| Pathway | Step | Score | Similar to | Id. | Cov. | Bits | Other hit | Other id. | Other bits |
|---|
| L-asparagine catabolism | bgtA | med | ATPase (characterized, see rationale) | 42% | 73% | 135.6 | ModC aka CHLD aka NARD aka B0765, component of Molybdate porter consisting of three proteins | 37% | 197.2 |
| L-aspartate catabolism | bgtA | med | ATPase (characterized, see rationale) | 42% | 73% | 135.6 | ModC aka CHLD aka NARD aka B0765, component of Molybdate porter consisting of three proteins | 37% | 197.2 |
| D-maltose catabolism | malK_Aa | lo | ABC-type maltose transporter (EC 7.5.2.1) (characterized) | 36% | 65% | 151.4 | ModC aka CHLD aka NARD aka B0765, component of Molybdate porter consisting of three proteins | 37% | 197.2 |
| D-maltose catabolism | malK | lo | Maltose/maltodextrin import ATP-binding protein MalK; EC 7.5.2.1 (characterized) | 32% | 98% | 146.4 | ModC aka CHLD aka NARD aka B0765, component of Molybdate porter consisting of three proteins | 37% | 197.2 |
| N-acetyl-D-glucosamine catabolism | SMc02869 | lo | N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized) | 39% | 77% | 144.8 | ModC aka CHLD aka NARD aka B0765, component of Molybdate porter consisting of three proteins | 37% | 197.2 |
| D-glucosamine (chitosamine) catabolism | SMc02869 | lo | N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized) | 39% | 77% | 144.8 | ModC aka CHLD aka NARD aka B0765, component of Molybdate porter consisting of three proteins | 37% | 197.2 |
| D-cellobiose catabolism | gtsD | lo | Sugar ABC transporter ATP-binding protein (characterized, see rationale) | 34% | 75% | 144.4 | ModC aka CHLD aka NARD aka B0765, component of Molybdate porter consisting of three proteins | 37% | 197.2 |
| D-glucose catabolism | gtsD | lo | Sugar ABC transporter ATP-binding protein (characterized, see rationale) | 34% | 75% | 144.4 | ModC aka CHLD aka NARD aka B0765, component of Molybdate porter consisting of three proteins | 37% | 197.2 |
| lactose catabolism | gtsD | lo | Sugar ABC transporter ATP-binding protein (characterized, see rationale) | 34% | 75% | 144.4 | ModC aka CHLD aka NARD aka B0765, component of Molybdate porter consisting of three proteins | 37% | 197.2 |
| D-maltose catabolism | gtsD | lo | Sugar ABC transporter ATP-binding protein (characterized, see rationale) | 34% | 75% | 144.4 | ModC aka CHLD aka NARD aka B0765, component of Molybdate porter consisting of three proteins | 37% | 197.2 |
| sucrose catabolism | gtsD | lo | Sugar ABC transporter ATP-binding protein (characterized, see rationale) | 34% | 75% | 144.4 | ModC aka CHLD aka NARD aka B0765, component of Molybdate porter consisting of three proteins | 37% | 197.2 |
| trehalose catabolism | gtsD | lo | Sugar ABC transporter ATP-binding protein (characterized, see rationale) | 34% | 75% | 144.4 | ModC aka CHLD aka NARD aka B0765, component of Molybdate porter consisting of three proteins | 37% | 197.2 |
| 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% | 52% | 141 | ModC aka CHLD aka NARD aka B0765, component of Molybdate porter consisting of three proteins | 37% | 197.2 |
| 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) | 38% | 52% | 141 | ModC aka CHLD aka NARD aka B0765, component of Molybdate porter consisting of three proteins | 37% | 197.2 |
| xylitol catabolism | HSERO_RS17020 | lo | ABC-type sugar transport system, ATPase component protein (characterized, see rationale) | 33% | 82% | 141 | ModC aka CHLD aka NARD aka B0765, component of Molybdate porter consisting of three proteins | 37% | 197.2 |
| L-arabinose catabolism | xacK | lo | Xylose/arabinose import ATP-binding protein XacK; EC 7.5.2.13 (characterized, see rationale) | 39% | 51% | 140.6 | ModC aka CHLD aka NARD aka B0765, component of Molybdate porter consisting of three proteins | 37% | 197.2 |
| D-glucosamine (chitosamine) catabolism | SM_b21216 | lo | ABC transporter for D-Glucosamine, ATPase component (characterized) | 33% | 83% | 140.6 | ModC aka CHLD aka NARD aka B0765, component of Molybdate porter consisting of three proteins | 37% | 197.2 |
| 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% | 55% | 139.8 | ModC aka CHLD aka NARD aka B0765, component of Molybdate porter consisting of three proteins | 37% | 197.2 |
| D-mannitol catabolism | mtlK | lo | ABC transporter for D-Mannitol, D-Mannose, and D-Sorbitol, ATPase component (characterized) | 31% | 93% | 139.8 | ModC aka CHLD aka NARD aka B0765, component of Molybdate porter consisting of three proteins | 37% | 197.2 |
| 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% | 55% | 139.8 | ModC aka CHLD aka NARD aka B0765, component of Molybdate porter consisting of three proteins | 37% | 197.2 |
| D-sorbitol (glucitol) catabolism | mtlK | lo | ABC transporter for D-Mannitol, D-Mannose, and D-Sorbitol, ATPase component (characterized) | 31% | 93% | 139.8 | ModC aka CHLD aka NARD aka B0765, component of Molybdate porter consisting of three proteins | 37% | 197.2 |
| 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% | 55% | 139.8 | ModC aka CHLD aka NARD aka B0765, component of Molybdate porter consisting of three proteins | 37% | 197.2 |
| xylitol catabolism | Dshi_0546 | lo | ABC transporter for Xylitol, ATPase component (characterized) | 36% | 74% | 137.5 | ModC aka CHLD aka NARD aka B0765, component of Molybdate porter consisting of three proteins | 37% | 197.2 |
| D-xylose catabolism | gtsD | lo | ABC transporter for D-Glucose-6-Phosphate, ATPase component (characterized) | 37% | 52% | 137.5 | ModC aka CHLD aka NARD aka B0765, component of Molybdate porter consisting of three proteins | 37% | 197.2 |
| 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) | 34% | 71% | 136.7 | ModC aka CHLD aka NARD aka B0765, component of Molybdate porter consisting of three proteins | 37% | 197.2 |
| D-cellobiose catabolism | SMc04256 | lo | ABC transporter for D-Cellobiose and D-Salicin, ATPase component (characterized) | 34% | 80% | 136.3 | ModC aka CHLD aka NARD aka B0765, component of Molybdate porter consisting of three proteins | 37% | 197.2 |
| D-maltose catabolism | malK_Bb | lo | ABC-type maltose transport, ATP binding protein (characterized, see rationale) | 33% | 80% | 136.3 | ModC aka CHLD aka NARD aka B0765, component of Molybdate porter consisting of three proteins | 37% | 197.2 |
| D-cellobiose catabolism | aglK' | lo | Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) | 33% | 72% | 135.2 | ModC aka CHLD aka NARD aka B0765, component of Molybdate porter consisting of three proteins | 37% | 197.2 |
| D-glucose catabolism | aglK' | lo | Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) | 33% | 72% | 135.2 | ModC aka CHLD aka NARD aka B0765, component of Molybdate porter consisting of three proteins | 37% | 197.2 |
| lactose catabolism | aglK' | lo | Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) | 33% | 72% | 135.2 | ModC aka CHLD aka NARD aka B0765, component of Molybdate porter consisting of three proteins | 37% | 197.2 |
| lactose catabolism | lacK | lo | LacK, component of Lactose porter (characterized) | 34% | 76% | 135.2 | ModC aka CHLD aka NARD aka B0765, component of Molybdate porter consisting of three proteins | 37% | 197.2 |
| D-maltose catabolism | aglK | lo | Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) | 33% | 72% | 135.2 | ModC aka CHLD aka NARD aka B0765, component of Molybdate porter consisting of three proteins | 37% | 197.2 |
| D-maltose catabolism | aglK' | lo | Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) | 33% | 72% | 135.2 | ModC aka CHLD aka NARD aka B0765, component of Molybdate porter consisting of three proteins | 37% | 197.2 |
| sucrose catabolism | aglK | lo | Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) | 33% | 72% | 135.2 | ModC aka CHLD aka NARD aka B0765, component of Molybdate porter consisting of three proteins | 37% | 197.2 |
| sucrose catabolism | aglK' | lo | Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) | 33% | 72% | 135.2 | ModC aka CHLD aka NARD aka B0765, component of Molybdate porter consisting of three proteins | 37% | 197.2 |
| trehalose catabolism | aglK | lo | Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) | 33% | 72% | 135.2 | ModC aka CHLD aka NARD aka B0765, component of Molybdate porter consisting of three proteins | 37% | 197.2 |
| trehalose catabolism | aglK' | lo | Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) | 33% | 72% | 135.2 | ModC aka CHLD aka NARD aka B0765, component of Molybdate porter consisting of three proteins | 37% | 197.2 |
| D-maltose catabolism | musK | lo | ABC-type maltose transporter (EC 7.5.2.1) (characterized) | 32% | 71% | 132.5 | ModC aka CHLD aka NARD aka B0765, component of Molybdate porter consisting of three proteins | 37% | 197.2 |
| L-fucose catabolism | SM_b21106 | lo | ABC transporter for L-Fucose, ATPase component (characterized) | 31% | 85% | 132.1 | ModC aka CHLD aka NARD aka B0765, component of Molybdate porter consisting of three proteins | 37% | 197.2 |
| D-cellobiose catabolism | glcV | lo | monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) | 33% | 75% | 129 | ModC aka CHLD aka NARD aka B0765, component of Molybdate porter consisting of three proteins | 37% | 197.2 |
| D-galactose catabolism | glcV | lo | monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) | 33% | 75% | 129 | ModC aka CHLD aka NARD aka B0765, component of Molybdate porter consisting of three proteins | 37% | 197.2 |
| D-glucose catabolism | glcV | lo | monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) | 33% | 75% | 129 | ModC aka CHLD aka NARD aka B0765, component of Molybdate porter consisting of three proteins | 37% | 197.2 |
| L-glutamate catabolism | gltL | lo | GluA aka CGL1950, component of Glutamate porter (characterized) | 36% | 95% | 129 | ModC aka CHLD aka NARD aka B0765, component of Molybdate porter consisting of three proteins | 37% | 197.2 |
| lactose catabolism | glcV | lo | monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) | 33% | 75% | 129 | ModC aka CHLD aka NARD aka B0765, component of Molybdate porter consisting of three proteins | 37% | 197.2 |
| D-maltose catabolism | glcV | lo | monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) | 33% | 75% | 129 | ModC aka CHLD aka NARD aka B0765, component of Molybdate porter consisting of three proteins | 37% | 197.2 |
| D-mannose catabolism | glcV | lo | monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) | 33% | 75% | 129 | ModC aka CHLD aka NARD aka B0765, component of Molybdate porter consisting of three proteins | 37% | 197.2 |
| sucrose catabolism | glcV | lo | monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) | 33% | 75% | 129 | ModC aka CHLD aka NARD aka B0765, component of Molybdate porter consisting of three proteins | 37% | 197.2 |
| trehalose catabolism | glcV | lo | monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) | 33% | 75% | 129 | ModC aka CHLD aka NARD aka B0765, component of Molybdate porter consisting of three proteins | 37% | 197.2 |
| putrescine catabolism | potA | lo | Spermidine/putrescine import ATP-binding protein PotA, component of The spermidine/putrescine uptake porter, PotABCD (characterized) | 31% | 76% | 124.8 | ModC aka CHLD aka NARD aka B0765, component of Molybdate porter consisting of three proteins | 37% | 197.2 |
| trehalose catabolism | treV | lo | TreV, component of Trehalose porter (characterized) | 32% | 68% | 123.2 | ModC aka CHLD aka NARD aka B0765, component of Molybdate porter consisting of three proteins | 37% | 197.2 |
| L-tryptophan catabolism | ecfA2 | lo | Energy-coupling factor transporter ATP-binding protein EcfA2; Short=ECF transporter A component EcfA2; EC 7.-.-.- (characterized, see rationale) | 34% | 75% | 113.2 | ModC aka CHLD aka NARD aka B0765, component of Molybdate porter consisting of three proteins | 37% | 197.2 |
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