| Pathway | Step | Score | Similar to | Id. | Cov. | Bits | Other hit | Other id. | Other bits |
|---|
| L-arginine catabolism | artP | med | Arginine transport ATP-binding protein ArtM (characterized) | 40% | 89% | 142.1 | lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- | 48% | 206.1 |
| L-glutamate catabolism | gltL | lo | GluA aka CGL1950, component of Glutamate porter (characterized) | 39% | 88% | 147.1 | lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- | 48% | 206.1 |
| D-cellobiose catabolism | glcV | lo | monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) | 38% | 61% | 141.7 | lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- | 48% | 206.1 |
| D-galactose catabolism | glcV | lo | monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) | 38% | 61% | 141.7 | lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- | 48% | 206.1 |
| D-glucose catabolism | glcV | lo | monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) | 38% | 61% | 141.7 | lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- | 48% | 206.1 |
| lactose catabolism | glcV | lo | monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) | 38% | 61% | 141.7 | lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- | 48% | 206.1 |
| D-maltose catabolism | glcV | lo | monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) | 38% | 61% | 141.7 | lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- | 48% | 206.1 |
| D-mannose catabolism | glcV | lo | monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) | 38% | 61% | 141.7 | lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- | 48% | 206.1 |
| sucrose catabolism | glcV | lo | monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) | 38% | 61% | 141.7 | lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- | 48% | 206.1 |
| trehalose catabolism | glcV | lo | monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) | 38% | 61% | 141.7 | lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- | 48% | 206.1 |
| D-glucosamine (chitosamine) catabolism | AO353_21725 | lo | ABC transporter for D-glucosamine, ATPase component (characterized) | 38% | 85% | 139.8 | lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- | 48% | 206.1 |
| putrescine catabolism | potA | lo | spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31 (characterized) | 34% | 56% | 137.5 | lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- | 48% | 206.1 |
| D-maltose catabolism | malK_Bb | lo | ABC-type maltose transport, ATP binding protein (characterized, see rationale) | 36% | 61% | 136 | lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- | 48% | 206.1 |
| 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) | 34% | 58% | 134.4 | lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- | 48% | 206.1 |
| 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) | 34% | 58% | 134.4 | lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- | 48% | 206.1 |
| sucrose catabolism | thuK | lo | ABC transporter (characterized, see rationale) | 34% | 54% | 132.9 | lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- | 48% | 206.1 |
| D-maltose catabolism | thuK | lo | Trehalose/maltose import ATP-binding protein MalK; EC 7.5.2.1 (characterized) | 31% | 58% | 132.1 | lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- | 48% | 206.1 |
| lactose catabolism | lacK | lo | ABC transporter for Lactose, ATPase component (characterized) | 35% | 59% | 131.3 | lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- | 48% | 206.1 |
| L-histidine catabolism | aapP | lo | ABC transporter for L-Glutamine, L-Histidine, and other L-amino acids, ATPase component (characterized) | 33% | 83% | 131 | lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- | 48% | 206.1 |
| L-citrulline catabolism | AO353_03040 | lo | ABC transporter for L-Arginine and L-Citrulline, ATPase component (characterized) | 35% | 89% | 130.2 | lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- | 48% | 206.1 |
| D-alanine catabolism | Pf6N2E2_5405 | lo | ABC transporter for D-Alanine, ATPase component (characterized) | 32% | 84% | 128.6 | lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- | 48% | 206.1 |
| D-cellobiose catabolism | gtsD | 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) | 33% | 56% | 127.5 | lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- | 48% | 206.1 |
| D-glucose catabolism | gtsD | 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) | 33% | 56% | 127.5 | lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- | 48% | 206.1 |
| lactose catabolism | gtsD | 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) | 33% | 56% | 127.5 | lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- | 48% | 206.1 |
| D-maltose catabolism | gtsD | 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) | 33% | 56% | 127.5 | lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- | 48% | 206.1 |
| 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) | 33% | 56% | 127.5 | lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- | 48% | 206.1 |
| sucrose catabolism | gtsD | 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) | 33% | 56% | 127.5 | lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- | 48% | 206.1 |
| trehalose catabolism | gtsD | 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) | 33% | 56% | 127.5 | lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- | 48% | 206.1 |
| D-glucosamine (chitosamine) catabolism | SM_b21216 | lo | ABC transporter for D-Glucosamine, ATPase component (characterized) | 31% | 59% | 124.8 | lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- | 48% | 206.1 |
| D-sorbitol (glucitol) catabolism | mtlK | lo | ABC transporter for D-Sorbitol, ATPase component (characterized) | 32% | 60% | 124.8 | lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- | 48% | 206.1 |
| D-xylose catabolism | gtsD | lo | ABC transporter for D-Glucose-6-Phosphate, ATPase component (characterized) | 32% | 55% | 123.2 | lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- | 48% | 206.1 |
| D-cellobiose catabolism | SMc04256 | lo | ABC transporter for D-Cellobiose and D-Salicin, ATPase component (characterized) | 34% | 58% | 121.3 | lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- | 48% | 206.1 |
| D-galactose catabolism | PfGW456L13_1897 | lo | ABC transporter for D-Galactose and D-Glucose, ATPase component (characterized) | 32% | 55% | 120.9 | lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- | 48% | 206.1 |
| xylitol catabolism | HSERO_RS17020 | lo | ABC-type sugar transport system, ATPase component protein (characterized, see rationale) | 35% | 52% | 120.2 | lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- | 48% | 206.1 |
| D-maltose catabolism | malK | lo | Maltose-transporting ATPase (EC 3.6.3.19) (characterized) | 31% | 57% | 118.2 | lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- | 48% | 206.1 |
| 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% | 55% | 115.2 | lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- | 48% | 206.1 |
| 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% | 55% | 115.2 | lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- | 48% | 206.1 |
| 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% | 74% | 114.4 | lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- | 48% | 206.1 |
| L-arginine catabolism | braG | lo | ATP-binding component of a broad range amino acid ABC transporter (characterized, see rationale) | 30% | 86% | 106.3 | lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- | 48% | 206.1 |
| L-glutamate catabolism | braG | lo | ATP-binding component of a broad range amino acid ABC transporter (characterized, see rationale) | 30% | 86% | 106.3 | lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- | 48% | 206.1 |
| L-histidine catabolism | braG | lo | ATP-binding component of a broad range amino acid ABC transporter (characterized, see rationale) | 30% | 86% | 106.3 | lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- | 48% | 206.1 |
| L-isoleucine catabolism | livF | lo | ATP-binding component of a broad range amino acid ABC transporter (characterized, see rationale) | 30% | 86% | 106.3 | lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- | 48% | 206.1 |
| L-leucine catabolism | livF | lo | ATP-binding component of a broad range amino acid ABC transporter (characterized, see rationale) | 30% | 86% | 106.3 | lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- | 48% | 206.1 |
| L-valine catabolism | livF | lo | ATP-binding component of a broad range amino acid ABC transporter (characterized, see rationale) | 30% | 86% | 106.3 | lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- | 48% | 206.1 |
| L-phenylalanine catabolism | livF | lo | high-affinity branched-chain amino acid ABC transporter, ATP-binding protein LivF (characterized) | 32% | 91% | 104.8 | lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- | 48% | 206.1 |
| L-proline catabolism | HSERO_RS00900 | lo | ABC transporter ATP-binding protein (characterized, see rationale) | 31% | 88% | 99 | lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- | 48% | 206.1 |
| L-serine catabolism | Ac3H11_1692 | lo | ABC transporter ATP-binding protein (characterized, see rationale) | 31% | 88% | 99 | lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- | 48% | 206.1 |
| L-tyrosine catabolism | Ac3H11_1692 | lo | ABC transporter ATP-binding protein (characterized, see rationale) | 31% | 88% | 99 | lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- | 48% | 206.1 |
| L-alanine catabolism | braG | lo | NatE aka LivF aka SLR1881, component of Leucine/proline/alanine/serine/glycine (and possibly histidine) porter, NatABCDE (characterized) | 31% | 83% | 96.3 | lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- | 48% | 206.1 |
| L-histidine catabolism | natE | lo | NatE aka LivF aka SLR1881, component of Leucine/proline/alanine/serine/glycine (and possibly histidine) porter, NatABCDE (characterized) | 31% | 83% | 96.3 | lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- | 48% | 206.1 |
| L-leucine catabolism | natE | lo | NatE aka LivF aka SLR1881, component of Leucine/proline/alanine/serine/glycine (and possibly histidine) porter, NatABCDE (characterized) | 31% | 83% | 96.3 | lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- | 48% | 206.1 |
| L-proline catabolism | natE | lo | NatE aka LivF aka SLR1881, component of Leucine/proline/alanine/serine/glycine (and possibly histidine) porter, NatABCDE (characterized) | 31% | 83% | 96.3 | lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- | 48% | 206.1 |
| L-serine catabolism | braG | lo | NatE aka LivF aka SLR1881, component of Leucine/proline/alanine/serine/glycine (and possibly histidine) porter, NatABCDE (characterized) | 31% | 83% | 96.3 | lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- | 48% | 206.1 |
| L-threonine catabolism | braG | lo | NatE aka LivF aka SLR1881, component of Leucine/proline/alanine/serine/glycine (and possibly histidine) porter, NatABCDE (characterized) | 31% | 83% | 96.3 | lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- | 48% | 206.1 |
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