GapMind for catabolism of small carbon sources

 

Protein 203725 in Shewanella oneidensis MR-1

Annotation: SO4655 sulfate ABC transporter, ATP-binding protein (NCBI ptt file)

Length: 354 amino acids

Source: MR1 in FitnessBrowser

Candidate for 96 steps in catabolism of small carbon sources

Pathway Step Score Similar to Id. Cov. Bits Other hit Other id. Other bits
xylitol catabolism Dshi_0546 med ABC transporter for Xylitol, ATPase component (characterized) 46% 72% 222.6 CysA aka B2422, component of Sulfate/thiosulfate porter 56% 323.2
D-mannitol catabolism mtlK med SmoK aka POLK, component of Hexitol (glucitol; mannitol) porter (characterized) 45% 82% 221.9 CysA aka B2422, component of Sulfate/thiosulfate porter 56% 323.2
N-acetyl-D-glucosamine catabolism SMc02869 med N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized) 43% 76% 218.8 CysA aka B2422, component of Sulfate/thiosulfate porter 56% 323.2
D-glucosamine (chitosamine) catabolism SMc02869 med N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized) 43% 76% 218.8 CysA aka B2422, component of Sulfate/thiosulfate porter 56% 323.2
D-maltose catabolism thuK med ThuK aka RB0314 aka SMB20328, component of Trehalose/maltose/sucrose porter (trehalose inducible) (characterized) 41% 78% 211.1 CysA aka B2422, component of Sulfate/thiosulfate porter 56% 323.2
sucrose catabolism thuK med ThuK aka RB0314 aka SMB20328, component of Trehalose/maltose/sucrose porter (trehalose inducible) (characterized) 41% 78% 211.1 CysA aka B2422, component of Sulfate/thiosulfate porter 56% 323.2
trehalose catabolism thuK med ThuK aka RB0314 aka SMB20328, component of Trehalose/maltose/sucrose porter (trehalose inducible) (characterized) 41% 78% 211.1 CysA aka B2422, component of Sulfate/thiosulfate porter 56% 323.2
D-maltose catabolism malK_Bb med ABC-type maltose transport, ATP binding protein (characterized, see rationale) 41% 76% 208.8 CysA aka B2422, component of Sulfate/thiosulfate porter 56% 323.2
D-maltose catabolism musK med ABC-type maltose transporter (EC 7.5.2.1) (characterized) 41% 78% 206.1 CysA aka B2422, component of Sulfate/thiosulfate porter 56% 323.2
D-sorbitol (glucitol) catabolism mtlK med ABC transporter for D-Sorbitol, ATPase component (characterized) 42% 80% 205.3 CysA aka B2422, component of Sulfate/thiosulfate porter 56% 323.2
trehalose catabolism treV med TreV, component of Trehalose porter (characterized) 41% 73% 200.3 CysA aka B2422, component of Sulfate/thiosulfate porter 56% 323.2
L-arginine catabolism artP med Arginine transport ATP-binding protein ArtP; EC 7.4.2.- (characterized) 40% 92% 151 CysA aka B2422, component of Sulfate/thiosulfate porter 56% 323.2
putrescine catabolism potA lo spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31 (characterized) 52% 64% 238.8 CysA aka B2422, component of Sulfate/thiosulfate porter 56% 323.2
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) 38% 92% 225.3 CysA aka B2422, component of Sulfate/thiosulfate porter 56% 323.2
lactose catabolism lacK lo LacK, component of Lactose porter (characterized) 38% 90% 215.3 CysA aka B2422, component of Sulfate/thiosulfate porter 56% 323.2
L-arabinose catabolism xacJ lo Xylose/arabinose import ATP-binding protein XacJ; EC 7.5.2.13 (characterized, see rationale) 37% 93% 213.8 CysA aka B2422, component of Sulfate/thiosulfate porter 56% 323.2
D-maltose catabolism malK lo ABC-type maltose transporter (subunit 3/3) (EC 7.5.2.1) (characterized) 38% 87% 212.6 CysA aka B2422, component of Sulfate/thiosulfate porter 56% 323.2
D-cellobiose catabolism gtsD lo ABC transporter for D-Galactose and D-Glucose, ATPase component (characterized) 37% 81% 211.5 CysA aka B2422, component of Sulfate/thiosulfate porter 56% 323.2
D-galactose catabolism PfGW456L13_1897 lo ABC transporter for D-Galactose and D-Glucose, ATPase component (characterized) 37% 81% 211.5 CysA aka B2422, component of Sulfate/thiosulfate porter 56% 323.2
D-glucose catabolism gtsD lo ABC transporter for D-Galactose and D-Glucose, ATPase component (characterized) 37% 81% 211.5 CysA aka B2422, component of Sulfate/thiosulfate porter 56% 323.2
lactose catabolism gtsD lo ABC transporter for D-Galactose and D-Glucose, ATPase component (characterized) 37% 81% 211.5 CysA aka B2422, component of Sulfate/thiosulfate porter 56% 323.2
D-maltose catabolism gtsD lo ABC transporter for D-Galactose and D-Glucose, ATPase component (characterized) 37% 81% 211.5 CysA aka B2422, component of Sulfate/thiosulfate porter 56% 323.2
sucrose catabolism gtsD lo ABC transporter for D-Galactose and D-Glucose, ATPase component (characterized) 37% 81% 211.5 CysA aka B2422, component of Sulfate/thiosulfate porter 56% 323.2
trehalose catabolism gtsD lo ABC transporter for D-Galactose and D-Glucose, ATPase component (characterized) 37% 81% 211.5 CysA aka B2422, component of Sulfate/thiosulfate porter 56% 323.2
D-maltose catabolism aglK lo ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized) 35% 96% 211.1 CysA aka B2422, component of Sulfate/thiosulfate porter 56% 323.2
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) 37% 87% 211.1 CysA aka B2422, component of Sulfate/thiosulfate porter 56% 323.2
sucrose catabolism aglK lo ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized) 35% 96% 211.1 CysA aka B2422, component of Sulfate/thiosulfate porter 56% 323.2
trehalose catabolism aglK lo ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized) 35% 96% 211.1 CysA aka B2422, component of Sulfate/thiosulfate porter 56% 323.2
trehalose catabolism malK lo MsmK aka SMU.882, component of The raffinose/stachyose transporter, MsmEFGK (MalK (3.A.1.1.27) can probably substitute for MsmK; Webb et al., 2008). This system may also transport melibiose, isomaltotriose and sucrose as well as isomaltosaccharides (characterized) 33% 97% 209.1 CysA aka B2422, component of Sulfate/thiosulfate porter 56% 323.2
xylitol catabolism HSERO_RS17020 lo ABC-type sugar transport system, ATPase component protein (characterized, see rationale) 39% 78% 208.8 CysA aka B2422, component of Sulfate/thiosulfate porter 56% 323.2
D-xylose catabolism gtsD lo ABC transporter for D-Glucose-6-Phosphate, ATPase component (characterized) 34% 92% 208 CysA aka B2422, component of Sulfate/thiosulfate porter 56% 323.2
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) 37% 80% 203.8 CysA aka B2422, component of Sulfate/thiosulfate porter 56% 323.2
L-fucose catabolism SM_b21106 lo ABC transporter for L-Fucose, ATPase component (characterized) 38% 77% 203.4 CysA aka B2422, component of Sulfate/thiosulfate porter 56% 323.2
D-maltose catabolism malK_Aa lo ABC-type maltose transporter (EC 7.5.2.1) (characterized) 36% 92% 201.8 CysA aka B2422, component of Sulfate/thiosulfate porter 56% 323.2
D-cellobiose catabolism SMc04256 lo ABC transporter for D-Cellobiose and D-Salicin, ATPase component (characterized) 40% 83% 201.4 CysA aka B2422, component of Sulfate/thiosulfate porter 56% 323.2
D-cellobiose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 35% 86% 196.8 CysA aka B2422, component of Sulfate/thiosulfate porter 56% 323.2
D-galactose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 35% 86% 196.8 CysA aka B2422, component of Sulfate/thiosulfate porter 56% 323.2
D-glucose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 35% 86% 196.8 CysA aka B2422, component of Sulfate/thiosulfate porter 56% 323.2
lactose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 35% 86% 196.8 CysA aka B2422, component of Sulfate/thiosulfate porter 56% 323.2
D-maltose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 35% 86% 196.8 CysA aka B2422, component of Sulfate/thiosulfate porter 56% 323.2
D-mannose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 35% 86% 196.8 CysA aka B2422, component of Sulfate/thiosulfate porter 56% 323.2
sucrose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 35% 86% 196.8 CysA aka B2422, component of Sulfate/thiosulfate porter 56% 323.2
trehalose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 35% 86% 196.8 CysA aka B2422, component of Sulfate/thiosulfate porter 56% 323.2
L-arabinose catabolism araV lo AraV, component of Arabinose, fructose, xylose porter (characterized) 33% 95% 196.4 CysA aka B2422, component of Sulfate/thiosulfate porter 56% 323.2
D-fructose catabolism araV lo AraV, component of Arabinose, fructose, xylose porter (characterized) 33% 95% 196.4 CysA aka B2422, component of Sulfate/thiosulfate porter 56% 323.2
sucrose catabolism araV lo AraV, component of Arabinose, fructose, xylose porter (characterized) 33% 95% 196.4 CysA aka B2422, component of Sulfate/thiosulfate porter 56% 323.2
D-xylose catabolism araV lo AraV, component of Arabinose, fructose, xylose porter (characterized) 33% 95% 196.4 CysA aka B2422, component of Sulfate/thiosulfate porter 56% 323.2
D-cellobiose catabolism aglK' lo Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 41% 66% 191.4 CysA aka B2422, component of Sulfate/thiosulfate porter 56% 323.2
D-glucose catabolism aglK' lo Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 41% 66% 191.4 CysA aka B2422, component of Sulfate/thiosulfate porter 56% 323.2
lactose catabolism aglK' lo Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 41% 66% 191.4 CysA aka B2422, component of Sulfate/thiosulfate porter 56% 323.2
D-maltose catabolism aglK' lo Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 41% 66% 191.4 CysA aka B2422, component of Sulfate/thiosulfate porter 56% 323.2
sucrose catabolism aglK' lo Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 41% 66% 191.4 CysA aka B2422, component of Sulfate/thiosulfate porter 56% 323.2
trehalose catabolism aglK' lo Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 41% 66% 191.4 CysA aka B2422, component of Sulfate/thiosulfate porter 56% 323.2
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) 34% 98% 178.7 CysA aka B2422, component of Sulfate/thiosulfate porter 56% 323.2
L-proline catabolism proV lo Glycine betaine/proline betaine transport system ATP-binding protein ProV (characterized) 36% 65% 167.9 CysA aka B2422, component of Sulfate/thiosulfate porter 56% 323.2
D-glucosamine (chitosamine) catabolism AO353_21725 lo ABC transporter for D-glucosamine, ATPase component (characterized) 38% 94% 167.2 CysA aka B2422, component of Sulfate/thiosulfate porter 56% 323.2
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% 97% 166.8 CysA aka B2422, component of Sulfate/thiosulfate porter 56% 323.2
L-glutamate catabolism gltL 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% 97% 166.8 CysA aka B2422, component of Sulfate/thiosulfate porter 56% 323.2
L-histidine catabolism hutV lo ABC transporter for L-Histidine, ATPase component (characterized) 39% 85% 166 CysA aka B2422, component of Sulfate/thiosulfate porter 56% 323.2
D-alanine catabolism Pf6N2E2_5405 lo ABC transporter for D-Alanine, ATPase component (characterized) 38% 94% 164.5 CysA aka B2422, component of Sulfate/thiosulfate porter 56% 323.2
glycerol catabolism glpT lo GlpT, component of Glycerol uptake porter, GlpSTPQV (characterized) 37% 71% 163.7 CysA aka B2422, component of Sulfate/thiosulfate porter 56% 323.2
L-asparagine catabolism peb1C lo PEB1C, component of Uptake system for glutamate and aspartate (characterized) 38% 98% 163.3 CysA aka B2422, component of Sulfate/thiosulfate porter 56% 323.2
L-aspartate catabolism peb1C lo PEB1C, component of Uptake system for glutamate and aspartate (characterized) 38% 98% 163.3 CysA aka B2422, component of Sulfate/thiosulfate porter 56% 323.2
L-histidine catabolism aapP lo ABC transporter for L-Glutamine, L-Histidine, and other L-amino acids, ATPase component (characterized) 38% 93% 162.5 CysA aka B2422, component of Sulfate/thiosulfate porter 56% 323.2
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) 37% 93% 162.2 CysA aka B2422, component of Sulfate/thiosulfate porter 56% 323.2
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) 37% 93% 162.2 CysA aka B2422, component of Sulfate/thiosulfate porter 56% 323.2
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) 37% 93% 162.2 CysA aka B2422, component of Sulfate/thiosulfate porter 56% 323.2
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) 37% 93% 162.2 CysA aka B2422, component of Sulfate/thiosulfate porter 56% 323.2
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) 37% 93% 162.2 CysA aka B2422, component of Sulfate/thiosulfate porter 56% 323.2
L-asparagine catabolism bztD lo BztD, component of Glutamate/glutamine/aspartate/asparagine porter (characterized) 37% 91% 161 CysA aka B2422, component of Sulfate/thiosulfate porter 56% 323.2
L-aspartate catabolism bztD lo BztD, component of Glutamate/glutamine/aspartate/asparagine porter (characterized) 37% 91% 161 CysA aka B2422, component of Sulfate/thiosulfate porter 56% 323.2
L-histidine catabolism bgtA lo BgtA aka SLR1735, component of Arginine/lysine/histidine/glutamine porter (characterized) 36% 96% 159.8 CysA aka B2422, component of Sulfate/thiosulfate porter 56% 323.2
L-lysine catabolism hisP lo BgtA aka SLR1735, component of Arginine/lysine/histidine/glutamine porter (characterized) 36% 96% 159.8 CysA aka B2422, component of Sulfate/thiosulfate porter 56% 323.2
L-asparagine catabolism bgtA lo ATPase (characterized, see rationale) 38% 92% 157.1 CysA aka B2422, component of Sulfate/thiosulfate porter 56% 323.2
L-aspartate catabolism bgtA lo ATPase (characterized, see rationale) 38% 92% 157.1 CysA aka B2422, component of Sulfate/thiosulfate porter 56% 323.2
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) 38% 87% 156.4 CysA aka B2422, component of Sulfate/thiosulfate porter 56% 323.2
L-asparagine catabolism aatP lo PP1068, component of Acidic amino acid uptake porter, AatJMQP (characterized) 40% 89% 155.6 CysA aka B2422, component of Sulfate/thiosulfate porter 56% 323.2
L-aspartate catabolism aatP lo PP1068, component of Acidic amino acid uptake porter, AatJMQP (characterized) 40% 89% 155.6 CysA aka B2422, component of Sulfate/thiosulfate porter 56% 323.2
L-histidine catabolism hisP lo Histidine transport ATP-binding protein HisP (characterized) 35% 96% 155.2 CysA aka B2422, component of Sulfate/thiosulfate porter 56% 323.2
L-histidine catabolism BPHYT_RS24015 lo ABC transporter related (characterized, see rationale) 37% 90% 154.8 CysA aka B2422, component of Sulfate/thiosulfate porter 56% 323.2
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) 35% 90% 154.5 CysA aka B2422, component of Sulfate/thiosulfate porter 56% 323.2
glycerol catabolism glpS lo ABC transporter for Glycerol, ATPase component 1 (characterized) 31% 96% 154.5 CysA aka B2422, component of Sulfate/thiosulfate porter 56% 323.2
L-citrulline catabolism AO353_03040 lo ABC transporter for L-Arginine and L-Citrulline, ATPase component (characterized) 34% 98% 150.2 CysA aka B2422, component of Sulfate/thiosulfate porter 56% 323.2
L-histidine catabolism Ac3H11_2560 lo ABC transporter for L-Histidine, ATPase component (characterized) 39% 84% 145.6 CysA aka B2422, component of Sulfate/thiosulfate porter 56% 323.2
L-proline catabolism HSERO_RS00895 lo ABC-type branched-chain amino acid transport system, ATPase component protein (characterized, see rationale) 34% 97% 136.3 CysA aka B2422, component of Sulfate/thiosulfate porter 56% 323.2
L-tryptophan catabolism ecfA1 lo Energy-coupling factor transporter ATP-binding protein EcfA1; Short=ECF transporter A component EcfA; EC 7.-.-.- (characterized, see rationale) 37% 74% 129.8 CysA aka B2422, component of Sulfate/thiosulfate porter 56% 323.2
L-arabinose catabolism xylGsa lo Xylose/arabinose import ATP-binding protein XylG; EC 7.5.2.13 (characterized, see rationale) 33% 98% 120.9 CysA aka B2422, component of Sulfate/thiosulfate porter 56% 323.2
L-isoleucine catabolism livF lo High-affinity branched-chain amino acid transport ATP-binding protein (characterized, see rationale) 31% 96% 120.9 CysA aka B2422, component of Sulfate/thiosulfate porter 56% 323.2
L-phenylalanine catabolism livF lo High-affinity branched-chain amino acid transport ATP-binding protein (characterized, see rationale) 31% 96% 120.9 CysA aka B2422, component of Sulfate/thiosulfate porter 56% 323.2
myo-inositol catabolism PGA1_c07320 lo Inositol transport system ATP-binding protein (characterized) 32% 90% 112.5 CysA aka B2422, component of Sulfate/thiosulfate porter 56% 323.2
L-alanine catabolism braG lo NatE aka LivF aka SLR1881, component of Leucine/proline/alanine/serine/glycine (and possibly histidine) porter, NatABCDE (characterized) 31% 92% 105.1 CysA aka B2422, component of Sulfate/thiosulfate porter 56% 323.2
L-histidine catabolism natE lo NatE aka LivF aka SLR1881, component of Leucine/proline/alanine/serine/glycine (and possibly histidine) porter, NatABCDE (characterized) 31% 92% 105.1 CysA aka B2422, component of Sulfate/thiosulfate porter 56% 323.2
L-leucine catabolism natE lo NatE aka LivF aka SLR1881, component of Leucine/proline/alanine/serine/glycine (and possibly histidine) porter, NatABCDE (characterized) 31% 92% 105.1 CysA aka B2422, component of Sulfate/thiosulfate porter 56% 323.2
L-proline catabolism natE lo NatE aka LivF aka SLR1881, component of Leucine/proline/alanine/serine/glycine (and possibly histidine) porter, NatABCDE (characterized) 31% 92% 105.1 CysA aka B2422, component of Sulfate/thiosulfate porter 56% 323.2
L-serine catabolism braG lo NatE aka LivF aka SLR1881, component of Leucine/proline/alanine/serine/glycine (and possibly histidine) porter, NatABCDE (characterized) 31% 92% 105.1 CysA aka B2422, component of Sulfate/thiosulfate porter 56% 323.2
L-threonine catabolism braG lo NatE aka LivF aka SLR1881, component of Leucine/proline/alanine/serine/glycine (and possibly histidine) porter, NatABCDE (characterized) 31% 92% 105.1 CysA aka B2422, component of Sulfate/thiosulfate porter 56% 323.2

Sequence Analysis Tools

View 203725 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

Fitness BLAST: loading...

Sequence

MSIHIQQVNKHFGNFVAVDSVNLEIKTGELTALLGPSGSGKTTLLRIIAGLEQADSGIVK
FNGEDITTQHVSERGVGFVFQHYALFKHMTVFENVAYGLTVRPRKTRPSKAEIAEKVHSL
LKLVQLDWTADRYPSQLSGGQRQRIALARALAVEPKVLLLDEPFGALDAKVRAELRRWLR
RLHDEINVTTVFVTHDQEEALEVADKIVVMNKGRIEQQGTPEEVYDTPSNPFVYEFLGNV
NLFHARVKHGHSTIGNIHIPSPEHAGGEEQQGLAYVRPHEIEVLTQPTENAIKVNLDLVT
IVGPVARLEVLTEIDEQLIHVELSKVQFKQLGISKGDNAWIQPRYSKVFLGEGI

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