| Pathway | Step | Score | Similar to | Id. | Cov. | Bits | Other hit | Other id. | Other bits |
|---|
| D-cellobiose catabolism | gtsD | hi | GtsD (GLcK), component of Glucose porter, GtsABCD (characterized) | 54% | 95% | 382.1 | 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 | 53% | 357.5 |
| D-glucose catabolism | gtsD | hi | GtsD (GLcK), component of Glucose porter, GtsABCD (characterized) | 54% | 95% | 382.1 | 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 | 53% | 357.5 |
| lactose catabolism | gtsD | hi | GtsD (GLcK), component of Glucose porter, GtsABCD (characterized) | 54% | 95% | 382.1 | 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 | 53% | 357.5 |
| D-maltose catabolism | gtsD | hi | GtsD (GLcK), component of Glucose porter, GtsABCD (characterized) | 54% | 95% | 382.1 | 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 | 53% | 357.5 |
| sucrose catabolism | gtsD | hi | GtsD (GLcK), component of Glucose porter, GtsABCD (characterized) | 54% | 95% | 382.1 | 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 | 53% | 357.5 |
| trehalose catabolism | gtsD | hi | GtsD (GLcK), component of Glucose porter, GtsABCD (characterized) | 54% | 95% | 382.1 | 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 | 53% | 357.5 |
| D-galactose catabolism | PfGW456L13_1897 | hi | ABC transporter for D-Galactose and D-Glucose, ATPase component (characterized) | 53% | 95% | 370.9 | 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 | 53% | 357.5 |
| D-xylose catabolism | gtsD | med | ABC transporter for D-Glucose-6-Phosphate, ATPase component (characterized) | 54% | 95% | 374.4 | ABC transporter for D-Galactose and D-Glucose, ATPase component | 53% | 370.9 |
| 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) | 53% | 99% | 357.5 | GtsD (GLcK), component of Glucose porter, GtsABCD | 54% | 382.1 |
| 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) | 53% | 99% | 357.5 | GtsD (GLcK), component of Glucose porter, GtsABCD | 54% | 382.1 |
| D-glucosamine (chitosamine) catabolism | SM_b21216 | med | ABC transporter for D-Glucosamine, ATPase component (characterized) | 52% | 99% | 356.3 | GtsD (GLcK), component of Glucose porter, GtsABCD | 54% | 382.1 |
| L-fucose catabolism | SM_b21106 | med | ABC transporter for L-Fucose, ATPase component (characterized) | 49% | 100% | 338.2 | GtsD (GLcK), component of Glucose porter, GtsABCD | 54% | 382.1 |
| D-maltose catabolism | malK_Aa | med | ABC-type maltose transporter (EC 7.5.2.1) (characterized) | 48% | 96% | 337.4 | GtsD (GLcK), component of Glucose porter, GtsABCD | 54% | 382.1 |
| 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) | 48% | 97% | 336.7 | GtsD (GLcK), component of Glucose porter, GtsABCD | 54% | 382.1 |
| 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) | 48% | 97% | 336.7 | GtsD (GLcK), component of Glucose porter, GtsABCD | 54% | 382.1 |
| 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) | 48% | 97% | 336.7 | GtsD (GLcK), component of Glucose porter, GtsABCD | 54% | 382.1 |
| D-cellobiose catabolism | SMc04256 | med | ABC transporter for D-Cellobiose and D-Salicin, ATPase component (characterized) | 49% | 100% | 335.5 | GtsD (GLcK), component of Glucose porter, GtsABCD | 54% | 382.1 |
| D-maltose catabolism | malK_Bb | med | ABC-type maltose transport, ATP binding protein (characterized, see rationale) | 48% | 98% | 320.1 | GtsD (GLcK), component of Glucose porter, GtsABCD | 54% | 382.1 |
| trehalose catabolism | malK | med | MsmK aka SMU.882, component of The raffinose/stachyose transporter, MsmEFGK (MalK (3.A.1.1.27) can probably substitute for MsmK; Webb et al., 2008). This system may also transport melibiose, isomaltotriose and sucrose as well as isomaltosaccharides (characterized) | 45% | 100% | 317.8 | GtsD (GLcK), component of Glucose porter, GtsABCD | 54% | 382.1 |
| D-mannitol catabolism | mtlK | med | ABC transporter for D-Mannitol, D-Mannose, and D-Mannose, ATPase component (characterized) | 47% | 96% | 317.4 | GtsD (GLcK), component of Glucose porter, GtsABCD | 54% | 382.1 |
| D-sorbitol (glucitol) catabolism | mtlK | med | ABC transporter for D-Mannitol, D-Mannose, and D-Sorbitol, ATPase component (characterized) | 47% | 96% | 316.6 | GtsD (GLcK), component of Glucose porter, GtsABCD | 54% | 382.1 |
| 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) | 45% | 100% | 314.3 | GtsD (GLcK), component of Glucose porter, GtsABCD | 54% | 382.1 |
| lactose catabolism | lacK | med | ABC transporter for Lactose, ATPase component (characterized) | 48% | 89% | 307 | GtsD (GLcK), component of Glucose porter, GtsABCD | 54% | 382.1 |
| D-maltose catabolism | malK | med | Maltose-transporting ATPase (EC 3.6.3.19) (characterized) | 51% | 80% | 303.9 | GtsD (GLcK), component of Glucose porter, GtsABCD | 54% | 382.1 |
| xylitol catabolism | HSERO_RS17020 | med | ABC-type sugar transport system, ATPase component protein (characterized, see rationale) | 46% | 88% | 300.4 | GtsD (GLcK), component of Glucose porter, GtsABCD | 54% | 382.1 |
| D-maltose catabolism | aglK | med | ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized) | 46% | 98% | 295.4 | GtsD (GLcK), component of Glucose porter, GtsABCD | 54% | 382.1 |
| sucrose catabolism | aglK | med | ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized) | 46% | 98% | 295.4 | GtsD (GLcK), component of Glucose porter, GtsABCD | 54% | 382.1 |
| trehalose catabolism | aglK | med | ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized) | 46% | 98% | 295.4 | GtsD (GLcK), component of Glucose porter, GtsABCD | 54% | 382.1 |
| L-arabinose catabolism | xacJ | med | Xylose/arabinose import ATP-binding protein XacJ; EC 7.5.2.13 (characterized, see rationale) | 45% | 96% | 292.4 | GtsD (GLcK), component of Glucose porter, GtsABCD | 54% | 382.1 |
| xylitol catabolism | Dshi_0546 | med | ABC transporter for Xylitol, ATPase component (characterized) | 51% | 85% | 289.7 | GtsD (GLcK), component of Glucose porter, GtsABCD | 54% | 382.1 |
| 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) | 44% | 98% | 287.7 | GtsD (GLcK), component of Glucose porter, GtsABCD | 54% | 382.1 |
| N-acetyl-D-glucosamine catabolism | SMc02869 | med | N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized) | 55% | 81% | 287 | GtsD (GLcK), component of Glucose porter, GtsABCD | 54% | 382.1 |
| D-glucosamine (chitosamine) catabolism | SMc02869 | med | N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized) | 55% | 81% | 287 | GtsD (GLcK), component of Glucose porter, GtsABCD | 54% | 382.1 |
| D-maltose catabolism | musK | med | ABC-type maltose transporter (EC 7.5.2.1) (characterized) | 47% | 86% | 285.8 | GtsD (GLcK), component of Glucose porter, GtsABCD | 54% | 382.1 |
| L-arabinose catabolism | xacK | med | Xylose/arabinose import ATP-binding protein XacK; EC 7.5.2.13 (characterized, see rationale) | 42% | 96% | 283.9 | GtsD (GLcK), component of Glucose porter, GtsABCD | 54% | 382.1 |
| D-cellobiose catabolism | aglK' | med | Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) | 43% | 95% | 272.3 | GtsD (GLcK), component of Glucose porter, GtsABCD | 54% | 382.1 |
| D-glucose catabolism | aglK' | med | Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) | 43% | 95% | 272.3 | GtsD (GLcK), component of Glucose porter, GtsABCD | 54% | 382.1 |
| lactose catabolism | aglK' | med | Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) | 43% | 95% | 272.3 | GtsD (GLcK), component of Glucose porter, GtsABCD | 54% | 382.1 |
| D-maltose catabolism | aglK' | med | Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) | 43% | 95% | 272.3 | GtsD (GLcK), component of Glucose porter, GtsABCD | 54% | 382.1 |
| sucrose catabolism | aglK' | med | Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) | 43% | 95% | 272.3 | GtsD (GLcK), component of Glucose porter, GtsABCD | 54% | 382.1 |
| trehalose catabolism | aglK' | med | Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) | 43% | 95% | 272.3 | GtsD (GLcK), component of Glucose porter, GtsABCD | 54% | 382.1 |
| putrescine catabolism | potA | med | Spermidine/putrescine import ATP-binding protein PotA, component of The spermidine/putrescine uptake porter, PotABCD (characterized) | 44% | 89% | 245.7 | GtsD (GLcK), component of Glucose porter, GtsABCD | 54% | 382.1 |
| trehalose catabolism | treV | med | TreV, component of Trehalose porter (characterized) | 49% | 77% | 239.6 | GtsD (GLcK), component of Glucose porter, GtsABCD | 54% | 382.1 |
| L-arabinose catabolism | araV | lo | AraV, component of Arabinose, fructose, xylose porter (characterized) | 39% | 79% | 204.5 | GtsD (GLcK), component of Glucose porter, GtsABCD | 54% | 382.1 |
| D-fructose catabolism | araV | lo | AraV, component of Arabinose, fructose, xylose porter (characterized) | 39% | 79% | 204.5 | GtsD (GLcK), component of Glucose porter, GtsABCD | 54% | 382.1 |
| sucrose catabolism | araV | lo | AraV, component of Arabinose, fructose, xylose porter (characterized) | 39% | 79% | 204.5 | GtsD (GLcK), component of Glucose porter, GtsABCD | 54% | 382.1 |
| D-xylose catabolism | araV | lo | AraV, component of Arabinose, fructose, xylose porter (characterized) | 39% | 79% | 204.5 | GtsD (GLcK), component of Glucose porter, GtsABCD | 54% | 382.1 |
| glycerol catabolism | glpS | lo | ABC transporter for Glycerol, ATPase component 1 (characterized) | 33% | 94% | 179.5 | GtsD (GLcK), component of Glucose porter, GtsABCD | 54% | 382.1 |
| L-histidine catabolism | BPHYT_RS24015 | lo | ABC transporter related (characterized, see rationale) | 36% | 90% | 143.7 | GtsD (GLcK), component of Glucose porter, GtsABCD | 54% | 382.1 |
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