| Pathway | Step | Score | Similar to | Id. | Cov. | Bits | Other hit | Other id. | Other bits |
|---|
| L-proline catabolism | proV | hi | glycine betaine/l-proline transport atp-binding protein prov (characterized) | 60% | 98% | 454.5 | OtaA, component of The salt-induced glycine betaine OtaABC transporter | 50% | 389.4 |
| 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) | 48% | 97% | 371.3 | Glycine betaine/choline transport system ATP-binding protein OusV | 61% | 456.8 |
| L-histidine catabolism | hutV | med | ABC transporter for L-Histidine, ATPase component (characterized) | 60% | 95% | 311.2 | Glycine betaine/choline transport system ATP-binding protein OusV | 61% | 456.8 |
| 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) | 58% | 95% | 300.4 | Glycine betaine/choline transport system ATP-binding protein OusV | 61% | 456.8 |
| putrescine catabolism | potA | lo | PotG aka B0855, component of Putrescine porter (characterized) | 41% | 66% | 184.1 | Glycine betaine/choline transport system ATP-binding protein OusV | 61% | 456.8 |
| D-maltose catabolism | thuK | lo | Trehalose/maltose import ATP-binding protein MalK; EC 7.5.2.1 (characterized) | 42% | 65% | 177.6 | Glycine betaine/choline transport system ATP-binding protein OusV | 61% | 456.8 |
| trehalose catabolism | thuK | lo | Trehalose/maltose import ATP-binding protein MalK; EC 7.5.2.1 (characterized) | 42% | 65% | 177.6 | Glycine betaine/choline transport system ATP-binding protein OusV | 61% | 456.8 |
| sucrose catabolism | thuK | lo | ABC transporter (characterized, see rationale) | 41% | 59% | 176.8 | Glycine betaine/choline transport system ATP-binding protein OusV | 61% | 456.8 |
| L-arabinose catabolism | xacJ | lo | Xylose/arabinose import ATP-binding protein XacJ; EC 7.5.2.13 (characterized, see rationale) | 41% | 62% | 172.2 | Glycine betaine/choline transport system ATP-binding protein OusV | 61% | 456.8 |
| 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% | 62% | 171.4 | Glycine betaine/choline transport system ATP-binding protein OusV | 61% | 456.8 |
| L-fucose catabolism | SM_b21106 | lo | ABC transporter for L-Fucose, ATPase component (characterized) | 36% | 73% | 169.9 | Glycine betaine/choline transport system ATP-binding protein OusV | 61% | 456.8 |
| D-maltose catabolism | malK | lo | Maltose/maltodextrin import ATP-binding protein MalK; EC 7.5.2.1 (characterized) | 40% | 65% | 169.9 | Glycine betaine/choline transport system ATP-binding protein OusV | 61% | 456.8 |
| 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) | 36% | 73% | 167.5 | Glycine betaine/choline transport system ATP-binding protein OusV | 61% | 456.8 |
| D-maltose catabolism | aglK | lo | ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized) | 37% | 68% | 163.7 | Glycine betaine/choline transport system ATP-binding protein OusV | 61% | 456.8 |
| sucrose catabolism | aglK | lo | ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized) | 37% | 68% | 163.7 | Glycine betaine/choline transport system ATP-binding protein OusV | 61% | 456.8 |
| trehalose catabolism | aglK | lo | ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized) | 37% | 68% | 163.7 | Glycine betaine/choline transport system ATP-binding protein OusV | 61% | 456.8 |
| D-mannitol catabolism | mtlK | lo | ABC transporter for D-mannitol and D-mannose, ATPase component (characterized) | 34% | 74% | 162.9 | Glycine betaine/choline transport system ATP-binding protein OusV | 61% | 456.8 |
| D-glucosamine (chitosamine) catabolism | SM_b21216 | lo | ABC transporter for D-Glucosamine, ATPase component (characterized) | 35% | 74% | 162.2 | Glycine betaine/choline transport system ATP-binding protein OusV | 61% | 456.8 |
| L-asparagine catabolism | glnQ | lo | Glutamine ABC transporter ATP-binding protein, component of Glutamine transporter, GlnQP. Takes up glutamine, asparagine and glutamate which compete for each other for binding both substrate and the transmembrane protein constituent of the system (Fulyani et al. 2015). Tandem substrate binding domains (SBDs) differ in substrate specificity and affinity, allowing cells to efficiently accumulate different amino acids via a single ABC transporter. Analysis revealed the roles of individual residues in determining the substrate affinity (characterized) | 36% | 97% | 161 | Glycine betaine/choline transport system ATP-binding protein OusV | 61% | 456.8 |
| L-glutamate catabolism | gltL | lo | Glutamine ABC transporter ATP-binding protein, component of Glutamine transporter, GlnQP. Takes up glutamine, asparagine and glutamate which compete for each other for binding both substrate and the transmembrane protein constituent of the system (Fulyani et al. 2015). Tandem substrate binding domains (SBDs) differ in substrate specificity and affinity, allowing cells to efficiently accumulate different amino acids via a single ABC transporter. Analysis revealed the roles of individual residues in determining the substrate affinity (characterized) | 36% | 97% | 161 | Glycine betaine/choline transport system ATP-binding protein OusV | 61% | 456.8 |
| L-arabinose catabolism | xacK | lo | Xylose/arabinose import ATP-binding protein XacK; EC 7.5.2.13 (characterized, see rationale) | 39% | 61% | 160.2 | Glycine betaine/choline transport system ATP-binding protein OusV | 61% | 456.8 |
| D-sorbitol (glucitol) catabolism | mtlK | lo | MtlK, component of The polyol (mannitol, glucitol (sorbitol), arabitol (arabinitol; lyxitol)) uptake porter, MtlEFGK (characterized) | 35% | 63% | 160.2 | Glycine betaine/choline transport system ATP-binding protein OusV | 61% | 456.8 |
| N-acetyl-D-glucosamine catabolism | SMc02869 | lo | N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized) | 33% | 78% | 159.8 | Glycine betaine/choline transport system ATP-binding protein OusV | 61% | 456.8 |
| D-glucosamine (chitosamine) catabolism | SMc02869 | lo | N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized) | 33% | 78% | 159.8 | Glycine betaine/choline transport system ATP-binding protein OusV | 61% | 456.8 |
| xylitol catabolism | Dshi_0546 | lo | ABC transporter for Xylitol, ATPase component (characterized) | 35% | 73% | 159.5 | Glycine betaine/choline transport system ATP-binding protein OusV | 61% | 456.8 |
| D-cellobiose catabolism | aglK' | lo | Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) | 37% | 68% | 158.3 | Glycine betaine/choline transport system ATP-binding protein OusV | 61% | 456.8 |
| D-glucose catabolism | aglK' | lo | Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) | 37% | 68% | 158.3 | Glycine betaine/choline transport system ATP-binding protein OusV | 61% | 456.8 |
| lactose catabolism | aglK' | lo | Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) | 37% | 68% | 158.3 | Glycine betaine/choline transport system ATP-binding protein OusV | 61% | 456.8 |
| lactose catabolism | lacK | lo | LacK, component of Lactose porter (characterized) | 38% | 66% | 158.3 | Glycine betaine/choline transport system ATP-binding protein OusV | 61% | 456.8 |
| D-maltose catabolism | aglK' | lo | Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) | 37% | 68% | 158.3 | Glycine betaine/choline transport system ATP-binding protein OusV | 61% | 456.8 |
| sucrose catabolism | aglK' | lo | Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) | 37% | 68% | 158.3 | Glycine betaine/choline transport system ATP-binding protein OusV | 61% | 456.8 |
| trehalose catabolism | aglK' | lo | Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) | 37% | 68% | 158.3 | Glycine betaine/choline transport system ATP-binding protein OusV | 61% | 456.8 |
| D-cellobiose catabolism | gtsD | lo | GtsD (GLcK), component of Glucose porter, GtsABCD (characterized) | 34% | 65% | 156.8 | Glycine betaine/choline transport system ATP-binding protein OusV | 61% | 456.8 |
| D-glucose catabolism | gtsD | lo | GtsD (GLcK), component of Glucose porter, GtsABCD (characterized) | 34% | 65% | 156.8 | Glycine betaine/choline transport system ATP-binding protein OusV | 61% | 456.8 |
| lactose catabolism | gtsD | lo | GtsD (GLcK), component of Glucose porter, GtsABCD (characterized) | 34% | 65% | 156.8 | Glycine betaine/choline transport system ATP-binding protein OusV | 61% | 456.8 |
| L-lysine catabolism | hisP | lo | Amino-acid ABC transporter, ATP-binding protein (characterized, see rationale) | 34% | 99% | 156.8 | Glycine betaine/choline transport system ATP-binding protein OusV | 61% | 456.8 |
| D-maltose catabolism | gtsD | lo | GtsD (GLcK), component of Glucose porter, GtsABCD (characterized) | 34% | 65% | 156.8 | Glycine betaine/choline transport system ATP-binding protein OusV | 61% | 456.8 |
| sucrose catabolism | gtsD | lo | GtsD (GLcK), component of Glucose porter, GtsABCD (characterized) | 34% | 65% | 156.8 | Glycine betaine/choline transport system ATP-binding protein OusV | 61% | 456.8 |
| trehalose catabolism | gtsD | lo | GtsD (GLcK), component of Glucose porter, GtsABCD (characterized) | 34% | 65% | 156.8 | Glycine betaine/choline transport system ATP-binding protein OusV | 61% | 456.8 |
| L-arabinose catabolism | araV | lo | AraV, component of Arabinose, fructose, xylose porter (characterized) | 38% | 63% | 156 | Glycine betaine/choline transport system ATP-binding protein OusV | 61% | 456.8 |
| D-fructose catabolism | araV | lo | AraV, component of Arabinose, fructose, xylose porter (characterized) | 38% | 63% | 156 | Glycine betaine/choline transport system ATP-binding protein OusV | 61% | 456.8 |
| D-maltose catabolism | musK | lo | ABC-type maltose transporter (EC 7.5.2.1) (characterized) | 38% | 60% | 156 | Glycine betaine/choline transport system ATP-binding protein OusV | 61% | 456.8 |
| sucrose catabolism | araV | lo | AraV, component of Arabinose, fructose, xylose porter (characterized) | 38% | 63% | 156 | Glycine betaine/choline transport system ATP-binding protein OusV | 61% | 456.8 |
| D-xylose catabolism | araV | lo | AraV, component of Arabinose, fructose, xylose porter (characterized) | 38% | 63% | 156 | Glycine betaine/choline transport system ATP-binding protein OusV | 61% | 456.8 |
| D-maltose catabolism | malK_Bb | lo | ABC-type maltose transport, ATP binding protein (characterized, see rationale) | 35% | 69% | 155.6 | Glycine betaine/choline transport system ATP-binding protein OusV | 61% | 456.8 |
| L-arginine catabolism | artP | lo | ABC transporter for L-Arginine, putative ATPase component (characterized) | 34% | 97% | 155.2 | Glycine betaine/choline transport system ATP-binding protein OusV | 61% | 456.8 |
| 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% | 78% | 154.8 | Glycine betaine/choline transport system ATP-binding protein OusV | 61% | 456.8 |
| L-histidine catabolism | Ac3H11_2560 | lo | ABC transporter for L-Histidine, ATPase component (characterized) | 40% | 79% | 154.5 | Glycine betaine/choline transport system ATP-binding protein OusV | 61% | 456.8 |
| L-asparagine catabolism | bztD | lo | BztD, component of Glutamate/glutamine/aspartate/asparagine porter (characterized) | 36% | 85% | 154.1 | Glycine betaine/choline transport system ATP-binding protein OusV | 61% | 456.8 |
| L-aspartate catabolism | bztD | lo | BztD, component of Glutamate/glutamine/aspartate/asparagine porter (characterized) | 36% | 85% | 154.1 | Glycine betaine/choline transport system ATP-binding protein OusV | 61% | 456.8 |
| L-histidine catabolism | aapP | lo | ABC transporter for L-Glutamine, L-Histidine, and other L-amino acids, ATPase component (characterized) | 36% | 86% | 153.7 | Glycine betaine/choline transport system ATP-binding protein OusV | 61% | 456.8 |
| L-asparagine catabolism | aatP | lo | ABC transporter for L-aspartate, L-asparagine, L-glutamate, and L-glutamine, ATPase component (characterized) | 38% | 91% | 152.9 | Glycine betaine/choline transport system ATP-binding protein OusV | 61% | 456.8 |
| L-aspartate catabolism | aatP | lo | ABC transporter for L-aspartate, L-asparagine, L-glutamate, and L-glutamine, ATPase component (characterized) | 38% | 91% | 152.9 | Glycine betaine/choline transport system ATP-binding protein OusV | 61% | 456.8 |
| D-alanine catabolism | Pf6N2E2_5405 | lo | ABC transporter for D-Alanine, ATPase component (characterized) | 36% | 88% | 152.1 | Glycine betaine/choline transport system ATP-binding protein OusV | 61% | 456.8 |
| D-xylose catabolism | gtsD | lo | ABC transporter for D-Glucose-6-Phosphate, ATPase component (characterized) | 36% | 58% | 152.1 | Glycine betaine/choline transport system ATP-binding protein OusV | 61% | 456.8 |
| L-histidine catabolism | hisP | lo | Histidine transport ATP-binding protein HisP (characterized) | 36% | 91% | 151.8 | Glycine betaine/choline transport system ATP-binding protein OusV | 61% | 456.8 |
| D-galactose catabolism | PfGW456L13_1897 | lo | ABC transporter for D-Galactose and D-Glucose, ATPase component (characterized) | 36% | 58% | 151.4 | Glycine betaine/choline transport system ATP-binding protein OusV | 61% | 456.8 |
| trehalose catabolism | treV | lo | TreV, component of Trehalose porter (characterized) | 35% | 72% | 151 | Glycine betaine/choline transport system ATP-binding protein OusV | 61% | 456.8 |
| L-asparagine catabolism | aapP | lo | AapP, component of General L-amino acid porter; transports basic and acidic amino acids preferentially, but also transports aliphatic amino acids (catalyzes both uptake and efflux) (characterized) | 35% | 87% | 150.2 | Glycine betaine/choline transport system ATP-binding protein OusV | 61% | 456.8 |
| L-aspartate catabolism | aapP | lo | AapP, component of General L-amino acid porter; transports basic and acidic amino acids preferentially, but also transports aliphatic amino acids (catalyzes both uptake and efflux) (characterized) | 35% | 87% | 150.2 | Glycine betaine/choline transport system ATP-binding protein OusV | 61% | 456.8 |
| 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% | 63% | 150.2 | Glycine betaine/choline transport system ATP-binding protein OusV | 61% | 456.8 |
| L-glutamate catabolism | aapP | lo | AapP, component of General L-amino acid porter; transports basic and acidic amino acids preferentially, but also transports aliphatic amino acids (catalyzes both uptake and efflux) (characterized) | 35% | 87% | 150.2 | Glycine betaine/choline transport system ATP-binding protein OusV | 61% | 456.8 |
| L-leucine catabolism | aapP | lo | AapP, component of General L-amino acid porter; transports basic and acidic amino acids preferentially, but also transports aliphatic amino acids (catalyzes both uptake and efflux) (characterized) | 35% | 87% | 150.2 | Glycine betaine/choline transport system ATP-binding protein OusV | 61% | 456.8 |
| L-proline catabolism | aapP | lo | AapP, component of General L-amino acid porter; transports basic and acidic amino acids preferentially, but also transports aliphatic amino acids (catalyzes both uptake and efflux) (characterized) | 35% | 87% | 150.2 | Glycine betaine/choline transport system ATP-binding protein OusV | 61% | 456.8 |
| L-asparagine catabolism | peb1C | lo | PEB1C, component of Uptake system for glutamate and aspartate (characterized) | 37% | 91% | 146 | Glycine betaine/choline transport system ATP-binding protein OusV | 61% | 456.8 |
| L-aspartate catabolism | peb1C | lo | PEB1C, component of Uptake system for glutamate and aspartate (characterized) | 37% | 91% | 146 | Glycine betaine/choline transport system ATP-binding protein OusV | 61% | 456.8 |
| D-cellobiose catabolism | SMc04256 | lo | ABC transporter for D-Cellobiose and D-Salicin, ATPase component (characterized) | 32% | 87% | 146 | Glycine betaine/choline transport system ATP-binding protein OusV | 61% | 456.8 |
| D-glucosamine (chitosamine) catabolism | AO353_21725 | lo | ABC transporter for D-Glucosamine, putative ATPase component (characterized) | 34% | 97% | 145.2 | Glycine betaine/choline transport system ATP-binding protein OusV | 61% | 456.8 |
| L-tryptophan catabolism | ecfA1 | lo | Energy-coupling factor transporter ATP-binding protein EcfA1; Short=ECF transporter A component EcfA; EC 7.-.-.- (characterized, see rationale) | 37% | 77% | 144.4 | Glycine betaine/choline transport system ATP-binding protein OusV | 61% | 456.8 |
| L-citrulline catabolism | AO353_03040 | lo | ABC transporter for L-Arginine and L-Citrulline, ATPase component (characterized) | 35% | 92% | 142.9 | Glycine betaine/choline transport system ATP-binding protein OusV | 61% | 456.8 |
| L-asparagine catabolism | bgtA | lo | ATPase (characterized, see rationale) | 35% | 97% | 140.6 | Glycine betaine/choline transport system ATP-binding protein OusV | 61% | 456.8 |
| L-aspartate catabolism | bgtA | lo | ATPase (characterized, see rationale) | 35% | 97% | 140.6 | Glycine betaine/choline transport system ATP-binding protein OusV | 61% | 456.8 |
| L-citrulline catabolism | PS417_17605 | lo | ATP-binding cassette domain-containing protein; SubName: Full=Amino acid transporter; SubName: Full=Histidine ABC transporter ATP-binding protein; SubName: Full=Histidine transport system ATP-binding protein (characterized, see rationale) | 35% | 95% | 136 | Glycine betaine/choline transport system ATP-binding protein OusV | 61% | 456.8 |
| glycerol catabolism | glpS | lo | GlpS, component of Glycerol uptake porter, GlpSTPQV (characterized) | 31% | 65% | 125.6 | Glycine betaine/choline transport system ATP-binding protein OusV | 61% | 456.8 |
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