| Pathway | Step | Score | Similar to | Id. | Cov. | Bits | Other hit | Other id. | Other bits |
|---|
| L-arginine catabolism | artP | lo | Arginine transport ATP-binding protein ArtM (characterized) | 38% | 90% | 148.3 | HrtA, component of Probable Heme exporter, HrtAB | 41% | 183.0 |
| 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) | 37% | 90% | 144.4 | HrtA, component of Probable Heme exporter, HrtAB | 41% | 183.0 |
| L-glutamate catabolism | gltL | 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) | 37% | 90% | 144.4 | HrtA, component of Probable Heme exporter, HrtAB | 41% | 183.0 |
| L-lysine catabolism | hisP | lo | ABC transporter for L-Lysine, ATPase component (characterized) | 35% | 91% | 135.2 | HrtA, component of Probable Heme exporter, HrtAB | 41% | 183.0 |
| L-histidine catabolism | bgtA | lo | BgtA aka SLR1735, component of Arginine/lysine/histidine/glutamine porter (characterized) | 37% | 90% | 132.1 | HrtA, component of Probable Heme exporter, HrtAB | 41% | 183.0 |
| L-asparagine catabolism | peb1C | lo | PEB1C, component of Uptake system for glutamate and aspartate (characterized) | 34% | 90% | 130.6 | HrtA, component of Probable Heme exporter, HrtAB | 41% | 183.0 |
| L-aspartate catabolism | peb1C | lo | PEB1C, component of Uptake system for glutamate and aspartate (characterized) | 34% | 90% | 130.6 | HrtA, component of Probable Heme exporter, HrtAB | 41% | 183.0 |
| L-histidine catabolism | hisP | lo | 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) | 34% | 93% | 130.6 | HrtA, component of Probable Heme exporter, HrtAB | 41% | 183.0 |
| L-asparagine catabolism | aatP | lo | Glutamate/aspartate transport ATP-binding protein GltL aka B0652, component of Glutamate/aspartate porter (characterized) | 37% | 88% | 130.2 | HrtA, component of Probable Heme exporter, HrtAB | 41% | 183.0 |
| L-aspartate catabolism | aatP | lo | Glutamate/aspartate transport ATP-binding protein GltL aka B0652, component of Glutamate/aspartate porter (characterized) | 37% | 88% | 130.2 | HrtA, component of Probable Heme exporter, HrtAB | 41% | 183.0 |
| D-maltose catabolism | thuK | lo | Trehalose/maltose import ATP-binding protein MalK; EC 7.5.2.1 (characterized) | 34% | 58% | 129.8 | HrtA, component of Probable Heme exporter, HrtAB | 41% | 183.0 |
| trehalose catabolism | thuK | lo | Trehalose/maltose import ATP-binding protein MalK; EC 7.5.2.1 (characterized) | 34% | 58% | 129.8 | HrtA, component of Probable Heme exporter, HrtAB | 41% | 183.0 |
| L-asparagine catabolism | bztD | lo | BztD, component of Glutamate/glutamine/aspartate/asparagine porter (characterized) | 38% | 74% | 129 | HrtA, component of Probable Heme exporter, HrtAB | 41% | 183.0 |
| L-aspartate catabolism | bztD | lo | BztD, component of Glutamate/glutamine/aspartate/asparagine porter (characterized) | 38% | 74% | 129 | HrtA, component of Probable Heme exporter, HrtAB | 41% | 183.0 |
| 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) | 35% | 86% | 127.5 | HrtA, component of Probable Heme exporter, HrtAB | 41% | 183.0 |
| 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) | 35% | 86% | 127.5 | HrtA, component of Probable Heme exporter, HrtAB | 41% | 183.0 |
| D-cellobiose catabolism | gtsD | lo | Sugar ABC transporter ATP-binding protein (characterized, see rationale) | 36% | 55% | 127.5 | HrtA, component of Probable Heme exporter, HrtAB | 41% | 183.0 |
| D-glucose catabolism | gtsD | lo | Sugar ABC transporter ATP-binding protein (characterized, see rationale) | 36% | 55% | 127.5 | HrtA, component of Probable Heme exporter, HrtAB | 41% | 183.0 |
| 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) | 35% | 86% | 127.5 | HrtA, component of Probable Heme exporter, HrtAB | 41% | 183.0 |
| 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) | 35% | 86% | 127.5 | HrtA, component of Probable Heme exporter, HrtAB | 41% | 183.0 |
| lactose catabolism | gtsD | lo | Sugar ABC transporter ATP-binding protein (characterized, see rationale) | 36% | 55% | 127.5 | HrtA, component of Probable Heme exporter, HrtAB | 41% | 183.0 |
| 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) | 35% | 86% | 127.5 | HrtA, component of Probable Heme exporter, HrtAB | 41% | 183.0 |
| D-maltose catabolism | gtsD | lo | Sugar ABC transporter ATP-binding protein (characterized, see rationale) | 36% | 55% | 127.5 | HrtA, component of Probable Heme exporter, HrtAB | 41% | 183.0 |
| 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) | 35% | 86% | 127.5 | HrtA, component of Probable Heme exporter, HrtAB | 41% | 183.0 |
| sucrose catabolism | gtsD | lo | Sugar ABC transporter ATP-binding protein (characterized, see rationale) | 36% | 55% | 127.5 | HrtA, component of Probable Heme exporter, HrtAB | 41% | 183.0 |
| trehalose catabolism | gtsD | lo | Sugar ABC transporter ATP-binding protein (characterized, see rationale) | 36% | 55% | 127.5 | HrtA, component of Probable Heme exporter, HrtAB | 41% | 183.0 |
| L-arabinose catabolism | araV | lo | AraV, component of Arabinose, fructose, xylose porter (characterized) | 35% | 54% | 125.6 | HrtA, component of Probable Heme exporter, HrtAB | 41% | 183.0 |
| D-fructose catabolism | araV | lo | AraV, component of Arabinose, fructose, xylose porter (characterized) | 35% | 54% | 125.6 | HrtA, component of Probable Heme exporter, HrtAB | 41% | 183.0 |
| sucrose catabolism | araV | lo | AraV, component of Arabinose, fructose, xylose porter (characterized) | 35% | 54% | 125.6 | HrtA, component of Probable Heme exporter, HrtAB | 41% | 183.0 |
| D-xylose catabolism | araV | lo | AraV, component of Arabinose, fructose, xylose porter (characterized) | 35% | 54% | 125.6 | HrtA, component of Probable Heme exporter, HrtAB | 41% | 183.0 |
| D-cellobiose catabolism | cbtF | lo | CbtF, component of Cellobiose and cellooligosaccharide porter (characterized) | 34% | 68% | 118.2 | HrtA, component of Probable Heme exporter, HrtAB | 41% | 183.0 |
| D-mannitol catabolism | mtlK | lo | ABC transporter for D-mannitol and D-mannose, ATPase component (characterized) | 35% | 57% | 117.5 | HrtA, component of Probable Heme exporter, HrtAB | 41% | 183.0 |
| 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) | 33% | 74% | 117.1 | HrtA, component of Probable Heme exporter, HrtAB | 41% | 183.0 |
| 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) | 31% | 89% | 116.7 | HrtA, component of Probable Heme exporter, HrtAB | 41% | 183.0 |
| 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) | 31% | 89% | 116.7 | HrtA, component of Probable Heme exporter, HrtAB | 41% | 183.0 |
| 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) | 31% | 89% | 116.7 | HrtA, component of Probable Heme exporter, HrtAB | 41% | 183.0 |
| 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% | 72% | 115.2 | HrtA, component of Probable Heme exporter, HrtAB | 41% | 183.0 |
| D-sorbitol (glucitol) catabolism | mtlK | lo | ABC transporter for D-Mannitol, D-Mannose, and D-Sorbitol, ATPase component (characterized) | 34% | 57% | 114.4 | HrtA, component of Probable Heme exporter, HrtAB | 41% | 183.0 |
| 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) | 36% | 76% | 112.8 | HrtA, component of Probable Heme exporter, HrtAB | 41% | 183.0 |
| D-cellobiose catabolism | SMc04256 | lo | ABC transporter for D-Cellobiose and D-Salicin, ATPase component (characterized) | 31% | 61% | 110.5 | HrtA, component of Probable Heme exporter, HrtAB | 41% | 183.0 |
| D-cellobiose catabolism | cbtD | lo | CbtD, component of Cellobiose and cellooligosaccharide porter (characterized) | 34% | 62% | 109.4 | HrtA, component of Probable Heme exporter, HrtAB | 41% | 183.0 |
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