Pathway | Step | Score | Similar to | Id. | Cov. | Bits | Other hit | Other id. | Other bits |
L-histidine catabolism | Ac3H11_2554 | med | ABC transporter for L-Histidine, permease component 1 (characterized) | 48% | 96% | 197.2 | BgtB aka GLNH aka SLL1270, component of Arginine/lysine/histidine/glutamine porter | 50% | 195.7 |
L-lysine catabolism | hisM | lo | ABC transporter for L-Lysine, permease component 2 (characterized) | 36% | 97% | 153.7 | ABC transporter for L-Histidine, permease component 1 | 48% | 197.2 |
L-asparagine catabolism | peb1B | lo | PEP1B, component of Uptake system for glutamate and aspartate (characterized) | 39% | 81% | 148.7 | ABC transporter for L-Histidine, permease component 1 | 48% | 197.2 |
L-aspartate catabolism | peb1B | lo | PEP1B, component of Uptake system for glutamate and aspartate (characterized) | 39% | 81% | 148.7 | ABC transporter for L-Histidine, permease component 1 | 48% | 197.2 |
L-glutamate catabolism | peb1B | lo | PEP1B, component of Uptake system for glutamate and aspartate (characterized) | 39% | 81% | 148.7 | ABC transporter for L-Histidine, permease component 1 | 48% | 197.2 |
D-glucosamine (chitosamine) catabolism | AO353_21715 | lo | ABC transporter for D-Glucosamine Hydrochloride, permease component 2 (characterized) | 35% | 97% | 144.8 | ABC transporter for L-Histidine, permease component 1 | 48% | 197.2 |
L-arginine catabolism | artM | lo | L-Arginine ABC transporter, permease protein AotM (characterized) | 35% | 95% | 144.4 | ABC transporter for L-Histidine, permease component 1 | 48% | 197.2 |
L-citrulline catabolism | AO353_03045 | lo | ABC transporter for L-Arginine and L-Citrulline, permease component 1 (characterized) | 34% | 95% | 140.6 | ABC transporter for L-Histidine, permease component 1 | 48% | 197.2 |
L-asparagine catabolism | natG | lo | NatG, component of Acidic and neutral amino acid uptake transporter NatFGH/BgtA. BgtA is shared with BgtAB (characterized) | 35% | 74% | 137.9 | ABC transporter for L-Histidine, permease component 1 | 48% | 197.2 |
L-aspartate catabolism | natG | lo | NatG, component of Acidic and neutral amino acid uptake transporter NatFGH/BgtA. BgtA is shared with BgtAB (characterized) | 35% | 74% | 137.9 | ABC transporter for L-Histidine, permease component 1 | 48% | 197.2 |
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) | 33% | 96% | 134.4 | ABC transporter for L-Histidine, permease component 1 | 48% | 197.2 |
L-lysine catabolism | hisQ | lo | ABC transporter for L-Lysine, permease component 1 (characterized) | 35% | 88% | 134.4 | ABC transporter for L-Histidine, permease component 1 | 48% | 197.2 |
L-histidine catabolism | BPHYT_RS24005 | lo | Polar amino acid ABC transporter, inner membrane subunit; Flags: Precursor (characterized, see rationale) | 34% | 90% | 132.9 | ABC transporter for L-Histidine, permease component 1 | 48% | 197.2 |
D-glucosamine (chitosamine) catabolism | AO353_21720 | lo | ABC transporter for D-glucosamine, permease component 2 (characterized) | 36% | 90% | 132.5 | ABC transporter for L-Histidine, permease component 1 | 48% | 197.2 |
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% | 93% | 129 | ABC transporter for L-Histidine, permease component 1 | 48% | 197.2 |
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) | 34% | 88% | 129 | ABC transporter for L-Histidine, permease component 1 | 48% | 197.2 |
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% | 93% | 129 | ABC transporter for L-Histidine, permease component 1 | 48% | 197.2 |
L-asparagine catabolism | aatQ | lo | PP1070, component of Acidic amino acid uptake porter, AatJMQP (characterized) | 35% | 88% | 127.1 | ABC transporter for L-Histidine, permease component 1 | 48% | 197.2 |
L-aspartate catabolism | aatQ | lo | PP1070, component of Acidic amino acid uptake porter, AatJMQP (characterized) | 35% | 88% | 127.1 | ABC transporter for L-Histidine, permease component 1 | 48% | 197.2 |
L-asparagine catabolism | aatM | lo | PP1069, component of Acidic amino acid uptake porter, AatJMQP (characterized) | 32% | 99% | 126.7 | ABC transporter for L-Histidine, permease component 1 | 48% | 197.2 |
L-aspartate catabolism | aatM | lo | PP1069, component of Acidic amino acid uptake porter, AatJMQP (characterized) | 32% | 99% | 126.7 | ABC transporter for L-Histidine, permease component 1 | 48% | 197.2 |
L-glutamate catabolism | gltK | lo | PP1069, component of Acidic amino acid uptake porter, AatJMQP (characterized) | 32% | 99% | 126.7 | ABC transporter for L-Histidine, permease component 1 | 48% | 197.2 |
L-histidine catabolism | aapM | lo | ABC transporter for L-Glutamine, L-Histidine, and other L-amino acids, permease component 2 (characterized) | 33% | 57% | 125.6 | ABC transporter for L-Histidine, permease component 1 | 48% | 197.2 |
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) | 32% | 53% | 122.9 | ABC transporter for L-Histidine, permease component 1 | 48% | 197.2 |
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) | 32% | 53% | 122.9 | ABC transporter for L-Histidine, permease component 1 | 48% | 197.2 |
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) | 32% | 53% | 122.9 | ABC transporter for L-Histidine, permease component 1 | 48% | 197.2 |
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) | 32% | 53% | 122.9 | ABC transporter for L-Histidine, permease component 1 | 48% | 197.2 |
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) | 32% | 53% | 122.9 | ABC transporter for L-Histidine, permease component 1 | 48% | 197.2 |
L-histidine catabolism | BPHYT_RS24010 | lo | Polar amino acid ABC transporter, inner membrane subunit (characterized, see rationale) | 30% | 90% | 120.2 | ABC transporter for L-Histidine, permease component 1 | 48% | 197.2 |
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) | 33% | 95% | 117.9 | ABC transporter for L-Histidine, permease component 1 | 48% | 197.2 |
L-glutamate catabolism | gluD | lo | GluD aka CGL1953, component of Glutamate porter (characterized) | 32% | 76% | 113.6 | ABC transporter for L-Histidine, permease component 1 | 48% | 197.2 |
D-alanine catabolism | Pf6N2E2_5404 | lo | ABC transporter for D-Alanine, permease component 1 (characterized) | 31% | 56% | 111.7 | ABC transporter for L-Histidine, permease component 1 | 48% | 197.2 |
L-glutamate catabolism | gluC | lo | GluC aka CGL1952, component of Glutamate porter (characterized) | 33% | 91% | 110.9 | ABC transporter for L-Histidine, permease component 1 | 48% | 197.2 |
L-asparagine catabolism | natH | lo | NatH, component of Acidic and neutral amino acid uptake transporter NatFGH/BgtA. BgtA is shared with BgtAB (characterized) | 30% | 60% | 110.5 | ABC transporter for L-Histidine, permease component 1 | 48% | 197.2 |
L-aspartate catabolism | natH | lo | NatH, component of Acidic and neutral amino acid uptake transporter NatFGH/BgtA. BgtA is shared with BgtAB (characterized) | 30% | 60% | 110.5 | ABC transporter for L-Histidine, permease component 1 | 48% | 197.2 |
L-asparagine catabolism | peb1D | lo | Amino acid ABC transporter, permease protein PEB1 (characterized, see rationale) | 30% | 95% | 102.4 | ABC transporter for L-Histidine, permease component 1 | 48% | 197.2 |
L-aspartate catabolism | peb1D | lo | Amino acid ABC transporter, permease protein PEB1 (characterized, see rationale) | 30% | 95% | 102.4 | ABC transporter for L-Histidine, permease component 1 | 48% | 197.2 |
L-asparagine catabolism | bztB | lo | glutamate/glutamine/aspartate/asparagine transport system permease protein BztB (characterized) | 31% | 50% | 97.8 | ABC transporter for L-Histidine, permease component 1 | 48% | 197.2 |
L-aspartate catabolism | bztB | lo | glutamate/glutamine/aspartate/asparagine transport system permease protein BztB (characterized) | 31% | 50% | 97.8 | ABC transporter for L-Histidine, permease component 1 | 48% | 197.2 |
L-glutamate catabolism | bztB | lo | glutamate/glutamine/aspartate/asparagine transport system permease protein BztB (characterized) | 31% | 50% | 97.8 | ABC transporter for L-Histidine, permease component 1 | 48% | 197.2 |
L-asparagine catabolism | aapQ | lo | AapQ, 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) | 31% | 54% | 95.9 | ABC transporter for L-Histidine, permease component 1 | 48% | 197.2 |
L-aspartate catabolism | aapQ | lo | AapQ, 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) | 31% | 54% | 95.9 | ABC transporter for L-Histidine, permease component 1 | 48% | 197.2 |
L-glutamate catabolism | aapQ | lo | AapQ, 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) | 31% | 54% | 95.9 | ABC transporter for L-Histidine, permease component 1 | 48% | 197.2 |
L-histidine catabolism | aapQ | lo | AapQ, 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) | 31% | 54% | 95.9 | ABC transporter for L-Histidine, permease component 1 | 48% | 197.2 |
L-leucine catabolism | aapQ | lo | AapQ, 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) | 31% | 54% | 95.9 | ABC transporter for L-Histidine, permease component 1 | 48% | 197.2 |
L-proline catabolism | aapQ | lo | AapQ, 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) | 31% | 54% | 95.9 | ABC transporter for L-Histidine, permease component 1 | 48% | 197.2 |
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