fmod MODIFICATIONOPS is
     inc MODIFICATION .

op acetyl : -> Modification .          *** acetylated
op acetyl : Site -> Modification .     *** acetylated on a specific site
op act : -> Modification .             *** activated
op cleaved : -> Modification .         *** cleaved by a protease
op degraded : -> Modification .        *** used in rules to show the little man on the stairs
op dimer : -> Modification .           *** dimerized
op GDP : -> Modification .             *** bound to GDP
op GDPbS : -> Modification [ctor] .    *** bound to GDPbS
op GMPPCP : -> Modification [ctor] .   *** bound to GMPPCP
op GMPPNP : -> Modification [ctor] .   *** bound to GMPPNP
op GTP : -> Modification .             *** bound to GTP
op GTPgS  : -> Modification [ctor] .   *** bound to GTPgS
op K48poly : -> Modification .         *** polymerized via K48 linkages
op K48ubiq : -> Modification .         *** covalently bound to ubiquitin polymerized via K48 linkages
op K63poly : -> Modification .         *** polymerized via K63 linkages
op K63ubiq : -> Modification .         *** covalently bound to ubiquitin polymerized via K48 linkages
op methyl : -> Modification .          *** methylated
op methyl : Site -> Modification .     *** methylated on a specific site
op nedd : -> Modification .            *** neddylated
op NucFree : -> Modification [ctor] .  *** not bound to any nucleotide
op on : -> Modification .              *** gene transcription is on
op p25 : -> Modification .             *** Cdk5r1 processing
op p34 : -> Modification .             *** TgfbR1 cleavage product
op p50 : -> Modification .             *** Nfkb1 processing
op p52 : -> Modification .             *** Nfkb2 processing
op p100 : -> Modification .            *** Nfkb2 processing
op p105 : -> Modification .            *** Nfkb1 processing
op phos :       -> Modification .      *** phosphorylated
op phos : Site  -> Modification .      *** phosphorylated on a specific site
op poly : -> Modification .            *** polymerized
op poly1 : -> Modification .           *** used for free Ubiq-poly chains
op poly2 : -> Modification .           *** used for free Ubiq-poly chains
op poly3 : -> Modification .           *** used for free Ubiq-poly chains
op sumo : -> Modification .            *** sumoylated
op thiophos : -> Modification [ctor] . *** phosed with thiophosphate
op ubiq : -> Modification .            *** covalently conjugated to ubiquitin
op ubiq : Site -> Modification .       *** covalently conjugated with ubiquitin at a specific site
op unphos : -> Modification .          *** used for datums only to highlight change in phos
op Yphos : -> Modification .           *** phosphorylated on Tyrosine
op conj : -> Modification .            *** used for mono or poly ubiquitin bound to any protein (FK2 antibody)
op mono : -> Modification .            *** not polymerized

op glyc : -> Modification .          *** glycosylated
op glyc : Gcode -> Modification .    *** glycosylated with Gcode
op gpi : -> Modification .          *** attached to protein via gpi linkage
op gpi : Gcode -> Modification .    *** Gcode attached to protein via gpi linkage that includes carrier lipid




***( not used
  op act1 : -> Modification .
  op act2 : -> Modification .
  op act3 : -> Modification .
  op bound :      -> Modification .
  op bound : Site -> Modification .
  op clustered : -> Modification .   *** used for integrins
  op deact : -> Modification .
  op dephos : -> Modification .
  op disrupted : -> Modification .
  op done : -> Modification .       *** used to prevent recycling
  op downreg : -> Modification .
  op gact : -> Modification .         *** activation of a Gef
  op gone : -> Modification .
  op inhib : -> Modification .  *** inhibited by: inhibitor binding
  op mem  : -> Modification .   *** at the membrane for TTZ
  op mito : -> Modification .  *** in the mito for TTZ
  op Nhydrox : -> Modification .       *** hydroxylation on Asparagine (N)
  op notthere : -> Modification .
  op phosbound : Site -> Modification .
  op Phydrox : -> Modification .       *** hydroxylation on Proline (P)
  op PL : -> Modification .  *** covalent conjugation with a phospholipid
  op pre : -> Modification .            *** Precursor
  op primed : -> Modification .    *** used for integrins
  op reloc : -> Modification .         *** Relocated
  op reloc2 : -> Modification .         *** Relocated again
  op WT : -> Modification [ctor] . 
  sorts GXP GTPS .
  subsorts GTPS < GXP < Modification .
  op GDP : -> GXP .    *** used for small GTPases
  ops GTP GTPmut : -> GTPS . 
  sort ACTS .
  subsort ACTS < Modification .
  ops act actmut : -> ACTS .
  op closed : -> Modification .
  op new : -> Modification .
  op num : Nat -> Modification .
  op off : -> Modification .
  op oligo : -> Modification .      *** oligomerized
  op one : -> Modification .
  op open : -> Modification .
  op ox    : -> Modification .  *** oxidized and reduced
  op pro1 : -> Modification .
  op pro2 : -> Modification .
  op red    : -> Modification .  *** oxidized and reduced
  op STphos : -> Modification . *** Serine/Threonine phosphorylation
  op STphos1 : -> Modification .
  op STphos2 : -> Modification .
  op three : -> Modification .
  op Tphos : -> Modification .
  op trimer : -> Modification .
  op trunc : -> Modification .  *** Truncated
  op two : -> Modification .
  op hydrox : -> Modification .          *** hydroxylation
  op hydrox : Site -> Modification .     *** hydroxylation with site
  op Sphos : -> Modification .

)

endfm
