TABLE 2.

Conserved motifs in initiator proteins of RC replicons^a

Familyb	Sequence ofc:
	Motif 2	Motif 3
φX174	GRLHFHAVHFM	VGFYVAKYVNKKSDM
cons	gxuHUHuxuux	ugxYuakYuxkxxxx
pC194	YNPHFHVLIAV	ELYEMAKYSGKDSDY
cons	yxxHUHvLUxV	xxxExxKYxxKxxDU
pMV158	KKAHYHVLYIA	NVENMYLYLTHESKD
cons	KkxHYHUUUxx	xxxgxUxYUtHxxxD
pT181		SNRFIRIYNKKQERK
cons		SdRFIRIYNKKqERK

^aThe two motifs found in Rep proteins of plasmids representing the main plasmid families, and their comparison with those found in the initiator proteins of ssDNA coliphages (162). 

^bBelow each Rep protein, a derived consensus is shown. 

^cMotif 2, termed the HUH motif, is thought to be the metal-binding domain of the Rep proteins. Note that this motif is not found in the Rep proteins of plasmids of the pT181 family or in the initiator gpII protein of filamentous coliphages. Motif 3 (the catalytic motif) contains the conserved Tyr residue involved in the nucleophilic attack to the plasmid DNA at initiation of replication. Capital letters denote totally conserved residues; lowercase letters denote residues conserved in many but not all proteins within the family; U and u denote hydrophobic residues; x denotes any residue.