| Pathway | Step | Score | Similar to | Id. | Cov. | Bits | Other hit | Other id. | Other bits |
|---|
| L-histidine catabolism | hutV | med | ABC transporter for L-Histidine, ATPase component (characterized) | 55% | 97% | 297.7 | OtaA, component of The salt-induced glycine betaine OtaABC transporter | 58% | 325.1 |
| 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) | 44% | 87% | 295.4 | OtaA, component of The salt-induced glycine betaine OtaABC transporter | 58% | 325.1 |
| L-proline catabolism | proV | med | glycine betaine/l-proline transport atp-binding protein prov (characterized) | 43% | 91% | 294.3 | OtaA, component of The salt-induced glycine betaine OtaABC transporter | 58% | 325.1 |
| 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) | 53% | 95% | 280.4 | OtaA, component of The salt-induced glycine betaine OtaABC transporter | 58% | 325.1 |
| D-cellobiose catabolism | gtsD | med | Sugar ABC transporter ATP-binding protein (characterized, see rationale) | 41% | 76% | 199.1 | OtaA, component of The salt-induced glycine betaine OtaABC transporter | 58% | 325.1 |
| D-glucose catabolism | gtsD | med | Sugar ABC transporter ATP-binding protein (characterized, see rationale) | 41% | 76% | 199.1 | OtaA, component of The salt-induced glycine betaine OtaABC transporter | 58% | 325.1 |
| lactose catabolism | gtsD | med | Sugar ABC transporter ATP-binding protein (characterized, see rationale) | 41% | 76% | 199.1 | OtaA, component of The salt-induced glycine betaine OtaABC transporter | 58% | 325.1 |
| D-maltose catabolism | gtsD | med | Sugar ABC transporter ATP-binding protein (characterized, see rationale) | 41% | 76% | 199.1 | OtaA, component of The salt-induced glycine betaine OtaABC transporter | 58% | 325.1 |
| sucrose catabolism | gtsD | med | Sugar ABC transporter ATP-binding protein (characterized, see rationale) | 41% | 76% | 199.1 | OtaA, component of The salt-induced glycine betaine OtaABC transporter | 58% | 325.1 |
| trehalose catabolism | gtsD | med | Sugar ABC transporter ATP-binding protein (characterized, see rationale) | 41% | 76% | 199.1 | OtaA, component of The salt-induced glycine betaine OtaABC transporter | 58% | 325.1 |
| L-asparagine catabolism | aatP | med | ABC transporter for L-asparagine and L-glutamate, ATPase component (characterized) | 41% | 86% | 156.4 | OtaA, component of The salt-induced glycine betaine OtaABC transporter | 58% | 325.1 |
| L-aspartate catabolism | aatP | med | ABC transporter for L-asparagine and L-glutamate, ATPase component (characterized) | 41% | 86% | 156.4 | OtaA, component of The salt-induced glycine betaine OtaABC transporter | 58% | 325.1 |
| L-glutamate catabolism | gltL | med | ABC transporter for L-asparagine and L-glutamate, ATPase component (characterized) | 41% | 86% | 156.4 | OtaA, component of The salt-induced glycine betaine OtaABC transporter | 58% | 325.1 |
| L-histidine catabolism | Ac3H11_2560 | med | ABC transporter for L-Histidine, ATPase component (characterized) | 43% | 76% | 156.4 | OtaA, component of The salt-induced glycine betaine OtaABC transporter | 58% | 325.1 |
| D-maltose catabolism | thuK | lo | Trehalose/maltose import ATP-binding protein MalK; EC 7.5.2.1 (characterized) | 42% | 61% | 188 | OtaA, component of The salt-induced glycine betaine OtaABC transporter | 58% | 325.1 |
| trehalose catabolism | thuK | lo | Trehalose/maltose import ATP-binding protein MalK; EC 7.5.2.1 (characterized) | 42% | 61% | 188 | OtaA, component of The salt-induced glycine betaine OtaABC transporter | 58% | 325.1 |
| putrescine catabolism | potA | lo | PotG aka B0855, component of Putrescine porter (characterized) | 42% | 58% | 185.3 | OtaA, component of The salt-induced glycine betaine OtaABC transporter | 58% | 325.1 |
| L-arabinose catabolism | xacK | lo | Xylose/arabinose import ATP-binding protein XacK; EC 7.5.2.13 (characterized, see rationale) | 41% | 66% | 182.2 | OtaA, component of The salt-induced glycine betaine OtaABC transporter | 58% | 325.1 |
| D-maltose catabolism | musK | lo | ABC-type maltose transporter (EC 7.5.2.1) (characterized) | 33% | 95% | 179.9 | OtaA, component of The salt-induced glycine betaine OtaABC transporter | 58% | 325.1 |
| D-glucosamine (chitosamine) catabolism | SM_b21216 | lo | ABC transporter for D-Glucosamine, ATPase component (characterized) | 34% | 87% | 178.3 | OtaA, component of The salt-induced glycine betaine OtaABC transporter | 58% | 325.1 |
| N-acetyl-D-glucosamine catabolism | SMc02869 | lo | N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized) | 35% | 85% | 177.6 | OtaA, component of The salt-induced glycine betaine OtaABC transporter | 58% | 325.1 |
| D-glucosamine (chitosamine) catabolism | SMc02869 | lo | N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized) | 35% | 85% | 177.6 | OtaA, component of The salt-induced glycine betaine OtaABC transporter | 58% | 325.1 |
| 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) | 38% | 59% | 176.8 | OtaA, component of The salt-induced glycine betaine OtaABC transporter | 58% | 325.1 |
| D-maltose catabolism | malK_Bb | lo | ABC-type maltose transport, ATP binding protein (characterized, see rationale) | 36% | 72% | 176.8 | OtaA, component of The salt-induced glycine betaine OtaABC transporter | 58% | 325.1 |
| L-arabinose catabolism | xacJ | lo | Xylose/arabinose import ATP-binding protein XacJ; EC 7.5.2.13 (characterized, see rationale) | 41% | 60% | 174.9 | OtaA, component of The salt-induced glycine betaine OtaABC transporter | 58% | 325.1 |
| D-galactose catabolism | PfGW456L13_1897 | lo | ABC transporter for D-Galactose and D-Glucose, ATPase component (characterized) | 38% | 57% | 172.6 | OtaA, component of The salt-induced glycine betaine OtaABC transporter | 58% | 325.1 |
| trehalose catabolism | treV | lo | TreV, component of Trehalose porter (characterized) | 37% | 70% | 172.2 | OtaA, component of The salt-induced glycine betaine OtaABC transporter | 58% | 325.1 |
| 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) | 38% | 60% | 170.6 | OtaA, component of The salt-induced glycine betaine OtaABC transporter | 58% | 325.1 |
| D-maltose catabolism | aglK | lo | ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized) | 32% | 88% | 167.9 | OtaA, component of The salt-induced glycine betaine OtaABC transporter | 58% | 325.1 |
| sucrose catabolism | aglK | lo | ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized) | 32% | 88% | 167.9 | OtaA, component of The salt-induced glycine betaine OtaABC transporter | 58% | 325.1 |
| trehalose catabolism | aglK | lo | ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized) | 32% | 88% | 167.9 | OtaA, component of The salt-induced glycine betaine OtaABC transporter | 58% | 325.1 |
| D-sorbitol (glucitol) catabolism | mtlK | lo | ABC transporter for D-Sorbitol, ATPase component (characterized) | 31% | 84% | 167.5 | OtaA, component of The salt-induced glycine betaine OtaABC transporter | 58% | 325.1 |
| L-arginine catabolism | artP | lo | ABC transporter for L-Arginine, putative ATPase component (characterized) | 36% | 92% | 162.5 | OtaA, component of The salt-induced glycine betaine OtaABC transporter | 58% | 325.1 |
| 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% | 61% | 162.5 | OtaA, component of The salt-induced glycine betaine OtaABC transporter | 58% | 325.1 |
| 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) | 35% | 61% | 162.5 | OtaA, component of The salt-induced glycine betaine OtaABC transporter | 58% | 325.1 |
| 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) | 35% | 98% | 159.1 | OtaA, component of The salt-induced glycine betaine OtaABC transporter | 58% | 325.1 |
| D-maltose catabolism | malK | lo | Maltose-transporting ATPase (EC 3.6.3.19) (characterized) | 35% | 61% | 158.7 | OtaA, component of The salt-induced glycine betaine OtaABC transporter | 58% | 325.1 |
| D-cellobiose catabolism | SMc04256 | lo | ABC transporter for D-Cellobiose and D-Salicin, ATPase component (characterized) | 35% | 61% | 156.4 | OtaA, component of The salt-induced glycine betaine OtaABC transporter | 58% | 325.1 |
| L-asparagine catabolism | bztD | lo | BztD, component of Glutamate/glutamine/aspartate/asparagine porter (characterized) | 38% | 85% | 156 | OtaA, component of The salt-induced glycine betaine OtaABC transporter | 58% | 325.1 |
| L-aspartate catabolism | bztD | lo | BztD, component of Glutamate/glutamine/aspartate/asparagine porter (characterized) | 38% | 85% | 156 | OtaA, component of The salt-induced glycine betaine OtaABC transporter | 58% | 325.1 |
| D-glucosamine (chitosamine) catabolism | AO353_21725 | lo | ABC transporter for D-Glucosamine, putative ATPase component (characterized) | 35% | 92% | 154.1 | OtaA, component of The salt-induced glycine betaine OtaABC transporter | 58% | 325.1 |
| L-lysine catabolism | hisP | lo | Amino-acid ABC transporter, ATP-binding protein (characterized, see rationale) | 37% | 90% | 154.1 | OtaA, component of The salt-induced glycine betaine OtaABC transporter | 58% | 325.1 |
| L-histidine catabolism | hisP | lo | Histidine transport ATP-binding protein HisP (characterized) | 35% | 93% | 149.4 | OtaA, component of The salt-induced glycine betaine OtaABC transporter | 58% | 325.1 |
| L-histidine catabolism | BPHYT_RS24015 | lo | ABC transporter related (characterized, see rationale) | 35% | 95% | 148.7 | OtaA, component of The salt-induced glycine betaine OtaABC transporter | 58% | 325.1 |
| L-histidine catabolism | aapP | lo | ABC transporter for L-Glutamine, L-Histidine, and other L-amino acids, ATPase component (characterized) | 37% | 87% | 148.7 | OtaA, component of The salt-induced glycine betaine OtaABC transporter | 58% | 325.1 |
| 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) | 36% | 87% | 147.9 | OtaA, component of The salt-induced glycine betaine OtaABC transporter | 58% | 325.1 |
| 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) | 36% | 87% | 147.9 | OtaA, component of The salt-induced glycine betaine OtaABC transporter | 58% | 325.1 |
| 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) | 36% | 87% | 147.9 | OtaA, component of The salt-induced glycine betaine OtaABC transporter | 58% | 325.1 |
| 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) | 36% | 87% | 147.9 | OtaA, component of The salt-induced glycine betaine OtaABC transporter | 58% | 325.1 |
| 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) | 36% | 87% | 147.9 | OtaA, component of The salt-induced glycine betaine OtaABC transporter | 58% | 325.1 |
| L-citrulline catabolism | AO353_03040 | lo | ABC transporter for L-Arginine and L-Citrulline, ATPase component (characterized) | 32% | 98% | 146 | OtaA, component of The salt-induced glycine betaine OtaABC transporter | 58% | 325.1 |
| L-histidine catabolism | bgtA | lo | BgtA aka SLR1735, component of Arginine/lysine/histidine/glutamine porter (characterized) | 35% | 94% | 145.6 | OtaA, component of The salt-induced glycine betaine OtaABC transporter | 58% | 325.1 |
| D-alanine catabolism | Pf6N2E2_5405 | lo | ABC transporter for D-Alanine, ATPase component (characterized) | 37% | 88% | 144.8 | OtaA, component of The salt-induced glycine betaine OtaABC transporter | 58% | 325.1 |
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