| Pathway | Step | Score | Similar to | Id. | Cov. | Bits | Other hit | Other id. | Other bits |
|---|
| L-lysine catabolism | hisP | med | Amino-acid ABC transporter, ATP-binding protein (characterized, see rationale) | 56% | 93% | 262.3 | Glutamine transport ATP-binding protein GlnQ; EC 7.4.2.- | 56% | 270.0 |
| L-arginine catabolism | artP | 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) | 53% | 97% | 254.2 | Glutamine transport ATP-binding protein GlnQ; EC 7.4.2.- | 56% | 270.0 |
| 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) | 53% | 97% | 254.2 | Glutamine transport ATP-binding protein GlnQ; EC 7.4.2.- | 56% | 270.0 |
| 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) | 52% | 98% | 252.7 | Glutamine transport ATP-binding protein GlnQ; EC 7.4.2.- | 56% | 270.0 |
| 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) | 52% | 98% | 252.7 | Glutamine transport ATP-binding protein GlnQ; EC 7.4.2.- | 56% | 270.0 |
| L-histidine catabolism | bgtA | med | BgtA aka SLR1735, component of Arginine/lysine/histidine/glutamine porter (characterized) | 53% | 96% | 246.9 | Glutamine transport ATP-binding protein GlnQ; EC 7.4.2.- | 56% | 270.0 |
| L-histidine catabolism | BPHYT_RS24015 | med | ABC transporter related (characterized, see rationale) | 52% | 94% | 245.7 | Glutamine transport ATP-binding protein GlnQ; EC 7.4.2.- | 56% | 270.0 |
| L-citrulline catabolism | AO353_03040 | med | ABC transporter for L-Arginine and L-Citrulline, ATPase component (characterized) | 52% | 97% | 245 | Glutamine transport ATP-binding protein GlnQ; EC 7.4.2.- | 56% | 270.0 |
| L-asparagine catabolism | bztD | med | BztD, component of Glutamate/glutamine/aspartate/asparagine porter (characterized) | 52% | 91% | 241.1 | Glutamine transport ATP-binding protein GlnQ; EC 7.4.2.- | 56% | 270.0 |
| L-aspartate catabolism | bztD | med | BztD, component of Glutamate/glutamine/aspartate/asparagine porter (characterized) | 52% | 91% | 241.1 | Glutamine transport ATP-binding protein GlnQ; EC 7.4.2.- | 56% | 270.0 |
| L-asparagine catabolism | aatP | med | Glutamate/aspartate transport ATP-binding protein GltL aka B0652, component of Glutamate/aspartate porter (characterized) | 50% | 100% | 238 | Glutamine transport ATP-binding protein GlnQ; EC 7.4.2.- | 56% | 270.0 |
| L-aspartate catabolism | aatP | med | Glutamate/aspartate transport ATP-binding protein GltL aka B0652, component of Glutamate/aspartate porter (characterized) | 50% | 100% | 238 | Glutamine transport ATP-binding protein GlnQ; EC 7.4.2.- | 56% | 270.0 |
| L-asparagine catabolism | bgtA | med | ATPase (characterized, see rationale) | 52% | 92% | 237.3 | Glutamine transport ATP-binding protein GlnQ; EC 7.4.2.- | 56% | 270.0 |
| L-aspartate catabolism | bgtA | med | ATPase (characterized, see rationale) | 52% | 92% | 237.3 | Glutamine transport ATP-binding protein GlnQ; EC 7.4.2.- | 56% | 270.0 |
| 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) | 53% | 90% | 236.1 | Glutamine transport ATP-binding protein GlnQ; EC 7.4.2.- | 56% | 270.0 |
| 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) | 51% | 93% | 235.7 | Glutamine transport ATP-binding protein GlnQ; EC 7.4.2.- | 56% | 270.0 |
| 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) | 51% | 93% | 235.7 | Glutamine transport ATP-binding protein GlnQ; EC 7.4.2.- | 56% | 270.0 |
| 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) | 51% | 93% | 235.7 | Glutamine transport ATP-binding protein GlnQ; EC 7.4.2.- | 56% | 270.0 |
| 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) | 51% | 93% | 235.7 | Glutamine transport ATP-binding protein GlnQ; EC 7.4.2.- | 56% | 270.0 |
| 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) | 51% | 93% | 235.7 | Glutamine transport ATP-binding protein GlnQ; EC 7.4.2.- | 56% | 270.0 |
| 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) | 51% | 93% | 235.7 | Glutamine transport ATP-binding protein GlnQ; EC 7.4.2.- | 56% | 270.0 |
| D-alanine catabolism | Pf6N2E2_5405 | med | ABC transporter for D-Alanine, ATPase component (characterized) | 50% | 95% | 232.3 | Glutamine transport ATP-binding protein GlnQ; EC 7.4.2.- | 56% | 270.0 |
| D-glucosamine (chitosamine) catabolism | AO353_21725 | med | ABC transporter for D-glucosamine, ATPase component (characterized) | 51% | 93% | 228.4 | Glutamine transport ATP-binding protein GlnQ; EC 7.4.2.- | 56% | 270.0 |
| L-asparagine catabolism | peb1C | med | PEB1C, component of Uptake system for glutamate and aspartate (characterized) | 47% | 99% | 224.6 | Glutamine transport ATP-binding protein GlnQ; EC 7.4.2.- | 56% | 270.0 |
| L-aspartate catabolism | peb1C | med | PEB1C, component of Uptake system for glutamate and aspartate (characterized) | 47% | 99% | 224.6 | Glutamine transport ATP-binding protein GlnQ; EC 7.4.2.- | 56% | 270.0 |
| L-histidine catabolism | PA5503 | med | Methionine import ATP-binding protein MetN 2, component of L-Histidine uptake porter, MetIQN (characterized) | 41% | 75% | 179.9 | Glutamine transport ATP-binding protein GlnQ; EC 7.4.2.- | 56% | 270.0 |
| N-acetyl-D-glucosamine catabolism | SMc02869 | lo | N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized) | 39% | 64% | 156.4 | Glutamine transport ATP-binding protein GlnQ; EC 7.4.2.- | 56% | 270.0 |
| D-glucosamine (chitosamine) catabolism | SMc02869 | lo | N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized) | 39% | 64% | 156.4 | Glutamine transport ATP-binding protein GlnQ; EC 7.4.2.- | 56% | 270.0 |
| lactose catabolism | lacK | lo | LacK, component of Lactose porter (characterized) | 37% | 61% | 150.6 | Glutamine transport ATP-binding protein GlnQ; EC 7.4.2.- | 56% | 270.0 |
| D-cellobiose catabolism | gtsD | lo | ABC transporter for D-Glucose-6-Phosphate, ATPase component (characterized) | 37% | 60% | 142.5 | Glutamine transport ATP-binding protein GlnQ; EC 7.4.2.- | 56% | 270.0 |
| D-glucose catabolism | gtsD | lo | ABC transporter for D-Glucose-6-Phosphate, ATPase component (characterized) | 37% | 60% | 142.5 | Glutamine transport ATP-binding protein GlnQ; EC 7.4.2.- | 56% | 270.0 |
| lactose catabolism | gtsD | lo | ABC transporter for D-Glucose-6-Phosphate, ATPase component (characterized) | 37% | 60% | 142.5 | Glutamine transport ATP-binding protein GlnQ; EC 7.4.2.- | 56% | 270.0 |
| D-maltose catabolism | gtsD | lo | ABC transporter for D-Glucose-6-Phosphate, ATPase component (characterized) | 37% | 60% | 142.5 | Glutamine transport ATP-binding protein GlnQ; EC 7.4.2.- | 56% | 270.0 |
| sucrose catabolism | gtsD | lo | ABC transporter for D-Glucose-6-Phosphate, ATPase component (characterized) | 37% | 60% | 142.5 | Glutamine transport ATP-binding protein GlnQ; EC 7.4.2.- | 56% | 270.0 |
| trehalose catabolism | gtsD | lo | ABC transporter for D-Glucose-6-Phosphate, ATPase component (characterized) | 37% | 60% | 142.5 | Glutamine transport ATP-binding protein GlnQ; EC 7.4.2.- | 56% | 270.0 |
| D-xylose catabolism | gtsD | lo | ABC transporter for D-Glucose-6-Phosphate, ATPase component (characterized) | 37% | 60% | 142.5 | Glutamine transport ATP-binding protein GlnQ; EC 7.4.2.- | 56% | 270.0 |
| L-arabinose catabolism | xacK | lo | Xylose/arabinose import ATP-binding protein XacK; EC 7.5.2.13 (characterized, see rationale) | 37% | 58% | 140.2 | Glutamine transport ATP-binding protein GlnQ; EC 7.4.2.- | 56% | 270.0 |
| D-maltose catabolism | malK | lo | Maltose/maltodextrin import ATP-binding protein MalK; EC 7.5.2.1 (characterized) | 36% | 63% | 139 | Glutamine transport ATP-binding protein GlnQ; EC 7.4.2.- | 56% | 270.0 |
| 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) | 32% | 97% | 138.7 | Glutamine transport ATP-binding protein GlnQ; EC 7.4.2.- | 56% | 270.0 |
| 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) | 32% | 97% | 138.7 | Glutamine transport ATP-binding protein GlnQ; EC 7.4.2.- | 56% | 270.0 |
| 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) | 32% | 97% | 138.7 | Glutamine transport ATP-binding protein GlnQ; EC 7.4.2.- | 56% | 270.0 |
| 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) | 30% | 98% | 106.7 | Glutamine transport ATP-binding protein GlnQ; EC 7.4.2.- | 56% | 270.0 |
| 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) | 30% | 98% | 106.7 | Glutamine transport ATP-binding protein GlnQ; EC 7.4.2.- | 56% | 270.0 |
| 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) | 30% | 98% | 106.7 | Glutamine transport ATP-binding protein GlnQ; EC 7.4.2.- | 56% | 270.0 |
| 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) | 30% | 98% | 106.7 | Glutamine transport ATP-binding protein GlnQ; EC 7.4.2.- | 56% | 270.0 |
| 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) | 30% | 98% | 106.7 | Glutamine transport ATP-binding protein GlnQ; EC 7.4.2.- | 56% | 270.0 |
| 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) | 30% | 98% | 106.7 | Glutamine transport ATP-binding protein GlnQ; EC 7.4.2.- | 56% | 270.0 |
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