Table 1.

Fold recognition from 3D-PSSM and FUGUE servers for the C-terminal region of BMV 1a

PBD code	Name	SF	Description	3D-PSSM		FUGUE
				e-Value	Percentage of identity	Z-score	Percentage of identity
1pjr and 3pjr	PcrA	1	DNA helicase from Bacillus stearothermophilus	–	–	2.33	6% (of 632 residues)
1uaa	RepA	1	DNA helicase from E.Coli	1.01	12% (of 306 residues)	2.33	5% (of 623 residues)
1hv8	MjDEAD	2	RNA helicase from Methanococcus jannaschii	1.53	12% (of 353 residues)	–	–
1a1v	NS3	2	RNA helicase from Hepatitis C virus	0.176	11% (of 135 residues)	–	–

First ranked e-values (and Z-scores) for the alignment of BMV 1a C-terminal region (residues 448–961) with the sequences of helicases with known structure hinted by means of the fold recognition server 3D-PSSM. Scores and alignments obtained by FUGUE are also given for the UvrD-helicases (sequences of PcrA and RepA). The percentage of identity and the total number of residues aligned with the query are shown. PDB codes are used to identify the helicase proteins: HCV helicase NS3 (1a1v), MjDEAD (1hv8), UvrD helicase RepA (1uaa), and PcrA (1pjr). The largest number of residues aligned is obtained with MjDEAD