Table 1 List of domains and associated reactions as implemented in BiGMeC
From: Automatic reconstruction of metabolic pathways from identified biosynthetic gene clusters
Abbrv. | Name | Note | Reaction |
|---|---|---|---|
A | Adenylation | Activates and attaches AA to PCP | ATP + AA + PCP\(\rightarrow\)AA-PCP + AMP + Pii |
ACP | Acyl carrier protein | Facilitates transport in PKSs | Â |
AT | Acyltransferase | Loads extender unit onto ACP | Acyl-CoA + ACP \(\rightarrow\) Acyl-ACP + CoA |
C | Condensation | Elongates the peptide by condensation | AA-PCP + Xn \(\rightarrow\) Xn+1 + H2O + ACP |
CAL | Coenzyme A ligase | Catalyzes the incorporation of different starter units, e.g. fatty acids, AHBA, and shikimic acid [32, 56, 57] | Y + PCP \(\rightarrow\) Y-PCP + H2O |
cMT | Carbon methyltransferase | Methylates peptide/polyketide | SAM + Xn \(\rightarrow\) Xn + SAH |
Cy | Heterocylization | Elongates the peptide by condensation and cyclization | AA-PCP + Xn \(\rightarrow\) Xn+1 + H2O + ACP |
DH | Dehydratase | Forms double bound by removal of H2O | Xn \(\rightarrow\) Xn + H2O |
E | Epimerase | Stereochemical inversion | Xn \(\rightarrow\) Xn |
ECH | Enoyl-CoA hydratase/isomerase | Not able to discriminate, so BiGMeC assumes isomerase | Xn \(\rightarrow\) Xn |
ER | Enoyl reductase | Reduces double bound formed by the DH domain to a methylene group | NADPH + H+ + Xn \(\rightarrow\) Xn + NADP+ |
FkbH | FkbH-like domain | Domain in an alternative loading module. Dephosphorylates 1,3-bpg [58] | 1,3-bpg + ACP \(\rightarrow\) D-lactate-ACP + 2 Pi |
GNAT | GCN5-related N-acetyl transferase | Alt. load module that decarboxylates malonyl-CoA and adds acetyl group to ACP [59] | Malonyl-CoA + ACP \(\rightarrow\) Acetyl-ACP + CoA + CO2 |
KR | Keto reductase | Reduces carbonyl group to hydroxyl group | NADPH + H+ + Xn \(\rightarrow\) Xn + NADP+ |
KS | Keto synthase | Appends extender unit to polyketide | Acyl-ACP + Xn \(\rightarrow\) Xn+1 + CO2 + ACP |
nMT | Nitrogen methyltransferase | Methylates peptide/polyketide | SAM + Xn \(\rightarrow\) Xn + SAH |
oMT | Oxygen methyltransferase | Methylates peptide/polyketide | SAM + Xn \(\rightarrow\) Xn + SAH |
PCP | Peptidyl carrier domain | Facilitates transport in NRPSs | Â |
TD | Thioester reductase | Releases product from ACP/PCP | NADPH + H+ + Xn \(\rightarrow\) detached product + NADP+ |
TE | Thioesterase | Releases product from ACP/PCP | H2O + Xn \(\rightarrow\) detached product |