GapMind for catabolism of small carbon sources

 

Protein WP_051335598.1 in Methylocapsa acidiphila B2

Annotation: NCBI__GCF_000427445.1:WP_051335598.1

Length: 390 amino acids

Source: GCF_000427445.1 in NCBI

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) 45% 99% 332.8 Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD 40% 264.2
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% 91% 244.6 PotG aka B0855, component of Putrescine porter 45% 332.8
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% 91% 244.6 PotG aka B0855, component of Putrescine porter 45% 332.8
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% 91% 244.6 PotG aka B0855, component of Putrescine porter 45% 332.8
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% 91% 244.6 PotG aka B0855, component of Putrescine porter 45% 332.8
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% 91% 244.6 PotG aka B0855, component of Putrescine porter 45% 332.8
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% 91% 244.6 PotG aka B0855, component of Putrescine porter 45% 332.8
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% 91% 244.6 PotG aka B0855, component of Putrescine porter 45% 332.8
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% 91% 244.6 PotG aka B0855, component of Putrescine porter 45% 332.8
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% 91% 244.6 PotG aka B0855, component of Putrescine porter 45% 332.8
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% 91% 244.6 PotG aka B0855, component of Putrescine porter 45% 332.8
L-fucose catabolism SM_b21106 med ABC transporter for L-Fucose, ATPase component (characterized) 42% 82% 233 PotG aka B0855, component of Putrescine porter 45% 332.8
D-glucosamine (chitosamine) catabolism SM_b21216 med ABC transporter for D-Glucosamine, ATPase component (characterized) 43% 81% 231.9 PotG aka B0855, component of Putrescine porter 45% 332.8
xylitol catabolism Dshi_0546 med ABC transporter for Xylitol, ATPase component (characterized) 40% 88% 230.7 PotG aka B0855, component of Putrescine porter 45% 332.8
N-acetyl-D-glucosamine catabolism SMc02869 med N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized) 48% 70% 228 PotG aka B0855, component of Putrescine porter 45% 332.8
D-glucosamine (chitosamine) catabolism SMc02869 med N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized) 48% 70% 228 PotG aka B0855, component of Putrescine porter 45% 332.8
trehalose catabolism treV med TreV, component of Trehalose porter (characterized) 44% 75% 223.4 PotG aka B0855, component of Putrescine porter 45% 332.8
D-maltose catabolism malK_Bb med ABC-type maltose transport, ATP binding protein (characterized, see rationale) 44% 70% 221.9 PotG aka B0855, component of Putrescine porter 45% 332.8
D-mannitol catabolism mtlK med SmoK aka POLK, component of Hexitol (glucitol; mannitol) porter (characterized) 44% 81% 220.3 PotG aka B0855, component of Putrescine porter 45% 332.8
D-cellobiose catabolism aglK' med Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 40% 83% 215.3 PotG aka B0855, component of Putrescine porter 45% 332.8
D-glucose catabolism aglK' med Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 40% 83% 215.3 PotG aka B0855, component of Putrescine porter 45% 332.8
lactose catabolism aglK' med Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 40% 83% 215.3 PotG aka B0855, component of Putrescine porter 45% 332.8
D-maltose catabolism aglK med Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 40% 83% 215.3 PotG aka B0855, component of Putrescine porter 45% 332.8
D-maltose catabolism aglK' med Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 40% 83% 215.3 PotG aka B0855, component of Putrescine porter 45% 332.8
D-sorbitol (glucitol) catabolism mtlK med ABC transporter for D-Sorbitol, ATPase component (characterized) 45% 73% 215.3 PotG aka B0855, component of Putrescine porter 45% 332.8
sucrose catabolism aglK med Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 40% 83% 215.3 PotG aka B0855, component of Putrescine porter 45% 332.8
sucrose catabolism aglK' med Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 40% 83% 215.3 PotG aka B0855, component of Putrescine porter 45% 332.8
trehalose catabolism aglK med Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 40% 83% 215.3 PotG aka B0855, component of Putrescine porter 45% 332.8
trehalose catabolism aglK' med Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 40% 83% 215.3 PotG aka B0855, component of Putrescine porter 45% 332.8
D-xylose catabolism gtsD med ABC transporter for D-Glucose-6-Phosphate, ATPase component (characterized) 40% 77% 213.8 PotG aka B0855, component of Putrescine porter 45% 332.8
lactose catabolism lacK lo ABC transporter for Lactose, ATPase component (characterized) 37% 97% 236.9 PotG aka B0855, component of Putrescine porter 45% 332.8
D-maltose catabolism malK lo ABC-type maltose transporter (subunit 3/3) (EC 7.5.2.1) (characterized) 39% 94% 227.3 PotG aka B0855, component of Putrescine porter 45% 332.8
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) 39% 91% 226.5 PotG aka B0855, component of Putrescine porter 45% 332.8
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) 40% 91% 224.9 PotG aka B0855, component of Putrescine porter 45% 332.8
L-arabinose catabolism xacJ lo Xylose/arabinose import ATP-binding protein XacJ; EC 7.5.2.13 (characterized, see rationale) 39% 92% 223 PotG aka B0855, component of Putrescine porter 45% 332.8
L-arabinose catabolism xacK lo Xylose/arabinose import ATP-binding protein XacK; EC 7.5.2.13 (characterized, see rationale) 37% 92% 215.3 PotG aka B0855, component of Putrescine porter 45% 332.8
D-cellobiose catabolism SMc04256 lo ABC transporter for D-Cellobiose and D-Salicin, ATPase component (characterized) 37% 98% 214.5 PotG aka B0855, component of Putrescine porter 45% 332.8
D-galactose catabolism PfGW456L13_1897 lo ABC transporter for D-Galactose and D-Glucose, ATPase component (characterized) 37% 84% 211.5 PotG aka B0855, component of Putrescine porter 45% 332.8
D-cellobiose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 37% 88% 209.9 PotG aka B0855, component of Putrescine porter 45% 332.8
D-galactose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 37% 88% 209.9 PotG aka B0855, component of Putrescine porter 45% 332.8
D-glucose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 37% 88% 209.9 PotG aka B0855, component of Putrescine porter 45% 332.8
lactose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 37% 88% 209.9 PotG aka B0855, component of Putrescine porter 45% 332.8
D-maltose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 37% 88% 209.9 PotG aka B0855, component of Putrescine porter 45% 332.8
D-mannose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 37% 88% 209.9 PotG aka B0855, component of Putrescine porter 45% 332.8
sucrose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 37% 88% 209.9 PotG aka B0855, component of Putrescine porter 45% 332.8
trehalose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 37% 88% 209.9 PotG aka B0855, component of Putrescine porter 45% 332.8
D-maltose catabolism musK lo ABC-type maltose transporter (EC 7.5.2.1) (characterized) 39% 74% 208 PotG aka B0855, component of Putrescine porter 45% 332.8
D-maltose catabolism malK_Aa lo ABC-type maltose transporter (EC 7.5.2.1) (characterized) 38% 76% 206.5 PotG aka B0855, component of Putrescine porter 45% 332.8
xylitol catabolism HSERO_RS17020 lo ABC-type sugar transport system, ATPase component protein (characterized, see rationale) 36% 91% 204.1 PotG aka B0855, component of Putrescine porter 45% 332.8
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) 35% 89% 201.8 PotG aka B0855, component of Putrescine porter 45% 332.8
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) 34% 93% 200.3 PotG aka B0855, component of Putrescine porter 45% 332.8
L-arabinose catabolism araV lo AraV, component of Arabinose, fructose, xylose porter (characterized) 42% 68% 197.6 PotG aka B0855, component of Putrescine porter 45% 332.8
D-fructose catabolism araV lo AraV, component of Arabinose, fructose, xylose porter (characterized) 42% 68% 197.6 PotG aka B0855, component of Putrescine porter 45% 332.8
sucrose catabolism araV lo AraV, component of Arabinose, fructose, xylose porter (characterized) 42% 68% 197.6 PotG aka B0855, component of Putrescine porter 45% 332.8
D-xylose catabolism araV lo AraV, component of Arabinose, fructose, xylose porter (characterized) 42% 68% 197.6 PotG aka B0855, component of Putrescine porter 45% 332.8
L-proline catabolism opuBA lo BusAA, component of Uptake system for glycine-betaine (high affinity) and proline (low affinity) (OpuAA-OpuABC) or BusAA-ABC of Lactococcus lactis). BusAA, the ATPase subunit, has a C-terminal tandem cystathionine β-synthase (CBS) domain which is the cytoplasmic K+ sensor for osmotic stress (osmotic strength)while the BusABC subunit has the membrane and receptor domains fused to each other (Biemans-Oldehinkel et al., 2006; Mahmood et al., 2006; Gul et al. 2012). An N-terminal amphipathic α-helix of OpuA is necessary for high activity but is not critical for biogenesis or the ionic regulation of transport (characterized) 39% 62% 177.6 PotG aka B0855, component of Putrescine porter 45% 332.8
L-proline catabolism proV lo Glycine betaine/proline betaine transport system ATP-binding protein ProV (characterized) 38% 60% 173.7 PotG aka B0855, component of Putrescine porter 45% 332.8
L-histidine catabolism hutV lo ABC transporter for L-Histidine, ATPase component (characterized) 38% 90% 171 PotG aka B0855, component of Putrescine porter 45% 332.8
glycerol catabolism glpS lo ABC transporter for Glycerol, ATPase component 1 (characterized) 34% 94% 169.1 PotG aka B0855, component of Putrescine porter 45% 332.8
glycerol catabolism glpT lo GlpT, component of Glycerol uptake porter, GlpSTPQV (characterized) 36% 71% 164.5 PotG aka B0855, component of Putrescine porter 45% 332.8
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% 84% 158.3 PotG aka B0855, component of Putrescine porter 45% 332.8
D-glucosamine (chitosamine) catabolism AO353_21725 lo ABC transporter for D-Glucosamine, putative ATPase component (characterized) 38% 97% 157.5 PotG aka B0855, component of Putrescine porter 45% 332.8
L-asparagine catabolism bgtA lo ATPase (characterized, see rationale) 35% 98% 154.5 PotG aka B0855, component of Putrescine porter 45% 332.8
L-aspartate catabolism bgtA lo ATPase (characterized, see rationale) 35% 98% 154.5 PotG aka B0855, component of Putrescine porter 45% 332.8
D-alanine catabolism Pf6N2E2_5405 lo ABC transporter for D-Alanine, ATPase component (characterized) 35% 99% 153.7 PotG aka B0855, component of Putrescine porter 45% 332.8
L-lysine catabolism hisP lo Amino-acid ABC transporter, ATP-binding protein (characterized, see rationale) 35% 97% 151.8 PotG aka B0855, component of Putrescine porter 45% 332.8
L-asparagine catabolism bztD lo BztD, component of Glutamate/glutamine/aspartate/asparagine porter (characterized) 33% 91% 148.7 PotG aka B0855, component of Putrescine porter 45% 332.8
L-aspartate catabolism bztD lo BztD, component of Glutamate/glutamine/aspartate/asparagine porter (characterized) 33% 91% 148.7 PotG aka B0855, component of Putrescine porter 45% 332.8
L-arginine catabolism artP lo Arginine transport ATP-binding protein ArtM (characterized) 35% 100% 146.4 PotG aka B0855, component of Putrescine porter 45% 332.8
L-histidine catabolism aapP lo ABC transporter for L-Glutamine, L-Histidine, and other L-amino acids, ATPase component (characterized) 32% 99% 142.9 PotG aka B0855, component of Putrescine porter 45% 332.8
L-histidine catabolism bgtA lo BgtA aka SLR1735, component of Arginine/lysine/histidine/glutamine porter (characterized) 34% 99% 140.2 PotG aka B0855, component of Putrescine porter 45% 332.8
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% 99% 139 PotG aka B0855, component of Putrescine porter 45% 332.8
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% 99% 139 PotG aka B0855, component of Putrescine porter 45% 332.8
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% 99% 139 PotG aka B0855, component of Putrescine porter 45% 332.8
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% 99% 139 PotG aka B0855, component of Putrescine porter 45% 332.8
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% 99% 139 PotG aka B0855, component of Putrescine porter 45% 332.8
L-asparagine catabolism aatP lo Glutamate/aspartate transport ATP-binding protein GltL aka B0652, component of Glutamate/aspartate porter (characterized) 34% 99% 137.9 PotG aka B0855, component of Putrescine porter 45% 332.8
L-aspartate catabolism aatP lo Glutamate/aspartate transport ATP-binding protein GltL aka B0652, component of Glutamate/aspartate porter (characterized) 34% 99% 137.9 PotG aka B0855, component of Putrescine porter 45% 332.8
D-mannose catabolism TM1750 lo TM1750, component of Probable mannose/mannoside porter. Induced by beta-mannan (Conners et al., 2005). Regulated by mannose-responsive regulator manR (characterized) 34% 73% 127.9 PotG aka B0855, component of Putrescine porter 45% 332.8
L-tryptophan catabolism ecfA1 lo Energy-coupling factor transporter ATP-binding protein EcfA1; Short=ECF transporter A component EcfA; EC 7.-.-.- (characterized, see rationale) 34% 80% 127.9 PotG aka B0855, component of Putrescine porter 45% 332.8
L-isoleucine catabolism livG lo ABC transporter ATP-binding protein-branched chain amino acid transport, component of The branched chain hydrophobic amino acid transporter, LivJFGHM (characterized) 31% 98% 123.6 PotG aka B0855, component of Putrescine porter 45% 332.8
L-leucine catabolism livG lo ABC transporter ATP-binding protein-branched chain amino acid transport, component of The branched chain hydrophobic amino acid transporter, LivJFGHM (characterized) 31% 98% 123.6 PotG aka B0855, component of Putrescine porter 45% 332.8
L-valine catabolism livG lo ABC transporter ATP-binding protein-branched chain amino acid transport, component of The branched chain hydrophobic amino acid transporter, LivJFGHM (characterized) 31% 98% 123.6 PotG aka B0855, component of Putrescine porter 45% 332.8
D-cellobiose catabolism mglA lo glucose transporter, ATPase component (characterized) 32% 90% 110.9 PotG aka B0855, component of Putrescine porter 45% 332.8
D-glucose catabolism mglA lo glucose transporter, ATPase component (characterized) 32% 90% 110.9 PotG aka B0855, component of Putrescine porter 45% 332.8
lactose catabolism mglA lo glucose transporter, ATPase component (characterized) 32% 90% 110.9 PotG aka B0855, component of Putrescine porter 45% 332.8
D-maltose catabolism mglA lo glucose transporter, ATPase component (characterized) 32% 90% 110.9 PotG aka B0855, component of Putrescine porter 45% 332.8
sucrose catabolism mglA lo glucose transporter, ATPase component (characterized) 32% 90% 110.9 PotG aka B0855, component of Putrescine porter 45% 332.8
trehalose catabolism mglA lo glucose transporter, ATPase component (characterized) 32% 90% 110.9 PotG aka B0855, component of Putrescine porter 45% 332.8

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Sequence

MAAFQNSSRRGEARRGGGSNAVSAPSESAAPVVRLEGVTKRHGRLTAVDNLSLSLRRGEF
FALLGPSGCGKTSLLRLIGGFEAPDSGRIFIDGVDVTETPPHRRPVNMMFQTYALFPHLN
VACNIGFGLVQEGMPKAKIKTRVEEMLRFVQLEGLGERRPDQLSGGQKQRVALARALAKR
PKLLLLDEPLAALDRRLREETQFELMRLQKTFGVTFLVVTHDQREAMAMAGRIAVMREGR
IEQIGTPEQIYETPSSRYVARFVGEINLLDGKVATTTGGRVSVATAAGAVEIACAAAYAP
GWPVAVALRPERILVCPSEAAPDAPGLNLLHGVIEEKAYLGEVTLYRIGLSGGLALRAAR
QNHEPGASAFEPGDKVAAGFTPDAAIILPS

This GapMind analysis is from Sep 24 2021. The underlying query database was built on Sep 17 2021.

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About GapMind

Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.

A candidate for a step is "high confidence" if either:

where "other" refers to the best ublast hit to a sequence that is not annotated as performing this step (and is not "ignored").

Otherwise, a candidate is "medium confidence" if either:

Other blast hits with at least 50% coverage are "low confidence."

Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:

GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).

For more information, see:

If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know

by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory