| Pathway | Step | Score | Similar to | Id. | Cov. | Bits | Other hit | Other id. | Other bits |
|---|
| L-arginine catabolism | bgtB | hi | Basic amino acid uptake transporter, BgtAB (characterized) | 96% | 100% | 929.1 | Glutamine ABC transporter permease and substrate binding protein 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 | 34% | 268.9 |
| L-asparagine catabolism | bgtA | hi | Basic amino acid uptake transporter, BgtAB (characterized) | 96% | 100% | 929.1 | BgtB aka GLNH aka SLL1270, component of Arginine/lysine/histidine/glutamine porter | 51% | 481.1 |
| L-aspartate catabolism | bgtA | hi | Basic amino acid uptake transporter, BgtAB (characterized) | 96% | 100% | 929.1 | BgtB aka GLNH aka SLL1270, component of Arginine/lysine/histidine/glutamine porter | 51% | 481.1 |
| L-histidine catabolism | bgtB | hi | Basic amino acid uptake transporter, BgtAB (characterized) | 96% | 100% | 929.1 | Glutamine ABC transporter permease and substrate binding protein 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 | 34% | 268.9 |
| L-lysine catabolism | bgtB | hi | Basic amino acid uptake transporter, BgtAB (characterized) | 96% | 100% | 929.1 | Glutamine ABC transporter permease and substrate binding protein 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 | 34% | 268.9 |
| L-histidine catabolism | Ac3H11_2554 | med | ABC transporter for L-Histidine, permease component 1 (characterized) | 46% | 91% | 183.3 | Basic amino acid uptake transporter, BgtAB | 96% | 929.1 |
| L-lysine catabolism | hisQ | med | ABC transporter for L-Lysine, permease component 1 (characterized) | 40% | 92% | 141.4 | Basic amino acid uptake transporter, BgtAB | 96% | 929.1 |
| L-asparagine catabolism | glnP | lo | Glutamine ABC transporter permease and substrate binding protein 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) | 34% | 63% | 268.9 | Basic amino acid uptake transporter, BgtAB | 96% | 929.1 |
| L-glutamate catabolism | glnP | lo | Glutamine ABC transporter permease and substrate binding protein 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) | 34% | 63% | 268.9 | Basic amino acid uptake transporter, BgtAB | 96% | 929.1 |
| L-asparagine catabolism | aatM | lo | Glutamate/aspartate import permease protein GltK (characterized) | 39% | 95% | 152.5 | Basic amino acid uptake transporter, BgtAB | 96% | 929.1 |
| L-aspartate catabolism | aatM | lo | Glutamate/aspartate import permease protein GltK (characterized) | 39% | 95% | 152.5 | Basic amino acid uptake transporter, BgtAB | 96% | 929.1 |
| L-glutamate catabolism | gltK | lo | Glutamate/aspartate import permease protein GltK (characterized) | 39% | 95% | 152.5 | Basic amino acid uptake transporter, BgtAB | 96% | 929.1 |
| L-lysine catabolism | hisM | lo | ABC transporter for L-Lysine, permease component 2 (characterized) | 34% | 95% | 139.4 | Basic amino acid uptake transporter, BgtAB | 96% | 929.1 |
| L-arginine catabolism | artM | lo | Amino acid (Lysine/arginine/ornithine/histidine/octopine) ABC transporter membrane protein, 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) | 30% | 97% | 134 | Basic amino acid uptake transporter, BgtAB | 96% | 929.1 |
| L-histidine catabolism | hisM | lo | Amino acid (Lysine/arginine/ornithine/histidine/octopine) ABC transporter membrane protein, 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) | 30% | 97% | 134 | Basic amino acid uptake transporter, BgtAB | 96% | 929.1 |
| L-histidine catabolism | Ac3H11_2555 | lo | ABC transporter for L-Histidine, periplasmic substrate-binding component 1 (characterized) | 31% | 96% | 131 | Basic amino acid uptake transporter, BgtAB | 96% | 929.1 |
| D-glucosamine (chitosamine) catabolism | AO353_21715 | lo | ABC transporter for D-glucosamine, permease component 1 (characterized) | 37% | 90% | 130.6 | Basic amino acid uptake transporter, BgtAB | 96% | 929.1 |
| L-histidine catabolism | BPHYT_RS24005 | lo | Polar amino acid ABC transporter, inner membrane subunit; Flags: Precursor (characterized, see rationale) | 33% | 91% | 130.6 | Basic amino acid uptake transporter, BgtAB | 96% | 929.1 |
| L-asparagine catabolism | natG | lo | NatG, component of Acidic and neutral amino acid uptake transporter NatFGH/BgtA. BgtA is shared with BgtAB (characterized) | 32% | 80% | 128.6 | Basic amino acid uptake transporter, BgtAB | 96% | 929.1 |
| L-aspartate catabolism | natG | lo | NatG, component of Acidic and neutral amino acid uptake transporter NatFGH/BgtA. BgtA is shared with BgtAB (characterized) | 32% | 80% | 128.6 | Basic amino acid uptake transporter, BgtAB | 96% | 929.1 |
| L-citrulline catabolism | PS417_17595 | lo | ABC transporter permease subunit; SubName: Full=Amino acid ABC transporter permease; SubName: Full=Histidine transport system permease protein (characterized, see rationale) | 36% | 95% | 127.9 | Basic amino acid uptake transporter, BgtAB | 96% | 929.1 |
| L-asparagine catabolism | peb1B | lo | PEP1B, component of Uptake system for glutamate and aspartate (characterized) | 33% | 81% | 125.2 | Basic amino acid uptake transporter, BgtAB | 96% | 929.1 |
| L-aspartate catabolism | peb1B | lo | PEP1B, component of Uptake system for glutamate and aspartate (characterized) | 33% | 81% | 125.2 | Basic amino acid uptake transporter, BgtAB | 96% | 929.1 |
| L-glutamate catabolism | peb1B | lo | PEP1B, component of Uptake system for glutamate and aspartate (characterized) | 33% | 81% | 125.2 | Basic amino acid uptake transporter, BgtAB | 96% | 929.1 |
| L-arginine catabolism | artJ | lo | Putative ABC transporter arginine-binding protein 2 (characterized) | 34% | 98% | 124.8 | Basic amino acid uptake transporter, BgtAB | 96% | 929.1 |
| L-arginine catabolism | artQ | lo | Probable permease 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% | 92% | 123.6 | Basic amino acid uptake transporter, BgtAB | 96% | 929.1 |
| L-asparagine catabolism | natH | lo | Amino acid ABC transporter, permease protein, 3-TM region, His/Glu/Gln/Arg/opine (characterized, see rationale) | 35% | 60% | 123.6 | Basic amino acid uptake transporter, BgtAB | 96% | 929.1 |
| L-aspartate catabolism | natH | lo | Amino acid ABC transporter, permease protein, 3-TM region, His/Glu/Gln/Arg/opine (characterized, see rationale) | 35% | 60% | 123.6 | Basic amino acid uptake transporter, BgtAB | 96% | 929.1 |
| L-histidine catabolism | hisQ | lo | Probable permease 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% | 92% | 123.6 | Basic amino acid uptake transporter, BgtAB | 96% | 929.1 |
| L-histidine catabolism | BPHYT_RS24010 | lo | Polar amino acid ABC transporter, inner membrane subunit (characterized, see rationale) | 31% | 90% | 122.9 | Basic amino acid uptake transporter, BgtAB | 96% | 929.1 |
| L-histidine catabolism | aapM | lo | ABC transporter for L-Glutamine, L-Histidine, and other L-amino acids, permease component 2 (characterized) | 34% | 57% | 119.8 | Basic amino acid uptake transporter, BgtAB | 96% | 929.1 |
| L-glutamate catabolism | gluC | lo | GluC aka CGL1952, component of Glutamate porter (characterized) | 36% | 93% | 117.9 | Basic amino acid uptake transporter, BgtAB | 96% | 929.1 |
| D-alanine catabolism | Pf6N2E2_5404 | lo | ABC transporter for D-Alanine, permease component 1 (characterized) | 35% | 55% | 115.9 | Basic amino acid uptake transporter, BgtAB | 96% | 929.1 |
| L-asparagine catabolism | aapM | lo | AapM, 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% | 50% | 114.8 | Basic amino acid uptake transporter, BgtAB | 96% | 929.1 |
| L-aspartate catabolism | aapM | lo | AapM, 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% | 50% | 114.8 | Basic amino acid uptake transporter, BgtAB | 96% | 929.1 |
| L-glutamate catabolism | aapM | lo | AapM, 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% | 50% | 114.8 | Basic amino acid uptake transporter, BgtAB | 96% | 929.1 |
| L-leucine catabolism | aapM | lo | AapM, 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% | 50% | 114.8 | Basic amino acid uptake transporter, BgtAB | 96% | 929.1 |
| L-proline catabolism | aapM | lo | AapM, 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% | 50% | 114.8 | Basic amino acid uptake transporter, BgtAB | 96% | 929.1 |
| L-glutamate catabolism | gltJ | lo | Amino acid ABC transporter membrane protein, component of Amino acid transporter, AatJMQP. Probably transports L-glutamic acid, D-glutamine acid, L-glutamine and N-acetyl L-glutamic acid (Johnson et al. 2008). Very similar to 3.A.1.3.19 of P. putida (characterized) | 32% | 86% | 113.6 | Basic amino acid uptake transporter, BgtAB | 96% | 929.1 |
| L-asparagine catabolism | peb1D | lo | Amino acid ABC transporter, permease protein PEB1 (characterized, see rationale) | 32% | 90% | 109.8 | Basic amino acid uptake transporter, BgtAB | 96% | 929.1 |
| L-aspartate catabolism | peb1D | lo | Amino acid ABC transporter, permease protein PEB1 (characterized, see rationale) | 32% | 90% | 109.8 | Basic amino acid uptake transporter, BgtAB | 96% | 929.1 |
| L-asparagine catabolism | aatQ | lo | PP1070, component of Acidic amino acid uptake porter, AatJMQP (characterized) | 32% | 82% | 107.1 | Basic amino acid uptake transporter, BgtAB | 96% | 929.1 |
| L-aspartate catabolism | aatQ | lo | PP1070, component of Acidic amino acid uptake porter, AatJMQP (characterized) | 32% | 82% | 107.1 | Basic amino acid uptake transporter, BgtAB | 96% | 929.1 |
| L-histidine catabolism | aapQ | lo | ABC transporter for L-Glutamine, L-Histidine, and other L-amino acids, permease component 1 (characterized) | 34% | 52% | 106.3 | Basic amino acid uptake transporter, BgtAB | 96% | 929.1 |
| L-citrulline catabolism | PS417_17600 | lo | ABC transporter permease; SubName: Full=Amino acid ABC transporter permease; SubName: Full=Histidine ABC transporter permease HisM; SubName: Full=Histidine transport system permease protein; SubName: Full=Histidine/lysine/arginine/ornithine ABC transporter permease HisM (characterized, see rationale) | 32% | 91% | 100.5 | Basic amino acid uptake transporter, BgtAB | 96% | 929.1 |
| D-alanine catabolism | Pf6N2E2_5403 | lo | ABC transporter for D-Alanine, permease component 2 (characterized) | 33% | 55% | 100.1 | Basic amino acid uptake transporter, BgtAB | 96% | 929.1 |
| L-citrulline catabolism | AO353_03050 | lo | ABC transporter for L-Arginine and L-Citrulline, permease component 2 (characterized) | 31% | 92% | 99.8 | Basic amino acid uptake transporter, BgtAB | 96% | 929.1 |
| L-lysine catabolism | argT | lo | ABC transporter for L-Lysine, periplasmic substrate-binding component (characterized) | 31% | 91% | 97.8 | Basic amino acid uptake transporter, BgtAB | 96% | 929.1 |
| L-glutamate catabolism | gluD | lo | GluD aka CGL1953, component of Glutamate porter (characterized) | 32% | 75% | 95.1 | Basic amino acid uptake transporter, BgtAB | 96% | 929.1 |
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