| 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) | 51% | 98% | 394.8 | OtaA, component of The salt-induced glycine betaine OtaABC transporter | 62% | 472.2 |
| L-proline catabolism | proV | med | glycine betaine/l-proline transport atp-binding protein prov (characterized) | 50% | 98% | 379.4 | OtaA, component of The salt-induced glycine betaine OtaABC transporter | 62% | 472.2 |
| L-histidine catabolism | hutV | med | HutV aka HISV aka R02702 aka SMC00670, component of Uptake system for hisitidine, proline, proline-betaine and glycine-betaine (characterized) | 56% | 95% | 300.4 | OtaA, component of The salt-induced glycine betaine OtaABC transporter | 62% | 472.2 |
| 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% | 95% | 300.4 | OtaA, component of The salt-induced glycine betaine OtaABC transporter | 62% | 472.2 |
| L-histidine catabolism | Ac3H11_2560 | med | ABC transporter for L-Histidine, ATPase component (characterized) | 40% | 84% | 159.5 | OtaA, component of The salt-induced glycine betaine OtaABC transporter | 62% | 472.2 |
| L-asparagine catabolism | aatP | med | ABC transporter for L-asparagine and L-glutamate, ATPase component (characterized) | 40% | 87% | 152.5 | OtaA, component of The salt-induced glycine betaine OtaABC transporter | 62% | 472.2 |
| L-aspartate catabolism | aatP | med | ABC transporter for L-asparagine and L-glutamate, ATPase component (characterized) | 40% | 87% | 152.5 | OtaA, component of The salt-induced glycine betaine OtaABC transporter | 62% | 472.2 |
| L-glutamate catabolism | gltL | med | ABC transporter for L-asparagine and L-glutamate, ATPase component (characterized) | 40% | 87% | 152.5 | OtaA, component of The salt-induced glycine betaine OtaABC transporter | 62% | 472.2 |
| putrescine catabolism | potA | lo | Spermidine/putrescine import ATP-binding protein PotA, component of The spermidine/putrescine uptake porter, PotABCD (characterized) | 42% | 63% | 196.1 | OtaA, component of The salt-induced glycine betaine OtaABC transporter | 62% | 472.2 |
| L-arabinose catabolism | xacK | lo | Xylose/arabinose import ATP-binding protein XacK; EC 7.5.2.13 (characterized, see rationale) | 40% | 62% | 182.2 | OtaA, component of The salt-induced glycine betaine OtaABC transporter | 62% | 472.2 |
| L-histidine catabolism | PA5503 | lo | Methionine import ATP-binding protein MetN 2, component of L-Histidine uptake porter, MetIQN (characterized) | 40% | 72% | 178.7 | OtaA, component of The salt-induced glycine betaine OtaABC transporter | 62% | 472.2 |
| D-cellobiose catabolism | gtsD | lo | ABC transporter for D-Galactose and D-Glucose, ATPase component (characterized) | 40% | 57% | 172.6 | OtaA, component of The salt-induced glycine betaine OtaABC transporter | 62% | 472.2 |
| D-galactose catabolism | PfGW456L13_1897 | lo | ABC transporter for D-Galactose and D-Glucose, ATPase component (characterized) | 40% | 57% | 172.6 | OtaA, component of The salt-induced glycine betaine OtaABC transporter | 62% | 472.2 |
| D-glucose catabolism | gtsD | lo | ABC transporter for D-Galactose and D-Glucose, ATPase component (characterized) | 40% | 57% | 172.6 | OtaA, component of The salt-induced glycine betaine OtaABC transporter | 62% | 472.2 |
| lactose catabolism | gtsD | lo | ABC transporter for D-Galactose and D-Glucose, ATPase component (characterized) | 40% | 57% | 172.6 | OtaA, component of The salt-induced glycine betaine OtaABC transporter | 62% | 472.2 |
| D-maltose catabolism | gtsD | lo | ABC transporter for D-Galactose and D-Glucose, ATPase component (characterized) | 40% | 57% | 172.6 | OtaA, component of The salt-induced glycine betaine OtaABC transporter | 62% | 472.2 |
| sucrose catabolism | gtsD | lo | ABC transporter for D-Galactose and D-Glucose, ATPase component (characterized) | 40% | 57% | 172.6 | OtaA, component of The salt-induced glycine betaine OtaABC transporter | 62% | 472.2 |
| trehalose catabolism | gtsD | lo | ABC transporter for D-Galactose and D-Glucose, ATPase component (characterized) | 40% | 57% | 172.6 | OtaA, component of The salt-induced glycine betaine OtaABC transporter | 62% | 472.2 |
| D-maltose catabolism | thuK | lo | ThuK aka RB0314 aka SMB20328, component of Trehalose/maltose/sucrose porter (trehalose inducible) (characterized) | 38% | 75% | 170.6 | OtaA, component of The salt-induced glycine betaine OtaABC transporter | 62% | 472.2 |
| sucrose catabolism | thuK | lo | ThuK aka RB0314 aka SMB20328, component of Trehalose/maltose/sucrose porter (trehalose inducible) (characterized) | 38% | 75% | 170.6 | OtaA, component of The salt-induced glycine betaine OtaABC transporter | 62% | 472.2 |
| trehalose catabolism | thuK | lo | ThuK aka RB0314 aka SMB20328, component of Trehalose/maltose/sucrose porter (trehalose inducible) (characterized) | 38% | 75% | 170.6 | OtaA, component of The salt-induced glycine betaine OtaABC transporter | 62% | 472.2 |
| D-cellobiose catabolism | SMc04256 | lo | ABC transporter for D-Cellobiose and D-Salicin, ATPase component (characterized) | 40% | 66% | 167.2 | OtaA, component of The salt-induced glycine betaine OtaABC transporter | 62% | 472.2 |
| L-arginine catabolism | artP | lo | Arginine transport ATP-binding protein ArtM (characterized) | 37% | 98% | 160.6 | OtaA, component of The salt-induced glycine betaine OtaABC transporter | 62% | 472.2 |
| L-asparagine catabolism | bztD | lo | BztD, component of Glutamate/glutamine/aspartate/asparagine porter (characterized) | 35% | 96% | 159.8 | OtaA, component of The salt-induced glycine betaine OtaABC transporter | 62% | 472.2 |
| L-aspartate catabolism | bztD | lo | BztD, component of Glutamate/glutamine/aspartate/asparagine porter (characterized) | 35% | 96% | 159.8 | OtaA, component of The salt-induced glycine betaine OtaABC transporter | 62% | 472.2 |
| L-citrulline catabolism | AO353_03040 | lo | ABC transporter for L-Arginine and L-Citrulline, ATPase component (characterized) | 36% | 96% | 157.9 | OtaA, component of The salt-induced glycine betaine OtaABC transporter | 62% | 472.2 |
| L-asparagine catabolism | bgtA | lo | ATPase (characterized, see rationale) | 38% | 86% | 155.6 | OtaA, component of The salt-induced glycine betaine OtaABC transporter | 62% | 472.2 |
| L-aspartate catabolism | bgtA | lo | ATPase (characterized, see rationale) | 38% | 86% | 155.6 | OtaA, component of The salt-induced glycine betaine OtaABC transporter | 62% | 472.2 |
| L-histidine catabolism | aapP | lo | ABC transporter for L-Glutamine, L-Histidine, and other L-amino acids, ATPase component (characterized) | 38% | 88% | 155.6 | OtaA, component of The salt-induced glycine betaine OtaABC transporter | 62% | 472.2 |
| D-glucosamine (chitosamine) catabolism | AO353_21725 | lo | ABC transporter for D-Glucosamine, putative ATPase component (characterized) | 38% | 92% | 155.2 | OtaA, component of The salt-induced glycine betaine OtaABC transporter | 62% | 472.2 |
| 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% | 89% | 153.7 | OtaA, component of The salt-induced glycine betaine OtaABC transporter | 62% | 472.2 |
| 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% | 89% | 153.7 | OtaA, component of The salt-induced glycine betaine OtaABC transporter | 62% | 472.2 |
| 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% | 89% | 153.7 | OtaA, component of The salt-induced glycine betaine OtaABC transporter | 62% | 472.2 |
| 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% | 89% | 153.7 | OtaA, component of The salt-induced glycine betaine OtaABC transporter | 62% | 472.2 |
| 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% | 89% | 153.7 | OtaA, component of The salt-induced glycine betaine OtaABC transporter | 62% | 472.2 |
| L-lysine catabolism | hisP | lo | Amino-acid ABC transporter, ATP-binding protein (characterized, see rationale) | 37% | 88% | 153.3 | OtaA, component of The salt-induced glycine betaine OtaABC transporter | 62% | 472.2 |
| 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% | 96% | 152.5 | OtaA, component of The salt-induced glycine betaine OtaABC transporter | 62% | 472.2 |
| D-alanine catabolism | Pf6N2E2_5405 | lo | ABC transporter for D-Alanine, ATPase component (characterized) | 35% | 93% | 151.4 | OtaA, component of The salt-induced glycine betaine OtaABC transporter | 62% | 472.2 |
| L-histidine catabolism | hisP | lo | Probable ATP-binding component of ABC transporter, component of Amino acid transporter, PA5152-PA5155. Probably transports numerous amino acids including lysine, arginine, histidine, D-alanine and D-valine (Johnson et al. 2008). Regulated by ArgR (characterized) | 34% | 95% | 149.1 | OtaA, component of The salt-induced glycine betaine OtaABC transporter | 62% | 472.2 |
| L-histidine catabolism | bgtA | lo | BgtA aka SLR1735, component of Arginine/lysine/histidine/glutamine porter (characterized) | 35% | 96% | 148.7 | OtaA, component of The salt-induced glycine betaine OtaABC transporter | 62% | 472.2 |
| L-histidine catabolism | BPHYT_RS24015 | lo | ABC transporter related (characterized, see rationale) | 36% | 94% | 147.1 | OtaA, component of The salt-induced glycine betaine OtaABC transporter | 62% | 472.2 |
| D-mannose catabolism | TM1750 | lo | TM1750, component of Probable mannose/mannoside porter. Induced by beta-mannan (Conners et al., 2005). Regulated by mannose-responsive regulator manR (characterized) | 34% | 77% | 145.6 | OtaA, component of The salt-induced glycine betaine OtaABC transporter | 62% | 472.2 |
| L-tryptophan catabolism | ecfA1 | lo | Energy-coupling factor transporter ATP-binding protein EcfA1; Short=ECF transporter A component EcfA; EC 7.-.-.- (characterized, see rationale) | 40% | 77% | 145.2 | OtaA, component of The salt-induced glycine betaine OtaABC transporter | 62% | 472.2 |
| glycerol catabolism | glpT | lo | GlpT, component of Glycerol uptake porter, GlpSTPQV (characterized) | 32% | 62% | 140.2 | OtaA, component of The salt-induced glycine betaine OtaABC transporter | 62% | 472.2 |
| L-asparagine catabolism | peb1C | lo | PEB1C, component of Uptake system for glutamate and aspartate (characterized) | 34% | 94% | 139.8 | OtaA, component of The salt-induced glycine betaine OtaABC transporter | 62% | 472.2 |
| L-aspartate catabolism | peb1C | lo | PEB1C, component of Uptake system for glutamate and aspartate (characterized) | 34% | 94% | 139.8 | OtaA, component of The salt-induced glycine betaine OtaABC transporter | 62% | 472.2 |
| 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) | 36% | 88% | 137.1 | OtaA, component of The salt-induced glycine betaine OtaABC transporter | 62% | 472.2 |
| D-cellobiose catabolism | cbtD | lo | CbtD, component of Cellobiose and cellooligosaccharide porter (characterized) | 32% | 81% | 131 | OtaA, component of The salt-induced glycine betaine OtaABC transporter | 62% | 472.2 |
| D-mannose catabolism | TM1749 | lo | TM1749, component of Probable mannose/mannoside porter. Induced by beta-mannan (Conners et al., 2005). Regulated by mannose-responsive regulator manR (characterized) | 33% | 77% | 128.6 | OtaA, component of The salt-induced glycine betaine OtaABC transporter | 62% | 472.2 |
| D-cellobiose catabolism | TM0028 | lo | TM0028, component of β-glucoside porter (Conners et al., 2005). Binds cellobiose, laminaribiose (Nanavati et al. 2006). Regulated by cellobiose-responsive repressor BglR (characterized) | 33% | 72% | 100.9 | OtaA, component of The salt-induced glycine betaine OtaABC transporter | 62% | 472.2 |
This GapMind analysis is from Sep 24 2021. 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