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Tc1 being a tail completion protein involved in long tail assembly [ 26, 48], we anticipated that a neck containing Tc1 would not be found in Podoviridae phages.
In addition, some yet not identified genes probably encoding a head completion protein and other hypothetical proteins were detected in the amplified DNA.
We show that the contigs represent modules linked by long repeat regions enclosing some yet not identified ORFs (e.g., for a head completion protein).
Similarly, in B. pseudomallei 1106a chromosome 2, the AMP nucleosidase (BURPS1106A_A2416) and integrase (BURPS1106A_A2415) genes are adjacent to genes annotated as encoding a phage portal domain protein (BURPS1106A_A2414) and phage tail completion protein (BURPS1106A_A2413).
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Gp6 is essential at early steps of DNA packaging and for DNA translocation to the capsid interior, it affects the efficiency of DNA packaging, it is a central component of the headful sensor that determines the size of the packaged DNA molecule, and is essential for closure of the portal pore by the head completion proteins to prevent exit of the DNA encapsidated.
In particular, SPP1, λ and HK97 are gathered within the same phage type because they are predicted as exhibiting homologous head- and tail completion proteins.
Therefore, we identified from the literature several proteins characterized as head- and tail- completion proteins in a number of model phages (Table 1), and we search for homologs of these proteins within the genomes of the same 447 completely sequenced phages.
They comprise two head-completion proteins homologous to T4 gp13 (noted Ad2) and T4 gp14 (noted Hc2), and a tail-completion protein homologous to T4 gp15 (noted Tc2).
They adopt a structural organisation similar to that of the Siphoviridae phage SPP1 and comprise three head-to-tail connection proteins: two head-completion proteins homologous to SPP1 gp15 (Adaptor, noted Ad1) and SPP1 gp16 (Head closure, noted Hc1) and a tail-completion protein homologous to SPP1 gp17 (noted Tc1).
Head- and tail-completion proteins extracted from the literature are listed in this table.
We detected 633 phage head- and tail-completion proteins (compared to only 282 when using PSI-Blast, see Table 2).
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