Pathway | Step | Score | Similar to | Id. | Cov. | Bits | Other hit | Other id. | Other bits |
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) | 43% | 63% | 199.1 | WtpC, component of Tungsten (KM=20pM)/molybdate (KM=10nM) porter | 52% | 260.4 |
trehalose catabolism | thuK | 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) | 43% | 63% | 199.1 | WtpC, component of Tungsten (KM=20pM)/molybdate (KM=10nM) porter | 52% | 260.4 |
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) | 39% | 67% | 195.3 | WtpC, component of Tungsten (KM=20pM)/molybdate (KM=10nM) porter | 52% | 260.4 |
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) | 39% | 67% | 195.3 | WtpC, component of Tungsten (KM=20pM)/molybdate (KM=10nM) porter | 52% | 260.4 |
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) | 39% | 67% | 195.3 | WtpC, component of Tungsten (KM=20pM)/molybdate (KM=10nM) porter | 52% | 260.4 |
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) | 39% | 67% | 195.3 | WtpC, component of Tungsten (KM=20pM)/molybdate (KM=10nM) porter | 52% | 260.4 |
D-maltose 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% | 67% | 195.3 | WtpC, component of Tungsten (KM=20pM)/molybdate (KM=10nM) porter | 52% | 260.4 |
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% | 67% | 195.3 | WtpC, component of Tungsten (KM=20pM)/molybdate (KM=10nM) porter | 52% | 260.4 |
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) | 39% | 67% | 195.3 | WtpC, component of Tungsten (KM=20pM)/molybdate (KM=10nM) porter | 52% | 260.4 |
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% | 67% | 195.3 | WtpC, component of Tungsten (KM=20pM)/molybdate (KM=10nM) porter | 52% | 260.4 |
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) | 39% | 67% | 195.3 | WtpC, component of Tungsten (KM=20pM)/molybdate (KM=10nM) porter | 52% | 260.4 |
D-maltose catabolism | malK_Aa | lo | ABC-type maltose transporter (EC 7.5.2.1) (characterized) | 39% | 60% | 190.3 | WtpC, component of Tungsten (KM=20pM)/molybdate (KM=10nM) porter | 52% | 260.4 |
D-maltose catabolism | malK_Bb | lo | ABC-type maltose transport, ATP binding protein (characterized, see rationale) | 44% | 63% | 189.1 | WtpC, component of Tungsten (KM=20pM)/molybdate (KM=10nM) porter | 52% | 260.4 |
D-galactose catabolism | PfGW456L13_1897 | lo | ABC transporter for D-Galactose and D-Glucose, ATPase component (characterized) | 42% | 56% | 185.3 | WtpC, component of Tungsten (KM=20pM)/molybdate (KM=10nM) porter | 52% | 260.4 |
D-maltose catabolism | malK | lo | Maltose-transporting ATPase (EC 3.6.3.19) (characterized) | 38% | 68% | 184.5 | WtpC, component of Tungsten (KM=20pM)/molybdate (KM=10nM) porter | 52% | 260.4 |
D-xylose catabolism | gtsD | lo | ABC transporter for D-Glucose-6-Phosphate, ATPase component (characterized) | 41% | 56% | 182.2 | WtpC, component of Tungsten (KM=20pM)/molybdate (KM=10nM) porter | 52% | 260.4 |
trehalose catabolism | treV | lo | TreV, component of Trehalose porter (characterized) | 38% | 88% | 181.4 | WtpC, component of Tungsten (KM=20pM)/molybdate (KM=10nM) porter | 52% | 260.4 |
D-mannitol catabolism | mtlK | lo | ABC transporter for D-mannitol and D-mannose, ATPase component (characterized) | 41% | 63% | 181 | WtpC, component of Tungsten (KM=20pM)/molybdate (KM=10nM) porter | 52% | 260.4 |
N-acetyl-D-glucosamine catabolism | SMc02869 | lo | N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized) | 32% | 95% | 177.6 | WtpC, component of Tungsten (KM=20pM)/molybdate (KM=10nM) porter | 52% | 260.4 |
D-glucosamine (chitosamine) catabolism | SMc02869 | lo | N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized) | 32% | 95% | 177.6 | WtpC, component of Tungsten (KM=20pM)/molybdate (KM=10nM) porter | 52% | 260.4 |
D-sorbitol (glucitol) catabolism | mtlK | lo | ABC transporter for D-Mannitol, D-Mannose, and D-Sorbitol, ATPase component (characterized) | 41% | 63% | 177.2 | WtpC, component of Tungsten (KM=20pM)/molybdate (KM=10nM) porter | 52% | 260.4 |
D-cellobiose catabolism | SMc04256 | lo | ABC transporter for D-Cellobiose and D-Salicin, ATPase component (characterized) | 42% | 60% | 176 | WtpC, component of Tungsten (KM=20pM)/molybdate (KM=10nM) porter | 52% | 260.4 |
D-maltose catabolism | aglK | lo | ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized) | 38% | 66% | 174.1 | WtpC, component of Tungsten (KM=20pM)/molybdate (KM=10nM) porter | 52% | 260.4 |
sucrose catabolism | aglK | lo | ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized) | 38% | 66% | 174.1 | WtpC, component of Tungsten (KM=20pM)/molybdate (KM=10nM) porter | 52% | 260.4 |
trehalose catabolism | aglK | lo | ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized) | 38% | 66% | 174.1 | WtpC, component of Tungsten (KM=20pM)/molybdate (KM=10nM) porter | 52% | 260.4 |
L-fucose catabolism | SM_b21106 | lo | ABC transporter for L-Fucose, ATPase component (characterized) | 36% | 69% | 171.8 | WtpC, component of Tungsten (KM=20pM)/molybdate (KM=10nM) porter | 52% | 260.4 |
xylitol catabolism | HSERO_RS17020 | lo | ABC-type sugar transport system, ATPase component protein (characterized, see rationale) | 38% | 53% | 170.6 | WtpC, component of Tungsten (KM=20pM)/molybdate (KM=10nM) porter | 52% | 260.4 |
D-cellobiose catabolism | aglK' | lo | Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) | 39% | 62% | 170.2 | WtpC, component of Tungsten (KM=20pM)/molybdate (KM=10nM) porter | 52% | 260.4 |
D-glucose catabolism | aglK' | lo | Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) | 39% | 62% | 170.2 | WtpC, component of Tungsten (KM=20pM)/molybdate (KM=10nM) porter | 52% | 260.4 |
lactose catabolism | aglK' | lo | Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) | 39% | 62% | 170.2 | WtpC, component of Tungsten (KM=20pM)/molybdate (KM=10nM) porter | 52% | 260.4 |
D-maltose catabolism | aglK' | lo | Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) | 39% | 62% | 170.2 | WtpC, component of Tungsten (KM=20pM)/molybdate (KM=10nM) porter | 52% | 260.4 |
sucrose catabolism | aglK' | lo | Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) | 39% | 62% | 170.2 | WtpC, component of Tungsten (KM=20pM)/molybdate (KM=10nM) porter | 52% | 260.4 |
trehalose catabolism | aglK' | lo | Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) | 39% | 62% | 170.2 | WtpC, component of Tungsten (KM=20pM)/molybdate (KM=10nM) porter | 52% | 260.4 |
lactose catabolism | lacK | lo | ABC transporter for Lactose, ATPase component (characterized) | 34% | 78% | 167.9 | WtpC, component of Tungsten (KM=20pM)/molybdate (KM=10nM) porter | 52% | 260.4 |
putrescine catabolism | potA | lo | PotG aka B0855, component of Putrescine porter (characterized) | 35% | 81% | 167.5 | WtpC, component of Tungsten (KM=20pM)/molybdate (KM=10nM) porter | 52% | 260.4 |
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) | 37% | 65% | 167.5 | WtpC, component of Tungsten (KM=20pM)/molybdate (KM=10nM) porter | 52% | 260.4 |
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) | 39% | 57% | 166.4 | WtpC, component of Tungsten (KM=20pM)/molybdate (KM=10nM) porter | 52% | 260.4 |
glycerol catabolism | glpS | lo | GlpS, component of Glycerol uptake porter, GlpSTPQV (characterized) | 39% | 54% | 141.7 | WtpC, component of Tungsten (KM=20pM)/molybdate (KM=10nM) porter | 52% | 260.4 |
glycerol catabolism | glpT | lo | GlpT, component of Glycerol uptake porter, GlpSTPQV (characterized) | 31% | 71% | 140.2 | WtpC, component of Tungsten (KM=20pM)/molybdate (KM=10nM) porter | 52% | 260.4 |
L-alanine catabolism | braG | lo | NatE aka LivF aka SLR1881, component of Leucine/proline/alanine/serine/glycine (and possibly histidine) porter, NatABCDE (characterized) | 34% | 84% | 109.4 | WtpC, component of Tungsten (KM=20pM)/molybdate (KM=10nM) porter | 52% | 260.4 |
L-histidine catabolism | natE | lo | NatE aka LivF aka SLR1881, component of Leucine/proline/alanine/serine/glycine (and possibly histidine) porter, NatABCDE (characterized) | 34% | 84% | 109.4 | WtpC, component of Tungsten (KM=20pM)/molybdate (KM=10nM) porter | 52% | 260.4 |
L-leucine catabolism | natE | lo | NatE aka LivF aka SLR1881, component of Leucine/proline/alanine/serine/glycine (and possibly histidine) porter, NatABCDE (characterized) | 34% | 84% | 109.4 | WtpC, component of Tungsten (KM=20pM)/molybdate (KM=10nM) porter | 52% | 260.4 |
L-proline catabolism | natE | lo | NatE aka LivF aka SLR1881, component of Leucine/proline/alanine/serine/glycine (and possibly histidine) porter, NatABCDE (characterized) | 34% | 84% | 109.4 | WtpC, component of Tungsten (KM=20pM)/molybdate (KM=10nM) porter | 52% | 260.4 |
L-serine catabolism | braG | lo | NatE aka LivF aka SLR1881, component of Leucine/proline/alanine/serine/glycine (and possibly histidine) porter, NatABCDE (characterized) | 34% | 84% | 109.4 | WtpC, component of Tungsten (KM=20pM)/molybdate (KM=10nM) porter | 52% | 260.4 |
L-threonine catabolism | braG | lo | NatE aka LivF aka SLR1881, component of Leucine/proline/alanine/serine/glycine (and possibly histidine) porter, NatABCDE (characterized) | 34% | 84% | 109.4 | WtpC, component of Tungsten (KM=20pM)/molybdate (KM=10nM) porter | 52% | 260.4 |
L-isoleucine catabolism | livF | lo | ABC transporter ATP-binding protein-branched chain amino acid transport, component of The branched chain hydrophobic amino acid transporter, LivJFGHM (characterized) | 32% | 81% | 101.3 | WtpC, component of Tungsten (KM=20pM)/molybdate (KM=10nM) porter | 52% | 260.4 |
L-leucine catabolism | livF | lo | ABC transporter ATP-binding protein-branched chain amino acid transport, component of The branched chain hydrophobic amino acid transporter, LivJFGHM (characterized) | 32% | 81% | 101.3 | WtpC, component of Tungsten (KM=20pM)/molybdate (KM=10nM) porter | 52% | 260.4 |
L-valine catabolism | livF | lo | ABC transporter ATP-binding protein-branched chain amino acid transport, component of The branched chain hydrophobic amino acid transporter, LivJFGHM (characterized) | 32% | 81% | 101.3 | WtpC, component of Tungsten (KM=20pM)/molybdate (KM=10nM) porter | 52% | 260.4 |
myo-inositol catabolism | PGA1_c07320 | lo | Inositol transport system ATP-binding protein (characterized) | 35% | 78% | 100.1 | WtpC, component of Tungsten (KM=20pM)/molybdate (KM=10nM) porter | 52% | 260.4 |
L-phenylalanine catabolism | livF | lo | high-affinity branched-chain amino acid ABC transporter, ATP-binding protein LivF (characterized) | 31% | 98% | 95.9 | WtpC, component of Tungsten (KM=20pM)/molybdate (KM=10nM) porter | 52% | 260.4 |
D-fructose catabolism | frcA | lo | Fructose import ATP-binding protein FrcA; EC 7.5.2.- (characterized) | 33% | 86% | 94.4 | WtpC, component of Tungsten (KM=20pM)/molybdate (KM=10nM) porter | 52% | 260.4 |
D-mannose catabolism | frcA | lo | Fructose import ATP-binding protein FrcA; EC 7.5.2.- (characterized) | 33% | 86% | 94.4 | WtpC, component of Tungsten (KM=20pM)/molybdate (KM=10nM) porter | 52% | 260.4 |
D-ribose catabolism | frcA | lo | Fructose import ATP-binding protein FrcA; EC 7.5.2.- (characterized) | 33% | 86% | 94.4 | WtpC, component of Tungsten (KM=20pM)/molybdate (KM=10nM) porter | 52% | 260.4 |
sucrose catabolism | frcA | lo | Fructose import ATP-binding protein FrcA; EC 7.5.2.- (characterized) | 33% | 86% | 94.4 | WtpC, component of Tungsten (KM=20pM)/molybdate (KM=10nM) porter | 52% | 260.4 |
L-proline catabolism | HSERO_RS00895 | lo | ABC-type branched-chain amino acid transport system, ATPase component protein (characterized, see rationale) | 30% | 97% | 92.4 | WtpC, component of Tungsten (KM=20pM)/molybdate (KM=10nM) porter | 52% | 260.4 |
D-cellobiose catabolism | mglA | lo | glucose transporter, ATPase component (characterized) | 34% | 76% | 85.9 | WtpC, component of Tungsten (KM=20pM)/molybdate (KM=10nM) porter | 52% | 260.4 |
D-glucose catabolism | mglA | lo | glucose transporter, ATPase component (characterized) | 34% | 76% | 85.9 | WtpC, component of Tungsten (KM=20pM)/molybdate (KM=10nM) porter | 52% | 260.4 |
lactose catabolism | mglA | lo | glucose transporter, ATPase component (characterized) | 34% | 76% | 85.9 | WtpC, component of Tungsten (KM=20pM)/molybdate (KM=10nM) porter | 52% | 260.4 |
D-maltose catabolism | mglA | lo | glucose transporter, ATPase component (characterized) | 34% | 76% | 85.9 | WtpC, component of Tungsten (KM=20pM)/molybdate (KM=10nM) porter | 52% | 260.4 |
sucrose catabolism | mglA | lo | glucose transporter, ATPase component (characterized) | 34% | 76% | 85.9 | WtpC, component of Tungsten (KM=20pM)/molybdate (KM=10nM) porter | 52% | 260.4 |
trehalose catabolism | mglA | lo | glucose transporter, ATPase component (characterized) | 34% | 76% | 85.9 | WtpC, component of Tungsten (KM=20pM)/molybdate (KM=10nM) porter | 52% | 260.4 |
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