Analysis of the complete nucleotide sequence of the group IV RNA coliphage SP

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Abstract
We report the nucleotide sequence of the Group IV RNA bacteriophage SP. The entire sequence is 4276 nucleotides long. Four cistrons have been identified by comparison with the related Group III phage Qβ The maturation protein contains 449 amino acids, the coat protein contains 131 amino acids, the read-through protein contains 330 amino acids and the replicase β-subunit contains 575 amino acids. SP is 59 nucleotides longer than Qβ We have analyzed both sequence and structural conservation between SP and Qβ and shown that the sequences for the coat and central region of the replicase are strongly conserved between the two genomes. We also show that the S and M replicase binding sites of Qβ are strongly conserved in SP. Interestingly, the base composition of SP and Qβ differ significantly from one another , and most of the differences can be accounted for by a strong preponderance of U in the third position of each codon of Qβ relative to SP. We also compare conserved hairpins associated with potential coat protein and replicase binding sites.