| Pathway | Step | Score | Similar to | Id. | Cov. | Bits | Other hit | Other id. | Other bits |
|---|
| putrescine catabolism | potA | lo | PotG aka B0855, component of Putrescine porter (characterized) | 40% | 75% | 196.8 | ABC-type molybdate transporter (EC 7.3.2.5) | 36% | 199.9 |
| D-maltose catabolism | thuK | lo | Trehalose/maltose import ATP-binding protein MalK; EC 7.5.2.1 (characterized) | 33% | 98% | 194.9 | ABC-type molybdate transporter (EC 7.3.2.5) | 36% | 199.9 |
| trehalose catabolism | thuK | lo | Trehalose/maltose import ATP-binding protein MalK; EC 7.5.2.1 (characterized) | 33% | 98% | 194.9 | ABC-type molybdate transporter (EC 7.3.2.5) | 36% | 199.9 |
| D-cellobiose catabolism | gtsD | lo | Sugar ABC transporter ATP-binding protein (characterized, see rationale) | 38% | 74% | 178.3 | ABC-type molybdate transporter (EC 7.3.2.5) | 36% | 199.9 |
| D-glucose catabolism | gtsD | lo | Sugar ABC transporter ATP-binding protein (characterized, see rationale) | 38% | 74% | 178.3 | ABC-type molybdate transporter (EC 7.3.2.5) | 36% | 199.9 |
| lactose catabolism | gtsD | lo | Sugar ABC transporter ATP-binding protein (characterized, see rationale) | 38% | 74% | 178.3 | ABC-type molybdate transporter (EC 7.3.2.5) | 36% | 199.9 |
| D-maltose catabolism | gtsD | lo | Sugar ABC transporter ATP-binding protein (characterized, see rationale) | 38% | 74% | 178.3 | ABC-type molybdate transporter (EC 7.3.2.5) | 36% | 199.9 |
| sucrose catabolism | gtsD | lo | Sugar ABC transporter ATP-binding protein (characterized, see rationale) | 38% | 74% | 178.3 | ABC-type molybdate transporter (EC 7.3.2.5) | 36% | 199.9 |
| trehalose catabolism | gtsD | lo | Sugar ABC transporter ATP-binding protein (characterized, see rationale) | 38% | 74% | 178.3 | ABC-type molybdate transporter (EC 7.3.2.5) | 36% | 199.9 |
| L-fucose catabolism | SM_b21106 | lo | ABC transporter for L-Fucose, ATPase component (characterized) | 38% | 72% | 177.2 | ABC-type molybdate transporter (EC 7.3.2.5) | 36% | 199.9 |
| sucrose catabolism | thuK | lo | ABC transporter (characterized, see rationale) | 37% | 74% | 177.2 | ABC-type molybdate transporter (EC 7.3.2.5) | 36% | 199.9 |
| xylitol catabolism | HSERO_RS17020 | lo | ABC-type sugar transport system, ATPase component protein (characterized, see rationale) | 33% | 85% | 176.8 | ABC-type molybdate transporter (EC 7.3.2.5) | 36% | 199.9 |
| D-mannitol catabolism | mtlK | lo | ABC transporter for D-Mannitol, D-Mannose, and D-Sorbitol, ATPase component (characterized) | 36% | 79% | 174.9 | ABC-type molybdate transporter (EC 7.3.2.5) | 36% | 199.9 |
| D-sorbitol (glucitol) catabolism | mtlK | lo | ABC transporter for D-Mannitol, D-Mannose, and D-Sorbitol, ATPase component (characterized) | 36% | 79% | 174.9 | ABC-type molybdate transporter (EC 7.3.2.5) | 36% | 199.9 |
| D-maltose catabolism | malK | lo | ABC-type maltose transporter (subunit 3/3) (EC 7.5.2.1) (characterized) | 36% | 75% | 172.6 | ABC-type molybdate transporter (EC 7.3.2.5) | 36% | 199.9 |
| 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) | 39% | 71% | 171 | ABC-type molybdate transporter (EC 7.3.2.5) | 36% | 199.9 |
| 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) | 33% | 90% | 171 | ABC-type molybdate transporter (EC 7.3.2.5) | 36% | 199.9 |
| D-maltose catabolism | malK_Aa | lo | ABC-type maltose transporter (EC 7.5.2.1) (characterized) | 32% | 90% | 168.3 | ABC-type molybdate transporter (EC 7.3.2.5) | 36% | 199.9 |
| D-maltose catabolism | malK_Bb | lo | ABC-type maltose transport, ATP binding protein (characterized, see rationale) | 38% | 78% | 167.9 | ABC-type molybdate transporter (EC 7.3.2.5) | 36% | 199.9 |
| D-cellobiose catabolism | glcV | lo | monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) | 34% | 77% | 167.5 | ABC-type molybdate transporter (EC 7.3.2.5) | 36% | 199.9 |
| D-galactose catabolism | glcV | lo | monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) | 34% | 77% | 167.5 | ABC-type molybdate transporter (EC 7.3.2.5) | 36% | 199.9 |
| D-glucose catabolism | glcV | lo | monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) | 34% | 77% | 167.5 | ABC-type molybdate transporter (EC 7.3.2.5) | 36% | 199.9 |
| lactose catabolism | glcV | lo | monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) | 34% | 77% | 167.5 | ABC-type molybdate transporter (EC 7.3.2.5) | 36% | 199.9 |
| D-maltose catabolism | glcV | lo | monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) | 34% | 77% | 167.5 | ABC-type molybdate transporter (EC 7.3.2.5) | 36% | 199.9 |
| D-mannose catabolism | glcV | lo | monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) | 34% | 77% | 167.5 | ABC-type molybdate transporter (EC 7.3.2.5) | 36% | 199.9 |
| sucrose catabolism | glcV | lo | monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) | 34% | 77% | 167.5 | ABC-type molybdate transporter (EC 7.3.2.5) | 36% | 199.9 |
| trehalose catabolism | glcV | lo | monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) | 34% | 77% | 167.5 | ABC-type molybdate transporter (EC 7.3.2.5) | 36% | 199.9 |
| L-arabinose catabolism | xacJ | lo | Xylose/arabinose import ATP-binding protein XacJ; EC 7.5.2.13 (characterized, see rationale) | 34% | 79% | 166.4 | ABC-type molybdate transporter (EC 7.3.2.5) | 36% | 199.9 |
| L-arabinose catabolism | xacK | lo | Xylose/arabinose import ATP-binding protein XacK; EC 7.5.2.13 (characterized, see rationale) | 37% | 69% | 166 | ABC-type molybdate transporter (EC 7.3.2.5) | 36% | 199.9 |
| D-cellobiose catabolism | SMc04256 | lo | ABC transporter for D-Cellobiose and D-Salicin, ATPase component (characterized) | 38% | 76% | 164.9 | ABC-type molybdate transporter (EC 7.3.2.5) | 36% | 199.9 |
| 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) | 33% | 82% | 164.1 | ABC-type molybdate transporter (EC 7.3.2.5) | 36% | 199.9 |
| 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) | 33% | 82% | 164.1 | ABC-type molybdate transporter (EC 7.3.2.5) | 36% | 199.9 |
| xylitol catabolism | Dshi_0546 | lo | ABC transporter for Xylitol, ATPase component (characterized) | 35% | 75% | 163.3 | ABC-type molybdate transporter (EC 7.3.2.5) | 36% | 199.9 |
| 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) | 39% | 69% | 161 | ABC-type molybdate transporter (EC 7.3.2.5) | 36% | 199.9 |
| trehalose catabolism | treV | lo | TreV, component of Trehalose porter (characterized) | 39% | 76% | 161 | ABC-type molybdate transporter (EC 7.3.2.5) | 36% | 199.9 |
| D-maltose catabolism | musK | lo | ABC-type maltose transporter (EC 7.5.2.1) (characterized) | 35% | 73% | 160.2 | ABC-type molybdate transporter (EC 7.3.2.5) | 36% | 199.9 |
| D-glucosamine (chitosamine) catabolism | SM_b21216 | lo | ABC transporter for D-Glucosamine, ATPase component (characterized) | 33% | 76% | 158.7 | ABC-type molybdate transporter (EC 7.3.2.5) | 36% | 199.9 |
| lactose catabolism | lacK | lo | ABC transporter for Lactose, ATPase component (characterized) | 36% | 74% | 155.2 | ABC-type molybdate transporter (EC 7.3.2.5) | 36% | 199.9 |
| D-xylose catabolism | gtsD | lo | ABC transporter for D-Glucose-6-Phosphate, ATPase component (characterized) | 34% | 77% | 155.2 | ABC-type molybdate transporter (EC 7.3.2.5) | 36% | 199.9 |
| D-galactose catabolism | PfGW456L13_1897 | lo | ABC transporter for D-Galactose and D-Glucose, ATPase component (characterized) | 35% | 77% | 153.3 | ABC-type molybdate transporter (EC 7.3.2.5) | 36% | 199.9 |
| D-cellobiose catabolism | aglK' | lo | Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) | 33% | 72% | 152.5 | ABC-type molybdate transporter (EC 7.3.2.5) | 36% | 199.9 |
| D-glucose catabolism | aglK' | lo | Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) | 33% | 72% | 152.5 | ABC-type molybdate transporter (EC 7.3.2.5) | 36% | 199.9 |
| lactose catabolism | aglK' | lo | Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) | 33% | 72% | 152.5 | ABC-type molybdate transporter (EC 7.3.2.5) | 36% | 199.9 |
| D-maltose catabolism | aglK | lo | Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) | 33% | 72% | 152.5 | ABC-type molybdate transporter (EC 7.3.2.5) | 36% | 199.9 |
| D-maltose catabolism | aglK' | lo | Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) | 33% | 72% | 152.5 | ABC-type molybdate transporter (EC 7.3.2.5) | 36% | 199.9 |
| sucrose catabolism | aglK | lo | Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) | 33% | 72% | 152.5 | ABC-type molybdate transporter (EC 7.3.2.5) | 36% | 199.9 |
| sucrose catabolism | aglK' | lo | Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) | 33% | 72% | 152.5 | ABC-type molybdate transporter (EC 7.3.2.5) | 36% | 199.9 |
| trehalose catabolism | aglK | lo | Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) | 33% | 72% | 152.5 | ABC-type molybdate transporter (EC 7.3.2.5) | 36% | 199.9 |
| trehalose catabolism | aglK' | lo | Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) | 33% | 72% | 152.5 | ABC-type molybdate transporter (EC 7.3.2.5) | 36% | 199.9 |
| N-acetyl-D-glucosamine catabolism | SMc02869 | lo | N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized) | 38% | 67% | 152.1 | ABC-type molybdate transporter (EC 7.3.2.5) | 36% | 199.9 |
| D-glucosamine (chitosamine) catabolism | SMc02869 | lo | N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized) | 38% | 67% | 152.1 | ABC-type molybdate transporter (EC 7.3.2.5) | 36% | 199.9 |
| 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) | 34% | 71% | 145.2 | ABC-type molybdate transporter (EC 7.3.2.5) | 36% | 199.9 |
| L-histidine catabolism | Ac3H11_2560 | lo | ABC transporter for L-Histidine, ATPase component (characterized) | 38% | 69% | 131.7 | ABC-type molybdate transporter (EC 7.3.2.5) | 36% | 199.9 |
| glycerol catabolism | glpS | lo | ABC transporter for Glycerol, ATPase component 1 (characterized) | 32% | 73% | 129.4 | ABC-type molybdate transporter (EC 7.3.2.5) | 36% | 199.9 |
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