Pathway | Step | Score | Similar to | Id. | Cov. | Bits | Other hit | Other id. | Other bits |
D-maltose catabolism | thuK | med | Trehalose/maltose import ATP-binding protein MalK; EC 7.5.2.1 (characterized) | 41% | 97% | 259.2 | Glycerol-3-phosphate-transporting ATPase, component of Inositol phosphate porter (Rodionova et al. 2013). Binds inositol phosphate with low Kd and inositol with a lower affinity | 46% | 293.9 |
trehalose catabolism | thuK | med | Trehalose/maltose import ATP-binding protein MalK; EC 7.5.2.1 (characterized) | 41% | 97% | 259.2 | Glycerol-3-phosphate-transporting ATPase, component of Inositol phosphate porter (Rodionova et al. 2013). Binds inositol phosphate with low Kd and inositol with a lower affinity | 46% | 293.9 |
xylitol catabolism | HSERO_RS17020 | med | ABC-type sugar transport system, ATPase component protein (characterized, see rationale) | 42% | 86% | 257.7 | Glycerol-3-phosphate-transporting ATPase, component of Inositol phosphate porter (Rodionova et al. 2013). Binds inositol phosphate with low Kd and inositol with a lower affinity | 46% | 293.9 |
D-mannitol catabolism | mtlK | med | SmoK aka POLK, component of Hexitol (glucitol; mannitol) porter (characterized) | 44% | 88% | 251.5 | Glycerol-3-phosphate-transporting ATPase, component of Inositol phosphate porter (Rodionova et al. 2013). Binds inositol phosphate with low Kd and inositol with a lower affinity | 46% | 293.9 |
sucrose catabolism | thuK | med | ThuK aka RB0314 aka SMB20328, component of Trehalose/maltose/sucrose porter (trehalose inducible) (characterized) | 41% | 96% | 248.8 | Glycerol-3-phosphate-transporting ATPase, component of Inositol phosphate porter (Rodionova et al. 2013). Binds inositol phosphate with low Kd and inositol with a lower affinity | 46% | 293.9 |
D-maltose catabolism | malK_Sm | med | 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) | 41% | 95% | 248.4 | Glycerol-3-phosphate-transporting ATPase, component of Inositol phosphate porter (Rodionova et al. 2013). Binds inositol phosphate with low Kd and inositol with a lower affinity | 46% | 293.9 |
trehalose catabolism | malK | med | 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) | 41% | 95% | 248.4 | Glycerol-3-phosphate-transporting ATPase, component of Inositol phosphate porter (Rodionova et al. 2013). Binds inositol phosphate with low Kd and inositol with a lower affinity | 46% | 293.9 |
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% | 94% | 248.1 | Glycerol-3-phosphate-transporting ATPase, component of Inositol phosphate porter (Rodionova et al. 2013). Binds inositol phosphate with low Kd and inositol with a lower affinity | 46% | 293.9 |
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% | 94% | 248.1 | Glycerol-3-phosphate-transporting ATPase, component of Inositol phosphate porter (Rodionova et al. 2013). Binds inositol phosphate with low Kd and inositol with a lower affinity | 46% | 293.9 |
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% | 94% | 248.1 | Glycerol-3-phosphate-transporting ATPase, component of Inositol phosphate porter (Rodionova et al. 2013). Binds inositol phosphate with low Kd and inositol with a lower affinity | 46% | 293.9 |
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% | 94% | 248.1 | Glycerol-3-phosphate-transporting ATPase, component of Inositol phosphate porter (Rodionova et al. 2013). Binds inositol phosphate with low Kd and inositol with a lower affinity | 46% | 293.9 |
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% | 94% | 248.1 | Glycerol-3-phosphate-transporting ATPase, component of Inositol phosphate porter (Rodionova et al. 2013). Binds inositol phosphate with low Kd and inositol with a lower affinity | 46% | 293.9 |
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% | 94% | 248.1 | Glycerol-3-phosphate-transporting ATPase, component of Inositol phosphate porter (Rodionova et al. 2013). Binds inositol phosphate with low Kd and inositol with a lower affinity | 46% | 293.9 |
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% | 94% | 248.1 | Glycerol-3-phosphate-transporting ATPase, component of Inositol phosphate porter (Rodionova et al. 2013). Binds inositol phosphate with low Kd and inositol with a lower affinity | 46% | 293.9 |
L-arabinose catabolism | xacK | med | Xylose/arabinose import ATP-binding protein XacK; EC 7.5.2.13 (characterized, see rationale) | 41% | 91% | 247.3 | Glycerol-3-phosphate-transporting ATPase, component of Inositol phosphate porter (Rodionova et al. 2013). Binds inositol phosphate with low Kd and inositol with a lower affinity | 46% | 293.9 |
D-maltose catabolism | aglK | med | ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized) | 40% | 99% | 246.1 | Glycerol-3-phosphate-transporting ATPase, component of Inositol phosphate porter (Rodionova et al. 2013). Binds inositol phosphate with low Kd and inositol with a lower affinity | 46% | 293.9 |
sucrose catabolism | aglK | med | ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized) | 40% | 99% | 246.1 | Glycerol-3-phosphate-transporting ATPase, component of Inositol phosphate porter (Rodionova et al. 2013). Binds inositol phosphate with low Kd and inositol with a lower affinity | 46% | 293.9 |
trehalose catabolism | aglK | med | ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized) | 40% | 99% | 246.1 | Glycerol-3-phosphate-transporting ATPase, component of Inositol phosphate porter (Rodionova et al. 2013). Binds inositol phosphate with low Kd and inositol with a lower affinity | 46% | 293.9 |
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) | 40% | 92% | 243.4 | Glycerol-3-phosphate-transporting ATPase, component of Inositol phosphate porter (Rodionova et al. 2013). Binds inositol phosphate with low Kd and inositol with a lower affinity | 46% | 293.9 |
N-acetyl-D-glucosamine catabolism | SMc02869 | med | N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized) | 41% | 82% | 243 | Glycerol-3-phosphate-transporting ATPase, component of Inositol phosphate porter (Rodionova et al. 2013). Binds inositol phosphate with low Kd and inositol with a lower affinity | 46% | 293.9 |
D-glucosamine (chitosamine) catabolism | SMc02869 | med | N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized) | 41% | 82% | 243 | Glycerol-3-phosphate-transporting ATPase, component of Inositol phosphate porter (Rodionova et al. 2013). Binds inositol phosphate with low Kd and inositol with a lower affinity | 46% | 293.9 |
trehalose catabolism | treV | med | TreV, component of Trehalose porter (characterized) | 46% | 75% | 219.9 | Glycerol-3-phosphate-transporting ATPase, component of Inositol phosphate porter (Rodionova et al. 2013). Binds inositol phosphate with low Kd and inositol with a lower affinity | 46% | 293.9 |
L-fucose catabolism | SM_b21106 | lo | ABC transporter for L-Fucose, ATPase component (characterized) | 40% | 99% | 256.1 | Glycerol-3-phosphate-transporting ATPase, component of Inositol phosphate porter (Rodionova et al. 2013). Binds inositol phosphate with low Kd and inositol with a lower affinity | 46% | 293.9 |
D-glucosamine (chitosamine) catabolism | SM_b21216 | lo | ABC transporter for D-Glucosamine, ATPase component (characterized) | 39% | 99% | 246.9 | Glycerol-3-phosphate-transporting ATPase, component of Inositol phosphate porter (Rodionova et al. 2013). Binds inositol phosphate with low Kd and inositol with a lower affinity | 46% | 293.9 |
D-sorbitol (glucitol) catabolism | mtlK | lo | ABC transporter for D-Sorbitol, ATPase component (characterized) | 39% | 96% | 245 | Glycerol-3-phosphate-transporting ATPase, component of Inositol phosphate porter (Rodionova et al. 2013). Binds inositol phosphate with low Kd and inositol with a lower affinity | 46% | 293.9 |
xylitol catabolism | Dshi_0546 | lo | ABC transporter for Xylitol, ATPase component (characterized) | 39% | 99% | 243 | Glycerol-3-phosphate-transporting ATPase, component of Inositol phosphate porter (Rodionova et al. 2013). Binds inositol phosphate with low Kd and inositol with a lower affinity | 46% | 293.9 |
D-cellobiose catabolism | SMc04256 | lo | ABC transporter for D-Cellobiose and D-Salicin, ATPase component (characterized) | 38% | 99% | 241.9 | Glycerol-3-phosphate-transporting ATPase, component of Inositol phosphate porter (Rodionova et al. 2013). Binds inositol phosphate with low Kd and inositol with a lower affinity | 46% | 293.9 |
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% | 95% | 241.9 | Glycerol-3-phosphate-transporting ATPase, component of Inositol phosphate porter (Rodionova et al. 2013). Binds inositol phosphate with low Kd and inositol with a lower affinity | 46% | 293.9 |
D-maltose catabolism | malK_Aa | lo | ABC-type maltose transporter (EC 7.5.2.1) (characterized) | 39% | 93% | 241.1 | Glycerol-3-phosphate-transporting ATPase, component of Inositol phosphate porter (Rodionova et al. 2013). Binds inositol phosphate with low Kd and inositol with a lower affinity | 46% | 293.9 |
D-maltose catabolism | malK | lo | Maltose-transporting ATPase (EC 3.6.3.19) (characterized) | 39% | 96% | 240 | Glycerol-3-phosphate-transporting ATPase, component of Inositol phosphate porter (Rodionova et al. 2013). Binds inositol phosphate with low Kd and inositol with a lower affinity | 46% | 293.9 |
lactose catabolism | lacK | lo | ABC transporter for Lactose, ATPase component (characterized) | 40% | 99% | 239.2 | Glycerol-3-phosphate-transporting ATPase, component of Inositol phosphate porter (Rodionova et al. 2013). Binds inositol phosphate with low Kd and inositol with a lower affinity | 46% | 293.9 |
D-maltose catabolism | musK | lo | ABC-type maltose transporter (EC 7.5.2.1) (characterized) | 38% | 99% | 233 | Glycerol-3-phosphate-transporting ATPase, component of Inositol phosphate porter (Rodionova et al. 2013). Binds inositol phosphate with low Kd and inositol with a lower affinity | 46% | 293.9 |
D-cellobiose catabolism | aglK' | lo | Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) | 39% | 90% | 229.6 | Glycerol-3-phosphate-transporting ATPase, component of Inositol phosphate porter (Rodionova et al. 2013). Binds inositol phosphate with low Kd and inositol with a lower affinity | 46% | 293.9 |
D-glucose catabolism | aglK' | lo | Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) | 39% | 90% | 229.6 | Glycerol-3-phosphate-transporting ATPase, component of Inositol phosphate porter (Rodionova et al. 2013). Binds inositol phosphate with low Kd and inositol with a lower affinity | 46% | 293.9 |
lactose catabolism | aglK' | lo | Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) | 39% | 90% | 229.6 | Glycerol-3-phosphate-transporting ATPase, component of Inositol phosphate porter (Rodionova et al. 2013). Binds inositol phosphate with low Kd and inositol with a lower affinity | 46% | 293.9 |
D-maltose catabolism | aglK' | lo | Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) | 39% | 90% | 229.6 | Glycerol-3-phosphate-transporting ATPase, component of Inositol phosphate porter (Rodionova et al. 2013). Binds inositol phosphate with low Kd and inositol with a lower affinity | 46% | 293.9 |
sucrose catabolism | aglK' | lo | Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) | 39% | 90% | 229.6 | Glycerol-3-phosphate-transporting ATPase, component of Inositol phosphate porter (Rodionova et al. 2013). Binds inositol phosphate with low Kd and inositol with a lower affinity | 46% | 293.9 |
trehalose catabolism | aglK' | lo | Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) | 39% | 90% | 229.6 | Glycerol-3-phosphate-transporting ATPase, component of Inositol phosphate porter (Rodionova et al. 2013). Binds inositol phosphate with low Kd and inositol with a lower affinity | 46% | 293.9 |
D-galactose catabolism | PfGW456L13_1897 | lo | ABC transporter for D-Galactose and D-Glucose, ATPase component (characterized) | 46% | 62% | 229.2 | Glycerol-3-phosphate-transporting ATPase, component of Inositol phosphate porter (Rodionova et al. 2013). Binds inositol phosphate with low Kd and inositol with a lower affinity | 46% | 293.9 |
D-maltose catabolism | malK_Bb | lo | ABC-type maltose transport, ATP binding protein (characterized, see rationale) | 47% | 69% | 228.8 | Glycerol-3-phosphate-transporting ATPase, component of Inositol phosphate porter (Rodionova et al. 2013). Binds inositol phosphate with low Kd and inositol with a lower affinity | 46% | 293.9 |
D-xylose catabolism | gtsD | lo | ABC transporter for D-Glucose-6-Phosphate, ATPase component (characterized) | 45% | 62% | 227.6 | Glycerol-3-phosphate-transporting ATPase, component of Inositol phosphate porter (Rodionova et al. 2013). Binds inositol phosphate with low Kd and inositol with a lower affinity | 46% | 293.9 |
D-cellobiose catabolism | glcV | lo | monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) | 36% | 98% | 218 | Glycerol-3-phosphate-transporting ATPase, component of Inositol phosphate porter (Rodionova et al. 2013). Binds inositol phosphate with low Kd and inositol with a lower affinity | 46% | 293.9 |
D-galactose catabolism | glcV | lo | monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) | 36% | 98% | 218 | Glycerol-3-phosphate-transporting ATPase, component of Inositol phosphate porter (Rodionova et al. 2013). Binds inositol phosphate with low Kd and inositol with a lower affinity | 46% | 293.9 |
D-glucose catabolism | glcV | lo | monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) | 36% | 98% | 218 | Glycerol-3-phosphate-transporting ATPase, component of Inositol phosphate porter (Rodionova et al. 2013). Binds inositol phosphate with low Kd and inositol with a lower affinity | 46% | 293.9 |
lactose catabolism | glcV | lo | monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) | 36% | 98% | 218 | Glycerol-3-phosphate-transporting ATPase, component of Inositol phosphate porter (Rodionova et al. 2013). Binds inositol phosphate with low Kd and inositol with a lower affinity | 46% | 293.9 |
D-maltose catabolism | glcV | lo | monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) | 36% | 98% | 218 | Glycerol-3-phosphate-transporting ATPase, component of Inositol phosphate porter (Rodionova et al. 2013). Binds inositol phosphate with low Kd and inositol with a lower affinity | 46% | 293.9 |
D-mannose catabolism | glcV | lo | monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) | 36% | 98% | 218 | Glycerol-3-phosphate-transporting ATPase, component of Inositol phosphate porter (Rodionova et al. 2013). Binds inositol phosphate with low Kd and inositol with a lower affinity | 46% | 293.9 |
sucrose catabolism | glcV | lo | monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) | 36% | 98% | 218 | Glycerol-3-phosphate-transporting ATPase, component of Inositol phosphate porter (Rodionova et al. 2013). Binds inositol phosphate with low Kd and inositol with a lower affinity | 46% | 293.9 |
trehalose catabolism | glcV | lo | monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) | 36% | 98% | 218 | Glycerol-3-phosphate-transporting ATPase, component of Inositol phosphate porter (Rodionova et al. 2013). Binds inositol phosphate with low Kd and inositol with a lower affinity | 46% | 293.9 |
glycerol catabolism | glpT | lo | GlpT, component of Glycerol uptake porter, GlpSTPQV (characterized) | 35% | 85% | 204.1 | Glycerol-3-phosphate-transporting ATPase, component of Inositol phosphate porter (Rodionova et al. 2013). Binds inositol phosphate with low Kd and inositol with a lower affinity | 46% | 293.9 |
glycerol catabolism | glpS | lo | GlpS, component of Glycerol uptake porter, GlpSTPQV (characterized) | 35% | 99% | 189.9 | Glycerol-3-phosphate-transporting ATPase, component of Inositol phosphate porter (Rodionova et al. 2013). Binds inositol phosphate with low Kd and inositol with a lower affinity | 46% | 293.9 |
L-citrulline catabolism | AO353_03040 | lo | ABC transporter for L-Arginine and L-Citrulline, ATPase component (characterized) | 35% | 94% | 147.1 | Glycerol-3-phosphate-transporting ATPase, component of Inositol phosphate porter (Rodionova et al. 2013). Binds inositol phosphate with low Kd and inositol with a lower affinity | 46% | 293.9 |
L-histidine catabolism | hisP | lo | Probable ATP-binding component of ABC transporter, component of Amino acid transporter, PA5152-PA5155. Probably transports numerous amino acids including lysine, arginine, histidine, D-alanine and D-valine (Johnson et al. 2008). Regulated by ArgR (characterized) | 35% | 97% | 146.7 | Glycerol-3-phosphate-transporting ATPase, component of Inositol phosphate porter (Rodionova et al. 2013). Binds inositol phosphate with low Kd and inositol with a lower affinity | 46% | 293.9 |
L-lysine catabolism | hisP | lo | Probable ATP-binding component of ABC transporter, component of Amino acid transporter, PA5152-PA5155. Probably transports numerous amino acids including lysine, arginine, histidine, D-alanine and D-valine (Johnson et al. 2008). Regulated by ArgR (characterized) | 35% | 97% | 146.7 | Glycerol-3-phosphate-transporting ATPase, component of Inositol phosphate porter (Rodionova et al. 2013). Binds inositol phosphate with low Kd and inositol with a lower affinity | 46% | 293.9 |
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