PHYRE Protein Fold Recognition Server

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Protein Homology/analogY Recognition Engine V 2.0

Fold library entry viewer: c5flmB_

Fold library id	PDB Header	Molecule	Title
c5flmB_	3.40	PDB header: transcription	Chain: B: PDB Molecule: dna-directed rna polymerase ii subunit rpb2;

Links to external resources
Added to library: Sat Jan 23 08:41:30 2016

1 . . . . . . . . 10 . . . . . . . . . 20 . . . . . . . . . 30 . . . . . . . . . 40 . . . . . . . . . 50 . . . . . . . . . 60 . . . . . . . . . 70

Sequence E I T P D L W Q E A C W I V I S S Y F D E K G L V R Q Q L D S F D E F I Q M S V Q R I V E D A P P I D L Q P P R Y L L K F E Q I Y L S K P T

Predicted secondary structure

SS confidence

Known secondary structure (DSSP)
S
S
S
T S S
S

. . . . . . . . . 80 . . . . . . . . . 90 . . . . . . . . . 100 . . . . . . . . . 110 . . . . . . . . . 120 . . . . . . . . . 130 . . . . . . . . . 140

Sequence H W E R D G A P S P M M P N E A R L R N L T Y S A P L Y V D I T K T V I K E G E E Q L Q T Q H Q K T F I G K I P I M L R S T Y C L L N G L T

Predicted secondary structure

SS confidence

Known secondary structure (DSSP)
T T
T T
S S S
T T S T T S T T T T

. . . . . . . . . 150 . . . . . . . . . 160 . . . . . . . . . 170 . . . . . . . . . 180 . . . . . . . . . 190 . . . . . . . . . 200 . . . . . . . . . 210

Sequence D R D L C E L N E C P L D P G G Y F I I N G S E K V L I A Q E K M A T N T V Y V F A K K D S K Y A Y T G E C R S C L E N S S R P T S T I W V

Predicted secondary structure

SS confidence

Known secondary structure (DSSP) T T
T T
T T
S S
S S S S T T T

. . . . . . . . . 220 . . . . . . . . . 230 . . . . . . . . . 240 . . . . . . . . . 250 . . . . . . . . . 260 . . . . . . . . . 270 . . . . . . . . . 280

Sequence S M L A R G G Q G A K K S A I G Q R I V A T L P Y I K Q E V P I I I V F R A L G F V S D R D I L E H I I Y D F E D P E M M E M V K P S L D E

Predicted secondary structure

SS confidence

Known secondary structure (DSSP)
T T
S
T T B S S
T T
S
S
T T

. . . . . . . . . 290 . . . . . . . . . 300 . . . . . . . . . 310 . . . . . . . . . 320 . . . . . . . . . 330 . . . . . . . . . 340 . . . . . . . . . 350

Sequence A F V I Q E Q N V A L N F I G S R G A K P G V T K E K R I K Y A K E V L Q K E M L P H V G V S D F C E T K K A Y F L G Y M V H R L L L A A L

Predicted secondary structure

SS confidence

Known secondary structure (DSSP) T T T
S T T B S S
S S T T S
T T T
S S T T T

. . . . . . . . . 360 . . . . . . . . . 370 . . . . . . . . . 380 . . . . . . . . . 390 . . . . . . . . . 400 . . . . . . . . . 410 . . . . . . . . . 420

Sequence G R R E L D D R D H Y G N K R L D L A G P L L A F L F R G M F K N L L K E V R I Y A Q K F I D R G K D F N L E L A I K T R I I S D G L K Y S

Predicted secondary structure

SS confidence

Known secondary structure (DSSP) T S S
T T
T T S
T T
S
S T T T

. . . . . . . . . 430 . . . . . . . . . 440 . . . . . . . . . 450 . . . . . . . . . 460 . . . . . . . . . 470 . . . . . . . . . 480 . . . . . . . . . 490

Sequence L A T G N W G D Q K K A H Q A R A G V S Q V L N R L T F A S T L S H L R R L N S P I G R D G K L A K P R Q L H N T L W G M V C P A E T P E G

Predicted secondary structure

SS confidence

Known secondary structure (DSSP) S
B S
S T T T T T S B
S
S
S
S
S S
S S S S S
G G G T T T B
S S
S

. . . . . . . . . 500 . . . . . . . . . 510 . . . . . . . . . 520 . . . . . . . . . 530 . . . . . . . . . 540 . . . . . . . . . 550 . . . . . . . . . 560

Sequence H A V G L V K N L A L M A Y I S V G S Q P S P I L E F L E E W S M E N L E E I S P A A I A D A T K I F V N G C W V G I H K D P E Q L M N T L

Predicted secondary structure

SS confidence

Known secondary structure (DSSP) T T T T T B B T T
S T
S T T
T T S T T T S T T S

. . . . . . . . . 570 . . . . . . . . . 580 . . . . . . . . . 590 . . . . . . . . . 600 . . . . . . . . . 610 . . . . . . . . . 620 . . . . . . . . . 630

Sequence R K L R R Q M D I I V S E V S M I R D I R E R E I R I Y T D A G R I C R P L L I V E K Q K L L L K K R H I D Q L K E R E Y N N Y S W Q D L V

Predicted secondary structure

SS confidence

Known secondary structure (DSSP) T T S S S
T T
S T T
S
T T S
T
T T T T

. . . . . . . . . 640 . . . . . . . . . 650 . . . . . . . . . 660 . . . . . . . . . 670 . . . . . . . . . 680 . . . . . . . . . 690 . . . . . . . . . 700

Sequence A S G V V E Y I D T L E E E T V M L A M T P D D L Q E K E V A Y C S T Y T H C E I H P S M I L G V C A S I I P F P D H N Q S P R N T Y Q S A

Predicted secondary structure

SS confidence

Known secondary structure (DSSP) T T T S T T
S
T S
S S
S
S
S
G G G G S B T G G G G S S S G G G B

. . . . . . . . . 710 . . . . . . . . . 720 . . . . . . . . . 730 . . . . . . . . . 740 . . . . . . . . . 750 . . . . . . . . . 760 . . . . . . . . . 770

Sequence M G K Q A M G V Y I T N F H V R M D T L A H V L Y Y P Q K P L V T T R S M E Y L R F R E L P A G I N S I V A I A S Y T G Y N Q E D S V I M N

Predicted secondary structure

SS confidence

Known secondary structure (DSSP) T T S B
S
T T T T T
S S S S
S
G G G G G G T T T T S
S
S S S S
T T

. . . . . . . . . 780 . . . . . . . . . 790 . . . . . . . . . 800 . . . . . . . . . 810 . . . . . . . . . 820 . . . . . . . . . 830 . . . . . . . . . 840

Sequence R S A V D R G F F R S V F Y R S Y K E Q E S K K G F D Q E E V F E K P T R E T C Q G M R H A I Y D K L D D D G L I A P G V R V S G D D V I I

Predicted secondary structure

SS confidence

Known secondary structure (DSSP) T T T T T
B
S S S
B
T T T B S
S S
T T
T T S B
T T
T T

. . . . . . . . . 850 . . . . . . . . . 860 . . . . . . . . . 870 . . . . . . . . . 880 . . . . . . . . . 890 . . . . . . . . . 900 . . . . . . . . . 910

Sequence G K T V T L P T K R D C S T F L R T S E T G I V D Q V M V T L N Q E G Y K F C K I R V R S V R I P Q I G D K F A S R H G Q K G T C G I Q Y R

Predicted secondary structure

SS confidence

Known secondary structure (DSSP)
T T
S S
S S
T T S

. . . . . . . . . 920 . . . . . . . . . 930 . . . . . . . . . 940 . . . . . . . . . 950 . . . . . . . . . 960 . . . . . . . . . 970 . . . . . . . . . 980

Sequence Q E D M P F T C E G I T P D I I I N P H A I P S R M T I G H L I E C L Q G K V S A N K G E I G D A T P F N D A V N V Q K I S N L L S D Y G Y

Predicted secondary structure

SS confidence

Known secondary structure (DSSP) T T T S
B
T T
S
T T
B
S S
S
S S
G G G T S

. . . . . . . . . 990 . . . . . . . . . 1000 . . . . . . . . . 1010 . . . . . . . . . 1020 . . . . . . . . . 1030 . . . . . . . . . 1040 . . . . . . . . . 1050

Sequence H L R G N E V L Y N G F T G R K I T S Q I F I G P T Y Y Q R L K H M V D D K I H S R A R G P I Q I L N R Q P M E G R S R D G G L R F G E M E

Predicted secondary structure

SS confidence

Known secondary structure (DSSP)
T T S
B
T T T
B
S S
B S
S S
B
T T T
S B
S S T T T T

. . . . . . . . . 1060 . . . . . . . . . 1070 . . . . . . . . . 1080 . . . . . . . . . 1090 . . . . . . . . . 1100 . . . . . . . . . 1110 . . . . . . . . . 1120

Sequence R D C Q I A H G A A Q F L R E R L F E A S D P Y Q V H V C N L C G I M A I A N T R T H T Y E C R G C R N K T Q I S L V R M P Y A C K L L F Q

Predicted secondary structure

SS confidence

Known secondary structure (DSSP) T
T T S S
S S S S S B
T T T
B T T T T B
S

. . . . . . . . . 1130 . . . .

Sequence E L M S M S I A P R M M S V

Predicted secondary structure

SS confidence

Known secondary structure (DSSP) T T T

Download: PDB structure FASTA sequence
Hidden Markov model

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Please cite: The Phyre2 web portal for protein modeling, prediction and analysis

Kelley LA et al. Nature Protocols 10, 845-858 (2015) [paper] [Citation link]

© Structural Bioinformatics Group, Imperial College, London

Michael Sternberg

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	1	.	.	.	.	.	.	.	.	10	.	.	.	.	.	.	.	.	.	20	.	.	.	.	.	.	.	.	.	30	.	.	.	.	.	.	.	.	.	40	.	.	.	.	.	.	.	.	.	50	.	.	.	.	.	.	.	.	.	60	.	.	.	.	.	.	.	.	.	70
Sequence	E	I	T	P	D	L	W	Q	E	A	C	W	I	V	I	S	S	Y	F	D	E	K	G	L	V	R	Q	Q	L	D	S	F	D	E	F	I	Q	M	S	V	Q	R	I	V	E	D	A	P	P	I	D	L	Q	P	P	R	Y	L	L	K	F	E	Q	I	Y	L	S	K	P	T
Predicted secondary structure
SS confidence
Known secondary structure (DSSP)					S																	S		S														T								S	S																					S
	.	.	.	.	.	.	.	.	.	80	.	.	.	.	.	.	.	.	.	90	.	.	.	.	.	.	.	.	.	100	.	.	.	.	.	.	.	.	.	110	.	.	.	.	.	.	.	.	.	120	.	.	.	.	.	.	.	.	.	130	.	.	.	.	.	.	.	.	.	140
Sequence	H	W	E	R	D	G	A	P	S	P	M	M	P	N	E	A	R	L	R	N	L	T	Y	S	A	P	L	Y	V	D	I	T	K	T	V	I	K	E	G	E	E	Q	L	Q	T	Q	H	Q	K	T	F	I	G	K	I	P	I	M	L	R	S	T	Y	C	L	L	N	G	L	T
Predicted secondary structure
SS confidence
Known secondary structure (DSSP)				T	T														T	T																		S	S	S																			T	T	S	T	T	S	T	T	T	T
	.	.	.	.	.	.	.	.	.	150	.	.	.	.	.	.	.	.	.	160	.	.	.	.	.	.	.	.	.	170	.	.	.	.	.	.	.	.	.	180	.	.	.	.	.	.	.	.	.	190	.	.	.	.	.	.	.	.	.	200	.	.	.	.	.	.	.	.	.	210
Sequence	D	R	D	L	C	E	L	N	E	C	P	L	D	P	G	G	Y	F	I	I	N	G	S	E	K	V	L	I	A	Q	E	K	M	A	T	N	T	V	Y	V	F	A	K	K	D	S	K	Y	A	Y	T	G	E	C	R	S	C	L	E	N	S	S	R	P	T	S	T	I	W	V
Predicted secondary structure
SS confidence
Known secondary structure (DSSP)							T	T			T	T									T	T													S	S								S	S	S	S												T	T	T
	.	.	.	.	.	.	.	.	.	220	.	.	.	.	.	.	.	.	.	230	.	.	.	.	.	.	.	.	.	240	.	.	.	.	.	.	.	.	.	250	.	.	.	.	.	.	.	.	.	260	.	.	.	.	.	.	.	.	.	270	.	.	.	.	.	.	.	.	.	280
Sequence	S	M	L	A	R	G	G	Q	G	A	K	K	S	A	I	G	Q	R	I	V	A	T	L	P	Y	I	K	Q	E	V	P	I	I	I	V	F	R	A	L	G	F	V	S	D	R	D	I	L	E	H	I	I	Y	D	F	E	D	P	E	M	M	E	M	V	K	P	S	L	D	E
Predicted secondary structure
SS confidence
Known secondary structure (DSSP)					T	T			S															T	T	B	S	S											T	T			S										S		T	T
	.	.	.	.	.	.	.	.	.	290	.	.	.	.	.	.	.	.	.	300	.	.	.	.	.	.	.	.	.	310	.	.	.	.	.	.	.	.	.	320	.	.	.	.	.	.	.	.	.	330	.	.	.	.	.	.	.	.	.	340	.	.	.	.	.	.	.	.	.	350
Sequence	A	F	V	I	Q	E	Q	N	V	A	L	N	F	I	G	S	R	G	A	K	P	G	V	T	K	E	K	R	I	K	Y	A	K	E	V	L	Q	K	E	M	L	P	H	V	G	V	S	D	F	C	E	T	K	K	A	Y	F	L	G	Y	M	V	H	R	L	L	L	A	A	L
Predicted secondary structure
SS confidence
Known secondary structure (DSSP)	T	T	T			S										T	T	B	S	S			S	S														T	T	S		T	T	T		S	S	T	T																					T
	.	.	.	.	.	.	.	.	.	360	.	.	.	.	.	.	.	.	.	370	.	.	.	.	.	.	.	.	.	380	.	.	.	.	.	.	.	.	.	390	.	.	.	.	.	.	.	.	.	400	.	.	.	.	.	.	.	.	.	410	.	.	.	.	.	.	.	.	.	420
Sequence	G	R	R	E	L	D	D	R	D	H	Y	G	N	K	R	L	D	L	A	G	P	L	L	A	F	L	F	R	G	M	F	K	N	L	L	K	E	V	R	I	Y	A	Q	K	F	I	D	R	G	K	D	F	N	L	E	L	A	I	K	T	R	I	I	S	D	G	L	K	Y	S
Predicted secondary structure
SS confidence
Known secondary structure (DSSP)	T	S	S					T	T		T	T	S																																		T	T		S				S	T	T	T
	.	.	.	.	.	.	.	.	.	430	.	.	.	.	.	.	.	.	.	440	.	.	.	.	.	.	.	.	.	450	.	.	.	.	.	.	.	.	.	460	.	.	.	.	.	.	.	.	.	470	.	.	.	.	.	.	.	.	.	480	.	.	.	.	.	.	.	.	.	490
Sequence	L	A	T	G	N	W	G	D	Q	K	K	A	H	Q	A	R	A	G	V	S	Q	V	L	N	R	L	T	F	A	S	T	L	S	H	L	R	R	L	N	S	P	I	G	R	D	G	K	L	A	K	P	R	Q	L	H	N	T	L	W	G	M	V	C	P	A	E	T	P	E	G
Predicted secondary structure
SS confidence
Known secondary structure (DSSP)			S			B	S		S	T	T	T	T	T	S	B				S						S										S						S		S	S				S	S	S	S	S			G	G	G	T	T	T	B		S	S					S
	.	.	.	.	.	.	.	.	.	500	.	.	.	.	.	.	.	.	.	510	.	.	.	.	.	.	.	.	.	520	.	.	.	.	.	.	.	.	.	530	.	.	.	.	.	.	.	.	.	540	.	.	.	.	.	.	.	.	.	550	.	.	.	.	.	.	.	.	.	560
Sequence	H	A	V	G	L	V	K	N	L	A	L	M	A	Y	I	S	V	G	S	Q	P	S	P	I	L	E	F	L	E	E	W	S	M	E	N	L	E	E	I	S	P	A	A	I	A	D	A	T	K	I	F	V	N	G	C	W	V	G	I	H	K	D	P	E	Q	L	M	N	T	L
Predicted secondary structure
SS confidence
Known secondary structure (DSSP)	T	T	T	T	T				B	B	T	T									S										T					S	T	T			T	T	S	T	T	T	S						T	T							S
	.	.	.	.	.	.	.	.	.	570	.	.	.	.	.	.	.	.	.	580	.	.	.	.	.	.	.	.	.	590	.	.	.	.	.	.	.	.	.	600	.	.	.	.	.	.	.	.	.	610	.	.	.	.	.	.	.	.	.	620	.	.	.	.	.	.	.	.	.	630
Sequence	R	K	L	R	R	Q	M	D	I	I	V	S	E	V	S	M	I	R	D	I	R	E	R	E	I	R	I	Y	T	D	A	G	R	I	C	R	P	L	L	I	V	E	K	Q	K	L	L	L	K	K	R	H	I	D	Q	L	K	E	R	E	Y	N	N	Y	S	W	Q	D	L	V
Predicted secondary structure
SS confidence
Known secondary structure (DSSP)						T	T	S	S	S		T	T							S	T	T									S												T	T			S											T		T	T	T	T
	.	.	.	.	.	.	.	.	.	640	.	.	.	.	.	.	.	.	.	650	.	.	.	.	.	.	.	.	.	660	.	.	.	.	.	.	.	.	.	670	.	.	.	.	.	.	.	.	.	680	.	.	.	.	.	.	.	.	.	690	.	.	.	.	.	.	.	.	.	700
Sequence	A	S	G	V	V	E	Y	I	D	T	L	E	E	E	T	V	M	L	A	M	T	P	D	D	L	Q	E	K	E	V	A	Y	C	S	T	Y	T	H	C	E	I	H	P	S	M	I	L	G	V	C	A	S	I	I	P	F	P	D	H	N	Q	S	P	R	N	T	Y	Q	S	A
Predicted secondary structure
SS confidence
Known secondary structure (DSSP)	T	T	T	S										T	T					S						T	S		S	S		S		S							S		G	G	G	G	S	B	T	G	G	G	G	S	S	S	G	G	G	B
	.	.	.	.	.	.	.	.	.	710	.	.	.	.	.	.	.	.	.	720	.	.	.	.	.	.	.	.	.	730	.	.	.	.	.	.	.	.	.	740	.	.	.	.	.	.	.	.	.	750	.	.	.	.	.	.	.	.	.	760	.	.	.	.	.	.	.	.	.	770
Sequence	M	G	K	Q	A	M	G	V	Y	I	T	N	F	H	V	R	M	D	T	L	A	H	V	L	Y	Y	P	Q	K	P	L	V	T	T	R	S	M	E	Y	L	R	F	R	E	L	P	A	G	I	N	S	I	V	A	I	A	S	Y	T	G	Y	N	Q	E	D	S	V	I	M	N
Predicted secondary structure
SS confidence
Known secondary structure (DSSP)		T	T	S	B		S				T	T	T	T	T				S	S					S	S					S				G	G	G	G	G	G	T	T	T	T	S			S											S	S	S	S		T	T
	.	.	.	.	.	.	.	.	.	780	.	.	.	.	.	.	.	.	.	790	.	.	.	.	.	.	.	.	.	800	.	.	.	.	.	.	.	.	.	810	.	.	.	.	.	.	.	.	.	820	.	.	.	.	.	.	.	.	.	830	.	.	.	.	.	.	.	.	.	840
Sequence	R	S	A	V	D	R	G	F	F	R	S	V	F	Y	R	S	Y	K	E	Q	E	S	K	K	G	F	D	Q	E	E	V	F	E	K	P	T	R	E	T	C	Q	G	M	R	H	A	I	Y	D	K	L	D	D	D	G	L	I	A	P	G	V	R	V	S	G	D	D	V	I	I
Predicted secondary structure
SS confidence
Known secondary structure (DSSP)					T	T	T	T	T														B		S	S	S		B								T	T	T	B	S				S	S			T	T			T	T	S	B			T	T					T	T
	.	.	.	.	.	.	.	.	.	850	.	.	.	.	.	.	.	.	.	860	.	.	.	.	.	.	.	.	.	870	.	.	.	.	.	.	.	.	.	880	.	.	.	.	.	.	.	.	.	890	.	.	.	.	.	.	.	.	.	900	.	.	.	.	.	.	.	.	.	910
Sequence	G	K	T	V	T	L	P	T	K	R	D	C	S	T	F	L	R	T	S	E	T	G	I	V	D	Q	V	M	V	T	L	N	Q	E	G	Y	K	F	C	K	I	R	V	R	S	V	R	I	P	Q	I	G	D	K	F	A	S	R	H	G	Q	K	G	T	C	G	I	Q	Y	R
Predicted secondary structure
SS confidence
Known secondary structure (DSSP)																		T	T														S	S																	S	S						T	T	S
	.	.	.	.	.	.	.	.	.	920	.	.	.	.	.	.	.	.	.	930	.	.	.	.	.	.	.	.	.	940	.	.	.	.	.	.	.	.	.	950	.	.	.	.	.	.	.	.	.	960	.	.	.	.	.	.	.	.	.	970	.	.	.	.	.	.	.	.	.	980
Sequence	Q	E	D	M	P	F	T	C	E	G	I	T	P	D	I	I	I	N	P	H	A	I	P	S	R	M	T	I	G	H	L	I	E	C	L	Q	G	K	V	S	A	N	K	G	E	I	G	D	A	T	P	F	N	D	A	V	N	V	Q	K	I	S	N	L	L	S	D	Y	G	Y
Predicted secondary structure
SS confidence
Known secondary structure (DSSP)	T	T	T	S		B		T	T					S					T	T							B																	S	S						S			S	S											G	G	G	T	S
	.	.	.	.	.	.	.	.	.	990	.	.	.	.	.	.	.	.	.	1000	.	.	.	.	.	.	.	.	.	1010	.	.	.	.	.	.	.	.	.	1020	.	.	.	.	.	.	.	.	.	1030	.	.	.	.	.	.	.	.	.	1040	.	.	.	.	.	.	.	.	.	1050
Sequence	H	L	R	G	N	E	V	L	Y	N	G	F	T	G	R	K	I	T	S	Q	I	F	I	G	P	T	Y	Y	Q	R	L	K	H	M	V	D	D	K	I	H	S	R	A	R	G	P	I	Q	I	L	N	R	Q	P	M	E	G	R	S	R	D	G	G	L	R	F	G	E	M	E
Predicted secondary structure
SS confidence
Known secondary structure (DSSP)		T	T	S					B		T	T	T			B		S	S												B	S											S	S			B		T	T	T		S	B		S	S	T	T	T	T
	.	.	.	.	.	.	.	.	.	1060	.	.	.	.	.	.	.	.	.	1070	.	.	.	.	.	.	.	.	.	1080	.	.	.	.	.	.	.	.	.	1090	.	.	.	.	.	.	.	.	.	1100	.	.	.	.	.	.	.	.	.	1110	.	.	.	.	.	.	.	.	.	1120
Sequence	R	D	C	Q	I	A	H	G	A	A	Q	F	L	R	E	R	L	F	E	A	S	D	P	Y	Q	V	H	V	C	N	L	C	G	I	M	A	I	A	N	T	R	T	H	T	Y	E	C	R	G	C	R	N	K	T	Q	I	S	L	V	R	M	P	Y	A	C	K	L	L	F	Q
Predicted secondary structure
SS confidence
Known secondary structure (DSSP)								T										T	T	S	S									S	S	S	S	S	B					T	T	T					B	T	T	T	T	B		S
	.	.	.	.	.	.	.	.	.	1130	.	.	.	.
Sequence	E	L	M	S	M	S	I	A	P	R	M	M	S	V
Predicted secondary structure
SS confidence
Known secondary structure (DSSP)				T	T	T