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) | 49% | 98% | 328.6 | sn-glycerol-3-phosphate import ATP-binding protein UgpC; EC 7.6.2.10 | 50% | 337.4 |
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) | 49% | 98% | 328.6 | sn-glycerol-3-phosphate import ATP-binding protein UgpC; EC 7.6.2.10 | 50% | 337.4 |
D-mannitol catabolism | mtlK | med | ABC transporter for D-Mannitol, D-Mannose, and D-Mannose, ATPase component (characterized) | 48% | 97% | 323.9 | sn-glycerol-3-phosphate import ATP-binding protein UgpC; EC 7.6.2.10 | 50% | 337.4 |
D-sorbitol (glucitol) catabolism | mtlK | med | ABC transporter for D-sorbitol, ATPase component (characterized) | 49% | 99% | 323.9 | sn-glycerol-3-phosphate import ATP-binding protein UgpC; EC 7.6.2.10 | 50% | 337.4 |
N-acetyl-D-glucosamine catabolism | SMc02869 | med | N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized) | 48% | 94% | 314.7 | sn-glycerol-3-phosphate import ATP-binding protein UgpC; EC 7.6.2.10 | 50% | 337.4 |
D-glucosamine (chitosamine) catabolism | SMc02869 | med | N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized) | 48% | 94% | 314.7 | sn-glycerol-3-phosphate import ATP-binding protein UgpC; EC 7.6.2.10 | 50% | 337.4 |
xylitol catabolism | Dshi_0546 | med | ABC transporter for Xylitol, ATPase component (characterized) | 46% | 95% | 310.1 | sn-glycerol-3-phosphate import ATP-binding protein UgpC; EC 7.6.2.10 | 50% | 337.4 |
D-maltose catabolism | aglK | med | ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized) | 47% | 99% | 309.3 | sn-glycerol-3-phosphate import ATP-binding protein UgpC; EC 7.6.2.10 | 50% | 337.4 |
D-maltose catabolism | thuK | med | ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized) | 47% | 99% | 309.3 | sn-glycerol-3-phosphate import ATP-binding protein UgpC; EC 7.6.2.10 | 50% | 337.4 |
sucrose catabolism | aglK | med | ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized) | 47% | 99% | 309.3 | sn-glycerol-3-phosphate import ATP-binding protein UgpC; EC 7.6.2.10 | 50% | 337.4 |
trehalose catabolism | aglK | med | ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized) | 47% | 99% | 309.3 | sn-glycerol-3-phosphate import ATP-binding protein UgpC; EC 7.6.2.10 | 50% | 337.4 |
D-cellobiose catabolism | gtsD | med | ABC transporter for D-Glucose-6-Phosphate, ATPase component (characterized) | 47% | 98% | 308.9 | sn-glycerol-3-phosphate import ATP-binding protein UgpC; EC 7.6.2.10 | 50% | 337.4 |
D-glucose catabolism | gtsD | med | ABC transporter for D-Glucose-6-Phosphate, ATPase component (characterized) | 47% | 98% | 308.9 | sn-glycerol-3-phosphate import ATP-binding protein UgpC; EC 7.6.2.10 | 50% | 337.4 |
lactose catabolism | gtsD | med | ABC transporter for D-Glucose-6-Phosphate, ATPase component (characterized) | 47% | 98% | 308.9 | sn-glycerol-3-phosphate import ATP-binding protein UgpC; EC 7.6.2.10 | 50% | 337.4 |
D-maltose catabolism | gtsD | med | ABC transporter for D-Glucose-6-Phosphate, ATPase component (characterized) | 47% | 98% | 308.9 | sn-glycerol-3-phosphate import ATP-binding protein UgpC; EC 7.6.2.10 | 50% | 337.4 |
sucrose catabolism | gtsD | med | ABC transporter for D-Glucose-6-Phosphate, ATPase component (characterized) | 47% | 98% | 308.9 | sn-glycerol-3-phosphate import ATP-binding protein UgpC; EC 7.6.2.10 | 50% | 337.4 |
trehalose catabolism | gtsD | med | ABC transporter for D-Glucose-6-Phosphate, ATPase component (characterized) | 47% | 98% | 308.9 | sn-glycerol-3-phosphate import ATP-binding protein UgpC; EC 7.6.2.10 | 50% | 337.4 |
D-xylose catabolism | gtsD | med | ABC transporter for D-Glucose-6-Phosphate, ATPase component (characterized) | 47% | 98% | 308.9 | sn-glycerol-3-phosphate import ATP-binding protein UgpC; EC 7.6.2.10 | 50% | 337.4 |
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) | 46% | 98% | 308.5 | sn-glycerol-3-phosphate import ATP-binding protein UgpC; EC 7.6.2.10 | 50% | 337.4 |
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) | 46% | 98% | 308.5 | sn-glycerol-3-phosphate import ATP-binding protein UgpC; EC 7.6.2.10 | 50% | 337.4 |
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) | 48% | 95% | 307.8 | sn-glycerol-3-phosphate import ATP-binding protein UgpC; EC 7.6.2.10 | 50% | 337.4 |
sucrose catabolism | thuK | 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) | 48% | 95% | 307.8 | sn-glycerol-3-phosphate import ATP-binding protein UgpC; EC 7.6.2.10 | 50% | 337.4 |
D-maltose catabolism | malK | med | Maltose-transporting ATPase (EC 3.6.3.19) (characterized) | 45% | 96% | 303.9 | sn-glycerol-3-phosphate import ATP-binding protein UgpC; EC 7.6.2.10 | 50% | 337.4 |
D-maltose catabolism | malK_Aa | med | ABC-type maltose transporter (EC 7.5.2.1) (characterized) | 47% | 93% | 303.9 | sn-glycerol-3-phosphate import ATP-binding protein UgpC; EC 7.6.2.10 | 50% | 337.4 |
L-fucose catabolism | SM_b21106 | med | ABC transporter for L-Fucose, ATPase component (characterized) | 47% | 99% | 303.5 | sn-glycerol-3-phosphate import ATP-binding protein UgpC; EC 7.6.2.10 | 50% | 337.4 |
lactose catabolism | lacK | med | ABC transporter for Lactose, ATPase component (characterized) | 45% | 99% | 301.6 | sn-glycerol-3-phosphate import ATP-binding protein UgpC; EC 7.6.2.10 | 50% | 337.4 |
D-galactose catabolism | PfGW456L13_1897 | med | ABC transporter for D-Galactose and D-Glucose, ATPase component (characterized) | 46% | 98% | 300.8 | sn-glycerol-3-phosphate import ATP-binding protein UgpC; EC 7.6.2.10 | 50% | 337.4 |
D-cellobiose catabolism | msiK | med | 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) | 47% | 95% | 299.7 | sn-glycerol-3-phosphate import ATP-binding protein UgpC; EC 7.6.2.10 | 50% | 337.4 |
L-arabinose catabolism | xacK | med | Xylose/arabinose import ATP-binding protein XacK; EC 7.5.2.13 (characterized, see rationale) | 46% | 95% | 298.9 | sn-glycerol-3-phosphate import ATP-binding protein UgpC; EC 7.6.2.10 | 50% | 337.4 |
D-maltose catabolism | malK_Bb | med | ABC-type maltose transport, ATP binding protein (characterized, see rationale) | 46% | 99% | 298.1 | sn-glycerol-3-phosphate import ATP-binding protein UgpC; EC 7.6.2.10 | 50% | 337.4 |
D-maltose catabolism | musK | med | ABC-type maltose transporter (EC 7.5.2.1) (characterized) | 49% | 85% | 295.4 | sn-glycerol-3-phosphate import ATP-binding protein UgpC; EC 7.6.2.10 | 50% | 337.4 |
xylitol catabolism | HSERO_RS17020 | med | ABC-type sugar transport system, ATPase component protein (characterized, see rationale) | 45% | 88% | 289.7 | sn-glycerol-3-phosphate import ATP-binding protein UgpC; EC 7.6.2.10 | 50% | 337.4 |
L-arabinose catabolism | xacJ | med | Xylose/arabinose import ATP-binding protein XacJ; EC 7.5.2.13 (characterized, see rationale) | 45% | 93% | 287 | sn-glycerol-3-phosphate import ATP-binding protein UgpC; EC 7.6.2.10 | 50% | 337.4 |
D-glucosamine (chitosamine) catabolism | SM_b21216 | med | ABC transporter for D-Glucosamine, ATPase component (characterized) | 44% | 99% | 276.6 | sn-glycerol-3-phosphate import ATP-binding protein UgpC; EC 7.6.2.10 | 50% | 337.4 |
D-cellobiose catabolism | SMc04256 | med | ABC transporter for D-Cellobiose and D-Salicin, ATPase component (characterized) | 48% | 82% | 268.9 | sn-glycerol-3-phosphate import ATP-binding protein UgpC; EC 7.6.2.10 | 50% | 337.4 |
D-cellobiose catabolism | aglK' | med | Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) | 47% | 84% | 268.1 | sn-glycerol-3-phosphate import ATP-binding protein UgpC; EC 7.6.2.10 | 50% | 337.4 |
D-glucose catabolism | aglK' | med | Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) | 47% | 84% | 268.1 | sn-glycerol-3-phosphate import ATP-binding protein UgpC; EC 7.6.2.10 | 50% | 337.4 |
lactose catabolism | aglK' | med | Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) | 47% | 84% | 268.1 | sn-glycerol-3-phosphate import ATP-binding protein UgpC; EC 7.6.2.10 | 50% | 337.4 |
D-maltose catabolism | aglK' | med | Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) | 47% | 84% | 268.1 | sn-glycerol-3-phosphate import ATP-binding protein UgpC; EC 7.6.2.10 | 50% | 337.4 |
sucrose catabolism | aglK' | med | Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) | 47% | 84% | 268.1 | sn-glycerol-3-phosphate import ATP-binding protein UgpC; EC 7.6.2.10 | 50% | 337.4 |
trehalose catabolism | aglK' | med | Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) | 47% | 84% | 268.1 | sn-glycerol-3-phosphate import ATP-binding protein UgpC; EC 7.6.2.10 | 50% | 337.4 |
trehalose catabolism | treV | med | TreV, component of Trehalose porter (characterized) | 40% | 94% | 240.4 | sn-glycerol-3-phosphate import ATP-binding protein UgpC; EC 7.6.2.10 | 50% | 337.4 |
putrescine catabolism | potA | med | spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31 (characterized) | 41% | 76% | 224.9 | sn-glycerol-3-phosphate import ATP-binding protein UgpC; EC 7.6.2.10 | 50% | 337.4 |
glycerol catabolism | glpT | lo | GlpT, component of Glycerol uptake porter, GlpSTPQV (characterized) | 37% | 85% | 214.9 | sn-glycerol-3-phosphate import ATP-binding protein UgpC; EC 7.6.2.10 | 50% | 337.4 |
L-arabinose catabolism | araV | lo | AraV, component of Arabinose, fructose, xylose porter (characterized) | 34% | 97% | 208.8 | sn-glycerol-3-phosphate import ATP-binding protein UgpC; EC 7.6.2.10 | 50% | 337.4 |
D-fructose catabolism | araV | lo | AraV, component of Arabinose, fructose, xylose porter (characterized) | 34% | 97% | 208.8 | sn-glycerol-3-phosphate import ATP-binding protein UgpC; EC 7.6.2.10 | 50% | 337.4 |
sucrose catabolism | araV | lo | AraV, component of Arabinose, fructose, xylose porter (characterized) | 34% | 97% | 208.8 | sn-glycerol-3-phosphate import ATP-binding protein UgpC; EC 7.6.2.10 | 50% | 337.4 |
D-xylose catabolism | araV | lo | AraV, component of Arabinose, fructose, xylose porter (characterized) | 34% | 97% | 208.8 | sn-glycerol-3-phosphate import ATP-binding protein UgpC; EC 7.6.2.10 | 50% | 337.4 |
D-cellobiose catabolism | glcV | lo | monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) | 36% | 99% | 203 | sn-glycerol-3-phosphate import ATP-binding protein UgpC; EC 7.6.2.10 | 50% | 337.4 |
D-galactose catabolism | glcV | lo | monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) | 36% | 99% | 203 | sn-glycerol-3-phosphate import ATP-binding protein UgpC; EC 7.6.2.10 | 50% | 337.4 |
D-glucose catabolism | glcV | lo | monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) | 36% | 99% | 203 | sn-glycerol-3-phosphate import ATP-binding protein UgpC; EC 7.6.2.10 | 50% | 337.4 |
lactose catabolism | glcV | lo | monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) | 36% | 99% | 203 | sn-glycerol-3-phosphate import ATP-binding protein UgpC; EC 7.6.2.10 | 50% | 337.4 |
D-maltose catabolism | glcV | lo | monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) | 36% | 99% | 203 | sn-glycerol-3-phosphate import ATP-binding protein UgpC; EC 7.6.2.10 | 50% | 337.4 |
D-mannose catabolism | glcV | lo | monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) | 36% | 99% | 203 | sn-glycerol-3-phosphate import ATP-binding protein UgpC; EC 7.6.2.10 | 50% | 337.4 |
sucrose catabolism | glcV | lo | monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) | 36% | 99% | 203 | sn-glycerol-3-phosphate import ATP-binding protein UgpC; EC 7.6.2.10 | 50% | 337.4 |
trehalose catabolism | glcV | lo | monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) | 36% | 99% | 203 | sn-glycerol-3-phosphate import ATP-binding protein UgpC; EC 7.6.2.10 | 50% | 337.4 |
glycerol catabolism | glpS | lo | GlpS, component of Glycerol uptake porter, GlpSTPQV (characterized) | 32% | 100% | 178.7 | sn-glycerol-3-phosphate import ATP-binding protein UgpC; EC 7.6.2.10 | 50% | 337.4 |
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