| Pathway | Step | Score | Similar to | Id. | Cov. | Bits | Other hit | Other id. | Other bits |
|---|
| 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) | 41% | 89% | 159.5 | Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD | 41% | 170.2 |
| L-glutamate catabolism | gltL | 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) | 41% | 89% | 159.5 | Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD | 41% | 170.2 |
| putrescine catabolism | potA | lo | spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31 (characterized) | 42% | 59% | 164.5 | Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD | 41% | 170.2 |
| D-maltose catabolism | thuK | lo | Trehalose/maltose import ATP-binding protein MalK; EC 7.5.2.1 (characterized) | 38% | 73% | 163.7 | Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD | 41% | 170.2 |
| trehalose catabolism | thuK | lo | Trehalose/maltose import ATP-binding protein MalK; EC 7.5.2.1 (characterized) | 38% | 73% | 163.7 | Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD | 41% | 170.2 |
| D-maltose catabolism | malK | lo | ABC-type maltose transporter (subunit 3/3) (EC 7.5.2.1) (characterized) | 40% | 60% | 160.2 | Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD | 41% | 170.2 |
| sucrose catabolism | thuK | lo | ABC transporter (characterized, see rationale) | 40% | 68% | 159.8 | Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD | 41% | 170.2 |
| D-sorbitol (glucitol) catabolism | mtlK | lo | ABC transporter for D-Sorbitol, ATPase component (characterized) | 36% | 72% | 156.4 | Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD | 41% | 170.2 |
| L-arabinose catabolism | araV | lo | AraV, component of Arabinose, fructose, xylose porter (characterized) | 38% | 68% | 152.9 | Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD | 41% | 170.2 |
| D-fructose catabolism | araV | lo | AraV, component of Arabinose, fructose, xylose porter (characterized) | 38% | 68% | 152.9 | Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD | 41% | 170.2 |
| 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) | 35% | 83% | 152.9 | Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD | 41% | 170.2 |
| sucrose catabolism | araV | lo | AraV, component of Arabinose, fructose, xylose porter (characterized) | 38% | 68% | 152.9 | Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD | 41% | 170.2 |
| D-xylose catabolism | araV | lo | AraV, component of Arabinose, fructose, xylose porter (characterized) | 38% | 68% | 152.9 | Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD | 41% | 170.2 |
| L-fucose catabolism | SM_b21106 | lo | ABC transporter for L-Fucose, ATPase component (characterized) | 37% | 67% | 152.1 | Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD | 41% | 170.2 |
| L-proline catabolism | proV | lo | glycine betaine/l-proline transport atp-binding protein prov (characterized) | 32% | 66% | 149.1 | Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD | 41% | 170.2 |
| xylitol catabolism | HSERO_RS17020 | lo | ABC-type sugar transport system, ATPase component protein (characterized, see rationale) | 39% | 55% | 147.1 | Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD | 41% | 170.2 |
| L-asparagine catabolism | aatP | lo | ABC transporter for L-Asparagine and possibly other L-amino acids, putative ATPase component (characterized) | 38% | 85% | 145.2 | Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD | 41% | 170.2 |
| L-aspartate catabolism | aatP | lo | ABC transporter for L-Asparagine and possibly other L-amino acids, putative ATPase component (characterized) | 38% | 85% | 145.2 | Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD | 41% | 170.2 |
| D-alanine catabolism | Pf6N2E2_5405 | lo | ABC transporter for D-Alanine, ATPase component (characterized) | 35% | 87% | 141.4 | Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD | 41% | 170.2 |
| L-asparagine catabolism | bgtA | lo | ATPase (characterized, see rationale) | 35% | 85% | 139.8 | Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD | 41% | 170.2 |
| L-aspartate catabolism | bgtA | lo | ATPase (characterized, see rationale) | 35% | 85% | 139.8 | Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD | 41% | 170.2 |
| L-arabinose catabolism | xacK | lo | Xylose/arabinose import ATP-binding protein XacK; EC 7.5.2.13 (characterized, see rationale) | 36% | 53% | 138.3 | Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD | 41% | 170.2 |
| L-histidine catabolism | aapP | lo | ABC transporter for L-Glutamine, L-Histidine, and other L-amino acids, ATPase component (characterized) | 38% | 80% | 137.5 | Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD | 41% | 170.2 |
| L-arginine catabolism | artP | lo | Arginine transport ATP-binding protein ArtP; EC 7.4.2.- (characterized) | 39% | 84% | 136.3 | Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD | 41% | 170.2 |
| D-glucosamine (chitosamine) catabolism | AO353_21725 | lo | ABC transporter for D-Glucosamine, putative ATPase component (characterized) | 36% | 89% | 134.8 | Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD | 41% | 170.2 |
| L-tryptophan catabolism | ecfA1 | lo | Energy-coupling factor transporter ATP-binding protein EcfA1; Short=ECF transporter A component EcfA; EC 7.-.-.- (characterized, see rationale) | 36% | 75% | 127.5 | Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD | 41% | 170.2 |
| glycerol catabolism | glpT | lo | ABC transporter for Glycerol, ATPase component 2 (characterized) | 33% | 61% | 114.8 | Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD | 41% | 170.2 |
| glycerol catabolism | glpS | lo | ABC transporter for Glycerol, ATPase component 1 (characterized) | 35% | 58% | 110.9 | Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD | 41% | 170.2 |
| 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) | 31% | 81% | 96.3 | Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD | 41% | 170.2 |
| 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) | 31% | 81% | 96.3 | Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD | 41% | 170.2 |
| 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) | 31% | 81% | 96.3 | Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD | 41% | 170.2 |
| 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) | 31% | 81% | 96.3 | Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD | 41% | 170.2 |
| 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) | 31% | 81% | 96.3 | Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD | 41% | 170.2 |
| 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) | 31% | 81% | 96.3 | Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD | 41% | 170.2 |
| 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) | 31% | 81% | 96.3 | Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD | 41% | 170.2 |
| L-alanine catabolism | braF | lo | NatA, 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) | 32% | 53% | 73.2 | Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD | 41% | 170.2 |
| L-isoleucine catabolism | natA | lo | NatA, 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) | 32% | 53% | 73.2 | Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD | 41% | 170.2 |
| L-leucine catabolism | natA | lo | NatA, 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) | 32% | 53% | 73.2 | Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD | 41% | 170.2 |
| L-proline catabolism | natA | lo | NatA, 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) | 32% | 53% | 73.2 | Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD | 41% | 170.2 |
| L-serine catabolism | braF | lo | NatA, 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) | 32% | 53% | 73.2 | Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD | 41% | 170.2 |
| L-threonine catabolism | braF | lo | NatA, 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) | 32% | 53% | 73.2 | Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD | 41% | 170.2 |
| L-valine catabolism | natA | lo | NatA, 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) | 32% | 53% | 73.2 | Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD | 41% | 170.2 |
This GapMind analysis is from Sep 17 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