Job Description P46837 Confidence 100.00% Date Thu Jan 5 12:04:18 GMT 2012 Rank 3 Aligned Residues 646 % Identity 19% Template c3psfA_ PDB info PDB header:transcription Chain: A: PDB Molecule:transcription elongation factor spt6; PDBTitle: crystal structure of the spt6 core domain from saccharomyces2 cerevisiae, form spt6(236-1259) Resolution 2.59 Å

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		6	.	.	.	10	.	.	.	.	.	.	.	.									.	20	.	.	.	.	.	.	.	.		.	30	.	.	.	.	.	.	.	.	.	40	.	.	.	.	.	.	.								.	.	50	.	.	.	.	.	.	.	.	.	60	.	.	.	.	.	.	.	.	.
Predicted Secondary structure															.	.	.	.	.	.	.	.											.																				.	.	.	.	.	.	.
Query SS confidence															.	.	.	.	.	.	.	.											.																				.	.	.	.	.	.	.
Query Sequence		F	C	R	I	I	A	G	E	I	Q	A	R	P	.	.	.	.	.	.	.	.	E	Q	V	D	A	A	V	R	L	L	.	D	E	G	N	T	V	P	F	I	A	R	Y	R	K	E	I	T	G	G	.	.	.	.	.	.	.	L	D	D	T	Q	L	R	N	L	E	T	R	L	S	Y	L	R	E	L	E	E	R
Query Conservation															.	.	.	.	.	.	.	.											.																				.	.	.	.	.	.	.
Alig confidence															.	.	.	.	.	.	.	.											.																				.	.	.	.	.	.	.
Template Conservation
Template Sequence		I	A	E	K	I	S	V	D	K	N	F	D	A	N	Y	D	L	T	E	F	K	E	A	I	G	N	A	I	K	F	I	T	K	E	N	L	E	V	P	F	I	Y	A	Y	R	R	N	Y	I	S	S	R	E	K	D	G	F	L	L	T	E	D	D	L	W	D	I	V	S	L	D	I	E	F	H	S	L	V	N	K
Template Known Secondary structure														S	S																			T	S												G	G	G	S	B		S	S	T	T	S		B
Template Predicted Secondary structure
Template SS confidence
		351	.	.	.	.	.	.	.	.	360	.	.	.	.	.	.	.	.	.	370	.	.	.	.	.	.	.	.	.	380	.	.	.	.	.	.	.	.	.	390	.	.	.	.	.	.	.	.	.	400	.	.	.	.	.	.	.	.	.	410	.	.	.	.	.	.	.	.	.	420	.	.	.	.	.	.	.	.	.	430
		70	.	.	.	.	.	.	.	.	.	80	.	.	.	.	.	.	.	.	.	90	.	.	.	.	.	.	.	.	.	100	.	.			.	.	.	.	.	.	.	110	.	.	.	.	.	.	.	.	.	120	.	.	.	.	.	.	.	.	.	130
Predicted Secondary structure																																			.	.																													.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.
Query SS confidence																																			.	.																													.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.
Query Sequence		R	Q	A	I	L	K	S	I	S	E	Q	G	K	L	T	D	D	L	A	K	A	I	N	A	T	L	S	K	T	E	L	E	D	.	.	L	Y	L	P	Y	K	P	K	R	R	T	R	G	Q	I	A	I	E	A	G	L	E	P	L	A	D	L	L	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.
Query Conservation																																			.	.																													.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.
Alig confidence																																			.	.																													.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.
Template Conservation
Template Sequence		K	D	Y	V	Q	R	F	Y	A	E	L	H	I	D	D	P	I	V	T	E	Y	F	K	N	Q	N	S	L	Q	D	I	Y	D	Y	L	E	F	K	Y	A	N	E	I	N	E	M	S	Y	E	K	F	K	A	S	P	L	Y	Q	A	V	S	D	I	G	I	S	A	E	D	V	G	E	N	I	S	S	Q	H	Q	I
Template Known Secondary structure																																								T													T	T	S	T	T						T	T	S	S												T	S		S
Template Predicted Secondary structure
Template SS confidence
		431	.	.	.	.	.	.	.	.	440	.	.	.	.	.	.	.	.	.	450	.	.	.	.	.	.	.	.	.	460	.	.	.	.	.	.	.	.	.	470	.	.	.	.	.	.	.	.	.	480	.	.	.	.	.	.	.	.	.	490	.	.	.	.	.	.	.	.	.	500	.	.	.	.	.	.	.	.	.	510
					131	.	.	.	.	.	.	.	.	140	.	.	.	.	.	.	.	.	.	150	.	.	.	.	.	.	.	.	.	160	.	.	.	.	.	.	.	.	.	170	.	.	.	.	.	.	.	.	.	180	.	.	.	.	.	.	.	.	.	190	.	.	.	.	.	.	.	.	.	200	.	.	.	.	.	.	.
Predicted Secondary structure		.	.	.
Query SS confidence		.	.	.
Query Sequence		.	.	.	W	S	D	P	S	H	T	P	E	V	A	A	A	Q	Y	V	Y	A	D	K	G	V	A	D	T	K	A	A	L	D	G	A	R	Y	I	L	M	E	R	F	A	E	D	A	A	L	L	A	K	V	R	D	Y	L	W	K	N	A	H	L	V	S	T	V	V	S	G	K	E	E	E	G	A	K	F	R	D
Query Conservation		.	.	.
Alig confidence		.	.	.
Template Conservation
Template Sequence		H	P	P	V	D	H	P	S	S	K	P	V	E	V	I	E	S	I	L	N	A	N	S	G	D	L	Q	T	K	L	A	I	D	T	V	Q	K	Y	Y	S	L	E	L	S	K	N	T	K	I	R	E	K	V	R	S	D	F	S	K	Y	Y	L	A	D	V	V	L	T	A	K	G	K	K	E	I	Q	K	G	S	L
Template Known Secondary structure		S						S	S													T	T	T	T	T																				T															S																T	T	T	S	T
Template Predicted Secondary structure
Template SS confidence
		535	.	.	.	.	540	.	.	.	.	.	.	.	.	.	550	.	.	.	.	.	.	.	.	.	560	.	.	.	.	.	.	.	.	.	570	.	.	.	.	.	.	.	.	.	580	.	.	.	.	.	.	.	.	.	590	.	.	.	.	.	.	.	.	.	600	.	.	.	.	.	.	.	.	.	610	.	.	.	.
		208	.	210	.	.					.	.	.	.	.	.			.	220	.	.	.	.	.	.	.	.	.	230	.	.	.	.	.	.	.	.	.	240	.	.	.	.	.	.	.	.	.	250	.	.	.	.	.	.	.	.	.	260	.	.	.	.	.	.	.	.	.	270	.	.	.	.	.	.	.	.	.	280	.
Predicted Secondary structure							.	.	.	.							.	.
Query SS confidence							.	.	.	.							.	.
Query Sequence		Y	F	D	H	H	.	.	.	.	E	P	L	S	T	V	.	.	P	S	H	R	A	L	A	M	F	R	G	R	N	E	G	V	L	Q	L	S	L	N	A	D	P	Q	F	D	E	P	P	K	E	S	Y	C	E	Q	I	I	M	D	H	L	G	L	R	L	N	N	A	P	A	D	S	W	R	K	G	V	V	S	W
Query Conservation							.	.	.	.							.	.
Alig confidence							.	.	.	.							.	.																														.	.	.
Template Conservation																																																.	.	.
Template Sequence		Y	E	D	I	K	Y	A	I	N	R	T	P	M	H	F	R	R	D	P	D	V	F	L	K	M	V	E	A	E	S	L	N	L	L	S	V	K	L	H	M	S	S	Q	A	Q	Y	.	.	.	I	E	H	L	F	Q	I	A	L	E	T	T	N	T	S	D	I	A	I	E	W	N	N	F	R	K	L	A	F	N	Q
Template Known Secondary structure		T	T	T	T	T	T	B			B		T	T						T												T	T	S								T	T					.	.	.									T						S
Template Predicted Secondary structure																																																.	.	.
Template SS confidence
		620	.	.	.	.	.	.	.	.	.	630	.	.	.	.	.	.	.	.	.	640	.	.	.	.	.	.	.	.	.	650	.	.	.	.	.	.	.	.	.	660	.	.	.	.	.				.	.	.	.	670	.	.	.	.	.	.	.	.	.	680	.	.	.	.	.	.	.	.	.	690	.	.	.	.	.	.
		282	.	.	.	.	.	.	.	290	.	.	.	.	.	.	.	.	.	300	.	.	.	.	.	.	.	.	.	310	.	.	.	.	.	.	.	.	.	320	.	.	.	.	.	.	.								.	.	330	.	.	.	.	.					.	.	.	.	340	.	.	.	.	.	.	.	.	.	350
Predicted Secondary structure																																																.	.	.	.	.	.	.									.	.	.	.
Query SS confidence																																																.	.	.	.	.	.	.									.	.	.	.
Query Sequence		T	W	R	I	K	V	L	M	H	L	E	T	E	L	M	G	T	V	R	E	R	A	E	D	E	A	I	N	V	F	A	R	N	L	H	D	L	L	M	A	A	P	A	G	L	R	.	.	.	.	.	.	.	A	T	M	G	L	D	P	G	.	.	.	.	L	R	T	G	V	K	V	A	V	V	D	A	T	G	K
Query Conservation																																																.	.	.	.	.	.	.									.	.	.	.
Alig confidence								.																																								.	.	.	.	.	.	.									.	.	.	.
Template Conservation								.
Template Sequence		A	M	D	K	I	F	.	Q	D	I	S	Q	E	V	K	D	N	L	T	K	N	C	Q	K	L	V	A	K	T	V	R	H	K	F	M	T	K	L	D	Q	A	P	F	I	P	N	V	R	D	P	K	I	P	K	I	L	S	L	T	C	G	Q	G	R	F	G	A	D	A	I	I	A	V	Y	V	N	R	K	G	D
Template Known Secondary structure								.																																						S		T	T	S												T	T			T	T	T	S									T	T	S
Template Predicted Secondary structure								.
Template SS confidence
		697	.	.	700	.	.		.	.	.	.	.	.	.	710	.	.	.	.	.	.	.	.	.	720	.	.	.	.	.	.	.	.	.	730	.	.	.	.	.	.	.	.	.	740	.	.	.	.	.	.	.	.	.	750	.	.	.	.	.	.	.	.	.	760	.	.	.	.	.	.	.	.	.	770	.	.	.	.	.
		351	.	.	.	.	.	.	.	.	360	.	.				.	.	.	.	.	.	.	370	.	.	.	.	.	.	.	.	.	380	.	.	.	.	.	.		.	.	.	390	.	.	.	.	.	.	.	.	.	400	.	.	.	.	.	.						.	.	.	410	.	.	.	.	.	.	.	.	.	420	.
Predicted Secondary structure														.	.	.																									.																					.	.	.	.	.
Query SS confidence														.	.	.																									.																					.	.	.	.	.
Query Sequence		L	V	A	T	D	T	I	Y	P	H	T	G	.	.	.	Q	A	A	K	A	A	M	T	V	A	A	L	C	E	K	H	N	V	E	L	V	A	I	G	.	N	G	T	A	S	R	E	T	E	R	F	Y	L	D	V	Q	K	Q	F	P	.	.	.	.	.	K	V	T	A	Q	K	V	I	V	S	E	A	G	A	S
Query Conservation														.	.	.																									.																					.	.	.	.	.
Alig confidence														.	.	.																									.																					.	.	.	.	.
Template Conservation
Template Sequence		F	I	R	D	Y	K	I	V	D	N	P	F	D	K	T	N	P	E	K	F	E	D	T	L	D	N	I	I	Q	S	C	Q	P	N	A	I	G	I	N	G	P	N	P	K	T	Q	K	F	Y	K	R	L	Q	E	V	L	H	K	K	Q	I	V	D	S	R	G	H	T	I	P	I	I	Y	V	E	D	E	V	A	I
Template Known Secondary structure										S		T	T		S	S																			S							S	S	T																T	T		B		T	T	S		B									T	T
Template Predicted Secondary structure
Template SS confidence
		776	.	.	.	780	.	.	.	.	.	.	.	.	.	790	.	.	.	.	.	.	.	.	.	800	.	.	.	.	.	.	.	.	.	810	.	.	.	.	.	.	.	.	.	820	.	.	.	.	.	.	.	.	.	830	.	.	.	.	.	.	.	.	.	840	.	.	.	.	.	.	.	.	.	850	.	.	.	.	.
		422	.	.	.	.	.	.	.	430	.	.	.	.	.	.	.	.	.	440	.	.	.	.	.	.	.	.	.	450	.	.	.	.	.	.	.	.	.	460				.	.	.	.	.	.	.	.	.	470	.	.	.	.	.	.	.	.	.	480	.	.	.	.	.	.	.	.	.	490	.	.	.	.	.	.	.	.
Predicted Secondary structure																																									.	.	.
Query SS confidence																																									.	.	.
Query Sequence		V	Y	S	A	S	E	L	A	A	Q	E	F	P	D	L	D	V	S	L	R	G	A	V	S	I	A	R	R	L	Q	D	P	L	A	E	L	V	K	I	.	.	.	D	P	K	S	I	G	V	G	Q	Y	Q	H	D	V	S	Q	T	Q	L	A	R	K	L	D	A	V	V	E	D	C	V	N	A	V	G	V	D	L
Query Conservation																																									.	.	.
Alig confidence																																									.	.	.
Template Conservation
Template Sequence		R	Y	Q	N	S	E	R	A	A	Q	E	F	P	N	K	P	P	L	V	K	Y	C	I	A	L	A	R	Y	M	H	S	P	L	L	E	Y	A	N	L	T	S	E	E	V	R	S	L	S	I	H	P	H	Q	N	L	L	S	S	E	Q	L	S	W	A	L	E	T	A	F	V	D	I	V	N	L	V	S	V	E	V
Template Known Secondary structure					T	S							S	T	T																								T	S							T	S				T	T	G	G	G	S
Template Predicted Secondary structure
Template SS confidence
		856	.	.	.	860	.	.	.	.	.	.	.	.	.	870	.	.	.	.	.	.	.	.	.	880	.	.	.	.	.	.	.	.	.	890	.	.	.	.	.	.	.	.	.	900	.	.	.	.	.	.	.	.	.	910	.	.	.	.	.	.	.	.	.	920	.	.	.	.	.	.	.	.	.	930	.	.	.	.	.
		499	500	.	.						.	.	.	.	.	.	.	510	.	.	.	.	.	.	.	.	.	520	.	.		.	.	.	.	.	.	.	530	.	.	.	.	.	.	.	.	.	540	.	.	.	.	.	.	.	.	.	550	.	.	.	.	.	.	.	.	.	560	.					.	.	.	.	.	.	.
Predicted Secondary structure						.	.	.	.	.																					.																																								.	.	.	.
Query SS confidence						.	.	.	.	.																					.																																								.	.	.	.
Query Sequence		N	T	A	S	.	.	.	.	.	V	P	L	L	T	R	V	A	G	L	T	R	M	M	A	Q	N	I	V	A	.	W	R	D	E	N	G	Q	F	Q	N	R	Q	Q	L	L	K	V	S	R	L	G	P	K	A	F	E	Q	C	A	G	F	L	R	I	N	H	G	D	N	.	.	.	.	P	L	D	A	S	T	V
Query Conservation						.	.	.	.	.																					.																																								.	.	.	.
Alig confidence						.	.	.	.	.																					.																																								.	.	.	.
Template Conservation
Template Sequence		N	K	A	T	D	N	N	Y	Y	A	S	A	L	K	Y	I	S	G	F	G	K	R	K	A	I	D	F	L	Q	S	L	Q	R	L	N	E	P	L	L	A	R	Q	Q	L	I	T	H	N	I	L	H	K	T	I	F	M	N	S	A	G	F	L	Y	I	S	W	N	E	D	L	E	H	D	Q	L	D	S	T	R	I
Template Known Secondary structure						T						T	T	G	G	G	S	T	T																T		S					T	T					T	T	S	S									T	T	T									T	T			G	G	G	G	S	S
Template Predicted Secondary structure
Template SS confidence
		936	.	.	.	940	.	.	.	.	.	.	.	.	.	950	.	.	.	.	.	.	.	.	.	960	.	.	.	.	.	.	.	.	.	970	.	.	.	.	.	.	.	.	.	980	.	.	.	.	.	.	.	.	.	990	.	.	.	.	.	.	.	.	.	1000	.	.	.	.	.	.	.	.	.	1010	.	.	.	.	.
		569	570	.	.	.	.	.	.	.	.	.	580	.	.		.	.	.	.	.	.	.	590	.																				.	.	.	.	.	.	.	.	600	.	.	.	.	.	.	.	.							.	610	.	.	.	.	.	.	.	.	.	620	.	.
Predicted Secondary structure																.										.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.																		.	.	.	.	.	.
Query SS confidence																.										.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.																		.	.	.	.	.	.
Query Sequence		H	P	E	A	Y	P	V	V	E	R	I	L	A	A	.	T	Q	Q	A	L	K	D	L	M	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	G	N	S	S	E	L	R	N	L	K	A	S	D	F	T	D	E	.	.	.	.	.	.	K	F	G	V	P	T	V	T	D	I	I	K	E	L
Query Conservation																.										.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.																		.	.	.	.	.	.
Alig confidence																.										.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.																		.	.	.	.	.	.
Template Conservation
Template Sequence		H	P	E	D	Y	H	L	A	T	K	V	A	A	D	A	L	E	Y	D	P	D	T	I	A	E	K	E	E	Q	G	T	M	S	E	F	I	E	L	L	R	E	D	P	D	R	R	A	K	L	E	S	L	N	L	E	S	Y	A	E	E	L	E	K	N	T	G	L	R	K	L	N	N	L	N	T	I	V	L	E	L
Template Known Secondary structure			G	G	G												T	T													T		T	T										T	T						T	T	S
Template Predicted Secondary structure
Template SS confidence
		1022	.	.	.	.	.	.	.	1030	.	.	.	.	.	.	.	.	.	1040	.	.	.	.	.	.	.	.	.	1050	.	.	.	.	.	.	.	.	.	1060	.	.	.	.	.	.	.	.	.	1070	.	.	.	.	.	.	.	.	.	1080	.	.	.	.	.	.	.	.	.	1090	.	.	.	.	.	.	.	.	.	1100	.
		623	.	.	.	.	.	.	630	.	.	.	.	.	.	.	.	.	640	.	.	.	.	.						.	.	.	.	650	.	.	.	.	.
Predicted Secondary structure																									.	.	.	.	.
Query SS confidence																									.	.	.	.	.
Query Sequence		E	K	P	G	R	D	P	R	P	E	F	K	T	A	Q	F	A	D	G	V	E	T	M	.	.	.	.	.	N	D	L	Q	P	G	M	I	L	E
Query Conservation																									.	.	.	.	.
Alig confidence																									.	.	.	.	.
Template Conservation
Template Sequence		L	D	G	F	E	E	L	R	N	D	F	H	P	L	Q	G	D	E	I	F	Q	S	L	T	G	E	S	S	K	D	P	S	I	W	D	L	K	Q
Template Known Secondary structure			S	T	T				S																							T	T	T	B
Template Predicted Secondary structure
Template SS confidence
		1102	.	.	.	.	.	.	.	1110	.	.	.	.	.	.	.	.	.	1120	.	.	.	.	.	.	.	.	.	1130	.	.	.	.	.	.	.	.	.