| Pathway | Step | Score | Similar to | Id. | Cov. | Bits | Other hit | Other id. | Other bits |
|---|
| D-mannitol catabolism | mtlK | med | ABC transporter for D-Mannitol, D-Mannose, and D-Mannose, ATPase component (characterized) | 49% | 96% | 352.1 | AlgS, component of Alginate (MW 27,000 Da) (and Alginate oligosaccharides) uptake porter. Sphingomonas species A1 is a 'pit-forming' bacterium that directly incorporates alginate into its cytoplasm through a pit-dependent transport system, termed a 'superchannel' (Murata et al., 2008). The pit is a novel organ acquired through the fluidity and reconstitution of cell surface molecules, and through cooperation with the transport machinery in the cells. It confers upon bacterial cells a more efficient way to secure and assimilate macromolecules | 50% | 349.0 |
| D-sorbitol (glucitol) catabolism | mtlK | med | MtlK, component of The polyol (mannitol, glucitol (sorbitol), arabitol (arabinitol; lyxitol)) uptake porter, MtlEFGK (characterized) | 48% | 96% | 341.3 | AlgS, component of Alginate (MW 27,000 Da) (and Alginate oligosaccharides) uptake porter. Sphingomonas species A1 is a 'pit-forming' bacterium that directly incorporates alginate into its cytoplasm through a pit-dependent transport system, termed a 'superchannel' (Murata et al., 2008). The pit is a novel organ acquired through the fluidity and reconstitution of cell surface molecules, and through cooperation with the transport machinery in the cells. It confers upon bacterial cells a more efficient way to secure and assimilate macromolecules | 50% | 349.0 |
| D-maltose catabolism | malK | med | Maltose-transporting ATPase (EC 3.6.3.19) (characterized) | 51% | 96% | 339.7 | ABC transporter for D-Mannitol, D-Mannose, and D-Mannose, ATPase component | 49% | 352.1 |
| lactose catabolism | lacK | med | ABC transporter for Lactose, ATPase component (characterized) | 52% | 96% | 338.6 | ABC transporter for D-Mannitol, D-Mannose, and D-Mannose, ATPase component | 49% | 352.1 |
| 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) | 50% | 97% | 334.3 | ABC transporter for D-Mannitol, D-Mannose, and D-Mannose, ATPase component | 49% | 352.1 |
| 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) | 50% | 97% | 334.3 | ABC transporter for D-Mannitol, D-Mannose, and D-Mannose, ATPase component | 49% | 352.1 |
| xylitol catabolism | Dshi_0546 | med | ABC transporter for Xylitol, ATPase component (characterized) | 51% | 98% | 325.5 | ABC transporter for D-Mannitol, D-Mannose, and D-Mannose, ATPase component | 49% | 352.1 |
| D-cellobiose catabolism | SMc04256 | med | ABC transporter for D-Cellobiose and D-Salicin, ATPase component (characterized) | 48% | 98% | 324.3 | ABC transporter for D-Mannitol, D-Mannose, and D-Mannose, ATPase component | 49% | 352.1 |
| D-maltose catabolism | aglK | med | ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized) | 48% | 98% | 322.4 | ABC transporter for D-Mannitol, D-Mannose, and D-Mannose, ATPase component | 49% | 352.1 |
| D-maltose catabolism | thuK | med | ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized) | 48% | 98% | 322.4 | ABC transporter for D-Mannitol, D-Mannose, and D-Mannose, ATPase component | 49% | 352.1 |
| sucrose catabolism | aglK | med | ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized) | 48% | 98% | 322.4 | ABC transporter for D-Mannitol, D-Mannose, and D-Mannose, ATPase component | 49% | 352.1 |
| trehalose catabolism | aglK | med | ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized) | 48% | 98% | 322.4 | ABC transporter for D-Mannitol, D-Mannose, and D-Mannose, ATPase component | 49% | 352.1 |
| L-fucose catabolism | SM_b21106 | med | ABC transporter for L-Fucose, ATPase component (characterized) | 48% | 97% | 319.3 | ABC transporter for D-Mannitol, D-Mannose, and D-Mannose, ATPase component | 49% | 352.1 |
| sucrose catabolism | thuK | med | ABC transporter (characterized, see rationale) | 49% | 92% | 318.5 | ABC transporter for D-Mannitol, D-Mannose, and D-Mannose, ATPase component | 49% | 352.1 |
| D-maltose catabolism | malK_Sm | med | 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) | 47% | 99% | 317.8 | ABC transporter for D-Mannitol, D-Mannose, and D-Mannose, ATPase component | 49% | 352.1 |
| trehalose catabolism | malK | med | 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) | 47% | 99% | 317.8 | ABC transporter for D-Mannitol, D-Mannose, and D-Mannose, ATPase component | 49% | 352.1 |
| D-cellobiose catabolism | gtsD | med | ABC transporter for D-Galactose and D-Glucose, ATPase component (characterized) | 46% | 91% | 317 | ABC transporter for D-Mannitol, D-Mannose, and D-Mannose, ATPase component | 49% | 352.1 |
| D-galactose catabolism | PfGW456L13_1897 | med | ABC transporter for D-Galactose and D-Glucose, ATPase component (characterized) | 46% | 91% | 317 | ABC transporter for D-Mannitol, D-Mannose, and D-Mannose, ATPase component | 49% | 352.1 |
| D-glucose catabolism | gtsD | med | ABC transporter for D-Galactose and D-Glucose, ATPase component (characterized) | 46% | 91% | 317 | ABC transporter for D-Mannitol, D-Mannose, and D-Mannose, ATPase component | 49% | 352.1 |
| lactose catabolism | gtsD | med | ABC transporter for D-Galactose and D-Glucose, ATPase component (characterized) | 46% | 91% | 317 | ABC transporter for D-Mannitol, D-Mannose, and D-Mannose, ATPase component | 49% | 352.1 |
| D-maltose catabolism | gtsD | med | ABC transporter for D-Galactose and D-Glucose, ATPase component (characterized) | 46% | 91% | 317 | ABC transporter for D-Mannitol, D-Mannose, and D-Mannose, ATPase component | 49% | 352.1 |
| sucrose catabolism | gtsD | med | ABC transporter for D-Galactose and D-Glucose, ATPase component (characterized) | 46% | 91% | 317 | ABC transporter for D-Mannitol, D-Mannose, and D-Mannose, ATPase component | 49% | 352.1 |
| trehalose catabolism | gtsD | med | ABC transporter for D-Galactose and D-Glucose, ATPase component (characterized) | 46% | 91% | 317 | ABC transporter for D-Mannitol, D-Mannose, and D-Mannose, ATPase component | 49% | 352.1 |
| D-xylose catabolism | gtsD | med | ABC transporter for D-Glucose-6-Phosphate, ATPase component (characterized) | 46% | 92% | 315.1 | ABC transporter for D-Mannitol, D-Mannose, and D-Mannose, ATPase component | 49% | 352.1 |
| N-acetyl-D-glucosamine catabolism | SMc02869 | med | N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized) | 54% | 84% | 305.1 | ABC transporter for D-Mannitol, D-Mannose, and D-Mannose, ATPase component | 49% | 352.1 |
| D-glucosamine (chitosamine) catabolism | SMc02869 | med | N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized) | 54% | 84% | 305.1 | ABC transporter for D-Mannitol, D-Mannose, and D-Mannose, ATPase component | 49% | 352.1 |
| D-cellobiose catabolism | aglK' | med | Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) | 48% | 91% | 302.4 | ABC transporter for D-Mannitol, D-Mannose, and D-Mannose, ATPase component | 49% | 352.1 |
| D-glucose catabolism | aglK' | med | Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) | 48% | 91% | 302.4 | ABC transporter for D-Mannitol, D-Mannose, and D-Mannose, ATPase component | 49% | 352.1 |
| lactose catabolism | aglK' | med | Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) | 48% | 91% | 302.4 | ABC transporter for D-Mannitol, D-Mannose, and D-Mannose, ATPase component | 49% | 352.1 |
| D-maltose catabolism | aglK' | med | Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) | 48% | 91% | 302.4 | ABC transporter for D-Mannitol, D-Mannose, and D-Mannose, ATPase component | 49% | 352.1 |
| sucrose catabolism | aglK' | med | Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) | 48% | 91% | 302.4 | ABC transporter for D-Mannitol, D-Mannose, and D-Mannose, ATPase component | 49% | 352.1 |
| trehalose catabolism | aglK' | med | Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) | 48% | 91% | 302.4 | ABC transporter for D-Mannitol, D-Mannose, and D-Mannose, ATPase component | 49% | 352.1 |
| L-arabinose catabolism | xacK | med | Xylose/arabinose import ATP-binding protein XacK; EC 7.5.2.13 (characterized, see rationale) | 44% | 90% | 299.3 | ABC transporter for D-Mannitol, D-Mannose, and D-Mannose, ATPase component | 49% | 352.1 |
| D-glucosamine (chitosamine) catabolism | SM_b21216 | med | ABC transporter for D-Glucosamine, ATPase component (characterized) | 45% | 97% | 294.3 | ABC transporter for D-Mannitol, D-Mannose, and D-Mannose, ATPase component | 49% | 352.1 |
| xylitol catabolism | HSERO_RS17020 | med | ABC-type sugar transport system, ATPase component protein (characterized, see rationale) | 43% | 87% | 293.5 | ABC transporter for D-Mannitol, D-Mannose, and D-Mannose, ATPase component | 49% | 352.1 |
| D-maltose catabolism | malK_Bb | med | ABC-type maltose transport, ATP binding protein (characterized, see rationale) | 57% | 72% | 292.4 | ABC transporter for D-Mannitol, D-Mannose, and D-Mannose, ATPase component | 49% | 352.1 |
| D-maltose catabolism | musK | med | ABC-type maltose transporter (EC 7.5.2.1) (characterized) | 48% | 86% | 290.4 | ABC transporter for D-Mannitol, D-Mannose, and D-Mannose, ATPase component | 49% | 352.1 |
| L-arabinose catabolism | xacJ | med | Xylose/arabinose import ATP-binding protein XacJ; EC 7.5.2.13 (characterized, see rationale) | 45% | 85% | 275.8 | ABC transporter for D-Mannitol, D-Mannose, and D-Mannose, ATPase component | 49% | 352.1 |
| putrescine catabolism | potA | med | spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31 (characterized) | 41% | 93% | 259.6 | ABC transporter for D-Mannitol, D-Mannose, and D-Mannose, ATPase component | 49% | 352.1 |
| trehalose catabolism | treV | med | TreV, component of Trehalose porter (characterized) | 48% | 82% | 240 | ABC transporter for D-Mannitol, D-Mannose, and D-Mannose, ATPase component | 49% | 352.1 |
| glycerol catabolism | glpT | lo | ABC transporter for Glycerol, ATPase component 2 (characterized) | 35% | 99% | 224.2 | ABC transporter for D-Mannitol, D-Mannose, and D-Mannose, ATPase component | 49% | 352.1 |
| L-arabinose catabolism | araV | lo | AraV, component of Arabinose, fructose, xylose porter (characterized) | 35% | 92% | 201.1 | ABC transporter for D-Mannitol, D-Mannose, and D-Mannose, ATPase component | 49% | 352.1 |
| D-fructose catabolism | araV | lo | AraV, component of Arabinose, fructose, xylose porter (characterized) | 35% | 92% | 201.1 | ABC transporter for D-Mannitol, D-Mannose, and D-Mannose, ATPase component | 49% | 352.1 |
| sucrose catabolism | araV | lo | AraV, component of Arabinose, fructose, xylose porter (characterized) | 35% | 92% | 201.1 | ABC transporter for D-Mannitol, D-Mannose, and D-Mannose, ATPase component | 49% | 352.1 |
| D-xylose catabolism | araV | lo | AraV, component of Arabinose, fructose, xylose porter (characterized) | 35% | 92% | 201.1 | ABC transporter for D-Mannitol, D-Mannose, and D-Mannose, ATPase component | 49% | 352.1 |
| glycerol catabolism | glpS | lo | GlpS, component of Glycerol uptake porter, GlpSTPQV (characterized) | 34% | 97% | 200.3 | ABC transporter for D-Mannitol, D-Mannose, and D-Mannose, ATPase component | 49% | 352.1 |
| 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) | 40% | 73% | 189.1 | ABC transporter for D-Mannitol, D-Mannose, and D-Mannose, ATPase component | 49% | 352.1 |
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