| Pathway | Step | Score | Similar to | Id. | Cov. | Bits | Other hit | Other id. | Other bits |
|---|
| L-proline catabolism | opuBA | med | 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) | 55% | 98% | 427.6 | OtaA, component of The salt-induced glycine betaine OtaABC transporter | 62% | 482.3 |
| L-proline catabolism | proV | med | glycine betaine/l-proline transport atp-binding protein prov (characterized) | 50% | 99% | 380.2 | OtaA, component of The salt-induced glycine betaine OtaABC transporter | 62% | 482.3 |
| L-histidine catabolism | hutV | med | ABC transporter for L-Histidine, ATPase component (characterized) | 59% | 96% | 319.3 | OtaA, component of The salt-induced glycine betaine OtaABC transporter | 62% | 482.3 |
| L-proline catabolism | hutV | med | HutV aka HISV aka R02702 aka SMC00670, component of Uptake system for hisitidine, proline, proline-betaine and glycine-betaine (characterized) | 56% | 96% | 302.8 | OtaA, component of The salt-induced glycine betaine OtaABC transporter | 62% | 482.3 |
| putrescine catabolism | potA | lo | spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31 (characterized) | 36% | 83% | 181 | OtaA, component of The salt-induced glycine betaine OtaABC transporter | 62% | 482.3 |
| 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% | 64% | 179.1 | OtaA, component of The salt-induced glycine betaine OtaABC transporter | 62% | 482.3 |
| trehalose catabolism | thuK | 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% | 64% | 179.1 | OtaA, component of The salt-induced glycine betaine OtaABC transporter | 62% | 482.3 |
| D-maltose catabolism | thuK | lo | Trehalose/maltose import ATP-binding protein MalK; EC 7.5.2.1 (characterized) | 40% | 65% | 177.6 | OtaA, component of The salt-induced glycine betaine OtaABC transporter | 62% | 482.3 |
| D-cellobiose catabolism | gtsD | lo | ABC transporter for D-Glucose-6-Phosphate, ATPase component (characterized) | 39% | 62% | 173.3 | OtaA, component of The salt-induced glycine betaine OtaABC transporter | 62% | 482.3 |
| D-glucose catabolism | gtsD | lo | ABC transporter for D-Glucose-6-Phosphate, ATPase component (characterized) | 39% | 62% | 173.3 | OtaA, component of The salt-induced glycine betaine OtaABC transporter | 62% | 482.3 |
| lactose catabolism | gtsD | lo | ABC transporter for D-Glucose-6-Phosphate, ATPase component (characterized) | 39% | 62% | 173.3 | OtaA, component of The salt-induced glycine betaine OtaABC transporter | 62% | 482.3 |
| D-maltose catabolism | gtsD | lo | ABC transporter for D-Glucose-6-Phosphate, ATPase component (characterized) | 39% | 62% | 173.3 | OtaA, component of The salt-induced glycine betaine OtaABC transporter | 62% | 482.3 |
| sucrose catabolism | gtsD | lo | ABC transporter for D-Glucose-6-Phosphate, ATPase component (characterized) | 39% | 62% | 173.3 | OtaA, component of The salt-induced glycine betaine OtaABC transporter | 62% | 482.3 |
| trehalose catabolism | gtsD | lo | ABC transporter for D-Glucose-6-Phosphate, ATPase component (characterized) | 39% | 62% | 173.3 | OtaA, component of The salt-induced glycine betaine OtaABC transporter | 62% | 482.3 |
| D-xylose catabolism | gtsD | lo | ABC transporter for D-Glucose-6-Phosphate, ATPase component (characterized) | 39% | 62% | 173.3 | OtaA, component of The salt-induced glycine betaine OtaABC transporter | 62% | 482.3 |
| D-galactose catabolism | PfGW456L13_1897 | lo | ABC transporter for D-Galactose and D-Glucose, ATPase component (characterized) | 40% | 58% | 172.6 | OtaA, component of The salt-induced glycine betaine OtaABC transporter | 62% | 482.3 |
| L-arabinose catabolism | xacK | lo | Xylose/arabinose import ATP-binding protein XacK; EC 7.5.2.13 (characterized, see rationale) | 34% | 64% | 169.1 | OtaA, component of The salt-induced glycine betaine OtaABC transporter | 62% | 482.3 |
| D-maltose catabolism | aglK | lo | ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized) | 34% | 87% | 166 | OtaA, component of The salt-induced glycine betaine OtaABC transporter | 62% | 482.3 |
| D-maltose catabolism | musK | lo | ABC-type maltose transporter (EC 7.5.2.1) (characterized) | 39% | 60% | 166 | OtaA, component of The salt-induced glycine betaine OtaABC transporter | 62% | 482.3 |
| sucrose catabolism | aglK | lo | ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized) | 34% | 87% | 166 | OtaA, component of The salt-induced glycine betaine OtaABC transporter | 62% | 482.3 |
| trehalose catabolism | aglK | lo | ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized) | 34% | 87% | 166 | OtaA, component of The salt-induced glycine betaine OtaABC transporter | 62% | 482.3 |
| trehalose catabolism | treV | lo | TreV, component of Trehalose porter (characterized) | 37% | 76% | 165.6 | OtaA, component of The salt-induced glycine betaine OtaABC transporter | 62% | 482.3 |
| L-arabinose catabolism | xacJ | lo | Xylose/arabinose import ATP-binding protein XacJ; EC 7.5.2.13 (characterized, see rationale) | 41% | 58% | 164.9 | OtaA, component of The salt-induced glycine betaine OtaABC transporter | 62% | 482.3 |
| L-fucose catabolism | SM_b21106 | lo | ABC transporter for L-Fucose, ATPase component (characterized) | 38% | 64% | 164.5 | OtaA, component of The salt-induced glycine betaine OtaABC transporter | 62% | 482.3 |
| D-maltose catabolism | malK_Bb | lo | ABC-type maltose transport, ATP binding protein (characterized, see rationale) | 34% | 87% | 164.1 | OtaA, component of The salt-induced glycine betaine OtaABC transporter | 62% | 482.3 |
| sucrose catabolism | thuK | lo | ThuK aka RB0314 aka SMB20328, component of Trehalose/maltose/sucrose porter (trehalose inducible) (characterized) | 32% | 91% | 164.1 | OtaA, component of The salt-induced glycine betaine OtaABC transporter | 62% | 482.3 |
| 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) | 33% | 79% | 163.7 | OtaA, component of The salt-induced glycine betaine OtaABC transporter | 62% | 482.3 |
| xylitol catabolism | Dshi_0546 | lo | ABC transporter for Xylitol, ATPase component (characterized) | 36% | 76% | 161.8 | OtaA, component of The salt-induced glycine betaine OtaABC transporter | 62% | 482.3 |
| D-cellobiose catabolism | glcV | lo | monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) | 32% | 73% | 160.2 | OtaA, component of The salt-induced glycine betaine OtaABC transporter | 62% | 482.3 |
| D-galactose catabolism | glcV | lo | monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) | 32% | 73% | 160.2 | OtaA, component of The salt-induced glycine betaine OtaABC transporter | 62% | 482.3 |
| D-glucosamine (chitosamine) catabolism | SM_b21216 | lo | ABC transporter for D-Glucosamine, ATPase component (characterized) | 37% | 71% | 160.2 | OtaA, component of The salt-induced glycine betaine OtaABC transporter | 62% | 482.3 |
| D-glucose catabolism | glcV | lo | monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) | 32% | 73% | 160.2 | OtaA, component of The salt-induced glycine betaine OtaABC transporter | 62% | 482.3 |
| lactose catabolism | glcV | lo | monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) | 32% | 73% | 160.2 | OtaA, component of The salt-induced glycine betaine OtaABC transporter | 62% | 482.3 |
| D-maltose catabolism | glcV | lo | monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) | 32% | 73% | 160.2 | OtaA, component of The salt-induced glycine betaine OtaABC transporter | 62% | 482.3 |
| D-mannose catabolism | glcV | lo | monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) | 32% | 73% | 160.2 | OtaA, component of The salt-induced glycine betaine OtaABC transporter | 62% | 482.3 |
| sucrose catabolism | glcV | lo | monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) | 32% | 73% | 160.2 | OtaA, component of The salt-induced glycine betaine OtaABC transporter | 62% | 482.3 |
| trehalose catabolism | glcV | lo | monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) | 32% | 73% | 160.2 | OtaA, component of The salt-induced glycine betaine OtaABC transporter | 62% | 482.3 |
| N-acetyl-D-glucosamine catabolism | SMc02869 | lo | N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized) | 38% | 65% | 159.1 | OtaA, component of The salt-induced glycine betaine OtaABC transporter | 62% | 482.3 |
| D-glucosamine (chitosamine) catabolism | SMc02869 | lo | N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized) | 38% | 65% | 159.1 | OtaA, component of The salt-induced glycine betaine OtaABC transporter | 62% | 482.3 |
| D-sorbitol (glucitol) catabolism | mtlK | lo | ABC transporter for D-Sorbitol, ATPase component (characterized) | 36% | 64% | 159.1 | OtaA, component of The salt-induced glycine betaine OtaABC transporter | 62% | 482.3 |
| D-cellobiose catabolism | SMc04256 | lo | ABC transporter for D-Cellobiose and D-Salicin, ATPase component (characterized) | 38% | 61% | 158.7 | OtaA, component of The salt-induced glycine betaine OtaABC transporter | 62% | 482.3 |
| 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) | 31% | 81% | 157.9 | OtaA, component of The salt-induced glycine betaine OtaABC transporter | 62% | 482.3 |
| D-maltose catabolism | malK | lo | Maltose-transporting ATPase (EC 3.6.3.19) (characterized) | 34% | 65% | 156.4 | OtaA, component of The salt-induced glycine betaine OtaABC transporter | 62% | 482.3 |
| D-mannitol catabolism | mtlK | lo | ABC transporter for D-Mannitol, D-Mannose, and D-Sorbitol, ATPase component (characterized) | 40% | 59% | 155.6 | OtaA, component of The salt-induced glycine betaine OtaABC transporter | 62% | 482.3 |
| 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) | 35% | 62% | 153.3 | OtaA, component of The salt-induced glycine betaine OtaABC transporter | 62% | 482.3 |
| xylitol catabolism | HSERO_RS17020 | lo | ABC-type sugar transport system, ATPase component protein (characterized, see rationale) | 36% | 59% | 144.4 | OtaA, component of The salt-induced glycine betaine OtaABC transporter | 62% | 482.3 |
| glycerol catabolism | glpS | lo | ABC transporter for Glycerol, ATPase component 1 (characterized) | 32% | 66% | 135.6 | OtaA, component of The salt-induced glycine betaine OtaABC transporter | 62% | 482.3 |
| L-isoleucine catabolism | livG | lo | High-affinity branched-chain amino acid transport ATP-binding protein LivG aka B3455, component of Leucine; leucine/isoleucine/valine porter (characterized) | 31% | 89% | 115.5 | OtaA, component of The salt-induced glycine betaine OtaABC transporter | 62% | 482.3 |
| L-leucine catabolism | livG | lo | High-affinity branched-chain amino acid transport ATP-binding protein LivG aka B3455, component of Leucine; leucine/isoleucine/valine porter (characterized) | 31% | 89% | 115.5 | OtaA, component of The salt-induced glycine betaine OtaABC transporter | 62% | 482.3 |
| L-phenylalanine catabolism | livG | lo | High-affinity branched-chain amino acid transport ATP-binding protein LivG aka B3455, component of Leucine; leucine/isoleucine/valine porter (characterized) | 31% | 89% | 115.5 | OtaA, component of The salt-induced glycine betaine OtaABC transporter | 62% | 482.3 |
| L-valine catabolism | livG | lo | High-affinity branched-chain amino acid transport ATP-binding protein LivG aka B3455, component of Leucine; leucine/isoleucine/valine porter (characterized) | 31% | 89% | 115.5 | OtaA, component of The salt-induced glycine betaine OtaABC transporter | 62% | 482.3 |
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