Job Description P06612 Confidence 100.00% Date Thu Jan 5 10:59:12 GMT 2012 Rank 3 Aligned Residues 568 % Identity 25% Template c2o59B_ PDB info PDB header:isomerase/dna Chain: B: PDB Molecule:dna topoisomerase 3; PDBTitle: structure of e. coli topoisomerase iii in complex with an 8-2 base single stranded oligonucleotide. frozen in glycerol3 ph 8.0 Resolution 2.50 Å

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		4	.	.	.	.	.	10	.	.	.	.	.	.	.	.	.	20	.														.	.	.	.	.	.	.	.	30	.	.	.	.	.	.	.	.	.	40	.	.	.	.	.	.	.	.	.	50	.	.	.	.	.	.	.	.	.	60	.	.	.	.	.	.	.	.	.	70
Predicted Secondary structure																				.	.	.	.	.	.	.	.	.	.	.	.	.
Query SS confidence																				.	.	.	.	.	.	.	.	.	.	.	.	.
Query Sequence		A	L	V	I	V	E	S	P	A	K	A	K	T	I	N	K	Y	L	.	.	.	.	.	.	.	.	.	.	.	.	.	G	S	D	Y	V	V	K	S	S	V	G	H	I	R	D	L	P	T	S	G	S	A	A	K	K	S	A	D	S	T	S	T	K	T	A	K	K	P	K	K	D	E	R	G	A	L	V	N	R
Query Conservation																				.	.	.	.	.	.	.	.	.	.	.	.	.
Alig confidence																				.	.	.	.	.	.	.	.	.	.	.	.	.																																								.	.	.	.	.	.	.	.	.	.
Template Conservation																																																																								.	.	.	.	.	.	.	.	.	.
Template Sequence		R	L	F	I	A	E	K	P	S	L	A	R	A	I	A	D	V	L	P	K	P	H	R	K	G	D	G	F	I	E	C	G	N	G	Q	V	V	T	W	C	I	G	H	L	L	E	Q	A	Q	P	D	A	Y	D	S	R	Y	A	R	W	N	L	A	D	L	P	I	V	P	E	.	.	.	.	.	.	.	.	.	.
Template Known Secondary structure							S	S									T	T	S		S						S	S					T	T	T								S		S						G	G	G	T		G	G	G	G	S			S	T	T		S				S	.	.	.	.	.	.	.	.	.	.
Template Predicted Secondary structure																																																																								.	.	.	.	.	.	.	.	.	.
Template SS confidence
		2	.	.	.	.	.	.	.	10	.	.	.	.	.	.	.	.	.	20	.	.	.	.	.	.	.	.	.	30	.	.	.	.	.	.	.	.	.	40	.	.	.	.	.	.	.	.	.	50	.	.	.	.	.	.	.	.	.	60	.	.	.	.	.	.	.	.	.	70	.
		71	.	.	.	.	.	.	.	.	80	.	.	.	.	.	.	.	.	.	90	.	.	.	.	.	.	.	.	.	100	.	.	.	.	.	.	.	.	.	110	.	.	.	.	.	.	.	.	.	120	.	.	.	.	.	.	.	.	.				130	.	.	.	.	.	.	.	.	.	140	.	.	.	.	.	.	.
Predicted Secondary structure																																																													.	.	.
Query SS confidence																																																													.	.	.
Query Sequence		M	G	V	D	P	W	H	N	W	E	A	H	Y	E	V	L	P	G	K	E	K	V	V	S	E	L	K	Q	L	A	E	K	A	D	H	I	Y	L	A	T	D	L	D	R	E	G	E	A	I	A	W	H	L	R	E	V	I	G	G	.	.	.	D	D	A	R	Y	S	R	V	V	F	N	E	I	T	K	N	A	I
Query Conservation																																																													.	.	.
Alig confidence		.	.	.	.	.	.	.	.	.																																																			.	.	.
Template Conservation		.	.	.	.	.	.	.	.	.
Template Sequence		.	.	.	.	.	.	.	.	.	K	W	Q	L	Q	P	R	P	S	V	T	K	Q	L	N	V	I	K	R	F	L	H	E	A	S	E	I	V	H	A	G	D	P	D	R	E	G	Q	L	L	V	D	E	V	L	D	Y	L	Q	L	A	P	E	K	R	Q	Q	V	Q	R	C	L	I	N	D	L	N	P	Q	A	V
Template Known Secondary structure		.	.	.	.	.	.	.	.	.	S							S	T	T															S								S	S														T	T							T	T							S			S
Template Predicted Secondary structure		.	.	.	.	.	.	.	.	.
Template SS confidence
											72	.	.	.	.	.	.	.	80	.	.	.	.	.	.	.	.	.	90	.	.	.	.	.	.	.	.	.	100	.	.	.	.	.	.	.	.	.	110	.	.	.	.	.	.	.	.	.	120	.	.	.	.	.	.	.	.	.	130	.	.	.	.	.	.	.	.	.	140	.	.
		148	.	150	.	.	.	.	.	.	.	.			.	160	.	.	.	.	.	.	.	.	.	170	.	.	.	.	.	.	.	.	.	180	.	.	.	.	.	.	.	.	.	190						.	.	.	.	.	.	.	.	.	200	.	.	.	.	.	.	.	.	.	210	.	.	.	.	.	.	.	.	.	220
Predicted Secondary structure													.	.																																	.	.	.	.	.
Query SS confidence													.	.																																	.	.	.	.	.
Query Sequence		R	Q	A	F	N	K	P	G	E	L	N	.	.	I	D	R	V	N	A	Q	Q	A	R	R	F	M	D	R	V	V	G	Y	M	V	S	P	L	L	W	K	K	I	A	R	G	.	.	.	.	.	L	S	A	G	R	V	Q	S	V	A	V	R	L	V	V	E	R	E	R	E	I	K	A	F	V	P	E	E	F	W
Query Conservation													.	.																																	.	.	.	.	.
Alig confidence													.	.																																	.	.	.	.	.
Template Conservation
Template Sequence		E	R	A	I	D	R	L	R	S	N	S	E	F	V	P	L	C	V	S	A	L	A	R	A	R	A	D	W	L	Y	G	I	N	M	T	R	A	Y	T	I	L	G	R	N	A	G	Y	Q	G	V	L	S	V	G	R	V	Q	T	P	V	L	G	L	V	V	R	R	D	E	E	I	E	N	F	V	A	K	D	F	F
Template Known Secondary structure							S				G	G	G	G																																T	T			S						T	T
Template Predicted Secondary structure
Template SS confidence
		143	.	.	.	.	.	.	150	.	.	.	.	.	.	.	.	.	160	.	.	.	.	.	.	.	.	.	170	.	.	.	.	.	.	.	.	.	180	.	.	.	.	.	.	.	.	.	190	.	.	.	.	.	.	.	.	.	200	.	.	.	.	.	.	.	.	.	210	.	.	.	.	.	.	.	.	.	220	.	.
		221	.	.	.	.	.	.	.	.	230	.	.	.	.	.	.	.	.	.	240							.	.	.	.	.	.	.	.	.	250	.	.	.	.	.	.	.	.	.	260	.	.	.	.	.	.	.	.	.	270	.	.	.	.	.	.	.	.	.	280	.	.	.	.	.	.	.	.	.	290	.	.	.	.
Predicted Secondary structure																						.	.	.	.	.	.
Query SS confidence																						.	.	.	.	.	.
Query Sequence		E	V	D	A	S	T	T	T	P	S	G	E	A	L	A	L	Q	V	T	H	.	.	.	.	.	.	Q	N	D	K	P	F	R	P	V	N	K	E	Q	T	Q	A	A	V	S	L	L	E	K	A	R	Y	S	V	L	E	R	E	D	K	P	T	T	S	K	P	G	A	P	F	I	T	S	T	L	Q	Q	A	A	S
Query Conservation																						.	.	.	.	.	.
Alig confidence																						.	.	.	.	.	.
Template Conservation
Template Sequence		E	V	K	A	H	I	V	T	P	A	D	E	R	F	T	A	I	W	Q	P	S	E	A	C	E	P	Y	Q	D	E	E	G	R	L	L	H	R	P	L	A	E	H	V	V	N	R	I	S	G	Q	P	A	I	V	T	S	Y	N	D	K	R	E	S	E	S	A	P	L	P	F	S	L	S	A	L	Q	I	E	A	A
Template Known Secondary structure										T	T	S											G	G	G	G	G	G	B		T	T			B														T	T
Template Predicted Secondary structure
Template SS confidence
		223	.	.	.	.	.	.	230	.	.	.	.	.	.	.	.	.	240	.	.	.	.	.	.	.	.	.	250	.	.	.	.	.	.	.	.	.	260	.	.	.	.	.	.	.	.	.	270	.	.	.	.	.	.	.	.	.	280	.	.	.	.	.	.	.	.	.	290	.	.	.	.	.	.	.	.	.	300	.	.
		295	.	.	.	.	300	.	.	.	.	.	.	.	.	.	310	.	.	.	.		.	.	.	.	.	320	.	.	.	.	.	.	.	.	.	330	.	.	.	.	.	.	.	.	.	340	.	.								.	.	.	.	.	.	.	350	.	.	.	.	.	.	.	.	.	360	.	.	.	.	.	.
Predicted Secondary structure																						.																													.	.	.	.	.	.	.
Query SS confidence																						.																													.	.	.	.	.	.	.
Query Sequence		T	R	L	G	F	G	V	K	K	T	M	M	M	A	Q	R	L	Y	E	A	.	G	Y	I	T	Y	M	R	T	D	S	T	N	L	S	Q	D	A	V	N	M	V	R	G	Y	I	S	D	N	.	.	.	.	.	.	.	F	G	K	K	Y	L	P	E	S	P	N	Q	Y	A	S	K	E	N	S	Q	E	A	H	E
Query Conservation																						.																													.	.	.	.	.	.	.
Alig confidence																						.																													.	.	.	.	.	.	.
Template Conservation
Template Sequence		K	R	F	G	L	S	A	Q	N	V	L	D	I	C	Q	K	L	Y	E	T	H	K	L	I	T	Y	P	R	S	D	C	R	Y	L	P	E	E	H	F	A	G	R	H	A	V	M	N	A	I	S	V	H	A	P	D	L	L	P	Q	P	V	V	D	P	D	I	R	N	R	C	W	D	D	K	K	V	D	A	H	H
Template Known Secondary structure																					T	S			B			S	S						B		G	G	G	G	G	G												S	T	T	T				T	T			T	T				T	T	B		G	G	G		S	S
Template Predicted Secondary structure
Template SS confidence
		303	.	.	.	.	.	.	310	.	.	.	.	.	.	.	.	.	320	.	.	.	.	.	.	.	.	.	330	.	.	.	.	.	.	.	.	.	340	.	.	.	.	.	.	.	.	.	350	.	.	.	.	.	.	.	.	.	360	.	.	.	.	.	.	.	.	.	370	.	.	.	.	.	.	.	.	.	380	.	.
		367	.	.	370	.	.	.	.	.	.	.	.	.	380	.	.	.	.	.	.	.	.	.	390	.	.	.	.	.	.	.	.	.	400	.	.	.	.	.	.	.	.	.	410	.	.	.	.	.	.	.	.	.	420	.	.	.	.	.	.	.	.	.	430	.	.	.	.	.	.	.	.	.	440	.	.	.	.	.	.
Predicted Secondary structure
Query SS confidence
Query Sequence		A	I	R	P	S	D	V	N	V	M	A	E	S	L	K	D	M	E	A	D	A	Q	K	L	Y	Q	L	I	W	R	Q	F	V	A	C	Q	M	T	P	A	K	Y	D	S	T	T	L	T	V	G	A	G	D	F	R	L	K	A	R	G	R	I	L	R	F	D	G	W	T	K	V	M	P	A	L	R	K	G	D	E
Query Conservation
Alig confidence										.	.	.	.
Template Conservation										.	.	.	.
Template Sequence		A	I	I	P	T	A	R	S	.	.	.	.	S	A	I	N	L	T	E	N	E	A	K	V	Y	N	L	I	A	R	Q	Y	L	M	Q	F	C	P	D	A	V	F	R	K	C	V	I	E	L	D	I	A	K	G	K	F	V	A	K	A	R	F	L	A	E	A	G	W	R	T	L	L	G	S	K	E	R	D	E	E
Template Known Secondary structure					B		S			.	.	.	.	S																						T	T	S															T	T														G	G	G	G	G	S							T	T
Template Predicted Secondary structure										.	.	.	.
Template SS confidence
		383	.	.	.	.	.	.	390					.	.	.	.	.	.	.	.	.	400	.	.	.	.	.	.	.	.	.	410	.	.	.	.	.	.	.	.	.	420	.	.	.	.	.	.	.	.	.	430	.	.	.	.	.	.	.	.	.	440	.	.	.	.	.	.	.	.	.	450	.	.	.	.	.	.	.	.
		447			.	.	450	.	.	.	.	.	.	.	.	.	460	.	.	.	.	.	.	.	.	.	470	.	.	.	.	.	.	.	.	.	480	.	.	.	.	.	.	.	.	.																		490	.	.	.	.	.	.	.	.	.	500	.	.	.	.	.	.	.
Predicted Secondary structure			.	.																																											.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.
Query SS confidence			.	.																																											.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.
Query Sequence		D	.	.	R	I	L	P	A	V	N	K	G	D	A	L	T	L	V	E	L	T	P	A	Q	H	F	T	K	P	P	A	R	F	S	E	A	S	L	V	K	E	L	E	K	R	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	G	I	G	R	P	S	T	Y	A	S	I	I	S	T	I	Q	D	R
Query Conservation			.	.																																											.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.
Alig confidence			.	.																																											.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.
Template Conservation
Template Sequence		N	D	G	T	P	L	P	V	V	A	K	G	D	E	L	L	C	E	K	G	E	V	V	E	R	Q	T	Q	P	P	R	H	F	T	D	A	T	L	L	S	A	M	T	G	I	A	R	F	V	Q	D	K	D	L	K	K	I	L	R	A	T	D	G	L	G	T	E	A	T	R	A	G	I	I	E	L	L	F	K	R
Template Known Secondary structure			B	S								T	T																																T	G	G	G	G													T	T	S	S	S		T	T	T											T
Template Predicted Secondary structure
Template SS confidence
		459	460	.	.	.	.	.	.	.	.	.	470	.	.	.	.	.	.	.	.	.	480	.	.	.	.	.	.	.	.	.	490	.	.	.	.	.	.	.	.	.	500	.	.	.	.	.	.	.	.	.	510	.	.	.	.	.	.	.	.	.	520	.	.	.	.	.	.	.	.	.	530	.	.	.	.	.	.	.	.
		508	.	510	.	.	.	.	.	.	.	.	.	520	.	.	.	.	.	.	.	.	.	530	.	.	.	.	.	.	.	.	.	540	.	.	.	.	.	.	.	.	.	550	.	.	.	.	.	.	.	.	.	560	.	.	.	.	.	.	.	.	.	570	.	.	.	.	.	.	.	.	.	580	.	.	.	.	.	.	.
Predicted Secondary structure
Query SS confidence
Query Sequence		G	Y	V	R	V	E	N	R	R	F	Y	A	E	K	M	G	E	I	V	T	D	R	L	E	E	N	F	R	E	L	M	N	Y	D	F	T	A	Q	M	E	N	S	L	D	Q	V	A	N	H	E	A	E	W	K	A	V	L	D	H	F	F	S	D	F	T	Q	Q	L	D	K	A	E	K	D	P	E	E	G	G	M
Query Conservation
Alig confidence																												.	.	.																																																			.
Template Conservation																												.	.	.																																																			.
Template Sequence		G	F	L	T	K	K	G	R	Y	I	H	S	T	D	A	G	K	A	L	F	H	S	L	P	E	M	.	.	.	A	T	R	P	D	M	T	A	H	W	E	S	V	L	T	Q	I	S	E	K	Q	C	R	Y	Q	D	F	M	Q	P	L	V	G	T	L	Y	Q	L	I	D	Q	A	K	R	T	P	V	R	Q	F	.
Template Known Secondary structure		T	S				S	S	S															S				.	.	.			S	S															T	T	S	S																						T			G	G	G	G	.
Template Predicted Secondary structure																												.	.	.																																																			.
Template SS confidence
		539	540	.	.	.	.	.	.	.	.	.	550	.	.	.	.	.	.	.	.	.	560	.	.	.	.				.	.	.	.	.	570	.	.	.	.	.	.	.	.	.	580	.	.	.	.	.	.	.	.	.	590	.	.	.	.	.	.	.	.	.	600	.	.	.	.	.	.	.	.	.	610	.	.	.	.
		588	.	590	.	.	.	.	.	.	.	.	.	600	.	.	.	.	.
Predicted Secondary structure
Query SS confidence
Query Sequence		R	P	N	Q	M	V	L	T	S	I	D	C	P	T	C	G	R	K
Query Conservation
Alig confidence		.	.	.	.	.	.	.
Template Conservation		.	.	.	.	.	.	.
Template Sequence		.	.	.	.	.	.	.	R	G	I	V	A	P	A	I	A	H	H
Template Known Secondary structure		.	.	.	.	.	.	.	T	T							T	T
Template Predicted Secondary structure		.	.	.	.	.	.	.
Template SS confidence
									615	.	.	.	.	620	.	.	.	.	.