| Pathway | Step | Score | Similar to | Id. | Cov. | Bits | Other hit | Other id. | Other bits |
|---|
| D-maltose catabolism | thuK | lo | Trehalose/maltose import ATP-binding protein MalK; EC 7.5.2.1 (characterized) | 40% | 63% | 171 | Sulfate/thiosulfate import ATP-binding protein CysA aka RV2397C aka MT2468 aka MTCY253.24, component of Sulfate porter | 42% | 178.3 |
| trehalose catabolism | thuK | lo | Trehalose/maltose import ATP-binding protein MalK; EC 7.5.2.1 (characterized) | 40% | 63% | 171 | Sulfate/thiosulfate import ATP-binding protein CysA aka RV2397C aka MT2468 aka MTCY253.24, component of Sulfate porter | 42% | 178.3 |
| putrescine catabolism | potA | lo | spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31 (characterized) | 45% | 53% | 170.6 | Sulfate/thiosulfate import ATP-binding protein CysA aka RV2397C aka MT2468 aka MTCY253.24, component of Sulfate porter | 42% | 178.3 |
| lactose catabolism | lacK | lo | ABC transporter for Lactose, ATPase component (characterized) | 37% | 70% | 169.1 | Sulfate/thiosulfate import ATP-binding protein CysA aka RV2397C aka MT2468 aka MTCY253.24, component of Sulfate porter | 42% | 178.3 |
| D-maltose catabolism | malK | lo | Maltose-transporting ATPase (EC 3.6.3.19) (characterized) | 38% | 64% | 167.5 | Sulfate/thiosulfate import ATP-binding protein CysA aka RV2397C aka MT2468 aka MTCY253.24, component of Sulfate porter | 42% | 178.3 |
| D-glucosamine (chitosamine) catabolism | SM_b21216 | lo | ABC transporter for D-Glucosamine, ATPase component (characterized) | 34% | 71% | 165.6 | Sulfate/thiosulfate import ATP-binding protein CysA aka RV2397C aka MT2468 aka MTCY253.24, component of Sulfate porter | 42% | 178.3 |
| D-cellobiose catabolism | gtsD | lo | ABC transporter for D-Glucose-6-Phosphate, ATPase component (characterized) | 36% | 61% | 164.9 | Sulfate/thiosulfate import ATP-binding protein CysA aka RV2397C aka MT2468 aka MTCY253.24, component of Sulfate porter | 42% | 178.3 |
| D-glucose catabolism | gtsD | lo | ABC transporter for D-Glucose-6-Phosphate, ATPase component (characterized) | 36% | 61% | 164.9 | Sulfate/thiosulfate import ATP-binding protein CysA aka RV2397C aka MT2468 aka MTCY253.24, component of Sulfate porter | 42% | 178.3 |
| lactose catabolism | gtsD | lo | ABC transporter for D-Glucose-6-Phosphate, ATPase component (characterized) | 36% | 61% | 164.9 | Sulfate/thiosulfate import ATP-binding protein CysA aka RV2397C aka MT2468 aka MTCY253.24, component of Sulfate porter | 42% | 178.3 |
| D-maltose catabolism | gtsD | lo | ABC transporter for D-Glucose-6-Phosphate, ATPase component (characterized) | 36% | 61% | 164.9 | Sulfate/thiosulfate import ATP-binding protein CysA aka RV2397C aka MT2468 aka MTCY253.24, component of Sulfate porter | 42% | 178.3 |
| D-sorbitol (glucitol) catabolism | mtlK | lo | ABC transporter for D-Sorbitol, ATPase component (characterized) | 34% | 73% | 164.9 | Sulfate/thiosulfate import ATP-binding protein CysA aka RV2397C aka MT2468 aka MTCY253.24, component of Sulfate porter | 42% | 178.3 |
| sucrose catabolism | gtsD | lo | ABC transporter for D-Glucose-6-Phosphate, ATPase component (characterized) | 36% | 61% | 164.9 | Sulfate/thiosulfate import ATP-binding protein CysA aka RV2397C aka MT2468 aka MTCY253.24, component of Sulfate porter | 42% | 178.3 |
| trehalose catabolism | gtsD | lo | ABC transporter for D-Glucose-6-Phosphate, ATPase component (characterized) | 36% | 61% | 164.9 | Sulfate/thiosulfate import ATP-binding protein CysA aka RV2397C aka MT2468 aka MTCY253.24, component of Sulfate porter | 42% | 178.3 |
| D-xylose catabolism | gtsD | lo | ABC transporter for D-Glucose-6-Phosphate, ATPase component (characterized) | 36% | 61% | 164.9 | Sulfate/thiosulfate import ATP-binding protein CysA aka RV2397C aka MT2468 aka MTCY253.24, component of Sulfate porter | 42% | 178.3 |
| sucrose catabolism | thuK | lo | ABC transporter (characterized, see rationale) | 38% | 58% | 164.5 | Sulfate/thiosulfate import ATP-binding protein CysA aka RV2397C aka MT2468 aka MTCY253.24, component of Sulfate porter | 42% | 178.3 |
| 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) | 43% | 53% | 164.1 | Sulfate/thiosulfate import ATP-binding protein CysA aka RV2397C aka MT2468 aka MTCY253.24, component of Sulfate porter | 42% | 178.3 |
| 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) | 37% | 63% | 164.1 | Sulfate/thiosulfate import ATP-binding protein CysA aka RV2397C aka MT2468 aka MTCY253.24, component of Sulfate porter | 42% | 178.3 |
| D-maltose catabolism | malK_Aa | lo | ABC-type maltose transporter (EC 7.5.2.1) (characterized) | 38% | 59% | 162.9 | Sulfate/thiosulfate import ATP-binding protein CysA aka RV2397C aka MT2468 aka MTCY253.24, component of Sulfate porter | 42% | 178.3 |
| D-maltose catabolism | malK_Bb | lo | ABC-type maltose transport, ATP binding protein (characterized, see rationale) | 41% | 62% | 162.9 | Sulfate/thiosulfate import ATP-binding protein CysA aka RV2397C aka MT2468 aka MTCY253.24, component of Sulfate porter | 42% | 178.3 |
| D-mannitol catabolism | mtlK | lo | MtlK, component of The polyol (mannitol, glucitol (sorbitol), arabitol (arabinitol; lyxitol)) uptake porter, MtlEFGK (characterized) | 38% | 60% | 161.8 | Sulfate/thiosulfate import ATP-binding protein CysA aka RV2397C aka MT2468 aka MTCY253.24, component of Sulfate porter | 42% | 178.3 |
| xylitol catabolism | Dshi_0546 | lo | ABC transporter for Xylitol, ATPase component (characterized) | 36% | 68% | 161.4 | Sulfate/thiosulfate import ATP-binding protein CysA aka RV2397C aka MT2468 aka MTCY253.24, component of Sulfate porter | 42% | 178.3 |
| D-galactose catabolism | PfGW456L13_1897 | lo | ABC transporter for D-Galactose and D-Glucose, ATPase component (characterized) | 36% | 61% | 160.6 | Sulfate/thiosulfate import ATP-binding protein CysA aka RV2397C aka MT2468 aka MTCY253.24, component of Sulfate porter | 42% | 178.3 |
| L-arabinose catabolism | xacJ | lo | Xylose/arabinose import ATP-binding protein XacJ; EC 7.5.2.13 (characterized, see rationale) | 40% | 54% | 160.2 | Sulfate/thiosulfate import ATP-binding protein CysA aka RV2397C aka MT2468 aka MTCY253.24, component of Sulfate porter | 42% | 178.3 |
| L-fucose catabolism | SM_b21106 | lo | ABC transporter for L-Fucose, ATPase component (characterized) | 39% | 67% | 159.5 | Sulfate/thiosulfate import ATP-binding protein CysA aka RV2397C aka MT2468 aka MTCY253.24, component of Sulfate porter | 42% | 178.3 |
| D-cellobiose catabolism | SMc04256 | lo | ABC transporter for D-Cellobiose and D-Salicin, ATPase component (characterized) | 42% | 56% | 156 | Sulfate/thiosulfate import ATP-binding protein CysA aka RV2397C aka MT2468 aka MTCY253.24, component of Sulfate porter | 42% | 178.3 |
| D-cellobiose catabolism | glcV | lo | monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) | 36% | 75% | 155.6 | Sulfate/thiosulfate import ATP-binding protein CysA aka RV2397C aka MT2468 aka MTCY253.24, component of Sulfate porter | 42% | 178.3 |
| D-galactose catabolism | glcV | lo | monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) | 36% | 75% | 155.6 | Sulfate/thiosulfate import ATP-binding protein CysA aka RV2397C aka MT2468 aka MTCY253.24, component of Sulfate porter | 42% | 178.3 |
| D-glucose catabolism | glcV | lo | monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) | 36% | 75% | 155.6 | Sulfate/thiosulfate import ATP-binding protein CysA aka RV2397C aka MT2468 aka MTCY253.24, component of Sulfate porter | 42% | 178.3 |
| lactose catabolism | glcV | lo | monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) | 36% | 75% | 155.6 | Sulfate/thiosulfate import ATP-binding protein CysA aka RV2397C aka MT2468 aka MTCY253.24, component of Sulfate porter | 42% | 178.3 |
| D-maltose catabolism | glcV | lo | monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) | 36% | 75% | 155.6 | Sulfate/thiosulfate import ATP-binding protein CysA aka RV2397C aka MT2468 aka MTCY253.24, component of Sulfate porter | 42% | 178.3 |
| D-mannose catabolism | glcV | lo | monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) | 36% | 75% | 155.6 | Sulfate/thiosulfate import ATP-binding protein CysA aka RV2397C aka MT2468 aka MTCY253.24, component of Sulfate porter | 42% | 178.3 |
| sucrose catabolism | glcV | lo | monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) | 36% | 75% | 155.6 | Sulfate/thiosulfate import ATP-binding protein CysA aka RV2397C aka MT2468 aka MTCY253.24, component of Sulfate porter | 42% | 178.3 |
| trehalose catabolism | glcV | lo | monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) | 36% | 75% | 155.6 | Sulfate/thiosulfate import ATP-binding protein CysA aka RV2397C aka MT2468 aka MTCY253.24, component of Sulfate porter | 42% | 178.3 |
| L-arabinose catabolism | araV | lo | AraV, component of Arabinose, fructose, xylose porter (characterized) | 33% | 76% | 154.8 | Sulfate/thiosulfate import ATP-binding protein CysA aka RV2397C aka MT2468 aka MTCY253.24, component of Sulfate porter | 42% | 178.3 |
| D-fructose catabolism | araV | lo | AraV, component of Arabinose, fructose, xylose porter (characterized) | 33% | 76% | 154.8 | Sulfate/thiosulfate import ATP-binding protein CysA aka RV2397C aka MT2468 aka MTCY253.24, component of Sulfate porter | 42% | 178.3 |
| sucrose catabolism | araV | lo | AraV, component of Arabinose, fructose, xylose porter (characterized) | 33% | 76% | 154.8 | Sulfate/thiosulfate import ATP-binding protein CysA aka RV2397C aka MT2468 aka MTCY253.24, component of Sulfate porter | 42% | 178.3 |
| trehalose catabolism | treV | lo | TreV, component of Trehalose porter (characterized) | 41% | 65% | 154.8 | Sulfate/thiosulfate import ATP-binding protein CysA aka RV2397C aka MT2468 aka MTCY253.24, component of Sulfate porter | 42% | 178.3 |
| D-xylose catabolism | araV | lo | AraV, component of Arabinose, fructose, xylose porter (characterized) | 33% | 76% | 154.8 | Sulfate/thiosulfate import ATP-binding protein CysA aka RV2397C aka MT2468 aka MTCY253.24, component of Sulfate porter | 42% | 178.3 |
| L-arabinose catabolism | xacK | lo | Xylose/arabinose import ATP-binding protein XacK; EC 7.5.2.13 (characterized, see rationale) | 39% | 54% | 154.5 | Sulfate/thiosulfate import ATP-binding protein CysA aka RV2397C aka MT2468 aka MTCY253.24, component of Sulfate porter | 42% | 178.3 |
| N-acetyl-D-glucosamine catabolism | SMc02869 | lo | N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized) | 37% | 67% | 154.1 | Sulfate/thiosulfate import ATP-binding protein CysA aka RV2397C aka MT2468 aka MTCY253.24, component of Sulfate porter | 42% | 178.3 |
| D-glucosamine (chitosamine) catabolism | SMc02869 | lo | N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized) | 37% | 67% | 154.1 | Sulfate/thiosulfate import ATP-binding protein CysA aka RV2397C aka MT2468 aka MTCY253.24, component of Sulfate porter | 42% | 178.3 |
| 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) | 33% | 68% | 150.6 | Sulfate/thiosulfate import ATP-binding protein CysA aka RV2397C aka MT2468 aka MTCY253.24, component of Sulfate porter | 42% | 178.3 |
| D-maltose catabolism | musK | lo | ABC-type maltose transporter (EC 7.5.2.1) (characterized) | 41% | 52% | 150.6 | Sulfate/thiosulfate import ATP-binding protein CysA aka RV2397C aka MT2468 aka MTCY253.24, component of Sulfate porter | 42% | 178.3 |
| trehalose catabolism | malK | lo | MsmK aka SMU.882, component of The raffinose/stachyose transporter, MsmEFGK (MalK (3.A.1.1.27) can probably substitute for MsmK; Webb et al., 2008). This system may also transport melibiose, isomaltotriose and sucrose as well as isomaltosaccharides (characterized) | 34% | 78% | 149.1 | Sulfate/thiosulfate import ATP-binding protein CysA aka RV2397C aka MT2468 aka MTCY253.24, component of Sulfate porter | 42% | 178.3 |
| D-maltose catabolism | aglK | lo | ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized) | 39% | 56% | 148.3 | Sulfate/thiosulfate import ATP-binding protein CysA aka RV2397C aka MT2468 aka MTCY253.24, component of Sulfate porter | 42% | 178.3 |
| sucrose catabolism | aglK | lo | ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized) | 39% | 56% | 148.3 | Sulfate/thiosulfate import ATP-binding protein CysA aka RV2397C aka MT2468 aka MTCY253.24, component of Sulfate porter | 42% | 178.3 |
| trehalose catabolism | aglK | lo | ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized) | 39% | 56% | 148.3 | Sulfate/thiosulfate import ATP-binding protein CysA aka RV2397C aka MT2468 aka MTCY253.24, component of Sulfate porter | 42% | 178.3 |
| 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) | 37% | 64% | 146.7 | Sulfate/thiosulfate import ATP-binding protein CysA aka RV2397C aka MT2468 aka MTCY253.24, component of Sulfate porter | 42% | 178.3 |
| D-cellobiose catabolism | aglK' | lo | Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) | 37% | 64% | 146 | Sulfate/thiosulfate import ATP-binding protein CysA aka RV2397C aka MT2468 aka MTCY253.24, component of Sulfate porter | 42% | 178.3 |
| D-glucose catabolism | aglK' | lo | Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) | 37% | 64% | 146 | Sulfate/thiosulfate import ATP-binding protein CysA aka RV2397C aka MT2468 aka MTCY253.24, component of Sulfate porter | 42% | 178.3 |
| lactose catabolism | aglK' | lo | Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) | 37% | 64% | 146 | Sulfate/thiosulfate import ATP-binding protein CysA aka RV2397C aka MT2468 aka MTCY253.24, component of Sulfate porter | 42% | 178.3 |
| D-maltose catabolism | aglK' | lo | Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) | 37% | 64% | 146 | Sulfate/thiosulfate import ATP-binding protein CysA aka RV2397C aka MT2468 aka MTCY253.24, component of Sulfate porter | 42% | 178.3 |
| sucrose catabolism | aglK' | lo | Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) | 37% | 64% | 146 | Sulfate/thiosulfate import ATP-binding protein CysA aka RV2397C aka MT2468 aka MTCY253.24, component of Sulfate porter | 42% | 178.3 |
| trehalose catabolism | aglK' | lo | Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) | 37% | 64% | 146 | Sulfate/thiosulfate import ATP-binding protein CysA aka RV2397C aka MT2468 aka MTCY253.24, component of Sulfate porter | 42% | 178.3 |
| L-proline catabolism | opuBA | lo | BusAA, component of Uptake system for glycine-betaine (high affinity) and proline (low affinity) (OpuAA-OpuABC) or BusAA-ABC of Lactococcus lactis). BusAA, the ATPase subunit, has a C-terminal tandem cystathionine β-synthase (CBS) domain which is the cytoplasmic K+ sensor for osmotic stress (osmotic strength)while the BusABC subunit has the membrane and receptor domains fused to each other (Biemans-Oldehinkel et al., 2006; Mahmood et al., 2006; Gul et al. 2012). An N-terminal amphipathic α-helix of OpuA is necessary for high activity but is not critical for biogenesis or the ionic regulation of transport (characterized) | 34% | 61% | 141.7 | Sulfate/thiosulfate import ATP-binding protein CysA aka RV2397C aka MT2468 aka MTCY253.24, component of Sulfate porter | 42% | 178.3 |
| L-arginine catabolism | artP | lo | Arginine transport ATP-binding protein ArtP; EC 7.4.2.- (characterized) | 39% | 92% | 138.7 | Sulfate/thiosulfate import ATP-binding protein CysA aka RV2397C aka MT2468 aka MTCY253.24, component of Sulfate porter | 42% | 178.3 |
| L-asparagine catabolism | peb1C | lo | PEB1C, component of Uptake system for glutamate and aspartate (characterized) | 37% | 99% | 137.1 | Sulfate/thiosulfate import ATP-binding protein CysA aka RV2397C aka MT2468 aka MTCY253.24, component of Sulfate porter | 42% | 178.3 |
| L-aspartate catabolism | peb1C | lo | PEB1C, component of Uptake system for glutamate and aspartate (characterized) | 37% | 99% | 137.1 | Sulfate/thiosulfate import ATP-binding protein CysA aka RV2397C aka MT2468 aka MTCY253.24, component of Sulfate porter | 42% | 178.3 |
| L-histidine catabolism | Ac3H11_2560 | lo | ABC transporter for L-Histidine, ATPase component (characterized) | 36% | 76% | 132.9 | Sulfate/thiosulfate import ATP-binding protein CysA aka RV2397C aka MT2468 aka MTCY253.24, component of Sulfate porter | 42% | 178.3 |
| L-tryptophan catabolism | ecfA2 | lo | Energy-coupling factor transporter ATP-binding protein EcfA2; Short=ECF transporter A component EcfA2; EC 7.-.-.- (characterized, see rationale) | 32% | 82% | 122.9 | Sulfate/thiosulfate import ATP-binding protein CysA aka RV2397C aka MT2468 aka MTCY253.24, component of Sulfate porter | 42% | 178.3 |
| glycerol catabolism | glpS | lo | ABC transporter for Glycerol, ATPase component 1 (characterized) | 35% | 55% | 121.3 | Sulfate/thiosulfate import ATP-binding protein CysA aka RV2397C aka MT2468 aka MTCY253.24, component of Sulfate porter | 42% | 178.3 |
| D-fructose catabolism | frcA | lo | Fructose import ATP-binding protein FrcA; EC 7.5.2.- (characterized) | 30% | 75% | 89 | Sulfate/thiosulfate import ATP-binding protein CysA aka RV2397C aka MT2468 aka MTCY253.24, component of Sulfate porter | 42% | 178.3 |
| D-mannose catabolism | frcA | lo | Fructose import ATP-binding protein FrcA; EC 7.5.2.- (characterized) | 30% | 75% | 89 | Sulfate/thiosulfate import ATP-binding protein CysA aka RV2397C aka MT2468 aka MTCY253.24, component of Sulfate porter | 42% | 178.3 |
| D-ribose catabolism | frcA | lo | Fructose import ATP-binding protein FrcA; EC 7.5.2.- (characterized) | 30% | 75% | 89 | Sulfate/thiosulfate import ATP-binding protein CysA aka RV2397C aka MT2468 aka MTCY253.24, component of Sulfate porter | 42% | 178.3 |
| sucrose catabolism | frcA | lo | Fructose import ATP-binding protein FrcA; EC 7.5.2.- (characterized) | 30% | 75% | 89 | Sulfate/thiosulfate import ATP-binding protein CysA aka RV2397C aka MT2468 aka MTCY253.24, component of Sulfate porter | 42% | 178.3 |
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