GapMind for catabolism of small carbon sources

 

Protein Dsui_0258 in Dechlorosoma suillum PS

Annotation: Dsui_0258 sulfate ABC transporter, ATP-binding protein

Length: 360 amino acids

Source: PS in FitnessBrowser

Candidate for 87 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) 43% 86% 253.1 CysA aka B2422, component of Sulfate/thiosulfate porter 58% 342.0
xylitol catabolism Dshi_0546 med ABC transporter for Xylitol, ATPase component (characterized) 43% 79% 218.4 CysA aka B2422, component of Sulfate/thiosulfate porter 58% 342.0
N-acetyl-D-glucosamine catabolism SMc02869 med N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized) 44% 70% 214.5 CysA aka B2422, component of Sulfate/thiosulfate porter 58% 342.0
D-glucosamine (chitosamine) catabolism SMc02869 med N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized) 44% 70% 214.5 CysA aka B2422, component of Sulfate/thiosulfate porter 58% 342.0
D-maltose catabolism thuK med ThuK aka RB0314 aka SMB20328, component of Trehalose/maltose/sucrose porter (trehalose inducible) (characterized) 41% 77% 212.6 CysA aka B2422, component of Sulfate/thiosulfate porter 58% 342.0
sucrose catabolism thuK med ThuK aka RB0314 aka SMB20328, component of Trehalose/maltose/sucrose porter (trehalose inducible) (characterized) 41% 77% 212.6 CysA aka B2422, component of Sulfate/thiosulfate porter 58% 342.0
trehalose catabolism thuK med ThuK aka RB0314 aka SMB20328, component of Trehalose/maltose/sucrose porter (trehalose inducible) (characterized) 41% 77% 212.6 CysA aka B2422, component of Sulfate/thiosulfate porter 58% 342.0
trehalose catabolism treV med TreV, component of Trehalose porter (characterized) 41% 73% 198.7 CysA aka B2422, component of Sulfate/thiosulfate porter 58% 342.0
L-glutamate catabolism gltL med GluA aka CGL1950, component of Glutamate porter (characterized) 42% 98% 171.8 CysA aka B2422, component of Sulfate/thiosulfate porter 58% 342.0
D-mannitol catabolism mtlK lo SmoK aka POLK, component of Hexitol (glucitol; mannitol) porter (characterized) 40% 99% 231.1 CysA aka B2422, component of Sulfate/thiosulfate porter 58% 342.0
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% 87% 224.6 CysA aka B2422, component of Sulfate/thiosulfate porter 58% 342.0
D-glucosamine (chitosamine) catabolism SM_b21216 lo ABC transporter for D-Glucosamine, ATPase component (characterized) 39% 85% 223 CysA aka B2422, component of Sulfate/thiosulfate porter 58% 342.0
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) 37% 88% 216.5 CysA aka B2422, component of Sulfate/thiosulfate porter 58% 342.0
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) 37% 88% 216.5 CysA aka B2422, component of Sulfate/thiosulfate porter 58% 342.0
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) 37% 88% 216.5 CysA aka B2422, component of Sulfate/thiosulfate porter 58% 342.0
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) 37% 88% 216.5 CysA aka B2422, component of Sulfate/thiosulfate porter 58% 342.0
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% 88% 216.5 CysA aka B2422, component of Sulfate/thiosulfate porter 58% 342.0
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) 37% 88% 216.5 CysA aka B2422, component of Sulfate/thiosulfate porter 58% 342.0
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) 37% 88% 216.5 CysA aka B2422, component of Sulfate/thiosulfate porter 58% 342.0
D-maltose catabolism malK lo ABC-type maltose transporter (subunit 3/3) (EC 7.5.2.1) (characterized) 38% 91% 216.1 CysA aka B2422, component of Sulfate/thiosulfate porter 58% 342.0
D-maltose catabolism malK_Bb lo ABC-type maltose transport, ATP binding protein (characterized, see rationale) 38% 88% 215.7 CysA aka B2422, component of Sulfate/thiosulfate porter 58% 342.0
lactose catabolism lacK lo ABC transporter for Lactose, ATPase component (characterized) 36% 98% 215.3 CysA aka B2422, component of Sulfate/thiosulfate porter 58% 342.0
D-sorbitol (glucitol) catabolism mtlK lo ABC transporter for D-Sorbitol, ATPase component (characterized) 36% 96% 214.5 CysA aka B2422, component of Sulfate/thiosulfate porter 58% 342.0
L-arabinose catabolism xacJ lo Xylose/arabinose import ATP-binding protein XacJ; EC 7.5.2.13 (characterized, see rationale) 37% 81% 211.5 CysA aka B2422, component of Sulfate/thiosulfate porter 58% 342.0
L-fucose catabolism SM_b21106 lo ABC transporter for L-Fucose, ATPase component (characterized) 37% 85% 211.1 CysA aka B2422, component of Sulfate/thiosulfate porter 58% 342.0
D-xylose catabolism gtsD lo ABC transporter for D-Glucose-6-Phosphate, ATPase component (characterized) 35% 97% 211.1 CysA aka B2422, component of Sulfate/thiosulfate porter 58% 342.0
xylitol catabolism HSERO_RS17020 lo ABC-type sugar transport system, ATPase component protein (characterized, see rationale) 47% 58% 210.3 CysA aka B2422, component of Sulfate/thiosulfate porter 58% 342.0
D-maltose catabolism aglK lo ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized) 38% 88% 209.1 CysA aka B2422, component of Sulfate/thiosulfate porter 58% 342.0
sucrose catabolism aglK lo ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized) 38% 88% 209.1 CysA aka B2422, component of Sulfate/thiosulfate porter 58% 342.0
trehalose catabolism aglK lo ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized) 38% 88% 209.1 CysA aka B2422, component of Sulfate/thiosulfate porter 58% 342.0
L-arabinose catabolism xacK lo Xylose/arabinose import ATP-binding protein XacK; EC 7.5.2.13 (characterized, see rationale) 38% 77% 207.6 CysA aka B2422, component of Sulfate/thiosulfate porter 58% 342.0
D-galactose catabolism PfGW456L13_1897 lo ABC transporter for D-Galactose and D-Glucose, ATPase component (characterized) 35% 92% 207.2 CysA aka B2422, component of Sulfate/thiosulfate porter 58% 342.0
D-cellobiose catabolism SMc04256 lo ABC transporter for D-Cellobiose and D-Salicin, ATPase component (characterized) 36% 94% 203.8 CysA aka B2422, component of Sulfate/thiosulfate porter 58% 342.0
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) 36% 83% 201.1 CysA aka B2422, component of Sulfate/thiosulfate porter 58% 342.0
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) 36% 83% 201.1 CysA aka B2422, component of Sulfate/thiosulfate porter 58% 342.0
D-maltose catabolism malK_Aa lo ABC-type maltose transporter (EC 7.5.2.1) (characterized) 34% 92% 200.3 CysA aka B2422, component of Sulfate/thiosulfate porter 58% 342.0
D-cellobiose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 33% 99% 199.9 CysA aka B2422, component of Sulfate/thiosulfate porter 58% 342.0
D-galactose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 33% 99% 199.9 CysA aka B2422, component of Sulfate/thiosulfate porter 58% 342.0
D-glucose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 33% 99% 199.9 CysA aka B2422, component of Sulfate/thiosulfate porter 58% 342.0
lactose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 33% 99% 199.9 CysA aka B2422, component of Sulfate/thiosulfate porter 58% 342.0
D-maltose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 33% 99% 199.9 CysA aka B2422, component of Sulfate/thiosulfate porter 58% 342.0
D-mannose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 33% 99% 199.9 CysA aka B2422, component of Sulfate/thiosulfate porter 58% 342.0
sucrose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 33% 99% 199.9 CysA aka B2422, component of Sulfate/thiosulfate porter 58% 342.0
trehalose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 33% 99% 199.9 CysA aka B2422, component of Sulfate/thiosulfate porter 58% 342.0
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) 33% 94% 198 CysA aka B2422, component of Sulfate/thiosulfate porter 58% 342.0
D-maltose catabolism musK lo ABC-type maltose transporter (EC 7.5.2.1) (characterized) 36% 80% 198 CysA aka B2422, component of Sulfate/thiosulfate porter 58% 342.0
D-cellobiose catabolism aglK' lo Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 34% 95% 192.2 CysA aka B2422, component of Sulfate/thiosulfate porter 58% 342.0
D-glucose catabolism aglK' lo Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 34% 95% 192.2 CysA aka B2422, component of Sulfate/thiosulfate porter 58% 342.0
lactose catabolism aglK' lo Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 34% 95% 192.2 CysA aka B2422, component of Sulfate/thiosulfate porter 58% 342.0
D-maltose catabolism aglK' lo Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 34% 95% 192.2 CysA aka B2422, component of Sulfate/thiosulfate porter 58% 342.0
sucrose catabolism aglK' lo Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 34% 95% 192.2 CysA aka B2422, component of Sulfate/thiosulfate porter 58% 342.0
trehalose catabolism aglK' lo Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 34% 95% 192.2 CysA aka B2422, component of Sulfate/thiosulfate porter 58% 342.0
L-arabinose catabolism araV lo AraV, component of Arabinose, fructose, xylose porter (characterized) 32% 98% 188 CysA aka B2422, component of Sulfate/thiosulfate porter 58% 342.0
D-fructose catabolism araV lo AraV, component of Arabinose, fructose, xylose porter (characterized) 32% 98% 188 CysA aka B2422, component of Sulfate/thiosulfate porter 58% 342.0
sucrose catabolism araV lo AraV, component of Arabinose, fructose, xylose porter (characterized) 32% 98% 188 CysA aka B2422, component of Sulfate/thiosulfate porter 58% 342.0
D-xylose catabolism araV lo AraV, component of Arabinose, fructose, xylose porter (characterized) 32% 98% 188 CysA aka B2422, component of Sulfate/thiosulfate porter 58% 342.0
L-proline catabolism proV lo Glycine betaine/proline betaine transport system ATP-binding protein ProV (characterized) 37% 64% 177.9 CysA aka B2422, component of Sulfate/thiosulfate porter 58% 342.0
glycerol catabolism glpT lo GlpT, component of Glycerol uptake porter, GlpSTPQV (characterized) 32% 92% 168.7 CysA aka B2422, component of Sulfate/thiosulfate porter 58% 342.0
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) 36% 75% 167.5 CysA aka B2422, component of Sulfate/thiosulfate porter 58% 342.0
L-histidine catabolism hutV lo ABC transporter for L-Histidine, ATPase component (characterized) 36% 82% 165.2 CysA aka B2422, component of Sulfate/thiosulfate porter 58% 342.0
L-histidine catabolism aapP lo ABC transporter for L-Glutamine, L-Histidine, and other L-amino acids, ATPase component (characterized) 37% 93% 162.9 CysA aka B2422, component of Sulfate/thiosulfate porter 58% 342.0
L-asparagine catabolism bgtA lo ATPase (characterized, see rationale) 39% 92% 162.2 CysA aka B2422, component of Sulfate/thiosulfate porter 58% 342.0
L-aspartate catabolism bgtA lo ATPase (characterized, see rationale) 39% 92% 162.2 CysA aka B2422, component of Sulfate/thiosulfate porter 58% 342.0
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) 37% 91% 160.2 CysA aka B2422, component of Sulfate/thiosulfate porter 58% 342.0
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) 36% 93% 159.5 CysA aka B2422, component of Sulfate/thiosulfate porter 58% 342.0
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) 36% 93% 159.5 CysA aka B2422, component of Sulfate/thiosulfate porter 58% 342.0
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) 36% 93% 159.5 CysA aka B2422, component of Sulfate/thiosulfate porter 58% 342.0
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) 36% 93% 159.5 CysA aka B2422, component of Sulfate/thiosulfate porter 58% 342.0
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) 36% 93% 159.5 CysA aka B2422, component of Sulfate/thiosulfate porter 58% 342.0
D-alanine catabolism Pf6N2E2_5405 lo ABC transporter for D-Alanine, ATPase component (characterized) 36% 94% 159.1 CysA aka B2422, component of Sulfate/thiosulfate porter 58% 342.0
L-asparagine catabolism aatP lo Glutamate/aspartate transport ATP-binding protein GltL aka B0652, component of Glutamate/aspartate porter (characterized) 35% 99% 159.1 CysA aka B2422, component of Sulfate/thiosulfate porter 58% 342.0
L-aspartate catabolism aatP lo Glutamate/aspartate transport ATP-binding protein GltL aka B0652, component of Glutamate/aspartate porter (characterized) 35% 99% 159.1 CysA aka B2422, component of Sulfate/thiosulfate porter 58% 342.0
L-histidine catabolism bgtA lo BgtA aka SLR1735, component of Arginine/lysine/histidine/glutamine porter (characterized) 38% 96% 157.5 CysA aka B2422, component of Sulfate/thiosulfate porter 58% 342.0
L-lysine catabolism hisP lo BgtA aka SLR1735, component of Arginine/lysine/histidine/glutamine porter (characterized) 38% 96% 157.5 CysA aka B2422, component of Sulfate/thiosulfate porter 58% 342.0
L-asparagine catabolism bztD lo BztD, component of Glutamate/glutamine/aspartate/asparagine porter (characterized) 35% 91% 157.1 CysA aka B2422, component of Sulfate/thiosulfate porter 58% 342.0
L-aspartate catabolism bztD lo BztD, component of Glutamate/glutamine/aspartate/asparagine porter (characterized) 35% 91% 157.1 CysA aka B2422, component of Sulfate/thiosulfate porter 58% 342.0
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% 97% 155.2 CysA aka B2422, component of Sulfate/thiosulfate porter 58% 342.0
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% 97% 155.2 CysA aka B2422, component of Sulfate/thiosulfate porter 58% 342.0
D-glucosamine (chitosamine) catabolism AO353_21725 lo ABC transporter for D-Glucosamine, putative ATPase component (characterized) 36% 95% 154.8 CysA aka B2422, component of Sulfate/thiosulfate porter 58% 342.0
glycerol catabolism glpS lo ABC transporter for Glycerol, ATPase component 1 (characterized) 32% 99% 153.3 CysA aka B2422, component of Sulfate/thiosulfate porter 58% 342.0
L-histidine catabolism BPHYT_RS24015 lo ABC transporter related (characterized, see rationale) 37% 95% 151.8 CysA aka B2422, component of Sulfate/thiosulfate porter 58% 342.0
L-asparagine catabolism peb1C lo PEB1C, component of Uptake system for glutamate and aspartate (characterized) 34% 98% 149.8 CysA aka B2422, component of Sulfate/thiosulfate porter 58% 342.0
L-aspartate catabolism peb1C lo PEB1C, component of Uptake system for glutamate and aspartate (characterized) 34% 98% 149.8 CysA aka B2422, component of Sulfate/thiosulfate porter 58% 342.0
L-tryptophan catabolism ecfA2 lo Energy-coupling factor transporter ATP-binding protein EcfA2; Short=ECF transporter A component EcfA2; EC 7.-.-.- (characterized, see rationale) 36% 78% 133.7 CysA aka B2422, component of Sulfate/thiosulfate porter 58% 342.0
L-arabinose catabolism xylGsa lo Xylose/arabinose import ATP-binding protein XylG; EC 7.5.2.13 (characterized, see rationale) 34% 98% 123.2 CysA aka B2422, component of Sulfate/thiosulfate porter 58% 342.0
citrate catabolism fecE lo iron(III) dicitrate transport ATP-binding protein FecE (characterized) 34% 89% 120.2 CysA aka B2422, component of Sulfate/thiosulfate porter 58% 342.0
myo-inositol catabolism PGA1_c07320 lo Inositol transport system ATP-binding protein (characterized) 31% 84% 107.5 CysA aka B2422, component of Sulfate/thiosulfate porter 58% 342.0

Sequence Analysis Tools

View Dsui_0258 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

MSIEIRNIAKRFGNFVALDDVSLSIPTGELVALLGPSGCGKTTLLRIIAGMETADEGQVM
FEGSEATHLHARERQVGFVFQHYALFRHMNVFENVAFGLRVKPRKERPCESEIRKRVMDL
LSLVQLDWLADRYPTQLSGGQRQRIALARALAVEPKVLLLDEPFGALDTKVRKELRRWLR
RLHDEMHISSVFVTHDQEEALEVADRVVVMNKGRIEQVGSPDEVYSNPASPFVYQFLGNV
NVFHSRVHGAWAEVARDDVPAGQEAVAFIRPHDIDIDTVATPESLEAKVSYVQTIGPLVR
VEVIHQGELVEVELTRERQQVLGLTAGQQVWLKPRQVKVFANGEGAVAPAQAQEKQPFLF

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, the preprint on GapMind for carbon sources, 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