| Pathway | Step | Score | Similar to | Id. | Cov. | Bits | Other hit | Other id. | Other bits |
|---|
| L-arginine catabolism | artP | med | Arginine transport ATP-binding protein ArtM (characterized) | 42% | 90% | 149.4 | lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- | 44% | 194.1 |
| L-asparagine catabolism | aatP | lo | ABC transporter for L-aspartate, L-asparagine, L-glutamate, and L-glutamine, ATPase component (characterized) | 39% | 89% | 143.3 | lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- | 44% | 194.1 |
| L-aspartate catabolism | aatP | lo | ABC transporter for L-aspartate, L-asparagine, L-glutamate, and L-glutamine, ATPase component (characterized) | 39% | 89% | 143.3 | lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- | 44% | 194.1 |
| D-maltose catabolism | malK | lo | Maltose/maltodextrin import ATP-binding protein MalK; EC 7.5.2.1 (characterized) | 34% | 57% | 133.7 | lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- | 44% | 194.1 |
| D-cellobiose catabolism | gtsD | 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) | 33% | 56% | 131 | lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- | 44% | 194.1 |
| D-glucose catabolism | gtsD | 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) | 33% | 56% | 131 | lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- | 44% | 194.1 |
| lactose catabolism | gtsD | 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) | 33% | 56% | 131 | lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- | 44% | 194.1 |
| D-maltose catabolism | gtsD | 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) | 33% | 56% | 131 | lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- | 44% | 194.1 |
| D-maltose catabolism | thuK | 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) | 33% | 56% | 131 | lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- | 44% | 194.1 |
| 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) | 33% | 56% | 131 | lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- | 44% | 194.1 |
| sucrose catabolism | gtsD | 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) | 33% | 56% | 131 | lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- | 44% | 194.1 |
| sucrose catabolism | thuK | 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) | 33% | 56% | 131 | lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- | 44% | 194.1 |
| trehalose catabolism | gtsD | 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) | 33% | 56% | 131 | lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- | 44% | 194.1 |
| trehalose catabolism | thuK | 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) | 33% | 56% | 131 | lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- | 44% | 194.1 |
| D-cellobiose catabolism | aglK' | lo | Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) | 35% | 56% | 125.6 | lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- | 44% | 194.1 |
| D-glucose catabolism | aglK' | lo | Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) | 35% | 56% | 125.6 | lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- | 44% | 194.1 |
| lactose catabolism | aglK' | lo | Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) | 35% | 56% | 125.6 | lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- | 44% | 194.1 |
| D-maltose catabolism | aglK | lo | Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) | 35% | 56% | 125.6 | lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- | 44% | 194.1 |
| D-maltose catabolism | aglK' | lo | Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) | 35% | 56% | 125.6 | lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- | 44% | 194.1 |
| sucrose catabolism | aglK | lo | Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) | 35% | 56% | 125.6 | lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- | 44% | 194.1 |
| sucrose catabolism | aglK' | lo | Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) | 35% | 56% | 125.6 | lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- | 44% | 194.1 |
| trehalose catabolism | aglK | lo | Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) | 35% | 56% | 125.6 | lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- | 44% | 194.1 |
| trehalose catabolism | aglK' | lo | Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) | 35% | 56% | 125.6 | lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- | 44% | 194.1 |
| D-alanine catabolism | AZOBR_RS08250 | lo | Leucine//isoleucine/valine ABC transporter,ATPase component; EC 3.6.3.- (characterized, see rationale) | 32% | 90% | 106.7 | lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- | 44% | 194.1 |
| L-proline catabolism | AZOBR_RS08250 | lo | Leucine//isoleucine/valine ABC transporter,ATPase component; EC 3.6.3.- (characterized, see rationale) | 32% | 90% | 106.7 | lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- | 44% | 194.1 |
| L-isoleucine catabolism | livG | lo | ABC transporter ATP-binding protein (characterized, see rationale) | 30% | 88% | 105.9 | lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- | 44% | 194.1 |
| L-leucine catabolism | livG | lo | ABC transporter ATP-binding protein (characterized, see rationale) | 30% | 88% | 105.9 | lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- | 44% | 194.1 |
| L-phenylalanine catabolism | livG | lo | ABC transporter ATP-binding protein (characterized, see rationale) | 30% | 88% | 105.9 | lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- | 44% | 194.1 |
| L-proline catabolism | HSERO_RS00895 | lo | ABC transporter ATP-binding protein (characterized, see rationale) | 30% | 88% | 105.9 | lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- | 44% | 194.1 |
| L-serine catabolism | Ac3H11_1693 | lo | ABC transporter ATP-binding protein (characterized, see rationale) | 30% | 88% | 105.9 | lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- | 44% | 194.1 |
| L-tyrosine catabolism | Ac3H11_1693 | lo | ABC transporter ATP-binding protein (characterized, see rationale) | 30% | 88% | 105.9 | lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- | 44% | 194.1 |
| L-isoleucine catabolism | livF | lo | ABC transporter ATP-binding protein (characterized, see rationale) | 33% | 88% | 100.5 | lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- | 44% | 194.1 |
| L-leucine catabolism | livF | lo | ABC transporter ATP-binding protein (characterized, see rationale) | 33% | 88% | 100.5 | lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- | 44% | 194.1 |
| L-phenylalanine catabolism | livF | lo | ABC transporter ATP-binding protein (characterized, see rationale) | 33% | 88% | 100.5 | lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- | 44% | 194.1 |
| L-proline catabolism | HSERO_RS00900 | lo | ABC transporter ATP-binding protein (characterized, see rationale) | 33% | 88% | 100.5 | lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- | 44% | 194.1 |
| L-serine catabolism | Ac3H11_1692 | lo | ABC transporter ATP-binding protein (characterized, see rationale) | 33% | 88% | 100.5 | lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- | 44% | 194.1 |
| L-tyrosine catabolism | Ac3H11_1692 | lo | ABC transporter ATP-binding protein (characterized, see rationale) | 33% | 88% | 100.5 | lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- | 44% | 194.1 |
This GapMind analysis is from Sep 24 2021. 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