GapMind for catabolism of small carbon sources

 

Protein 6938538 in Shewanella amazonensis SB2B

Annotation: Sama_2641 polyamine ABC transporter, ATP-binding protein (RefSeq)

Length: 378 amino acids

Source: SB2B in FitnessBrowser

Candidate for 103 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% 444.9 Uncharacterized ABC transporter ATP-binding protein YdcT 41% 254.6
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) 40% 92% 248.4 PotG aka B0855, component of Putrescine porter 63% 444.9
trehalose catabolism thuK 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) 40% 92% 248.4 PotG aka B0855, component of Putrescine porter 63% 444.9
D-maltose catabolism thuK med Trehalose/maltose import ATP-binding protein MalK; EC 7.5.2.1 (characterized) 41% 88% 241.1 PotG aka B0855, component of Putrescine porter 63% 444.9
xylitol catabolism Dshi_0546 med ABC transporter for Xylitol, ATPase component (characterized) 47% 73% 238.8 PotG aka B0855, component of Putrescine porter 63% 444.9
D-cellobiose catabolism aglK' med Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 42% 87% 234.2 PotG aka B0855, component of Putrescine porter 63% 444.9
D-glucose catabolism aglK' med Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 42% 87% 234.2 PotG aka B0855, component of Putrescine porter 63% 444.9
lactose catabolism aglK' med Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 42% 87% 234.2 PotG aka B0855, component of Putrescine porter 63% 444.9
D-maltose catabolism aglK med Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 42% 87% 234.2 PotG aka B0855, component of Putrescine porter 63% 444.9
D-maltose catabolism aglK' med Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 42% 87% 234.2 PotG aka B0855, component of Putrescine porter 63% 444.9
sucrose catabolism aglK med Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 42% 87% 234.2 PotG aka B0855, component of Putrescine porter 63% 444.9
sucrose catabolism aglK' med Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 42% 87% 234.2 PotG aka B0855, component of Putrescine porter 63% 444.9
trehalose catabolism aglK med Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 42% 87% 234.2 PotG aka B0855, component of Putrescine porter 63% 444.9
trehalose catabolism aglK' med Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 42% 87% 234.2 PotG aka B0855, component of Putrescine porter 63% 444.9
N-acetyl-D-glucosamine catabolism SMc02869 med N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized) 46% 70% 226.9 PotG aka B0855, component of Putrescine porter 63% 444.9
D-glucosamine (chitosamine) catabolism SMc02869 med N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized) 46% 70% 226.9 PotG aka B0855, component of Putrescine porter 63% 444.9
D-maltose catabolism malK_Aa med ABC-type maltose transporter (EC 7.5.2.1) (characterized) 45% 71% 226.5 PotG aka B0855, component of Putrescine porter 63% 444.9
D-mannitol catabolism mtlK med SmoK aka POLK, component of Hexitol (glucitol; mannitol) porter (characterized) 41% 82% 226.5 PotG aka B0855, component of Putrescine porter 63% 444.9
L-arabinose catabolism xacJ med Xylose/arabinose import ATP-binding protein XacJ; EC 7.5.2.13 (characterized, see rationale) 42% 75% 225.3 PotG aka B0855, component of Putrescine porter 63% 444.9
D-cellobiose catabolism msiK med 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) 41% 75% 221.1 PotG aka B0855, component of Putrescine porter 63% 444.9
D-cellobiose catabolism gtsD med GtsD (GLcK), component of Glucose porter, GtsABCD (characterized) 41% 77% 219.9 PotG aka B0855, component of Putrescine porter 63% 444.9
D-glucose catabolism gtsD med GtsD (GLcK), component of Glucose porter, GtsABCD (characterized) 41% 77% 219.9 PotG aka B0855, component of Putrescine porter 63% 444.9
lactose catabolism gtsD med GtsD (GLcK), component of Glucose porter, GtsABCD (characterized) 41% 77% 219.9 PotG aka B0855, component of Putrescine porter 63% 444.9
D-maltose catabolism gtsD med GtsD (GLcK), component of Glucose porter, GtsABCD (characterized) 41% 77% 219.9 PotG aka B0855, component of Putrescine porter 63% 444.9
sucrose catabolism gtsD med GtsD (GLcK), component of Glucose porter, GtsABCD (characterized) 41% 77% 219.9 PotG aka B0855, component of Putrescine porter 63% 444.9
trehalose catabolism gtsD med GtsD (GLcK), component of Glucose porter, GtsABCD (characterized) 41% 77% 219.9 PotG aka B0855, component of Putrescine porter 63% 444.9
D-maltose catabolism musK med ABC-type maltose transporter (EC 7.5.2.1) (characterized) 42% 73% 216.9 PotG aka B0855, component of Putrescine porter 63% 444.9
D-maltose catabolism malK_Bb med ABC-type maltose transport, ATP binding protein (characterized, see rationale) 42% 78% 215.7 PotG aka B0855, component of Putrescine porter 63% 444.9
lactose catabolism lacK med ABC transporter for Lactose, ATPase component (characterized) 41% 79% 214.9 PotG aka B0855, component of Putrescine porter 63% 444.9
L-fucose catabolism SM_b21106 med ABC transporter for L-Fucose, ATPase component (characterized) 42% 71% 213 PotG aka B0855, component of Putrescine porter 63% 444.9
trehalose catabolism treV med TreV, component of Trehalose porter (characterized) 42% 76% 203.4 PotG aka B0855, component of Putrescine porter 63% 444.9
L-arabinose catabolism araV med AraV, component of Arabinose, fructose, xylose porter (characterized) 41% 71% 202.2 PotG aka B0855, component of Putrescine porter 63% 444.9
D-fructose catabolism araV med AraV, component of Arabinose, fructose, xylose porter (characterized) 41% 71% 202.2 PotG aka B0855, component of Putrescine porter 63% 444.9
sucrose catabolism araV med AraV, component of Arabinose, fructose, xylose porter (characterized) 41% 71% 202.2 PotG aka B0855, component of Putrescine porter 63% 444.9
D-xylose catabolism araV med AraV, component of Arabinose, fructose, xylose porter (characterized) 41% 71% 202.2 PotG aka B0855, component of Putrescine porter 63% 444.9
L-histidine catabolism hutV med ABC transporter for L-Histidine, ATPase component (characterized) 41% 86% 179.1 PotG aka B0855, component of Putrescine porter 63% 444.9
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) 40% 81% 171.8 PotG aka B0855, component of Putrescine porter 63% 444.9
L-histidine catabolism Ac3H11_2560 med ABC transporter for L-Histidine, ATPase component (characterized) 42% 80% 161.4 PotG aka B0855, component of Putrescine porter 63% 444.9
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) 40% 87% 240.7 PotG aka B0855, component of Putrescine porter 63% 444.9
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) 40% 87% 240.7 PotG aka B0855, component of Putrescine porter 63% 444.9
D-sorbitol (glucitol) catabolism mtlK lo ABC transporter for D-Sorbitol, ATPase component (characterized) 38% 85% 232.6 PotG aka B0855, component of Putrescine porter 63% 444.9
D-maltose catabolism malK lo Maltose-transporting ATPase (EC 3.6.3.19) (characterized) 37% 88% 230.7 PotG aka B0855, component of Putrescine porter 63% 444.9
D-xylose catabolism gtsD lo ABC transporter for D-Glucose-6-Phosphate, ATPase component (characterized) 39% 84% 224.6 PotG aka B0855, component of Putrescine porter 63% 444.9
D-galactose catabolism PfGW456L13_1897 lo ABC transporter for D-Galactose and D-Glucose, ATPase component (characterized) 40% 84% 223.8 PotG aka B0855, component of Putrescine porter 63% 444.9
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% 96% 223 PotG aka B0855, component of Putrescine porter 63% 444.9
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) 37% 96% 223 PotG aka B0855, component of Putrescine porter 63% 444.9
L-arabinose catabolism xacK lo Xylose/arabinose import ATP-binding protein XacK; EC 7.5.2.13 (characterized, see rationale) 44% 66% 216.1 PotG aka B0855, component of Putrescine porter 63% 444.9
D-cellobiose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 36% 88% 213.4 PotG aka B0855, component of Putrescine porter 63% 444.9
D-galactose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 36% 88% 213.4 PotG aka B0855, component of Putrescine porter 63% 444.9
D-glucose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 36% 88% 213.4 PotG aka B0855, component of Putrescine porter 63% 444.9
lactose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 36% 88% 213.4 PotG aka B0855, component of Putrescine porter 63% 444.9
D-maltose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 36% 88% 213.4 PotG aka B0855, component of Putrescine porter 63% 444.9
D-mannose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 36% 88% 213.4 PotG aka B0855, component of Putrescine porter 63% 444.9
sucrose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 36% 88% 213.4 PotG aka B0855, component of Putrescine porter 63% 444.9
trehalose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 36% 88% 213.4 PotG aka B0855, component of Putrescine porter 63% 444.9
xylitol catabolism HSERO_RS17020 lo ABC-type sugar transport system, ATPase component protein (characterized, see rationale) 43% 67% 207.2 PotG aka B0855, component of Putrescine porter 63% 444.9
D-glucosamine (chitosamine) catabolism SM_b21216 lo ABC transporter for D-Glucosamine, ATPase component (characterized) 38% 78% 205.7 PotG aka B0855, component of Putrescine porter 63% 444.9
D-cellobiose catabolism SMc04256 lo ABC transporter for D-Cellobiose and D-Salicin, ATPase component (characterized) 39% 81% 204.5 PotG aka B0855, component of Putrescine porter 63% 444.9
L-proline catabolism proV lo glycine betaine/l-proline transport atp-binding protein prov (characterized) 40% 63% 180.3 PotG aka B0855, component of Putrescine porter 63% 444.9
L-proline catabolism opuBA lo BilEA aka OpuBA protein, component of A proline/glycine betaine uptake system. Also reported to be a bile exclusion system that exports oxgall and other bile compounds, BilEA/EB or OpuBA/BB (required for normal virulence) (characterized) 38% 76% 176 PotG aka B0855, component of Putrescine porter 63% 444.9
glycerol catabolism glpT lo GlpT, component of Glycerol uptake porter, GlpSTPQV (characterized) 33% 77% 166 PotG aka B0855, component of Putrescine porter 63% 444.9
L-glutamate catabolism gltL lo GluA aka CGL1950, component of Glutamate porter (characterized) 38% 99% 165.2 PotG aka B0855, component of Putrescine porter 63% 444.9
glycerol catabolism glpS lo ABC transporter for Glycerol, ATPase component 1 (characterized) 32% 90% 162.9 PotG aka B0855, component of Putrescine porter 63% 444.9
L-asparagine catabolism bztD lo BztD, component of Glutamate/glutamine/aspartate/asparagine porter (characterized) 33% 93% 162.2 PotG aka B0855, component of Putrescine porter 63% 444.9
L-aspartate catabolism bztD lo BztD, component of Glutamate/glutamine/aspartate/asparagine porter (characterized) 33% 93% 162.2 PotG aka B0855, component of Putrescine porter 63% 444.9
L-arginine catabolism artP lo Arginine transport ATP-binding protein ArtM (characterized) 37% 100% 159.8 PotG aka B0855, component of Putrescine porter 63% 444.9
L-histidine catabolism aapP lo ABC transporter for L-Glutamine, L-Histidine, and other L-amino acids, ATPase component (characterized) 34% 99% 154.5 PotG aka B0855, component of Putrescine porter 63% 444.9
L-asparagine catabolism bgtA lo ATPase (characterized, see rationale) 34% 98% 153.7 PotG aka B0855, component of Putrescine porter 63% 444.9
L-aspartate catabolism bgtA lo ATPase (characterized, see rationale) 34% 98% 153.7 PotG aka B0855, component of Putrescine porter 63% 444.9
D-alanine catabolism Pf6N2E2_5405 lo ABC transporter for D-Alanine, ATPase component (characterized) 36% 95% 152.9 PotG aka B0855, component of Putrescine porter 63% 444.9
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) 36% 96% 152.5 PotG aka B0855, component of Putrescine porter 63% 444.9
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% 151.4 PotG aka B0855, component of Putrescine porter 63% 444.9
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% 151.4 PotG aka B0855, component of Putrescine porter 63% 444.9
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% 151.4 PotG aka B0855, component of Putrescine porter 63% 444.9
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% 151.4 PotG aka B0855, component of Putrescine porter 63% 444.9
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% 151.4 PotG aka B0855, component of Putrescine porter 63% 444.9
D-glucosamine (chitosamine) catabolism AO353_21725 lo ABC transporter for D-glucosamine, ATPase component (characterized) 35% 96% 149.8 PotG aka B0855, component of Putrescine porter 63% 444.9
L-asparagine catabolism aatP lo Glutamate/aspartate transport ATP-binding protein GltL aka B0652, component of Glutamate/aspartate porter (characterized) 34% 99% 146.4 PotG aka B0855, component of Putrescine porter 63% 444.9
L-aspartate catabolism aatP lo Glutamate/aspartate transport ATP-binding protein GltL aka B0652, component of Glutamate/aspartate porter (characterized) 34% 99% 146.4 PotG aka B0855, component of Putrescine porter 63% 444.9
L-histidine catabolism BPHYT_RS24015 lo ABC transporter related (characterized, see rationale) 33% 95% 140.6 PotG aka B0855, component of Putrescine porter 63% 444.9
L-asparagine catabolism peb1C lo PEB1C, component of Uptake system for glutamate and aspartate (characterized) 33% 99% 136 PotG aka B0855, component of Putrescine porter 63% 444.9
L-aspartate catabolism peb1C lo PEB1C, component of Uptake system for glutamate and aspartate (characterized) 33% 99% 136 PotG aka B0855, component of Putrescine porter 63% 444.9
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% 444.9
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% 92% 133.7 PotG aka B0855, component of Putrescine porter 63% 444.9
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% 74% 132.5 PotG aka B0855, component of Putrescine porter 63% 444.9
L-histidine catabolism bgtA lo BgtA aka SLR1735, component of Arginine/lysine/histidine/glutamine porter (characterized) 32% 96% 132.1 PotG aka B0855, component of Putrescine porter 63% 444.9
L-histidine catabolism hisP lo histidine transport ATP-binding protein hisP (characterized) 32% 98% 132.1 PotG aka B0855, component of Putrescine porter 63% 444.9
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% 444.9
L-proline catabolism HSERO_RS00895 lo ABC-type branched-chain amino acid transport system, ATPase component protein (characterized, see rationale) 31% 99% 128.3 PotG aka B0855, component of Putrescine porter 63% 444.9
L-arabinose catabolism xylGsa lo Xylose/arabinose import ATP-binding protein XylG; EC 7.5.2.13 (characterized, see rationale) 32% 97% 119 PotG aka B0855, component of Putrescine porter 63% 444.9
L-arginine catabolism braG lo ATP-binding component of a broad range amino acid ABC transporter (characterized, see rationale) 31% 96% 115.9 PotG aka B0855, component of Putrescine porter 63% 444.9
L-glutamate catabolism braG lo ATP-binding component of a broad range amino acid ABC transporter (characterized, see rationale) 31% 96% 115.9 PotG aka B0855, component of Putrescine porter 63% 444.9
L-histidine catabolism braG lo ATP-binding component of a broad range amino acid ABC transporter (characterized, see rationale) 31% 96% 115.9 PotG aka B0855, component of Putrescine porter 63% 444.9
L-isoleucine catabolism livF lo ATP-binding component of a broad range amino acid ABC transporter (characterized, see rationale) 31% 96% 115.9 PotG aka B0855, component of Putrescine porter 63% 444.9
L-leucine catabolism livF lo ATP-binding component of a broad range amino acid ABC transporter (characterized, see rationale) 31% 96% 115.9 PotG aka B0855, component of Putrescine porter 63% 444.9
L-valine catabolism livF lo ATP-binding component of a broad range amino acid ABC transporter (characterized, see rationale) 31% 96% 115.9 PotG aka B0855, component of Putrescine porter 63% 444.9
D-alanine catabolism AZOBR_RS08250 lo Leucine//isoleucine/valine ABC transporter,ATPase component; EC 3.6.3.- (characterized, see rationale) 30% 97% 110.2 PotG aka B0855, component of Putrescine porter 63% 444.9
L-proline catabolism AZOBR_RS08250 lo Leucine//isoleucine/valine ABC transporter,ATPase component; EC 3.6.3.- (characterized, see rationale) 30% 97% 110.2 PotG aka B0855, component of Putrescine porter 63% 444.9
myo-inositol catabolism PGA1_c07320 lo Inositol transport system ATP-binding protein (characterized) 31% 85% 105.5 PotG aka B0855, component of Putrescine porter 63% 444.9
D-fructose catabolism frcA lo Fructose import ATP-binding protein FrcA; EC 7.5.2.- (characterized) 30% 90% 98.2 PotG aka B0855, component of Putrescine porter 63% 444.9
D-mannose catabolism frcA lo Fructose import ATP-binding protein FrcA; EC 7.5.2.- (characterized) 30% 90% 98.2 PotG aka B0855, component of Putrescine porter 63% 444.9
D-ribose catabolism frcA lo Fructose import ATP-binding protein FrcA; EC 7.5.2.- (characterized) 30% 90% 98.2 PotG aka B0855, component of Putrescine porter 63% 444.9
sucrose catabolism frcA lo Fructose import ATP-binding protein FrcA; EC 7.5.2.- (characterized) 30% 90% 98.2 PotG aka B0855, component of Putrescine porter 63% 444.9

Sequence Analysis Tools

View 6938538 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: TMHMM

Check the SEED with FIGfam search

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Sequence

MAMTSGVTNKPTTKTQDEVLLKIERVSKLFDDVRAVDDVSLTINKGEIFALLGGSGSGKS
TLLRMLAGFERPTEGRIYLDGQDITDLPPYERPINMMFQSYALFPHMTVEQNIAFGLKQD
KMSKADISQRVQEMLKLVHMEQYAKRKPHQLSGGQRQRVALARSLAKRPKLLLLDEPMGA
LDKKLRTQMQLEVVEILERVGVTCVMVTHDQEEAMTMAGRIAIMSDGWIAQVGSPMDIYE
SPNSRMIAEFIGTVNLFDCEIIEDEADHAILKSPTLPQPFLIGHGVTTSLEDKHVWLAVR
PEKTLITREQPEGEYNWARGKVHDIAYLGGLSVYYIKLEDDKIIQCSMTNTERRADHPTW
GDDIYISWEATSGVVLRS

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