| 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) | 44% | 72% | 218 | CP4-6 prophage; ABC transporter ATP-binding protein AfuC | 40% | 231.1 |
| 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) | 44% | 72% | 218 | CP4-6 prophage; ABC transporter ATP-binding protein AfuC | 40% | 231.1 |
| xylitol catabolism | Dshi_0546 | med | ABC transporter for Xylitol, ATPase component (characterized) | 40% | 95% | 218 | CP4-6 prophage; ABC transporter ATP-binding protein AfuC | 40% | 231.1 |
| trehalose catabolism | treV | med | TreV, component of Trehalose porter (characterized) | 45% | 72% | 214.2 | CP4-6 prophage; ABC transporter ATP-binding protein AfuC | 40% | 231.1 |
| D-mannitol catabolism | mtlK | med | ABC transporter for D-mannitol and D-mannose, ATPase component (characterized) | 42% | 72% | 211.5 | CP4-6 prophage; ABC transporter ATP-binding protein AfuC | 40% | 231.1 |
| D-sorbitol (glucitol) catabolism | mtlK | med | ABC transporter for D-Sorbitol, ATPase component (characterized) | 43% | 71% | 208.8 | CP4-6 prophage; ABC transporter ATP-binding protein AfuC | 40% | 231.1 |
| D-glucosamine (chitosamine) catabolism | SM_b21216 | med | ABC transporter for D-Glucosamine, ATPase component (characterized) | 42% | 71% | 208 | CP4-6 prophage; ABC transporter ATP-binding protein AfuC | 40% | 231.1 |
| putrescine catabolism | potA | med | PotG aka B0855, component of Putrescine porter (characterized) | 41% | 84% | 207.2 | CP4-6 prophage; ABC transporter ATP-binding protein AfuC | 40% | 231.1 |
| lactose catabolism | lacK | med | LacK, component of Lactose porter (characterized) | 43% | 71% | 206.8 | CP4-6 prophage; ABC transporter ATP-binding protein AfuC | 40% | 231.1 |
| N-acetyl-D-glucosamine catabolism | SMc02869 | med | N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized) | 45% | 71% | 201.4 | CP4-6 prophage; ABC transporter ATP-binding protein AfuC | 40% | 231.1 |
| D-glucosamine (chitosamine) catabolism | SMc02869 | med | N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized) | 45% | 71% | 201.4 | CP4-6 prophage; ABC transporter ATP-binding protein AfuC | 40% | 231.1 |
| L-proline catabolism | opuBA | med | BilEA aka OpuBA protein, component of A proline/glycine betaine uptake system. Also reported to be a bile exclusion system that exports oxgall and other bile compounds, BilEA/EB or OpuBA/BB (required for normal virulence) (characterized) | 40% | 73% | 174.9 | CP4-6 prophage; ABC transporter ATP-binding protein AfuC | 40% | 231.1 |
| L-fucose catabolism | SM_b21106 | lo | ABC transporter for L-Fucose, ATPase component (characterized) | 45% | 66% | 222.2 | CP4-6 prophage; ABC transporter ATP-binding protein AfuC | 40% | 231.1 |
| D-maltose catabolism | thuK | lo | Trehalose/maltose import ATP-binding protein MalK; EC 7.5.2.1 (characterized) | 47% | 67% | 219.5 | CP4-6 prophage; ABC transporter ATP-binding protein AfuC | 40% | 231.1 |
| D-maltose catabolism | malK_Bb | lo | ABC-type maltose transport, ATP binding protein (characterized, see rationale) | 45% | 68% | 213 | CP4-6 prophage; ABC transporter ATP-binding protein AfuC | 40% | 231.1 |
| D-maltose catabolism | malK | lo | ABC-type maltose transporter (subunit 3/3) (EC 7.5.2.1) (characterized) | 46% | 70% | 209.9 | CP4-6 prophage; ABC transporter ATP-binding protein AfuC | 40% | 231.1 |
| 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) | 42% | 70% | 209.5 | CP4-6 prophage; ABC transporter ATP-binding protein AfuC | 40% | 231.1 |
| D-maltose catabolism | musK | lo | ABC-type maltose transporter (EC 7.5.2.1) (characterized) | 44% | 67% | 206.5 | CP4-6 prophage; ABC transporter ATP-binding protein AfuC | 40% | 231.1 |
| D-cellobiose catabolism | gtsD | 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) | 45% | 63% | 200.3 | CP4-6 prophage; ABC transporter ATP-binding protein AfuC | 40% | 231.1 |
| D-glucose catabolism | gtsD | 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) | 45% | 63% | 200.3 | CP4-6 prophage; ABC transporter ATP-binding protein AfuC | 40% | 231.1 |
| lactose catabolism | gtsD | 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) | 45% | 63% | 200.3 | CP4-6 prophage; ABC transporter ATP-binding protein AfuC | 40% | 231.1 |
| D-maltose catabolism | gtsD | 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) | 45% | 63% | 200.3 | CP4-6 prophage; ABC transporter ATP-binding protein AfuC | 40% | 231.1 |
| 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) | 45% | 63% | 200.3 | CP4-6 prophage; ABC transporter ATP-binding protein AfuC | 40% | 231.1 |
| sucrose catabolism | gtsD | 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) | 45% | 63% | 200.3 | CP4-6 prophage; ABC transporter ATP-binding protein AfuC | 40% | 231.1 |
| 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) | 45% | 63% | 200.3 | CP4-6 prophage; ABC transporter ATP-binding protein AfuC | 40% | 231.1 |
| trehalose catabolism | gtsD | 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) | 45% | 63% | 200.3 | CP4-6 prophage; ABC transporter ATP-binding protein AfuC | 40% | 231.1 |
| D-xylose catabolism | gtsD | lo | ABC transporter for D-Glucose-6-Phosphate, ATPase component (characterized) | 38% | 84% | 200.3 | CP4-6 prophage; ABC transporter ATP-binding protein AfuC | 40% | 231.1 |
| D-maltose catabolism | malK_Aa | lo | ABC-type maltose transporter (EC 7.5.2.1) (characterized) | 41% | 66% | 194.5 | CP4-6 prophage; ABC transporter ATP-binding protein AfuC | 40% | 231.1 |
| D-cellobiose catabolism | aglK' | lo | Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) | 46% | 64% | 194.1 | CP4-6 prophage; ABC transporter ATP-binding protein AfuC | 40% | 231.1 |
| D-glucose catabolism | aglK' | lo | Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) | 46% | 64% | 194.1 | CP4-6 prophage; ABC transporter ATP-binding protein AfuC | 40% | 231.1 |
| lactose catabolism | aglK' | lo | Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) | 46% | 64% | 194.1 | CP4-6 prophage; ABC transporter ATP-binding protein AfuC | 40% | 231.1 |
| D-maltose catabolism | aglK | lo | Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) | 46% | 64% | 194.1 | CP4-6 prophage; ABC transporter ATP-binding protein AfuC | 40% | 231.1 |
| D-maltose catabolism | aglK' | lo | Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) | 46% | 64% | 194.1 | CP4-6 prophage; ABC transporter ATP-binding protein AfuC | 40% | 231.1 |
| sucrose catabolism | aglK | lo | Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) | 46% | 64% | 194.1 | CP4-6 prophage; ABC transporter ATP-binding protein AfuC | 40% | 231.1 |
| sucrose catabolism | aglK' | lo | Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) | 46% | 64% | 194.1 | CP4-6 prophage; ABC transporter ATP-binding protein AfuC | 40% | 231.1 |
| trehalose catabolism | aglK | lo | Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) | 46% | 64% | 194.1 | CP4-6 prophage; ABC transporter ATP-binding protein AfuC | 40% | 231.1 |
| trehalose catabolism | aglK' | lo | Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) | 46% | 64% | 194.1 | CP4-6 prophage; ABC transporter ATP-binding protein AfuC | 40% | 231.1 |
| L-arabinose catabolism | araV | lo | AraV, component of Arabinose, fructose, xylose porter (characterized) | 43% | 66% | 193 | CP4-6 prophage; ABC transporter ATP-binding protein AfuC | 40% | 231.1 |
| D-fructose catabolism | araV | lo | AraV, component of Arabinose, fructose, xylose porter (characterized) | 43% | 66% | 193 | CP4-6 prophage; ABC transporter ATP-binding protein AfuC | 40% | 231.1 |
| sucrose catabolism | araV | lo | AraV, component of Arabinose, fructose, xylose porter (characterized) | 43% | 66% | 193 | CP4-6 prophage; ABC transporter ATP-binding protein AfuC | 40% | 231.1 |
| D-xylose catabolism | araV | lo | AraV, component of Arabinose, fructose, xylose porter (characterized) | 43% | 66% | 193 | CP4-6 prophage; ABC transporter ATP-binding protein AfuC | 40% | 231.1 |
| D-cellobiose catabolism | glcV | lo | monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) | 42% | 69% | 192.2 | CP4-6 prophage; ABC transporter ATP-binding protein AfuC | 40% | 231.1 |
| D-galactose catabolism | glcV | lo | monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) | 42% | 69% | 192.2 | CP4-6 prophage; ABC transporter ATP-binding protein AfuC | 40% | 231.1 |
| D-glucose catabolism | glcV | lo | monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) | 42% | 69% | 192.2 | CP4-6 prophage; ABC transporter ATP-binding protein AfuC | 40% | 231.1 |
| lactose catabolism | glcV | lo | monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) | 42% | 69% | 192.2 | CP4-6 prophage; ABC transporter ATP-binding protein AfuC | 40% | 231.1 |
| D-maltose catabolism | glcV | lo | monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) | 42% | 69% | 192.2 | CP4-6 prophage; ABC transporter ATP-binding protein AfuC | 40% | 231.1 |
| D-mannose catabolism | glcV | lo | monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) | 42% | 69% | 192.2 | CP4-6 prophage; ABC transporter ATP-binding protein AfuC | 40% | 231.1 |
| sucrose catabolism | glcV | lo | monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) | 42% | 69% | 192.2 | CP4-6 prophage; ABC transporter ATP-binding protein AfuC | 40% | 231.1 |
| trehalose catabolism | glcV | lo | monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) | 42% | 69% | 192.2 | CP4-6 prophage; ABC transporter ATP-binding protein AfuC | 40% | 231.1 |
| xylitol catabolism | HSERO_RS17020 | lo | ABC-type sugar transport system, ATPase component protein (characterized, see rationale) | 35% | 88% | 192.2 | CP4-6 prophage; ABC transporter ATP-binding protein AfuC | 40% | 231.1 |
| L-arabinose catabolism | xacK | lo | Xylose/arabinose import ATP-binding protein XacK; EC 7.5.2.13 (characterized, see rationale) | 42% | 63% | 191.8 | CP4-6 prophage; ABC transporter ATP-binding protein AfuC | 40% | 231.1 |
| L-arabinose catabolism | xacJ | lo | Xylose/arabinose import ATP-binding protein XacJ; EC 7.5.2.13 (characterized, see rationale) | 42% | 63% | 191 | CP4-6 prophage; ABC transporter ATP-binding protein AfuC | 40% | 231.1 |
| D-galactose catabolism | PfGW456L13_1897 | lo | ABC transporter for D-Galactose and D-Glucose, ATPase component (characterized) | 41% | 68% | 189.9 | CP4-6 prophage; ABC transporter ATP-binding protein AfuC | 40% | 231.1 |
| glycerol catabolism | glpS | lo | ABC transporter for Glycerol, ATPase component 1 (characterized) | 34% | 68% | 148.3 | CP4-6 prophage; ABC transporter ATP-binding protein AfuC | 40% | 231.1 |
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