# Contains rules for poorly defined clusters and/or clusters which are likely to
# match primary metabolism

# Cutoffs and neighbourhoods are given in kilobases

RULE saccharide
    CATEGORY saccharide
    DESCRIPTION Saccharide cluster definition from clusterfinder
    CUTOFF 20
    NEIGHBOURHOOD 10
    CONDITIONS minimum(2,[Alpha-amylase, Alpha-amylase_C, Bac_transf,
                          Capsule_synth, CBM_48, DegT_DnrJ_EryC1, dTDP_sugar_isom,
                          Epimerase_2, Glycos_transf_1, Glycos_transf_2,
                          Glycos_transf_4, Glyco_tran_28_C, Glyco_transf_28,
                          Glyco_transf_8, Glyco_transf_8C, Glyco_transf_9,
                          MannoseP_isomer, PIG-L, Poly_export, Polysacc_synt,
                          Polysacc_synt_2, RmlD_sub_bind, Wzy_C])

RULE fatty_acid
    CATEGORY other
    DESCRIPTION Fatty acid definition from clusterfinder
    CUTOFF 20
    NEIGHBOURHOOD 10
    CONDITIONS  bt1fas or ft1fas or t2fas or fabH

RULE fungal-RiPP-like
    CATEGORY RiPP
    DESCRIPTION fungal RiPP-like clusters
    SUPERIORS fungal-RiPP
    CUTOFF 20
    NEIGHBOURHOOD 30
    CONDITIONS DUF3328

RULE lysine
    CATEGORY NRPS
    DESCRIPTION Fungal lysine primary metabolism
    EXAMPLE NCBI NP_009673.1 1-1392 lysine
    CUTOFF 5
    NEIGHBOURHOOD 20
    CONDITIONS alpha_am_amid

RULE quinone_isoprenoid_chain
    CATEGORY terpene
    DESCRIPTION Prenyltransferase involved in biosynthesis of the isoprenoid side chain
                of quinones (e.g. coenzyme Q, menaquinone)
    EXAMPLE NCBI J05547.2 752-2173 hexaprenyl diphosphate
    CUTOFF 5
    NEIGHBOURHOOD 5
    CONDITIONS PT_HPP

RULE halogenated
    CATEGORY other
    DESCRIPTION Halogenases are frequently involved in secondary metabolite biosynthesis
    SUPERIORS polyhalogenated-pyrrole
    CUTOFF 5
    NEIGHBOURHOOD 10
    CONDITIONS Trp_halogenase
