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Figure 2 | Virology Journal

Figure 2

From: Transcription of the T4 late genes

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.)

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