Pathway | Step | Score | Similar to | Id. | Cov. | Bits | Other hit | Other id. | Other bits |
L-histidine catabolism | PA5503 | hi | Methionine import ATP-binding protein MetN 2, component of L-Histidine uptake porter, MetIQN (characterized) | 73% | 100% | 477.6 | Methionine import ATP-binding protein MetN; EC 7.4.2.11 | 52% | 315.5 |
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) | 42% | 96% | 186 | Methionine import ATP-binding protein MetN 2, component of L-Histidine uptake porter, MetIQN | 73% | 477.6 |
L-glutamate catabolism | gltL | 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) | 42% | 96% | 186 | Methionine import ATP-binding protein MetN 2, component of L-Histidine uptake porter, MetIQN | 73% | 477.6 |
L-arginine catabolism | artP | med | BgtA aka SLR1735, component of Arginine/lysine/histidine/glutamine porter (characterized) | 43% | 96% | 181.4 | Methionine import ATP-binding protein MetN 2, component of L-Histidine uptake porter, MetIQN | 73% | 477.6 |
L-histidine catabolism | bgtA | med | BgtA aka SLR1735, component of Arginine/lysine/histidine/glutamine porter (characterized) | 43% | 96% | 181.4 | Methionine import ATP-binding protein MetN 2, component of L-Histidine uptake porter, MetIQN | 73% | 477.6 |
L-lysine catabolism | hisP | med | BgtA aka SLR1735, component of Arginine/lysine/histidine/glutamine porter (characterized) | 43% | 96% | 181.4 | Methionine import ATP-binding protein MetN 2, component of L-Histidine uptake porter, MetIQN | 73% | 477.6 |
L-histidine catabolism | hutV | med | ABC transporter for L-Histidine, ATPase component (characterized) | 42% | 83% | 179.1 | Methionine import ATP-binding protein MetN 2, component of L-Histidine uptake porter, MetIQN | 73% | 477.6 |
L-asparagine catabolism | bgtA | med | ATPase (characterized, see rationale) | 41% | 92% | 174.5 | Methionine import ATP-binding protein MetN 2, component of L-Histidine uptake porter, MetIQN | 73% | 477.6 |
L-aspartate catabolism | bgtA | med | ATPase (characterized, see rationale) | 41% | 92% | 174.5 | Methionine import ATP-binding protein MetN 2, component of L-Histidine uptake porter, MetIQN | 73% | 477.6 |
L-histidine catabolism | hisP | med | Histidine transport ATP-binding protein HisP (characterized) | 42% | 95% | 171.4 | Methionine import ATP-binding protein MetN 2, component of L-Histidine uptake porter, MetIQN | 73% | 477.6 |
L-proline catabolism | hutV | med | HutV aka HISV aka R02702 aka SMC00670, component of Uptake system for hisitidine, proline, proline-betaine and glycine-betaine (characterized) | 41% | 85% | 166.8 | Methionine import ATP-binding protein MetN 2, component of L-Histidine uptake porter, MetIQN | 73% | 477.6 |
L-asparagine catabolism | aatP | med | ABC transporter for L-aspartate, L-asparagine, L-glutamate, and L-glutamine, ATPase component (characterized) | 40% | 89% | 161.4 | Methionine import ATP-binding protein MetN 2, component of L-Histidine uptake porter, MetIQN | 73% | 477.6 |
L-aspartate catabolism | aatP | med | ABC transporter for L-aspartate, L-asparagine, L-glutamate, and L-glutamine, ATPase component (characterized) | 40% | 89% | 161.4 | Methionine import ATP-binding protein MetN 2, component of L-Histidine uptake porter, MetIQN | 73% | 477.6 |
L-proline catabolism | proV | lo | glycine betaine/l-proline transport atp-binding protein prov (characterized) | 42% | 60% | 180.6 | Methionine import ATP-binding protein MetN 2, component of L-Histidine uptake porter, MetIQN | 73% | 477.6 |
D-alanine catabolism | Pf6N2E2_5405 | lo | ABC transporter for D-Alanine, ATPase component (characterized) | 39% | 95% | 172.6 | Methionine import ATP-binding protein MetN 2, component of L-Histidine uptake porter, MetIQN | 73% | 477.6 |
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) | 39% | 93% | 171.8 | Methionine import ATP-binding protein MetN 2, component of L-Histidine uptake porter, MetIQN | 73% | 477.6 |
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) | 39% | 93% | 171.8 | Methionine import ATP-binding protein MetN 2, component of L-Histidine uptake porter, MetIQN | 73% | 477.6 |
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) | 39% | 93% | 171.8 | Methionine import ATP-binding protein MetN 2, component of L-Histidine uptake porter, MetIQN | 73% | 477.6 |
L-histidine 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) | 39% | 93% | 171.8 | Methionine import ATP-binding protein MetN 2, component of L-Histidine uptake porter, MetIQN | 73% | 477.6 |
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) | 39% | 93% | 171.8 | Methionine import ATP-binding protein MetN 2, component of L-Histidine uptake porter, MetIQN | 73% | 477.6 |
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) | 39% | 93% | 171.8 | Methionine import ATP-binding protein MetN 2, component of L-Histidine uptake porter, MetIQN | 73% | 477.6 |
D-glucosamine (chitosamine) catabolism | AO353_21725 | lo | ABC transporter for D-glucosamine, ATPase component (characterized) | 39% | 94% | 169.1 | Methionine import ATP-binding protein MetN 2, component of L-Histidine uptake porter, MetIQN | 73% | 477.6 |
L-asparagine catabolism | bztD | lo | BztD, component of Glutamate/glutamine/aspartate/asparagine porter (characterized) | 37% | 90% | 167.9 | Methionine import ATP-binding protein MetN 2, component of L-Histidine uptake porter, MetIQN | 73% | 477.6 |
L-aspartate catabolism | bztD | lo | BztD, component of Glutamate/glutamine/aspartate/asparagine porter (characterized) | 37% | 90% | 167.9 | Methionine import ATP-binding protein MetN 2, component of L-Histidine uptake porter, MetIQN | 73% | 477.6 |
L-citrulline catabolism | AO353_03040 | lo | ABC transporter for L-Arginine and L-Citrulline, ATPase component (characterized) | 38% | 98% | 166.8 | Methionine import ATP-binding protein MetN 2, component of L-Histidine uptake porter, MetIQN | 73% | 477.6 |
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) | 36% | 77% | 163.3 | Methionine import ATP-binding protein MetN 2, component of L-Histidine uptake porter, MetIQN | 73% | 477.6 |
putrescine catabolism | potA | lo | PotG aka B0855, component of Putrescine porter (characterized) | 37% | 64% | 161.4 | Methionine import ATP-binding protein MetN 2, component of L-Histidine uptake porter, MetIQN | 73% | 477.6 |
L-histidine catabolism | BPHYT_RS24015 | lo | ABC transporter related (characterized, see rationale) | 38% | 97% | 157.1 | Methionine import ATP-binding protein MetN 2, component of L-Histidine uptake porter, MetIQN | 73% | 477.6 |
L-asparagine catabolism | peb1C | lo | PEB1C, component of Uptake system for glutamate and aspartate (characterized) | 37% | 98% | 156.4 | Methionine import ATP-binding protein MetN 2, component of L-Histidine uptake porter, MetIQN | 73% | 477.6 |
L-aspartate catabolism | peb1C | lo | PEB1C, component of Uptake system for glutamate and aspartate (characterized) | 37% | 98% | 156.4 | Methionine import ATP-binding protein MetN 2, component of L-Histidine uptake porter, MetIQN | 73% | 477.6 |
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) | 38% | 89% | 156.4 | Methionine import ATP-binding protein MetN 2, component of L-Histidine uptake porter, MetIQN | 73% | 477.6 |
D-maltose catabolism | thuK | lo | Trehalose/maltose import ATP-binding protein MalK; EC 7.5.2.1 (characterized) | 32% | 88% | 154.8 | Methionine import ATP-binding protein MetN 2, component of L-Histidine uptake porter, MetIQN | 73% | 477.6 |
trehalose catabolism | thuK | lo | Trehalose/maltose import ATP-binding protein MalK; EC 7.5.2.1 (characterized) | 32% | 88% | 154.8 | Methionine import ATP-binding protein MetN 2, component of L-Histidine uptake porter, MetIQN | 73% | 477.6 |
L-arabinose catabolism | xacK | lo | Xylose/arabinose import ATP-binding protein XacK; EC 7.5.2.13 (characterized, see rationale) | 33% | 77% | 149.1 | Methionine import ATP-binding protein MetN 2, component of L-Histidine uptake porter, MetIQN | 73% | 477.6 |
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) | 33% | 84% | 147.9 | Methionine import ATP-binding protein MetN 2, component of L-Histidine uptake porter, MetIQN | 73% | 477.6 |
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) | 32% | 84% | 147.5 | Methionine import ATP-binding protein MetN 2, component of L-Histidine uptake porter, MetIQN | 73% | 477.6 |
D-sorbitol (glucitol) catabolism | mtlK | lo | ABC transporter for D-Sorbitol, ATPase component (characterized) | 30% | 85% | 146.4 | Methionine import ATP-binding protein MetN 2, component of L-Histidine uptake porter, MetIQN | 73% | 477.6 |
lactose catabolism | lacK | lo | ABC transporter for Lactose, ATPase component (characterized) | 33% | 80% | 144.8 | Methionine import ATP-binding protein MetN 2, component of L-Histidine uptake porter, MetIQN | 73% | 477.6 |
N-acetyl-D-glucosamine catabolism | SMc02869 | lo | N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized) | 31% | 85% | 143.7 | Methionine import ATP-binding protein MetN 2, component of L-Histidine uptake porter, MetIQN | 73% | 477.6 |
D-glucosamine (chitosamine) catabolism | SMc02869 | lo | N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized) | 31% | 85% | 143.7 | Methionine import ATP-binding protein MetN 2, component of L-Histidine uptake porter, MetIQN | 73% | 477.6 |
xylitol catabolism | Dshi_0546 | lo | ABC transporter for Xylitol, ATPase component (characterized) | 34% | 68% | 143.3 | Methionine import ATP-binding protein MetN 2, component of L-Histidine uptake porter, MetIQN | 73% | 477.6 |
L-fucose catabolism | SM_b21106 | lo | ABC transporter for L-Fucose, ATPase component (characterized) | 33% | 67% | 142.9 | Methionine import ATP-binding protein MetN 2, component of L-Histidine uptake porter, MetIQN | 73% | 477.6 |
D-mannitol catabolism | mtlK | lo | ABC transporter for D-Mannitol, D-Mannose, and D-Mannose, ATPase component (characterized) | 33% | 61% | 142.1 | Methionine import ATP-binding protein MetN 2, component of L-Histidine uptake porter, MetIQN | 73% | 477.6 |
L-tryptophan catabolism | ecfA1 | lo | Energy-coupling factor transporter ATP-binding protein EcfA1; Short=ECF transporter A component EcfA; EC 7.-.-.- (characterized, see rationale) | 38% | 74% | 138.3 | Methionine import ATP-binding protein MetN 2, component of L-Histidine uptake porter, MetIQN | 73% | 477.6 |
D-glucosamine (chitosamine) catabolism | SM_b21216 | lo | ABC transporter for D-Glucosamine, ATPase component (characterized) | 33% | 62% | 137.1 | Methionine import ATP-binding protein MetN 2, component of L-Histidine uptake porter, MetIQN | 73% | 477.6 |
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) | 35% | 77% | 137.1 | Methionine import ATP-binding protein MetN 2, component of L-Histidine uptake porter, MetIQN | 73% | 477.6 |
D-cellobiose catabolism | gtsD | lo | ABC transporter for D-Glucose-6-Phosphate, ATPase component (characterized) | 33% | 61% | 136 | Methionine import ATP-binding protein MetN 2, component of L-Histidine uptake porter, MetIQN | 73% | 477.6 |
D-glucose catabolism | gtsD | lo | ABC transporter for D-Glucose-6-Phosphate, ATPase component (characterized) | 33% | 61% | 136 | Methionine import ATP-binding protein MetN 2, component of L-Histidine uptake porter, MetIQN | 73% | 477.6 |
lactose catabolism | gtsD | lo | ABC transporter for D-Glucose-6-Phosphate, ATPase component (characterized) | 33% | 61% | 136 | Methionine import ATP-binding protein MetN 2, component of L-Histidine uptake porter, MetIQN | 73% | 477.6 |
D-maltose catabolism | gtsD | lo | ABC transporter for D-Glucose-6-Phosphate, ATPase component (characterized) | 33% | 61% | 136 | Methionine import ATP-binding protein MetN 2, component of L-Histidine uptake porter, MetIQN | 73% | 477.6 |
sucrose catabolism | gtsD | lo | ABC transporter for D-Glucose-6-Phosphate, ATPase component (characterized) | 33% | 61% | 136 | Methionine import ATP-binding protein MetN 2, component of L-Histidine uptake porter, MetIQN | 73% | 477.6 |
trehalose catabolism | gtsD | lo | ABC transporter for D-Glucose-6-Phosphate, ATPase component (characterized) | 33% | 61% | 136 | Methionine import ATP-binding protein MetN 2, component of L-Histidine uptake porter, MetIQN | 73% | 477.6 |
D-xylose catabolism | gtsD | lo | ABC transporter for D-Glucose-6-Phosphate, ATPase component (characterized) | 33% | 61% | 136 | Methionine import ATP-binding protein MetN 2, component of L-Histidine uptake porter, MetIQN | 73% | 477.6 |
D-maltose catabolism | malK | lo | ABC-type maltose transporter (subunit 3/3) (EC 7.5.2.1) (characterized) | 33% | 61% | 135.2 | Methionine import ATP-binding protein MetN 2, component of L-Histidine uptake porter, MetIQN | 73% | 477.6 |
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) | 32% | 60% | 134.8 | Methionine import ATP-binding protein MetN 2, component of L-Histidine uptake porter, MetIQN | 73% | 477.6 |
trehalose catabolism | treV | lo | TreV, component of Trehalose porter (characterized) | 32% | 65% | 132.1 | Methionine import ATP-binding protein MetN 2, component of L-Histidine uptake porter, MetIQN | 73% | 477.6 |
D-galactose catabolism | PfGW456L13_1897 | lo | ABC transporter for D-Galactose and D-Glucose, ATPase component (characterized) | 33% | 61% | 131.7 | Methionine import ATP-binding protein MetN 2, component of L-Histidine uptake porter, MetIQN | 73% | 477.6 |
D-maltose catabolism | malK_Bb | lo | ABC-type maltose transport, ATP binding protein (characterized, see rationale) | 31% | 68% | 130.6 | Methionine import ATP-binding protein MetN 2, component of L-Histidine uptake porter, MetIQN | 73% | 477.6 |
sucrose catabolism | thuK | lo | ABC transporter (characterized, see rationale) | 34% | 61% | 130.2 | Methionine import ATP-binding protein MetN 2, component of L-Histidine uptake porter, MetIQN | 73% | 477.6 |
L-tryptophan catabolism | ecfA2 | lo | Energy-coupling factor transporter ATP-binding protein EcfA2; Short=ECF transporter A component EcfA2; EC 7.-.-.- (characterized, see rationale) | 33% | 78% | 127.5 | Methionine import ATP-binding protein MetN 2, component of L-Histidine uptake porter, MetIQN | 73% | 477.6 |
D-cellobiose catabolism | SMc04256 | lo | ABC transporter for D-Cellobiose and D-Salicin, ATPase component (characterized) | 31% | 83% | 126.7 | Methionine import ATP-binding protein MetN 2, component of L-Histidine uptake porter, MetIQN | 73% | 477.6 |
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) | 31% | 66% | 126.7 | Methionine import ATP-binding protein MetN 2, component of L-Histidine uptake porter, MetIQN | 73% | 477.6 |
D-cellobiose catabolism | cbtD | lo | CbtD, component of Cellobiose and cellooligosaccharide porter (characterized) | 34% | 70% | 126.3 | Methionine import ATP-binding protein MetN 2, component of L-Histidine uptake porter, MetIQN | 73% | 477.6 |
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) | 31% | 88% | 122.1 | Methionine import ATP-binding protein MetN 2, component of L-Histidine uptake porter, MetIQN | 73% | 477.6 |
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) | 31% | 60% | 120.6 | Methionine import ATP-binding protein MetN 2, component of L-Histidine uptake porter, MetIQN | 73% | 477.6 |
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% | 93% | 119.8 | Methionine import ATP-binding protein MetN 2, component of L-Histidine uptake porter, MetIQN | 73% | 477.6 |
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% | 93% | 119.8 | Methionine import ATP-binding protein MetN 2, component of L-Histidine uptake porter, MetIQN | 73% | 477.6 |
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% | 93% | 119.8 | Methionine import ATP-binding protein MetN 2, component of L-Histidine uptake porter, MetIQN | 73% | 477.6 |
D-cellobiose catabolism | cbtF | lo | CbtF, component of Cellobiose and cellooligosaccharide porter (characterized) | 31% | 76% | 119.4 | Methionine import ATP-binding protein MetN 2, component of L-Histidine uptake porter, MetIQN | 73% | 477.6 |
D-cellobiose catabolism | mglA | lo | glucose transporter, ATPase component (characterized) | 32% | 85% | 111.7 | Methionine import ATP-binding protein MetN 2, component of L-Histidine uptake porter, MetIQN | 73% | 477.6 |
D-glucose catabolism | mglA | lo | glucose transporter, ATPase component (characterized) | 32% | 85% | 111.7 | Methionine import ATP-binding protein MetN 2, component of L-Histidine uptake porter, MetIQN | 73% | 477.6 |
lactose catabolism | mglA | lo | glucose transporter, ATPase component (characterized) | 32% | 85% | 111.7 | Methionine import ATP-binding protein MetN 2, component of L-Histidine uptake porter, MetIQN | 73% | 477.6 |
D-maltose catabolism | mglA | lo | glucose transporter, ATPase component (characterized) | 32% | 85% | 111.7 | Methionine import ATP-binding protein MetN 2, component of L-Histidine uptake porter, MetIQN | 73% | 477.6 |
sucrose catabolism | mglA | lo | glucose transporter, ATPase component (characterized) | 32% | 85% | 111.7 | Methionine import ATP-binding protein MetN 2, component of L-Histidine uptake porter, MetIQN | 73% | 477.6 |
trehalose catabolism | mglA | lo | glucose transporter, ATPase component (characterized) | 32% | 85% | 111.7 | Methionine import ATP-binding protein MetN 2, component of L-Histidine uptake porter, MetIQN | 73% | 477.6 |
L-phenylalanine catabolism | livG | lo | ABC transporter ATP-binding protein (characterized, see rationale) | 32% | 86% | 110.5 | Methionine import ATP-binding protein MetN 2, component of L-Histidine uptake porter, MetIQN | 73% | 477.6 |
L-proline catabolism | HSERO_RS00895 | lo | ABC transporter ATP-binding protein (characterized, see rationale) | 32% | 86% | 110.5 | Methionine import ATP-binding protein MetN 2, component of L-Histidine uptake porter, MetIQN | 73% | 477.6 |
L-serine catabolism | Ac3H11_1693 | lo | ABC transporter ATP-binding protein (characterized, see rationale) | 32% | 86% | 110.5 | Methionine import ATP-binding protein MetN 2, component of L-Histidine uptake porter, MetIQN | 73% | 477.6 |
L-tyrosine catabolism | Ac3H11_1693 | lo | ABC transporter ATP-binding protein (characterized, see rationale) | 32% | 86% | 110.5 | Methionine import ATP-binding protein MetN 2, component of L-Histidine uptake porter, MetIQN | 73% | 477.6 |
This GapMind analysis is from Apr 09 2024. The underlying query database was built on Sep 17 2021.
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.
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).
If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know