GapMind for catabolism of small carbon sources

 

Protein WP_067078050.1 in Methanoculleus horonobensis T10

Annotation: NCBI__GCF_001602375.1:WP_067078050.1

Length: 349 amino acids

Source: GCF_001602375.1 in NCBI

Candidate for 88 steps in catabolism of small carbon sources

Pathway Step Score Similar to Id. Cov. Bits Other hit Other id. Other bits
D-maltose catabolism musK med ABC-type maltose transporter (EC 7.5.2.1) (characterized) 41% 71% 210.7 WtpC, component of Tungsten (KM=20pM)/molybdate (KM=10nM) porter 45% 298.1
xylitol catabolism HSERO_RS17020 med ABC-type sugar transport system, ATPase component protein (characterized, see rationale) 40% 75% 204.9 WtpC, component of Tungsten (KM=20pM)/molybdate (KM=10nM) porter 45% 298.1
D-cellobiose catabolism SMc04256 med ABC transporter for D-Cellobiose and D-Salicin, ATPase component (characterized) 41% 75% 192.2 WtpC, component of Tungsten (KM=20pM)/molybdate (KM=10nM) porter 45% 298.1
trehalose catabolism treV med TreV, component of Trehalose porter (characterized) 41% 72% 184.5 WtpC, component of Tungsten (KM=20pM)/molybdate (KM=10nM) porter 45% 298.1
D-cellobiose catabolism gtsD lo Sugar ABC transporter ATP-binding protein (characterized, see rationale) 35% 96% 220.3 WtpC, component of Tungsten (KM=20pM)/molybdate (KM=10nM) porter 45% 298.1
L-fucose catabolism SM_b21106 lo ABC transporter for L-Fucose, ATPase component (characterized) 37% 95% 220.3 WtpC, component of Tungsten (KM=20pM)/molybdate (KM=10nM) porter 45% 298.1
D-glucose catabolism gtsD lo Sugar ABC transporter ATP-binding protein (characterized, see rationale) 35% 96% 220.3 WtpC, component of Tungsten (KM=20pM)/molybdate (KM=10nM) porter 45% 298.1
lactose catabolism gtsD lo Sugar ABC transporter ATP-binding protein (characterized, see rationale) 35% 96% 220.3 WtpC, component of Tungsten (KM=20pM)/molybdate (KM=10nM) porter 45% 298.1
D-maltose catabolism gtsD lo Sugar ABC transporter ATP-binding protein (characterized, see rationale) 35% 96% 220.3 WtpC, component of Tungsten (KM=20pM)/molybdate (KM=10nM) porter 45% 298.1
D-sorbitol (glucitol) catabolism mtlK lo ABC transporter for D-Sorbitol, ATPase component (characterized) 39% 96% 220.3 WtpC, component of Tungsten (KM=20pM)/molybdate (KM=10nM) porter 45% 298.1
sucrose catabolism gtsD lo Sugar ABC transporter ATP-binding protein (characterized, see rationale) 35% 96% 220.3 WtpC, component of Tungsten (KM=20pM)/molybdate (KM=10nM) porter 45% 298.1
trehalose catabolism gtsD lo Sugar ABC transporter ATP-binding protein (characterized, see rationale) 35% 96% 220.3 WtpC, component of Tungsten (KM=20pM)/molybdate (KM=10nM) porter 45% 298.1
D-glucosamine (chitosamine) catabolism SM_b21216 lo ABC transporter for D-Glucosamine, ATPase component (characterized) 39% 96% 219.2 WtpC, component of Tungsten (KM=20pM)/molybdate (KM=10nM) porter 45% 298.1
D-mannitol catabolism mtlK lo ABC transporter for D-mannitol and D-mannose, ATPase component (characterized) 38% 95% 216.9 WtpC, component of Tungsten (KM=20pM)/molybdate (KM=10nM) porter 45% 298.1
N-acetyl-D-glucosamine catabolism SMc02869 lo N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized) 36% 89% 214.9 WtpC, component of Tungsten (KM=20pM)/molybdate (KM=10nM) porter 45% 298.1
D-glucosamine (chitosamine) catabolism SMc02869 lo N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized) 36% 89% 214.9 WtpC, component of Tungsten (KM=20pM)/molybdate (KM=10nM) porter 45% 298.1
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) 36% 93% 214.2 WtpC, component of Tungsten (KM=20pM)/molybdate (KM=10nM) porter 45% 298.1
trehalose catabolism thuK 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) 36% 93% 214.2 WtpC, component of Tungsten (KM=20pM)/molybdate (KM=10nM) porter 45% 298.1
D-maltose catabolism malK_Bb lo ABC-type maltose transport, ATP binding protein (characterized, see rationale) 40% 83% 213.8 WtpC, component of Tungsten (KM=20pM)/molybdate (KM=10nM) porter 45% 298.1
putrescine catabolism potA lo PotG aka B0855, component of Putrescine porter (characterized) 38% 90% 212.2 WtpC, component of Tungsten (KM=20pM)/molybdate (KM=10nM) porter 45% 298.1
D-galactose catabolism PfGW456L13_1897 lo ABC transporter for D-Galactose and D-Glucose, ATPase component (characterized) 37% 88% 211.5 WtpC, component of Tungsten (KM=20pM)/molybdate (KM=10nM) porter 45% 298.1
D-xylose catabolism gtsD lo ABC transporter for D-Glucose-6-Phosphate, ATPase component (characterized) 38% 88% 211.5 WtpC, component of Tungsten (KM=20pM)/molybdate (KM=10nM) porter 45% 298.1
sucrose catabolism thuK lo ABC transporter (characterized, see rationale) 37% 82% 210.7 WtpC, component of Tungsten (KM=20pM)/molybdate (KM=10nM) porter 45% 298.1
D-maltose catabolism thuK lo Trehalose/maltose import ATP-binding protein MalK; EC 7.5.2.1 (characterized) 36% 97% 208.4 WtpC, component of Tungsten (KM=20pM)/molybdate (KM=10nM) porter 45% 298.1
L-arabinose catabolism xacK lo Xylose/arabinose import ATP-binding protein XacK; EC 7.5.2.13 (characterized, see rationale) 36% 89% 202.6 WtpC, component of Tungsten (KM=20pM)/molybdate (KM=10nM) porter 45% 298.1
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% 71% 200.7 WtpC, component of Tungsten (KM=20pM)/molybdate (KM=10nM) porter 45% 298.1
xylitol catabolism Dshi_0546 lo ABC transporter for Xylitol, ATPase component (characterized) 39% 74% 199.9 WtpC, component of Tungsten (KM=20pM)/molybdate (KM=10nM) porter 45% 298.1
D-maltose catabolism malK_Aa lo ABC-type maltose transporter (EC 7.5.2.1) (characterized) 36% 88% 199.1 WtpC, component of Tungsten (KM=20pM)/molybdate (KM=10nM) porter 45% 298.1
D-maltose catabolism malK lo Maltose/maltodextrin import ATP-binding protein MalK; EC 7.5.2.1 (characterized) 33% 95% 198.4 WtpC, component of Tungsten (KM=20pM)/molybdate (KM=10nM) porter 45% 298.1
lactose catabolism lacK lo ABC transporter for Lactose, ATPase component (characterized) 37% 90% 197.2 WtpC, component of Tungsten (KM=20pM)/molybdate (KM=10nM) porter 45% 298.1
L-arabinose catabolism xacJ lo Xylose/arabinose import ATP-binding protein XacJ; EC 7.5.2.13 (characterized, see rationale) 39% 74% 194.9 WtpC, component of Tungsten (KM=20pM)/molybdate (KM=10nM) porter 45% 298.1
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) 33% 97% 194.1 WtpC, component of Tungsten (KM=20pM)/molybdate (KM=10nM) porter 45% 298.1
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) 33% 97% 194.1 WtpC, component of Tungsten (KM=20pM)/molybdate (KM=10nM) porter 45% 298.1
D-cellobiose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 38% 84% 189.9 WtpC, component of Tungsten (KM=20pM)/molybdate (KM=10nM) porter 45% 298.1
D-galactose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 38% 84% 189.9 WtpC, component of Tungsten (KM=20pM)/molybdate (KM=10nM) porter 45% 298.1
D-glucose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 38% 84% 189.9 WtpC, component of Tungsten (KM=20pM)/molybdate (KM=10nM) porter 45% 298.1
lactose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 38% 84% 189.9 WtpC, component of Tungsten (KM=20pM)/molybdate (KM=10nM) porter 45% 298.1
D-maltose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 38% 84% 189.9 WtpC, component of Tungsten (KM=20pM)/molybdate (KM=10nM) porter 45% 298.1
D-mannose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 38% 84% 189.9 WtpC, component of Tungsten (KM=20pM)/molybdate (KM=10nM) porter 45% 298.1
sucrose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 38% 84% 189.9 WtpC, component of Tungsten (KM=20pM)/molybdate (KM=10nM) porter 45% 298.1
trehalose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 38% 84% 189.9 WtpC, component of Tungsten (KM=20pM)/molybdate (KM=10nM) porter 45% 298.1
D-cellobiose catabolism aglK' lo Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 33% 94% 188.7 WtpC, component of Tungsten (KM=20pM)/molybdate (KM=10nM) porter 45% 298.1
D-glucose catabolism aglK' lo Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 33% 94% 188.7 WtpC, component of Tungsten (KM=20pM)/molybdate (KM=10nM) porter 45% 298.1
lactose catabolism aglK' lo Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 33% 94% 188.7 WtpC, component of Tungsten (KM=20pM)/molybdate (KM=10nM) porter 45% 298.1
D-maltose catabolism aglK lo Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 33% 94% 188.7 WtpC, component of Tungsten (KM=20pM)/molybdate (KM=10nM) porter 45% 298.1
D-maltose catabolism aglK' lo Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 33% 94% 188.7 WtpC, component of Tungsten (KM=20pM)/molybdate (KM=10nM) porter 45% 298.1
sucrose catabolism aglK lo Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 33% 94% 188.7 WtpC, component of Tungsten (KM=20pM)/molybdate (KM=10nM) porter 45% 298.1
sucrose catabolism aglK' lo Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 33% 94% 188.7 WtpC, component of Tungsten (KM=20pM)/molybdate (KM=10nM) porter 45% 298.1
trehalose catabolism aglK lo Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 33% 94% 188.7 WtpC, component of Tungsten (KM=20pM)/molybdate (KM=10nM) porter 45% 298.1
trehalose catabolism aglK' lo Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 33% 94% 188.7 WtpC, component of Tungsten (KM=20pM)/molybdate (KM=10nM) porter 45% 298.1
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) 34% 94% 185.3 WtpC, component of Tungsten (KM=20pM)/molybdate (KM=10nM) porter 45% 298.1
L-arabinose catabolism araV lo AraV, component of Arabinose, fructose, xylose porter (characterized) 38% 73% 181.8 WtpC, component of Tungsten (KM=20pM)/molybdate (KM=10nM) porter 45% 298.1
D-fructose catabolism araV lo AraV, component of Arabinose, fructose, xylose porter (characterized) 38% 73% 181.8 WtpC, component of Tungsten (KM=20pM)/molybdate (KM=10nM) porter 45% 298.1
sucrose catabolism araV lo AraV, component of Arabinose, fructose, xylose porter (characterized) 38% 73% 181.8 WtpC, component of Tungsten (KM=20pM)/molybdate (KM=10nM) porter 45% 298.1
D-xylose catabolism araV lo AraV, component of Arabinose, fructose, xylose porter (characterized) 38% 73% 181.8 WtpC, component of Tungsten (KM=20pM)/molybdate (KM=10nM) porter 45% 298.1
glycerol catabolism glpT lo ABC transporter for Glycerol, ATPase component 2 (characterized) 34% 84% 168.3 WtpC, component of Tungsten (KM=20pM)/molybdate (KM=10nM) porter 45% 298.1
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) 35% 74% 161.4 WtpC, component of Tungsten (KM=20pM)/molybdate (KM=10nM) porter 45% 298.1
glycerol catabolism glpS lo GlpS, component of Glycerol uptake porter, GlpSTPQV (characterized) 40% 63% 154.1 WtpC, component of Tungsten (KM=20pM)/molybdate (KM=10nM) porter 45% 298.1
L-proline catabolism HSERO_RS00895 lo ABC-type branched-chain amino acid transport system, ATPase component protein (characterized, see rationale) 34% 97% 142.5 WtpC, component of Tungsten (KM=20pM)/molybdate (KM=10nM) porter 45% 298.1
L-isoleucine catabolism livG lo ABC transporter ATP-binding protein (characterized, see rationale) 34% 95% 134.4 WtpC, component of Tungsten (KM=20pM)/molybdate (KM=10nM) porter 45% 298.1
L-leucine catabolism livG lo ABC transporter ATP-binding protein (characterized, see rationale) 34% 95% 134.4 WtpC, component of Tungsten (KM=20pM)/molybdate (KM=10nM) porter 45% 298.1
L-phenylalanine catabolism livG lo ABC transporter ATP-binding protein (characterized, see rationale) 34% 95% 134.4 WtpC, component of Tungsten (KM=20pM)/molybdate (KM=10nM) porter 45% 298.1
L-serine catabolism Ac3H11_1693 lo ABC transporter ATP-binding protein (characterized, see rationale) 34% 95% 134.4 WtpC, component of Tungsten (KM=20pM)/molybdate (KM=10nM) porter 45% 298.1
L-tyrosine catabolism Ac3H11_1693 lo ABC transporter ATP-binding protein (characterized, see rationale) 34% 95% 134.4 WtpC, component of Tungsten (KM=20pM)/molybdate (KM=10nM) porter 45% 298.1
D-fructose catabolism fruK lo Fructose import ATP-binding protein FruK; EC 7.5.2.- (characterized) 31% 53% 119.8 WtpC, component of Tungsten (KM=20pM)/molybdate (KM=10nM) porter 45% 298.1
sucrose catabolism fruK lo Fructose import ATP-binding protein FruK; EC 7.5.2.- (characterized) 31% 53% 119.8 WtpC, component of Tungsten (KM=20pM)/molybdate (KM=10nM) porter 45% 298.1
L-alanine catabolism braF lo High-affinity branched-chain amino acid transport ATP-binding protein BraF, component of Branched chain amino acid uptake transporter. Transports alanine (characterized) 31% 98% 119.4 WtpC, component of Tungsten (KM=20pM)/molybdate (KM=10nM) porter 45% 298.1
L-serine catabolism braF lo High-affinity branched-chain amino acid transport ATP-binding protein BraF, component of Branched chain amino acid uptake transporter. Transports alanine (characterized) 31% 98% 119.4 WtpC, component of Tungsten (KM=20pM)/molybdate (KM=10nM) porter 45% 298.1
L-threonine catabolism braF lo High-affinity branched-chain amino acid transport ATP-binding protein BraF, component of Branched chain amino acid uptake transporter. Transports alanine (characterized) 31% 98% 119.4 WtpC, component of Tungsten (KM=20pM)/molybdate (KM=10nM) porter 45% 298.1
L-valine catabolism livG lo High-affinity branched-chain amino acid transport ATP-binding protein BraF, component of Branched chain amino acid uptake transporter. Transports alanine (characterized) 31% 98% 119.4 WtpC, component of Tungsten (KM=20pM)/molybdate (KM=10nM) porter 45% 298.1
L-alanine catabolism braG lo NatE aka LivF aka SLR1881, component of Leucine/proline/alanine/serine/glycine (and possibly histidine) porter, NatABCDE (characterized) 34% 86% 110.5 WtpC, component of Tungsten (KM=20pM)/molybdate (KM=10nM) porter 45% 298.1
L-histidine catabolism natE lo NatE aka LivF aka SLR1881, component of Leucine/proline/alanine/serine/glycine (and possibly histidine) porter, NatABCDE (characterized) 34% 86% 110.5 WtpC, component of Tungsten (KM=20pM)/molybdate (KM=10nM) porter 45% 298.1
L-leucine catabolism natE lo NatE aka LivF aka SLR1881, component of Leucine/proline/alanine/serine/glycine (and possibly histidine) porter, NatABCDE (characterized) 34% 86% 110.5 WtpC, component of Tungsten (KM=20pM)/molybdate (KM=10nM) porter 45% 298.1
L-proline catabolism natE lo NatE aka LivF aka SLR1881, component of Leucine/proline/alanine/serine/glycine (and possibly histidine) porter, NatABCDE (characterized) 34% 86% 110.5 WtpC, component of Tungsten (KM=20pM)/molybdate (KM=10nM) porter 45% 298.1
L-serine catabolism braG lo NatE aka LivF aka SLR1881, component of Leucine/proline/alanine/serine/glycine (and possibly histidine) porter, NatABCDE (characterized) 34% 86% 110.5 WtpC, component of Tungsten (KM=20pM)/molybdate (KM=10nM) porter 45% 298.1
L-threonine catabolism braG lo NatE aka LivF aka SLR1881, component of Leucine/proline/alanine/serine/glycine (and possibly histidine) porter, NatABCDE (characterized) 34% 86% 110.5 WtpC, component of Tungsten (KM=20pM)/molybdate (KM=10nM) porter 45% 298.1
D-alanine catabolism AZOBR_RS08250 lo Leucine//isoleucine/valine ABC transporter,ATPase component; EC 3.6.3.- (characterized, see rationale) 33% 94% 109.4 WtpC, component of Tungsten (KM=20pM)/molybdate (KM=10nM) porter 45% 298.1
L-proline catabolism AZOBR_RS08250 lo Leucine//isoleucine/valine ABC transporter,ATPase component; EC 3.6.3.- (characterized, see rationale) 33% 94% 109.4 WtpC, component of Tungsten (KM=20pM)/molybdate (KM=10nM) porter 45% 298.1
L-isoleucine catabolism livF lo ABC transporter ATP-binding protein (characterized, see rationale) 30% 96% 109 WtpC, component of Tungsten (KM=20pM)/molybdate (KM=10nM) porter 45% 298.1
L-leucine catabolism livF lo ABC transporter ATP-binding protein (characterized, see rationale) 30% 96% 109 WtpC, component of Tungsten (KM=20pM)/molybdate (KM=10nM) porter 45% 298.1
L-phenylalanine catabolism livF lo ABC transporter ATP-binding protein (characterized, see rationale) 30% 96% 109 WtpC, component of Tungsten (KM=20pM)/molybdate (KM=10nM) porter 45% 298.1
L-proline catabolism HSERO_RS00900 lo ABC transporter ATP-binding protein (characterized, see rationale) 30% 96% 109 WtpC, component of Tungsten (KM=20pM)/molybdate (KM=10nM) porter 45% 298.1
L-serine catabolism Ac3H11_1692 lo ABC transporter ATP-binding protein (characterized, see rationale) 30% 96% 109 WtpC, component of Tungsten (KM=20pM)/molybdate (KM=10nM) porter 45% 298.1
L-tyrosine catabolism Ac3H11_1692 lo ABC transporter ATP-binding protein (characterized, see rationale) 30% 96% 109 WtpC, component of Tungsten (KM=20pM)/molybdate (KM=10nM) porter 45% 298.1
L-arginine catabolism braG lo ATP-binding component of a broad range amino acid ABC transporter (characterized, see rationale) 33% 94% 107.1 WtpC, component of Tungsten (KM=20pM)/molybdate (KM=10nM) porter 45% 298.1
L-glutamate catabolism braG lo ATP-binding component of a broad range amino acid ABC transporter (characterized, see rationale) 33% 94% 107.1 WtpC, component of Tungsten (KM=20pM)/molybdate (KM=10nM) porter 45% 298.1
L-histidine catabolism braG lo ATP-binding component of a broad range amino acid ABC transporter (characterized, see rationale) 33% 94% 107.1 WtpC, component of Tungsten (KM=20pM)/molybdate (KM=10nM) porter 45% 298.1
L-valine catabolism livF lo ATP-binding component of a broad range amino acid ABC transporter (characterized, see rationale) 33% 94% 107.1 WtpC, component of Tungsten (KM=20pM)/molybdate (KM=10nM) porter 45% 298.1

Sequence Analysis Tools

View WP_067078050.1 at NCBI

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Find functional residues: SitesBLAST

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Predict transmenbrane helices: Phobius

Predict protein localization: PSORTb

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Sequence

MLRIAGLAKRLGDFALDGVDLTVADGEYFVVLGPTGAGKTILLETLAGIYAPDAGTIDLD
GRDITHTDPKDRGIGMVYQDYMLFPHLTVGENIGFGLKQGKADPARIRESVQETAALLGI
GHLLERTTGTLSGGEQQRAAIARALVLRPRVLLLDEPLSALDTVTRERLRRELKAIHRAT
GTTVIHITHHFEDIFALADRVAVMQDGRIVQAGTPDEVFRRPATEFVAAFTGMENVYCGV
SRVRNGEAAIDLGEIVVRTVTAIEGDVCVGIRPEEVILSRRPFESSAANTFPGTVAEIRQ
NGMFSRVVVDTGLLFVAVLTRQSVARLGLVEGEPASVTFKASAVHVFKR

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