| Pathway | Step | Score | Similar to | Id. | Cov. | Bits | Other hit | Other id. | Other bits |
|---|
| putrescine catabolism | potA | med | spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31 (characterized) | 42% | 86% | 252.3 | CysA aka B2422, component of Sulfate/thiosulfate porter | 59% | 353.6 |
| sucrose catabolism | thuK | med | ABC transporter (characterized, see rationale) | 41% | 82% | 247.7 | CysA aka B2422, component of Sulfate/thiosulfate porter | 59% | 353.6 |
| D-mannitol catabolism | mtlK | med | SmoK aka POLK, component of Hexitol (glucitol; mannitol) porter (characterized) | 44% | 80% | 226.5 | CysA aka B2422, component of Sulfate/thiosulfate porter | 59% | 353.6 |
| D-maltose catabolism | malK_Bb | med | ABC-type maltose transport, ATP binding protein (characterized, see rationale) | 42% | 74% | 224.6 | CysA aka B2422, component of Sulfate/thiosulfate porter | 59% | 353.6 |
| D-glucosamine (chitosamine) catabolism | SM_b21216 | med | ABC transporter for D-Glucosamine, ATPase component (characterized) | 41% | 82% | 223.8 | CysA aka B2422, component of Sulfate/thiosulfate porter | 59% | 353.6 |
| D-sorbitol (glucitol) catabolism | mtlK | med | MtlK, component of The polyol (mannitol, glucitol (sorbitol), arabitol (arabinitol; lyxitol)) uptake porter, MtlEFGK (characterized) | 41% | 80% | 223.4 | CysA aka B2422, component of Sulfate/thiosulfate porter | 59% | 353.6 |
| D-maltose catabolism | malK1 | med | 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% | 78% | 221.5 | CysA aka B2422, component of Sulfate/thiosulfate porter | 59% | 353.6 |
| trehalose catabolism | thuK | med | 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% | 78% | 221.5 | CysA aka B2422, component of Sulfate/thiosulfate porter | 59% | 353.6 |
| D-maltose catabolism | malK_Aa | med | ABC-type maltose transporter (EC 7.5.2.1) (characterized) | 42% | 72% | 219.9 | CysA aka B2422, component of Sulfate/thiosulfate porter | 59% | 353.6 |
| N-acetyl-D-glucosamine catabolism | SMc02869 | med | N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized) | 44% | 70% | 219.5 | CysA aka B2422, component of Sulfate/thiosulfate porter | 59% | 353.6 |
| D-glucosamine (chitosamine) catabolism | SMc02869 | med | N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized) | 44% | 70% | 219.5 | CysA aka B2422, component of Sulfate/thiosulfate porter | 59% | 353.6 |
| lactose catabolism | lacK | med | ABC transporter for Lactose, ATPase component (characterized) | 42% | 73% | 218.8 | CysA aka B2422, component of Sulfate/thiosulfate porter | 59% | 353.6 |
| D-maltose catabolism | aglK | med | ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized) | 41% | 79% | 213 | CysA aka B2422, component of Sulfate/thiosulfate porter | 59% | 353.6 |
| D-maltose catabolism | thuK | med | ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized) | 41% | 79% | 213 | CysA aka B2422, component of Sulfate/thiosulfate porter | 59% | 353.6 |
| sucrose catabolism | aglK | med | ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized) | 41% | 79% | 213 | CysA aka B2422, component of Sulfate/thiosulfate porter | 59% | 353.6 |
| trehalose catabolism | aglK | med | ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized) | 41% | 79% | 213 | CysA aka B2422, component of Sulfate/thiosulfate porter | 59% | 353.6 |
| L-arabinose catabolism | xacK | med | Xylose/arabinose import ATP-binding protein XacK; EC 7.5.2.13 (characterized, see rationale) | 41% | 75% | 210.3 | CysA aka B2422, component of Sulfate/thiosulfate porter | 59% | 353.6 |
| D-cellobiose catabolism | SMc04256 | med | ABC transporter for D-Cellobiose and D-Salicin, ATPase component (characterized) | 40% | 82% | 205.7 | CysA aka B2422, component of Sulfate/thiosulfate porter | 59% | 353.6 |
| trehalose catabolism | treV | med | TreV, component of Trehalose porter (characterized) | 40% | 75% | 191 | CysA aka B2422, component of Sulfate/thiosulfate porter | 59% | 353.6 |
| D-maltose catabolism | malK | lo | Maltose/maltodextrin import ATP-binding protein MalK; EC 7.5.2.1 (characterized) | 38% | 92% | 224.2 | CysA aka B2422, component of Sulfate/thiosulfate porter | 59% | 353.6 |
| L-fucose catabolism | SM_b21106 | lo | ABC transporter for L-Fucose, ATPase component (characterized) | 39% | 79% | 223.8 | CysA aka B2422, component of Sulfate/thiosulfate porter | 59% | 353.6 |
| D-cellobiose catabolism | gtsD | lo | GtsD (GLcK), component of Glucose porter, GtsABCD (characterized) | 36% | 93% | 221.1 | CysA aka B2422, component of Sulfate/thiosulfate porter | 59% | 353.6 |
| D-glucose catabolism | gtsD | lo | GtsD (GLcK), component of Glucose porter, GtsABCD (characterized) | 36% | 93% | 221.1 | CysA aka B2422, component of Sulfate/thiosulfate porter | 59% | 353.6 |
| lactose catabolism | gtsD | lo | GtsD (GLcK), component of Glucose porter, GtsABCD (characterized) | 36% | 93% | 221.1 | CysA aka B2422, component of Sulfate/thiosulfate porter | 59% | 353.6 |
| D-maltose catabolism | gtsD | lo | GtsD (GLcK), component of Glucose porter, GtsABCD (characterized) | 36% | 93% | 221.1 | CysA aka B2422, component of Sulfate/thiosulfate porter | 59% | 353.6 |
| sucrose catabolism | gtsD | lo | GtsD (GLcK), component of Glucose porter, GtsABCD (characterized) | 36% | 93% | 221.1 | CysA aka B2422, component of Sulfate/thiosulfate porter | 59% | 353.6 |
| trehalose catabolism | gtsD | lo | GtsD (GLcK), component of Glucose porter, GtsABCD (characterized) | 36% | 93% | 221.1 | CysA aka B2422, component of Sulfate/thiosulfate porter | 59% | 353.6 |
| L-arabinose catabolism | xacJ | lo | Xylose/arabinose import ATP-binding protein XacJ; EC 7.5.2.13 (characterized, see rationale) | 39% | 80% | 218.8 | CysA aka B2422, component of Sulfate/thiosulfate porter | 59% | 353.6 |
| 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) | 43% | 65% | 213.8 | CysA aka B2422, component of Sulfate/thiosulfate porter | 59% | 353.6 |
| 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% | 93% | 213.4 | CysA aka B2422, component of Sulfate/thiosulfate porter | 59% | 353.6 |
| xylitol catabolism | HSERO_RS17020 | lo | ABC-type sugar transport system, ATPase component protein (characterized, see rationale) | 43% | 64% | 212.2 | CysA aka B2422, component of Sulfate/thiosulfate porter | 59% | 353.6 |
| 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% | 80% | 202.2 | CysA aka B2422, component of Sulfate/thiosulfate porter | 59% | 353.6 |
| D-cellobiose catabolism | aglK' | lo | Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) | 39% | 78% | 199.5 | CysA aka B2422, component of Sulfate/thiosulfate porter | 59% | 353.6 |
| D-glucose catabolism | aglK' | lo | Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) | 39% | 78% | 199.5 | CysA aka B2422, component of Sulfate/thiosulfate porter | 59% | 353.6 |
| lactose catabolism | aglK' | lo | Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) | 39% | 78% | 199.5 | CysA aka B2422, component of Sulfate/thiosulfate porter | 59% | 353.6 |
| D-maltose catabolism | aglK' | lo | Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) | 39% | 78% | 199.5 | CysA aka B2422, component of Sulfate/thiosulfate porter | 59% | 353.6 |
| sucrose catabolism | aglK' | lo | Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) | 39% | 78% | 199.5 | CysA aka B2422, component of Sulfate/thiosulfate porter | 59% | 353.6 |
| trehalose catabolism | aglK' | lo | Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) | 39% | 78% | 199.5 | CysA aka B2422, component of Sulfate/thiosulfate porter | 59% | 353.6 |
| L-arabinose catabolism | araV | lo | AraV, component of Arabinose, fructose, xylose porter (characterized) | 34% | 95% | 192.6 | CysA aka B2422, component of Sulfate/thiosulfate porter | 59% | 353.6 |
| D-fructose catabolism | araV | lo | AraV, component of Arabinose, fructose, xylose porter (characterized) | 34% | 95% | 192.6 | CysA aka B2422, component of Sulfate/thiosulfate porter | 59% | 353.6 |
| sucrose catabolism | araV | lo | AraV, component of Arabinose, fructose, xylose porter (characterized) | 34% | 95% | 192.6 | CysA aka B2422, component of Sulfate/thiosulfate porter | 59% | 353.6 |
| D-xylose catabolism | araV | lo | AraV, component of Arabinose, fructose, xylose porter (characterized) | 34% | 95% | 192.6 | CysA aka B2422, component of Sulfate/thiosulfate porter | 59% | 353.6 |
| L-proline catabolism | opuBA | lo | BilEA aka OpuBA protein, component of A proline/glycine betaine uptake system. Also reported to be a bile exclusion system that exports oxgall and other bile compounds, BilEA/EB or OpuBA/BB (required for normal virulence) (characterized) | 35% | 94% | 178.7 | CysA aka B2422, component of Sulfate/thiosulfate porter | 59% | 353.6 |
| L-proline catabolism | proV | lo | Glycine betaine/proline betaine transport system ATP-binding protein ProV (characterized) | 37% | 60% | 174.5 | CysA aka B2422, component of Sulfate/thiosulfate porter | 59% | 353.6 |
| glycerol catabolism | glpS | lo | ABC transporter for Glycerol, ATPase component 1 (characterized) | 32% | 94% | 163.3 | CysA aka B2422, component of Sulfate/thiosulfate porter | 59% | 353.6 |
| L-histidine catabolism | hutV | lo | ABC transporter for L-Histidine, ATPase component (characterized) | 37% | 84% | 162.9 | CysA aka B2422, component of Sulfate/thiosulfate porter | 59% | 353.6 |
| 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% | 87% | 161.4 | CysA aka B2422, component of Sulfate/thiosulfate porter | 59% | 353.6 |
| L-tryptophan catabolism | ecfA2 | lo | Energy-coupling factor transporter ATP-binding protein EcfA2; Short=ECF transporter A component EcfA2; EC 7.-.-.- (characterized, see rationale) | 37% | 77% | 137.9 | CysA aka B2422, component of Sulfate/thiosulfate porter | 59% | 353.6 |
This GapMind analysis is from Apr 09 2024. 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