| Pathway | Step | Score | Similar to | Id. | Cov. | Bits | Other hit | Other id. | Other bits |
|---|
| L-asparagine catabolism | bztD | med | BztD, component of Glutamate/glutamine/aspartate/asparagine porter (characterized) | 51% | 94% | 235 | GluA aka CGL1950, component of Glutamate porter | 50% | 230.7 |
| L-aspartate catabolism | bztD | med | BztD, component of Glutamate/glutamine/aspartate/asparagine porter (characterized) | 51% | 94% | 235 | GluA aka CGL1950, component of Glutamate porter | 50% | 230.7 |
| L-glutamate catabolism | gltL | med | BztD, component of Glutamate/glutamine/aspartate/asparagine porter (characterized) | 51% | 94% | 235 | Glutamine transport ATP-binding protein GlnQ; EC 7.4.2.- | 50% | 228.4 |
| L-histidine catabolism | aapP | med | ABC transporter for L-Glutamine, L-Histidine, and other L-amino acids, ATPase component (characterized) | 48% | 100% | 230.7 | BztD, component of Glutamate/glutamine/aspartate/asparagine porter | 51% | 233.0 |
| L-asparagine catabolism | aatP | med | Glutamate/aspartate transport ATP-binding protein GltL aka B0652, component of Glutamate/aspartate porter (characterized) | 50% | 100% | 229.2 | BztD, component of Glutamate/glutamine/aspartate/asparagine porter | 51% | 233.0 |
| L-aspartate catabolism | aatP | med | Glutamate/aspartate transport ATP-binding protein GltL aka B0652, component of Glutamate/aspartate porter (characterized) | 50% | 100% | 229.2 | BztD, component of Glutamate/glutamine/aspartate/asparagine porter | 51% | 233.0 |
| L-asparagine catabolism | aapP | med | 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) | 50% | 95% | 228 | BztD, component of Glutamate/glutamine/aspartate/asparagine porter | 51% | 233.0 |
| L-aspartate catabolism | aapP | med | 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) | 50% | 95% | 228 | BztD, component of Glutamate/glutamine/aspartate/asparagine porter | 51% | 233.0 |
| L-glutamate catabolism | aapP | med | 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) | 50% | 95% | 228 | BztD, component of Glutamate/glutamine/aspartate/asparagine porter | 51% | 233.0 |
| L-leucine catabolism | aapP | med | 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) | 50% | 95% | 228 | BztD, component of Glutamate/glutamine/aspartate/asparagine porter | 51% | 233.0 |
| L-proline catabolism | aapP | med | 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) | 50% | 95% | 228 | BztD, component of Glutamate/glutamine/aspartate/asparagine porter | 51% | 233.0 |
| D-alanine catabolism | Pf6N2E2_5405 | med | ABC transporter for D-Alanine, ATPase component (characterized) | 51% | 95% | 224.9 | BztD, component of Glutamate/glutamine/aspartate/asparagine porter | 51% | 233.0 |
| L-lysine catabolism | hisP | med | Amino-acid ABC transporter, ATP-binding protein (characterized, see rationale) | 50% | 93% | 223.8 | BztD, component of Glutamate/glutamine/aspartate/asparagine porter | 51% | 233.0 |
| L-asparagine catabolism | glnQ | med | 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) | 49% | 96% | 222.6 | BztD, component of Glutamate/glutamine/aspartate/asparagine porter | 51% | 233.0 |
| L-arginine catabolism | artP | med | Arginine transport ATP-binding protein ArtM (characterized) | 47% | 99% | 218.4 | BztD, component of Glutamate/glutamine/aspartate/asparagine porter | 51% | 233.0 |
| L-histidine catabolism | bgtA | med | BgtA aka SLR1735, component of Arginine/lysine/histidine/glutamine porter (characterized) | 50% | 96% | 217.2 | BztD, component of Glutamate/glutamine/aspartate/asparagine porter | 51% | 233.0 |
| D-glucosamine (chitosamine) catabolism | AO353_21725 | med | ABC transporter for D-glucosamine, ATPase component (characterized) | 46% | 98% | 214.2 | BztD, component of Glutamate/glutamine/aspartate/asparagine porter | 51% | 233.0 |
| L-histidine catabolism | BPHYT_RS24015 | med | ABC transporter related (characterized, see rationale) | 47% | 97% | 212.6 | BztD, component of Glutamate/glutamine/aspartate/asparagine porter | 51% | 233.0 |
| L-citrulline catabolism | PS417_17605 | med | 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) | 48% | 89% | 208.8 | BztD, component of Glutamate/glutamine/aspartate/asparagine porter | 51% | 233.0 |
| L-asparagine catabolism | bgtA | med | ATPase (characterized, see rationale) | 44% | 98% | 208 | BztD, component of Glutamate/glutamine/aspartate/asparagine porter | 51% | 233.0 |
| L-aspartate catabolism | bgtA | med | ATPase (characterized, see rationale) | 44% | 98% | 208 | BztD, component of Glutamate/glutamine/aspartate/asparagine porter | 51% | 233.0 |
| L-asparagine catabolism | peb1C | med | PEB1C, component of Uptake system for glutamate and aspartate (characterized) | 48% | 98% | 206.1 | BztD, component of Glutamate/glutamine/aspartate/asparagine porter | 51% | 233.0 |
| L-aspartate catabolism | peb1C | med | PEB1C, component of Uptake system for glutamate and aspartate (characterized) | 48% | 98% | 206.1 | BztD, component of Glutamate/glutamine/aspartate/asparagine porter | 51% | 233.0 |
| L-histidine catabolism | hisP | med | 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) | 48% | 97% | 204.9 | BztD, component of Glutamate/glutamine/aspartate/asparagine porter | 51% | 233.0 |
| L-histidine catabolism | Ac3H11_2560 | med | ABC transporter for L-Histidine, ATPase component (characterized) | 40% | 72% | 127.5 | BztD, component of Glutamate/glutamine/aspartate/asparagine porter | 51% | 233.0 |
| L-arginine catabolism | artQ | med | ABC transporter for L-Arginine, permease component 2 (characterized) | 34% | 94% | 115.2 | | | |
| L-lysine catabolism | hisM | med | ABC transporter for L-Lysine, permease component 2 (characterized) | 31% | 97% | 114.8 | | | |
| L-citrulline catabolism | PS417_17595 | med | ABC transporter permease subunit; SubName: Full=Amino acid ABC transporter permease; SubName: Full=Histidine transport system permease protein (characterized, see rationale) | 33% | 91% | 109.8 | | | |
| L-lysine catabolism | hisQ | med | ABC transporter for L-Lysine, permease component 1 (characterized) | 31% | 91% | 108.6 | | | |
| D-glucosamine (chitosamine) catabolism | AO353_21715 | med | ABC transporter for D-Glucosamine, permease component 2 (characterized) | 31% | 89% | 105.5 | | | |
| D-glucosamine (chitosamine) catabolism | AO353_21720 | med | ABC transporter for D-glucosamine, permease component 2 (characterized) | 33% | 87% | 99.8 | | | |
| L-arginine catabolism | artM | med | Arginine ABC transporter permease protein ArtM (characterized) | 31% | 99% | 97.8 | | | |
| L-glutamate catabolism | gluC | med | GluC aka CGL1952, component of Glutamate porter (characterized) | 30% | 89% | 91.3 | | | |
| L-isoleucine catabolism | livG | lo | ABC transporter ATP-binding protein-branched chain amino acid transport, component of The branched chain hydrophobic amino acid transporter, LivJFGHM (characterized) | 32% | 98% | 128.3 | BztD, component of Glutamate/glutamine/aspartate/asparagine porter | 51% | 233.0 |
| L-leucine catabolism | livG | lo | ABC transporter ATP-binding protein-branched chain amino acid transport, component of The branched chain hydrophobic amino acid transporter, LivJFGHM (characterized) | 32% | 98% | 128.3 | BztD, component of Glutamate/glutamine/aspartate/asparagine porter | 51% | 233.0 |
| L-valine catabolism | livG | lo | ABC transporter ATP-binding protein-branched chain amino acid transport, component of The branched chain hydrophobic amino acid transporter, LivJFGHM (characterized) | 32% | 98% | 128.3 | BztD, component of Glutamate/glutamine/aspartate/asparagine porter | 51% | 233.0 |
| L-alanine catabolism | braF | lo | High-affinity branched-chain amino acid transport ATP-binding protein BraF, component of Branched chain amino acid uptake transporter. Transports alanine (characterized) | 30% | 96% | 125.2 | BztD, component of Glutamate/glutamine/aspartate/asparagine porter | 51% | 233.0 |
| L-serine catabolism | braF | lo | High-affinity branched-chain amino acid transport ATP-binding protein BraF, component of Branched chain amino acid uptake transporter. Transports alanine (characterized) | 30% | 96% | 125.2 | BztD, component of Glutamate/glutamine/aspartate/asparagine porter | 51% | 233.0 |
| L-threonine catabolism | braF | lo | High-affinity branched-chain amino acid transport ATP-binding protein BraF, component of Branched chain amino acid uptake transporter. Transports alanine (characterized) | 30% | 96% | 125.2 | BztD, component of Glutamate/glutamine/aspartate/asparagine porter | 51% | 233.0 |
| 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) | 30% | 96% | 120.9 | BztD, component of Glutamate/glutamine/aspartate/asparagine porter | 51% | 233.0 |
| D-fructose catabolism | frcA | lo | Fructose import ATP-binding protein FrcA; EC 7.5.2.- (characterized) | 31% | 83% | 113.2 | BztD, component of Glutamate/glutamine/aspartate/asparagine porter | 51% | 233.0 |
| D-mannose catabolism | frcA | lo | Fructose import ATP-binding protein FrcA; EC 7.5.2.- (characterized) | 31% | 83% | 113.2 | BztD, component of Glutamate/glutamine/aspartate/asparagine porter | 51% | 233.0 |
| D-ribose catabolism | frcA | lo | Fructose import ATP-binding protein FrcA; EC 7.5.2.- (characterized) | 31% | 83% | 113.2 | BztD, component of Glutamate/glutamine/aspartate/asparagine porter | 51% | 233.0 |
| sucrose catabolism | frcA | lo | Fructose import ATP-binding protein FrcA; EC 7.5.2.- (characterized) | 31% | 83% | 113.2 | BztD, component of Glutamate/glutamine/aspartate/asparagine porter | 51% | 233.0 |
| L-proline catabolism | HSERO_RS00900 | lo | ABC-type branched-chain amino acid transport system, ATPase component protein (characterized, see rationale) | 32% | 89% | 109.4 | BztD, component of Glutamate/glutamine/aspartate/asparagine porter | 51% | 233.0 |
| L-alanine catabolism | braG | lo | NatE, component of The neutral amino acid permease, N-1 (transports pro, phe, leu, gly, ala, ser, gln and his, but gln and his are not transported via NatB) (characterized) | 30% | 85% | 104.8 | BztD, component of Glutamate/glutamine/aspartate/asparagine porter | 51% | 233.0 |
| L-isoleucine catabolism | natE | lo | NatE, component of The neutral amino acid permease, N-1 (transports pro, phe, leu, gly, ala, ser, gln and his, but gln and his are not transported via NatB) (characterized) | 30% | 85% | 104.8 | BztD, component of Glutamate/glutamine/aspartate/asparagine porter | 51% | 233.0 |
| L-leucine catabolism | natE | lo | NatE, component of The neutral amino acid permease, N-1 (transports pro, phe, leu, gly, ala, ser, gln and his, but gln and his are not transported via NatB) (characterized) | 30% | 85% | 104.8 | BztD, component of Glutamate/glutamine/aspartate/asparagine porter | 51% | 233.0 |
| L-proline catabolism | natE | lo | NatE, component of The neutral amino acid permease, N-1 (transports pro, phe, leu, gly, ala, ser, gln and his, but gln and his are not transported via NatB) (characterized) | 30% | 85% | 104.8 | BztD, component of Glutamate/glutamine/aspartate/asparagine porter | 51% | 233.0 |
| L-serine catabolism | braG | lo | NatE, component of The neutral amino acid permease, N-1 (transports pro, phe, leu, gly, ala, ser, gln and his, but gln and his are not transported via NatB) (characterized) | 30% | 85% | 104.8 | BztD, component of Glutamate/glutamine/aspartate/asparagine porter | 51% | 233.0 |
| L-threonine catabolism | braG | lo | NatE, component of The neutral amino acid permease, N-1 (transports pro, phe, leu, gly, ala, ser, gln and his, but gln and his are not transported via NatB) (characterized) | 30% | 85% | 104.8 | BztD, component of Glutamate/glutamine/aspartate/asparagine porter | 51% | 233.0 |
| L-valine catabolism | natE | lo | NatE, component of The neutral amino acid permease, N-1 (transports pro, phe, leu, gly, ala, ser, gln and his, but gln and his are not transported via NatB) (characterized) | 30% | 85% | 104.8 | BztD, component of Glutamate/glutamine/aspartate/asparagine porter | 51% | 233.0 |
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