TABLE 2.
Phages, prophages, and phage-related elements with homology to phage B3a
| Phage or elementb | Bacterial hostc | Gene(s)d |
|---|---|---|
| Phage A118 | Listeria monocytogenes | ORF1-ORF72 |
| Phage BcepMu | Burkholderia cenocepacia | gp1-gp53 |
| BorMu | Bordetella bronchiseptica RB50 | BB3606-BB3657 |
| Brs1* | Brucella suis 1330 | ?BR0584-BR0599? (ext) |
| Bruc1* | Brucella melitensis 16M | BMEI1340-BMEI1350 |
| Cc1* | Caulobacter crescentus CB215 | ?CC2776-CC2790 (ext) |
| CP-933T* | Escherichia coli O157:H7 EDL933 | Z2966-Z2994 |
| CV1* | Chromobacterium violaceum ATCC 12472 | CV0406-CV0432 |
| CV2* | Chromobacterium violaceum ATCC 12472 | ?CV1474-CV1479? |
| Phage D108 | Escherichia coli | Probably 50 to 60 genese |
| Phage D3112 | Pseudomonas aeruginosa | p01-p55f |
| DucMu1 | Haemophilus ducreyi 35000HP | HD0089-HD0156 |
| DucMu2 | Haemophilus ducreyi 35000HP | HD0479-HD0540 |
| DucMu3 | Haemophilus ducreyi 35000HP | HD1517-HD1581 |
| FluMu | Haemophilus influenzae Rd KW20 | HI1476-HI1523 |
| Phage HF2 | Haloferax volcanii | ORF1-ORF121 |
| Phage K139 | Vibrio cholerae | ORF1-ORF44 |
| MiniFluMu* | Haemophilus influenzae Rd KW20 | HI1568-HI1571 |
| Phage Mu | Escherichia coli | gp1-gp55 |
| MuSo1 | Shewanella oneidensis MR-1 | SO0641-SO0683 |
| MuSo2 | Shewanella oneidensis MR-1 | SO2652-SO2704 |
| NeisMu1* | Neisseria meningitidis B MC58 | NMB1078-NMB1121 |
| NeisMu2*g | Neisseria meningitidis B MC58 | NMB0985-NMB0991 |
| NMB1* | Neisseria meningitidis B MC58 | NMB1002-NMB1007 |
| Pnm1 | Neisseria meningitidis A Z2491 | NMA1821-NMA1884 |
| Pnm2* | Neisseria meningitidis A Z2491 | NMA1281-NMA1330 |
| Pnm3* | Neisseria meningitidis A Z2491 | NMA1185-NMA1199? |
| Pnm4/5*h | Neisseria meningitidis A Z2491 | NMA1208-NMA1231? |
| Phage 03 | Pseudomonas syringae DC3000 | PSPTO3385-PSPTO3429 |
| Phage V | Shigella flexneri | SfV ORF1-ORF53 |
| Phage 186 | Escherichia coli | ORF1-ORF97 |
| Phage P2 | Escherichia coli | ORF1-ORF42 |
| Phage φP27 | Escherichia coli | ORF1-ORF58 |
| Phage φE125 | Burkholderia mallei | ORF1-ORF70 |
| Phage PP01 | Pseudomonas putida KT2440 | PP3849-PP3920 |
| RadMu | Deinococcus radiodurans R1 | DRA0074-DRA0119 |
| RS1* | Ralstonia solanacearum GMI1000 | ?RSc0839-RSc0892? |
| RS6 | Ralstonia solanacearum GMI1000 | RSc1896-RSc1948 |
| SP14* | Escherichia coli O157:H7 Sakai | ?ECs2713-ECs2774 |
| SP18 | Escherichia coli O157:H7 Sakai | ECs4943-ECs4998 |
| Sti3i | Salmonella serovar Typhi CT18j | STY1591-STY1643 |
| Phage ST64B | Salmonella serovar Typhimuriumj | Sb1-Sb56 |
| Stm7* | Salmonella serovar Typhimurium LT2j | STM4196-STM4219 |
| Tum2 | Agrobacterium tumefaciens C58 | AGR_C_1731-AGR_C_1774 |
| VibMu* | Vibrio cholerae N16961 | ?VC1788-VC1803 (ext) |
| VioMuk | Chromobacterium violaceum ATCC 12472 | ?CV2111-CV2165? |
| XacP1* | Xanthomonas axonopodis 903 | ?XAC 2640-XAC2655? (ext) |
| XccP1 | Xanthomonas campestris ATCC33913 | XCC2962-3012 |
| XfP1 | Xylella fastidiosa 9a5c | XF0678-XF0733 |
| XfP4* | Xylella fastidiosa 9a5c | XF1642-XF1711 |
| XfP5* | Xylella fastidiosa 9a5c | XF0485-XF0536? |
| XfP6* | Xylella fastidiosa 9a5c | XF2110-XF2132 (ext) |
Much of the information given here for prophages and phage-related elements found in bacterial genome sequences was taken from the review by Casjens (13). The genome sequences for Bordetella bronchiseptica, Chromobacterium violaceum, and Haemophilus ducreyi were completed after that review; their B3-homologous prophages and elements are named here using the conventions of Morgan et al. (68) and Casjens (13). Specifically, new Mu-like prophages were named by adding a three-letter prefix to Mu (e.g., VioMu), and short phage-related elements are identified by a strain designator and asterisk (e.g., CV1*). For other phages and phage elements that were named by viral and bacterial genome sequencing teams, we use the names given by those teams.
The names of phages known to be capable of infection and multiplication are designated Phage. Elements that appear to be too short to allow independent multiplication are marked with an asterisk. Newly identified prophages with high homology to Mu are designated BorMu, DucMu (pronounced duke), and VioMu according to the convention of Morgan et al. (68).
For infectious phage, a common host is listed. For prophages and elements, the strain whose genome was sequenced is given.
The genes included in each phage, prophage, or element are listed using the genomic sequential ORF numbering system. A question mark is added when the terminal gene is uncertain. (ext) indicates that the identification of B3-homologous genes has resulted in the extension of the likely outer limits of prophages and phage-related elements beyond those annotated by Casjens (13).
Phage D108 has not been sequenced, but it is very closely related to Mu (21); therefore, it probably has 50 to 60 genes.
The sequence database annotation for D3112 contains 55 genes, whereas the published paper lists only 53 genes (91).
NeisMu2 is also called MuMenB (62).
Pnm4 and Pnm5 were originally annotated as two separate elements (48, 71). Their close proximity and the identification of intervening genes as B3 homologues suggest that they may be a single longer element that we call Pnm4/5.
Sti3 is also called SalMu (86).
The complete names for Salmonella species are as follows: Salmonella serovar Typhi is Salmonella enterica subsp. enterica serovar Typhi (strain CT18), and Salmonella serovar Typhimurium LT2 is Salmonella enterica serovar Typhimurium (strain LT2).
VioMu is also called ChromoMu (86).