TABLE 1.
Criteria extracted from the literature that were used to evaluate the Phage Proteomic Treesa
| Criteriab | BLASTP result with E-value cutoff of:
|
Protein distance result with penalty value of:
|
|||||
|---|---|---|---|---|---|---|---|
| 0.001 | 0.01 | 0.1 | 0 | 5 | 10 | 100 | |
| dsDNA, ssDNA, and ssRNA phage are fundamentally different | Nc | Nc | Nc | Nd | Y | Y | Y |
| ssRNA phage fall into two groups: (i) leviviruses (fr, MS2, and GA) and (ii) alloleviviruses (SP, NL95, M11, and MX1); PP7 is an out group (7) | N | N | N | Y | Y | Y | Y |
| Leviviruses consist of two groups: group I (fr and MS2) and group II (GA and KU1) (28) | N | N | Y | Y | Y | Y | Y |
| φCPG1, φAR39, and Chp2 are more closely related to each other than to the avian Chlamydia psittaci φChp1 (53) | Y | N | N | Y | Y | Y | Y |
| α3 and φK ssDNA phage are more closely related to each other than to φX174 and G4 (36) | N | Y | N | Y | Y | Y | Y |
| ssDNA phages I2-2 and Ike are more closely related to each other than to F1 (58) | N | N | N | Y | Y | Y | Y |
| ssDNA phage Pf3 is only distantly related to M13, f1, and fd (42) | Y | Y | Y | Y | Y | Y | Y |
| Fs-2 is similar to f1, fd, M13, Ike, and Pf3 (33) | Y | Y | Y | Y | Y | Y | Y |
| ssDNA phage SVTS2 is related to Spiroplasma citri φSpVI (56) | Y | Y | Y | Y | Y | Y | Y |
| Among the podoviruses, PZA is more closely related to B103 than to GA1 (51) | Y | Y | Y | Y | Y | Y | N |
| Mycoplasma φP1 is related to other terminal protein-containing phage (e.g., φ29) (62) | Y | Y | Y | N | N | Y | Y |
| Podoviruses SIO1, T7, YeO3-12 are related (48, 49, 54) | Y | Y | Y | Y | Y | Y | Y |
| Lambdoid phage include lambda, 933W, N15, HK022, HK97, VT2-Sa, P22, D3, APSE-1, and HK620 (8, 13, 15, 37, 59, 64) | Y | Y | Y | N | Y | Y | Ne |
| D29, L5, and Bxb are closely related (24, 44) | Y | Y | Y | Y | Y | Y | Y |
| Relative relationships of Sfi21 > adh > PVL ≥ φ105 (18) | Y | Y | N | N | Y | Y | Y |
| Methanobacterium φM2 is closely related to Methanobacterium wolfeii prophage ψM100 (52) | Y | Y | Y | Y | Y | Y | Y |
| HP1, P2, and 186 are related (21) | Y | Y | Y | Y | Y | Y | Y |
a
“No” (N) indicates that the particular criteria were not met by the tree in question. A tree using the protein distance method with a penalty of 10 met all of the criteria (i.e., Yes [Y]) and is shown in Fig. 2.
b
Source references are indicated in parentheses.
c
dsDNA Fuselloviridae and Corticoviridae phage group with ssDNA phages due to one similar protein.
d
Inoviridae MV-L1 groups with Siphoviridae BK5-T.
e
T4 is forced into lambdoid phage by the penalty.