| Pathway | Step | Score | Similar to | Id. | Cov. | Bits | Other hit | Other id. | Other bits |
|---|
| putrescine catabolism | potA | lo | PotG aka B0855, component of Putrescine porter (characterized) | 34% | 70% | 157.9 | Ferric ABC transporter ATP-binding protein, component of Iron (Fe3+) uptake porter, AfuABC (FbpABC) (Chin et al. 1996). AfuA has been characterized | 37% | 166.4 |
| D-maltose catabolism | malK | lo | Maltose-transporting ATPase (EC 3.6.3.19) (characterized) | 34% | 73% | 149.1 | Ferric ABC transporter ATP-binding protein, component of Iron (Fe3+) uptake porter, AfuABC (FbpABC) (Chin et al. 1996). AfuA has been characterized | 37% | 166.4 |
| 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) | 34% | 59% | 144.8 | Ferric ABC transporter ATP-binding protein, component of Iron (Fe3+) uptake porter, AfuABC (FbpABC) (Chin et al. 1996). AfuA has been characterized | 37% | 166.4 |
| D-cellobiose catabolism | glcV | lo | monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) | 30% | 94% | 143.3 | Ferric ABC transporter ATP-binding protein, component of Iron (Fe3+) uptake porter, AfuABC (FbpABC) (Chin et al. 1996). AfuA has been characterized | 37% | 166.4 |
| D-galactose catabolism | glcV | lo | monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) | 30% | 94% | 143.3 | Ferric ABC transporter ATP-binding protein, component of Iron (Fe3+) uptake porter, AfuABC (FbpABC) (Chin et al. 1996). AfuA has been characterized | 37% | 166.4 |
| D-glucose catabolism | glcV | lo | monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) | 30% | 94% | 143.3 | Ferric ABC transporter ATP-binding protein, component of Iron (Fe3+) uptake porter, AfuABC (FbpABC) (Chin et al. 1996). AfuA has been characterized | 37% | 166.4 |
| lactose catabolism | glcV | lo | monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) | 30% | 94% | 143.3 | Ferric ABC transporter ATP-binding protein, component of Iron (Fe3+) uptake porter, AfuABC (FbpABC) (Chin et al. 1996). AfuA has been characterized | 37% | 166.4 |
| D-maltose catabolism | glcV | lo | monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) | 30% | 94% | 143.3 | Ferric ABC transporter ATP-binding protein, component of Iron (Fe3+) uptake porter, AfuABC (FbpABC) (Chin et al. 1996). AfuA has been characterized | 37% | 166.4 |
| D-mannose catabolism | glcV | lo | monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) | 30% | 94% | 143.3 | Ferric ABC transporter ATP-binding protein, component of Iron (Fe3+) uptake porter, AfuABC (FbpABC) (Chin et al. 1996). AfuA has been characterized | 37% | 166.4 |
| sucrose catabolism | glcV | lo | monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) | 30% | 94% | 143.3 | Ferric ABC transporter ATP-binding protein, component of Iron (Fe3+) uptake porter, AfuABC (FbpABC) (Chin et al. 1996). AfuA has been characterized | 37% | 166.4 |
| trehalose catabolism | glcV | lo | monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) | 30% | 94% | 143.3 | Ferric ABC transporter ATP-binding protein, component of Iron (Fe3+) uptake porter, AfuABC (FbpABC) (Chin et al. 1996). AfuA has been characterized | 37% | 166.4 |
| N-acetyl-D-glucosamine catabolism | SMc02869 | lo | N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized) | 35% | 70% | 140.6 | Ferric ABC transporter ATP-binding protein, component of Iron (Fe3+) uptake porter, AfuABC (FbpABC) (Chin et al. 1996). AfuA has been characterized | 37% | 166.4 |
| D-glucosamine (chitosamine) catabolism | SMc02869 | lo | N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized) | 35% | 70% | 140.6 | Ferric ABC transporter ATP-binding protein, component of Iron (Fe3+) uptake porter, AfuABC (FbpABC) (Chin et al. 1996). AfuA has been characterized | 37% | 166.4 |
| D-maltose catabolism | musK | lo | ABC-type maltose transporter (EC 7.5.2.1) (characterized) | 33% | 61% | 140.2 | Ferric ABC transporter ATP-binding protein, component of Iron (Fe3+) uptake porter, AfuABC (FbpABC) (Chin et al. 1996). AfuA has been characterized | 37% | 166.4 |
| D-mannitol catabolism | mtlK | lo | SmoK aka POLK, component of Hexitol (glucitol; mannitol) porter (characterized) | 31% | 70% | 139.8 | Ferric ABC transporter ATP-binding protein, component of Iron (Fe3+) uptake porter, AfuABC (FbpABC) (Chin et al. 1996). AfuA has been characterized | 37% | 166.4 |
| xylitol catabolism | Dshi_0546 | lo | ABC transporter for Xylitol, ATPase component (characterized) | 32% | 72% | 138.7 | Ferric ABC transporter ATP-binding protein, component of Iron (Fe3+) uptake porter, AfuABC (FbpABC) (Chin et al. 1996). AfuA has been characterized | 37% | 166.4 |
| D-sorbitol (glucitol) catabolism | mtlK | lo | ABC transporter for D-Sorbitol, ATPase component (characterized) | 33% | 64% | 134.8 | Ferric ABC transporter ATP-binding protein, component of Iron (Fe3+) uptake porter, AfuABC (FbpABC) (Chin et al. 1996). AfuA has been characterized | 37% | 166.4 |
| lactose catabolism | lacK | lo | LacK, component of Lactose porter (characterized) | 31% | 64% | 131 | Ferric ABC transporter ATP-binding protein, component of Iron (Fe3+) uptake porter, AfuABC (FbpABC) (Chin et al. 1996). AfuA has been characterized | 37% | 166.4 |
| D-cellobiose catabolism | SMc04256 | lo | ABC transporter for D-Cellobiose and D-Salicin, ATPase component (characterized) | 34% | 65% | 130.6 | Ferric ABC transporter ATP-binding protein, component of Iron (Fe3+) uptake porter, AfuABC (FbpABC) (Chin et al. 1996). AfuA has been characterized | 37% | 166.4 |
| 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) | 33% | 64% | 130.2 | Ferric ABC transporter ATP-binding protein, component of Iron (Fe3+) uptake porter, AfuABC (FbpABC) (Chin et al. 1996). AfuA has been characterized | 37% | 166.4 |
| 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) | 33% | 64% | 130.2 | Ferric ABC transporter ATP-binding protein, component of Iron (Fe3+) uptake porter, AfuABC (FbpABC) (Chin et al. 1996). AfuA has been characterized | 37% | 166.4 |
| D-cellobiose catabolism | gtsD | lo | Sugar ABC transporter ATP-binding protein (characterized, see rationale) | 32% | 65% | 129.4 | Ferric ABC transporter ATP-binding protein, component of Iron (Fe3+) uptake porter, AfuABC (FbpABC) (Chin et al. 1996). AfuA has been characterized | 37% | 166.4 |
| D-glucose catabolism | gtsD | lo | Sugar ABC transporter ATP-binding protein (characterized, see rationale) | 32% | 65% | 129.4 | Ferric ABC transporter ATP-binding protein, component of Iron (Fe3+) uptake porter, AfuABC (FbpABC) (Chin et al. 1996). AfuA has been characterized | 37% | 166.4 |
| lactose catabolism | gtsD | lo | Sugar ABC transporter ATP-binding protein (characterized, see rationale) | 32% | 65% | 129.4 | Ferric ABC transporter ATP-binding protein, component of Iron (Fe3+) uptake porter, AfuABC (FbpABC) (Chin et al. 1996). AfuA has been characterized | 37% | 166.4 |
| D-maltose catabolism | gtsD | lo | Sugar ABC transporter ATP-binding protein (characterized, see rationale) | 32% | 65% | 129.4 | Ferric ABC transporter ATP-binding protein, component of Iron (Fe3+) uptake porter, AfuABC (FbpABC) (Chin et al. 1996). AfuA has been characterized | 37% | 166.4 |
| sucrose catabolism | gtsD | lo | Sugar ABC transporter ATP-binding protein (characterized, see rationale) | 32% | 65% | 129.4 | Ferric ABC transporter ATP-binding protein, component of Iron (Fe3+) uptake porter, AfuABC (FbpABC) (Chin et al. 1996). AfuA has been characterized | 37% | 166.4 |
| trehalose catabolism | gtsD | lo | Sugar ABC transporter ATP-binding protein (characterized, see rationale) | 32% | 65% | 129.4 | Ferric ABC transporter ATP-binding protein, component of Iron (Fe3+) uptake porter, AfuABC (FbpABC) (Chin et al. 1996). AfuA has been characterized | 37% | 166.4 |
| trehalose catabolism | treV | lo | TreV, component of Trehalose porter (characterized) | 31% | 92% | 129 | Ferric ABC transporter ATP-binding protein, component of Iron (Fe3+) uptake porter, AfuABC (FbpABC) (Chin et al. 1996). AfuA has been characterized | 37% | 166.4 |
| L-arabinose catabolism | araV | lo | AraV, component of Arabinose, fructose, xylose porter (characterized) | 31% | 68% | 128.3 | Ferric ABC transporter ATP-binding protein, component of Iron (Fe3+) uptake porter, AfuABC (FbpABC) (Chin et al. 1996). AfuA has been characterized | 37% | 166.4 |
| D-fructose catabolism | araV | lo | AraV, component of Arabinose, fructose, xylose porter (characterized) | 31% | 68% | 128.3 | Ferric ABC transporter ATP-binding protein, component of Iron (Fe3+) uptake porter, AfuABC (FbpABC) (Chin et al. 1996). AfuA has been characterized | 37% | 166.4 |
| 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) | 32% | 76% | 128.3 | Ferric ABC transporter ATP-binding protein, component of Iron (Fe3+) uptake porter, AfuABC (FbpABC) (Chin et al. 1996). AfuA has been characterized | 37% | 166.4 |
| sucrose catabolism | araV | lo | AraV, component of Arabinose, fructose, xylose porter (characterized) | 31% | 68% | 128.3 | Ferric ABC transporter ATP-binding protein, component of Iron (Fe3+) uptake porter, AfuABC (FbpABC) (Chin et al. 1996). AfuA has been characterized | 37% | 166.4 |
| 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) | 32% | 76% | 128.3 | Ferric ABC transporter ATP-binding protein, component of Iron (Fe3+) uptake porter, AfuABC (FbpABC) (Chin et al. 1996). AfuA has been characterized | 37% | 166.4 |
| D-xylose catabolism | araV | lo | AraV, component of Arabinose, fructose, xylose porter (characterized) | 31% | 68% | 128.3 | Ferric ABC transporter ATP-binding protein, component of Iron (Fe3+) uptake porter, AfuABC (FbpABC) (Chin et al. 1996). AfuA has been characterized | 37% | 166.4 |
| L-fucose catabolism | SM_b21106 | lo | ABC transporter for L-Fucose, ATPase component (characterized) | 32% | 61% | 123.6 | Ferric ABC transporter ATP-binding protein, component of Iron (Fe3+) uptake porter, AfuABC (FbpABC) (Chin et al. 1996). AfuA has been characterized | 37% | 166.4 |
| D-cellobiose catabolism | aglK' | lo | Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) | 32% | 63% | 122.1 | Ferric ABC transporter ATP-binding protein, component of Iron (Fe3+) uptake porter, AfuABC (FbpABC) (Chin et al. 1996). AfuA has been characterized | 37% | 166.4 |
| D-glucose catabolism | aglK' | lo | Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) | 32% | 63% | 122.1 | Ferric ABC transporter ATP-binding protein, component of Iron (Fe3+) uptake porter, AfuABC (FbpABC) (Chin et al. 1996). AfuA has been characterized | 37% | 166.4 |
| lactose catabolism | aglK' | lo | Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) | 32% | 63% | 122.1 | Ferric ABC transporter ATP-binding protein, component of Iron (Fe3+) uptake porter, AfuABC (FbpABC) (Chin et al. 1996). AfuA has been characterized | 37% | 166.4 |
| D-maltose catabolism | aglK | lo | Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) | 32% | 63% | 122.1 | Ferric ABC transporter ATP-binding protein, component of Iron (Fe3+) uptake porter, AfuABC (FbpABC) (Chin et al. 1996). AfuA has been characterized | 37% | 166.4 |
| D-maltose catabolism | aglK' | lo | Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) | 32% | 63% | 122.1 | Ferric ABC transporter ATP-binding protein, component of Iron (Fe3+) uptake porter, AfuABC (FbpABC) (Chin et al. 1996). AfuA has been characterized | 37% | 166.4 |
| sucrose catabolism | aglK | lo | Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) | 32% | 63% | 122.1 | Ferric ABC transporter ATP-binding protein, component of Iron (Fe3+) uptake porter, AfuABC (FbpABC) (Chin et al. 1996). AfuA has been characterized | 37% | 166.4 |
| sucrose catabolism | aglK' | lo | Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) | 32% | 63% | 122.1 | Ferric ABC transporter ATP-binding protein, component of Iron (Fe3+) uptake porter, AfuABC (FbpABC) (Chin et al. 1996). AfuA has been characterized | 37% | 166.4 |
| trehalose catabolism | aglK | lo | Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) | 32% | 63% | 122.1 | Ferric ABC transporter ATP-binding protein, component of Iron (Fe3+) uptake porter, AfuABC (FbpABC) (Chin et al. 1996). AfuA has been characterized | 37% | 166.4 |
| trehalose catabolism | aglK' | lo | Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) | 32% | 63% | 122.1 | Ferric ABC transporter ATP-binding protein, component of Iron (Fe3+) uptake porter, AfuABC (FbpABC) (Chin et al. 1996). AfuA has been characterized | 37% | 166.4 |
| xylitol catabolism | HSERO_RS17020 | lo | ABC-type sugar transport system, ATPase component protein (characterized, see rationale) | 31% | 60% | 119 | Ferric ABC transporter ATP-binding protein, component of Iron (Fe3+) uptake porter, AfuABC (FbpABC) (Chin et al. 1996). AfuA has been characterized | 37% | 166.4 |
| glycerol catabolism | glpT | lo | GlpT, component of Glycerol uptake porter, GlpSTPQV (characterized) | 32% | 59% | 106.3 | Ferric ABC transporter ATP-binding protein, component of Iron (Fe3+) uptake porter, AfuABC (FbpABC) (Chin et al. 1996). AfuA has been characterized | 37% | 166.4 |
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