The open reading frame for native gIII sequence begins with 5’-GTG AAA AAA TTA … (see GTG start in review Kozak, M. (1999) Gene 234, 187-208 Initiation of translation in prokaryotes and eukaryotes; van Wezenbeek, P.M.G.F. et al (1980) Gene 129-148). The N-terminus of pIII includes a leader sequence necessary for processing the newly translated protein in the cell. The mature peptide as displayed on M13 phage has been cleaved at the leader peptidase site. Note, the random region will be in the same reading frame as the leader sequence.
gIII translation for M13KE or an insertless clone:
MKKLLFAIPLVVPFYSHS // AETVES
gIII translation for a PhD clone (X is a randomized position):
Ph.D.-12 clone #E8210S, E8111L
MKKLLFAIPLVVPFYSHS // X12-GGGS-AETVES…pIII→
Ph.D.-7 clone #E8211S
MKKLLFAIPLVVPFYSHS // X7-GGGS-AETVES… pIII→
Ph.D.-C7C clone #E8212S
MKKLLFAIPLVVPFYSHS // ACX7C-GGGS-AETVES…pIII→
An additional note, a Ph.D. clone will have 5 copies of the same pIII protein, i.e. (Ph.D.-7) X7-GGGS-AETVES…, at one end of the cylindrical particle.
// indicates leader peptidase cleavage site