The difference in gene order suggests that rearrangement of these genes had occurred during evolution. Orf25 to orf31, except orf29 that encoded
a possible membrane protein, encoded tail proteins, whereas TSA HDAC chemical structure orf32 encoded a late gene control protein. These genes corresponded to the P2 operon F I F II EE’TUD (Figure 3, Additional file 1: Table S1; ). In P2, E’ overlaps the start of gene T, lacks a potential ribosome binding site, and extends 37 nt back into E in the -1 reading frame. A run of 6 T residues (T6G slippery sequence) was located 20 nt upstream of the possible GUG start of E’ and an extension of gene E following a -1 translational Navitoclax in vitro frameshift has been designated as E + E’. The arrangement of E and E’ genes within the tail gene cluster and their coupling through
a translational frameshift is conserved among P2-related phages as well as in several other phages such as lambda although they share no similarity in amino acid sequence [31–33]. Near the 3′-end of orf27, there is a T7G similar selleck chemicals to the conserved T6G slippery sequence , nt 288–295 relative to the orf27 start codon. Thus, by analogy, a -1 translational frameshift may occur here during translation, thereby producing a protein product of orf27.1 (Additional file 4: Figure S2A). Instead of the T7G, a predicted T7C slippery sequence was observed in the corresponding tail genes of prophages of S. maltophilia K279a, X. campestris pv. campestris 33913, X. oryzae pv. oryzae strains KACC10331, MAFF311018, and PXO99A (Additional
file 4: Figure S2B). These findings indicate that this type of arrangement may be conserved in all P2-like phages. The protein predicted for isometheptene orf33 was a phage-related protein similar to gp17 of phage BcepMu; orf34 encoded a protein similar to that of P2 regulatory protein Ogr (see below); the products predicted for orf35-46 were all hypothetical proteins, except that orf39 and orf43 encoded a DNA primase-like protein and a tyrosine family integrase, respectively. Tyrosine family integrases are responsible for DNA cleavage, strand exchange, and religation steps with a covalently bound phosphotyrosine intermediate . As shown in Additional file 5: Figure S3, similarity search based on domain architecture  and sequence alignments showed that the predicted protein of orf43 possessed 4 residues of the pentad conserved residues (R241, K264, H348 and H366) and the possible catalytic site Tyr375 (Additional file 5: Figure S3). However, no significant similarity in amino acid sequence was observed between the N-terminal region of Smp131 integrase and those of other integrases. Varied degrees of identity were shared by Smp131 proteins with the analogous proteins from phages encompassing a wild host range (Figure 3, Additional file 6: Table S3). These homologues include 23 encoded by Pseudomonas phage phiCTX (27% to 73% identity), 22 by Burkholderia phage KL3 (34% to 62% identity), and 20 by Enterobacteria phage P2 (26% to 60% identity).