| Pathway | Step | Score | Similar to | Id. | Cov. | Bits | Other hit | Other id. | Other bits |
|---|
| L-histidine catabolism | PA5503 | med | Methionine import ATP-binding protein MetN 2, component of L-Histidine uptake porter, MetIQN (characterized) | 43% | 100% | 256.5 | Methionine import ATP-binding protein metN, component of L-Methionine uptake porter, MetQNI | 95% | 657.5 |
| L-arginine catabolism | artP | med | Arginine transport ATP-binding protein ArtM (characterized) | 44% | 99% | 198.7 | Methionine import ATP-binding protein metN, component of L-Methionine uptake porter, MetQNI | 95% | 657.5 |
| 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) | 42% | 98% | 193 | Methionine import ATP-binding protein metN, component of L-Methionine uptake porter, MetQNI | 95% | 657.5 |
| 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) | 42% | 98% | 193 | Methionine import ATP-binding protein metN, component of L-Methionine uptake porter, MetQNI | 95% | 657.5 |
| L-asparagine catabolism | bgtA | med | ATPase (characterized, see rationale) | 40% | 97% | 177.2 | Methionine import ATP-binding protein metN, component of L-Methionine uptake porter, MetQNI | 95% | 657.5 |
| L-aspartate catabolism | bgtA | med | ATPase (characterized, see rationale) | 40% | 97% | 177.2 | Methionine import ATP-binding protein metN, component of L-Methionine uptake porter, MetQNI | 95% | 657.5 |
| L-histidine catabolism | bgtA | med | BgtA aka SLR1735, component of Arginine/lysine/histidine/glutamine porter (characterized) | 44% | 89% | 176 | Methionine import ATP-binding protein metN, component of L-Methionine uptake porter, MetQNI | 95% | 657.5 |
| L-lysine catabolism | hisP | med | BgtA aka SLR1735, component of Arginine/lysine/histidine/glutamine porter (characterized) | 44% | 89% | 176 | Methionine import ATP-binding protein metN, component of L-Methionine uptake porter, MetQNI | 95% | 657.5 |
| L-histidine catabolism | hisP | med | histidine transport ATP-binding protein hisP (characterized) | 42% | 93% | 173.3 | Methionine import ATP-binding protein metN, component of L-Methionine uptake porter, MetQNI | 95% | 657.5 |
| D-glucosamine (chitosamine) catabolism | AO353_21725 | med | ABC transporter for D-glucosamine, ATPase component (characterized) | 40% | 97% | 168.7 | Methionine import ATP-binding protein metN, component of L-Methionine uptake porter, MetQNI | 95% | 657.5 |
| L-asparagine catabolism | bztD | med | BztD, component of Glutamate/glutamine/aspartate/asparagine porter (characterized) | 40% | 86% | 166.4 | Methionine import ATP-binding protein metN, component of L-Methionine uptake porter, MetQNI | 95% | 657.5 |
| L-aspartate catabolism | bztD | med | BztD, component of Glutamate/glutamine/aspartate/asparagine porter (characterized) | 40% | 86% | 166.4 | Methionine import ATP-binding protein metN, component of L-Methionine uptake porter, MetQNI | 95% | 657.5 |
| L-proline catabolism | proV | lo | glycine betaine/l-proline transport atp-binding protein prov (characterized) | 39% | 62% | 182.2 | Methionine import ATP-binding protein metN, component of L-Methionine uptake porter, MetQNI | 95% | 657.5 |
| L-asparagine catabolism | peb1C | lo | PEB1C, component of Uptake system for glutamate and aspartate (characterized) | 40% | 100% | 181 | Methionine import ATP-binding protein metN, component of L-Methionine uptake porter, MetQNI | 95% | 657.5 |
| L-aspartate catabolism | peb1C | lo | PEB1C, component of Uptake system for glutamate and aspartate (characterized) | 40% | 100% | 181 | Methionine import ATP-binding protein metN, component of L-Methionine uptake porter, MetQNI | 95% | 657.5 |
| L-proline catabolism | opuBA | lo | BusAA, component of Uptake system for glycine-betaine (high affinity) and proline (low affinity) (OpuAA-OpuABC) or BusAA-ABC of Lactococcus lactis). BusAA, the ATPase subunit, has a C-terminal tandem cystathionine β-synthase (CBS) domain which is the cytoplasmic K+ sensor for osmotic stress (osmotic strength)while the BusABC subunit has the membrane and receptor domains fused to each other (Biemans-Oldehinkel et al., 2006; Mahmood et al., 2006; Gul et al. 2012). An N-terminal amphipathic α-helix of OpuA is necessary for high activity but is not critical for biogenesis or the ionic regulation of transport (characterized) | 39% | 61% | 174.5 | Methionine import ATP-binding protein metN, component of L-Methionine uptake porter, MetQNI | 95% | 657.5 |
| L-asparagine catabolism | aatP | lo | Glutamate/aspartate transport ATP-binding protein GltL aka B0652, component of Glutamate/aspartate porter (characterized) | 39% | 100% | 171 | Methionine import ATP-binding protein metN, component of L-Methionine uptake porter, MetQNI | 95% | 657.5 |
| L-aspartate catabolism | aatP | lo | Glutamate/aspartate transport ATP-binding protein GltL aka B0652, component of Glutamate/aspartate porter (characterized) | 39% | 100% | 171 | Methionine import ATP-binding protein metN, component of L-Methionine uptake porter, MetQNI | 95% | 657.5 |
| L-citrulline catabolism | AO353_03040 | lo | ABC transporter for L-Arginine and L-Citrulline, ATPase component (characterized) | 37% | 99% | 169.1 | Methionine import ATP-binding protein metN, component of L-Methionine uptake porter, MetQNI | 95% | 657.5 |
| L-histidine catabolism | hutV | lo | ABC transporter for L-Histidine, ATPase component (characterized) | 37% | 95% | 166.4 | Methionine import ATP-binding protein metN, component of L-Methionine uptake porter, MetQNI | 95% | 657.5 |
| L-histidine catabolism | aapP | lo | ABC transporter for L-Glutamine, L-Histidine, and other L-amino acids, ATPase component (characterized) | 37% | 100% | 164.5 | Methionine import ATP-binding protein metN, component of L-Methionine uptake porter, MetQNI | 95% | 657.5 |
| L-proline catabolism | hutV | lo | HutV aka HISV aka R02702 aka SMC00670, component of Uptake system for hisitidine, proline, proline-betaine and glycine-betaine (characterized) | 39% | 88% | 164.5 | Methionine import ATP-binding protein metN, component of L-Methionine uptake porter, MetQNI | 95% | 657.5 |
| L-citrulline catabolism | PS417_17605 | lo | 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) | 35% | 99% | 163.3 | Methionine import ATP-binding protein metN, component of L-Methionine uptake porter, MetQNI | 95% | 657.5 |
| L-histidine catabolism | BPHYT_RS24015 | lo | ABC transporter related (characterized, see rationale) | 37% | 97% | 162.5 | Methionine import ATP-binding protein metN, component of L-Methionine uptake porter, MetQNI | 95% | 657.5 |
| 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) | 37% | 99% | 159.5 | Methionine import ATP-binding protein metN, component of L-Methionine uptake porter, MetQNI | 95% | 657.5 |
| 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) | 37% | 99% | 159.5 | Methionine import ATP-binding protein metN, component of L-Methionine uptake porter, MetQNI | 95% | 657.5 |
| 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) | 37% | 99% | 159.5 | Methionine import ATP-binding protein metN, component of L-Methionine uptake porter, MetQNI | 95% | 657.5 |
| 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) | 37% | 99% | 159.5 | Methionine import ATP-binding protein metN, component of L-Methionine uptake porter, MetQNI | 95% | 657.5 |
| 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) | 37% | 99% | 159.5 | Methionine import ATP-binding protein metN, component of L-Methionine uptake porter, MetQNI | 95% | 657.5 |
| D-alanine catabolism | Pf6N2E2_5405 | lo | ABC transporter for D-Alanine, ATPase component (characterized) | 36% | 96% | 158.3 | Methionine import ATP-binding protein metN, component of L-Methionine uptake porter, MetQNI | 95% | 657.5 |
| L-tryptophan catabolism | ecfA1 | lo | Energy-coupling factor transporter ATP-binding protein EcfA1; Short=ECF transporter A component EcfA; EC 7.-.-.- (characterized, see rationale) | 38% | 78% | 139.4 | Methionine import ATP-binding protein metN, component of L-Methionine uptake porter, MetQNI | 95% | 657.5 |
| L-tryptophan catabolism | ecfA2 | lo | Energy-coupling factor transporter ATP-binding protein EcfA2; Short=ECF transporter A component EcfA2; EC 7.-.-.- (characterized, see rationale) | 33% | 97% | 136.3 | Methionine import ATP-binding protein metN, component of L-Methionine uptake porter, MetQNI | 95% | 657.5 |
| 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% | 95% | 132.5 | Methionine import ATP-binding protein metN, component of L-Methionine uptake porter, MetQNI | 95% | 657.5 |
| 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% | 95% | 132.5 | Methionine import ATP-binding protein metN, component of L-Methionine uptake porter, MetQNI | 95% | 657.5 |
| 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% | 95% | 132.5 | Methionine import ATP-binding protein metN, component of L-Methionine uptake porter, MetQNI | 95% | 657.5 |
| 2'-deoxyinosine catabolism | nupA | lo | RnsB, component of The (deoxy)ribonucleoside permease; probably takes up all deoxy- and ribonucleosides (cytidine, uridine, adenosine and toxic analogues, fluorocytidine and fluorouridine tested), but not ribose or nucleobases (characterized) | 31% | 52% | 126.7 | Methionine import ATP-binding protein metN, component of L-Methionine uptake porter, MetQNI | 95% | 657.5 |
| 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% | 89% | 110.9 | Methionine import ATP-binding protein metN, component of L-Methionine uptake porter, MetQNI | 95% | 657.5 |
| 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% | 89% | 110.9 | Methionine import ATP-binding protein metN, component of L-Methionine uptake porter, MetQNI | 95% | 657.5 |
| 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% | 89% | 110.9 | Methionine import ATP-binding protein metN, component of L-Methionine uptake porter, MetQNI | 95% | 657.5 |
| L-phenylalanine catabolism | livG | lo | High-affinity branched-chain amino acid ABC transporter ATP-binding protein LivG (characterized, see rationale) | 30% | 89% | 109.4 | Methionine import ATP-binding protein metN, component of L-Methionine uptake porter, MetQNI | 95% | 657.5 |
| myo-inositol catabolism | PGA1_c07320 | lo | Inositol transport system ATP-binding protein (characterized) | 30% | 84% | 97.1 | Methionine import ATP-binding protein metN, component of L-Methionine uptake porter, MetQNI | 95% | 657.5 |
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