| Pathway | Step | Score | Similar to | Id. | Cov. | Bits | Other hit | Other id. | Other bits |
|---|
| L-proline catabolism | opuBA | med | 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) | 45% | 73% | 197.6 | Carnitine transport ATP-binding protein OpuCA; EC 7.6.2.9 | 45% | 221.9 |
| L-lysine catabolism | hisP | med | Amino-acid ABC transporter, ATP-binding protein (characterized, see rationale) | 41% | 91% | 167.9 | Carnitine transport ATP-binding protein OpuCA; EC 7.6.2.9 | 45% | 221.9 |
| L-glutamate catabolism | gltL | med | GluA aka CGL1950, component of Glutamate porter (characterized) | 42% | 91% | 162.5 | Carnitine transport ATP-binding protein OpuCA; EC 7.6.2.9 | 45% | 221.9 |
| L-asparagine catabolism | aatP | med | ABC transporter for L-asparagine and L-glutamate, ATPase component (characterized) | 41% | 89% | 160.2 | Carnitine transport ATP-binding protein OpuCA; EC 7.6.2.9 | 45% | 221.9 |
| L-aspartate catabolism | aatP | med | ABC transporter for L-asparagine and L-glutamate, ATPase component (characterized) | 41% | 89% | 160.2 | Carnitine transport ATP-binding protein OpuCA; EC 7.6.2.9 | 45% | 221.9 |
| putrescine catabolism | potA | lo | spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31 (characterized) | 42% | 58% | 171.8 | Carnitine transport ATP-binding protein OpuCA; EC 7.6.2.9 | 45% | 221.9 |
| N-acetyl-D-glucosamine catabolism | SMc02869 | lo | N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized) | 43% | 63% | 166.4 | Carnitine transport ATP-binding protein OpuCA; EC 7.6.2.9 | 45% | 221.9 |
| D-glucosamine (chitosamine) catabolism | SMc02869 | lo | N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized) | 43% | 63% | 166.4 | Carnitine transport ATP-binding protein OpuCA; EC 7.6.2.9 | 45% | 221.9 |
| xylitol catabolism | Dshi_0546 | lo | ABC transporter for Xylitol, ATPase component (characterized) | 37% | 75% | 164.1 | Carnitine transport ATP-binding protein OpuCA; EC 7.6.2.9 | 45% | 221.9 |
| L-asparagine catabolism | bztD | lo | BztD, component of Glutamate/glutamine/aspartate/asparagine porter (characterized) | 37% | 90% | 160.6 | Carnitine transport ATP-binding protein OpuCA; EC 7.6.2.9 | 45% | 221.9 |
| L-aspartate catabolism | bztD | lo | BztD, component of Glutamate/glutamine/aspartate/asparagine porter (characterized) | 37% | 90% | 160.6 | Carnitine transport ATP-binding protein OpuCA; EC 7.6.2.9 | 45% | 221.9 |
| D-sorbitol (glucitol) catabolism | mtlK | lo | ABC transporter for D-Sorbitol, ATPase component (characterized) | 36% | 76% | 159.1 | Carnitine transport ATP-binding protein OpuCA; EC 7.6.2.9 | 45% | 221.9 |
| lactose catabolism | lacK | lo | ABC transporter for Lactose, ATPase component (characterized) | 39% | 68% | 157.1 | Carnitine transport ATP-binding protein OpuCA; EC 7.6.2.9 | 45% | 221.9 |
| sucrose catabolism | thuK | lo | ABC transporter (characterized, see rationale) | 38% | 63% | 157.1 | Carnitine transport ATP-binding protein OpuCA; EC 7.6.2.9 | 45% | 221.9 |
| L-histidine catabolism | PA5503 | lo | Methionine import ATP-binding protein MetN 2, component of L-Histidine uptake porter, MetIQN (characterized) | 45% | 66% | 156.4 | Carnitine transport ATP-binding protein OpuCA; EC 7.6.2.9 | 45% | 221.9 |
| D-maltose catabolism | malK | lo | ABC-type maltose transporter (subunit 3/3) (EC 7.5.2.1) (characterized) | 38% | 63% | 155.6 | Carnitine transport ATP-binding protein OpuCA; EC 7.6.2.9 | 45% | 221.9 |
| L-fucose catabolism | SM_b21106 | lo | ABC transporter for L-Fucose, ATPase component (characterized) | 41% | 57% | 154.8 | Carnitine transport ATP-binding protein OpuCA; EC 7.6.2.9 | 45% | 221.9 |
| L-asparagine catabolism | bgtA | lo | ATPase (characterized, see rationale) | 38% | 91% | 153.7 | Carnitine transport ATP-binding protein OpuCA; EC 7.6.2.9 | 45% | 221.9 |
| L-aspartate catabolism | bgtA | lo | ATPase (characterized, see rationale) | 38% | 91% | 153.7 | Carnitine transport ATP-binding protein OpuCA; EC 7.6.2.9 | 45% | 221.9 |
| L-histidine catabolism | hutV | lo | ABC transporter for L-Histidine, ATPase component (characterized) | 37% | 83% | 153.7 | Carnitine transport ATP-binding protein OpuCA; EC 7.6.2.9 | 45% | 221.9 |
| D-mannitol catabolism | mtlK | lo | SmoK aka POLK, component of Hexitol (glucitol; mannitol) porter (characterized) | 36% | 76% | 153.7 | Carnitine transport ATP-binding protein OpuCA; EC 7.6.2.9 | 45% | 221.9 |
| 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) | 37% | 92% | 152.9 | Carnitine transport ATP-binding protein OpuCA; EC 7.6.2.9 | 45% | 221.9 |
| 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) | 37% | 92% | 152.9 | Carnitine transport ATP-binding protein OpuCA; EC 7.6.2.9 | 45% | 221.9 |
| 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) | 37% | 92% | 152.9 | Carnitine transport ATP-binding protein OpuCA; EC 7.6.2.9 | 45% | 221.9 |
| 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) | 37% | 92% | 152.9 | Carnitine transport ATP-binding protein OpuCA; EC 7.6.2.9 | 45% | 221.9 |
| 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) | 37% | 92% | 152.9 | Carnitine transport ATP-binding protein OpuCA; EC 7.6.2.9 | 45% | 221.9 |
| 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) | 37% | 92% | 152.9 | Carnitine transport ATP-binding protein OpuCA; EC 7.6.2.9 | 45% | 221.9 |
| D-alanine catabolism | Pf6N2E2_5405 | lo | ABC transporter for D-Alanine, ATPase component (characterized) | 36% | 93% | 150.2 | Carnitine transport ATP-binding protein OpuCA; EC 7.6.2.9 | 45% | 221.9 |
| 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) | 35% | 64% | 150.2 | Carnitine transport ATP-binding protein OpuCA; EC 7.6.2.9 | 45% | 221.9 |
| L-proline catabolism | proV | lo | glycine betaine/l-proline transport atp-binding protein prov (characterized) | 39% | 54% | 150.2 | Carnitine transport ATP-binding protein OpuCA; EC 7.6.2.9 | 45% | 221.9 |
| D-glucosamine (chitosamine) catabolism | AO353_21725 | lo | ABC transporter for D-Glucosamine, putative ATPase component (characterized) | 36% | 92% | 149.8 | Carnitine transport ATP-binding protein OpuCA; EC 7.6.2.9 | 45% | 221.9 |
| D-cellobiose catabolism | gtsD | 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) | 36% | 68% | 147.9 | Carnitine transport ATP-binding protein OpuCA; EC 7.6.2.9 | 45% | 221.9 |
| D-glucose catabolism | gtsD | 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) | 36% | 68% | 147.9 | Carnitine transport ATP-binding protein OpuCA; EC 7.6.2.9 | 45% | 221.9 |
| lactose catabolism | gtsD | 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) | 36% | 68% | 147.9 | Carnitine transport ATP-binding protein OpuCA; EC 7.6.2.9 | 45% | 221.9 |
| D-maltose catabolism | gtsD | 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) | 36% | 68% | 147.9 | Carnitine transport ATP-binding protein OpuCA; EC 7.6.2.9 | 45% | 221.9 |
| D-maltose catabolism | thuK | 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) | 36% | 68% | 147.9 | Carnitine transport ATP-binding protein OpuCA; EC 7.6.2.9 | 45% | 221.9 |
| 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) | 36% | 68% | 147.9 | Carnitine transport ATP-binding protein OpuCA; EC 7.6.2.9 | 45% | 221.9 |
| sucrose catabolism | gtsD | 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) | 36% | 68% | 147.9 | Carnitine transport ATP-binding protein OpuCA; EC 7.6.2.9 | 45% | 221.9 |
| trehalose catabolism | gtsD | 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) | 36% | 68% | 147.9 | Carnitine transport ATP-binding protein OpuCA; EC 7.6.2.9 | 45% | 221.9 |
| trehalose catabolism | thuK | 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) | 36% | 68% | 147.9 | Carnitine transport ATP-binding protein OpuCA; EC 7.6.2.9 | 45% | 221.9 |
| D-maltose catabolism | malK_Bb | lo | ABC-type maltose transport, ATP binding protein (characterized, see rationale) | 37% | 63% | 146 | Carnitine transport ATP-binding protein OpuCA; EC 7.6.2.9 | 45% | 221.9 |
| 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% | 86% | 145.6 | Carnitine transport ATP-binding protein OpuCA; EC 7.6.2.9 | 45% | 221.9 |
| L-arginine catabolism | artP | lo | BgtA aka SLR1735, component of Arginine/lysine/histidine/glutamine porter (characterized) | 36% | 97% | 143.7 | Carnitine transport ATP-binding protein OpuCA; EC 7.6.2.9 | 45% | 221.9 |
| 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) | 36% | 96% | 143.7 | Carnitine transport ATP-binding protein OpuCA; EC 7.6.2.9 | 45% | 221.9 |
| L-histidine catabolism | bgtA | lo | BgtA aka SLR1735, component of Arginine/lysine/histidine/glutamine porter (characterized) | 36% | 97% | 143.7 | Carnitine transport ATP-binding protein OpuCA; EC 7.6.2.9 | 45% | 221.9 |
| L-tryptophan catabolism | ecfA1 | lo | Energy-coupling factor transporter ATP-binding protein EcfA1; Short=ECF transporter A component EcfA; EC 7.-.-.- (characterized, see rationale) | 39% | 80% | 142.1 | Carnitine transport ATP-binding protein OpuCA; EC 7.6.2.9 | 45% | 221.9 |
| L-histidine catabolism | BPHYT_RS24015 | lo | ABC transporter related (characterized, see rationale) | 39% | 87% | 141.7 | Carnitine transport ATP-binding protein OpuCA; EC 7.6.2.9 | 45% | 221.9 |
| 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) | 35% | 70% | 141.7 | Carnitine transport ATP-binding protein OpuCA; EC 7.6.2.9 | 45% | 221.9 |
| D-xylose catabolism | gtsD | lo | ABC transporter for D-Glucose-6-Phosphate, ATPase component (characterized) | 37% | 61% | 140.2 | Carnitine transport ATP-binding protein OpuCA; EC 7.6.2.9 | 45% | 221.9 |
| D-cellobiose catabolism | SMc04256 | lo | ABC transporter for D-Cellobiose and D-Salicin, ATPase component (characterized) | 38% | 59% | 139.8 | Carnitine transport ATP-binding protein OpuCA; EC 7.6.2.9 | 45% | 221.9 |
| D-maltose catabolism | musK | lo | ABC-type maltose transporter (EC 7.5.2.1) (characterized) | 36% | 64% | 139.4 | Carnitine transport ATP-binding protein OpuCA; EC 7.6.2.9 | 45% | 221.9 |
| 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) | 37% | 56% | 139.4 | Carnitine transport ATP-binding protein OpuCA; EC 7.6.2.9 | 45% | 221.9 |
| 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) | 35% | 81% | 139 | Carnitine transport ATP-binding protein OpuCA; EC 7.6.2.9 | 45% | 221.9 |
| D-galactose catabolism | PfGW456L13_1897 | lo | ABC transporter for D-Galactose and D-Glucose, ATPase component (characterized) | 37% | 56% | 138.7 | Carnitine transport ATP-binding protein OpuCA; EC 7.6.2.9 | 45% | 221.9 |
| trehalose catabolism | treV | lo | TreV, component of Trehalose porter (characterized) | 34% | 66% | 138.3 | Carnitine transport ATP-binding protein OpuCA; EC 7.6.2.9 | 45% | 221.9 |
| L-arabinose catabolism | xacK | lo | Xylose/arabinose import ATP-binding protein XacK; EC 7.5.2.13 (characterized, see rationale) | 36% | 59% | 137.9 | Carnitine transport ATP-binding protein OpuCA; EC 7.6.2.9 | 45% | 221.9 |
| L-asparagine catabolism | peb1C | lo | PEB1C, component of Uptake system for glutamate and aspartate (characterized) | 34% | 95% | 137.9 | Carnitine transport ATP-binding protein OpuCA; EC 7.6.2.9 | 45% | 221.9 |
| L-aspartate catabolism | peb1C | lo | PEB1C, component of Uptake system for glutamate and aspartate (characterized) | 34% | 95% | 137.9 | Carnitine transport ATP-binding protein OpuCA; EC 7.6.2.9 | 45% | 221.9 |
| D-glucosamine (chitosamine) catabolism | SM_b21216 | lo | ABC transporter for D-Glucosamine, ATPase component (characterized) | 33% | 70% | 137.9 | Carnitine transport ATP-binding protein OpuCA; EC 7.6.2.9 | 45% | 221.9 |
| L-tryptophan catabolism | ecfA2 | lo | Energy-coupling factor transporter ATP-binding protein EcfA2; Short=ECF transporter A component EcfA2; EC 7.-.-.- (characterized, see rationale) | 36% | 78% | 136.3 | Carnitine transport ATP-binding protein OpuCA; EC 7.6.2.9 | 45% | 221.9 |
| 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) | 37% | 55% | 135.6 | Carnitine transport ATP-binding protein OpuCA; EC 7.6.2.9 | 45% | 221.9 |
| L-arabinose catabolism | xacJ | lo | Xylose/arabinose import ATP-binding protein XacJ; EC 7.5.2.13 (characterized, see rationale) | 35% | 58% | 131.3 | Carnitine transport ATP-binding protein OpuCA; EC 7.6.2.9 | 45% | 221.9 |
| glycerol catabolism | glpS | lo | ABC transporter for Glycerol, ATPase component 1 (characterized) | 34% | 70% | 127.5 | Carnitine transport ATP-binding protein OpuCA; EC 7.6.2.9 | 45% | 221.9 |
| L-histidine catabolism | Ac3H11_2560 | lo | ABC transporter for L-Histidine, ATPase component (characterized) | 39% | 76% | 124.4 | Carnitine transport ATP-binding protein OpuCA; EC 7.6.2.9 | 45% | 221.9 |
| 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% | 95% | 115.5 | Carnitine transport ATP-binding protein OpuCA; EC 7.6.2.9 | 45% | 221.9 |
| 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% | 95% | 115.5 | Carnitine transport ATP-binding protein OpuCA; EC 7.6.2.9 | 45% | 221.9 |
| 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% | 95% | 115.5 | Carnitine transport ATP-binding protein OpuCA; EC 7.6.2.9 | 45% | 221.9 |
| 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% | 95% | 115.5 | Carnitine transport ATP-binding protein OpuCA; EC 7.6.2.9 | 45% | 221.9 |
| 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% | 95% | 115.5 | Carnitine transport ATP-binding protein OpuCA; EC 7.6.2.9 | 45% | 221.9 |
| 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% | 95% | 115.5 | Carnitine transport ATP-binding protein OpuCA; EC 7.6.2.9 | 45% | 221.9 |
| L-arginine catabolism | braG | lo | ATP-binding component of a broad range amino acid ABC transporter (characterized, see rationale) | 32% | 93% | 115.2 | Carnitine transport ATP-binding protein OpuCA; EC 7.6.2.9 | 45% | 221.9 |
| L-glutamate catabolism | braG | lo | ATP-binding component of a broad range amino acid ABC transporter (characterized, see rationale) | 32% | 93% | 115.2 | Carnitine transport ATP-binding protein OpuCA; EC 7.6.2.9 | 45% | 221.9 |
| L-histidine catabolism | braG | lo | ATP-binding component of a broad range amino acid ABC transporter (characterized, see rationale) | 32% | 93% | 115.2 | Carnitine transport ATP-binding protein OpuCA; EC 7.6.2.9 | 45% | 221.9 |
| L-proline catabolism | HSERO_RS00895 | lo | ABC-type branched-chain amino acid transport system, ATPase component protein (characterized, see rationale) | 34% | 91% | 114.4 | Carnitine transport ATP-binding protein OpuCA; EC 7.6.2.9 | 45% | 221.9 |
| L-phenylalanine catabolism | livF | lo | high-affinity branched-chain amino acid ABC transporter, ATP-binding protein LivF (characterized) | 32% | 93% | 109.8 | Carnitine transport ATP-binding protein OpuCA; EC 7.6.2.9 | 45% | 221.9 |
| L-proline catabolism | HSERO_RS00900 | lo | ABC-type branched-chain amino acid transport system, ATPase component protein (characterized, see rationale) | 31% | 92% | 96.3 | Carnitine transport ATP-binding protein OpuCA; EC 7.6.2.9 | 45% | 221.9 |
| D-alanine catabolism | AZOBR_RS08250 | lo | Leucine//isoleucine/valine ABC transporter,ATPase component; EC 3.6.3.- (characterized, see rationale) | 31% | 90% | 95.5 | Carnitine transport ATP-binding protein OpuCA; EC 7.6.2.9 | 45% | 221.9 |
| L-proline catabolism | AZOBR_RS08250 | lo | Leucine//isoleucine/valine ABC transporter,ATPase component; EC 3.6.3.- (characterized, see rationale) | 31% | 90% | 95.5 | Carnitine transport ATP-binding protein OpuCA; EC 7.6.2.9 | 45% | 221.9 |
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