| Pathway | Step | Score | Similar to | Id. | Cov. | Bits | Other hit | Other id. | Other bits |
|---|
| D-mannitol catabolism | mtlK | med | SmoK aka POLK, component of Hexitol (glucitol; mannitol) porter (characterized) | 43% | 99% | 261.9 | Fe(3+) ions import ATP-binding protein FbpC, component of Hexose-phosphate transporter | 46% | 267.3 |
| D-sorbitol (glucitol) catabolism | mtlK | med | ABC transporter for D-Sorbitol, ATPase component (characterized) | 43% | 95% | 258.5 | Fe(3+) ions import ATP-binding protein FbpC, component of Hexose-phosphate transporter | 46% | 267.3 |
| putrescine catabolism | potA | med | PotG aka B0855, component of Putrescine porter (characterized) | 42% | 95% | 256.1 | Fe(3+) ions import ATP-binding protein FbpC, component of Hexose-phosphate transporter | 46% | 267.3 |
| N-acetyl-D-glucosamine catabolism | SMc02869 | med | N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized) | 44% | 84% | 251.5 | Fe(3+) ions import ATP-binding protein FbpC, component of Hexose-phosphate transporter | 46% | 267.3 |
| D-glucosamine (chitosamine) catabolism | SMc02869 | med | N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized) | 44% | 84% | 251.5 | Fe(3+) ions import ATP-binding protein FbpC, component of Hexose-phosphate transporter | 46% | 267.3 |
| 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) | 41% | 92% | 251.1 | Fe(3+) ions import ATP-binding protein FbpC, component of Hexose-phosphate transporter | 46% | 267.3 |
| 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) | 41% | 92% | 251.1 | Fe(3+) ions import ATP-binding protein FbpC, component of Hexose-phosphate transporter | 46% | 267.3 |
| 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) | 41% | 92% | 251.1 | Fe(3+) ions import ATP-binding protein FbpC, component of Hexose-phosphate transporter | 46% | 267.3 |
| 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) | 41% | 92% | 251.1 | Fe(3+) ions import ATP-binding protein FbpC, component of Hexose-phosphate transporter | 46% | 267.3 |
| 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) | 41% | 92% | 251.1 | Fe(3+) ions import ATP-binding protein FbpC, component of Hexose-phosphate transporter | 46% | 267.3 |
| 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) | 41% | 92% | 251.1 | Fe(3+) ions import ATP-binding protein FbpC, component of Hexose-phosphate transporter | 46% | 267.3 |
| 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) | 41% | 92% | 251.1 | Fe(3+) ions import ATP-binding protein FbpC, component of Hexose-phosphate transporter | 46% | 267.3 |
| 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) | 41% | 92% | 251.1 | Fe(3+) ions import ATP-binding protein FbpC, component of Hexose-phosphate transporter | 46% | 267.3 |
| 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) | 41% | 92% | 251.1 | Fe(3+) ions import ATP-binding protein FbpC, component of Hexose-phosphate transporter | 46% | 267.3 |
| trehalose 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) | 41% | 92% | 251.1 | Fe(3+) ions import ATP-binding protein FbpC, component of Hexose-phosphate transporter | 46% | 267.3 |
| lactose catabolism | lacK | med | ABC transporter for Lactose, ATPase component (characterized) | 40% | 92% | 247.3 | Fe(3+) ions import ATP-binding protein FbpC, component of Hexose-phosphate transporter | 46% | 267.3 |
| 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) | 42% | 78% | 242.7 | Fe(3+) ions import ATP-binding protein FbpC, component of Hexose-phosphate transporter | 46% | 267.3 |
| D-maltose catabolism | malK | med | ABC-type maltose transporter (subunit 3/3) (EC 7.5.2.1) (characterized) | 42% | 90% | 241.5 | Fe(3+) ions import ATP-binding protein FbpC, component of Hexose-phosphate transporter | 46% | 267.3 |
| D-cellobiose catabolism | SMc04256 | med | ABC transporter for D-Cellobiose and D-Salicin, ATPase component (characterized) | 43% | 82% | 236.5 | Fe(3+) ions import ATP-binding protein FbpC, component of Hexose-phosphate transporter | 46% | 267.3 |
| D-maltose catabolism | malK_Bb | med | ABC-type maltose transport, ATP binding protein (characterized, see rationale) | 43% | 78% | 232.3 | Fe(3+) ions import ATP-binding protein FbpC, component of Hexose-phosphate transporter | 46% | 267.3 |
| D-galactose catabolism | PfGW456L13_1897 | med | ABC transporter for D-Galactose and D-Glucose, ATPase component (characterized) | 43% | 78% | 229.9 | Fe(3+) ions import ATP-binding protein FbpC, component of Hexose-phosphate transporter | 46% | 267.3 |
| D-glucosamine (chitosamine) catabolism | SM_b21216 | med | ABC transporter for D-Glucosamine, ATPase component (characterized) | 43% | 81% | 229.9 | Fe(3+) ions import ATP-binding protein FbpC, component of Hexose-phosphate transporter | 46% | 267.3 |
| D-xylose catabolism | gtsD | med | ABC transporter for D-Glucose-6-Phosphate, ATPase component (characterized) | 43% | 77% | 229.6 | Fe(3+) ions import ATP-binding protein FbpC, component of Hexose-phosphate transporter | 46% | 267.3 |
| D-maltose catabolism | aglK | lo | ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized) | 39% | 94% | 245.4 | Fe(3+) ions import ATP-binding protein FbpC, component of Hexose-phosphate transporter | 46% | 267.3 |
| sucrose catabolism | aglK | lo | ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized) | 39% | 94% | 245.4 | Fe(3+) ions import ATP-binding protein FbpC, component of Hexose-phosphate transporter | 46% | 267.3 |
| trehalose catabolism | aglK | lo | ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized) | 39% | 94% | 245.4 | Fe(3+) ions import ATP-binding protein FbpC, component of Hexose-phosphate transporter | 46% | 267.3 |
| L-fucose catabolism | SM_b21106 | lo | ABC transporter for L-Fucose, ATPase component (characterized) | 40% | 91% | 236.9 | Fe(3+) ions import ATP-binding protein FbpC, component of Hexose-phosphate transporter | 46% | 267.3 |
| xylitol catabolism | Dshi_0546 | lo | ABC transporter for Xylitol, ATPase component (characterized) | 39% | 95% | 236.9 | Fe(3+) ions import ATP-binding protein FbpC, component of Hexose-phosphate transporter | 46% | 267.3 |
| D-cellobiose catabolism | aglK' | lo | Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) | 39% | 95% | 236.5 | Fe(3+) ions import ATP-binding protein FbpC, component of Hexose-phosphate transporter | 46% | 267.3 |
| D-glucose catabolism | aglK' | lo | Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) | 39% | 95% | 236.5 | Fe(3+) ions import ATP-binding protein FbpC, component of Hexose-phosphate transporter | 46% | 267.3 |
| lactose catabolism | aglK' | lo | Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) | 39% | 95% | 236.5 | Fe(3+) ions import ATP-binding protein FbpC, component of Hexose-phosphate transporter | 46% | 267.3 |
| D-maltose catabolism | aglK' | lo | Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) | 39% | 95% | 236.5 | Fe(3+) ions import ATP-binding protein FbpC, component of Hexose-phosphate transporter | 46% | 267.3 |
| sucrose catabolism | aglK' | lo | Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) | 39% | 95% | 236.5 | Fe(3+) ions import ATP-binding protein FbpC, component of Hexose-phosphate transporter | 46% | 267.3 |
| trehalose catabolism | aglK' | lo | Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) | 39% | 95% | 236.5 | Fe(3+) ions import ATP-binding protein FbpC, component of Hexose-phosphate transporter | 46% | 267.3 |
| xylitol catabolism | HSERO_RS17020 | lo | ABC-type sugar transport system, ATPase component protein (characterized, see rationale) | 44% | 67% | 228.8 | Fe(3+) ions import ATP-binding protein FbpC, component of Hexose-phosphate transporter | 46% | 267.3 |
| D-maltose catabolism | malK_Sm | lo | 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) | 39% | 93% | 225.7 | Fe(3+) ions import ATP-binding protein FbpC, component of Hexose-phosphate transporter | 46% | 267.3 |
| trehalose catabolism | malK | lo | 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) | 39% | 93% | 225.7 | Fe(3+) ions import ATP-binding protein FbpC, component of Hexose-phosphate transporter | 46% | 267.3 |
This GapMind analysis is from Sep 17 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