Pathway | Step | Score | Similar to | Id. | Cov. | Bits | Other hit | Other id. | Other bits |
D-maltose catabolism | thuK | lo | Trehalose/maltose import ATP-binding protein MalK; EC 7.5.2.1 (characterized) | 40% | 61% | 169.1 | Molybdate/tungstate import ATP-binding protein WtpC; EC 7.3.2.6 | 43% | 194.5 |
trehalose catabolism | thuK | lo | Trehalose/maltose import ATP-binding protein MalK; EC 7.5.2.1 (characterized) | 40% | 61% | 169.1 | Molybdate/tungstate import ATP-binding protein WtpC; EC 7.3.2.6 | 43% | 194.5 |
putrescine catabolism | potA | lo | PotG aka B0855, component of Putrescine porter (characterized) | 43% | 56% | 164.1 | Molybdate/tungstate import ATP-binding protein WtpC; EC 7.3.2.6 | 43% | 194.5 |
lactose catabolism | lacK | lo | ABC transporter for Lactose, ATPase component (characterized) | 39% | 62% | 163.7 | Molybdate/tungstate import ATP-binding protein WtpC; EC 7.3.2.6 | 43% | 194.5 |
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) | 40% | 60% | 161.4 | Molybdate/tungstate import ATP-binding protein WtpC; EC 7.3.2.6 | 43% | 194.5 |
D-mannitol catabolism | mtlK | lo | SmoK aka POLK, component of Hexitol (glucitol; mannitol) porter (characterized) | 38% | 69% | 160.6 | Molybdate/tungstate import ATP-binding protein WtpC; EC 7.3.2.6 | 43% | 194.5 |
D-sorbitol (glucitol) catabolism | mtlK | lo | ABC transporter for D-Sorbitol, ATPase component (characterized) | 40% | 66% | 160.6 | Molybdate/tungstate import ATP-binding protein WtpC; EC 7.3.2.6 | 43% | 194.5 |
D-maltose catabolism | malK | lo | Maltose-transporting ATPase (EC 3.6.3.19) (characterized) | 41% | 58% | 160.2 | Molybdate/tungstate import ATP-binding protein WtpC; EC 7.3.2.6 | 43% | 194.5 |
D-maltose catabolism | malK_Aa | lo | ABC-type maltose transporter (EC 7.5.2.1) (characterized) | 41% | 58% | 160.2 | Molybdate/tungstate import ATP-binding protein WtpC; EC 7.3.2.6 | 43% | 194.5 |
L-arabinose catabolism | xacJ | lo | Xylose/arabinose import ATP-binding protein XacJ; EC 7.5.2.13 (characterized, see rationale) | 39% | 58% | 158.3 | Molybdate/tungstate import ATP-binding protein WtpC; EC 7.3.2.6 | 43% | 194.5 |
L-fucose catabolism | SM_b21106 | lo | ABC transporter for L-Fucose, ATPase component (characterized) | 39% | 61% | 158.3 | Molybdate/tungstate import ATP-binding protein WtpC; EC 7.3.2.6 | 43% | 194.5 |
xylitol catabolism | HSERO_RS17020 | lo | ABC-type sugar transport system, ATPase component protein (characterized, see rationale) | 40% | 53% | 157.9 | Molybdate/tungstate import ATP-binding protein WtpC; EC 7.3.2.6 | 43% | 194.5 |
sucrose catabolism | thuK | lo | ABC transporter (characterized, see rationale) | 38% | 64% | 156.8 | Molybdate/tungstate import ATP-binding protein WtpC; EC 7.3.2.6 | 43% | 194.5 |
D-glucosamine (chitosamine) catabolism | SM_b21216 | lo | ABC transporter for D-Glucosamine, ATPase component (characterized) | 37% | 61% | 156.4 | Molybdate/tungstate import ATP-binding protein WtpC; EC 7.3.2.6 | 43% | 194.5 |
xylitol catabolism | Dshi_0546 | lo | ABC transporter for Xylitol, ATPase component (characterized) | 37% | 69% | 156 | Molybdate/tungstate import ATP-binding protein WtpC; EC 7.3.2.6 | 43% | 194.5 |
D-maltose catabolism | malK_Bb | lo | ABC-type maltose transport, ATP binding protein (characterized, see rationale) | 38% | 64% | 155.2 | Molybdate/tungstate import ATP-binding protein WtpC; EC 7.3.2.6 | 43% | 194.5 |
trehalose catabolism | treV | lo | TreV, component of Trehalose porter (characterized) | 40% | 68% | 152.5 | Molybdate/tungstate import ATP-binding protein WtpC; EC 7.3.2.6 | 43% | 194.5 |
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) | 36% | 69% | 151 | Molybdate/tungstate import ATP-binding protein WtpC; EC 7.3.2.6 | 43% | 194.5 |
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) | 36% | 69% | 151 | Molybdate/tungstate import ATP-binding protein WtpC; EC 7.3.2.6 | 43% | 194.5 |
D-cellobiose catabolism | SMc04256 | lo | ABC transporter for D-Cellobiose and D-Salicin, ATPase component (characterized) | 38% | 61% | 150.6 | Molybdate/tungstate import ATP-binding protein WtpC; EC 7.3.2.6 | 43% | 194.5 |
D-cellobiose catabolism | glcV | lo | monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) | 36% | 65% | 150.6 | Molybdate/tungstate import ATP-binding protein WtpC; EC 7.3.2.6 | 43% | 194.5 |
D-galactose catabolism | glcV | lo | monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) | 36% | 65% | 150.6 | Molybdate/tungstate import ATP-binding protein WtpC; EC 7.3.2.6 | 43% | 194.5 |
D-glucose catabolism | glcV | lo | monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) | 36% | 65% | 150.6 | Molybdate/tungstate import ATP-binding protein WtpC; EC 7.3.2.6 | 43% | 194.5 |
lactose catabolism | glcV | lo | monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) | 36% | 65% | 150.6 | Molybdate/tungstate import ATP-binding protein WtpC; EC 7.3.2.6 | 43% | 194.5 |
D-maltose catabolism | glcV | lo | monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) | 36% | 65% | 150.6 | Molybdate/tungstate import ATP-binding protein WtpC; EC 7.3.2.6 | 43% | 194.5 |
D-mannose catabolism | glcV | lo | monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) | 36% | 65% | 150.6 | Molybdate/tungstate import ATP-binding protein WtpC; EC 7.3.2.6 | 43% | 194.5 |
sucrose catabolism | glcV | lo | monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) | 36% | 65% | 150.6 | Molybdate/tungstate import ATP-binding protein WtpC; EC 7.3.2.6 | 43% | 194.5 |
trehalose catabolism | glcV | lo | monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) | 36% | 65% | 150.6 | Molybdate/tungstate import ATP-binding protein WtpC; EC 7.3.2.6 | 43% | 194.5 |
N-acetyl-D-glucosamine catabolism | SMc02869 | lo | N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized) | 37% | 62% | 149.4 | Molybdate/tungstate import ATP-binding protein WtpC; EC 7.3.2.6 | 43% | 194.5 |
D-glucosamine (chitosamine) catabolism | SMc02869 | lo | N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized) | 37% | 62% | 149.4 | Molybdate/tungstate import ATP-binding protein WtpC; EC 7.3.2.6 | 43% | 194.5 |
D-cellobiose catabolism | gtsD | lo | Sugar ABC transporter ATP-binding protein (characterized, see rationale) | 36% | 61% | 149.1 | Molybdate/tungstate import ATP-binding protein WtpC; EC 7.3.2.6 | 43% | 194.5 |
D-glucose catabolism | gtsD | lo | Sugar ABC transporter ATP-binding protein (characterized, see rationale) | 36% | 61% | 149.1 | Molybdate/tungstate import ATP-binding protein WtpC; EC 7.3.2.6 | 43% | 194.5 |
lactose catabolism | gtsD | lo | Sugar ABC transporter ATP-binding protein (characterized, see rationale) | 36% | 61% | 149.1 | Molybdate/tungstate import ATP-binding protein WtpC; EC 7.3.2.6 | 43% | 194.5 |
D-maltose catabolism | gtsD | lo | Sugar ABC transporter ATP-binding protein (characterized, see rationale) | 36% | 61% | 149.1 | Molybdate/tungstate import ATP-binding protein WtpC; EC 7.3.2.6 | 43% | 194.5 |
sucrose catabolism | gtsD | lo | Sugar ABC transporter ATP-binding protein (characterized, see rationale) | 36% | 61% | 149.1 | Molybdate/tungstate import ATP-binding protein WtpC; EC 7.3.2.6 | 43% | 194.5 |
trehalose catabolism | gtsD | lo | Sugar ABC transporter ATP-binding protein (characterized, see rationale) | 36% | 61% | 149.1 | Molybdate/tungstate import ATP-binding protein WtpC; EC 7.3.2.6 | 43% | 194.5 |
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) | 37% | 59% | 148.7 | Molybdate/tungstate import ATP-binding protein WtpC; EC 7.3.2.6 | 43% | 194.5 |
L-arabinose catabolism | xacK | lo | Xylose/arabinose import ATP-binding protein XacK; EC 7.5.2.13 (characterized, see rationale) | 36% | 60% | 147.9 | Molybdate/tungstate import ATP-binding protein WtpC; EC 7.3.2.6 | 43% | 194.5 |
L-arabinose catabolism | araV | lo | AraV, component of Arabinose, fructose, xylose porter (characterized) | 37% | 61% | 144.1 | Molybdate/tungstate import ATP-binding protein WtpC; EC 7.3.2.6 | 43% | 194.5 |
D-fructose catabolism | araV | lo | AraV, component of Arabinose, fructose, xylose porter (characterized) | 37% | 61% | 144.1 | Molybdate/tungstate import ATP-binding protein WtpC; EC 7.3.2.6 | 43% | 194.5 |
sucrose catabolism | araV | lo | AraV, component of Arabinose, fructose, xylose porter (characterized) | 37% | 61% | 144.1 | Molybdate/tungstate import ATP-binding protein WtpC; EC 7.3.2.6 | 43% | 194.5 |
D-xylose catabolism | araV | lo | AraV, component of Arabinose, fructose, xylose porter (characterized) | 37% | 61% | 144.1 | Molybdate/tungstate import ATP-binding protein WtpC; EC 7.3.2.6 | 43% | 194.5 |
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) | 34% | 60% | 141.7 | Molybdate/tungstate import ATP-binding protein WtpC; EC 7.3.2.6 | 43% | 194.5 |
D-galactose catabolism | PfGW456L13_1897 | lo | ABC transporter for D-Galactose and D-Glucose, ATPase component (characterized) | 37% | 56% | 140.6 | Molybdate/tungstate import ATP-binding protein WtpC; EC 7.3.2.6 | 43% | 194.5 |
D-maltose catabolism | musK | lo | ABC-type maltose transporter (EC 7.5.2.1) (characterized) | 37% | 58% | 140.6 | Molybdate/tungstate import ATP-binding protein WtpC; EC 7.3.2.6 | 43% | 194.5 |
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) | 38% | 57% | 139 | Molybdate/tungstate import ATP-binding protein WtpC; EC 7.3.2.6 | 43% | 194.5 |
L-proline catabolism | proV | lo | glycine betaine/l-proline transport atp-binding protein prov (characterized) | 34% | 61% | 137.9 | Molybdate/tungstate import ATP-binding protein WtpC; EC 7.3.2.6 | 43% | 194.5 |
D-xylose catabolism | gtsD | lo | ABC transporter for D-Glucose-6-Phosphate, ATPase component (characterized) | 37% | 54% | 137.9 | Molybdate/tungstate import ATP-binding protein WtpC; EC 7.3.2.6 | 43% | 194.5 |
D-maltose catabolism | aglK | lo | ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized) | 38% | 62% | 137.1 | Molybdate/tungstate import ATP-binding protein WtpC; EC 7.3.2.6 | 43% | 194.5 |
sucrose catabolism | aglK | lo | ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized) | 38% | 62% | 137.1 | Molybdate/tungstate import ATP-binding protein WtpC; EC 7.3.2.6 | 43% | 194.5 |
trehalose catabolism | aglK | lo | ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized) | 38% | 62% | 137.1 | Molybdate/tungstate import ATP-binding protein WtpC; EC 7.3.2.6 | 43% | 194.5 |
D-cellobiose catabolism | aglK' | lo | Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) | 37% | 60% | 134.8 | Molybdate/tungstate import ATP-binding protein WtpC; EC 7.3.2.6 | 43% | 194.5 |
D-glucose catabolism | aglK' | lo | Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) | 37% | 60% | 134.8 | Molybdate/tungstate import ATP-binding protein WtpC; EC 7.3.2.6 | 43% | 194.5 |
lactose catabolism | aglK' | lo | Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) | 37% | 60% | 134.8 | Molybdate/tungstate import ATP-binding protein WtpC; EC 7.3.2.6 | 43% | 194.5 |
D-maltose catabolism | aglK' | lo | Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) | 37% | 60% | 134.8 | Molybdate/tungstate import ATP-binding protein WtpC; EC 7.3.2.6 | 43% | 194.5 |
sucrose catabolism | aglK' | lo | Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) | 37% | 60% | 134.8 | Molybdate/tungstate import ATP-binding protein WtpC; EC 7.3.2.6 | 43% | 194.5 |
trehalose catabolism | aglK' | lo | Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) | 37% | 60% | 134.8 | Molybdate/tungstate import ATP-binding protein WtpC; EC 7.3.2.6 | 43% | 194.5 |
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) | 35% | 80% | 131.3 | Molybdate/tungstate import ATP-binding protein WtpC; EC 7.3.2.6 | 43% | 194.5 |
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) | 35% | 80% | 131.3 | Molybdate/tungstate import ATP-binding protein WtpC; EC 7.3.2.6 | 43% | 194.5 |
glycerol catabolism | glpS | lo | ABC transporter for Glycerol, ATPase component 1 (characterized) | 32% | 63% | 106.3 | Molybdate/tungstate import ATP-binding protein WtpC; EC 7.3.2.6 | 43% | 194.5 |
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