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% | 71% | 196.4 | WtpC, component of Tungsten (KM=20pM)/molybdate (KM=10nM) porter | 38% | 244.6 |
L-fucose catabolism | SM_b21106 | lo | ABC transporter for L-Fucose, ATPase component (characterized) | 38% | 92% | 197.6 | WtpC, component of Tungsten (KM=20pM)/molybdate (KM=10nM) porter | 38% | 244.6 |
L-arabinose catabolism | xacK | lo | Xylose/arabinose import ATP-binding protein XacK; EC 7.5.2.13 (characterized, see rationale) | 37% | 88% | 195.7 | WtpC, component of Tungsten (KM=20pM)/molybdate (KM=10nM) porter | 38% | 244.6 |
xylitol catabolism | Dshi_0546 | lo | ABC transporter for Xylitol, ATPase component (characterized) | 36% | 93% | 194.5 | WtpC, component of Tungsten (KM=20pM)/molybdate (KM=10nM) porter | 38% | 244.6 |
D-maltose catabolism | malK | lo | Maltose/maltodextrin import ATP-binding protein MalK; EC 7.5.2.1 (characterized) | 36% | 91% | 194.1 | WtpC, component of Tungsten (KM=20pM)/molybdate (KM=10nM) porter | 38% | 244.6 |
D-maltose catabolism | thuK | lo | Trehalose/maltose import ATP-binding protein MalK; EC 7.5.2.1 (characterized) | 36% | 96% | 190.3 | WtpC, component of Tungsten (KM=20pM)/molybdate (KM=10nM) porter | 38% | 244.6 |
trehalose catabolism | thuK | lo | Trehalose/maltose import ATP-binding protein MalK; EC 7.5.2.1 (characterized) | 36% | 96% | 190.3 | WtpC, component of Tungsten (KM=20pM)/molybdate (KM=10nM) porter | 38% | 244.6 |
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) | 34% | 90% | 188.7 | WtpC, component of Tungsten (KM=20pM)/molybdate (KM=10nM) porter | 38% | 244.6 |
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) | 34% | 90% | 188.7 | WtpC, component of Tungsten (KM=20pM)/molybdate (KM=10nM) porter | 38% | 244.6 |
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) | 34% | 90% | 188.7 | WtpC, component of Tungsten (KM=20pM)/molybdate (KM=10nM) porter | 38% | 244.6 |
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) | 34% | 90% | 188.7 | WtpC, component of Tungsten (KM=20pM)/molybdate (KM=10nM) porter | 38% | 244.6 |
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) | 34% | 90% | 188.7 | WtpC, component of Tungsten (KM=20pM)/molybdate (KM=10nM) porter | 38% | 244.6 |
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) | 34% | 90% | 188.7 | WtpC, component of Tungsten (KM=20pM)/molybdate (KM=10nM) porter | 38% | 244.6 |
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) | 34% | 90% | 188.7 | WtpC, component of Tungsten (KM=20pM)/molybdate (KM=10nM) porter | 38% | 244.6 |
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) | 34% | 90% | 188.7 | WtpC, component of Tungsten (KM=20pM)/molybdate (KM=10nM) porter | 38% | 244.6 |
N-acetyl-D-glucosamine catabolism | SMc02869 | lo | N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized) | 39% | 77% | 188 | WtpC, component of Tungsten (KM=20pM)/molybdate (KM=10nM) porter | 38% | 244.6 |
D-glucosamine (chitosamine) catabolism | SMc02869 | lo | N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized) | 39% | 77% | 188 | WtpC, component of Tungsten (KM=20pM)/molybdate (KM=10nM) porter | 38% | 244.6 |
D-mannitol catabolism | mtlK | lo | ABC transporter for D-Mannitol, D-Mannose, and D-Mannose, ATPase component (characterized) | 36% | 92% | 188 | WtpC, component of Tungsten (KM=20pM)/molybdate (KM=10nM) porter | 38% | 244.6 |
D-maltose catabolism | malK1 | lo | 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) | 38% | 77% | 186.8 | WtpC, component of Tungsten (KM=20pM)/molybdate (KM=10nM) porter | 38% | 244.6 |
D-sorbitol (glucitol) catabolism | mtlK | lo | ABC transporter for D-sorbitol, ATPase component (characterized) | 41% | 67% | 186 | WtpC, component of Tungsten (KM=20pM)/molybdate (KM=10nM) porter | 38% | 244.6 |
D-maltose catabolism | malK_Bb | lo | ABC-type maltose transport, ATP binding protein (characterized, see rationale) | 45% | 63% | 182.2 | WtpC, component of Tungsten (KM=20pM)/molybdate (KM=10nM) porter | 38% | 244.6 |
D-maltose catabolism | musK | lo | ABC-type maltose transporter (EC 7.5.2.1) (characterized) | 38% | 72% | 182.2 | WtpC, component of Tungsten (KM=20pM)/molybdate (KM=10nM) porter | 38% | 244.6 |
L-arabinose catabolism | xacJ | lo | Xylose/arabinose import ATP-binding protein XacJ; EC 7.5.2.13 (characterized, see rationale) | 44% | 56% | 179.1 | WtpC, component of Tungsten (KM=20pM)/molybdate (KM=10nM) porter | 38% | 244.6 |
D-maltose catabolism | malK_Aa | lo | ABC-type maltose transporter (EC 7.5.2.1) (characterized) | 40% | 61% | 177.9 | WtpC, component of Tungsten (KM=20pM)/molybdate (KM=10nM) porter | 38% | 244.6 |
trehalose catabolism | treV | lo | TreV, component of Trehalose porter (characterized) | 45% | 65% | 177.9 | WtpC, component of Tungsten (KM=20pM)/molybdate (KM=10nM) porter | 38% | 244.6 |
D-glucosamine (chitosamine) catabolism | SM_b21216 | lo | ABC transporter for D-Glucosamine, ATPase component (characterized) | 36% | 92% | 176.4 | WtpC, component of Tungsten (KM=20pM)/molybdate (KM=10nM) porter | 38% | 244.6 |
D-xylose catabolism | gtsD | lo | ABC transporter for D-Glucose-6-Phosphate, ATPase component (characterized) | 42% | 56% | 176.4 | WtpC, component of Tungsten (KM=20pM)/molybdate (KM=10nM) porter | 38% | 244.6 |
xylitol catabolism | HSERO_RS17020 | lo | ABC-type sugar transport system, ATPase component protein (characterized, see rationale) | 43% | 53% | 176 | WtpC, component of Tungsten (KM=20pM)/molybdate (KM=10nM) porter | 38% | 244.6 |
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) | 41% | 57% | 173.3 | WtpC, component of Tungsten (KM=20pM)/molybdate (KM=10nM) porter | 38% | 244.6 |
trehalose catabolism | malK | lo | 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) | 38% | 67% | 172.6 | WtpC, component of Tungsten (KM=20pM)/molybdate (KM=10nM) porter | 38% | 244.6 |
D-galactose catabolism | PfGW456L13_1897 | lo | ABC transporter for D-Galactose and D-Glucose, ATPase component (characterized) | 42% | 58% | 169.1 | WtpC, component of Tungsten (KM=20pM)/molybdate (KM=10nM) porter | 38% | 244.6 |
D-maltose catabolism | aglK | lo | ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized) | 38% | 79% | 167.9 | WtpC, component of Tungsten (KM=20pM)/molybdate (KM=10nM) porter | 38% | 244.6 |
sucrose catabolism | aglK | lo | ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized) | 38% | 79% | 167.9 | WtpC, component of Tungsten (KM=20pM)/molybdate (KM=10nM) porter | 38% | 244.6 |
trehalose catabolism | aglK | lo | ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized) | 38% | 79% | 167.9 | WtpC, component of Tungsten (KM=20pM)/molybdate (KM=10nM) porter | 38% | 244.6 |
lactose catabolism | lacK | lo | ABC transporter for Lactose, ATPase component (characterized) | 36% | 80% | 167.2 | WtpC, component of Tungsten (KM=20pM)/molybdate (KM=10nM) porter | 38% | 244.6 |
D-cellobiose catabolism | glcV | lo | monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) | 35% | 77% | 164.9 | WtpC, component of Tungsten (KM=20pM)/molybdate (KM=10nM) porter | 38% | 244.6 |
D-galactose catabolism | glcV | lo | monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) | 35% | 77% | 164.9 | WtpC, component of Tungsten (KM=20pM)/molybdate (KM=10nM) porter | 38% | 244.6 |
D-glucose catabolism | glcV | lo | monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) | 35% | 77% | 164.9 | WtpC, component of Tungsten (KM=20pM)/molybdate (KM=10nM) porter | 38% | 244.6 |
lactose catabolism | glcV | lo | monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) | 35% | 77% | 164.9 | WtpC, component of Tungsten (KM=20pM)/molybdate (KM=10nM) porter | 38% | 244.6 |
D-maltose catabolism | glcV | lo | monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) | 35% | 77% | 164.9 | WtpC, component of Tungsten (KM=20pM)/molybdate (KM=10nM) porter | 38% | 244.6 |
D-mannose catabolism | glcV | lo | monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) | 35% | 77% | 164.9 | WtpC, component of Tungsten (KM=20pM)/molybdate (KM=10nM) porter | 38% | 244.6 |
sucrose catabolism | glcV | lo | monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) | 35% | 77% | 164.9 | WtpC, component of Tungsten (KM=20pM)/molybdate (KM=10nM) porter | 38% | 244.6 |
trehalose catabolism | glcV | lo | monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) | 35% | 77% | 164.9 | WtpC, component of Tungsten (KM=20pM)/molybdate (KM=10nM) porter | 38% | 244.6 |
D-cellobiose catabolism | SMc04256 | lo | ABC transporter for D-Cellobiose and D-Salicin, ATPase component (characterized) | 38% | 75% | 163.7 | WtpC, component of Tungsten (KM=20pM)/molybdate (KM=10nM) porter | 38% | 244.6 |
L-arabinose catabolism | araV | lo | AraV, component of Arabinose, fructose, xylose porter (characterized) | 31% | 83% | 149.1 | WtpC, component of Tungsten (KM=20pM)/molybdate (KM=10nM) porter | 38% | 244.6 |
D-fructose catabolism | araV | lo | AraV, component of Arabinose, fructose, xylose porter (characterized) | 31% | 83% | 149.1 | WtpC, component of Tungsten (KM=20pM)/molybdate (KM=10nM) porter | 38% | 244.6 |
sucrose catabolism | araV | lo | AraV, component of Arabinose, fructose, xylose porter (characterized) | 31% | 83% | 149.1 | WtpC, component of Tungsten (KM=20pM)/molybdate (KM=10nM) porter | 38% | 244.6 |
D-xylose catabolism | araV | lo | AraV, component of Arabinose, fructose, xylose porter (characterized) | 31% | 83% | 149.1 | WtpC, component of Tungsten (KM=20pM)/molybdate (KM=10nM) porter | 38% | 244.6 |
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