| Pathway | Step | Score | Similar to | Id. | Cov. | Bits | Other hit | Other id. | Other bits |
|---|
| D-maltose catabolism | malK1 | med | 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) | 51% | 99% | 359.4 | CymD, component of Cyclodextrin porter | 62% | 451.4 |
| trehalose catabolism | thuK | med | 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) | 51% | 99% | 359.4 | CymD, component of Cyclodextrin porter | 62% | 451.4 |
| D-maltose catabolism | malK_Aa | med | ABC-type maltose transporter (EC 7.5.2.1) (characterized) | 51% | 96% | 359 | CymD, component of Cyclodextrin porter | 62% | 451.4 |
| D-cellobiose catabolism | gtsD | med | 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) | 50% | 97% | 350.9 | CymD, component of Cyclodextrin porter | 62% | 451.4 |
| D-glucose catabolism | gtsD | med | 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) | 50% | 97% | 350.9 | CymD, component of Cyclodextrin porter | 62% | 451.4 |
| lactose catabolism | gtsD | med | 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) | 50% | 97% | 350.9 | CymD, component of Cyclodextrin porter | 62% | 451.4 |
| D-maltose catabolism | gtsD | med | 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) | 50% | 97% | 350.9 | CymD, component of Cyclodextrin porter | 62% | 451.4 |
| D-maltose catabolism | thuK | med | 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) | 50% | 97% | 350.9 | CymD, component of Cyclodextrin porter | 62% | 451.4 |
| D-mannose catabolism | TT_C0211 | med | 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) | 50% | 97% | 350.9 | CymD, component of Cyclodextrin porter | 62% | 451.4 |
| sucrose catabolism | gtsD | med | 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) | 50% | 97% | 350.9 | CymD, component of Cyclodextrin porter | 62% | 451.4 |
| sucrose catabolism | thuK | med | 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) | 50% | 97% | 350.9 | CymD, component of Cyclodextrin porter | 62% | 451.4 |
| trehalose catabolism | gtsD | med | 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) | 50% | 97% | 350.9 | CymD, component of Cyclodextrin porter | 62% | 451.4 |
| D-maltose catabolism | malK | med | Maltose-transporting ATPase (EC 3.6.3.19) (characterized) | 50% | 95% | 332.4 | CymD, component of Cyclodextrin porter | 62% | 451.4 |
| D-maltose catabolism | malK_Sm | med | MalK, component of Maltose/Maltotriose/maltodextrin (up to 7 glucose units) transporters MalXFGK (MsmK (3.A.1.1.28) can probably substitute for MalK; Webb et al., 2008) (characterized) | 49% | 100% | 332 | CymD, component of Cyclodextrin porter | 62% | 451.4 |
| trehalose catabolism | malK | med | MalK, component of Maltose/Maltotriose/maltodextrin (up to 7 glucose units) transporters MalXFGK (MsmK (3.A.1.1.28) can probably substitute for MalK; Webb et al., 2008) (characterized) | 49% | 100% | 332 | CymD, component of Cyclodextrin porter | 62% | 451.4 |
| D-mannitol catabolism | mtlK | med | ABC transporter for D-Mannitol, D-Mannose, and D-Sorbitol, ATPase component (characterized) | 46% | 97% | 328.6 | CymD, component of Cyclodextrin porter | 62% | 451.4 |
| D-sorbitol (glucitol) catabolism | mtlK | med | ABC transporter for D-Mannitol, D-Mannose, and D-Sorbitol, ATPase component (characterized) | 46% | 97% | 328.6 | CymD, component of Cyclodextrin porter | 62% | 451.4 |
| L-fucose catabolism | SM_b21106 | med | ABC transporter for L-Fucose, ATPase component (characterized) | 48% | 100% | 325.1 | CymD, component of Cyclodextrin porter | 62% | 451.4 |
| D-maltose catabolism | aglK | med | ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized) | 49% | 99% | 317 | CymD, component of Cyclodextrin porter | 62% | 451.4 |
| sucrose catabolism | aglK | med | ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized) | 49% | 99% | 317 | CymD, component of Cyclodextrin porter | 62% | 451.4 |
| trehalose catabolism | aglK | med | ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized) | 49% | 99% | 317 | CymD, component of Cyclodextrin porter | 62% | 451.4 |
| 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) | 50% | 87% | 313.5 | CymD, component of Cyclodextrin porter | 62% | 451.4 |
| lactose catabolism | lacK | med | LacK, component of Lactose porter (characterized) | 52% | 90% | 307 | CymD, component of Cyclodextrin porter | 62% | 451.4 |
| D-xylose catabolism | gtsD | med | ABC transporter for D-Glucose-6-Phosphate, ATPase component (characterized) | 45% | 94% | 303.5 | CymD, component of Cyclodextrin porter | 62% | 451.4 |
| xylitol catabolism | Dshi_0546 | med | ABC transporter for Xylitol, ATPase component (characterized) | 46% | 98% | 296.6 | CymD, component of Cyclodextrin porter | 62% | 451.4 |
| xylitol catabolism | HSERO_RS17020 | med | ABC-type sugar transport system, ATPase component protein (characterized, see rationale) | 43% | 88% | 294.7 | CymD, component of Cyclodextrin porter | 62% | 451.4 |
| D-maltose catabolism | musK | med | ABC-type maltose transporter (EC 7.5.2.1) (characterized) | 50% | 86% | 294.3 | CymD, component of Cyclodextrin porter | 62% | 451.4 |
| D-cellobiose catabolism | SMc04256 | med | ABC transporter for D-Cellobiose and D-Salicin, ATPase component (characterized) | 46% | 97% | 289.7 | CymD, component of Cyclodextrin porter | 62% | 451.4 |
| D-galactose catabolism | PfGW456L13_1897 | med | ABC transporter for D-Galactose and D-Glucose, ATPase component (characterized) | 43% | 94% | 288.5 | CymD, component of Cyclodextrin porter | 62% | 451.4 |
| D-glucosamine (chitosamine) catabolism | SM_b21216 | med | ABC transporter for D-Glucosamine, ATPase component (characterized) | 42% | 99% | 285 | CymD, component of Cyclodextrin porter | 62% | 451.4 |
| N-acetyl-D-glucosamine catabolism | SMc02869 | med | N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized) | 56% | 72% | 283.5 | CymD, component of Cyclodextrin porter | 62% | 451.4 |
| D-glucosamine (chitosamine) catabolism | SMc02869 | med | N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized) | 56% | 72% | 283.5 | CymD, component of Cyclodextrin porter | 62% | 451.4 |
| D-maltose catabolism | malK_Bb | med | ABC-type maltose transport, ATP binding protein (characterized, see rationale) | 44% | 99% | 282.7 | CymD, component of Cyclodextrin porter | 62% | 451.4 |
| L-arabinose catabolism | xacK | med | Xylose/arabinose import ATP-binding protein XacK; EC 7.5.2.13 (characterized, see rationale) | 42% | 96% | 279.6 | CymD, component of Cyclodextrin porter | 62% | 451.4 |
| D-cellobiose catabolism | aglK' | med | Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) | 47% | 91% | 279.3 | CymD, component of Cyclodextrin porter | 62% | 451.4 |
| D-glucose catabolism | aglK' | med | Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) | 47% | 91% | 279.3 | CymD, component of Cyclodextrin porter | 62% | 451.4 |
| lactose catabolism | aglK' | med | Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) | 47% | 91% | 279.3 | CymD, component of Cyclodextrin porter | 62% | 451.4 |
| D-maltose catabolism | aglK' | med | Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) | 47% | 91% | 279.3 | CymD, component of Cyclodextrin porter | 62% | 451.4 |
| sucrose catabolism | aglK' | med | Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) | 47% | 91% | 279.3 | CymD, component of Cyclodextrin porter | 62% | 451.4 |
| trehalose catabolism | aglK' | med | Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) | 47% | 91% | 279.3 | CymD, component of Cyclodextrin porter | 62% | 451.4 |
| L-arabinose catabolism | xacJ | med | Xylose/arabinose import ATP-binding protein XacJ; EC 7.5.2.13 (characterized, see rationale) | 44% | 84% | 260.8 | CymD, component of Cyclodextrin porter | 62% | 451.4 |
| putrescine catabolism | potA | lo | PotG aka B0855, component of Putrescine porter (characterized) | 37% | 81% | 208 | CymD, component of Cyclodextrin porter | 62% | 451.4 |
| glycerol catabolism | glpT | lo | ABC transporter for Glycerol, ATPase component 2 (characterized) | 34% | 94% | 182.6 | CymD, component of Cyclodextrin porter | 62% | 451.4 |
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