Cp-1, a bacteriophage infecting Streptococcus pneumoniae, has a linear double-stranded DNA genome, with a terminal protein covalently linked to its 5' ends, that replicates by the protein-priming mechanism. We describe here the complete DNA sequence and transcriptional map of the Cp-1 genome. These analyses have led to the firm assignment of 10 genes and the localization of 19 additional open reading frames in the 19,345-bp Cp-1 DNA. Striking similarities and differences between some of these proteins and those of the Bacillus subtilis phage phi 29, a system that also replicates its DNA by the protein-priming mechanism, have been revealed. The genes coding for structural proteins and assembly factors are located in the central part of the Cp-1 genome. Several proteins corresponding to the predicted gene products were identified by in vitro and in vivo expression of the cloned genes. Mature major head protein from the virion particles results from hydrolysis of the primary gene product at the His-49 residue, whereas the phage gene is expressed in Escherichia coli without modification. We have also identified two open reading frames coding for proteins that show high degrees of similarity to the N- and C-terminal regions, respectively, of the single tail protein identified in phi 29. Sequencing and primer extension analysis suggest transcription of a small RNA showing a secondary structure similar to that of the prohead RNA required for the ATP-dependent packaging of phi 29 DNA. On the basis of its temporal expression, transcription of the Cp-1 genome takes place in two stages, early and late. Combined Northern (RNA) blot and primer extension experiments allowed us to map the 5' initiation sites of the transcripts, and we found that only three genes were transcribed from right to left. These analyses reveal that there are also noticeable differences between Cp-l and phi 29 in transcriptional organization. Considered together, the observations reported here provide new tangible evidence on phylogenetic relationships between B. subtilis and S. pneumoniae.