TABLE 1.

Criteria extracted from the literature that were used to evaluate the Phage Proteomic Treesa

CriteriabBLASTP result with E-value cutoff of:Protein distance result with penalty value of:
0.0010.010.10510100
dsDNA, ssDNA, and ssRNA phage are fundamentally differentNcNcNcNdYYY
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)NNNYYYY
Leviviruses consist of two groups: group I (fr and MS2) and group II (GA and KU1) (28)NNYYYYY
φCPG1, φAR39, and Chp2 are more closely related to each other than to the avian Chlamydia psittaci φChp1 (53)YNNYYYY
α3 and φK ssDNA phage are more closely related to each other than to φX174 and G4 (36)NYNYYYY
ssDNA phages I2-2 and Ike are more closely related to each other than to F1 (58)NNNYYYY
ssDNA phage Pf3 is only distantly related to M13, f1, and fd (42)YYYYYYY
Fs-2 is similar to f1, fd, M13, Ike, and Pf3 (33)YYYYYYY
ssDNA phage SVTS2 is related to Spiroplasma citri φSpVI (56)YYYYYYY
Among the podoviruses, PZA is more closely related to B103 than to GA1 (51)YYYYYYN
Mycoplasma φP1 is related to other terminal protein-containing phage (e.g., φ29) (62)YYYNNYY
Podoviruses SIO1, T7, YeO3-12 are related (48, 49, 54)YYYYYYY
Lambdoid phage include lambda, 933W, N15, HK022, HK97, VT2-Sa, P22, D3, APSE-1, and HK620 (8, 13, 15, 37, 59, 64)YYYNYYNe
D29, L5, and Bxb are closely related (24, 44)YYYYYYY
Relative relationships of Sfi21 > adh > PVL ≥ φ105 (18)YYNNYYY
Methanobacterium φM2 is closely related to Methanobacterium wolfeii prophage ψM100 (52)YYYYYYY
HP1, P2, and 186 are related (21)YYYYYYY
  • 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.