Job Description P43329 Confidence 100.00% Date Thu Jan 5 12:02:17 GMT 2012 Rank 3 Aligned Residues 415 % Identity 18% Template c1a1vA_ PDB info PDB header:hydrolase/dna Chain: A: PDB Molecule:protein (ns3 protein); PDBTitle: hepatitis c virus ns3 helicase domain complexed with single2 stranded sdna Resolution 2.20 Å

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		91	.	.	.	.	.	.	.	.	100	.	.	.	.	.	.	.	.	.	110	.	.	.	.	.	.	.	.	.	120	.	.	.	.	.	.	.	.	.	130	.	.	.	.	.	.	.	.	.	140	.	.	.	.	.	.	.	.	.	150	.	.	.	.	.	.	.	.	.	160	.	.	.	.	.	.	.	.	.	170
Predicted Secondary structure
Query SS confidence
Query Sequence		R	D	H	Q	V	V	I	V	A	G	E	T	G	S	G	K	T	T	Q	L	P	K	I	C	M	E	L	G	R	G	I	K	G	L	I	G	H	T	Q	P	R	R	L	A	A	R	T	V	A	N	R	I	A	E	E	L	K	T	E	P	G	G	C	I	G	Y	K	V	R	F	S	D	H	V	S	D	N	T	M	V
Query Conservation
Alig confidence																														.	.	.	.																																									.	.	.	.	.
Template Conservation																														.	.	.	.																																									.	.	.	.	.
Template Sequence		Q	S	F	Q	V	A	H	L	H	A	P	T	G	S	G	K	S	T	K	V	P	A	A	Y	A	A	Q	G	.	.	.	.	Y	K	V	L	V	L	N	P	S	V	A	A	T	L	G	F	G	A	Y	M	S	K	A	H	G	V	D	P	N	I	R	T	G	V	R	T	I	T	T	G	.	.	.	.	.	S	P	I
Template Known Secondary structure		S	S										T	T	S		T	T	T								T	T	T	.	.	.	.								S																	S								S	S							.	.	.	.	.		S
Template Predicted Secondary structure																														.	.	.	.																																									.	.	.	.	.
Template SS confidence
		195	.	.	.	.	200	.	.	.	.	.	.	.	.	.	210	.	.	.	.	.	.	.	.	.	220	.	.					.	.	.	.	.	.	.	230	.	.	.	.	.	.	.	.	.	240	.	.	.	.	.	.	.	.	.	250	.	.	.	.	.	.	.	.	.	260	.	.						.	.	.
		171	.	.	.	.	.	.	.	.	180	.	.	.	.	.	.	.	.	.	190	.	.	.	.	.	.	.	.	.	200	.	.	.	.	.	.	.	.	.	210	.	.	.	.	.	.	.	.	.	220	.	.	.	.	.	.	.	.	.	230	.	.	.	.	.	.	.	.	.	240	.	.	.	.	.	.	.	.	.	250
Predicted Secondary structure
Query SS confidence
Query Sequence		K	L	M	T	D	G	I	L	L	A	E	I	Q	Q	D	R	L	L	M	Q	Y	D	T	I	I	I	D	E	A	H	E	R	S	L	N	I	D	F	L	L	G	Y	L	K	E	L	L	P	R	R	P	D	L	K	I	I	I	T	S	A	T	I	D	P	E	R	F	S	R	H	F	N	N	A	P	I	I	E	V	S
Query Conservation
Alig confidence												.	.	.																																																			.	.	.	.
Template Conservation												.	.	.																																																			.	.	.	.
Template Sequence		T	Y	S	T	Y	G	K	F	L	A	.	.	.	D	G	G	S	G	G	A	Y	D	I	I	I	C	D	E	C	H	S	T	D	A	T	S	I	L	G	I	G	T	V	L	D	Q	A	E	T	A	G	A	R	L	V	V	L	A	T	A	T	P	P	.	.	.	.	G	S	V	T	V	P	H	P	N	I	E	E	V
Template Known Secondary structure												.	.	.	T	T							S						T	T	T			S														T	T	T	T	T		S							S	S		T	.	.	.	.	T							T	T
Template Predicted Secondary structure												.	.	.																																																			.	.	.	.
Template SS confidence
		266	.	.	.	270	.	.	.	.	.				.	.	.	.	280	.	.	.	.	.	.	.	.	.	290	.	.	.	.	.	.	.	.	.	300	.	.	.	.	.	.	.	.	.	310	.	.	.	.	.	.	.	.	.	320	.	.	.	.	.					.	.	.	.	330	.	.	.	.	.	.	.	.
		251	.	.	.	.	.	.	.	.	260	.	.	.	.	.	.	.	.	.	270	.	.	.	.	.	.	.	.	.	280	.	.	.	.	.	.	.	.	.	290	.	.	.	.	.	.	.	.	.	300	.	.	.	.	.	.	.	.	.	310	.	.	.	.	.	.	.	.	.	320	.	.	.	.	.	.	.	.	.	330
Predicted Secondary structure
Query SS confidence
Query Sequence		G	R	T	Y	P	V	E	V	R	Y	R	P	I	V	E	E	A	D	D	T	E	R	D	Q	L	Q	A	I	F	D	A	V	D	E	L	S	Q	E	S	H	G	D	I	L	I	F	M	S	G	E	R	E	I	R	D	T	A	D	A	L	N	K	L	N	L	R	H	T	E	I	L	P	L	Y	A	R	L	S	N	S
Query Conservation
Alig confidence																							.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.																									.	.	.
Template Conservation																							.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.																									.	.	.
Template Sequence		A	L	S	T	T	G	E	I	P	F	Y	G	K	A	I	P	L	E	V	I	K	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	G	G	R	H	L	I	F	C	H	S	K	K	K	C	D	E	L	A	A	K	L	V	A	L	.	.	.	G	I	N	A	V	A	Y	Y	R	G	L	D	V	S
Template Known Secondary structure					S		S	S				T	T					T					.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	S	S							S	S														T	.	.	.	T								T	T	S		G	G
Template Predicted Secondary structure																							.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.																									.	.	.
Template SS confidence
		340	.	.	.	.	.	.	.	.	.	350	.	.	.	.	.	.	.	.	.	360																			.	.	.	.	.	.	.	.	.	370	.	.	.	.	.	.	.	.	.	380	.	.	.	.				.	.	.	.	.	390	.	.	.	.	.	.	.	.
		331	.	.	.	.	.	.	.	.	340	.	.	.	.	.	.	.	.	.	350	.	.	.	.	.	.	.	.	.	360	.	.	.	.	.	.	.	.	.	370	.	.	.			.	.	.	.	.	.	380	.	.	.	.	.	.	.	.	.	390	.	.	.	.	.	.	.	.	.	400	.	.	.	.	.	.	.	.
Predicted Secondary structure																																													.	.
Query SS confidence																																													.	.
Query Sequence		E	Q	N	R	V	F	Q	S	H	S	G	R	R	I	V	L	A	T	N	V	A	E	T	S	L	T	V	P	G	I	K	Y	V	I	D	P	G	T	A	R	I	S	R	.	.	Y	S	Y	R	T	K	V	Q	R	L	P	I	E	P	I	S	Q	A	S	A	N	Q	R	K	G	R	C	G	R	V	S	E	G	I	C
Query Conservation																																													.	.
Alig confidence				.	.	.	.	.																		.	.	.	.																.	.
Template Conservation				.	.	.	.	.																		.	.	.	.
Template Sequence		V	I	.	.	.	.	.	P	T	S	G	D	V	V	V	V	A	T	D	A	L	F	T	G	.	.	.	.	D	F	D	S	V	I	D	C	N	T	V	T	Q	T	V	D	F	S	L	D	P	T	F	T	I	E	T	T	T	L	P	Q	D	A	V	S	R	T	Q	R	R	G	R	T	G	R	G	K	P	G	I	Y
Template Known Secondary structure		G	S	.	.	.	.	.		S	S	S	S							T	T					.	.	.	.		B	S																	S	S	S											B									T	T	B		S	S	S
Template Predicted Secondary structure				.	.	.	.	.																		.	.	.	.
Template SS confidence
		399	400						.	.	.	.	.	.	.	.	.	410	.	.	.	.	.	.	.					.	.	420	.	.	.	.	.	.	.	.	.	430	.	.	.	.	.	.	.	.	.	440	.	.	.	.	.	.	.	.	.	450	.	.	.	.	.	.	.	.	.	460	.	.	.	.	.	.	.	.	.
		409	410	.	.	.	.	.	.	.	.	.		420	.	.	.	.	.	.	.	.	.	430	.	.	.	.	.	.	.	.	.	440	.	.	.	.	.	.	.	.	.	450	.	.	.	.	.	.	.	.	.	460	.	.	.	.	.	.	.	.	.	470	.	.	.	.	.	.	.	.	.	480	.	.	.	.	.	.	.
Predicted Secondary structure													.
Query SS confidence													.
Query Sequence		I	R	L	Y	S	E	D	D	F	L	S	.	R	P	E	F	T	D	P	E	I	L	R	T	N	L	A	S	V	I	L	Q	M	T	A	L	G	L	G	D	I	A	A	F	P	F	V	E	A	P	D	K	R	N	I	Q	D	G	V	R	L	L	E	E	L	G	A	I	T	T	D	E	Q	A	S	A	Y	K	L	T
Query Conservation													.
Alig confidence													.																																																													.	.	.	.	.	.
Template Conservation																																																																										.	.	.	.	.	.
Template Sequence		R	F	V	A	P	G	E	R	P	S	G	M	F	D	S	S	V	L	C	E	C	Y	D	A	G	A	W	Y	E	L	T	P	A	E	T	T	V	R	L	R	A	Y	M	N	T	P	G	L	P	V	C	Q	D	H	L	E	F	W	E	G	V	F	T	G	L	T	H	I	D	A	H	F	.	.	.	.	.	.	L	S
Template Known Secondary structure				S		S			B		S		B																S																	S	T	T	S		B																	S						.	.	.	.	.	.
Template Predicted Secondary structure																																																																										.	.	.	.	.	.
Template SS confidence
		474	.	.	.	.	.	480	.	.	.	.	.	.	.	.	.	490	.	.	.	.	.	.	.	.	.	500	.	.	.	.	.	.	.	.	.	510	.	.	.	.	.	.	.	.	.	520	.	.	.	.	.	.	.	.	.	530	.	.	.	.	.	.	.	.	.	540	.	.	.	.	.							.	.
		488	.	490	.	.	.	.	.	.	.	.	.	500	.	.	.	.	.	.	.	.	.	510	.	.	.	.	.	.	.	.	.	520	.	.	.	.	.	.	.	.			.	530	.	.	.	.	.	.	.	.	.	540	.	.	.	.	.	.	.	.	.	550	.	.	.	.	.	.	.
Predicted Secondary structure																																											.	.
Query SS confidence																																											.	.
Query Sequence		P	L	G	R	Q	L	S	Q	L	P	V	D	P	R	L	A	R	M	V	L	E	A	Q	K	H	G	C	V	R	E	A	M	I	I	T	S	A	L	S	I	Q	.	.	D	P	R	E	R	P	M	D	K	Q	Q	A	S	D	E	K	H	R	R	F	H	D	K	E	S	D	F	L	A
Query Conservation																																											.	.
Alig confidence																																											.	.
Template Conservation
Template Sequence		Q	T	K	Q	S	G	E	N	F	P	Y	L	V	A	Y	Q	A	T	V	C	A	R	A	Q	A	P	P	P	S	W	D	Q	M	W	K	C	L	I	R	L	K	P	T	L	H	G	P	T	P	L	L	Y	R	L	G	A	V	Q	N	E	V	T	L	T	H	P	I	T	K	Y	I	M
Template Known Secondary structure						T	T		S	S															T				S			S	G	G	G	G	G	G	T	T	T	G	G	G			S						S	B	S	S				S						S
Template Predicted Secondary structure
Template SS confidence
		549	550	.	.	.	.	.	.	.	.	.	560	.	.	.	.	.	.	.	.	.	570	.	.	.	.	.	.	.	.	.	580	.	.	.	.	.	.	.	.	.	590	.	.	.	.	.	.	.	.	.	600	.	.	.	.	.	.	.	.	.	610	.	.	.	.	.	.	.	.	.	620