TABLE 3.
Phages and prophage elements related to Rhodococcus phage Pepy6, Poco6, Pine5, or DocB7
| Phage or prophage (host)a | Genome length (kb)b | Genomic terminic | No. of CDSd | No. of CDS with TMD (%)e | Relationship to Rhodococcus phage (no. of shared proteins)f |
|---|---|---|---|---|---|
| 1706 (Lactococcus lactis) | 55 | 3′ cos GCCCTGTCT | 76 | 12 (16) | 21 proteins shared with Pepy6 |
| BRYFOR.phiA (Bryantella formatexigens DSM 14469) | 57 | 3′ cos (based on TerL similarity to Pine5 gp14) | 73 | 17 (23) | 23 proteins shared with Pepy6; 21 proteins shared with 1706 |
| CLOSS21 (Clostridium sp. strain SS2/1) | 66 | 3′ cos (based on TerL similarity to Pine5 gp14) | 89 | 18 (20) | 24 proteins shared with Pepy6; 22 proteins shared with 1706 |
| CLOLEP (Clostridium leptum DSM 753) | 52 | 3′ cos (based on TerL similarity to Pine5 gp14) | 78 | 11 (14) | 34 proteins shared with Pepy6; 21 proteins shared with 1706 |
| Mycobacteriophage Rosebush-like phages | 67-71 | pac (based on TerL related to Rosebush gp7) | 81-104 | (∼10) | 31 proteins shared with Pine5 |
1706, Lactococcus lactis phage 1706 (NC_010576); BRYFOR, Bryantella formatexigens DSM 14469 prophage (derived from GenBank entry NZ_ACCL02000018.1 and includes coding region for locus tags BRYFOR_08569 to BRYFOR_08504); CLOSS21, Clostridium sp. strain SS2/1 prophage (derived from GenBank entry NZ_ABGC03000034 and includes locus tags CLOSS21_01580 to CLOSS21_01492); CLOLEP, Clostridium leptum DSM 753 (derived from GenBank entry NZ_ABCB02000017 and includes locus tags CLOLEP_01347 to CLOLEP_01425). Mycobacteriophage Rosebush-like phages (with GenBank entries in parentheses) included Rosebush (NC_004684), Qyrzula (NC_008204), Cooper (NC_008195), PG1 (NC_005259), Orion (NC_008197), Pipefish (NC_008199), Chah (NC_011284), Colbert (GQ303259.1), Nigel (NC_011044), Puhltonio (GQ303264.1), Phaedrus (NC_011057), Phlyer (NC_012027), and UncleHowie (GQ303266.1).
Genome length, genome nucleotide kilobase pair length.
The structure of the packaged genomic termini is shown. pac, headful packaging.
The number of protein-coding genes (CDS) is shown.
The numbers and percentages of the proteins encoded by the element that are predicted to have transmembrane domains (CDS with TMD) are shown.
Maximum E values of 1e−10 and scores over 50 were used to define shared proteins.