| Pathway | Step | Score | Similar to | Id. | Cov. | Bits | Other hit | Other id. | Other bits |
|---|
| L-glutamate catabolism | gltL | hi | GluA aka CGL1950, component of Glutamate porter (characterized) | 69% | 100% | 331.3 | Glutamine transport ATP-binding protein GlnQ; EC 7.4.2.- | 57% | 277.7 |
| L-asparagine catabolism | bgtA | med | ATPase (characterized, see rationale) | 63% | 91% | 285.4 | GluA aka CGL1950, component of Glutamate porter | 69% | 331.3 |
| L-aspartate catabolism | bgtA | med | ATPase (characterized, see rationale) | 63% | 91% | 285.4 | GluA aka CGL1950, component of Glutamate porter | 69% | 331.3 |
| L-asparagine catabolism | aatP | med | Glutamate/aspartate transport ATP-binding protein GltL aka B0652, component of Glutamate/aspartate porter (characterized) | 57% | 99% | 276.2 | GluA aka CGL1950, component of Glutamate porter | 69% | 331.3 |
| L-aspartate catabolism | aatP | med | Glutamate/aspartate transport ATP-binding protein GltL aka B0652, component of Glutamate/aspartate porter (characterized) | 57% | 99% | 276.2 | GluA aka CGL1950, component of Glutamate porter | 69% | 331.3 |
| L-lysine catabolism | hisP | med | Amino-acid ABC transporter, ATP-binding protein (characterized, see rationale) | 59% | 92% | 276.2 | GluA aka CGL1950, component of Glutamate porter | 69% | 331.3 |
| D-alanine catabolism | Pf6N2E2_5405 | med | ABC transporter for D-Alanine, ATPase component (characterized) | 56% | 94% | 258.5 | GluA aka CGL1950, component of Glutamate porter | 69% | 331.3 |
| L-asparagine catabolism | bztD | med | BztD, component of Glutamate/glutamine/aspartate/asparagine porter (characterized) | 55% | 92% | 258.1 | GluA aka CGL1950, component of Glutamate porter | 69% | 331.3 |
| L-aspartate catabolism | bztD | med | BztD, component of Glutamate/glutamine/aspartate/asparagine porter (characterized) | 55% | 92% | 258.1 | GluA aka CGL1950, component of Glutamate porter | 69% | 331.3 |
| L-histidine catabolism | aapP | med | ABC transporter for L-Glutamine, L-Histidine, and other L-amino acids, ATPase component (characterized) | 57% | 93% | 257.3 | GluA aka CGL1950, component of Glutamate porter | 69% | 331.3 |
| 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) | 57% | 93% | 255.4 | GluA aka CGL1950, component of Glutamate porter | 69% | 331.3 |
| 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) | 57% | 93% | 255.4 | GluA aka CGL1950, component of Glutamate porter | 69% | 331.3 |
| 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) | 57% | 93% | 255.4 | GluA aka CGL1950, component of Glutamate porter | 69% | 331.3 |
| 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) | 57% | 93% | 255.4 | GluA aka CGL1950, component of Glutamate porter | 69% | 331.3 |
| 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) | 57% | 93% | 255.4 | GluA aka CGL1950, component of Glutamate porter | 69% | 331.3 |
| L-arginine catabolism | artP | med | Arginine transport ATP-binding protein ArtM (characterized) | 54% | 100% | 255 | GluA aka CGL1950, component of Glutamate porter | 69% | 331.3 |
| 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) | 53% | 97% | 246.1 | GluA aka CGL1950, component of Glutamate porter | 69% | 331.3 |
| L-histidine catabolism | BPHYT_RS24015 | med | ABC transporter related (characterized, see rationale) | 50% | 94% | 244.2 | GluA aka CGL1950, component of Glutamate porter | 69% | 331.3 |
| 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% | 96% | 232.3 | GluA aka CGL1950, component of Glutamate porter | 69% | 331.3 |
| D-glucosamine (chitosamine) catabolism | AO353_21725 | med | ABC transporter for D-Glucosamine, putative ATPase component (characterized) | 50% | 93% | 228.4 | GluA aka CGL1950, component of Glutamate porter | 69% | 331.3 |
| L-asparagine catabolism | peb1C | med | PEB1C, component of Uptake system for glutamate and aspartate (characterized) | 49% | 100% | 226.5 | GluA aka CGL1950, component of Glutamate porter | 69% | 331.3 |
| L-aspartate catabolism | peb1C | med | PEB1C, component of Uptake system for glutamate and aspartate (characterized) | 49% | 100% | 226.5 | GluA aka CGL1950, component of Glutamate porter | 69% | 331.3 |
| 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) | 50% | 91% | 224.9 | GluA aka CGL1950, component of Glutamate porter | 69% | 331.3 |
| L-histidine catabolism | bgtA | med | BgtA aka SLR1735, component of Arginine/lysine/histidine/glutamine porter (characterized) | 52% | 94% | 224.2 | GluA aka CGL1950, component of Glutamate porter | 69% | 331.3 |
| L-citrulline catabolism | AO353_03040 | med | ABC transporter for L-Arginine and L-Citrulline, ATPase component (characterized) | 45% | 99% | 214.9 | GluA aka CGL1950, component of Glutamate porter | 69% | 331.3 |
| L-tryptophan catabolism | ecfA2 | med | Energy-coupling factor transporter ATP-binding protein EcfA2; Short=ECF transporter A component EcfA2; EC 7.-.-.- (characterized, see rationale) | 41% | 77% | 147.5 | GluA aka CGL1950, component of Glutamate porter | 69% | 331.3 |
| L-histidine catabolism | PA5503 | lo | Methionine import ATP-binding protein MetN 2, component of L-Histidine uptake porter, MetIQN (characterized) | 47% | 67% | 183.7 | GluA aka CGL1950, component of Glutamate porter | 69% | 331.3 |
| L-proline catabolism | opuBA | lo | BilEA aka OpuBA protein, component of A proline/glycine betaine uptake system. Also reported to be a bile exclusion system that exports oxgall and other bile compounds, BilEA/EB or OpuBA/BB (required for normal virulence) (characterized) | 38% | 73% | 159.5 | GluA aka CGL1950, component of Glutamate porter | 69% | 331.3 |
| putrescine catabolism | potA | lo | PotG aka B0855, component of Putrescine porter (characterized) | 37% | 62% | 153.3 | GluA aka CGL1950, component of Glutamate porter | 69% | 331.3 |
| D-mannitol catabolism | mtlK | lo | SmoK aka POLK, component of Hexitol (glucitol; mannitol) porter (characterized) | 38% | 67% | 150.2 | GluA aka CGL1950, component of Glutamate porter | 69% | 331.3 |
| L-fucose catabolism | SM_b21106 | lo | ABC transporter for L-Fucose, ATPase component (characterized) | 37% | 64% | 149.8 | GluA aka CGL1950, component of Glutamate porter | 69% | 331.3 |
| D-cellobiose catabolism | SMc04256 | lo | ABC transporter for D-Cellobiose and D-Salicin, ATPase component (characterized) | 36% | 65% | 133.7 | GluA aka CGL1950, component of Glutamate porter | 69% | 331.3 |
| L-isoleucine catabolism | livG | lo | ABC transporter ATP-binding protein (characterized, see rationale) | 31% | 90% | 121.7 | GluA aka CGL1950, component of Glutamate porter | 69% | 331.3 |
| L-leucine catabolism | livG | lo | ABC transporter ATP-binding protein (characterized, see rationale) | 31% | 90% | 121.7 | GluA aka CGL1950, component of Glutamate porter | 69% | 331.3 |
| L-phenylalanine catabolism | livG | lo | ABC transporter ATP-binding protein (characterized, see rationale) | 31% | 90% | 121.7 | GluA aka CGL1950, component of Glutamate porter | 69% | 331.3 |
| L-proline catabolism | HSERO_RS00895 | lo | ABC transporter ATP-binding protein (characterized, see rationale) | 31% | 90% | 121.7 | GluA aka CGL1950, component of Glutamate porter | 69% | 331.3 |
| L-serine catabolism | Ac3H11_1693 | lo | ABC transporter ATP-binding protein (characterized, see rationale) | 31% | 90% | 121.7 | GluA aka CGL1950, component of Glutamate porter | 69% | 331.3 |
| L-tyrosine catabolism | Ac3H11_1693 | lo | ABC transporter ATP-binding protein (characterized, see rationale) | 31% | 90% | 121.7 | GluA aka CGL1950, component of Glutamate porter | 69% | 331.3 |
| D-fructose catabolism | frcA | lo | Fructose import ATP-binding protein FrcA; EC 7.5.2.- (characterized) | 34% | 89% | 118.2 | GluA aka CGL1950, component of Glutamate porter | 69% | 331.3 |
| D-mannose catabolism | frcA | lo | Fructose import ATP-binding protein FrcA; EC 7.5.2.- (characterized) | 34% | 89% | 118.2 | GluA aka CGL1950, component of Glutamate porter | 69% | 331.3 |
| D-ribose catabolism | frcA | lo | Fructose import ATP-binding protein FrcA; EC 7.5.2.- (characterized) | 34% | 89% | 118.2 | GluA aka CGL1950, component of Glutamate porter | 69% | 331.3 |
| sucrose catabolism | frcA | lo | Fructose import ATP-binding protein FrcA; EC 7.5.2.- (characterized) | 34% | 89% | 118.2 | GluA aka CGL1950, component of Glutamate porter | 69% | 331.3 |
| L-arabinose catabolism | xylGsa | lo | Xylose/arabinose import ATP-binding protein XylG; EC 7.5.2.13 (characterized, see rationale) | 32% | 89% | 111.7 | GluA aka CGL1950, component of Glutamate porter | 69% | 331.3 |
| L-alanine catabolism | braG | lo | NatE aka LivF aka SLR1881, component of Leucine/proline/alanine/serine/glycine (and possibly histidine) porter, NatABCDE (characterized) | 31% | 88% | 102.4 | GluA aka CGL1950, component of Glutamate porter | 69% | 331.3 |
| L-histidine catabolism | natE | lo | NatE aka LivF aka SLR1881, component of Leucine/proline/alanine/serine/glycine (and possibly histidine) porter, NatABCDE (characterized) | 31% | 88% | 102.4 | GluA aka CGL1950, component of Glutamate porter | 69% | 331.3 |
| L-leucine catabolism | natE | lo | NatE aka LivF aka SLR1881, component of Leucine/proline/alanine/serine/glycine (and possibly histidine) porter, NatABCDE (characterized) | 31% | 88% | 102.4 | GluA aka CGL1950, component of Glutamate porter | 69% | 331.3 |
| L-proline catabolism | natE | lo | NatE aka LivF aka SLR1881, component of Leucine/proline/alanine/serine/glycine (and possibly histidine) porter, NatABCDE (characterized) | 31% | 88% | 102.4 | GluA aka CGL1950, component of Glutamate porter | 69% | 331.3 |
| L-serine catabolism | braG | lo | NatE aka LivF aka SLR1881, component of Leucine/proline/alanine/serine/glycine (and possibly histidine) porter, NatABCDE (characterized) | 31% | 88% | 102.4 | GluA aka CGL1950, component of Glutamate porter | 69% | 331.3 |
| L-threonine catabolism | braG | lo | NatE aka LivF aka SLR1881, component of Leucine/proline/alanine/serine/glycine (and possibly histidine) porter, NatABCDE (characterized) | 31% | 88% | 102.4 | GluA aka CGL1950, component of Glutamate porter | 69% | 331.3 |
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