GapMind for catabolism of small carbon sources

 

Protein WP_025331193.1 in Snodgrassella alvi wkB2

Annotation: NCBI__GCF_000600005.1:WP_025331193.1

Length: 376 amino acids

Source: GCF_000600005.1 in NCBI

Candidate for 97 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) 54% 99% 401.7 MotB, component of Mannopine porter 39% 251.1
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) 42% 89% 246.5 PotG aka B0855, component of Putrescine porter 54% 401.7
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) 42% 89% 246.5 PotG aka B0855, component of Putrescine porter 54% 401.7
D-maltose catabolism thuK med Trehalose/maltose import ATP-binding protein MalK; EC 7.5.2.1 (characterized) 42% 88% 242.3 PotG aka B0855, component of Putrescine porter 54% 401.7
L-arabinose catabolism xacK med Xylose/arabinose import ATP-binding protein XacK; EC 7.5.2.13 (characterized, see rationale) 42% 84% 239.2 PotG aka B0855, component of Putrescine porter 54% 401.7
L-arabinose catabolism xacJ med Xylose/arabinose import ATP-binding protein XacJ; EC 7.5.2.13 (characterized, see rationale) 43% 76% 238.4 PotG aka B0855, component of Putrescine porter 54% 401.7
xylitol catabolism Dshi_0546 med ABC transporter for Xylitol, ATPase component (characterized) 46% 80% 233.8 PotG aka B0855, component of Putrescine porter 54% 401.7
D-cellobiose catabolism gtsD med ABC transporter for D-Galactose and D-Glucose, ATPase component (characterized) 44% 75% 231.9 PotG aka B0855, component of Putrescine porter 54% 401.7
D-galactose catabolism PfGW456L13_1897 med ABC transporter for D-Galactose and D-Glucose, ATPase component (characterized) 44% 75% 231.9 PotG aka B0855, component of Putrescine porter 54% 401.7
D-glucose catabolism gtsD med ABC transporter for D-Galactose and D-Glucose, ATPase component (characterized) 44% 75% 231.9 PotG aka B0855, component of Putrescine porter 54% 401.7
lactose catabolism gtsD med ABC transporter for D-Galactose and D-Glucose, ATPase component (characterized) 44% 75% 231.9 PotG aka B0855, component of Putrescine porter 54% 401.7
D-maltose catabolism gtsD med ABC transporter for D-Galactose and D-Glucose, ATPase component (characterized) 44% 75% 231.9 PotG aka B0855, component of Putrescine porter 54% 401.7
sucrose catabolism gtsD med ABC transporter for D-Galactose and D-Glucose, ATPase component (characterized) 44% 75% 231.9 PotG aka B0855, component of Putrescine porter 54% 401.7
trehalose catabolism gtsD med ABC transporter for D-Galactose and D-Glucose, ATPase component (characterized) 44% 75% 231.9 PotG aka B0855, component of Putrescine porter 54% 401.7
N-acetyl-D-glucosamine catabolism SMc02869 med N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized) 47% 70% 231.5 PotG aka B0855, component of Putrescine porter 54% 401.7
D-glucosamine (chitosamine) catabolism SMc02869 med N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized) 47% 70% 231.5 PotG aka B0855, component of Putrescine porter 54% 401.7
D-xylose catabolism gtsD med ABC transporter for D-Glucose-6-Phosphate, ATPase component (characterized) 42% 75% 231.5 PotG aka B0855, component of Putrescine porter 54% 401.7
D-maltose catabolism malK_Aa med ABC-type maltose transporter (EC 7.5.2.1) (characterized) 42% 75% 224.9 PotG aka B0855, component of Putrescine porter 54% 401.7
L-fucose catabolism SM_b21106 med ABC transporter for L-Fucose, ATPase component (characterized) 43% 77% 224.2 PotG aka B0855, component of Putrescine porter 54% 401.7
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) 42% 72% 223.8 PotG aka B0855, component of Putrescine porter 54% 401.7
D-maltose catabolism malK_Bb med ABC-type maltose transport, ATP binding protein (characterized, see rationale) 48% 71% 222.6 PotG aka B0855, component of Putrescine porter 54% 401.7
D-maltose catabolism musK med ABC-type maltose transporter (EC 7.5.2.1) (characterized) 43% 73% 221.1 PotG aka B0855, component of Putrescine porter 54% 401.7
trehalose catabolism treV med TreV, component of Trehalose porter (characterized) 45% 77% 218.8 PotG aka B0855, component of Putrescine porter 54% 401.7
D-sorbitol (glucitol) catabolism mtlK med ABC transporter for D-Sorbitol, ATPase component (characterized) 41% 78% 216.5 PotG aka B0855, component of Putrescine porter 54% 401.7
sucrose catabolism thuK med ThuK aka RB0314 aka SMB20328, component of Trehalose/maltose/sucrose porter (trehalose inducible) (characterized) 41% 90% 216.1 PotG aka B0855, component of Putrescine porter 54% 401.7
D-cellobiose catabolism SMc04256 med ABC transporter for D-Cellobiose and D-Salicin, ATPase component (characterized) 41% 80% 215.7 PotG aka B0855, component of Putrescine porter 54% 401.7
L-histidine catabolism hutV med ABC transporter for L-Histidine, ATPase component (characterized) 41% 86% 166.4 PotG aka B0855, component of Putrescine porter 54% 401.7
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) 38% 88% 238.4 PotG aka B0855, component of Putrescine porter 54% 401.7
D-maltose catabolism malK lo Maltose-transporting ATPase (EC 3.6.3.19) (characterized) 39% 85% 232.6 PotG aka B0855, component of Putrescine porter 54% 401.7
D-cellobiose catabolism aglK' lo Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 40% 86% 230.3 PotG aka B0855, component of Putrescine porter 54% 401.7
D-glucose catabolism aglK' lo Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 40% 86% 230.3 PotG aka B0855, component of Putrescine porter 54% 401.7
lactose catabolism aglK' lo Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 40% 86% 230.3 PotG aka B0855, component of Putrescine porter 54% 401.7
D-maltose catabolism aglK lo Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 40% 86% 230.3 PotG aka B0855, component of Putrescine porter 54% 401.7
D-maltose catabolism aglK' lo Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 40% 86% 230.3 PotG aka B0855, component of Putrescine porter 54% 401.7
sucrose catabolism aglK lo Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 40% 86% 230.3 PotG aka B0855, component of Putrescine porter 54% 401.7
sucrose catabolism aglK' lo Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 40% 86% 230.3 PotG aka B0855, component of Putrescine porter 54% 401.7
trehalose catabolism aglK lo Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 40% 86% 230.3 PotG aka B0855, component of Putrescine porter 54% 401.7
trehalose catabolism aglK' lo Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 40% 86% 230.3 PotG aka B0855, component of Putrescine porter 54% 401.7
D-maltose catabolism malK_Sm lo MalK, component of Maltose/Maltotriose/maltodextrin (up to 7 glucose units) transporters MalXFGK (MsmK (3.A.1.1.28) can probably substitute for MalK; Webb et al., 2008) (characterized) 39% 89% 228 PotG aka B0855, component of Putrescine porter 54% 401.7
trehalose catabolism malK lo MalK, component of Maltose/Maltotriose/maltodextrin (up to 7 glucose units) transporters MalXFGK (MsmK (3.A.1.1.28) can probably substitute for MalK; Webb et al., 2008) (characterized) 39% 89% 228 PotG aka B0855, component of Putrescine porter 54% 401.7
D-glucosamine (chitosamine) catabolism SM_b21216 lo ABC transporter for D-Glucosamine, ATPase component (characterized) 39% 84% 223 PotG aka B0855, component of Putrescine porter 54% 401.7
D-mannitol catabolism mtlK lo ABC transporter for D-mannitol and D-mannose, ATPase component (characterized) 37% 93% 221.5 PotG aka B0855, component of Putrescine porter 54% 401.7
D-cellobiose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 37% 88% 217.6 PotG aka B0855, component of Putrescine porter 54% 401.7
D-galactose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 37% 88% 217.6 PotG aka B0855, component of Putrescine porter 54% 401.7
D-glucose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 37% 88% 217.6 PotG aka B0855, component of Putrescine porter 54% 401.7
lactose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 37% 88% 217.6 PotG aka B0855, component of Putrescine porter 54% 401.7
D-maltose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 37% 88% 217.6 PotG aka B0855, component of Putrescine porter 54% 401.7
D-mannose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 37% 88% 217.6 PotG aka B0855, component of Putrescine porter 54% 401.7
sucrose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 37% 88% 217.6 PotG aka B0855, component of Putrescine porter 54% 401.7
trehalose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 37% 88% 217.6 PotG aka B0855, component of Putrescine porter 54% 401.7
lactose catabolism lacK lo ABC transporter for Lactose, ATPase component (characterized) 40% 79% 213.8 PotG aka B0855, component of Putrescine porter 54% 401.7
xylitol catabolism HSERO_RS17020 lo ABC-type sugar transport system, ATPase component protein (characterized, see rationale) 40% 72% 201.8 PotG aka B0855, component of Putrescine porter 54% 401.7
L-arabinose catabolism araV lo AraV, component of Arabinose, fructose, xylose porter (characterized) 36% 80% 196.4 PotG aka B0855, component of Putrescine porter 54% 401.7
D-fructose catabolism araV lo AraV, component of Arabinose, fructose, xylose porter (characterized) 36% 80% 196.4 PotG aka B0855, component of Putrescine porter 54% 401.7
sucrose catabolism araV lo AraV, component of Arabinose, fructose, xylose porter (characterized) 36% 80% 196.4 PotG aka B0855, component of Putrescine porter 54% 401.7
D-xylose catabolism araV lo AraV, component of Arabinose, fructose, xylose porter (characterized) 36% 80% 196.4 PotG aka B0855, component of Putrescine porter 54% 401.7
L-proline catabolism proV lo glycine betaine/l-proline transport atp-binding protein prov (characterized) 40% 64% 179.9 PotG aka B0855, component of Putrescine porter 54% 401.7
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) 40% 58% 177.9 PotG aka B0855, component of Putrescine porter 54% 401.7
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% 90% 169.9 PotG aka B0855, component of Putrescine porter 54% 401.7
D-alanine catabolism Pf6N2E2_5405 lo ABC transporter for D-Alanine, ATPase component (characterized) 37% 99% 166 PotG aka B0855, component of Putrescine porter 54% 401.7
glycerol catabolism glpT lo GlpT, component of Glycerol uptake porter, GlpSTPQV (characterized) 31% 81% 164.9 PotG aka B0855, component of Putrescine porter 54% 401.7
L-asparagine catabolism bztD lo BztD, component of Glutamate/glutamine/aspartate/asparagine porter (characterized) 37% 90% 164.1 PotG aka B0855, component of Putrescine porter 54% 401.7
L-aspartate catabolism bztD lo BztD, component of Glutamate/glutamine/aspartate/asparagine porter (characterized) 37% 90% 164.1 PotG aka B0855, component of Putrescine porter 54% 401.7
L-glutamate catabolism gltL lo BztD, component of Glutamate/glutamine/aspartate/asparagine porter (characterized) 37% 90% 164.1 PotG aka B0855, component of Putrescine porter 54% 401.7
D-glucosamine (chitosamine) catabolism AO353_21725 lo ABC transporter for D-glucosamine, ATPase component (characterized) 36% 100% 163.7 PotG aka B0855, component of Putrescine porter 54% 401.7
glycerol catabolism glpS lo ABC transporter for Glycerol, ATPase component 1 (characterized) 31% 89% 161 PotG aka B0855, component of Putrescine porter 54% 401.7
L-histidine catabolism Ac3H11_2560 lo ABC transporter for L-Histidine, ATPase component (characterized) 39% 87% 157.9 PotG aka B0855, component of Putrescine porter 54% 401.7
L-asparagine catabolism glnQ lo Glutamine ABC transporter ATP-binding protein, component of Glutamine transporter, GlnQP. Takes up glutamine, asparagine and glutamate which compete for each other for binding both substrate and the transmembrane protein constituent of the system (Fulyani et al. 2015). Tandem substrate binding domains (SBDs) differ in substrate specificity and affinity, allowing cells to efficiently accumulate different amino acids via a single ABC transporter. Analysis revealed the roles of individual residues in determining the substrate affinity (characterized) 35% 96% 156.4 PotG aka B0855, component of Putrescine porter 54% 401.7
L-asparagine catabolism bgtA lo ATPase (characterized, see rationale) 33% 95% 155.6 PotG aka B0855, component of Putrescine porter 54% 401.7
L-aspartate catabolism bgtA lo ATPase (characterized, see rationale) 33% 95% 155.6 PotG aka B0855, component of Putrescine porter 54% 401.7
L-histidine catabolism BPHYT_RS24015 lo ABC transporter related (characterized, see rationale) 37% 92% 155.6 PotG aka B0855, component of Putrescine porter 54% 401.7
L-histidine catabolism PA5503 lo Methionine import ATP-binding protein MetN 2, component of L-Histidine uptake porter, MetIQN (characterized) 33% 82% 154.5 PotG aka B0855, component of Putrescine porter 54% 401.7
L-arginine catabolism artP 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% 98% 152.1 PotG aka B0855, component of Putrescine porter 54% 401.7
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% 98% 152.1 PotG aka B0855, component of Putrescine porter 54% 401.7
L-lysine 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% 98% 152.1 PotG aka B0855, component of Putrescine porter 54% 401.7
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% 95% 141.7 PotG aka B0855, component of Putrescine porter 54% 401.7
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% 94% 140.6 PotG aka B0855, component of Putrescine porter 54% 401.7
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% 74% 125.2 PotG aka B0855, component of Putrescine porter 54% 401.7
D-cellobiose catabolism cbtF lo CbtF, component of Cellobiose and cellooligosaccharide porter (characterized) 34% 58% 119.4 PotG aka B0855, component of Putrescine porter 54% 401.7
L-isoleucine catabolism livG lo High-affinity branched-chain amino acid ABC transporter ATP-binding protein LivG (characterized, see rationale) 30% 98% 117.5 PotG aka B0855, component of Putrescine porter 54% 401.7
L-phenylalanine catabolism livG lo High-affinity branched-chain amino acid ABC transporter ATP-binding protein LivG (characterized, see rationale) 30% 98% 117.5 PotG aka B0855, component of Putrescine porter 54% 401.7
L-alanine catabolism braG lo High-affinity branched-chain amino acid transport ATP-binding protein BraG, component of Branched chain amino acid uptake transporter. Transports alanine (characterized) 31% 96% 112.8 PotG aka B0855, component of Putrescine porter 54% 401.7
L-isoleucine catabolism livF lo High-affinity branched-chain amino acid transport ATP-binding protein BraG, component of Branched chain amino acid uptake transporter. Transports alanine (characterized) 31% 96% 112.8 PotG aka B0855, component of Putrescine porter 54% 401.7
L-leucine catabolism livF lo High-affinity branched-chain amino acid transport ATP-binding protein BraG, component of Branched chain amino acid uptake transporter. Transports alanine (characterized) 31% 96% 112.8 PotG aka B0855, component of Putrescine porter 54% 401.7
L-serine catabolism braG lo High-affinity branched-chain amino acid transport ATP-binding protein BraG, component of Branched chain amino acid uptake transporter. Transports alanine (characterized) 31% 96% 112.8 PotG aka B0855, component of Putrescine porter 54% 401.7
L-threonine catabolism braG lo High-affinity branched-chain amino acid transport ATP-binding protein BraG, component of Branched chain amino acid uptake transporter. Transports alanine (characterized) 31% 96% 112.8 PotG aka B0855, component of Putrescine porter 54% 401.7
L-valine catabolism livF lo High-affinity branched-chain amino acid transport ATP-binding protein BraG, component of Branched chain amino acid uptake transporter. Transports alanine (characterized) 31% 96% 112.8 PotG aka B0855, component of Putrescine porter 54% 401.7
D-cellobiose catabolism mglA lo glucose transporter, ATPase component (characterized) 33% 88% 109.4 PotG aka B0855, component of Putrescine porter 54% 401.7
D-glucose catabolism mglA lo glucose transporter, ATPase component (characterized) 33% 88% 109.4 PotG aka B0855, component of Putrescine porter 54% 401.7
lactose catabolism mglA lo glucose transporter, ATPase component (characterized) 33% 88% 109.4 PotG aka B0855, component of Putrescine porter 54% 401.7
D-maltose catabolism mglA lo glucose transporter, ATPase component (characterized) 33% 88% 109.4 PotG aka B0855, component of Putrescine porter 54% 401.7
sucrose catabolism mglA lo glucose transporter, ATPase component (characterized) 33% 88% 109.4 PotG aka B0855, component of Putrescine porter 54% 401.7
trehalose catabolism mglA lo glucose transporter, ATPase component (characterized) 33% 88% 109.4 PotG aka B0855, component of Putrescine porter 54% 401.7
L-histidine catabolism natE lo NatE aka LivF aka SLR1881, component of Leucine/proline/alanine/serine/glycine (and possibly histidine) porter, NatABCDE (characterized) 31% 93% 103.2 PotG aka B0855, component of Putrescine porter 54% 401.7
L-leucine catabolism natE lo NatE aka LivF aka SLR1881, component of Leucine/proline/alanine/serine/glycine (and possibly histidine) porter, NatABCDE (characterized) 31% 93% 103.2 PotG aka B0855, component of Putrescine porter 54% 401.7
L-proline catabolism natE lo NatE aka LivF aka SLR1881, component of Leucine/proline/alanine/serine/glycine (and possibly histidine) porter, NatABCDE (characterized) 31% 93% 103.2 PotG aka B0855, component of Putrescine porter 54% 401.7
L-phenylalanine catabolism livF lo high-affinity branched-chain amino acid ABC transporter, ATP-binding protein LivF (characterized) 30% 89% 101.7 PotG aka B0855, component of Putrescine porter 54% 401.7

Sequence Analysis Tools

View WP_025331193.1 at NCBI

Find papers: PaperBLAST

Find functional residues: SitesBLAST

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Predict transmenbrane helices: Phobius

Predict protein localization: PSORTb

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Sequence

MSENAITRPGADPAHYLQIKDIVKTYGDNYAVDHINLTIKKNEIFALLGSSGSGKSTLLR
MLAGMETPTQGQIILDGEDITKLQPYDRPINMMFQSYALFPHMTVEQNIAFGLKQDKLPK
DEISARVEEMLRLVQMSKYAKRKPHQLSGGQQQRVALARSLAKRPKLLLLDEPLGALDKK
LRQQTQLELVNTLEKVGATCIMVTHDQEEAMTMASRIAIMSDGQLQQVGTPSDIYDYPNS
RFTAEFMGETNILEGKVTEDGADHTIIHCPEMQQLVYLGHGISGPEDQKIWLSIRPEDIN
IYREQPQQEYNWSAGIVKEIAYLGSFGIFHIQLPSGKIIKSQVLSSYWEQYSIPMPTWEE
KVYISWPDNQVSPLTH

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