| Pathway | Step | Score | Similar to | Id. | Cov. | Bits | Other hit | Other id. | Other bits |
|---|
| 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) | 37% | 66% | 153.7 | Aliphatic sulfonates import ATP-binding protein SsuB; EC 7.6.2.- | 42% | 177.9 |
| putrescine catabolism | potA | lo | Spermidine/putrescine import ATP-binding protein PotA, component of The spermidine/putrescine uptake porter, PotABCD (characterized) | 41% | 53% | 142.1 | Aliphatic sulfonates import ATP-binding protein SsuB; EC 7.6.2.- | 42% | 177.9 |
| sucrose catabolism | thuK | lo | ABC transporter (characterized, see rationale) | 40% | 56% | 139.4 | Aliphatic sulfonates import ATP-binding protein SsuB; EC 7.6.2.- | 42% | 177.9 |
| L-histidine catabolism | Ac3H11_2560 | lo | ABC transporter for L-Histidine, ATPase component (characterized) | 35% | 82% | 139 | Aliphatic sulfonates import ATP-binding protein SsuB; EC 7.6.2.- | 42% | 177.9 |
| L-proline catabolism | proV | lo | glycine betaine/l-proline transport atp-binding protein prov (characterized) | 36% | 58% | 138.7 | Aliphatic sulfonates import ATP-binding protein SsuB; EC 7.6.2.- | 42% | 177.9 |
| 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) | 35% | 65% | 134.4 | Aliphatic sulfonates import ATP-binding protein SsuB; EC 7.6.2.- | 42% | 177.9 |
| 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) | 35% | 65% | 134.4 | Aliphatic sulfonates import ATP-binding protein SsuB; EC 7.6.2.- | 42% | 177.9 |
| 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) | 35% | 65% | 134.4 | Aliphatic sulfonates import ATP-binding protein SsuB; EC 7.6.2.- | 42% | 177.9 |
| 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) | 35% | 65% | 134.4 | Aliphatic sulfonates import ATP-binding protein SsuB; EC 7.6.2.- | 42% | 177.9 |
| 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) | 35% | 65% | 134.4 | Aliphatic sulfonates import ATP-binding protein SsuB; EC 7.6.2.- | 42% | 177.9 |
| 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) | 35% | 65% | 134.4 | Aliphatic sulfonates import ATP-binding protein SsuB; EC 7.6.2.- | 42% | 177.9 |
| 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) | 35% | 65% | 134.4 | Aliphatic sulfonates import ATP-binding protein SsuB; EC 7.6.2.- | 42% | 177.9 |
| 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) | 35% | 65% | 134.4 | Aliphatic sulfonates import ATP-binding protein SsuB; EC 7.6.2.- | 42% | 177.9 |
| trehalose 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) | 35% | 65% | 134.4 | Aliphatic sulfonates import ATP-binding protein SsuB; EC 7.6.2.- | 42% | 177.9 |
| D-maltose catabolism | malK | lo | ABC-type maltose transporter (subunit 3/3) (EC 7.5.2.1) (characterized) | 37% | 58% | 134 | Aliphatic sulfonates import ATP-binding protein SsuB; EC 7.6.2.- | 42% | 177.9 |
| D-mannitol catabolism | mtlK | lo | ABC transporter for D-mannitol and D-mannose, ATPase component (characterized) | 39% | 58% | 133.3 | Aliphatic sulfonates import ATP-binding protein SsuB; EC 7.6.2.- | 42% | 177.9 |
| D-sorbitol (glucitol) catabolism | mtlK | lo | ABC transporter for D-Mannitol, D-Mannose, and D-Sorbitol, ATPase component (characterized) | 39% | 58% | 132.9 | Aliphatic sulfonates import ATP-binding protein SsuB; EC 7.6.2.- | 42% | 177.9 |
| L-histidine catabolism | hutV | lo | ABC transporter for L-Histidine, ATPase component (characterized) | 37% | 82% | 130.6 | Aliphatic sulfonates import ATP-binding protein SsuB; EC 7.6.2.- | 42% | 177.9 |
| D-maltose catabolism | malK_Bb | lo | ABC-type maltose transport, ATP binding protein (characterized, see rationale) | 37% | 60% | 130.2 | Aliphatic sulfonates import ATP-binding protein SsuB; EC 7.6.2.- | 42% | 177.9 |
| N-acetyl-D-glucosamine catabolism | SMc02869 | lo | N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized) | 37% | 66% | 129.8 | Aliphatic sulfonates import ATP-binding protein SsuB; EC 7.6.2.- | 42% | 177.9 |
| D-glucosamine (chitosamine) catabolism | SMc02869 | lo | N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized) | 37% | 66% | 129.8 | Aliphatic sulfonates import ATP-binding protein SsuB; EC 7.6.2.- | 42% | 177.9 |
| D-maltose catabolism | malK_Aa | lo | ABC-type maltose transporter (EC 7.5.2.1) (characterized) | 35% | 60% | 128.6 | Aliphatic sulfonates import ATP-binding protein SsuB; EC 7.6.2.- | 42% | 177.9 |
| xylitol catabolism | Dshi_0546 | lo | ABC transporter for Xylitol, ATPase component (characterized) | 38% | 63% | 128.3 | Aliphatic sulfonates import ATP-binding protein SsuB; EC 7.6.2.- | 42% | 177.9 |
| lactose catabolism | lacK | lo | LacK, component of Lactose porter (characterized) | 35% | 62% | 126.3 | Aliphatic sulfonates import ATP-binding protein SsuB; EC 7.6.2.- | 42% | 177.9 |
| L-isoleucine catabolism | livG | lo | ABC transporter ATP-binding protein-branched chain amino acid transport, component of The branched chain hydrophobic amino acid transporter, LivJFGHM (characterized) | 35% | 100% | 125.9 | Aliphatic sulfonates import ATP-binding protein SsuB; EC 7.6.2.- | 42% | 177.9 |
| 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) | 35% | 100% | 125.9 | Aliphatic sulfonates import ATP-binding protein SsuB; EC 7.6.2.- | 42% | 177.9 |
| 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) | 35% | 100% | 125.9 | Aliphatic sulfonates import ATP-binding protein SsuB; EC 7.6.2.- | 42% | 177.9 |
| L-fucose catabolism | SM_b21106 | lo | ABC transporter for L-Fucose, ATPase component (characterized) | 35% | 57% | 124 | Aliphatic sulfonates import ATP-binding protein SsuB; EC 7.6.2.- | 42% | 177.9 |
| D-cellobiose catabolism | SMc04256 | lo | ABC transporter for D-Cellobiose and D-Salicin, ATPase component (characterized) | 36% | 58% | 123.6 | Aliphatic sulfonates import ATP-binding protein SsuB; EC 7.6.2.- | 42% | 177.9 |
| xylitol catabolism | HSERO_RS17020 | lo | ABC-type sugar transport system, ATPase component protein (characterized, see rationale) | 35% | 53% | 123.6 | Aliphatic sulfonates import ATP-binding protein SsuB; EC 7.6.2.- | 42% | 177.9 |
| L-arabinose catabolism | xacK | lo | Xylose/arabinose import ATP-binding protein XacK; EC 7.5.2.13 (characterized, see rationale) | 35% | 59% | 120.9 | Aliphatic sulfonates import ATP-binding protein SsuB; EC 7.6.2.- | 42% | 177.9 |
| 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% | 51% | 119.4 | Aliphatic sulfonates import ATP-binding protein SsuB; EC 7.6.2.- | 42% | 177.9 |
| L-proline catabolism | hutV | lo | HutV aka HISV aka R02702 aka SMC00670, component of Uptake system for hisitidine, proline, proline-betaine and glycine-betaine (characterized) | 36% | 79% | 119.4 | Aliphatic sulfonates import ATP-binding protein SsuB; EC 7.6.2.- | 42% | 177.9 |
| 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) | 35% | 58% | 119 | Aliphatic sulfonates import ATP-binding protein SsuB; EC 7.6.2.- | 42% | 177.9 |
| 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) | 35% | 58% | 119 | Aliphatic sulfonates import ATP-binding protein SsuB; EC 7.6.2.- | 42% | 177.9 |
| D-maltose catabolism | musK | lo | ABC-type maltose transporter (EC 7.5.2.1) (characterized) | 36% | 56% | 115.5 | Aliphatic sulfonates import ATP-binding protein SsuB; EC 7.6.2.- | 42% | 177.9 |
| trehalose catabolism | treV | lo | TreV, component of Trehalose porter (characterized) | 34% | 61% | 114 | Aliphatic sulfonates import ATP-binding protein SsuB; EC 7.6.2.- | 42% | 177.9 |
| L-tryptophan catabolism | ecfA1 | lo | Energy-coupling factor transporter ATP-binding protein EcfA1; Short=ECF transporter A component EcfA; EC 7.-.-.- (characterized, see rationale) | 32% | 85% | 104 | Aliphatic sulfonates import ATP-binding protein SsuB; EC 7.6.2.- | 42% | 177.9 |
| L-isoleucine catabolism | livF | lo | ABC transporter ATP-binding protein-branched chain amino acid transport, component of The branched chain hydrophobic amino acid transporter, LivJFGHM (characterized) | 33% | 93% | 103.6 | Aliphatic sulfonates import ATP-binding protein SsuB; EC 7.6.2.- | 42% | 177.9 |
| L-leucine catabolism | livF | lo | ABC transporter ATP-binding protein-branched chain amino acid transport, component of The branched chain hydrophobic amino acid transporter, LivJFGHM (characterized) | 33% | 93% | 103.6 | Aliphatic sulfonates import ATP-binding protein SsuB; EC 7.6.2.- | 42% | 177.9 |
| L-valine catabolism | livF | lo | ABC transporter ATP-binding protein-branched chain amino acid transport, component of The branched chain hydrophobic amino acid transporter, LivJFGHM (characterized) | 33% | 93% | 103.6 | Aliphatic sulfonates import ATP-binding protein SsuB; EC 7.6.2.- | 42% | 177.9 |
| L-phenylalanine catabolism | livG | lo | High-affinity branched-chain amino acid transport ATP-binding protein LivG aka B3455, component of Leucine; leucine/isoleucine/valine porter (characterized) | 31% | 87% | 90.1 | Aliphatic sulfonates import ATP-binding protein SsuB; EC 7.6.2.- | 42% | 177.9 |
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