| Pathway | Step | Score | Similar to | Id. | Cov. | Bits | Other hit | Other id. | Other bits |
|---|
| L-arginine catabolism | artP | 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) | 40% | 82% | 144.8 | Complete genome, strain BL23, component of Antimicrobial peptide exporter, ABC12 or YvoST | 49% | 211.8 |
| 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) | 40% | 82% | 144.8 | Complete genome, strain BL23, component of Antimicrobial peptide exporter, ABC12 or YvoST | 49% | 211.8 |
| L-lysine 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) | 40% | 82% | 144.8 | Complete genome, strain BL23, component of Antimicrobial peptide exporter, ABC12 or YvoST | 49% | 211.8 |
| D-glucosamine (chitosamine) catabolism | AO353_21725 | med | ABC transporter for D-glucosamine, ATPase component (characterized) | 41% | 77% | 135.2 | Complete genome, strain BL23, component of Antimicrobial peptide exporter, ABC12 or YvoST | 49% | 211.8 |
| L-asparagine catabolism | bztD | lo | BztD, component of Glutamate/glutamine/aspartate/asparagine porter (characterized) | 39% | 85% | 149.4 | Complete genome, strain BL23, component of Antimicrobial peptide exporter, ABC12 or YvoST | 49% | 211.8 |
| L-aspartate catabolism | bztD | lo | BztD, component of Glutamate/glutamine/aspartate/asparagine porter (characterized) | 39% | 85% | 149.4 | Complete genome, strain BL23, component of Antimicrobial peptide exporter, ABC12 or YvoST | 49% | 211.8 |
| L-glutamate catabolism | gltL | lo | BztD, component of Glutamate/glutamine/aspartate/asparagine porter (characterized) | 39% | 85% | 149.4 | Complete genome, strain BL23, component of Antimicrobial peptide exporter, ABC12 or YvoST | 49% | 211.8 |
| D-cellobiose catabolism | glcV | lo | monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) | 38% | 61% | 148.3 | Complete genome, strain BL23, component of Antimicrobial peptide exporter, ABC12 or YvoST | 49% | 211.8 |
| D-galactose catabolism | glcV | lo | monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) | 38% | 61% | 148.3 | Complete genome, strain BL23, component of Antimicrobial peptide exporter, ABC12 or YvoST | 49% | 211.8 |
| D-glucose catabolism | glcV | lo | monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) | 38% | 61% | 148.3 | Complete genome, strain BL23, component of Antimicrobial peptide exporter, ABC12 or YvoST | 49% | 211.8 |
| lactose catabolism | glcV | lo | monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) | 38% | 61% | 148.3 | Complete genome, strain BL23, component of Antimicrobial peptide exporter, ABC12 or YvoST | 49% | 211.8 |
| D-maltose catabolism | glcV | lo | monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) | 38% | 61% | 148.3 | Complete genome, strain BL23, component of Antimicrobial peptide exporter, ABC12 or YvoST | 49% | 211.8 |
| D-mannose catabolism | glcV | lo | monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) | 38% | 61% | 148.3 | Complete genome, strain BL23, component of Antimicrobial peptide exporter, ABC12 or YvoST | 49% | 211.8 |
| sucrose catabolism | glcV | lo | monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) | 38% | 61% | 148.3 | Complete genome, strain BL23, component of Antimicrobial peptide exporter, ABC12 or YvoST | 49% | 211.8 |
| trehalose catabolism | glcV | lo | monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) | 38% | 61% | 148.3 | Complete genome, strain BL23, component of Antimicrobial peptide exporter, ABC12 or YvoST | 49% | 211.8 |
| L-histidine catabolism | BPHYT_RS24015 | lo | ABC transporter related (characterized, see rationale) | 36% | 87% | 146.7 | Complete genome, strain BL23, component of Antimicrobial peptide exporter, ABC12 or YvoST | 49% | 211.8 |
| 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) | 39% | 84% | 142.5 | Complete genome, strain BL23, component of Antimicrobial peptide exporter, ABC12 or YvoST | 49% | 211.8 |
| 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) | 39% | 84% | 142.5 | Complete genome, strain BL23, component of Antimicrobial peptide exporter, ABC12 or YvoST | 49% | 211.8 |
| 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) | 39% | 84% | 142.5 | Complete genome, strain BL23, component of Antimicrobial peptide exporter, ABC12 or YvoST | 49% | 211.8 |
| L-histidine 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) | 39% | 84% | 142.5 | Complete genome, strain BL23, component of Antimicrobial peptide exporter, ABC12 or YvoST | 49% | 211.8 |
| 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) | 39% | 84% | 142.5 | Complete genome, strain BL23, component of Antimicrobial peptide exporter, ABC12 or YvoST | 49% | 211.8 |
| 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) | 39% | 84% | 142.5 | Complete genome, strain BL23, component of Antimicrobial peptide exporter, ABC12 or YvoST | 49% | 211.8 |
| L-histidine catabolism | bgtA | lo | BgtA aka SLR1735, component of Arginine/lysine/histidine/glutamine porter (characterized) | 38% | 87% | 142.1 | Complete genome, strain BL23, component of Antimicrobial peptide exporter, ABC12 or YvoST | 49% | 211.8 |
| D-sorbitol (glucitol) catabolism | mtlK | lo | ABC transporter for D-Sorbitol, ATPase component (characterized) | 38% | 60% | 139.8 | Complete genome, strain BL23, component of Antimicrobial peptide exporter, ABC12 or YvoST | 49% | 211.8 |
| L-asparagine catabolism | bgtA | lo | ATPase (characterized, see rationale) | 39% | 77% | 137.9 | Complete genome, strain BL23, component of Antimicrobial peptide exporter, ABC12 or YvoST | 49% | 211.8 |
| L-aspartate catabolism | bgtA | lo | ATPase (characterized, see rationale) | 39% | 77% | 137.9 | Complete genome, strain BL23, component of Antimicrobial peptide exporter, ABC12 or YvoST | 49% | 211.8 |
| D-cellobiose catabolism | gtsD | lo | Sugar ABC transporter ATP-binding protein (characterized, see rationale) | 34% | 61% | 134.8 | Complete genome, strain BL23, component of Antimicrobial peptide exporter, ABC12 or YvoST | 49% | 211.8 |
| D-glucose catabolism | gtsD | lo | Sugar ABC transporter ATP-binding protein (characterized, see rationale) | 34% | 61% | 134.8 | Complete genome, strain BL23, component of Antimicrobial peptide exporter, ABC12 or YvoST | 49% | 211.8 |
| lactose catabolism | gtsD | lo | Sugar ABC transporter ATP-binding protein (characterized, see rationale) | 34% | 61% | 134.8 | Complete genome, strain BL23, component of Antimicrobial peptide exporter, ABC12 or YvoST | 49% | 211.8 |
| D-maltose catabolism | gtsD | lo | Sugar ABC transporter ATP-binding protein (characterized, see rationale) | 34% | 61% | 134.8 | Complete genome, strain BL23, component of Antimicrobial peptide exporter, ABC12 or YvoST | 49% | 211.8 |
| sucrose catabolism | gtsD | lo | Sugar ABC transporter ATP-binding protein (characterized, see rationale) | 34% | 61% | 134.8 | Complete genome, strain BL23, component of Antimicrobial peptide exporter, ABC12 or YvoST | 49% | 211.8 |
| trehalose catabolism | gtsD | lo | Sugar ABC transporter ATP-binding protein (characterized, see rationale) | 34% | 61% | 134.8 | Complete genome, strain BL23, component of Antimicrobial peptide exporter, ABC12 or YvoST | 49% | 211.8 |
| L-citrulline catabolism | AO353_03040 | lo | ABC transporter for L-Arginine and L-Citrulline, ATPase component (characterized) | 35% | 89% | 134.4 | Complete genome, strain BL23, component of Antimicrobial peptide exporter, ABC12 or YvoST | 49% | 211.8 |
| L-histidine catabolism | Ac3H11_2560 | lo | ABC transporter for L-Histidine, ATPase component (characterized) | 36% | 83% | 132.9 | Complete genome, strain BL23, component of Antimicrobial peptide exporter, ABC12 or YvoST | 49% | 211.8 |
| D-mannitol catabolism | mtlK | lo | MtlK, component of The polyol (mannitol, glucitol (sorbitol), arabitol (arabinitol; lyxitol)) uptake porter, MtlEFGK (characterized) | 37% | 57% | 127.5 | Complete genome, strain BL23, component of Antimicrobial peptide exporter, ABC12 or YvoST | 49% | 211.8 |
| D-cellobiose catabolism | aglK' | lo | Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) | 37% | 57% | 127.1 | Complete genome, strain BL23, component of Antimicrobial peptide exporter, ABC12 or YvoST | 49% | 211.8 |
| D-glucose catabolism | aglK' | lo | Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) | 37% | 57% | 127.1 | Complete genome, strain BL23, component of Antimicrobial peptide exporter, ABC12 or YvoST | 49% | 211.8 |
| lactose catabolism | aglK' | lo | Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) | 37% | 57% | 127.1 | Complete genome, strain BL23, component of Antimicrobial peptide exporter, ABC12 or YvoST | 49% | 211.8 |
| D-maltose catabolism | aglK | lo | Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) | 37% | 57% | 127.1 | Complete genome, strain BL23, component of Antimicrobial peptide exporter, ABC12 or YvoST | 49% | 211.8 |
| D-maltose catabolism | aglK' | lo | Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) | 37% | 57% | 127.1 | Complete genome, strain BL23, component of Antimicrobial peptide exporter, ABC12 or YvoST | 49% | 211.8 |
| sucrose catabolism | aglK | lo | Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) | 37% | 57% | 127.1 | Complete genome, strain BL23, component of Antimicrobial peptide exporter, ABC12 or YvoST | 49% | 211.8 |
| sucrose catabolism | aglK' | lo | Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) | 37% | 57% | 127.1 | Complete genome, strain BL23, component of Antimicrobial peptide exporter, ABC12 or YvoST | 49% | 211.8 |
| trehalose catabolism | aglK | lo | Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) | 37% | 57% | 127.1 | Complete genome, strain BL23, component of Antimicrobial peptide exporter, ABC12 or YvoST | 49% | 211.8 |
| trehalose catabolism | aglK' | lo | Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) | 37% | 57% | 127.1 | Complete genome, strain BL23, component of Antimicrobial peptide exporter, ABC12 or YvoST | 49% | 211.8 |
| 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% | 72% | 114 | Complete genome, strain BL23, component of Antimicrobial peptide exporter, ABC12 or YvoST | 49% | 211.8 |
| L-isoleucine catabolism | livF | lo | ABC transporter ATP-binding protein-branched chain amino acid transport, component of The branched chain hydrophobic amino acid transporter, LivJFGHM (characterized) | 32% | 84% | 110.2 | Complete genome, strain BL23, component of Antimicrobial peptide exporter, ABC12 or YvoST | 49% | 211.8 |
| L-leucine catabolism | livF | lo | ABC transporter ATP-binding protein-branched chain amino acid transport, component of The branched chain hydrophobic amino acid transporter, LivJFGHM (characterized) | 32% | 84% | 110.2 | Complete genome, strain BL23, component of Antimicrobial peptide exporter, ABC12 or YvoST | 49% | 211.8 |
| L-valine catabolism | livF | lo | ABC transporter ATP-binding protein-branched chain amino acid transport, component of The branched chain hydrophobic amino acid transporter, LivJFGHM (characterized) | 32% | 84% | 110.2 | Complete genome, strain BL23, component of Antimicrobial peptide exporter, ABC12 or YvoST | 49% | 211.8 |
| glycerol catabolism | glpT | lo | GlpT, component of Glycerol uptake porter, GlpSTPQV (characterized) | 34% | 55% | 105.1 | Complete genome, strain BL23, component of Antimicrobial peptide exporter, ABC12 or YvoST | 49% | 211.8 |
| L-arginine catabolism | braG | lo | ATP-binding component of a broad range amino acid ABC transporter (characterized, see rationale) | 31% | 87% | 97.8 | Complete genome, strain BL23, component of Antimicrobial peptide exporter, ABC12 or YvoST | 49% | 211.8 |
| L-glutamate catabolism | braG | lo | ATP-binding component of a broad range amino acid ABC transporter (characterized, see rationale) | 31% | 87% | 97.8 | Complete genome, strain BL23, component of Antimicrobial peptide exporter, ABC12 or YvoST | 49% | 211.8 |
| L-histidine catabolism | braG | lo | ATP-binding component of a broad range amino acid ABC transporter (characterized, see rationale) | 31% | 87% | 97.8 | Complete genome, strain BL23, component of Antimicrobial peptide exporter, ABC12 or YvoST | 49% | 211.8 |
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