| Pathway | Step | Score | Similar to | Id. | Cov. | Bits | Other hit | Other id. | Other bits |
|---|
| putrescine catabolism | potA | hi | PotG aka B0855, component of Putrescine porter (characterized) | 60% | 97% | 426 | Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD | 44% | 250.8 |
| xylitol catabolism | Dshi_0546 | med | ABC transporter for Xylitol, ATPase component (characterized) | 47% | 72% | 232.6 | PotG aka B0855, component of Putrescine porter | 60% | 426.0 |
| N-acetyl-D-glucosamine catabolism | SMc02869 | med | N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized) | 46% | 70% | 223.8 | PotG aka B0855, component of Putrescine porter | 60% | 426.0 |
| D-glucosamine (chitosamine) catabolism | SMc02869 | med | N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized) | 46% | 70% | 223.8 | PotG aka B0855, component of Putrescine porter | 60% | 426.0 |
| D-cellobiose catabolism | gtsD | med | GtsD (GLcK), component of Glucose porter, GtsABCD (characterized) | 42% | 75% | 218 | PotG aka B0855, component of Putrescine porter | 60% | 426.0 |
| D-glucose catabolism | gtsD | med | GtsD (GLcK), component of Glucose porter, GtsABCD (characterized) | 42% | 75% | 218 | PotG aka B0855, component of Putrescine porter | 60% | 426.0 |
| lactose catabolism | gtsD | med | GtsD (GLcK), component of Glucose porter, GtsABCD (characterized) | 42% | 75% | 218 | PotG aka B0855, component of Putrescine porter | 60% | 426.0 |
| D-maltose catabolism | gtsD | med | GtsD (GLcK), component of Glucose porter, GtsABCD (characterized) | 42% | 75% | 218 | PotG aka B0855, component of Putrescine porter | 60% | 426.0 |
| sucrose catabolism | gtsD | med | GtsD (GLcK), component of Glucose porter, GtsABCD (characterized) | 42% | 75% | 218 | PotG aka B0855, component of Putrescine porter | 60% | 426.0 |
| trehalose catabolism | gtsD | med | GtsD (GLcK), component of Glucose porter, GtsABCD (characterized) | 42% | 75% | 218 | PotG aka B0855, component of Putrescine porter | 60% | 426.0 |
| trehalose catabolism | thuK | med | Trehalose import ATP-binding protein SugC; EC 7.5.2.- (characterized) | 41% | 72% | 218 | PotG aka B0855, component of Putrescine porter | 60% | 426.0 |
| D-maltose catabolism | malK_Bb | med | ABC-type maltose transport, ATP binding protein (characterized, see rationale) | 46% | 70% | 216.9 | PotG aka B0855, component of Putrescine porter | 60% | 426.0 |
| lactose catabolism | lacK | med | ABC transporter for Lactose, ATPase component (characterized) | 41% | 78% | 211.1 | PotG aka B0855, component of Putrescine porter | 60% | 426.0 |
| trehalose catabolism | treV | med | TreV, component of Trehalose porter (characterized) | 43% | 77% | 205.3 | PotG aka B0855, component of Putrescine porter | 60% | 426.0 |
| D-maltose catabolism | thuK | med | ThuK aka RB0314 aka SMB20328, component of Trehalose/maltose/sucrose porter (trehalose inducible) (characterized) | 44% | 71% | 197.2 | PotG aka B0855, component of Putrescine porter | 60% | 426.0 |
| sucrose catabolism | thuK | med | ThuK aka RB0314 aka SMB20328, component of Trehalose/maltose/sucrose porter (trehalose inducible) (characterized) | 44% | 71% | 197.2 | PotG aka B0855, component of Putrescine porter | 60% | 426.0 |
| L-histidine catabolism | hutV | med | ABC transporter for L-Histidine, ATPase component (characterized) | 40% | 89% | 179.5 | PotG aka B0855, component of Putrescine porter | 60% | 426.0 |
| L-proline catabolism | hutV | med | HutV aka HISV aka R02702 aka SMC00670, component of Uptake system for hisitidine, proline, proline-betaine and glycine-betaine (characterized) | 41% | 82% | 174.9 | PotG aka B0855, component of Putrescine porter | 60% | 426.0 |
| L-histidine catabolism | Ac3H11_2560 | med | ABC transporter for L-Histidine, ATPase component (characterized) | 44% | 80% | 159.5 | PotG aka B0855, component of Putrescine porter | 60% | 426.0 |
| D-mannitol catabolism | mtlK | lo | SmoK aka POLK, component of Hexitol (glucitol; mannitol) porter (characterized) | 40% | 87% | 234.2 | PotG aka B0855, component of Putrescine porter | 60% | 426.0 |
| D-maltose catabolism | malK | lo | Maltose-transporting ATPase (EC 3.6.3.19) (characterized) | 39% | 85% | 231.1 | PotG aka B0855, component of Putrescine porter | 60% | 426.0 |
| 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) | 40% | 89% | 229.6 | PotG aka B0855, component of Putrescine porter | 60% | 426.0 |
| 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% | 87% | 226.9 | PotG aka B0855, component of Putrescine porter | 60% | 426.0 |
| L-arabinose catabolism | xacJ | lo | Xylose/arabinose import ATP-binding protein XacJ; EC 7.5.2.13 (characterized, see rationale) | 39% | 81% | 224.6 | PotG aka B0855, component of Putrescine porter | 60% | 426.0 |
| D-sorbitol (glucitol) catabolism | mtlK | lo | ABC transporter for D-Sorbitol, ATPase component (characterized) | 37% | 88% | 224.6 | PotG aka B0855, component of Putrescine porter | 60% | 426.0 |
| D-galactose catabolism | PfGW456L13_1897 | lo | ABC transporter for D-Galactose and D-Glucose, ATPase component (characterized) | 39% | 84% | 221.5 | PotG aka B0855, component of Putrescine porter | 60% | 426.0 |
| D-xylose catabolism | gtsD | lo | ABC transporter for D-Glucose-6-Phosphate, ATPase component (characterized) | 38% | 84% | 221.1 | PotG aka B0855, component of Putrescine porter | 60% | 426.0 |
| D-maltose catabolism | malK_Aa | lo | ABC-type maltose transporter (EC 7.5.2.1) (characterized) | 39% | 86% | 220.3 | PotG aka B0855, component of Putrescine porter | 60% | 426.0 |
| D-cellobiose catabolism | SMc04256 | lo | ABC transporter for D-Cellobiose and D-Salicin, ATPase component (characterized) | 38% | 95% | 219.2 | PotG aka B0855, component of Putrescine porter | 60% | 426.0 |
| L-arabinose catabolism | xacK | lo | Xylose/arabinose import ATP-binding protein XacK; EC 7.5.2.13 (characterized, see rationale) | 46% | 62% | 215.7 | PotG aka B0855, component of Putrescine porter | 60% | 426.0 |
| D-maltose catabolism | aglK | lo | ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized) | 39% | 86% | 213.4 | PotG aka B0855, component of Putrescine porter | 60% | 426.0 |
| 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% | 89% | 213.4 | PotG aka B0855, component of Putrescine porter | 60% | 426.0 |
| sucrose catabolism | aglK | lo | ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized) | 39% | 86% | 213.4 | PotG aka B0855, component of Putrescine porter | 60% | 426.0 |
| trehalose catabolism | aglK | lo | ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized) | 39% | 86% | 213.4 | PotG aka B0855, component of Putrescine porter | 60% | 426.0 |
| 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) | 37% | 89% | 213.4 | PotG aka B0855, component of Putrescine porter | 60% | 426.0 |
| D-cellobiose catabolism | aglK' | lo | Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) | 37% | 96% | 211.1 | PotG aka B0855, component of Putrescine porter | 60% | 426.0 |
| D-glucose catabolism | aglK' | lo | Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) | 37% | 96% | 211.1 | PotG aka B0855, component of Putrescine porter | 60% | 426.0 |
| lactose catabolism | aglK' | lo | Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) | 37% | 96% | 211.1 | PotG aka B0855, component of Putrescine porter | 60% | 426.0 |
| D-maltose catabolism | aglK' | lo | Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) | 37% | 96% | 211.1 | PotG aka B0855, component of Putrescine porter | 60% | 426.0 |
| sucrose catabolism | aglK' | lo | Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) | 37% | 96% | 211.1 | PotG aka B0855, component of Putrescine porter | 60% | 426.0 |
| trehalose catabolism | aglK' | lo | Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) | 37% | 96% | 211.1 | PotG aka B0855, component of Putrescine porter | 60% | 426.0 |
| D-cellobiose catabolism | glcV | lo | monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) | 36% | 97% | 209.1 | PotG aka B0855, component of Putrescine porter | 60% | 426.0 |
| D-galactose catabolism | glcV | lo | monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) | 36% | 97% | 209.1 | PotG aka B0855, component of Putrescine porter | 60% | 426.0 |
| D-glucose catabolism | glcV | lo | monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) | 36% | 97% | 209.1 | PotG aka B0855, component of Putrescine porter | 60% | 426.0 |
| lactose catabolism | glcV | lo | monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) | 36% | 97% | 209.1 | PotG aka B0855, component of Putrescine porter | 60% | 426.0 |
| D-maltose catabolism | glcV | lo | monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) | 36% | 97% | 209.1 | PotG aka B0855, component of Putrescine porter | 60% | 426.0 |
| D-mannose catabolism | glcV | lo | monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) | 36% | 97% | 209.1 | PotG aka B0855, component of Putrescine porter | 60% | 426.0 |
| sucrose catabolism | glcV | lo | monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) | 36% | 97% | 209.1 | PotG aka B0855, component of Putrescine porter | 60% | 426.0 |
| trehalose catabolism | glcV | lo | monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) | 36% | 97% | 209.1 | PotG aka B0855, component of Putrescine porter | 60% | 426.0 |
| 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) | 37% | 80% | 208.4 | PotG aka B0855, component of Putrescine porter | 60% | 426.0 |
| L-fucose catabolism | SM_b21106 | lo | ABC transporter for L-Fucose, ATPase component (characterized) | 40% | 77% | 208.4 | PotG aka B0855, component of Putrescine porter | 60% | 426.0 |
| D-glucosamine (chitosamine) catabolism | SM_b21216 | lo | ABC transporter for D-Glucosamine, ATPase component (characterized) | 42% | 68% | 203 | PotG aka B0855, component of Putrescine porter | 60% | 426.0 |
| D-maltose catabolism | musK | lo | ABC-type maltose transporter (EC 7.5.2.1) (characterized) | 45% | 58% | 200.7 | PotG aka B0855, component of Putrescine porter | 60% | 426.0 |
| L-proline catabolism | proV | lo | glycine betaine/l-proline transport atp-binding protein prov (characterized) | 42% | 60% | 187.2 | PotG aka B0855, component of Putrescine porter | 60% | 426.0 |
| L-arabinose catabolism | araV | lo | AraV, component of Arabinose, fructose, xylose porter (characterized) | 37% | 69% | 181.8 | PotG aka B0855, component of Putrescine porter | 60% | 426.0 |
| D-fructose catabolism | araV | lo | AraV, component of Arabinose, fructose, xylose porter (characterized) | 37% | 69% | 181.8 | PotG aka B0855, component of Putrescine porter | 60% | 426.0 |
| sucrose catabolism | araV | lo | AraV, component of Arabinose, fructose, xylose porter (characterized) | 37% | 69% | 181.8 | PotG aka B0855, component of Putrescine porter | 60% | 426.0 |
| D-xylose catabolism | araV | lo | AraV, component of Arabinose, fructose, xylose porter (characterized) | 37% | 69% | 181.8 | PotG aka B0855, component of Putrescine porter | 60% | 426.0 |
| 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) | 35% | 76% | 175.3 | PotG aka B0855, component of Putrescine porter | 60% | 426.0 |
| L-glutamate catabolism | gltL | lo | GluA aka CGL1950, component of Glutamate porter (characterized) | 36% | 99% | 159.8 | PotG aka B0855, component of Putrescine porter | 60% | 426.0 |
| L-arginine catabolism | artP | lo | Arginine transport ATP-binding protein ArtM (characterized) | 36% | 100% | 159.1 | PotG aka B0855, component of Putrescine porter | 60% | 426.0 |
| L-histidine catabolism | aapP | lo | ABC transporter for L-Glutamine, L-Histidine, and other L-amino acids, ATPase component (characterized) | 34% | 99% | 155.6 | PotG aka B0855, component of Putrescine porter | 60% | 426.0 |
| D-alanine catabolism | Pf6N2E2_5405 | lo | ABC transporter for D-Alanine, ATPase component (characterized) | 34% | 98% | 155.2 | PotG aka B0855, component of Putrescine porter | 60% | 426.0 |
| glycerol catabolism | glpS | lo | ABC transporter for Glycerol, ATPase component 1 (characterized) | 36% | 63% | 154.5 | PotG aka B0855, component of Putrescine porter | 60% | 426.0 |
| L-asparagine catabolism | aapP | lo | AapP, component of General L-amino acid porter; transports basic and acidic amino acids preferentially, but also transports aliphatic amino acids (catalyzes both uptake and efflux) (characterized) | 33% | 99% | 151.4 | PotG aka B0855, component of Putrescine porter | 60% | 426.0 |
| L-aspartate catabolism | aapP | lo | AapP, component of General L-amino acid porter; transports basic and acidic amino acids preferentially, but also transports aliphatic amino acids (catalyzes both uptake and efflux) (characterized) | 33% | 99% | 151.4 | PotG aka B0855, component of Putrescine porter | 60% | 426.0 |
| L-glutamate catabolism | aapP | lo | AapP, component of General L-amino acid porter; transports basic and acidic amino acids preferentially, but also transports aliphatic amino acids (catalyzes both uptake and efflux) (characterized) | 33% | 99% | 151.4 | PotG aka B0855, component of Putrescine porter | 60% | 426.0 |
| L-leucine catabolism | aapP | lo | AapP, component of General L-amino acid porter; transports basic and acidic amino acids preferentially, but also transports aliphatic amino acids (catalyzes both uptake and efflux) (characterized) | 33% | 99% | 151.4 | PotG aka B0855, component of Putrescine porter | 60% | 426.0 |
| L-proline catabolism | aapP | lo | AapP, component of General L-amino acid porter; transports basic and acidic amino acids preferentially, but also transports aliphatic amino acids (catalyzes both uptake and efflux) (characterized) | 33% | 99% | 151.4 | PotG aka B0855, component of Putrescine porter | 60% | 426.0 |
| L-asparagine catabolism | aatP | lo | PP1068, component of Acidic amino acid uptake porter, AatJMQP (characterized) | 35% | 91% | 147.1 | PotG aka B0855, component of Putrescine porter | 60% | 426.0 |
| L-aspartate catabolism | aatP | lo | PP1068, component of Acidic amino acid uptake porter, AatJMQP (characterized) | 35% | 91% | 147.1 | PotG aka B0855, component of Putrescine porter | 60% | 426.0 |
| L-isoleucine catabolism | livG | lo | High-affinity branched-chain amino acid ABC transporter ATP-binding protein LivG (characterized, see rationale) | 32% | 95% | 132.1 | PotG aka B0855, component of Putrescine porter | 60% | 426.0 |
| L-phenylalanine catabolism | livG | lo | High-affinity branched-chain amino acid ABC transporter ATP-binding protein LivG (characterized, see rationale) | 32% | 95% | 132.1 | PotG aka B0855, component of Putrescine porter | 60% | 426.0 |
| L-leucine catabolism | livG | lo | ABC transporter ATP-binding protein-branched chain amino acid transport, component of The branched chain hydrophobic amino acid transporter, LivJFGHM (characterized) | 33% | 99% | 131.3 | PotG aka B0855, component of Putrescine porter | 60% | 426.0 |
| L-valine catabolism | livG | lo | ABC transporter ATP-binding protein-branched chain amino acid transport, component of The branched chain hydrophobic amino acid transporter, LivJFGHM (characterized) | 33% | 99% | 131.3 | PotG aka B0855, component of Putrescine porter | 60% | 426.0 |
| D-cellobiose catabolism | cbtD | lo | CbtD, component of Cellobiose and cellooligosaccharide porter (characterized) | 34% | 73% | 131 | PotG aka B0855, component of Putrescine porter | 60% | 426.0 |
| L-proline catabolism | HSERO_RS00895 | lo | ABC-type branched-chain amino acid transport system, ATPase component protein (characterized, see rationale) | 33% | 95% | 129.4 | PotG aka B0855, component of Putrescine porter | 60% | 426.0 |
| L-tryptophan catabolism | ecfA1 | lo | Energy-coupling factor transporter ATP-binding protein EcfA1; Short=ECF transporter A component EcfA; EC 7.-.-.- (characterized, see rationale) | 38% | 74% | 125.6 | PotG aka B0855, component of Putrescine porter | 60% | 426.0 |
| L-tryptophan catabolism | ecfA2 | lo | Energy-coupling factor transporter ATP-binding protein EcfA2; Short=ECF transporter A component EcfA2; EC 7.-.-.- (characterized, see rationale) | 35% | 78% | 123.2 | PotG aka B0855, component of Putrescine porter | 60% | 426.0 |
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