Focused Psi-Blast with rank order statistic

1. VpV262orfH/SIO1orf3+5 was suspected of being a divergent homologue of theT7 portal protein.
2. VpV262orfK was suspected of being a divergent homologue of T7/P60 capsid protein.

• Key: one of the 3 proteins of the suspected homologous family.
• Library:
1. All SIO1 + T7 proteins.
2. All P60 + VpV262 proteins.
• Method: 2-round Psi-Blast.
• Results:
1. VpV262 orfH forms PSSM with SIO1 orf3+5 on round 1 and finds T7 portal as best hit and E value = 0.008 on round 2.
2. T7 capsid forms PSSM with P60 capsid on round 1 and finds VpV262 as best hit and E value of 0.36 on round 2.
• Evaluation:
• The Blast E values are considered too soft to support a conclusion.
• The probablility of finding the hypothesized gene as the best T7 match =
fraction of total protein in T7 represented by the target =
0.02 and 0.04, respectively.
• Joint P value for the entire module being of common ancestry is P = 0.0008.
• Fig. 2, Hardies et al., 2003.
• Confirmation by secondary structure prediction: