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) | 48% | 100% | 235.3 | L-cystine import ATP-binding protein TcyN; EC 7.4.2.- | 57% | 278.1 |
L-histidine catabolism | BPHYT_RS24015 | med | ABC transporter related (characterized, see rationale) | 46% | 94% | 230.7 | L-cystine import ATP-binding protein TcyN; EC 7.4.2.- | 57% | 278.1 |
D-glucosamine (chitosamine) catabolism | AO353_21725 | med | ABC transporter for D-Glucosamine, putative ATPase component (characterized) | 49% | 94% | 225.3 | L-cystine import ATP-binding protein TcyN; EC 7.4.2.- | 57% | 278.1 |
L-histidine catabolism | hisP | med | Histidine transport ATP-binding protein HisP (characterized) | 46% | 96% | 223.8 | L-cystine import ATP-binding protein TcyN; EC 7.4.2.- | 57% | 278.1 |
L-lysine catabolism | hisP | med | Histidine transport ATP-binding protein HisP (characterized) | 46% | 96% | 223.8 | L-cystine import ATP-binding protein TcyN; EC 7.4.2.- | 57% | 278.1 |
L-citrulline catabolism | AO353_03040 | med | ABC transporter for L-Arginine and L-Citrulline, ATPase component (characterized) | 46% | 97% | 223.4 | L-cystine import ATP-binding protein TcyN; EC 7.4.2.- | 57% | 278.1 |
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) | 47% | 89% | 221.9 | L-cystine import ATP-binding protein TcyN; EC 7.4.2.- | 57% | 278.1 |
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% | 98% | 221.5 | L-cystine import ATP-binding protein TcyN; EC 7.4.2.- | 57% | 278.1 |
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% | 98% | 221.5 | L-cystine import ATP-binding protein TcyN; EC 7.4.2.- | 57% | 278.1 |
L-asparagine catabolism | aatP | med | ABC transporter for L-Asparagine and possibly other L-amino acids, putative ATPase component (characterized) | 48% | 99% | 219.5 | L-cystine import ATP-binding protein TcyN; EC 7.4.2.- | 57% | 278.1 |
L-aspartate catabolism | aatP | med | ABC transporter for L-Asparagine and possibly other L-amino acids, putative ATPase component (characterized) | 48% | 99% | 219.5 | L-cystine import ATP-binding protein TcyN; EC 7.4.2.- | 57% | 278.1 |
L-histidine catabolism | bgtA | med | BgtA aka SLR1735, component of Arginine/lysine/histidine/glutamine porter (characterized) | 43% | 97% | 215.3 | L-cystine import ATP-binding protein TcyN; EC 7.4.2.- | 57% | 278.1 |
D-alanine catabolism | Pf6N2E2_5405 | med | ABC transporter for D-Alanine, ATPase component (characterized) | 45% | 94% | 212.6 | L-cystine import ATP-binding protein TcyN; EC 7.4.2.- | 57% | 278.1 |
L-histidine catabolism | aapP | med | ABC transporter for L-Glutamine, L-Histidine, and other L-amino acids, ATPase component (characterized) | 44% | 92% | 209.5 | L-cystine import ATP-binding protein TcyN; EC 7.4.2.- | 57% | 278.1 |
L-asparagine catabolism | peb1C | med | PEB1C, component of Uptake system for glutamate and aspartate (characterized) | 46% | 99% | 208.8 | L-cystine import ATP-binding protein TcyN; EC 7.4.2.- | 57% | 278.1 |
L-aspartate catabolism | peb1C | med | PEB1C, component of Uptake system for glutamate and aspartate (characterized) | 46% | 99% | 208.8 | L-cystine import ATP-binding protein TcyN; EC 7.4.2.- | 57% | 278.1 |
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) | 44% | 93% | 208.4 | L-cystine import ATP-binding protein TcyN; EC 7.4.2.- | 57% | 278.1 |
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) | 44% | 93% | 208.4 | L-cystine import ATP-binding protein TcyN; EC 7.4.2.- | 57% | 278.1 |
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) | 44% | 93% | 208.4 | L-cystine import ATP-binding protein TcyN; EC 7.4.2.- | 57% | 278.1 |
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) | 44% | 93% | 208.4 | L-cystine import ATP-binding protein TcyN; EC 7.4.2.- | 57% | 278.1 |
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) | 44% | 93% | 208.4 | L-cystine import ATP-binding protein TcyN; EC 7.4.2.- | 57% | 278.1 |
L-asparagine catabolism | bztD | med | BztD, component of Glutamate/glutamine/aspartate/asparagine porter (characterized) | 45% | 86% | 205.7 | L-cystine import ATP-binding protein TcyN; EC 7.4.2.- | 57% | 278.1 |
L-aspartate catabolism | bztD | med | BztD, component of Glutamate/glutamine/aspartate/asparagine porter (characterized) | 45% | 86% | 205.7 | L-cystine import ATP-binding protein TcyN; EC 7.4.2.- | 57% | 278.1 |
L-asparagine catabolism | bgtA | med | ATPase (characterized, see rationale) | 44% | 85% | 199.1 | L-cystine import ATP-binding protein TcyN; EC 7.4.2.- | 57% | 278.1 |
L-aspartate catabolism | bgtA | med | ATPase (characterized, see rationale) | 44% | 85% | 199.1 | L-cystine import ATP-binding protein TcyN; EC 7.4.2.- | 57% | 278.1 |
putrescine catabolism | potA | lo | spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31 (characterized) | 40% | 64% | 155.2 | L-cystine import ATP-binding protein TcyN; EC 7.4.2.- | 57% | 278.1 |
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% | 96% | 134 | L-cystine import ATP-binding protein TcyN; EC 7.4.2.- | 57% | 278.1 |
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% | 96% | 134 | L-cystine import ATP-binding protein TcyN; EC 7.4.2.- | 57% | 278.1 |
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% | 96% | 134 | L-cystine import ATP-binding protein TcyN; EC 7.4.2.- | 57% | 278.1 |
L-phenylalanine catabolism | livG | lo | High-affinity branched-chain amino acid transport ATP-binding protein LivG aka B3455, component of Leucine; leucine/isoleucine/valine porter (characterized) | 31% | 93% | 125.2 | L-cystine import ATP-binding protein TcyN; EC 7.4.2.- | 57% | 278.1 |
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% | 93% | 122.9 | L-cystine import ATP-binding protein TcyN; EC 7.4.2.- | 57% | 278.1 |
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% | 93% | 122.9 | L-cystine import ATP-binding protein TcyN; EC 7.4.2.- | 57% | 278.1 |
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% | 93% | 122.9 | L-cystine import ATP-binding protein TcyN; EC 7.4.2.- | 57% | 278.1 |
L-histidine catabolism | natA | lo | NatA aka BRAF aka SLR0467, component of Leucine/proline/alanine/serine/glycine (and possibly histidine) porter, NatABCDE (characterized) | 32% | 90% | 122.5 | L-cystine import ATP-binding protein TcyN; EC 7.4.2.- | 57% | 278.1 |
L-leucine catabolism | natA | lo | NatA aka BRAF aka SLR0467, component of Leucine/proline/alanine/serine/glycine (and possibly histidine) porter, NatABCDE (characterized) | 32% | 90% | 122.5 | L-cystine import ATP-binding protein TcyN; EC 7.4.2.- | 57% | 278.1 |
L-proline catabolism | natA | lo | NatA aka BRAF aka SLR0467, component of Leucine/proline/alanine/serine/glycine (and possibly histidine) porter, NatABCDE (characterized) | 32% | 90% | 122.5 | L-cystine import ATP-binding protein TcyN; EC 7.4.2.- | 57% | 278.1 |
L-proline catabolism | HSERO_RS00895 | lo | ABC transporter ATP-binding protein (characterized, see rationale) | 30% | 91% | 121.3 | L-cystine import ATP-binding protein TcyN; EC 7.4.2.- | 57% | 278.1 |
L-serine catabolism | Ac3H11_1693 | lo | ABC transporter ATP-binding protein (characterized, see rationale) | 30% | 91% | 121.3 | L-cystine import ATP-binding protein TcyN; EC 7.4.2.- | 57% | 278.1 |
L-tyrosine catabolism | Ac3H11_1693 | lo | ABC transporter ATP-binding protein (characterized, see rationale) | 30% | 91% | 121.3 | L-cystine import ATP-binding protein TcyN; EC 7.4.2.- | 57% | 278.1 |
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) | 33% | 95% | 118.6 | L-cystine import ATP-binding protein TcyN; EC 7.4.2.- | 57% | 278.1 |
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) | 33% | 95% | 118.6 | L-cystine import ATP-binding protein TcyN; EC 7.4.2.- | 57% | 278.1 |
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) | 33% | 95% | 118.6 | L-cystine import ATP-binding protein TcyN; EC 7.4.2.- | 57% | 278.1 |
L-phenylalanine catabolism | livF | lo | ABC transporter ATP-binding protein (characterized, see rationale) | 30% | 93% | 108.2 | L-cystine import ATP-binding protein TcyN; EC 7.4.2.- | 57% | 278.1 |
L-proline catabolism | HSERO_RS00900 | lo | ABC transporter ATP-binding protein (characterized, see rationale) | 30% | 93% | 108.2 | L-cystine import ATP-binding protein TcyN; EC 7.4.2.- | 57% | 278.1 |
L-serine catabolism | Ac3H11_1692 | lo | ABC transporter ATP-binding protein (characterized, see rationale) | 30% | 93% | 108.2 | L-cystine import ATP-binding protein TcyN; EC 7.4.2.- | 57% | 278.1 |
L-tyrosine catabolism | Ac3H11_1692 | lo | ABC transporter ATP-binding protein (characterized, see rationale) | 30% | 93% | 108.2 | L-cystine import ATP-binding protein TcyN; EC 7.4.2.- | 57% | 278.1 |
glycerol catabolism | glpS | lo | GlpS, component of Glycerol uptake porter, GlpSTPQV (characterized) | 31% | 64% | 102.8 | L-cystine import ATP-binding protein TcyN; EC 7.4.2.- | 57% | 278.1 |
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