| Pathway | Step | Score | Similar to | Id. | Cov. | Bits | Other hit | Other id. | Other bits |
|---|
| L-arginine catabolism | artP | med | Arginine transport ATP-binding protein ArtM (characterized) | 52% | 98% | 240 | L-cystine import ATP-binding protein TcyN; EC 7.4.2.- | 52% | 257.3 |
| L-histidine catabolism | BPHYT_RS24015 | med | ABC transporter related (characterized, see rationale) | 45% | 96% | 221.9 | L-cystine import ATP-binding protein TcyN; EC 7.4.2.- | 52% | 257.3 |
| L-lysine catabolism | hisP | med | ABC transporter for L-Lysine, ATPase component (characterized) | 47% | 99% | 220.7 | L-cystine import ATP-binding protein TcyN; EC 7.4.2.- | 52% | 257.3 |
| L-histidine catabolism | hisP | med | Histidine transport ATP-binding protein HisP (characterized) | 47% | 95% | 220.3 | L-cystine import ATP-binding protein TcyN; EC 7.4.2.- | 52% | 257.3 |
| 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) | 47% | 96% | 217.6 | L-cystine import ATP-binding protein TcyN; EC 7.4.2.- | 52% | 257.3 |
| 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) | 47% | 96% | 217.6 | L-cystine import ATP-binding protein TcyN; EC 7.4.2.- | 52% | 257.3 |
| D-glucosamine (chitosamine) catabolism | AO353_21725 | med | ABC transporter for D-glucosamine, ATPase component (characterized) | 46% | 94% | 217.2 | L-cystine import ATP-binding protein TcyN; EC 7.4.2.- | 52% | 257.3 |
| L-citrulline catabolism | AO353_03040 | med | ABC transporter for L-Arginine and L-Citrulline, ATPase component (characterized) | 45% | 97% | 216.1 | L-cystine import ATP-binding protein TcyN; EC 7.4.2.- | 52% | 257.3 |
| 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) | 45% | 89% | 206.5 | L-cystine import ATP-binding protein TcyN; EC 7.4.2.- | 52% | 257.3 |
| D-alanine catabolism | Pf6N2E2_5405 | med | ABC transporter for D-Alanine, ATPase component (characterized) | 43% | 94% | 199.5 | L-cystine import ATP-binding protein TcyN; EC 7.4.2.- | 52% | 257.3 |
| L-histidine catabolism | aapP | med | ABC transporter for L-Glutamine, L-Histidine, and other L-amino acids, ATPase component (characterized) | 43% | 92% | 198.7 | L-cystine import ATP-binding protein TcyN; EC 7.4.2.- | 52% | 257.3 |
| L-asparagine catabolism | bztD | med | BztD, component of Glutamate/glutamine/aspartate/asparagine porter (characterized) | 43% | 90% | 198.4 | L-cystine import ATP-binding protein TcyN; EC 7.4.2.- | 52% | 257.3 |
| L-aspartate catabolism | bztD | med | BztD, component of Glutamate/glutamine/aspartate/asparagine porter (characterized) | 43% | 90% | 198.4 | L-cystine import ATP-binding protein TcyN; EC 7.4.2.- | 52% | 257.3 |
| L-asparagine catabolism | bgtA | med | ATPase (characterized, see rationale) | 42% | 92% | 196.1 | L-cystine import ATP-binding protein TcyN; EC 7.4.2.- | 52% | 257.3 |
| L-aspartate catabolism | bgtA | med | ATPase (characterized, see rationale) | 42% | 92% | 196.1 | L-cystine import ATP-binding protein TcyN; EC 7.4.2.- | 52% | 257.3 |
| L-histidine catabolism | bgtA | med | BgtA aka SLR1735, component of Arginine/lysine/histidine/glutamine porter (characterized) | 43% | 97% | 194.9 | L-cystine import ATP-binding protein TcyN; EC 7.4.2.- | 52% | 257.3 |
| 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) | 41% | 92% | 194.1 | L-cystine import ATP-binding protein TcyN; EC 7.4.2.- | 52% | 257.3 |
| 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) | 41% | 92% | 194.1 | L-cystine import ATP-binding protein TcyN; EC 7.4.2.- | 52% | 257.3 |
| 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) | 41% | 92% | 194.1 | L-cystine import ATP-binding protein TcyN; EC 7.4.2.- | 52% | 257.3 |
| 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) | 41% | 92% | 194.1 | L-cystine import ATP-binding protein TcyN; EC 7.4.2.- | 52% | 257.3 |
| 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) | 41% | 92% | 194.1 | L-cystine import ATP-binding protein TcyN; EC 7.4.2.- | 52% | 257.3 |
| L-asparagine catabolism | aatP | med | Glutamate/aspartate transport ATP-binding protein GltL aka B0652, component of Glutamate/aspartate porter (characterized) | 42% | 99% | 191.8 | L-cystine import ATP-binding protein TcyN; EC 7.4.2.- | 52% | 257.3 |
| L-aspartate catabolism | aatP | med | Glutamate/aspartate transport ATP-binding protein GltL aka B0652, component of Glutamate/aspartate porter (characterized) | 42% | 99% | 191.8 | L-cystine import ATP-binding protein TcyN; EC 7.4.2.- | 52% | 257.3 |
| L-histidine catabolism | hutV | med | ABC transporter for L-Histidine, ATPase component (characterized) | 40% | 80% | 159.1 | L-cystine import ATP-binding protein TcyN; EC 7.4.2.- | 52% | 257.3 |
| L-asparagine catabolism | peb1C | lo | PEB1C, component of Uptake system for glutamate and aspartate (characterized) | 40% | 98% | 183 | L-cystine import ATP-binding protein TcyN; EC 7.4.2.- | 52% | 257.3 |
| L-aspartate catabolism | peb1C | lo | PEB1C, component of Uptake system for glutamate and aspartate (characterized) | 40% | 98% | 183 | L-cystine import ATP-binding protein TcyN; EC 7.4.2.- | 52% | 257.3 |
| 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) | 43% | 56% | 177.9 | L-cystine import ATP-binding protein TcyN; EC 7.4.2.- | 52% | 257.3 |
| L-histidine catabolism | PA5503 | lo | Methionine import ATP-binding protein MetN 2, component of L-Histidine uptake porter, MetIQN (characterized) | 40% | 72% | 176.4 | L-cystine import ATP-binding protein TcyN; EC 7.4.2.- | 52% | 257.3 |
| L-proline catabolism | proV | lo | Glycine betaine/proline betaine transport system ATP-binding protein ProV (characterized) | 40% | 61% | 175.6 | L-cystine import ATP-binding protein TcyN; EC 7.4.2.- | 52% | 257.3 |
| D-cellobiose catabolism | glcV | lo | monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) | 41% | 65% | 156.4 | L-cystine import ATP-binding protein TcyN; EC 7.4.2.- | 52% | 257.3 |
| D-galactose catabolism | glcV | lo | monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) | 41% | 65% | 156.4 | L-cystine import ATP-binding protein TcyN; EC 7.4.2.- | 52% | 257.3 |
| D-glucose catabolism | glcV | lo | monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) | 41% | 65% | 156.4 | L-cystine import ATP-binding protein TcyN; EC 7.4.2.- | 52% | 257.3 |
| lactose catabolism | glcV | lo | monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) | 41% | 65% | 156.4 | L-cystine import ATP-binding protein TcyN; EC 7.4.2.- | 52% | 257.3 |
| D-maltose catabolism | glcV | lo | monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) | 41% | 65% | 156.4 | L-cystine import ATP-binding protein TcyN; EC 7.4.2.- | 52% | 257.3 |
| D-mannose catabolism | glcV | lo | monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) | 41% | 65% | 156.4 | L-cystine import ATP-binding protein TcyN; EC 7.4.2.- | 52% | 257.3 |
| sucrose catabolism | glcV | lo | monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) | 41% | 65% | 156.4 | L-cystine import ATP-binding protein TcyN; EC 7.4.2.- | 52% | 257.3 |
| trehalose catabolism | glcV | lo | monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) | 41% | 65% | 156.4 | L-cystine import ATP-binding protein TcyN; EC 7.4.2.- | 52% | 257.3 |
| L-proline catabolism | HSERO_RS00895 | lo | ABC-type branched-chain amino acid transport system, ATPase component protein (characterized, see rationale) | 32% | 94% | 125.6 | L-cystine import ATP-binding protein TcyN; EC 7.4.2.- | 52% | 257.3 |
| L-isoleucine catabolism | livG | lo | ABC transporter ATP-binding protein (characterized, see rationale) | 30% | 95% | 119.8 | L-cystine import ATP-binding protein TcyN; EC 7.4.2.- | 52% | 257.3 |
| L-leucine catabolism | livG | lo | ABC transporter ATP-binding protein (characterized, see rationale) | 30% | 95% | 119.8 | L-cystine import ATP-binding protein TcyN; EC 7.4.2.- | 52% | 257.3 |
| L-phenylalanine catabolism | livG | lo | ABC transporter ATP-binding protein (characterized, see rationale) | 30% | 95% | 119.8 | L-cystine import ATP-binding protein TcyN; EC 7.4.2.- | 52% | 257.3 |
| L-serine catabolism | Ac3H11_1693 | lo | ABC transporter ATP-binding protein (characterized, see rationale) | 30% | 95% | 119.8 | L-cystine import ATP-binding protein TcyN; EC 7.4.2.- | 52% | 257.3 |
| L-tyrosine catabolism | Ac3H11_1693 | lo | ABC transporter ATP-binding protein (characterized, see rationale) | 30% | 95% | 119.8 | L-cystine import ATP-binding protein TcyN; EC 7.4.2.- | 52% | 257.3 |
| citrate catabolism | fecE | lo | iron(III) dicitrate transport ATP-binding protein FecE (characterized) | 31% | 87% | 110.9 | L-cystine import ATP-binding protein TcyN; EC 7.4.2.- | 52% | 257.3 |
| L-histidine catabolism | natE | lo | NatE aka LivF aka SLR1881, component of Leucine/proline/alanine/serine/glycine (and possibly histidine) porter, NatABCDE (characterized) | 32% | 87% | 104.8 | L-cystine import ATP-binding protein TcyN; EC 7.4.2.- | 52% | 257.3 |
| L-leucine catabolism | natE | lo | NatE aka LivF aka SLR1881, component of Leucine/proline/alanine/serine/glycine (and possibly histidine) porter, NatABCDE (characterized) | 32% | 87% | 104.8 | L-cystine import ATP-binding protein TcyN; EC 7.4.2.- | 52% | 257.3 |
| L-proline catabolism | natE | lo | NatE aka LivF aka SLR1881, component of Leucine/proline/alanine/serine/glycine (and possibly histidine) porter, NatABCDE (characterized) | 32% | 87% | 104.8 | L-cystine import ATP-binding protein TcyN; EC 7.4.2.- | 52% | 257.3 |
| D-fructose catabolism | frcA | lo | Fructose import ATP-binding protein FrcA; EC 7.5.2.- (characterized) | 30% | 87% | 101.3 | L-cystine import ATP-binding protein TcyN; EC 7.4.2.- | 52% | 257.3 |
| D-mannose catabolism | frcA | lo | Fructose import ATP-binding protein FrcA; EC 7.5.2.- (characterized) | 30% | 87% | 101.3 | L-cystine import ATP-binding protein TcyN; EC 7.4.2.- | 52% | 257.3 |
| D-ribose catabolism | frcA | lo | Fructose import ATP-binding protein FrcA; EC 7.5.2.- (characterized) | 30% | 87% | 101.3 | L-cystine import ATP-binding protein TcyN; EC 7.4.2.- | 52% | 257.3 |
| sucrose catabolism | frcA | lo | Fructose import ATP-binding protein FrcA; EC 7.5.2.- (characterized) | 30% | 87% | 101.3 | L-cystine import ATP-binding protein TcyN; EC 7.4.2.- | 52% | 257.3 |
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