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#
- ACP
- acetyl carrier protein
- AMID
- amidase
- AMIN
- aminase
- AT
- acyltransferase
- 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
- CYC
- cyclase
- CYC_C7-C12
- connecting carbon 7 to 12
- CYC_C5-C14
- connecting carbon 5 to 14
- CYC_C5-C14/C3-C16
- connecting carbon 5 to 13 or carbon 3 to 16
- CYC_C1-C18|C2-C19
- connecting carbon 1 to 18 or carbon 2 to 19
- CYC_C2-C19
- connecting carbon 2 to 19
- CYC_C5-C18
- connecting carbon 5 to 18
- CYC_C4-C17/C2-C19
- connecting carbon 4 to 17 or carbon 2 to 19
- CYC_C4-C21/C2-C23|C2-C19
- connecting carbon 4 to 21, carbon 2 to 23, or carbon 2 to 19
- CYC_C9-C14
- connecting carbon 9 to 14
- DIMER
- dimerase
- GT
- glycosyltransferase
- HAL
- halogenase
- 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
- KSIII
- Non-acetate starter unit ketosynthase III
- LIG
- ligase
- 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
- OXY
- oxygenase