| Pathway | Step | Score | Similar to | Id. | Cov. | Bits | Other hit | Other id. | Other bits |
|---|
| trehalose catabolism | treV | lo | TreV, component of Trehalose porter (characterized) | 34% | 90% | 157.9 | Molybdenum ABC transporter, ATP-binding protein, component of The molybdate/tungstate ABC transporter, ModABC. The trans-inhibited 3-d structure of ModABC, is available (3D31.A and 3D31.B)(Gerber et al., 2008) | 41% | 199.5 |
| putrescine catabolism | potA | lo | PotG aka B0855, component of Putrescine porter (characterized) | 31% | 78% | 156.4 | Molybdenum ABC transporter, ATP-binding protein, component of The molybdate/tungstate ABC transporter, ModABC. The trans-inhibited 3-d structure of ModABC, is available (3D31.A and 3D31.B)(Gerber et al., 2008) | 41% | 199.5 |
| D-sorbitol (glucitol) catabolism | mtlK | lo | ABC transporter for D-Sorbitol, ATPase component (characterized) | 36% | 67% | 156 | Molybdenum ABC transporter, ATP-binding protein, component of The molybdate/tungstate ABC transporter, ModABC. The trans-inhibited 3-d structure of ModABC, is available (3D31.A and 3D31.B)(Gerber et al., 2008) | 41% | 199.5 |
| D-cellobiose catabolism | SMc04256 | lo | ABC transporter for D-Cellobiose and D-Salicin, ATPase component (characterized) | 34% | 71% | 149.1 | Molybdenum ABC transporter, ATP-binding protein, component of The molybdate/tungstate ABC transporter, ModABC. The trans-inhibited 3-d structure of ModABC, is available (3D31.A and 3D31.B)(Gerber et al., 2008) | 41% | 199.5 |
| D-mannitol catabolism | mtlK | lo | MtlK, component of The polyol (mannitol, glucitol (sorbitol), arabitol (arabinitol; lyxitol)) uptake porter, MtlEFGK (characterized) | 34% | 68% | 149.1 | Molybdenum ABC transporter, ATP-binding protein, component of The molybdate/tungstate ABC transporter, ModABC. The trans-inhibited 3-d structure of ModABC, is available (3D31.A and 3D31.B)(Gerber et al., 2008) | 41% | 199.5 |
| D-cellobiose catabolism | gtsD | lo | ABC transporter for D-Galactose and D-Glucose, ATPase component (characterized) | 35% | 62% | 146.4 | Molybdenum ABC transporter, ATP-binding protein, component of The molybdate/tungstate ABC transporter, ModABC. The trans-inhibited 3-d structure of ModABC, is available (3D31.A and 3D31.B)(Gerber et al., 2008) | 41% | 199.5 |
| D-galactose catabolism | PfGW456L13_1897 | lo | ABC transporter for D-Galactose and D-Glucose, ATPase component (characterized) | 35% | 62% | 146.4 | Molybdenum ABC transporter, ATP-binding protein, component of The molybdate/tungstate ABC transporter, ModABC. The trans-inhibited 3-d structure of ModABC, is available (3D31.A and 3D31.B)(Gerber et al., 2008) | 41% | 199.5 |
| D-glucose catabolism | gtsD | lo | ABC transporter for D-Galactose and D-Glucose, ATPase component (characterized) | 35% | 62% | 146.4 | Molybdenum ABC transporter, ATP-binding protein, component of The molybdate/tungstate ABC transporter, ModABC. The trans-inhibited 3-d structure of ModABC, is available (3D31.A and 3D31.B)(Gerber et al., 2008) | 41% | 199.5 |
| lactose catabolism | gtsD | lo | ABC transporter for D-Galactose and D-Glucose, ATPase component (characterized) | 35% | 62% | 146.4 | Molybdenum ABC transporter, ATP-binding protein, component of The molybdate/tungstate ABC transporter, ModABC. The trans-inhibited 3-d structure of ModABC, is available (3D31.A and 3D31.B)(Gerber et al., 2008) | 41% | 199.5 |
| D-maltose catabolism | gtsD | lo | ABC transporter for D-Galactose and D-Glucose, ATPase component (characterized) | 35% | 62% | 146.4 | Molybdenum ABC transporter, ATP-binding protein, component of The molybdate/tungstate ABC transporter, ModABC. The trans-inhibited 3-d structure of ModABC, is available (3D31.A and 3D31.B)(Gerber et al., 2008) | 41% | 199.5 |
| sucrose catabolism | gtsD | lo | ABC transporter for D-Galactose and D-Glucose, ATPase component (characterized) | 35% | 62% | 146.4 | Molybdenum ABC transporter, ATP-binding protein, component of The molybdate/tungstate ABC transporter, ModABC. The trans-inhibited 3-d structure of ModABC, is available (3D31.A and 3D31.B)(Gerber et al., 2008) | 41% | 199.5 |
| trehalose catabolism | gtsD | lo | ABC transporter for D-Galactose and D-Glucose, ATPase component (characterized) | 35% | 62% | 146.4 | Molybdenum ABC transporter, ATP-binding protein, component of The molybdate/tungstate ABC transporter, ModABC. The trans-inhibited 3-d structure of ModABC, is available (3D31.A and 3D31.B)(Gerber et al., 2008) | 41% | 199.5 |
| L-arabinose catabolism | xacJ | lo | Xylose/arabinose import ATP-binding protein XacJ; EC 7.5.2.13 (characterized, see rationale) | 33% | 62% | 145.2 | Molybdenum ABC transporter, ATP-binding protein, component of The molybdate/tungstate ABC transporter, ModABC. The trans-inhibited 3-d structure of ModABC, is available (3D31.A and 3D31.B)(Gerber et al., 2008) | 41% | 199.5 |
| D-xylose catabolism | gtsD | lo | ABC transporter for D-Glucose-6-Phosphate, ATPase component (characterized) | 36% | 61% | 145.2 | Molybdenum ABC transporter, ATP-binding protein, component of The molybdate/tungstate ABC transporter, ModABC. The trans-inhibited 3-d structure of ModABC, is available (3D31.A and 3D31.B)(Gerber et al., 2008) | 41% | 199.5 |
| N-acetyl-D-glucosamine catabolism | SMc02869 | lo | N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized) | 33% | 80% | 141.7 | Molybdenum ABC transporter, ATP-binding protein, component of The molybdate/tungstate ABC transporter, ModABC. The trans-inhibited 3-d structure of ModABC, is available (3D31.A and 3D31.B)(Gerber et al., 2008) | 41% | 199.5 |
| D-glucosamine (chitosamine) catabolism | SMc02869 | lo | N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized) | 33% | 80% | 141.7 | Molybdenum ABC transporter, ATP-binding protein, component of The molybdate/tungstate ABC transporter, ModABC. The trans-inhibited 3-d structure of ModABC, is available (3D31.A and 3D31.B)(Gerber et al., 2008) | 41% | 199.5 |
| D-maltose catabolism | malK | lo | Maltose-transporting ATPase (EC 3.6.3.19) (characterized) | 32% | 63% | 141.4 | Molybdenum ABC transporter, ATP-binding protein, component of The molybdate/tungstate ABC transporter, ModABC. The trans-inhibited 3-d structure of ModABC, is available (3D31.A and 3D31.B)(Gerber et al., 2008) | 41% | 199.5 |
| D-maltose catabolism | thuK | lo | ThuK aka RB0314 aka SMB20328, component of Trehalose/maltose/sucrose porter (trehalose inducible) (characterized) | 32% | 78% | 141.4 | Molybdenum ABC transporter, ATP-binding protein, component of The molybdate/tungstate ABC transporter, ModABC. The trans-inhibited 3-d structure of ModABC, is available (3D31.A and 3D31.B)(Gerber et al., 2008) | 41% | 199.5 |
| sucrose catabolism | thuK | lo | ThuK aka RB0314 aka SMB20328, component of Trehalose/maltose/sucrose porter (trehalose inducible) (characterized) | 32% | 78% | 141.4 | Molybdenum ABC transporter, ATP-binding protein, component of The molybdate/tungstate ABC transporter, ModABC. The trans-inhibited 3-d structure of ModABC, is available (3D31.A and 3D31.B)(Gerber et al., 2008) | 41% | 199.5 |
| trehalose catabolism | thuK | lo | ThuK aka RB0314 aka SMB20328, component of Trehalose/maltose/sucrose porter (trehalose inducible) (characterized) | 32% | 78% | 141.4 | Molybdenum ABC transporter, ATP-binding protein, component of The molybdate/tungstate ABC transporter, ModABC. The trans-inhibited 3-d structure of ModABC, is available (3D31.A and 3D31.B)(Gerber et al., 2008) | 41% | 199.5 |
| L-fucose catabolism | SM_b21106 | lo | ABC transporter for L-Fucose, ATPase component (characterized) | 35% | 64% | 141 | Molybdenum ABC transporter, ATP-binding protein, component of The molybdate/tungstate ABC transporter, ModABC. The trans-inhibited 3-d structure of ModABC, is available (3D31.A and 3D31.B)(Gerber et al., 2008) | 41% | 199.5 |
| xylitol catabolism | HSERO_RS17020 | lo | ABC-type sugar transport system, ATPase component protein (characterized, see rationale) | 34% | 53% | 140.6 | Molybdenum ABC transporter, ATP-binding protein, component of The molybdate/tungstate ABC transporter, ModABC. The trans-inhibited 3-d structure of ModABC, is available (3D31.A and 3D31.B)(Gerber et al., 2008) | 41% | 199.5 |
| D-maltose catabolism | malK_Bb | lo | ABC-type maltose transport, ATP binding protein (characterized, see rationale) | 34% | 68% | 138.3 | Molybdenum ABC transporter, ATP-binding protein, component of The molybdate/tungstate ABC transporter, ModABC. The trans-inhibited 3-d structure of ModABC, is available (3D31.A and 3D31.B)(Gerber et al., 2008) | 41% | 199.5 |
| 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) | 34% | 58% | 137.5 | Molybdenum ABC transporter, ATP-binding protein, component of The molybdate/tungstate ABC transporter, ModABC. The trans-inhibited 3-d structure of ModABC, is available (3D31.A and 3D31.B)(Gerber et al., 2008) | 41% | 199.5 |
| lactose catabolism | lacK | lo | ABC transporter for Lactose, ATPase component (characterized) | 33% | 68% | 134.4 | Molybdenum ABC transporter, ATP-binding protein, component of The molybdate/tungstate ABC transporter, ModABC. The trans-inhibited 3-d structure of ModABC, is available (3D31.A and 3D31.B)(Gerber et al., 2008) | 41% | 199.5 |
| D-glucosamine (chitosamine) catabolism | SM_b21216 | lo | ABC transporter for D-Glucosamine, ATPase component (characterized) | 34% | 67% | 134 | Molybdenum ABC transporter, ATP-binding protein, component of The molybdate/tungstate ABC transporter, ModABC. The trans-inhibited 3-d structure of ModABC, is available (3D31.A and 3D31.B)(Gerber et al., 2008) | 41% | 199.5 |
| D-cellobiose catabolism | aglK' | lo | Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) | 32% | 66% | 132.9 | Molybdenum ABC transporter, ATP-binding protein, component of The molybdate/tungstate ABC transporter, ModABC. The trans-inhibited 3-d structure of ModABC, is available (3D31.A and 3D31.B)(Gerber et al., 2008) | 41% | 199.5 |
| D-glucose catabolism | aglK' | lo | Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) | 32% | 66% | 132.9 | Molybdenum ABC transporter, ATP-binding protein, component of The molybdate/tungstate ABC transporter, ModABC. The trans-inhibited 3-d structure of ModABC, is available (3D31.A and 3D31.B)(Gerber et al., 2008) | 41% | 199.5 |
| lactose catabolism | aglK' | lo | Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) | 32% | 66% | 132.9 | Molybdenum ABC transporter, ATP-binding protein, component of The molybdate/tungstate ABC transporter, ModABC. The trans-inhibited 3-d structure of ModABC, is available (3D31.A and 3D31.B)(Gerber et al., 2008) | 41% | 199.5 |
| D-maltose catabolism | aglK | lo | Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) | 32% | 66% | 132.9 | Molybdenum ABC transporter, ATP-binding protein, component of The molybdate/tungstate ABC transporter, ModABC. The trans-inhibited 3-d structure of ModABC, is available (3D31.A and 3D31.B)(Gerber et al., 2008) | 41% | 199.5 |
| D-maltose catabolism | aglK' | lo | Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) | 32% | 66% | 132.9 | Molybdenum ABC transporter, ATP-binding protein, component of The molybdate/tungstate ABC transporter, ModABC. The trans-inhibited 3-d structure of ModABC, is available (3D31.A and 3D31.B)(Gerber et al., 2008) | 41% | 199.5 |
| sucrose catabolism | aglK | lo | Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) | 32% | 66% | 132.9 | Molybdenum ABC transporter, ATP-binding protein, component of The molybdate/tungstate ABC transporter, ModABC. The trans-inhibited 3-d structure of ModABC, is available (3D31.A and 3D31.B)(Gerber et al., 2008) | 41% | 199.5 |
| sucrose catabolism | aglK' | lo | Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) | 32% | 66% | 132.9 | Molybdenum ABC transporter, ATP-binding protein, component of The molybdate/tungstate ABC transporter, ModABC. The trans-inhibited 3-d structure of ModABC, is available (3D31.A and 3D31.B)(Gerber et al., 2008) | 41% | 199.5 |
| trehalose catabolism | aglK | lo | Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) | 32% | 66% | 132.9 | Molybdenum ABC transporter, ATP-binding protein, component of The molybdate/tungstate ABC transporter, ModABC. The trans-inhibited 3-d structure of ModABC, is available (3D31.A and 3D31.B)(Gerber et al., 2008) | 41% | 199.5 |
| trehalose catabolism | aglK' | lo | Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) | 32% | 66% | 132.9 | Molybdenum ABC transporter, ATP-binding protein, component of The molybdate/tungstate ABC transporter, ModABC. The trans-inhibited 3-d structure of ModABC, is available (3D31.A and 3D31.B)(Gerber et al., 2008) | 41% | 199.5 |
| 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) | 32% | 58% | 129.4 | Molybdenum ABC transporter, ATP-binding protein, component of The molybdate/tungstate ABC transporter, ModABC. The trans-inhibited 3-d structure of ModABC, is available (3D31.A and 3D31.B)(Gerber et al., 2008) | 41% | 199.5 |
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