aka B2422, component of Sulfate/thiosulfate porter 64% 318.2
L-serine catabolism Ac3H11_1693 lo ABC transporter ATP-binding protein (characterized, see rationale) 33% 92% 125.2 CysA aka B2422, component of Sulfate/thiosulfate porter 64% 318.2
L-tyrosine catabolism Ac3H11_1693 lo ABC transporter ATP-binding protein (characterized, see rationale) 33% 92% 125.2 CysA aka B2422, component of Sulfate/thiosulfate porter 64% 318.2
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) 31% 96% 121.7 CysA aka B2422, component of Sulfate/thiosulfate porter 64% 318.2
L-arabinose catabolism xylGsa lo Xylose/arabinose import ATP-binding protein XylG; EC 7.5.2.13 (characterized, see rationale) 33% 97% 120.9 CysA aka B2422, component of Sulfate/thiosulfate porter 64% 318.2
2'-deoxyinosine catabolism nupA lo Purine/cytidine ABC transporter ATP-binding protein, component of General nucleoside uptake porter, NupABC/BmpA (transports all common nucleosides as well as 5-fluorocytidine, inosine, deoxyuridine and xanthosine) (Martinussen et al., 2010) (Most similar to 3.A.1.2.12). NupA is 506aas with two ABC (C) domains. NupB has 8 predicted TMSs, NupC has 9 or 10 predicted TMSs in a 4 + 1 (or 2) + 4 arrangement (characterized) 30% 58% 120.6 CysA aka B2422, component of Sulfate/thiosulfate porter 64% 318.2
D-fructose catabolism frcA lo Fructose import ATP-binding protein FrcA; EC 7.5.2.- (characterized) 31% 95% 118.6 CysA aka B2422, component of Sulfate/thiosulfate porter 64% 318.2
D-mannose catabolism frcA lo Fructose import ATP-binding protein FrcA; EC 7.5.2.- (characterized) 31% 95% 118.6 CysA aka B2422, component of Sulfate/thiosulfate porter 64% 318.2
D-ribose catabolism frcA lo Fructose import ATP-binding protein FrcA; EC 7.5.2.- (characterized) 31% 95% 118.6 CysA aka B2422, component of Sulfate/thiosulfate porter 64% 318.2
sucrose catabolism frcA lo Fructose import ATP-binding protein FrcA; EC 7.5.2.- (characterized) 31% 95% 118.6 CysA aka B2422, component of Sulfate/thiosulfate porter 64% 318.2
L-alanine catabolism braG lo NatE aka LivF aka SLR1881, component of Leucine/proline/alanine/serine/glycine (and possibly histidine) porter, NatABCDE (characterized) 31% 93% 115.5 CysA aka B2422, component of Sulfate/thiosulfate porter 64% 318.2
L-histidine catabolism natE lo NatE aka LivF aka SLR1881, component of Leucine/proline/alanine/serine/glycine (and possibly histidine) porter, NatABCDE (characterized) 31% 93% 115.5 CysA aka B2422, component of Sulfate/thiosulfate porter 64% 318.2
L-leucine catabolism natE lo NatE aka LivF aka SLR1881, component of Leucine/proline/alanine/serine/glycine (and possibly histidine) porter, NatABCDE (characterized) 31% 93% 115.5 CysA aka B2422, component of Sulfate/thiosulfate porter 64% 318.2
L-proline catabolism natE lo NatE aka LivF aka SLR1881, component of Leucine/proline/alanine/serine/glycine (and possibly histidine) porter, NatABCDE (characterized) 31% 93% 115.5 CysA aka B2422, component of Sulfate/thiosulfate porter 64% 318.2
L-serine catabolism braG lo NatE aka LivF aka SLR1881, component of Leucine/proline/alanine/serine/glycine (and possibly histidine) porter, NatABCDE (characterized) 31% 93% 115.5 CysA aka B2422, component of Sulfate/thiosulfate porter 64% 318.2
L-threonine catabolism braG lo NatE aka LivF aka SLR1881, component of Leucine/proline/alanine/serine/glycine (and possibly histidine) porter, NatABCDE (characterized) 31% 93% 115.5 CysA aka B2422, component of Sulfate/thiosulfate porter 64% 318.2
L-isoleucine catabolism natE lo NatE, component of The neutral amino acid permease, N-1 (transports pro, phe, leu, gly, ala, ser, gln and his, but gln and his are not transported via NatB) (characterized) 32% 92% 113.2 CysA aka B2422, component of Sulfate/thiosulfate porter 64% 318.2
L-valine catabolism natE lo NatE, component of The neutral amino acid permease, N-1 (transports pro, phe, leu, gly, ala, ser, gln and his, but gln and his are not transported via NatB) (characterized) 32% 92% 113.2 CysA aka B2422, component of Sulfate/thiosulfate porter 64% 318.2
D-cellobiose catabolism cbtF lo CbtF, component of Cellobiose and cellooligosaccharide porter (characterized) 31% 74% 112.1 CysA aka B2422, component of Sulfate/thiosulfate porter 64% 318.2
D-cellobiose catabolism cbtD lo CbtD, component of Cellobiose and cellooligosaccharide porter (characterized) 30% 71% 111.7 CysA aka B2422, component of Sulfate/thiosulfate porter 64% 318.2
D-alanine catabolism AZOBR_RS08250 lo Leucine//isoleucine/valine ABC transporter,ATPase component; EC 3.6.3.- (characterized, see rationale) 31% 94% 111.3 CysA aka B2422, component of Sulfate/thiosulfate porter 64% 318.2
citrate catabolism fecE lo iron(III) dicitrate transport ATP-binding protein FecE (characterized) 34% 89% 111.3 CysA aka B2422, component of Sulfate/thiosulfate porter 64% 318.2
L-proline catabolism AZOBR_RS08250 lo Leucine//isoleucine/valine ABC transporter,ATPase component; EC 3.6.3.- (characterized, see rationale) 31% 94% 111.3 CysA aka B2422, component of Sulfate/thiosulfate porter 64% 318.2
L-proline catabolism HSERO_RS00900 lo ABC-type branched-chain amino acid transport system, ATPase component protein (characterized, see rationale) 31% 99% 111.3 CysA aka B2422, component of Sulfate/thiosulfate porter 64% 318.2
myo-inositol catabolism PS417_11890 lo m-Inositol ABC transporter, ATPase component (itaA) (characterized) 30% 52% 110.5 CysA aka B2422, component of Sulfate/thiosulfate porter 64% 318.2
myo-inositol catabolism PGA1_c07320 lo Inositol transport system ATP-binding protein (characterized) 32% 88% 109.4 CysA aka B2422, component of Sulfate/thiosulfate porter 64% 318.2
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) 30% 82% 107.5 CysA aka B2422, component of Sulfate/thiosulfate porter 64% 318.2

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Sequence

MALRPSLGSKTLIRVENITKRFGNYPALHGIDLEIQPGEFIALLGPSGSGKTTLLRIIAG
LEFQDEGHVHFNGDDVSDIPVGKRNVGFVFQQYALFRHMTVADNIAFGLTVRKASRRPAK
AEIKARAQELLRVVQLEGLGDRYPGQLSGGQRQRVALARALAIEPSLLLLDEPFGALDAK
VRKDLRRWLRDLHKQMGLTSIFVTHDQEEALELADRVVVMDHGRIDQIGTPEQVYMEPAT
AFVSHFVGETNRLPDGRHIRPHDFEIAAHGRDRVLVDNVFRKGGSWRVEGRLEEDGTIIE
IDVDAHEAPPAIGDTVTIAARRERTFSNPGD

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