GapMind for catabolism of small carbon sources

 

Protein WP_143709778.1 in Nautilia profundicola AmH

Annotation: NCBI__GCF_000021725.1:WP_143709778.1

Length: 242 amino acids

Source: GCF_000021725.1 in NCBI

Candidate for 84 steps in catabolism of small carbon sources

Pathway Step Score Similar to Id. Cov. Bits Other hit Other id. Other bits
L-histidine catabolism aapP med ABC transporter for L-Glutamine, L-Histidine, and other L-amino acids, ATPase component (characterized) 67% 93% 336.3 ABC transporter for D-Alanine, ATPase component 66% 335.1
D-alanine catabolism Pf6N2E2_5405 med ABC transporter for D-Alanine, ATPase component (characterized) 66% 95% 335.1 ABC transporter for L-Glutamine, L-Histidine, and other L-amino acids, ATPase component 67% 336.3
L-asparagine catabolism bztD med BztD, component of Glutamate/glutamine/aspartate/asparagine porter (characterized) 66% 92% 334 ABC transporter for D-Alanine, ATPase component 66% 335.1
L-aspartate catabolism bztD med BztD, component of Glutamate/glutamine/aspartate/asparagine porter (characterized) 66% 92% 334 ABC transporter for D-Alanine, ATPase component 66% 335.1
L-glutamate catabolism gltL med BztD, component of Glutamate/glutamine/aspartate/asparagine porter (characterized) 66% 92% 334 ABC transporter for D-Alanine, ATPase component 66% 335.1
L-asparagine catabolism aapP med 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) 66% 93% 333.2 ABC transporter for D-Alanine, ATPase component 66% 335.1
L-aspartate catabolism aapP med 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) 66% 93% 333.2 ABC transporter for D-Alanine, ATPase component 66% 335.1
L-glutamate catabolism aapP med 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) 66% 93% 333.2 ABC transporter for D-Alanine, ATPase component 66% 335.1
L-leucine catabolism aapP med 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) 66% 93% 333.2 ABC transporter for D-Alanine, ATPase component 66% 335.1
L-proline catabolism aapP med 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) 66% 93% 333.2 ABC transporter for D-Alanine, ATPase component 66% 335.1
L-asparagine catabolism aatP med ABC transporter for L-asparagine and L-glutamate, ATPase component (characterized) 59% 100% 299.3 ABC transporter for L-Glutamine, L-Histidine, and other L-amino acids, ATPase component 67% 336.3
L-aspartate catabolism aatP med ABC transporter for L-asparagine and L-glutamate, ATPase component (characterized) 59% 100% 299.3 ABC transporter for L-Glutamine, L-Histidine, and other L-amino acids, ATPase component 67% 336.3
L-lysine catabolism hisP med Amino-acid ABC transporter, ATP-binding protein (characterized, see rationale) 56% 93% 294.7 ABC transporter for L-Glutamine, L-Histidine, and other L-amino acids, ATPase component 67% 336.3
L-asparagine catabolism bgtA med ATPase (characterized, see rationale) 59% 92% 291.6 ABC transporter for L-Glutamine, L-Histidine, and other L-amino acids, ATPase component 67% 336.3
L-aspartate catabolism bgtA med ATPase (characterized, see rationale) 59% 92% 291.6 ABC transporter for L-Glutamine, L-Histidine, and other L-amino acids, ATPase component 67% 336.3
L-asparagine catabolism peb1C med PEB1C, component of Uptake system for glutamate and aspartate (characterized) 59% 100% 288.9 ABC transporter for L-Glutamine, L-Histidine, and other L-amino acids, ATPase component 67% 336.3
L-aspartate catabolism peb1C med PEB1C, component of Uptake system for glutamate and aspartate (characterized) 59% 100% 288.9 ABC transporter for L-Glutamine, L-Histidine, and other L-amino acids, ATPase component 67% 336.3
L-asparagine catabolism glnQ med 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) 56% 98% 280.4 ABC transporter for L-Glutamine, L-Histidine, and other L-amino acids, ATPase component 67% 336.3
L-arginine catabolism artP med Arginine transport ATP-binding protein ArtM (characterized) 56% 100% 272.7 ABC transporter for L-Glutamine, L-Histidine, and other L-amino acids, ATPase component 67% 336.3
L-histidine catabolism bgtA med BgtA aka SLR1735, component of Arginine/lysine/histidine/glutamine porter (characterized) 54% 96% 261.2 ABC transporter for L-Glutamine, L-Histidine, and other L-amino acids, ATPase component 67% 336.3
L-histidine catabolism hisP med 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) 49% 96% 245.7 ABC transporter for L-Glutamine, L-Histidine, and other L-amino acids, ATPase component 67% 336.3
D-glucosamine (chitosamine) catabolism AO353_21725 med ABC transporter for D-Glucosamine, putative ATPase component (characterized) 49% 94% 241.9 ABC transporter for L-Glutamine, L-Histidine, and other L-amino acids, ATPase component 67% 336.3
L-citrulline catabolism AO353_03040 med ABC transporter for L-Arginine and L-Citrulline, ATPase component (characterized) 48% 98% 238.8 ABC transporter for L-Glutamine, L-Histidine, and other L-amino acids, ATPase component 67% 336.3
L-histidine catabolism BPHYT_RS24015 med ABC transporter related (characterized, see rationale) 46% 94% 238.8 ABC transporter for L-Glutamine, L-Histidine, and other L-amino acids, ATPase component 67% 336.3
L-citrulline catabolism PS417_17605 med 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) 48% 90% 232.3 ABC transporter for L-Glutamine, L-Histidine, and other L-amino acids, ATPase component 67% 336.3
L-histidine catabolism PA5503 med Methionine import ATP-binding protein MetN 2, component of L-Histidine uptake porter, MetIQN (characterized) 42% 73% 186.8 ABC transporter for L-Glutamine, L-Histidine, and other L-amino acids, ATPase component 67% 336.3
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) 41% 58% 176 ABC transporter for L-Glutamine, L-Histidine, and other L-amino acids, ATPase component 67% 336.3
D-sorbitol (glucitol) catabolism mtlK lo ABC transporter for D-Sorbitol, ATPase component (characterized) 36% 66% 168.3 ABC transporter for L-Glutamine, L-Histidine, and other L-amino acids, ATPase component 67% 336.3
L-proline catabolism proV lo glycine betaine/l-proline transport atp-binding protein prov (characterized) 38% 56% 167.2 ABC transporter for L-Glutamine, L-Histidine, and other L-amino acids, ATPase component 67% 336.3
putrescine catabolism potA lo spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31 (characterized) 37% 62% 163.7 ABC transporter for L-Glutamine, L-Histidine, and other L-amino acids, ATPase component 67% 336.3
N-acetyl-D-glucosamine catabolism SMc02869 lo N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized) 37% 70% 161.8 ABC transporter for L-Glutamine, L-Histidine, and other L-amino acids, ATPase component 67% 336.3
D-glucosamine (chitosamine) catabolism SMc02869 lo N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized) 37% 70% 161.8 ABC transporter for L-Glutamine, L-Histidine, and other L-amino acids, ATPase component 67% 336.3
D-maltose catabolism malK_Bb lo ABC-type maltose transport, ATP binding protein (characterized, see rationale) 36% 67% 161 ABC transporter for L-Glutamine, L-Histidine, and other L-amino acids, ATPase component 67% 336.3
D-cellobiose catabolism gtsD lo ABC transporter for D-Galactose and D-Glucose, ATPase component (characterized) 38% 58% 160.2 ABC transporter for L-Glutamine, L-Histidine, and other L-amino acids, ATPase component 67% 336.3
D-galactose catabolism PfGW456L13_1897 lo ABC transporter for D-Galactose and D-Glucose, ATPase component (characterized) 38% 58% 160.2 ABC transporter for L-Glutamine, L-Histidine, and other L-amino acids, ATPase component 67% 336.3
D-glucose catabolism gtsD lo ABC transporter for D-Galactose and D-Glucose, ATPase component (characterized) 38% 58% 160.2 ABC transporter for L-Glutamine, L-Histidine, and other L-amino acids, ATPase component 67% 336.3
lactose catabolism gtsD lo ABC transporter for D-Galactose and D-Glucose, ATPase component (characterized) 38% 58% 160.2 ABC transporter for L-Glutamine, L-Histidine, and other L-amino acids, ATPase component 67% 336.3
D-maltose catabolism gtsD lo ABC transporter for D-Galactose and D-Glucose, ATPase component (characterized) 38% 58% 160.2 ABC transporter for L-Glutamine, L-Histidine, and other L-amino acids, ATPase component 67% 336.3
sucrose catabolism gtsD lo ABC transporter for D-Galactose and D-Glucose, ATPase component (characterized) 38% 58% 160.2 ABC transporter for L-Glutamine, L-Histidine, and other L-amino acids, ATPase component 67% 336.3
trehalose catabolism gtsD lo ABC transporter for D-Galactose and D-Glucose, ATPase component (characterized) 38% 58% 160.2 ABC transporter for L-Glutamine, L-Histidine, and other L-amino acids, ATPase component 67% 336.3
D-xylose catabolism gtsD lo ABC transporter for D-Glucose-6-Phosphate, ATPase component (characterized) 36% 61% 159.8 ABC transporter for L-Glutamine, L-Histidine, and other L-amino acids, ATPase component 67% 336.3
lactose catabolism lacK lo ABC transporter for Lactose, ATPase component (characterized) 38% 62% 159.5 ABC transporter for L-Glutamine, L-Histidine, and other L-amino acids, ATPase component 67% 336.3
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) 37% 61% 157.5 ABC transporter for L-Glutamine, L-Histidine, and other L-amino acids, ATPase component 67% 336.3
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) 37% 61% 157.5 ABC transporter for L-Glutamine, L-Histidine, and other L-amino acids, ATPase component 67% 336.3
L-histidine catabolism hutV lo ABC transporter for L-Histidine, ATPase component (characterized) 37% 87% 154.8 ABC transporter for L-Glutamine, L-Histidine, and other L-amino acids, ATPase component 67% 336.3
D-maltose catabolism malK lo Maltose-transporting ATPase (EC 3.6.3.19) (characterized) 35% 63% 154.1 ABC transporter for L-Glutamine, L-Histidine, and other L-amino acids, ATPase component 67% 336.3
D-cellobiose catabolism aglK' lo Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 34% 63% 153.3 ABC transporter for L-Glutamine, L-Histidine, and other L-amino acids, ATPase component 67% 336.3
D-glucose catabolism aglK' lo Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 34% 63% 153.3 ABC transporter for L-Glutamine, L-Histidine, and other L-amino acids, ATPase component 67% 336.3
lactose catabolism aglK' lo Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 34% 63% 153.3 ABC transporter for L-Glutamine, L-Histidine, and other L-amino acids, ATPase component 67% 336.3
D-maltose catabolism aglK lo Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 34% 63% 153.3 ABC transporter for L-Glutamine, L-Histidine, and other L-amino acids, ATPase component 67% 336.3
D-maltose catabolism aglK' lo Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 34% 63% 153.3 ABC transporter for L-Glutamine, L-Histidine, and other L-amino acids, ATPase component 67% 336.3
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% 87% 153.3 ABC transporter for L-Glutamine, L-Histidine, and other L-amino acids, ATPase component 67% 336.3
sucrose catabolism aglK lo Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 34% 63% 153.3 ABC transporter for L-Glutamine, L-Histidine, and other L-amino acids, ATPase component 67% 336.3
sucrose catabolism aglK' lo Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 34% 63% 153.3 ABC transporter for L-Glutamine, L-Histidine, and other L-amino acids, ATPase component 67% 336.3
trehalose catabolism aglK lo Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 34% 63% 153.3 ABC transporter for L-Glutamine, L-Histidine, and other L-amino acids, ATPase component 67% 336.3
trehalose catabolism aglK' lo Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 34% 63% 153.3 ABC transporter for L-Glutamine, L-Histidine, and other L-amino acids, ATPase component 67% 336.3
L-fucose catabolism SM_b21106 lo ABC transporter for L-Fucose, ATPase component (characterized) 35% 64% 152.5 ABC transporter for L-Glutamine, L-Histidine, and other L-amino acids, ATPase component 67% 336.3
D-mannitol catabolism mtlK lo SmoK aka POLK, component of Hexitol (glucitol; mannitol) porter (characterized) 34% 67% 151.4 ABC transporter for L-Glutamine, L-Histidine, and other L-amino acids, ATPase component 67% 336.3
D-maltose catabolism thuK lo ThuK aka RB0314 aka SMB20328, component of Trehalose/maltose/sucrose porter (trehalose inducible) (characterized) 36% 66% 150.2 ABC transporter for L-Glutamine, L-Histidine, and other L-amino acids, ATPase component 67% 336.3
sucrose catabolism thuK lo ThuK aka RB0314 aka SMB20328, component of Trehalose/maltose/sucrose porter (trehalose inducible) (characterized) 36% 66% 150.2 ABC transporter for L-Glutamine, L-Histidine, and other L-amino acids, ATPase component 67% 336.3
xylitol catabolism Dshi_0546 lo ABC transporter for Xylitol, ATPase component (characterized) 33% 68% 148.3 ABC transporter for L-Glutamine, L-Histidine, and other L-amino acids, ATPase component 67% 336.3
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) 35% 61% 147.9 ABC transporter for L-Glutamine, L-Histidine, and other L-amino acids, ATPase component 67% 336.3
L-arabinose catabolism xacJ lo Xylose/arabinose import ATP-binding protein XacJ; EC 7.5.2.13 (characterized, see rationale) 34% 61% 141 ABC transporter for L-Glutamine, L-Histidine, and other L-amino acids, ATPase component 67% 336.3
D-mannose catabolism TM1749 lo TM1749, component of Probable mannose/mannoside porter. Induced by beta-mannan (Conners et al., 2005). Regulated by mannose-responsive regulator manR (characterized) 34% 80% 139.8 ABC transporter for L-Glutamine, L-Histidine, and other L-amino acids, ATPase component 67% 336.3
D-glucosamine (chitosamine) catabolism SM_b21216 lo ABC transporter for D-Glucosamine, ATPase component (characterized) 33% 62% 137.9 ABC transporter for L-Glutamine, L-Histidine, and other L-amino acids, ATPase component 67% 336.3
D-cellobiose catabolism SMc04256 lo ABC transporter for D-Cellobiose and D-Salicin, ATPase component (characterized) 35% 62% 137.5 ABC transporter for L-Glutamine, L-Histidine, and other L-amino acids, ATPase component 67% 336.3
D-cellobiose catabolism cbtF lo CbtF, component of Cellobiose and cellooligosaccharide porter (characterized) 37% 70% 137.5 ABC transporter for L-Glutamine, L-Histidine, and other L-amino acids, ATPase component 67% 336.3
xylitol catabolism HSERO_RS17020 lo ABC-type sugar transport system, ATPase component protein (characterized, see rationale) 34% 57% 136 ABC transporter for L-Glutamine, L-Histidine, and other L-amino acids, ATPase component 67% 336.3
D-cellobiose catabolism TM0027 lo TM0027, component of β-glucoside porter (Conners et al., 2005). Binds cellobiose, laminaribiose (Nanavati et al. 2006). Regulated by cellobiose-responsive repressor BglR (characterized) 36% 88% 134.8 ABC transporter for L-Glutamine, L-Histidine, and other L-amino acids, ATPase component 67% 336.3
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% 64% 133.3 ABC transporter for L-Glutamine, L-Histidine, and other L-amino acids, ATPase component 67% 336.3
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% 64% 133.3 ABC transporter for L-Glutamine, L-Histidine, and other L-amino acids, ATPase component 67% 336.3
L-arabinose catabolism xylGsa lo Xylose/arabinose import ATP-binding protein XylG; EC 7.5.2.13 (characterized, see rationale) 35% 89% 131.7 ABC transporter for L-Glutamine, L-Histidine, and other L-amino acids, ATPase component 67% 336.3
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) 32% 76% 131.7 ABC transporter for L-Glutamine, L-Histidine, and other L-amino acids, ATPase component 67% 336.3
L-tryptophan catabolism ecfA2 lo Energy-coupling factor transporter ATP-binding protein EcfA2; Short=ECF transporter A component EcfA2; EC 7.-.-.- (characterized, see rationale) 37% 77% 131.3 ABC transporter for L-Glutamine, L-Histidine, and other L-amino acids, ATPase component 67% 336.3
L-tryptophan catabolism ecfA1 lo Energy-coupling factor transporter ATP-binding protein EcfA1; Short=ECF transporter A component EcfA; EC 7.-.-.- (characterized, see rationale) 36% 81% 129 ABC transporter for L-Glutamine, L-Histidine, and other L-amino acids, ATPase component 67% 336.3
D-cellobiose catabolism cbtD lo CbtD, component of Cellobiose and cellooligosaccharide porter (characterized) 36% 70% 124 ABC transporter for L-Glutamine, L-Histidine, and other L-amino acids, ATPase component 67% 336.3
L-histidine catabolism Ac3H11_2560 lo ABC transporter for L-Histidine, ATPase component (characterized) 37% 76% 121.7 ABC transporter for L-Glutamine, L-Histidine, and other L-amino acids, ATPase component 67% 336.3
citrate catabolism fecE lo iron(III) dicitrate transport ATP-binding protein FecE (characterized) 30% 87% 106.7 ABC transporter for L-Glutamine, L-Histidine, and other L-amino acids, ATPase component 67% 336.3
D-cellobiose catabolism mglA lo glucose transporter, ATPase component (characterized) 31% 84% 104 ABC transporter for L-Glutamine, L-Histidine, and other L-amino acids, ATPase component 67% 336.3
D-glucose catabolism mglA lo glucose transporter, ATPase component (characterized) 31% 84% 104 ABC transporter for L-Glutamine, L-Histidine, and other L-amino acids, ATPase component 67% 336.3
lactose catabolism mglA lo glucose transporter, ATPase component (characterized) 31% 84% 104 ABC transporter for L-Glutamine, L-Histidine, and other L-amino acids, ATPase component 67% 336.3
D-maltose catabolism mglA lo glucose transporter, ATPase component (characterized) 31% 84% 104 ABC transporter for L-Glutamine, L-Histidine, and other L-amino acids, ATPase component 67% 336.3
sucrose catabolism mglA lo glucose transporter, ATPase component (characterized) 31% 84% 104 ABC transporter for L-Glutamine, L-Histidine, and other L-amino acids, ATPase component 67% 336.3
trehalose catabolism mglA lo glucose transporter, ATPase component (characterized) 31% 84% 104 ABC transporter for L-Glutamine, L-Histidine, and other L-amino acids, ATPase component 67% 336.3

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Sequence

MIQMKDIEKYYGNFHALKGVNFNVDKGEVVVVCGPSGSGKSTLIRCINRLEDIDSGKIVV
DGQDLYNKKTNINKLRQEVGMVFQHFNLFPHLTIMENITIAPIKVKKMPKKEAEELAMQL
LERVKIPHQANKYPSELSGGQKQRVAIARTLAMKPKIILFDEPTSALDPEMIGEVLDVMK
ELARENYTIVCVTHEMGFAREVSDRIVFMDAGEIVEENTPEEFFNNPKTDRAKKFLSEIL
HH

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