| Pathway | Step | Score | Similar to | Id. | Cov. | Bits | Other hit | Other id. | Other bits |
|---|
| putrescine catabolism | potA | med | spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31 (characterized) | 42% | 87% | 236.5 | BitD, component of The iron transporter, BitABCDEF | 44% | 260.8 |
| D-sorbitol (glucitol) catabolism | mtlK | med | ABC transporter for D-Sorbitol, ATPase component (characterized) | 41% | 87% | 231.5 | BitD, component of The iron transporter, BitABCDEF | 44% | 260.8 |
| D-mannitol catabolism | mtlK | med | SmoK aka POLK, component of Hexitol (glucitol; mannitol) porter (characterized) | 41% | 99% | 224.9 | BitD, component of The iron transporter, BitABCDEF | 44% | 260.8 |
| 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) | 46% | 72% | 222.6 | BitD, component of The iron transporter, BitABCDEF | 44% | 260.8 |
| 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) | 46% | 72% | 222.6 | BitD, component of The iron transporter, BitABCDEF | 44% | 260.8 |
| D-maltose catabolism | malK_Bb | med | ABC-type maltose transport, ATP binding protein (characterized, see rationale) | 44% | 71% | 218 | BitD, component of The iron transporter, BitABCDEF | 44% | 260.8 |
| D-cellobiose catabolism | gtsD | med | GtsD (GLcK), component of Glucose porter, GtsABCD (characterized) | 42% | 73% | 216.1 | BitD, component of The iron transporter, BitABCDEF | 44% | 260.8 |
| D-glucose catabolism | gtsD | med | GtsD (GLcK), component of Glucose porter, GtsABCD (characterized) | 42% | 73% | 216.1 | BitD, component of The iron transporter, BitABCDEF | 44% | 260.8 |
| lactose catabolism | gtsD | med | GtsD (GLcK), component of Glucose porter, GtsABCD (characterized) | 42% | 73% | 216.1 | BitD, component of The iron transporter, BitABCDEF | 44% | 260.8 |
| D-maltose catabolism | gtsD | med | GtsD (GLcK), component of Glucose porter, GtsABCD (characterized) | 42% | 73% | 216.1 | BitD, component of The iron transporter, BitABCDEF | 44% | 260.8 |
| sucrose catabolism | gtsD | med | GtsD (GLcK), component of Glucose porter, GtsABCD (characterized) | 42% | 73% | 216.1 | BitD, component of The iron transporter, BitABCDEF | 44% | 260.8 |
| trehalose catabolism | gtsD | med | GtsD (GLcK), component of Glucose porter, GtsABCD (characterized) | 42% | 73% | 216.1 | BitD, component of The iron transporter, BitABCDEF | 44% | 260.8 |
| xylitol catabolism | HSERO_RS17020 | med | ABC-type sugar transport system, ATPase component protein (characterized, see rationale) | 43% | 71% | 214.9 | BitD, component of The iron transporter, BitABCDEF | 44% | 260.8 |
| D-glucosamine (chitosamine) catabolism | SM_b21216 | med | ABC transporter for D-Glucosamine, ATPase component (characterized) | 41% | 83% | 214.5 | BitD, component of The iron transporter, BitABCDEF | 44% | 260.8 |
| D-maltose catabolism | musK | med | ABC-type maltose transporter (EC 7.5.2.1) (characterized) | 43% | 74% | 214.5 | BitD, component of The iron transporter, BitABCDEF | 44% | 260.8 |
| 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) | 42% | 71% | 213.4 | BitD, component of The iron transporter, BitABCDEF | 44% | 260.8 |
| 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) | 42% | 71% | 213.4 | BitD, component of The iron transporter, BitABCDEF | 44% | 260.8 |
| trehalose catabolism | treV | med | TreV, component of Trehalose porter (characterized) | 47% | 76% | 211.1 | BitD, component of The iron transporter, BitABCDEF | 44% | 260.8 |
| D-maltose catabolism | malK | med | Maltose-transporting ATPase (EC 3.6.3.19) (characterized) | 43% | 70% | 203 | BitD, component of The iron transporter, BitABCDEF | 44% | 260.8 |
| lactose catabolism | lacK | med | LacK, component of Lactose porter (characterized) | 41% | 78% | 202.2 | BitD, component of The iron transporter, BitABCDEF | 44% | 260.8 |
| D-maltose catabolism | thuK | lo | Trehalose/maltose import ATP-binding protein MalK; EC 7.5.2.1 (characterized) | 51% | 64% | 248.4 | BitD, component of The iron transporter, BitABCDEF | 44% | 260.8 |
| 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) | 39% | 93% | 231.5 | BitD, component of The iron transporter, BitABCDEF | 44% | 260.8 |
| 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) | 39% | 93% | 231.5 | BitD, component of The iron transporter, BitABCDEF | 44% | 260.8 |
| xylitol catabolism | Dshi_0546 | lo | ABC transporter for Xylitol, ATPase component (characterized) | 38% | 99% | 221.9 | BitD, component of The iron transporter, BitABCDEF | 44% | 260.8 |
| 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) | 45% | 69% | 218.4 | BitD, component of The iron transporter, BitABCDEF | 44% | 260.8 |
| L-fucose catabolism | SM_b21106 | lo | ABC transporter for L-Fucose, ATPase component (characterized) | 37% | 87% | 216.9 | BitD, component of The iron transporter, BitABCDEF | 44% | 260.8 |
| D-maltose catabolism | malK_Aa | lo | ABC-type maltose transporter (EC 7.5.2.1) (characterized) | 36% | 91% | 215.7 | BitD, component of The iron transporter, BitABCDEF | 44% | 260.8 |
| L-arabinose catabolism | xacJ | lo | Xylose/arabinose import ATP-binding protein XacJ; EC 7.5.2.13 (characterized, see rationale) | 46% | 61% | 211.5 | BitD, component of The iron transporter, BitABCDEF | 44% | 260.8 |
| D-maltose catabolism | aglK | lo | ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized) | 45% | 65% | 209.1 | BitD, component of The iron transporter, BitABCDEF | 44% | 260.8 |
| sucrose catabolism | aglK | lo | ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized) | 45% | 65% | 209.1 | BitD, component of The iron transporter, BitABCDEF | 44% | 260.8 |
| trehalose catabolism | aglK | lo | ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized) | 45% | 65% | 209.1 | BitD, component of The iron transporter, BitABCDEF | 44% | 260.8 |
| L-arabinose catabolism | xacK | lo | Xylose/arabinose import ATP-binding protein XacK; EC 7.5.2.13 (characterized, see rationale) | 36% | 95% | 206.1 | BitD, component of The iron transporter, BitABCDEF | 44% | 260.8 |
| D-cellobiose catabolism | SMc04256 | lo | ABC transporter for D-Cellobiose and D-Salicin, ATPase component (characterized) | 45% | 65% | 203 | BitD, component of The iron transporter, BitABCDEF | 44% | 260.8 |
| D-cellobiose catabolism | aglK' | lo | Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) | 41% | 66% | 197.6 | BitD, component of The iron transporter, BitABCDEF | 44% | 260.8 |
| D-glucose catabolism | aglK' | lo | Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) | 41% | 66% | 197.6 | BitD, component of The iron transporter, BitABCDEF | 44% | 260.8 |
| lactose catabolism | aglK' | lo | Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) | 41% | 66% | 197.6 | BitD, component of The iron transporter, BitABCDEF | 44% | 260.8 |
| D-maltose catabolism | aglK' | lo | Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) | 41% | 66% | 197.6 | BitD, component of The iron transporter, BitABCDEF | 44% | 260.8 |
| sucrose catabolism | aglK' | lo | Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) | 41% | 66% | 197.6 | BitD, component of The iron transporter, BitABCDEF | 44% | 260.8 |
| trehalose catabolism | aglK' | lo | Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) | 41% | 66% | 197.6 | BitD, component of The iron transporter, BitABCDEF | 44% | 260.8 |
| glycerol catabolism | glpS | lo | ABC transporter for Glycerol, ATPase component 1 (characterized) | 35% | 98% | 166.4 | BitD, component of The iron transporter, BitABCDEF | 44% | 260.8 |
| glycerol catabolism | glpT | lo | ABC transporter for Glycerol, ATPase component 2 (characterized) | 33% | 93% | 163.3 | BitD, component of The iron transporter, BitABCDEF | 44% | 260.8 |
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