Figure 2

Amino acid sequence conservation of gp55. All T4-related phage genomes sequenced to date (see [59], which is a review by Petrov, et al., in this series) contain readily identifiable gp55 homologues [81]. Four segments of sequence conservation can be noted. The central and largest segment 2 allows the distant relationship to domain 2 of σ⁷⁰ to be discerned, primarily through correspondence with σ⁷⁰ conserved segments 2.1 and 2.2 and secondary structure. The presumption that segment 2.4 harbors the late promoter recognition element of gp55 is speculative. Conserved segment 4 is the sliding clamp-binding epitope. Conserved segments 1 and 3 share no recognizable sequence similarity with σ⁷⁰. Whether they correspond functionally with σ segment 1.1/1.2 and 3.1, respectively, is not known. The numbering of residues is continuous for the T4 protein. Amino acid sequences of the T4, RB14 and RB32 proteins are identical; only T4 is listed. RB49 and phi-1 gp55 are also identical except for Q30 (RB49)→E30 (phi-1); only RB49 is listed. A secondary structure prediction from HHpred, with α-helices as cylinders, is shown below the alignment. Vertical lines at the side cluster phages infecting (top to bottom): E. coli (133 was isolated as an Acinetobacter phage); Aeromonas species; and Vibrio species. The more divergent S-PM2 protein is the only representative of the completely sequenced cyanobacterial phages that has been included for this presentation. (The cyanobacterial RNAPs constitute a separate clade in the phylogeny of the multisubunit enzymes, as do the archaeal RNAPs and the individual eukaryotic nuclear RNAPs I-V.)