| Pathway | Step | Score | Similar to | Id. | Cov. | Bits | Other hit | Other id. | Other bits |
|---|
| D-cellobiose catabolism | gtsD | med | Sugar ABC transporter ATP-binding protein (characterized, see rationale) | 41% | 93% | 230.7 | FutC aka SLL1878, component of Ferric iron (Fe3+) porter | 40% | 239.6 |
| D-glucose catabolism | gtsD | med | Sugar ABC transporter ATP-binding protein (characterized, see rationale) | 41% | 93% | 230.7 | FutC aka SLL1878, component of Ferric iron (Fe3+) porter | 40% | 239.6 |
| lactose catabolism | gtsD | med | Sugar ABC transporter ATP-binding protein (characterized, see rationale) | 41% | 93% | 230.7 | FutC aka SLL1878, component of Ferric iron (Fe3+) porter | 40% | 239.6 |
| D-maltose catabolism | gtsD | med | Sugar ABC transporter ATP-binding protein (characterized, see rationale) | 41% | 93% | 230.7 | FutC aka SLL1878, component of Ferric iron (Fe3+) porter | 40% | 239.6 |
| sucrose catabolism | gtsD | med | Sugar ABC transporter ATP-binding protein (characterized, see rationale) | 41% | 93% | 230.7 | FutC aka SLL1878, component of Ferric iron (Fe3+) porter | 40% | 239.6 |
| trehalose catabolism | gtsD | med | Sugar ABC transporter ATP-binding protein (characterized, see rationale) | 41% | 93% | 230.7 | FutC aka SLL1878, component of Ferric iron (Fe3+) porter | 40% | 239.6 |
| D-cellobiose catabolism | msiK | med | 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) | 41% | 93% | 223.8 | FutC aka SLL1878, component of Ferric iron (Fe3+) porter | 40% | 239.6 |
| D-sorbitol (glucitol) catabolism | mtlK | med | ABC transporter for D-Sorbitol, ATPase component (characterized) | 44% | 79% | 222.2 | FutC aka SLL1878, component of Ferric iron (Fe3+) porter | 40% | 239.6 |
| L-fucose catabolism | SM_b21106 | med | ABC transporter for L-Fucose, ATPase component (characterized) | 40% | 90% | 221.1 | FutC aka SLL1878, component of Ferric iron (Fe3+) porter | 40% | 239.6 |
| lactose catabolism | lacK | med | LacK, component of Lactose porter (characterized) | 44% | 79% | 214.9 | FutC aka SLL1878, component of Ferric iron (Fe3+) porter | 40% | 239.6 |
| D-glucosamine (chitosamine) catabolism | SM_b21216 | med | ABC transporter for D-Glucosamine, ATPase component (characterized) | 43% | 81% | 213.8 | FutC aka SLL1878, component of Ferric iron (Fe3+) porter | 40% | 239.6 |
| N-acetyl-D-glucosamine catabolism | SMc02869 | med | N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized) | 41% | 89% | 210.7 | FutC aka SLL1878, component of Ferric iron (Fe3+) porter | 40% | 239.6 |
| D-glucosamine (chitosamine) catabolism | SMc02869 | med | N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized) | 41% | 89% | 210.7 | FutC aka SLL1878, component of Ferric iron (Fe3+) porter | 40% | 239.6 |
| D-cellobiose catabolism | aglK' | med | Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) | 41% | 79% | 206.8 | FutC aka SLL1878, component of Ferric iron (Fe3+) porter | 40% | 239.6 |
| D-glucose catabolism | aglK' | med | Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) | 41% | 79% | 206.8 | FutC aka SLL1878, component of Ferric iron (Fe3+) porter | 40% | 239.6 |
| lactose catabolism | aglK' | med | Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) | 41% | 79% | 206.8 | FutC aka SLL1878, component of Ferric iron (Fe3+) porter | 40% | 239.6 |
| D-maltose catabolism | aglK | med | Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) | 41% | 79% | 206.8 | FutC aka SLL1878, component of Ferric iron (Fe3+) porter | 40% | 239.6 |
| D-maltose catabolism | aglK' | med | Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) | 41% | 79% | 206.8 | FutC aka SLL1878, component of Ferric iron (Fe3+) porter | 40% | 239.6 |
| sucrose catabolism | aglK | med | Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) | 41% | 79% | 206.8 | FutC aka SLL1878, component of Ferric iron (Fe3+) porter | 40% | 239.6 |
| sucrose catabolism | aglK' | med | Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) | 41% | 79% | 206.8 | FutC aka SLL1878, component of Ferric iron (Fe3+) porter | 40% | 239.6 |
| trehalose catabolism | aglK | med | Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) | 41% | 79% | 206.8 | FutC aka SLL1878, component of Ferric iron (Fe3+) porter | 40% | 239.6 |
| trehalose catabolism | aglK' | med | Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) | 41% | 79% | 206.8 | FutC aka SLL1878, component of Ferric iron (Fe3+) porter | 40% | 239.6 |
| xylitol catabolism | Dshi_0546 | med | ABC transporter for Xylitol, ATPase component (characterized) | 47% | 70% | 206.5 | FutC aka SLL1878, component of Ferric iron (Fe3+) porter | 40% | 239.6 |
| D-maltose catabolism | musK | med | ABC-type maltose transporter (EC 7.5.2.1) (characterized) | 40% | 76% | 203.4 | FutC aka SLL1878, component of Ferric iron (Fe3+) porter | 40% | 239.6 |
| D-mannitol catabolism | mtlK | med | SmoK aka POLK, component of Hexitol (glucitol; mannitol) porter (characterized) | 44% | 70% | 203 | FutC aka SLL1878, component of Ferric iron (Fe3+) porter | 40% | 239.6 |
| L-arabinose catabolism | xacJ | med | Xylose/arabinose import ATP-binding protein XacJ; EC 7.5.2.13 (characterized, see rationale) | 40% | 77% | 195.7 | FutC aka SLL1878, component of Ferric iron (Fe3+) porter | 40% | 239.6 |
| xylitol catabolism | HSERO_RS17020 | lo | ABC-type sugar transport system, ATPase component protein (characterized, see rationale) | 38% | 99% | 226.9 | FutC aka SLL1878, component of Ferric iron (Fe3+) porter | 40% | 239.6 |
| D-maltose catabolism | malK_Bb | lo | ABC-type maltose transport, ATP binding protein (characterized, see rationale) | 38% | 90% | 218.8 | FutC aka SLL1878, component of Ferric iron (Fe3+) porter | 40% | 239.6 |
| D-maltose catabolism | malK1 | lo | MalK; aka Sugar ABC transporter, ATP-binding protein, component of The maltose, maltotriose, mannotetraose (MalE1)/maltose, maltotriose, trehalose (MalE2) porter (Nanavati et al., 2005). For MalG1 (823aas) and MalG2 (833aas), the C-terminal transmembrane domain with 6 putative TMSs is preceded by a single N-terminal TMS and a large (600 residue) hydrophilic region showing sequence similarity to MLP1 and 2 (9.A.14; e-12 & e-7) as well as other proteins (characterized) | 37% | 98% | 211.1 | FutC aka SLL1878, component of Ferric iron (Fe3+) porter | 40% | 239.6 |
| trehalose catabolism | thuK | lo | MalK; aka Sugar ABC transporter, ATP-binding protein, component of The maltose, maltotriose, mannotetraose (MalE1)/maltose, maltotriose, trehalose (MalE2) porter (Nanavati et al., 2005). For MalG1 (823aas) and MalG2 (833aas), the C-terminal transmembrane domain with 6 putative TMSs is preceded by a single N-terminal TMS and a large (600 residue) hydrophilic region showing sequence similarity to MLP1 and 2 (9.A.14; e-12 & e-7) as well as other proteins (characterized) | 37% | 98% | 211.1 | FutC aka SLL1878, component of Ferric iron (Fe3+) porter | 40% | 239.6 |
| sucrose catabolism | thuK | lo | ABC transporter (characterized, see rationale) | 35% | 99% | 205.7 | FutC aka SLL1878, component of Ferric iron (Fe3+) porter | 40% | 239.6 |
| 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) | 37% | 95% | 204.5 | FutC aka SLL1878, component of Ferric iron (Fe3+) porter | 40% | 239.6 |
| 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) | 37% | 95% | 204.5 | FutC aka SLL1878, component of Ferric iron (Fe3+) porter | 40% | 239.6 |
| D-cellobiose catabolism | glcV | lo | monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) | 39% | 80% | 199.9 | FutC aka SLL1878, component of Ferric iron (Fe3+) porter | 40% | 239.6 |
| D-galactose catabolism | glcV | lo | monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) | 39% | 80% | 199.9 | FutC aka SLL1878, component of Ferric iron (Fe3+) porter | 40% | 239.6 |
| D-glucose catabolism | glcV | lo | monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) | 39% | 80% | 199.9 | FutC aka SLL1878, component of Ferric iron (Fe3+) porter | 40% | 239.6 |
| lactose catabolism | glcV | lo | monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) | 39% | 80% | 199.9 | FutC aka SLL1878, component of Ferric iron (Fe3+) porter | 40% | 239.6 |
| D-maltose catabolism | glcV | lo | monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) | 39% | 80% | 199.9 | FutC aka SLL1878, component of Ferric iron (Fe3+) porter | 40% | 239.6 |
| D-mannose catabolism | glcV | lo | monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) | 39% | 80% | 199.9 | FutC aka SLL1878, component of Ferric iron (Fe3+) porter | 40% | 239.6 |
| sucrose catabolism | glcV | lo | monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) | 39% | 80% | 199.9 | FutC aka SLL1878, component of Ferric iron (Fe3+) porter | 40% | 239.6 |
| trehalose catabolism | glcV | lo | monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) | 39% | 80% | 199.9 | FutC aka SLL1878, component of Ferric iron (Fe3+) porter | 40% | 239.6 |
| D-maltose catabolism | malK | lo | Maltose-transporting ATPase (EC 3.6.3.19) (characterized) | 40% | 77% | 198 | FutC aka SLL1878, component of Ferric iron (Fe3+) porter | 40% | 239.6 |
| L-arabinose catabolism | araV | lo | AraV, component of Arabinose, fructose, xylose porter (characterized) | 42% | 65% | 193 | FutC aka SLL1878, component of Ferric iron (Fe3+) porter | 40% | 239.6 |
| D-fructose catabolism | araV | lo | AraV, component of Arabinose, fructose, xylose porter (characterized) | 42% | 65% | 193 | FutC aka SLL1878, component of Ferric iron (Fe3+) porter | 40% | 239.6 |
| sucrose catabolism | araV | lo | AraV, component of Arabinose, fructose, xylose porter (characterized) | 42% | 65% | 193 | FutC aka SLL1878, component of Ferric iron (Fe3+) porter | 40% | 239.6 |
| D-xylose catabolism | araV | lo | AraV, component of Arabinose, fructose, xylose porter (characterized) | 42% | 65% | 193 | FutC aka SLL1878, component of Ferric iron (Fe3+) porter | 40% | 239.6 |
| trehalose catabolism | treV | lo | TreV, component of Trehalose porter (characterized) | 43% | 69% | 189.5 | FutC aka SLL1878, component of Ferric iron (Fe3+) porter | 40% | 239.6 |
| glycerol catabolism | glpS | lo | GlpS, component of Glycerol uptake porter, GlpSTPQV (characterized) | 37% | 78% | 166.4 | FutC aka SLL1878, component of Ferric iron (Fe3+) porter | 40% | 239.6 |
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