| 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) | 40% | 82% | 154.1 | cell division ATP-binding protein ftsE | 54% | 224.6 |
| L-asparagine catabolism | bgtA | med | ATPase (characterized, see rationale) | 41% | 75% | 135.6 | cell division ATP-binding protein ftsE | 54% | 224.6 |
| L-aspartate catabolism | bgtA | med | ATPase (characterized, see rationale) | 41% | 75% | 135.6 | cell division ATP-binding protein ftsE | 54% | 224.6 |
| L-histidine catabolism | PA5503 | lo | Methionine import ATP-binding protein MetN 2, component of L-Histidine uptake porter, MetIQN (characterized) | 39% | 67% | 148.7 | cell division ATP-binding protein ftsE | 54% | 224.6 |
| L-asparagine catabolism | aatP | lo | Glutamate/aspartate transport ATP-binding protein GltL aka B0652, component of Glutamate/aspartate porter (characterized) | 38% | 89% | 141.7 | cell division ATP-binding protein ftsE | 54% | 224.6 |
| L-aspartate catabolism | aatP | lo | Glutamate/aspartate transport ATP-binding protein GltL aka B0652, component of Glutamate/aspartate porter (characterized) | 38% | 89% | 141.7 | cell division ATP-binding protein ftsE | 54% | 224.6 |
| L-glutamate catabolism | gltL | lo | Glutamate/aspartate transport ATP-binding protein GltL aka B0652, component of Glutamate/aspartate porter (characterized) | 38% | 89% | 141.7 | cell division ATP-binding protein ftsE | 54% | 224.6 |
| L-histidine catabolism | aapP | lo | ABC transporter for L-Glutamine, L-Histidine, and other L-amino acids, ATPase component (characterized) | 36% | 87% | 141.4 | cell division ATP-binding protein ftsE | 54% | 224.6 |
| L-arginine catabolism | artP | lo | BgtA aka SLR1735, component of Arginine/lysine/histidine/glutamine porter (characterized) | 37% | 89% | 139.8 | cell division ATP-binding protein ftsE | 54% | 224.6 |
| 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) | 35% | 86% | 139.8 | cell division ATP-binding protein ftsE | 54% | 224.6 |
| 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) | 35% | 86% | 139.8 | cell division ATP-binding protein ftsE | 54% | 224.6 |
| 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) | 35% | 86% | 139.8 | cell division ATP-binding protein ftsE | 54% | 224.6 |
| L-histidine catabolism | bgtA | lo | BgtA aka SLR1735, component of Arginine/lysine/histidine/glutamine porter (characterized) | 37% | 89% | 139.8 | cell division ATP-binding protein ftsE | 54% | 224.6 |
| 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) | 35% | 86% | 139.8 | cell division ATP-binding protein ftsE | 54% | 224.6 |
| 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) | 35% | 86% | 139.8 | cell division ATP-binding protein ftsE | 54% | 224.6 |
| D-alanine catabolism | Pf6N2E2_5405 | lo | ABC transporter for D-Alanine, ATPase component (characterized) | 36% | 84% | 139 | cell division ATP-binding protein ftsE | 54% | 224.6 |
| L-histidine catabolism | hisP | lo | histidine transport ATP-binding protein hisP (characterized) | 37% | 89% | 137.1 | cell division ATP-binding protein ftsE | 54% | 224.6 |
| 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) | 35% | 83% | 136.3 | cell division ATP-binding protein ftsE | 54% | 224.6 |
| L-asparagine catabolism | peb1C | lo | PEB1C, component of Uptake system for glutamate and aspartate (characterized) | 35% | 92% | 135.6 | cell division ATP-binding protein ftsE | 54% | 224.6 |
| L-aspartate catabolism | peb1C | lo | PEB1C, component of Uptake system for glutamate and aspartate (characterized) | 35% | 92% | 135.6 | cell division ATP-binding protein ftsE | 54% | 224.6 |
| xylitol catabolism | HSERO_RS17020 | lo | ABC-type sugar transport system, ATPase component protein (characterized, see rationale) | 36% | 52% | 133.7 | cell division ATP-binding protein ftsE | 54% | 224.6 |
| D-maltose catabolism | thuK | lo | ThuK aka RB0314 aka SMB20328, component of Trehalose/maltose/sucrose porter (trehalose inducible) (characterized) | 37% | 64% | 131.3 | cell division ATP-binding protein ftsE | 54% | 224.6 |
| sucrose catabolism | thuK | lo | ThuK aka RB0314 aka SMB20328, component of Trehalose/maltose/sucrose porter (trehalose inducible) (characterized) | 37% | 64% | 131.3 | cell division ATP-binding protein ftsE | 54% | 224.6 |
| trehalose catabolism | thuK | lo | ThuK aka RB0314 aka SMB20328, component of Trehalose/maltose/sucrose porter (trehalose inducible) (characterized) | 37% | 64% | 131.3 | cell division ATP-binding protein ftsE | 54% | 224.6 |
| D-sorbitol (glucitol) catabolism | mtlK | lo | ABC transporter for D-Sorbitol, ATPase component (characterized) | 34% | 61% | 127.9 | cell division ATP-binding protein ftsE | 54% | 224.6 |
| D-mannitol catabolism | mtlK | lo | MtlK, component of The polyol (mannitol, glucitol (sorbitol), arabitol (arabinitol; lyxitol)) uptake porter, MtlEFGK (characterized) | 35% | 58% | 125.6 | cell division ATP-binding protein ftsE | 54% | 224.6 |
| N-acetyl-D-glucosamine catabolism | SMc02869 | lo | N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized) | 34% | 58% | 124.8 | cell division ATP-binding protein ftsE | 54% | 224.6 |
| D-glucosamine (chitosamine) catabolism | SMc02869 | lo | N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized) | 34% | 58% | 124.8 | cell division ATP-binding protein ftsE | 54% | 224.6 |
| D-cellobiose catabolism | aglK' | lo | Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) | 35% | 58% | 124.4 | cell division ATP-binding protein ftsE | 54% | 224.6 |
| D-glucose catabolism | aglK' | lo | Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) | 35% | 58% | 124.4 | cell division ATP-binding protein ftsE | 54% | 224.6 |
| lactose catabolism | aglK' | lo | Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) | 35% | 58% | 124.4 | cell division ATP-binding protein ftsE | 54% | 224.6 |
| D-maltose catabolism | aglK | lo | Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) | 35% | 58% | 124.4 | cell division ATP-binding protein ftsE | 54% | 224.6 |
| D-maltose catabolism | aglK' | lo | Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) | 35% | 58% | 124.4 | cell division ATP-binding protein ftsE | 54% | 224.6 |
| sucrose catabolism | aglK | lo | Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) | 35% | 58% | 124.4 | cell division ATP-binding protein ftsE | 54% | 224.6 |
| sucrose catabolism | aglK' | lo | Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) | 35% | 58% | 124.4 | cell division ATP-binding protein ftsE | 54% | 224.6 |
| trehalose catabolism | aglK | lo | Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) | 35% | 58% | 124.4 | cell division ATP-binding protein ftsE | 54% | 224.6 |
| trehalose catabolism | aglK' | lo | Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) | 35% | 58% | 124.4 | cell division ATP-binding protein ftsE | 54% | 224.6 |
| D-maltose catabolism | malK | lo | Maltose-transporting ATPase (EC 3.6.3.19) (characterized) | 33% | 57% | 123.2 | cell division ATP-binding protein ftsE | 54% | 224.6 |
| trehalose catabolism | treV | lo | TreV, component of Trehalose porter (characterized) | 33% | 64% | 119.4 | cell division ATP-binding protein ftsE | 54% | 224.6 |
| D-cellobiose catabolism | gtsD | lo | ABC transporter for D-Galactose and D-Glucose, ATPase component (characterized) | 33% | 56% | 119 | cell division ATP-binding protein ftsE | 54% | 224.6 |
| D-galactose catabolism | PfGW456L13_1897 | lo | ABC transporter for D-Galactose and D-Glucose, ATPase component (characterized) | 33% | 56% | 119 | cell division ATP-binding protein ftsE | 54% | 224.6 |
| D-glucose catabolism | gtsD | lo | ABC transporter for D-Galactose and D-Glucose, ATPase component (characterized) | 33% | 56% | 119 | cell division ATP-binding protein ftsE | 54% | 224.6 |
| lactose catabolism | gtsD | lo | ABC transporter for D-Galactose and D-Glucose, ATPase component (characterized) | 33% | 56% | 119 | cell division ATP-binding protein ftsE | 54% | 224.6 |
| D-maltose catabolism | gtsD | lo | ABC transporter for D-Galactose and D-Glucose, ATPase component (characterized) | 33% | 56% | 119 | cell division ATP-binding protein ftsE | 54% | 224.6 |
| sucrose catabolism | gtsD | lo | ABC transporter for D-Galactose and D-Glucose, ATPase component (characterized) | 33% | 56% | 119 | cell division ATP-binding protein ftsE | 54% | 224.6 |
| trehalose catabolism | gtsD | lo | ABC transporter for D-Galactose and D-Glucose, ATPase component (characterized) | 33% | 56% | 119 | cell division ATP-binding protein ftsE | 54% | 224.6 |
| L-arabinose catabolism | xacK | lo | Xylose/arabinose import ATP-binding protein XacK; EC 7.5.2.13 (characterized, see rationale) | 35% | 56% | 118.6 | cell division ATP-binding protein ftsE | 54% | 224.6 |
| D-xylose catabolism | gtsD | lo | ABC transporter for D-Glucose-6-Phosphate, ATPase component (characterized) | 33% | 57% | 114.8 | cell division ATP-binding protein ftsE | 54% | 224.6 |
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