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. 2010 Nov 19;77(2):669–683. doi: 10.1128/AEM.01952-10

FIG. 3.

FIG. 3.

Genome maps of Pepy6 and Poco6 and related phages and prophages. (A) Genome maps of phages ReqiPepy6 and ReqiPoco6. Purple shading between the genome maps indicates segments of DNA that align with greater than 75% identity. The colors of the genes or proteins in the gene maps indicate the relationship of the encoded protein with other proteins as follows. Yellow indicates a homologue is encoded by phage 1706. Yellow genes with green outlines encode homologues of phage 1706 virion-associated proteins. The 1706 gene is indicated below the Rhodococcus phage gene. Turquoise indicates that there was no homologue in 1706, nor was a functional annotation possible. Dark blue indicates proteins for which a functional annotation could be made but lacked homologues in 1706. Green proteins possess 56 invariant, N-terminal amino acid residues, indicated by peach bars. Genes outlined in red encode proteins with predicted transmembrane helices. Regions shaded in peach indicate locations of gene insertions relative to phage 1706. (B) Genome maps of Lactococcus lactis phage 1706 and prophage elements BRYFOR and CLOSS21, present in the genomic sequences of Bryantella formatexigens DSM 14469 and Clostridium sp. strain SS2/1 genome, respectively. The phage 1706 genome map was derived from the GenBank entry with accession no. EU081845. The BRYFOR prophage encompasses the region encoding locus tags BRYFOR_08504 to BRYFOR_08569. The CLOSS21 prophage encompasses the region encoding locus tags CLOSS21_01492 to CLOSS21_01580. In order to align with phage 1706, the BRYFOR and CLOSS21 maps are drawn with the order of prophages changed. The locations of the prophage genomic termini, between the coding region of BRYFOR gene73 and gene1 and CLOSS21 gene89 and gene1, are indicated on the genome maps by turquoise shading. The colors of the genes or proteins indicate the relationship of the encoded protein with other proteins as follows: yellow, homologue encoded by Pepy6 and Poco6; gray, no homologue encoded by Pepy6 or Poco6. A green outline indicates that the protein encoded by the gene is a homologue of phage 1706 virion-associated protein. A red outline indicates that the protein encoded by the gene has predicted transmembrane helices. The gene number of the corresponding protein encoded by Pepy6 and 1706 is indicated below each map (-, no protein). Regions shaded in peach indicate locations of gene insertions in the map relative to phage 1706. Select functional annotations are shown above genes by the following abbreviations: e15, Salmonella phage epsilon15 tail fiber protein; lip, lipase; hol, holin; tmp, tape measure protein; Prim, primase; pol, DNA polymerase; HNH, homing endonuclease; Int, integrase; endo, endonuclease; ligA, ligase A domain; CMP deaminase, deoxycytidinylate deaminase. Homologous gene products in Pepy6 and 1706 (Pepy6yp and 1706yp, respectively) are indicated below each map.