Table 1.

Top-scoring structures that can serve as templates for the CPAF amino acid sequence in the program MODELLER [28] as identified by the program HHPRED [26, 27]. The column labeled “Prob” is the probability that the database match is a true positive. “E-values” are defined in the same way as in PSI-BLAST [46]. The “P-value” is equal to the “E-value” divided by the number of HMMs in the protein data bank. The “Score” column gives the total score that includes the score from the secondary structure comparison, which is listed in the column labeled “SS”. “Cols” contains the total number of matched columns in the query–template alignment and the remaining columns describe the range of aligned residues in the query and template [26, 27].

No. Hit	PDB Code	Protein	Prob	E-val	P-val	Score	SS	Cols	Query HMM	Template HMM
1	1k32 [25]	Tricorn Protease Thermatoga maritima	100	0	0	335.6	32.0	363	36-601	657-1040 (1045)
2	1fc6 [45]	PS II D1 Protease Scenedesmus obliquus	100	0	0	299.5	34.8	363	34-593	2-381 (388)
3	1j7x [47]	IRBP Interphotoreceptor Xenopus laevis	100	8.9E-38	7E-42	241.1	17.4	180	321-569	104-283 (302)
4	2ejy [48]	Erythrocyte membrane protein Homo sapiens	92.7	0.096	7.5E-6	28.0	5.2	49	108-156	16-69 (97))
5	2ev8 [49]	Erythrocyte membrane protein Homo sapiens	92.1	0.093	7.3E-6	28.0	4.6	49	108-156	16-69 (97)