| Pathway | Step | Score | Similar to | Id. | Cov. | Bits | Other hit | Other id. | Other bits |
|---|
| putrescine catabolism | potA | med | Spermidine/putrescine import ATP-binding protein PotA, component of The spermidine/putrescine uptake porter, PotABCD (characterized) | 42% | 80% | 238.8 | Uncharacterized ABC transporter ATP-binding protein YdcT | 44% | 252.3 |
| trehalose catabolism | treV | med | TreV, component of Trehalose porter (characterized) | 45% | 73% | 223.4 | Uncharacterized ABC transporter ATP-binding protein YdcT | 44% | 252.3 |
| D-maltose catabolism | thuK | med | ThuK aka RB0314 aka SMB20328, component of Trehalose/maltose/sucrose porter (trehalose inducible) (characterized) | 40% | 78% | 211.1 | Uncharacterized ABC transporter ATP-binding protein YdcT | 44% | 252.3 |
| sucrose catabolism | thuK | med | ThuK aka RB0314 aka SMB20328, component of Trehalose/maltose/sucrose porter (trehalose inducible) (characterized) | 40% | 78% | 211.1 | Uncharacterized ABC transporter ATP-binding protein YdcT | 44% | 252.3 |
| trehalose catabolism | thuK | med | ThuK aka RB0314 aka SMB20328, component of Trehalose/maltose/sucrose porter (trehalose inducible) (characterized) | 40% | 78% | 211.1 | Uncharacterized ABC transporter ATP-binding protein YdcT | 44% | 252.3 |
| D-maltose catabolism | musK | med | ABC-type maltose transporter (EC 7.5.2.1) (characterized) | 40% | 70% | 209.9 | Uncharacterized ABC transporter ATP-binding protein YdcT | 44% | 252.3 |
| D-sorbitol (glucitol) catabolism | mtlK | lo | ABC transporter for D-Sorbitol, ATPase component (characterized) | 39% | 91% | 231.1 | Uncharacterized ABC transporter ATP-binding protein YdcT | 44% | 252.3 |
| N-acetyl-D-glucosamine catabolism | SMc02869 | lo | N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized) | 39% | 88% | 225.3 | Uncharacterized ABC transporter ATP-binding protein YdcT | 44% | 252.3 |
| D-glucosamine (chitosamine) catabolism | SMc02869 | lo | N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized) | 39% | 88% | 225.3 | Uncharacterized ABC transporter ATP-binding protein YdcT | 44% | 252.3 |
| D-maltose catabolism | malK_Bb | lo | ABC-type maltose transport, ATP binding protein (characterized, see rationale) | 40% | 82% | 219.2 | Uncharacterized ABC transporter ATP-binding protein YdcT | 44% | 252.3 |
| D-glucosamine (chitosamine) catabolism | SM_b21216 | lo | ABC transporter for D-Glucosamine, ATPase component (characterized) | 43% | 69% | 217.2 | Uncharacterized ABC transporter ATP-binding protein YdcT | 44% | 252.3 |
| 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) | 41% | 69% | 216.9 | Uncharacterized ABC transporter ATP-binding protein YdcT | 44% | 252.3 |
| D-mannitol catabolism | mtlK | lo | SmoK aka POLK, component of Hexitol (glucitol; mannitol) porter (characterized) | 40% | 80% | 216.5 | Uncharacterized ABC transporter ATP-binding protein YdcT | 44% | 252.3 |
| L-arabinose catabolism | xacJ | lo | Xylose/arabinose import ATP-binding protein XacJ; EC 7.5.2.13 (characterized, see rationale) | 42% | 67% | 215.7 | Uncharacterized ABC transporter ATP-binding protein YdcT | 44% | 252.3 |
| 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) | 40% | 66% | 214.5 | Uncharacterized ABC transporter ATP-binding protein YdcT | 44% | 252.3 |
| 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) | 40% | 66% | 214.5 | Uncharacterized ABC transporter ATP-binding protein YdcT | 44% | 252.3 |
| 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) | 40% | 66% | 214.5 | Uncharacterized ABC transporter ATP-binding protein YdcT | 44% | 252.3 |
| 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) | 40% | 66% | 214.5 | Uncharacterized ABC transporter ATP-binding protein YdcT | 44% | 252.3 |
| 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) | 40% | 66% | 214.5 | Uncharacterized ABC transporter ATP-binding protein YdcT | 44% | 252.3 |
| 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) | 40% | 66% | 214.5 | Uncharacterized ABC transporter ATP-binding protein YdcT | 44% | 252.3 |
| 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) | 40% | 66% | 214.5 | Uncharacterized ABC transporter ATP-binding protein YdcT | 44% | 252.3 |
| xylitol catabolism | Dshi_0546 | lo | ABC transporter for Xylitol, ATPase component (characterized) | 40% | 80% | 214.5 | Uncharacterized ABC transporter ATP-binding protein YdcT | 44% | 252.3 |
| D-maltose catabolism | malK | lo | ABC-type maltose transporter (subunit 3/3) (EC 7.5.2.1) (characterized) | 41% | 68% | 211.8 | Uncharacterized ABC transporter ATP-binding protein YdcT | 44% | 252.3 |
| D-maltose catabolism | aglK | lo | ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized) | 41% | 69% | 211.1 | Uncharacterized ABC transporter ATP-binding protein YdcT | 44% | 252.3 |
| sucrose catabolism | aglK | lo | ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized) | 41% | 69% | 211.1 | Uncharacterized ABC transporter ATP-binding protein YdcT | 44% | 252.3 |
| trehalose catabolism | aglK | lo | ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized) | 41% | 69% | 211.1 | Uncharacterized ABC transporter ATP-binding protein YdcT | 44% | 252.3 |
| D-galactose catabolism | PfGW456L13_1897 | lo | ABC transporter for D-Galactose and D-Glucose, ATPase component (characterized) | 38% | 76% | 210.3 | Uncharacterized ABC transporter ATP-binding protein YdcT | 44% | 252.3 |
| xylitol catabolism | HSERO_RS17020 | lo | ABC-type sugar transport system, ATPase component protein (characterized, see rationale) | 43% | 59% | 210.3 | Uncharacterized ABC transporter ATP-binding protein YdcT | 44% | 252.3 |
| D-cellobiose catabolism | aglK' | lo | Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) | 36% | 88% | 209.1 | Uncharacterized ABC transporter ATP-binding protein YdcT | 44% | 252.3 |
| D-glucose catabolism | aglK' | lo | Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) | 36% | 88% | 209.1 | Uncharacterized ABC transporter ATP-binding protein YdcT | 44% | 252.3 |
| lactose catabolism | aglK' | lo | Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) | 36% | 88% | 209.1 | Uncharacterized ABC transporter ATP-binding protein YdcT | 44% | 252.3 |
| D-maltose catabolism | aglK' | lo | Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) | 36% | 88% | 209.1 | Uncharacterized ABC transporter ATP-binding protein YdcT | 44% | 252.3 |
| sucrose catabolism | aglK' | lo | Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) | 36% | 88% | 209.1 | Uncharacterized ABC transporter ATP-binding protein YdcT | 44% | 252.3 |
| trehalose catabolism | aglK' | lo | Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) | 36% | 88% | 209.1 | Uncharacterized ABC transporter ATP-binding protein YdcT | 44% | 252.3 |
| D-maltose catabolism | malK_Aa | lo | ABC-type maltose transporter (EC 7.5.2.1) (characterized) | 41% | 63% | 208 | Uncharacterized ABC transporter ATP-binding protein YdcT | 44% | 252.3 |
| D-xylose catabolism | gtsD | lo | ABC transporter for D-Glucose-6-Phosphate, ATPase component (characterized) | 38% | 76% | 208 | Uncharacterized ABC transporter ATP-binding protein YdcT | 44% | 252.3 |
| 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) | 42% | 59% | 206.5 | Uncharacterized ABC transporter ATP-binding protein YdcT | 44% | 252.3 |
| lactose catabolism | lacK | lo | ABC transporter for Lactose, ATPase component (characterized) | 35% | 92% | 206.1 | Uncharacterized ABC transporter ATP-binding protein YdcT | 44% | 252.3 |
| L-fucose catabolism | SM_b21106 | lo | ABC transporter for L-Fucose, ATPase component (characterized) | 39% | 68% | 204.9 | Uncharacterized ABC transporter ATP-binding protein YdcT | 44% | 252.3 |
| 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) | 39% | 69% | 204.5 | Uncharacterized ABC transporter ATP-binding protein YdcT | 44% | 252.3 |
| D-cellobiose catabolism | SMc04256 | lo | ABC transporter for D-Cellobiose and D-Salicin, ATPase component (characterized) | 37% | 80% | 201.8 | Uncharacterized ABC transporter ATP-binding protein YdcT | 44% | 252.3 |
| 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) | 39% | 67% | 201.4 | Uncharacterized ABC transporter ATP-binding protein YdcT | 44% | 252.3 |
| L-arabinose catabolism | araV | lo | AraV, component of Arabinose, fructose, xylose porter (characterized) | 40% | 67% | 189.1 | Uncharacterized ABC transporter ATP-binding protein YdcT | 44% | 252.3 |
| D-fructose catabolism | araV | lo | AraV, component of Arabinose, fructose, xylose porter (characterized) | 40% | 67% | 189.1 | Uncharacterized ABC transporter ATP-binding protein YdcT | 44% | 252.3 |
| sucrose catabolism | araV | lo | AraV, component of Arabinose, fructose, xylose porter (characterized) | 40% | 67% | 189.1 | Uncharacterized ABC transporter ATP-binding protein YdcT | 44% | 252.3 |
| D-xylose catabolism | araV | lo | AraV, component of Arabinose, fructose, xylose porter (characterized) | 40% | 67% | 189.1 | Uncharacterized ABC transporter ATP-binding protein YdcT | 44% | 252.3 |
| 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) | 41% | 60% | 184.5 | Uncharacterized ABC transporter ATP-binding protein YdcT | 44% | 252.3 |
| L-histidine catabolism | hutV | lo | HutV aka HISV aka R02702 aka SMC00670, component of Uptake system for hisitidine, proline, proline-betaine and glycine-betaine (characterized) | 37% | 86% | 166 | Uncharacterized ABC transporter ATP-binding protein YdcT | 44% | 252.3 |
| 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) | 37% | 86% | 166 | Uncharacterized ABC transporter ATP-binding protein YdcT | 44% | 252.3 |
| glycerol catabolism | glpS | lo | ABC transporter for Glycerol, ATPase component 1 (characterized) | 36% | 72% | 151.8 | Uncharacterized ABC transporter ATP-binding protein YdcT | 44% | 252.3 |
| L-histidine catabolism | Ac3H11_2560 | lo | ABC transporter for L-Histidine, ATPase component (characterized) | 39% | 84% | 148.7 | Uncharacterized ABC transporter ATP-binding protein YdcT | 44% | 252.3 |
| 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) | 36% | 97% | 129.8 | Uncharacterized ABC transporter ATP-binding protein YdcT | 44% | 252.3 |
| 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) | 36% | 97% | 129.8 | Uncharacterized ABC transporter ATP-binding protein YdcT | 44% | 252.3 |
| 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) | 36% | 97% | 129.8 | Uncharacterized ABC transporter ATP-binding protein YdcT | 44% | 252.3 |
| citrate catabolism | fecE | lo | iron(III) dicitrate transport ATP-binding protein FecE (characterized) | 30% | 87% | 119.4 | Uncharacterized ABC transporter ATP-binding protein YdcT | 44% | 252.3 |
| L-phenylalanine catabolism | livF | lo | high-affinity branched-chain amino acid ABC transporter, ATP-binding protein LivF (characterized) | 32% | 97% | 117.5 | Uncharacterized ABC transporter ATP-binding protein YdcT | 44% | 252.3 |
| L-alanine catabolism | braG | lo | High-affinity branched-chain amino acid transport ATP-binding protein BraG, component of Branched chain amino acid uptake transporter. Transports alanine (characterized) | 31% | 97% | 114.8 | Uncharacterized ABC transporter ATP-binding protein YdcT | 44% | 252.3 |
| L-serine catabolism | braG | lo | High-affinity branched-chain amino acid transport ATP-binding protein BraG, component of Branched chain amino acid uptake transporter. Transports alanine (characterized) | 31% | 97% | 114.8 | Uncharacterized ABC transporter ATP-binding protein YdcT | 44% | 252.3 |
| L-threonine catabolism | braG | lo | High-affinity branched-chain amino acid transport ATP-binding protein BraG, component of Branched chain amino acid uptake transporter. Transports alanine (characterized) | 31% | 97% | 114.8 | Uncharacterized ABC transporter ATP-binding protein YdcT | 44% | 252.3 |
| L-arginine catabolism | braG | lo | ATP-binding component of a broad range amino acid ABC transporter (characterized, see rationale) | 31% | 91% | 114.4 | Uncharacterized ABC transporter ATP-binding protein YdcT | 44% | 252.3 |
| L-glutamate catabolism | braG | lo | ATP-binding component of a broad range amino acid ABC transporter (characterized, see rationale) | 31% | 91% | 114.4 | Uncharacterized ABC transporter ATP-binding protein YdcT | 44% | 252.3 |
| L-histidine catabolism | braG | lo | ATP-binding component of a broad range amino acid ABC transporter (characterized, see rationale) | 31% | 91% | 114.4 | Uncharacterized ABC transporter ATP-binding protein YdcT | 44% | 252.3 |
| L-histidine catabolism | natE | lo | NatE aka LivF aka SLR1881, component of Leucine/proline/alanine/serine/glycine (and possibly histidine) porter, NatABCDE (characterized) | 31% | 87% | 105.5 | Uncharacterized ABC transporter ATP-binding protein YdcT | 44% | 252.3 |
| L-leucine catabolism | natE | lo | NatE aka LivF aka SLR1881, component of Leucine/proline/alanine/serine/glycine (and possibly histidine) porter, NatABCDE (characterized) | 31% | 87% | 105.5 | Uncharacterized ABC transporter ATP-binding protein YdcT | 44% | 252.3 |
| L-proline catabolism | natE | lo | NatE aka LivF aka SLR1881, component of Leucine/proline/alanine/serine/glycine (and possibly histidine) porter, NatABCDE (characterized) | 31% | 87% | 105.5 | Uncharacterized ABC transporter ATP-binding protein YdcT | 44% | 252.3 |
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