Although novel ORFs aren’t orthologs of T4 like genes, some seem to get paralogous duplications of adjacent, conserved genes, such as RB69ORF010c with motB, and RB49ORF183c, 44RRORF188c and T4 ORFs alt. 1 alt. 2, with alt. An extra ORF, 44RRORF187c, seems to be a full length duplication of alt, but displays only 54% similarity to 44RR alt. While none from the remaining novel ORFs showed any similarity to T4, 89 of them matched other novel ORFs from among the other five T4 like genomes in this review. A subset of ORFs in phages 44RR, Aeh1, and RB43 appear to be orthologs of the pyrimidine salvage pathway, previously described in the T4 like phage KVP40. This pathway contains an NAPRTase plus a bifunctional NUDIX hydrolase nucleoti dyl transferase, that’s distinct in the monofunctional NUDIX hydrolase, nudE, located in T4.

nudE orthologs had been also predicted for Aeh1, RB43 and RB69. It so seems that Aeh1 and RB43 possess both the bifunctional info NUDIX protein as well as T4 like monofunctional NudE protein. It really is unclear no matter whether these observations reflect a practical redundancy for RB43 and Aeh1, or if nudE and also the bifunctional NUDIX transferase deliver distinctive functions within the phage contaminated cell. Conversely, RB49 won’t appear to encode either nudE or even the bifunctional NUDIX protein. Several other novel ORFs could possibly be concerned in nucleotide modification and synthesis. These include DNA methyl ase, nucleotidyl transferase, nucleotide triphosphatase and sugar isomerase domain functions identified by Pfam matches.

Furthermore, phylogenetic analyses suggest that phage 44RR appears to have acquired ribonucleotide reductase and other thioredoxin genes from a bacterial host, as opposed to by conservation from the T4 like orthologs. A variety of the predicted ORFs likely to be concerned in gene regulation were also recognized, which includes DNA binding proteins, polyADP ribosylases and hydrolases, DNA helicases, an excision repair endonuclease and hom ing endonucleases, as indicated in Table 3. Other putative functions identified consist of membrane proteins, pepti dases, ATPases, an exotoxin, plus a putative DnaJ style pro tein chaperone. A number of ORFs that do not match identified genes in GenBank do match GenBank environmental sample sequences. It is actually unclear if these matches are to uncharacterized bacterial hosts, or to unknown bacteri ophages.

All ORFs have been also searched for matches to signal peptide and transmembrane motifs. Tables of ORFs matching these motifs for each genome are available. Mobile DNA elements The T4 genome encodes numerous mobile DNA ele ments, like three group I introns with integrated ORFs encoding homing endonucleases too as the freestand ing homing endonucleases genes, mob and seg. No group I introns were detected among any of the T4 like genomes sequenced here. Having said that, two ORFs bearing similarity to your mob genes of T4 were identified in Aeh1 and RB43. An ORF just like T4 segD has also been described for KVP40. So, T4 seems to carry many more mobile aspects than the genomes analyzed right here. Interestingly, each RB49 and RB43 exhibit matches to a just lately identified class of HEGs, AP2 HNH mobile DNA aspects, which are related to your AP2 DNA transcription aspect in plants. This class of HEGs continues to be postulated to have transferred from bacteriophages into plant genomes via the chloroplast genome.