GapMind for catabolism of small carbon sources

 

Protein 200449 in Shewanella oneidensis MR-1

Annotation: SO1271 polyamine ABC transporter, ATP-binding protein (NCBI ptt file)

Length: 378 amino acids

Source: MR1 in FitnessBrowser

Candidate for 89 steps in catabolism of small carbon sources

Pathway Step Score Similar to Id. Cov. Bits Other hit Other id. Other bits
putrescine catabolism potA hi PotG aka B0855, component of Putrescine porter (characterized) 63% 98% 437.6 Glycerol-3-phosphate-transporting ATPase, component of Inositol phosphate porter (Rodionova et al. 2013). Binds inositol phosphate with low Kd and inositol with a lower affinity 42% 253.8
xylitol catabolism Dshi_0546 med ABC transporter for Xylitol, ATPase component (characterized) 42% 89% 250.8 PotG aka B0855, component of Putrescine porter 63% 437.6
D-cellobiose catabolism gtsD med 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) 41% 87% 244.6 PotG aka B0855, component of Putrescine porter 63% 437.6
D-glucose catabolism gtsD med 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) 41% 87% 244.6 PotG aka B0855, component of Putrescine porter 63% 437.6
lactose catabolism gtsD med 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) 41% 87% 244.6 PotG aka B0855, component of Putrescine porter 63% 437.6
D-maltose catabolism gtsD med 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) 41% 87% 244.6 PotG aka B0855, component of Putrescine porter 63% 437.6
D-maltose catabolism thuK med 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) 41% 87% 244.6 PotG aka B0855, component of Putrescine porter 63% 437.6
D-mannose catabolism TT_C0211 med 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) 41% 87% 244.6 PotG aka B0855, component of Putrescine porter 63% 437.6
sucrose catabolism gtsD med 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) 41% 87% 244.6 PotG aka B0855, component of Putrescine porter 63% 437.6
sucrose catabolism thuK med 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) 41% 87% 244.6 PotG aka B0855, component of Putrescine porter 63% 437.6
trehalose catabolism gtsD med 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) 41% 87% 244.6 PotG aka B0855, component of Putrescine porter 63% 437.6
trehalose catabolism thuK med 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) 41% 87% 244.6 PotG aka B0855, component of Putrescine porter 63% 437.6
D-maltose catabolism malK1 med 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) 43% 88% 239.6 PotG aka B0855, component of Putrescine porter 63% 437.6
D-cellobiose catabolism aglK' med Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 42% 86% 237.7 PotG aka B0855, component of Putrescine porter 63% 437.6
D-glucose catabolism aglK' med Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 42% 86% 237.7 PotG aka B0855, component of Putrescine porter 63% 437.6
lactose catabolism aglK' med Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 42% 86% 237.7 PotG aka B0855, component of Putrescine porter 63% 437.6
D-maltose catabolism aglK med Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 42% 86% 237.7 PotG aka B0855, component of Putrescine porter 63% 437.6
D-maltose catabolism aglK' med Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 42% 86% 237.7 PotG aka B0855, component of Putrescine porter 63% 437.6
sucrose catabolism aglK med Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 42% 86% 237.7 PotG aka B0855, component of Putrescine porter 63% 437.6
sucrose catabolism aglK' med Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 42% 86% 237.7 PotG aka B0855, component of Putrescine porter 63% 437.6
trehalose catabolism aglK med Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 42% 86% 237.7 PotG aka B0855, component of Putrescine porter 63% 437.6
trehalose catabolism aglK' med Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 42% 86% 237.7 PotG aka B0855, component of Putrescine porter 63% 437.6
D-maltose catabolism malK_Aa med ABC-type maltose transporter (EC 7.5.2.1) (characterized) 45% 75% 228.8 PotG aka B0855, component of Putrescine porter 63% 437.6
L-arabinose catabolism xacJ med Xylose/arabinose import ATP-binding protein XacJ; EC 7.5.2.13 (characterized, see rationale) 43% 75% 226.1 PotG aka B0855, component of Putrescine porter 63% 437.6
N-acetyl-D-glucosamine catabolism SMc02869 med N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized) 46% 70% 225.7 PotG aka B0855, component of Putrescine porter 63% 437.6
D-glucosamine (chitosamine) catabolism SMc02869 med N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized) 46% 70% 225.7 PotG aka B0855, component of Putrescine porter 63% 437.6
D-sorbitol (glucitol) catabolism mtlK med ABC transporter for D-Sorbitol, ATPase component (characterized) 47% 72% 225.7 PotG aka B0855, component of Putrescine porter 63% 437.6
D-galactose catabolism PfGW456L13_1897 med ABC transporter for D-Galactose and D-Glucose, ATPase component (characterized) 42% 77% 224.9 PotG aka B0855, component of Putrescine porter 63% 437.6
D-mannitol catabolism mtlK med SmoK aka POLK, component of Hexitol (glucitol; mannitol) porter (characterized) 44% 80% 221.5 PotG aka B0855, component of Putrescine porter 63% 437.6
D-maltose catabolism malK_Bb med ABC-type maltose transport, ATP binding protein (characterized, see rationale) 44% 77% 218.4 PotG aka B0855, component of Putrescine porter 63% 437.6
D-maltose catabolism musK med ABC-type maltose transporter (EC 7.5.2.1) (characterized) 42% 73% 215.7 PotG aka B0855, component of Putrescine porter 63% 437.6
D-cellobiose catabolism SMc04256 med ABC transporter for D-Cellobiose and D-Salicin, ATPase component (characterized) 41% 81% 215.3 PotG aka B0855, component of Putrescine porter 63% 437.6
trehalose catabolism treV med TreV, component of Trehalose porter (characterized) 41% 78% 200.7 PotG aka B0855, component of Putrescine porter 63% 437.6
L-histidine catabolism hutV med ABC transporter for L-Histidine, ATPase component (characterized) 40% 91% 177.2 PotG aka B0855, component of Putrescine porter 63% 437.6
L-histidine catabolism Ac3H11_2560 med ABC transporter for L-Histidine, ATPase component (characterized) 42% 80% 162.2 PotG aka B0855, component of Putrescine porter 63% 437.6
L-tryptophan catabolism ecfA1 med Energy-coupling factor transporter ATP-binding protein EcfA1; Short=ECF transporter A component EcfA; EC 7.-.-.- (characterized, see rationale) 40% 74% 136.3 PotG aka B0855, component of Putrescine porter 63% 437.6
D-maltose catabolism malK lo Maltose-transporting ATPase (EC 3.6.3.19) (characterized) 38% 87% 231.1 PotG aka B0855, component of Putrescine porter 63% 437.6
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) 37% 93% 226.9 PotG aka B0855, component of Putrescine porter 63% 437.6
lactose catabolism lacK lo ABC transporter for Lactose, ATPase component (characterized) 38% 99% 226.5 PotG aka B0855, component of Putrescine porter 63% 437.6
D-xylose catabolism gtsD lo ABC transporter for D-Glucose-6-Phosphate, ATPase component (characterized) 38% 84% 219.9 PotG aka B0855, component of Putrescine porter 63% 437.6
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) 39% 88% 218.8 PotG aka B0855, component of Putrescine porter 63% 437.6
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) 39% 88% 218.8 PotG aka B0855, component of Putrescine porter 63% 437.6
L-arabinose catabolism xacK lo Xylose/arabinose import ATP-binding protein XacK; EC 7.5.2.13 (characterized, see rationale) 38% 84% 218 PotG aka B0855, component of Putrescine porter 63% 437.6
xylitol catabolism HSERO_RS17020 lo ABC-type sugar transport system, ATPase component protein (characterized, see rationale) 43% 67% 213.8 PotG aka B0855, component of Putrescine porter 63% 437.6
L-fucose catabolism SM_b21106 lo ABC transporter for L-Fucose, ATPase component (characterized) 46% 64% 212.6 PotG aka B0855, component of Putrescine porter 63% 437.6
D-glucosamine (chitosamine) catabolism SM_b21216 lo ABC transporter for D-Glucosamine, ATPase component (characterized) 38% 78% 210.3 PotG aka B0855, component of Putrescine porter 63% 437.6
D-cellobiose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 36% 88% 209.1 PotG aka B0855, component of Putrescine porter 63% 437.6
D-galactose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 36% 88% 209.1 PotG aka B0855, component of Putrescine porter 63% 437.6
D-glucose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 36% 88% 209.1 PotG aka B0855, component of Putrescine porter 63% 437.6
lactose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 36% 88% 209.1 PotG aka B0855, component of Putrescine porter 63% 437.6
D-maltose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 36% 88% 209.1 PotG aka B0855, component of Putrescine porter 63% 437.6
D-mannose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 36% 88% 209.1 PotG aka B0855, component of Putrescine porter 63% 437.6
sucrose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 36% 88% 209.1 PotG aka B0855, component of Putrescine porter 63% 437.6
trehalose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 36% 88% 209.1 PotG aka B0855, component of Putrescine porter 63% 437.6
L-arabinose catabolism araV lo AraV, component of Arabinose, fructose, xylose porter (characterized) 42% 67% 199.9 PotG aka B0855, component of Putrescine porter 63% 437.6
D-fructose catabolism araV lo AraV, component of Arabinose, fructose, xylose porter (characterized) 42% 67% 199.9 PotG aka B0855, component of Putrescine porter 63% 437.6
sucrose catabolism araV lo AraV, component of Arabinose, fructose, xylose porter (characterized) 42% 67% 199.9 PotG aka B0855, component of Putrescine porter 63% 437.6
D-xylose catabolism araV lo AraV, component of Arabinose, fructose, xylose porter (characterized) 42% 67% 199.9 PotG aka B0855, component of Putrescine porter 63% 437.6
L-proline catabolism proV lo glycine betaine/l-proline transport atp-binding protein prov (characterized) 40% 65% 179.5 PotG aka B0855, component of Putrescine porter 63% 437.6
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) 39% 81% 169.5 PotG aka B0855, component of Putrescine porter 63% 437.6
L-asparagine catabolism bztD lo BztD, component of Glutamate/glutamine/aspartate/asparagine porter (characterized) 34% 93% 166.4 PotG aka B0855, component of Putrescine porter 63% 437.6
L-aspartate catabolism bztD lo BztD, component of Glutamate/glutamine/aspartate/asparagine porter (characterized) 34% 93% 166.4 PotG aka B0855, component of Putrescine porter 63% 437.6
L-glutamate catabolism gltL lo BztD, component of Glutamate/glutamine/aspartate/asparagine porter (characterized) 34% 93% 166.4 PotG aka B0855, component of Putrescine porter 63% 437.6
glycerol catabolism glpT lo GlpT, component of Glycerol uptake porter, GlpSTPQV (characterized) 33% 77% 164.5 PotG aka B0855, component of Putrescine porter 63% 437.6
glycerol catabolism glpS lo ABC transporter for Glycerol, ATPase component 1 (characterized) 37% 63% 161.8 PotG aka B0855, component of Putrescine porter 63% 437.6
L-histidine catabolism aapP lo ABC transporter for L-Glutamine, L-Histidine, and other L-amino acids, ATPase component (characterized) 34% 99% 159.1 PotG aka B0855, component of Putrescine porter 63% 437.6
D-alanine catabolism Pf6N2E2_5405 lo ABC transporter for D-Alanine, ATPase component (characterized) 35% 94% 155.6 PotG aka B0855, component of Putrescine porter 63% 437.6
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% 97% 153.7 PotG aka B0855, component of Putrescine porter 63% 437.6
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% 97% 153.7 PotG aka B0855, component of Putrescine porter 63% 437.6
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% 97% 153.7 PotG aka B0855, component of Putrescine porter 63% 437.6
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% 97% 153.7 PotG aka B0855, component of Putrescine porter 63% 437.6
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% 97% 153.7 PotG aka B0855, component of Putrescine porter 63% 437.6
D-glucosamine (chitosamine) catabolism AO353_21725 lo ABC transporter for D-Glucosamine, putative ATPase component (characterized) 37% 97% 152.9 PotG aka B0855, component of Putrescine porter 63% 437.6
L-histidine catabolism PA5503 lo Methionine import ATP-binding protein MetN 2, component of L-Histidine uptake porter, MetIQN (characterized) 34% 73% 152.5 PotG aka B0855, component of Putrescine porter 63% 437.6
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% 96% 151 PotG aka B0855, component of Putrescine porter 63% 437.6
L-tryptophan catabolism ecfA2 lo Energy-coupling factor transporter ATP-binding protein EcfA2; Short=ECF transporter A component EcfA2; EC 7.-.-.- (characterized, see rationale) 37% 77% 134 PotG aka B0855, component of Putrescine porter 63% 437.6
D-cellobiose catabolism cbtF lo CbtF, component of Cellobiose and cellooligosaccharide porter (characterized) 32% 77% 129.4 PotG aka B0855, component of Putrescine porter 63% 437.6
L-arginine catabolism braG lo ATP-binding component of a broad range amino acid ABC transporter (characterized, see rationale) 32% 92% 117.9 PotG aka B0855, component of Putrescine porter 63% 437.6
L-glutamate catabolism braG lo ATP-binding component of a broad range amino acid ABC transporter (characterized, see rationale) 32% 92% 117.9 PotG aka B0855, component of Putrescine porter 63% 437.6
L-histidine catabolism braG lo ATP-binding component of a broad range amino acid ABC transporter (characterized, see rationale) 32% 92% 117.9 PotG aka B0855, component of Putrescine porter 63% 437.6
L-isoleucine catabolism livF lo ATP-binding component of a broad range amino acid ABC transporter (characterized, see rationale) 32% 92% 117.9 PotG aka B0855, component of Putrescine porter 63% 437.6
L-leucine catabolism livF lo ATP-binding component of a broad range amino acid ABC transporter (characterized, see rationale) 32% 92% 117.9 PotG aka B0855, component of Putrescine porter 63% 437.6
L-valine catabolism livF lo ATP-binding component of a broad range amino acid ABC transporter (characterized, see rationale) 32% 92% 117.9 PotG aka B0855, component of Putrescine porter 63% 437.6
D-cellobiose catabolism mglA lo glucose transporter, ATPase component (characterized) 31% 90% 112.8 PotG aka B0855, component of Putrescine porter 63% 437.6
D-glucose catabolism mglA lo glucose transporter, ATPase component (characterized) 31% 90% 112.8 PotG aka B0855, component of Putrescine porter 63% 437.6
lactose catabolism mglA lo glucose transporter, ATPase component (characterized) 31% 90% 112.8 PotG aka B0855, component of Putrescine porter 63% 437.6
D-maltose catabolism mglA lo glucose transporter, ATPase component (characterized) 31% 90% 112.8 PotG aka B0855, component of Putrescine porter 63% 437.6
sucrose catabolism mglA lo glucose transporter, ATPase component (characterized) 31% 90% 112.8 PotG aka B0855, component of Putrescine porter 63% 437.6
trehalose catabolism mglA lo glucose transporter, ATPase component (characterized) 31% 90% 112.8 PotG aka B0855, component of Putrescine porter 63% 437.6

Sequence Analysis Tools

View 200449 at FitnessBrowser

PaperBLAST (search for papers about homologs of this protein)

Search CDD (the Conserved Domains Database, which includes COG and superfam)

Search PFam (including for weak hits, up to E = 1)

Predict protein localization: PSORTb (Gram negative bacteria)

Predict transmembrane helices and signal peptides: Phobius

Check the SEED with FIGfam search

Fitness BLAST: loading...

Sequence

MASTSGVTNKPTTKTQEKVLLKIERVSKLFDDVRAVDDVSLTINKGEIFALLGGSGSGKS
TLLRMLAGFERPTSGRIYLDGEDITDLPPYERPINMMFQSYALFPHMTVAQNIAFGLKQD
KLPKAEIEQRVQEMLKLVHMEQYGKRKPHQLSGGQRQRVALARSLAKRPKLLLLDEPMGA
LDKKLRTQMQLEVVEILERVGVTCVMVTHDQEEAMTMAGRISIMSDGWIAQTGSPMDIYE
SPNSRMIAEFIGSVNLFSGEIEVDEVDHLIIKPNDLARSFYVGYGVTTSLEDKRVWLAVR
PEKTIISREQPEGEYNWAKGIVHDIAYLGGISVYYIRLENGQIVQCSMTNRERRADHATW
DDEVFISWEDTSGVVLRS

This GapMind analysis is from Sep 17 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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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 the paper from 2019 on GapMind for amino acid biosynthesis, or view the source code.

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