Job Description P23484 Confidence 99.28% Date Thu Jan 5 11:39:30 GMT 2012 Rank 11 Aligned Residues 166 % Identity 12% Template c3iydF_ PDB info PDB header:transcription/dna Chain: F: PDB Molecule:rna polymerase sigma factor rpod; PDBTitle: three-dimensional em structure of an intact activator-dependent2 transcription initiation complex Resolution 19.80 Å

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		1	.	.	.	.	.	.	.	.				10	.	.	.	.	.	.	.	.	.	20	.	.	.	.	.	.	.	.	.	30	.	.	.	.	.	.	.	.	.	40	.	.	.	.	.	.	.	.	.	50	.	.	.	.	.	.	.	.	.				60	.	.	.	.	.	.	.	.	.	70	.	.	.	.
Predicted Secondary structure											.	.	.																																																			.	.	.
Query SS confidence											.	.	.																																																			.	.	.
Query Sequence		M	S	D	R	A	T	T	T	A	.	.	.	S	L	T	F	E	S	L	Y	G	T	H	H	G	W	L	K	S	W	L	T	R	K	L	Q	S	A	F	D	A	D	D	I	A	Q	D	T	F	L	R	V	M	V	S	E	T	L	S	T	I	R	.	.	.	D	P	R	S	F	L	C	T	I	A	K	R	V	M	V
Query Conservation											.	.	.																																																			.	.	.
Alig confidence											.	.	.																																																			.	.	.
Template Conservation
Template Sequence		I	N	R	R	M	S	I	G	E	A	K	A	R	R	A	K	K	E	M	V	E	A	N	L	R	L	V	I	S	I	A	K	K	Y	T	N	R	G	L	Q	F	L	D	L	I	Q	E	G	N	I	G	L	M	K	A	V	D	K	F	E	Y	R	R	G	Y	K	F	S	T	Y	A	T	W	W	I	R	Q	A	I	T
Template Known Secondary structure					T													T	T	T	T	T	T	T	T						G	G	G	S	S	S	T	T	S	S		S	T	T	T	T											T	T	S			T	T	S	S	S		S	T	T	T
Template Predicted Secondary structure
Template SS confidence
		361	.	.	.	.	.	.	.	.	370	.	.	.	.	.	.	.	.	.	380	.	.	.	.	.	.	.	.	.	390	.	.	.	.	.	.	.	.	.	400	.	.	.	.	.	.	.	.	.	410	.	.	.	.	.	.	.	.	.	420	.	.	.	.	.	.	.	.	.	430	.	.	.	.	.	.	.	.	.	440
		75	.	.	.	.	80	.	.	.	.	.	.																																																																	.	.	.	90
Predicted Secondary structure														.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.
Query SS confidence														.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.
Query Sequence		D	L	F	R	R	N	A	L	E	K	A	Y	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	L	E	M	L
Query Conservation														.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.
Alig confidence														.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.
Template Conservation
Template Sequence		R	S	I	A	D	Q	A	R	T	I	R	I	P	V	H	M	I	E	T	I	N	K	L	N	R	I	S	R	Q	M	L	Q	E	M	G	R	E	P	T	P	E	E	L	A	E	R	M	L	M	P	E	D	K	I	R	K	V	L	K	I	A	K	E	P	I	S	M	E	T	P	I	G	D	D	E	D	S	H	L	G
Template Known Secondary structure				T	T	T	S		S	S	S				S					T	T	T	T	T	T	T	T	T	T	T	T	T	T	T	T		S				T	T	T	T	T	T	T	S	S			S	S									S						S	S				S	S	S	S	S			G	G
Template Predicted Secondary structure
Template SS confidence
		441	.	.	.	.	.	.	.	.	450	.	.	.	.	.	.	.	.	.	460	.	.	.	.	.	.	.	.	.	470	.	.	.	.	.	.	.	.	.	480	.	.	.	.	.	.	.	.	.	490	.	.	.	.	.	.	.	.	.	500	.	.	.	.	.	.	.	.	.	510	.	.	.	.	.	.	.	.	.	520
		91	.	.	.	.	.	.	.	.	100	.	.	.	.	.	.	.	.	.	110	.	.	.	.	.	.	.	.	.	120	.	.	.	.	.	.	.	.	.	130	.	.	.					.	.	.	.	.	.	140	.	.	.	.	.	.	.	.	.	150	.	.	.	.	.	.	.	.	.	160	.	.	.	.	.	.
Predicted Secondary structure																																													.	.	.	.
Query SS confidence																																													.	.	.	.
Query Sequence		A	L	M	P	E	G	G	A	P	S	P	E	E	R	E	S	Q	L	E	T	L	Q	L	L	D	S	M	L	D	G	L	N	G	K	T	R	E	A	F	L	L	S	Q	.	.	.	.	L	D	G	L	T	Y	S	E	I	A	H	K	L	G	V	S	I	S	S	V	K	K	Y	V	A	K	A	V	E	H	C	L	L
Query Conservation																																													.	.	.	.
Alig confidence																																													.	.	.	.
Template Conservation
Template Sequence		D	F	I	E	D	T	T	L	E	L	P	L	D	S	A	T	T	E	S	L	R	A	A	T	H	D	V	L	A	G	L	T	A	R	E	A	K	V	L	R	M	R	F	G	I	D	M	N	T	D	H	T	L	E	E	V	G	K	Q	F	D	V	T	R	E	R	I	R	Q	I	E	A	K	A	L	R	K	L	R	H
Template Known Secondary structure		G	S				S	S	S											T	T	S	S	S					T	T	S	S													T	S	S	S					S	T	T	G	G	G	T	T	T	S	S		S	S											T	T	T	T	S
Template Predicted Secondary structure
Template SS confidence
		521	.	.	.	.	.	.	.	.	530	.	.	.	.	.	.	.	.	.	540	.	.	.	.	.	.	.	.	.	550	.	.	.	.	.	.	.	.	.	560	.	.	.	.	.	.	.	.	.	570	.	.	.	.	.	.	.	.	.	580	.	.	.	.	.	.	.	.	.	590	.	.	.	.	.	.	.	.	.	600

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Please cite: Protein structure prediction on the web: a case study using the Phyre server
Kelley LA and Sternberg MJE. Nature Protocols 4, 363 - 371 (2009) [pdf] [Import into BibTeX]
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