Pathway | Step | Score | Similar to | Id. | Cov. | Bits | Other hit | Other id. | Other bits |
putrescine catabolism | potA | lo | spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31 (characterized) | 33% | 90% | 175.6 | WtpC, component of Tungsten (KM=20pM)/molybdate (KM=10nM) porter | 38% | 191.8 |
D-mannitol catabolism | mtlK | lo | ABC transporter for D-Mannitol, D-Mannose, and D-Mannose, ATPase component (characterized) | 34% | 86% | 171.4 | WtpC, component of Tungsten (KM=20pM)/molybdate (KM=10nM) porter | 38% | 191.8 |
D-maltose catabolism | malK | lo | ABC-type maltose transporter (subunit 3/3) (EC 7.5.2.1) (characterized) | 32% | 91% | 170.6 | WtpC, component of Tungsten (KM=20pM)/molybdate (KM=10nM) porter | 38% | 191.8 |
D-sorbitol (glucitol) catabolism | mtlK | lo | MtlK, component of The polyol (mannitol, glucitol (sorbitol), arabitol (arabinitol; lyxitol)) uptake porter, MtlEFGK (characterized) | 36% | 79% | 164.5 | WtpC, component of Tungsten (KM=20pM)/molybdate (KM=10nM) porter | 38% | 191.8 |
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) | 30% | 90% | 164.1 | WtpC, component of Tungsten (KM=20pM)/molybdate (KM=10nM) porter | 38% | 191.8 |
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) | 30% | 90% | 164.1 | WtpC, component of Tungsten (KM=20pM)/molybdate (KM=10nM) porter | 38% | 191.8 |
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) | 30% | 90% | 164.1 | WtpC, component of Tungsten (KM=20pM)/molybdate (KM=10nM) porter | 38% | 191.8 |
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) | 30% | 90% | 164.1 | WtpC, component of Tungsten (KM=20pM)/molybdate (KM=10nM) porter | 38% | 191.8 |
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) | 30% | 90% | 164.1 | WtpC, component of Tungsten (KM=20pM)/molybdate (KM=10nM) porter | 38% | 191.8 |
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) | 30% | 90% | 164.1 | WtpC, component of Tungsten (KM=20pM)/molybdate (KM=10nM) porter | 38% | 191.8 |
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) | 30% | 90% | 164.1 | WtpC, component of Tungsten (KM=20pM)/molybdate (KM=10nM) porter | 38% | 191.8 |
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) | 30% | 90% | 164.1 | WtpC, component of Tungsten (KM=20pM)/molybdate (KM=10nM) porter | 38% | 191.8 |
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) | 30% | 90% | 164.1 | WtpC, component of Tungsten (KM=20pM)/molybdate (KM=10nM) porter | 38% | 191.8 |
trehalose 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) | 30% | 90% | 164.1 | WtpC, component of Tungsten (KM=20pM)/molybdate (KM=10nM) porter | 38% | 191.8 |
D-xylose catabolism | gtsD | lo | ABC transporter for D-Glucose-6-Phosphate, ATPase component (characterized) | 35% | 71% | 161.8 | WtpC, component of Tungsten (KM=20pM)/molybdate (KM=10nM) porter | 38% | 191.8 |
L-arabinose catabolism | araV | lo | AraV, component of Arabinose, fructose, xylose porter (characterized) | 33% | 75% | 161.4 | WtpC, component of Tungsten (KM=20pM)/molybdate (KM=10nM) porter | 38% | 191.8 |
D-fructose catabolism | araV | lo | AraV, component of Arabinose, fructose, xylose porter (characterized) | 33% | 75% | 161.4 | WtpC, component of Tungsten (KM=20pM)/molybdate (KM=10nM) porter | 38% | 191.8 |
sucrose catabolism | araV | lo | AraV, component of Arabinose, fructose, xylose porter (characterized) | 33% | 75% | 161.4 | WtpC, component of Tungsten (KM=20pM)/molybdate (KM=10nM) porter | 38% | 191.8 |
D-xylose catabolism | araV | lo | AraV, component of Arabinose, fructose, xylose porter (characterized) | 33% | 75% | 161.4 | WtpC, component of Tungsten (KM=20pM)/molybdate (KM=10nM) porter | 38% | 191.8 |
lactose catabolism | lacK | lo | ABC transporter for Lactose, ATPase component (characterized) | 35% | 76% | 158.3 | WtpC, component of Tungsten (KM=20pM)/molybdate (KM=10nM) porter | 38% | 191.8 |
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) | 32% | 72% | 156.8 | WtpC, component of Tungsten (KM=20pM)/molybdate (KM=10nM) porter | 38% | 191.8 |
L-arabinose catabolism | xacK | lo | Xylose/arabinose import ATP-binding protein XacK; EC 7.5.2.13 (characterized, see rationale) | 36% | 70% | 156 | WtpC, component of Tungsten (KM=20pM)/molybdate (KM=10nM) porter | 38% | 191.8 |
D-galactose catabolism | PfGW456L13_1897 | lo | ABC transporter for D-Galactose and D-Glucose, ATPase component (characterized) | 33% | 73% | 154.5 | WtpC, component of Tungsten (KM=20pM)/molybdate (KM=10nM) porter | 38% | 191.8 |
D-maltose catabolism | aglK | lo | ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized) | 32% | 80% | 154.5 | WtpC, component of Tungsten (KM=20pM)/molybdate (KM=10nM) porter | 38% | 191.8 |
sucrose catabolism | aglK | lo | ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized) | 32% | 80% | 154.5 | WtpC, component of Tungsten (KM=20pM)/molybdate (KM=10nM) porter | 38% | 191.8 |
trehalose catabolism | aglK | lo | ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized) | 32% | 80% | 154.5 | WtpC, component of Tungsten (KM=20pM)/molybdate (KM=10nM) porter | 38% | 191.8 |
xylitol catabolism | Dshi_0546 | lo | ABC transporter for Xylitol, ATPase component (characterized) | 37% | 76% | 152.9 | WtpC, component of Tungsten (KM=20pM)/molybdate (KM=10nM) porter | 38% | 191.8 |
D-cellobiose catabolism | SMc04256 | lo | ABC transporter for D-Cellobiose and D-Salicin, ATPase component (characterized) | 37% | 80% | 152.5 | WtpC, component of Tungsten (KM=20pM)/molybdate (KM=10nM) porter | 38% | 191.8 |
D-cellobiose catabolism | aglK' | lo | Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) | 32% | 81% | 152.5 | WtpC, component of Tungsten (KM=20pM)/molybdate (KM=10nM) porter | 38% | 191.8 |
D-glucose catabolism | aglK' | lo | Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) | 32% | 81% | 152.5 | WtpC, component of Tungsten (KM=20pM)/molybdate (KM=10nM) porter | 38% | 191.8 |
lactose catabolism | aglK' | lo | Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) | 32% | 81% | 152.5 | WtpC, component of Tungsten (KM=20pM)/molybdate (KM=10nM) porter | 38% | 191.8 |
D-maltose catabolism | aglK' | lo | Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) | 32% | 81% | 152.5 | WtpC, component of Tungsten (KM=20pM)/molybdate (KM=10nM) porter | 38% | 191.8 |
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) | 31% | 80% | 152.5 | WtpC, component of Tungsten (KM=20pM)/molybdate (KM=10nM) porter | 38% | 191.8 |
sucrose catabolism | aglK' | lo | Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) | 32% | 81% | 152.5 | WtpC, component of Tungsten (KM=20pM)/molybdate (KM=10nM) porter | 38% | 191.8 |
trehalose catabolism | aglK' | lo | Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) | 32% | 81% | 152.5 | WtpC, component of Tungsten (KM=20pM)/molybdate (KM=10nM) porter | 38% | 191.8 |
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) | 31% | 80% | 152.5 | WtpC, component of Tungsten (KM=20pM)/molybdate (KM=10nM) porter | 38% | 191.8 |
N-acetyl-D-glucosamine catabolism | SMc02869 | lo | N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized) | 41% | 68% | 151.8 | WtpC, component of Tungsten (KM=20pM)/molybdate (KM=10nM) porter | 38% | 191.8 |
D-glucosamine (chitosamine) catabolism | SMc02869 | lo | N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized) | 41% | 68% | 151.8 | WtpC, component of Tungsten (KM=20pM)/molybdate (KM=10nM) porter | 38% | 191.8 |
trehalose catabolism | treV | lo | TreV, component of Trehalose porter (characterized) | 35% | 73% | 149.1 | WtpC, component of Tungsten (KM=20pM)/molybdate (KM=10nM) porter | 38% | 191.8 |
D-cellobiose catabolism | glcV | lo | monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) | 32% | 75% | 146.7 | WtpC, component of Tungsten (KM=20pM)/molybdate (KM=10nM) porter | 38% | 191.8 |
D-galactose catabolism | glcV | lo | monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) | 32% | 75% | 146.7 | WtpC, component of Tungsten (KM=20pM)/molybdate (KM=10nM) porter | 38% | 191.8 |
D-glucose catabolism | glcV | lo | monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) | 32% | 75% | 146.7 | WtpC, component of Tungsten (KM=20pM)/molybdate (KM=10nM) porter | 38% | 191.8 |
lactose catabolism | glcV | lo | monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) | 32% | 75% | 146.7 | WtpC, component of Tungsten (KM=20pM)/molybdate (KM=10nM) porter | 38% | 191.8 |
D-maltose catabolism | glcV | lo | monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) | 32% | 75% | 146.7 | WtpC, component of Tungsten (KM=20pM)/molybdate (KM=10nM) porter | 38% | 191.8 |
D-mannose catabolism | glcV | lo | monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) | 32% | 75% | 146.7 | WtpC, component of Tungsten (KM=20pM)/molybdate (KM=10nM) porter | 38% | 191.8 |
sucrose catabolism | glcV | lo | monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) | 32% | 75% | 146.7 | WtpC, component of Tungsten (KM=20pM)/molybdate (KM=10nM) porter | 38% | 191.8 |
trehalose catabolism | glcV | lo | monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) | 32% | 75% | 146.7 | WtpC, component of Tungsten (KM=20pM)/molybdate (KM=10nM) porter | 38% | 191.8 |
D-glucosamine (chitosamine) catabolism | SM_b21216 | lo | ABC transporter for D-Glucosamine, ATPase component (characterized) | 36% | 74% | 146.4 | WtpC, component of Tungsten (KM=20pM)/molybdate (KM=10nM) porter | 38% | 191.8 |
D-maltose catabolism | musK | lo | ABC-type maltose transporter (EC 7.5.2.1) (characterized) | 32% | 71% | 146.4 | WtpC, component of Tungsten (KM=20pM)/molybdate (KM=10nM) porter | 38% | 191.8 |
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) | 31% | 82% | 141.4 | WtpC, component of Tungsten (KM=20pM)/molybdate (KM=10nM) porter | 38% | 191.8 |
L-proline catabolism | opuBA | lo | 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) | 32% | 86% | 140.6 | WtpC, component of Tungsten (KM=20pM)/molybdate (KM=10nM) porter | 38% | 191.8 |
D-maltose catabolism | malK_Bb | lo | ABC-type maltose transport, ATP binding protein (characterized, see rationale) | 36% | 63% | 134.4 | WtpC, component of Tungsten (KM=20pM)/molybdate (KM=10nM) porter | 38% | 191.8 |
L-fucose catabolism | SM_b21106 | lo | ABC transporter for L-Fucose, ATPase component (characterized) | 32% | 73% | 133.7 | WtpC, component of Tungsten (KM=20pM)/molybdate (KM=10nM) porter | 38% | 191.8 |
L-alanine catabolism | braG | lo | NatE, component of The neutral amino acid permease, N-1 (transports pro, phe, leu, gly, ala, ser, gln and his, but gln and his are not transported via NatB) (characterized) | 37% | 87% | 109.8 | WtpC, component of Tungsten (KM=20pM)/molybdate (KM=10nM) porter | 38% | 191.8 |
L-isoleucine catabolism | natE | lo | NatE, component of The neutral amino acid permease, N-1 (transports pro, phe, leu, gly, ala, ser, gln and his, but gln and his are not transported via NatB) (characterized) | 37% | 87% | 109.8 | WtpC, component of Tungsten (KM=20pM)/molybdate (KM=10nM) porter | 38% | 191.8 |
L-leucine catabolism | natE | lo | NatE, component of The neutral amino acid permease, N-1 (transports pro, phe, leu, gly, ala, ser, gln and his, but gln and his are not transported via NatB) (characterized) | 37% | 87% | 109.8 | WtpC, component of Tungsten (KM=20pM)/molybdate (KM=10nM) porter | 38% | 191.8 |
L-proline catabolism | natE | lo | NatE, component of The neutral amino acid permease, N-1 (transports pro, phe, leu, gly, ala, ser, gln and his, but gln and his are not transported via NatB) (characterized) | 37% | 87% | 109.8 | WtpC, component of Tungsten (KM=20pM)/molybdate (KM=10nM) porter | 38% | 191.8 |
L-serine catabolism | braG | lo | NatE, component of The neutral amino acid permease, N-1 (transports pro, phe, leu, gly, ala, ser, gln and his, but gln and his are not transported via NatB) (characterized) | 37% | 87% | 109.8 | WtpC, component of Tungsten (KM=20pM)/molybdate (KM=10nM) porter | 38% | 191.8 |
L-threonine catabolism | braG | lo | NatE, component of The neutral amino acid permease, N-1 (transports pro, phe, leu, gly, ala, ser, gln and his, but gln and his are not transported via NatB) (characterized) | 37% | 87% | 109.8 | WtpC, component of Tungsten (KM=20pM)/molybdate (KM=10nM) porter | 38% | 191.8 |
L-valine catabolism | natE | lo | NatE, component of The neutral amino acid permease, N-1 (transports pro, phe, leu, gly, ala, ser, gln and his, but gln and his are not transported via NatB) (characterized) | 37% | 87% | 109.8 | WtpC, component of Tungsten (KM=20pM)/molybdate (KM=10nM) porter | 38% | 191.8 |
D-fructose catabolism | frcA | lo | Fructose import ATP-binding protein FrcA; EC 7.5.2.- (characterized) | 34% | 80% | 102.4 | WtpC, component of Tungsten (KM=20pM)/molybdate (KM=10nM) porter | 38% | 191.8 |
D-mannose catabolism | frcA | lo | Fructose import ATP-binding protein FrcA; EC 7.5.2.- (characterized) | 34% | 80% | 102.4 | WtpC, component of Tungsten (KM=20pM)/molybdate (KM=10nM) porter | 38% | 191.8 |
D-ribose catabolism | frcA | lo | Fructose import ATP-binding protein FrcA; EC 7.5.2.- (characterized) | 34% | 80% | 102.4 | WtpC, component of Tungsten (KM=20pM)/molybdate (KM=10nM) porter | 38% | 191.8 |
sucrose catabolism | frcA | lo | Fructose import ATP-binding protein FrcA; EC 7.5.2.- (characterized) | 34% | 80% | 102.4 | WtpC, component of Tungsten (KM=20pM)/molybdate (KM=10nM) porter | 38% | 191.8 |
This GapMind analysis is from Sep 24 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