| Pathway | Step | Score | Similar to | Id. | Cov. | Bits | Other hit | Other id. | Other bits |
|---|
| 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) | 63% | 98% | 306.2 | ABC transporter for D-Alanine, ATPase component | 61% | 305.1 |
| 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) | 63% | 98% | 306.2 | ABC transporter for D-Alanine, ATPase component | 61% | 305.1 |
| 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) | 63% | 98% | 306.2 | ABC transporter for D-Alanine, ATPase component | 61% | 305.1 |
| L-histidine 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) | 63% | 98% | 306.2 | ABC transporter for D-Alanine, ATPase component | 61% | 305.1 |
| 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) | 63% | 98% | 306.2 | ABC transporter for D-Alanine, ATPase component | 61% | 305.1 |
| 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) | 63% | 98% | 306.2 | ABC transporter for D-Alanine, ATPase component | 61% | 305.1 |
| D-alanine catabolism | Pf6N2E2_5405 | med | ABC transporter for D-Alanine, ATPase component (characterized) | 61% | 98% | 305.1 | 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) | 63% | 306.2 |
| L-glutamate catabolism | gltL | med | GluA aka CGL1950, component of Glutamate porter (characterized) | 65% | 99% | 301.2 | ABC transporter for D-Alanine, ATPase component | 61% | 305.1 |
| L-asparagine catabolism | bztD | med | BztD, component of Glutamate/glutamine/aspartate/asparagine porter (characterized) | 62% | 93% | 292.4 | ABC transporter for D-Alanine, ATPase component | 61% | 305.1 |
| L-aspartate catabolism | bztD | med | BztD, component of Glutamate/glutamine/aspartate/asparagine porter (characterized) | 62% | 93% | 292.4 | ABC transporter for D-Alanine, ATPase component | 61% | 305.1 |
| L-asparagine catabolism | aatP | med | Glutamate/aspartate transport ATP-binding protein GltL aka B0652, component of Glutamate/aspartate porter (characterized) | 61% | 100% | 279.3 | 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) | 63% | 306.2 |
| L-aspartate catabolism | aatP | med | Glutamate/aspartate transport ATP-binding protein GltL aka B0652, component of Glutamate/aspartate porter (characterized) | 61% | 100% | 279.3 | 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) | 63% | 306.2 |
| L-lysine catabolism | hisP | med | Amino-acid ABC transporter, ATP-binding protein (characterized, see rationale) | 56% | 97% | 273.9 | 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) | 63% | 306.2 |
| L-arginine catabolism | artP | med | Arginine transport ATP-binding protein ArtM (characterized) | 57% | 100% | 268.9 | 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) | 63% | 306.2 |
| 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% | 97% | 266.2 | 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) | 63% | 306.2 |
| L-asparagine catabolism | bgtA | med | ATPase (characterized, see rationale) | 57% | 95% | 265.8 | 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) | 63% | 306.2 |
| L-aspartate catabolism | bgtA | med | ATPase (characterized, see rationale) | 57% | 95% | 265.8 | 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) | 63% | 306.2 |
| L-asparagine catabolism | peb1C | med | PEB1C, component of Uptake system for glutamate and aspartate (characterized) | 54% | 100% | 260.8 | 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) | 63% | 306.2 |
| L-aspartate catabolism | peb1C | med | PEB1C, component of Uptake system for glutamate and aspartate (characterized) | 54% | 100% | 260.8 | 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) | 63% | 306.2 |
| 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) | 50% | 99% | 248.8 | 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) | 63% | 306.2 |
| L-histidine catabolism | bgtA | med | BgtA aka SLR1735, component of Arginine/lysine/histidine/glutamine porter (characterized) | 51% | 99% | 246.1 | 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) | 63% | 306.2 |
| L-histidine catabolism | BPHYT_RS24015 | med | ABC transporter related (characterized, see rationale) | 48% | 97% | 238.4 | 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) | 63% | 306.2 |
| D-glucosamine (chitosamine) catabolism | AO353_21725 | med | ABC transporter for D-Glucosamine, putative ATPase component (characterized) | 48% | 95% | 235.3 | 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) | 63% | 306.2 |
| 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% | 93% | 226.9 | 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) | 63% | 306.2 |
| L-citrulline catabolism | AO353_03040 | med | ABC transporter for L-Arginine and L-Citrulline, ATPase component (characterized) | 48% | 98% | 225.3 | 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) | 63% | 306.2 |
| L-histidine catabolism | PA5503 | med | Methionine import ATP-binding protein MetN 2, component of L-Histidine uptake porter, MetIQN (characterized) | 43% | 72% | 177.9 | 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) | 63% | 306.2 |
| L-proline catabolism | proV | lo | glycine betaine/l-proline transport atp-binding protein prov (characterized) | 40% | 61% | 172.6 | 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) | 63% | 306.2 |
| 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) | 39% | 73% | 157.9 | 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) | 63% | 306.2 |
| lactose catabolism | lacK | lo | ABC transporter for Lactose, ATPase component (characterized) | 37% | 63% | 155.2 | 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) | 63% | 306.2 |
| D-maltose catabolism | aglK | lo | ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized) | 37% | 64% | 153.7 | 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) | 63% | 306.2 |
| D-maltose catabolism | malK_Bb | lo | ABC-type maltose transport, ATP binding protein (characterized, see rationale) | 36% | 67% | 153.7 | 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) | 63% | 306.2 |
| D-maltose catabolism | thuK | lo | ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized) | 37% | 64% | 153.7 | 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) | 63% | 306.2 |
| sucrose catabolism | aglK | lo | ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized) | 37% | 64% | 153.7 | 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) | 63% | 306.2 |
| trehalose catabolism | aglK | lo | ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized) | 37% | 64% | 153.7 | 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) | 63% | 306.2 |
| N-acetyl-D-glucosamine catabolism | SMc02869 | lo | N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized) | 37% | 70% | 153.3 | 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) | 63% | 306.2 |
| D-glucosamine (chitosamine) catabolism | SMc02869 | lo | N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized) | 37% | 70% | 153.3 | 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) | 63% | 306.2 |
| putrescine catabolism | potA | lo | spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31 (characterized) | 36% | 65% | 152.1 | 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) | 63% | 306.2 |
| D-sorbitol (glucitol) catabolism | mtlK | lo | ABC transporter for D-Sorbitol, ATPase component (characterized) | 36% | 66% | 150.6 | 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) | 63% | 306.2 |
| D-mannitol catabolism | mtlK | lo | ABC transporter for D-Mannitol, D-Mannose, and D-Sorbitol, ATPase component (characterized) | 39% | 63% | 148.7 | 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) | 63% | 306.2 |
| D-cellobiose catabolism | aglK' | lo | Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) | 37% | 63% | 148.3 | 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) | 63% | 306.2 |
| D-glucose catabolism | aglK' | lo | Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) | 37% | 63% | 148.3 | 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) | 63% | 306.2 |
| lactose catabolism | aglK' | lo | Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) | 37% | 63% | 148.3 | 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) | 63% | 306.2 |
| D-maltose catabolism | aglK' | lo | Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) | 37% | 63% | 148.3 | 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) | 63% | 306.2 |
| sucrose catabolism | aglK' | lo | Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) | 37% | 63% | 148.3 | 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) | 63% | 306.2 |
| trehalose catabolism | aglK' | lo | Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) | 37% | 63% | 148.3 | 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) | 63% | 306.2 |
| sucrose catabolism | thuK | lo | ABC transporter (characterized, see rationale) | 38% | 61% | 147.9 | 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) | 63% | 306.2 |
| xylitol catabolism | Dshi_0546 | lo | ABC transporter for Xylitol, ATPase component (characterized) | 36% | 70% | 146.7 | 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) | 63% | 306.2 |
| trehalose catabolism | thuK | lo | Trehalose/maltose import ATP-binding protein MalK; EC 7.5.2.1 (characterized) | 35% | 62% | 146.4 | 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) | 63% | 306.2 |
| L-histidine catabolism | hutV | lo | ABC transporter for L-Histidine, ATPase component (characterized) | 38% | 86% | 146 | 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) | 63% | 306.2 |
| 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% | 61% | 141.4 | 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) | 63% | 306.2 |
| 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) | 36% | 91% | 141.4 | 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) | 63% | 306.2 |
| L-arabinose catabolism | xacJ | lo | Xylose/arabinose import ATP-binding protein XacJ; EC 7.5.2.13 (characterized, see rationale) | 35% | 61% | 139.8 | 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) | 63% | 306.2 |
| D-glucosamine (chitosamine) catabolism | SM_b21216 | lo | ABC transporter for D-Glucosamine, ATPase component (characterized) | 38% | 62% | 139.8 | 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) | 63% | 306.2 |
| D-maltose catabolism | malK | lo | ABC-type maltose transporter (subunit 3/3) (EC 7.5.2.1) (characterized) | 36% | 60% | 138.7 | 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) | 63% | 306.2 |
| D-cellobiose catabolism | gtsD | lo | ABC transporter for D-Galactose and D-Glucose, ATPase component (characterized) | 36% | 60% | 138.3 | 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) | 63% | 306.2 |
| D-galactose catabolism | PfGW456L13_1897 | lo | ABC transporter for D-Galactose and D-Glucose, ATPase component (characterized) | 36% | 60% | 138.3 | 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) | 63% | 306.2 |
| D-glucose catabolism | gtsD | lo | ABC transporter for D-Galactose and D-Glucose, ATPase component (characterized) | 36% | 60% | 138.3 | 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) | 63% | 306.2 |
| lactose catabolism | gtsD | lo | ABC transporter for D-Galactose and D-Glucose, ATPase component (characterized) | 36% | 60% | 138.3 | 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) | 63% | 306.2 |
| D-maltose catabolism | gtsD | lo | ABC transporter for D-Galactose and D-Glucose, ATPase component (characterized) | 36% | 60% | 138.3 | 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) | 63% | 306.2 |
| sucrose catabolism | gtsD | lo | ABC transporter for D-Galactose and D-Glucose, ATPase component (characterized) | 36% | 60% | 138.3 | 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) | 63% | 306.2 |
| trehalose catabolism | gtsD | lo | ABC transporter for D-Galactose and D-Glucose, ATPase component (characterized) | 36% | 60% | 138.3 | 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) | 63% | 306.2 |
| L-fucose catabolism | SM_b21106 | lo | ABC transporter for L-Fucose, ATPase component (characterized) | 34% | 61% | 137.9 | 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) | 63% | 306.2 |
| D-xylose catabolism | gtsD | lo | ABC transporter for D-Glucose-6-Phosphate, ATPase component (characterized) | 35% | 61% | 137.5 | 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) | 63% | 306.2 |
| D-cellobiose catabolism | glcV | lo | monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) | 38% | 65% | 136.7 | 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) | 63% | 306.2 |
| D-galactose catabolism | glcV | lo | monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) | 38% | 65% | 136.7 | 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) | 63% | 306.2 |
| D-glucose catabolism | glcV | lo | monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) | 38% | 65% | 136.7 | 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) | 63% | 306.2 |
| lactose catabolism | glcV | lo | monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) | 38% | 65% | 136.7 | 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) | 63% | 306.2 |
| D-maltose catabolism | glcV | lo | monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) | 38% | 65% | 136.7 | 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) | 63% | 306.2 |
| D-mannose catabolism | glcV | lo | monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) | 38% | 65% | 136.7 | 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) | 63% | 306.2 |
| sucrose catabolism | glcV | lo | monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) | 38% | 65% | 136.7 | 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) | 63% | 306.2 |
| trehalose catabolism | glcV | lo | monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) | 38% | 65% | 136.7 | 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) | 63% | 306.2 |
| trehalose catabolism | treV | lo | TreV, component of Trehalose porter (characterized) | 34% | 73% | 135.2 | 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) | 63% | 306.2 |
| xylitol catabolism | HSERO_RS17020 | lo | ABC-type sugar transport system, ATPase component protein (characterized, see rationale) | 37% | 55% | 134 | 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) | 63% | 306.2 |
| 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% | 82% | 132.9 | 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) | 63% | 306.2 |
| 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) | 32% | 95% | 131.3 | 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) | 63% | 306.2 |
| 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% | 79% | 131 | 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) | 63% | 306.2 |
| L-histidine catabolism | Ac3H11_2560 | lo | ABC transporter for L-Histidine, ATPase component (characterized) | 37% | 89% | 130.2 | 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) | 63% | 306.2 |
| L-arabinose catabolism | xacK | lo | Xylose/arabinose import ATP-binding protein XacK; EC 7.5.2.13 (characterized, see rationale) | 34% | 60% | 128.3 | 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) | 63% | 306.2 |
| 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) | 32% | 62% | 127.5 | 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) | 63% | 306.2 |
| L-proline catabolism | HSERO_RS00895 | lo | ABC-type branched-chain amino acid transport system, ATPase component protein (characterized, see rationale) | 30% | 95% | 127.5 | 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) | 63% | 306.2 |
| L-arabinose catabolism | araV | lo | AraV, component of Arabinose, fructose, xylose porter (characterized) | 31% | 68% | 125.6 | 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) | 63% | 306.2 |
| D-fructose catabolism | araV | lo | AraV, component of Arabinose, fructose, xylose porter (characterized) | 31% | 68% | 125.6 | 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) | 63% | 306.2 |
| sucrose catabolism | araV | lo | AraV, component of Arabinose, fructose, xylose porter (characterized) | 31% | 68% | 125.6 | 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) | 63% | 306.2 |
| D-xylose catabolism | araV | lo | AraV, component of Arabinose, fructose, xylose porter (characterized) | 31% | 68% | 125.6 | 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) | 63% | 306.2 |
| L-arabinose catabolism | xylGsa | lo | Xylose/arabinose import ATP-binding protein XylG; EC 7.5.2.13 (characterized, see rationale) | 34% | 95% | 124 | 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) | 63% | 306.2 |
| L-isoleucine catabolism | livF | lo | ABC transporter ATP-binding protein-branched chain amino acid transport, component of The branched chain hydrophobic amino acid transporter, LivJFGHM (characterized) | 30% | 99% | 124 | 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) | 63% | 306.2 |
| L-leucine catabolism | livF | lo | ABC transporter ATP-binding protein-branched chain amino acid transport, component of The branched chain hydrophobic amino acid transporter, LivJFGHM (characterized) | 30% | 99% | 124 | 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) | 63% | 306.2 |
| L-valine catabolism | livF | lo | ABC transporter ATP-binding protein-branched chain amino acid transport, component of The branched chain hydrophobic amino acid transporter, LivJFGHM (characterized) | 30% | 99% | 124 | 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) | 63% | 306.2 |
| D-maltose catabolism | musK | lo | ABC-type maltose transporter (EC 7.5.2.1) (characterized) | 33% | 56% | 122.9 | 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) | 63% | 306.2 |
| D-cellobiose catabolism | SMc04256 | lo | ABC transporter for D-Cellobiose and D-Salicin, ATPase component (characterized) | 34% | 62% | 120.2 | 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) | 63% | 306.2 |
| myo-inositol catabolism | PGA1_c07320 | lo | Inositol transport system ATP-binding protein (characterized) | 31% | 88% | 119 | 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) | 63% | 306.2 |
| L-phenylalanine catabolism | livF | lo | high-affinity branched-chain amino acid ABC transporter, ATP-binding protein LivF (characterized) | 30% | 95% | 119 | 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) | 63% | 306.2 |
| 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) | 34% | 56% | 117.9 | 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) | 63% | 306.2 |
| D-fructose catabolism | frcA | lo | Fructose import ATP-binding protein FrcA; EC 7.5.2.- (characterized) | 30% | 85% | 112.5 | 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) | 63% | 306.2 |
| D-mannose catabolism | frcA | lo | Fructose import ATP-binding protein FrcA; EC 7.5.2.- (characterized) | 30% | 85% | 112.5 | 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) | 63% | 306.2 |
| D-ribose catabolism | frcA | lo | Fructose import ATP-binding protein FrcA; EC 7.5.2.- (characterized) | 30% | 85% | 112.5 | 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) | 63% | 306.2 |
| sucrose catabolism | frcA | lo | Fructose import ATP-binding protein FrcA; EC 7.5.2.- (characterized) | 30% | 85% | 112.5 | 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) | 63% | 306.2 |
| glycerol catabolism | glpS | lo | ABC transporter for Glycerol, ATPase component 1 (characterized) | 32% | 62% | 105.9 | 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) | 63% | 306.2 |
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