Module description

The t2pks module predicts PKS type II biosynthetic gene cluster details.

Starter units

The following starter units are detected:

  • 2-methylbutyryl-CoA
  • acetyl-CoA
  • anthraniloyl-CoA
  • aziridinyl-CoA
  • benzoyl-CoA
  • butyryl-CoA
  • hexadienyl-CoA
  • hexanoyl-CoA
  • isobutyryl-CoA
  • malonamyl-CoA
  • propionyl-CoA

Malonyl elongation steps

Based on chain length factor classification, the module predicts the number of malonyl elongation steps.

Product class

Based on both the number of malonyl elongations and the detected cyclases, one or more product classes are predicted.

The following product classes are detected:

  • angucycline
  • anthracycline
  • aureolic acid
  • benzoisochromanequinone
  • pentangular polyphenol
  • tetracenomycin
  • tetracycline

Product molecular weight

Product molecular weights are predicted for all combinations of starter units and elongation steps, and modified based on the tailoring enzymes identified in the cluster.

Glossary of PKS type II specific terms

CLF
chain length factor
CLF_7
extending by 7 units
CLF_8|9
extending by 8 or 9 units
CLF_11|12
extending by 11 or 12 units
AT
acetyl transferase
CYC
cyclase
CYC_C7-C12
connecting carbons 7 and 12
CYC_C5-C14
connecting carbons 5 and 14
CYC_C5-C14/C3-C16
connecting carbons 5 or 3 and 14 or 16, respectively
CYC_C1-C18|C2-C19
connecting carbons 1 or 2 and 18 or 19, respectively
CYC_C2-C19
connecting carbons 2 and 19
CYC_C5-C18
connecting carbons 5 and 18
CYC_C4-C17/C2-C19
connecting carbons 4 or 2 and 17 or 19, respectively
CYC_C4-C21/C2-C23|C2-C19
connecting carbons 4 or 2 and 21, 23, or 19, respectively
CYC_C9-C14
connecting carbons 9 and 14
KSIII
Non-acetate starter unit ketosynthase III
ACP
acetyl carrier proteing
KR
ketoreductase
KR_C9
reducing carbon 9
KR_C11
reducing carbon 11
KR_C15
reducing carbon 15
KR_C17
reducing carbon 17
KR_C19
reducing carbon 19
KS
ketosynthase
OXY
oxygenase
GT
glycosyltransferase
MET
methyltransferase
MET_carboxy_O
carboxyl O-methyltransferase
MET_C2O|C2N
O- or N-methyltransferase acting on the oxygen or nitrogen at carbon 2, respectively
MET_C6|C8
methyltransferase acting at carbon 6 or 8
MET_C9O
O-methyltransferase acting on the oxygen at carbon 9
MET_C10
methyltransferase acting at carbon 10
MET_C11O
O-methyltransferase acting on the oxygen at carbon 11
MET_C13O|C17O
O-methyltransferase acting on the oxygen at carbon 13 or 17
MET_C18O
O-methyltransferase acting on the oxygen at carbon 18
DIMER
dimerase
LIG
ligase
HAL
halogenase
AMIN
aminase
AMID
amidase