Secondary structure and disorder prediction

		1	.	.	.	.	.	.	.	.	10	.	.	.	.	.	.	.	.	.	20	.	.	.	.	.	.	.	.	.	30	.	.	.	.	.	.	.	.	.	40	.	.	.	.	.	.	.	.	.	50	.	.	.	.	.	.	.	.	.	60
Sequence		M	Q	R	K	L	A	T	W	A	A	T	D	P	S	L	R	I	Q	R	L	L	R	L	I	T	Q	P	E	W	L	A	E	A	A	R	I	T	L	S	S	K	G	A	H	T	P	G	V	D	G	V	N	K	T	M	L	Q	A	R	L
Secondary structure
SS confidence
Disorder		?	?	?								?	?	?	?	?	?																							?	?	?	?	?	?	?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	70	.	.	.	.	.	.	.	.	.	80	.	.	.	.	.	.	.	.	.	90	.	.	.	.	.	.	.	.	.	100	.	.	.	.	.	.	.	.	.	110	.	.	.	.	.	.	.	.	.	120
Sequence		A	V	E	L	Q	I	L	R	D	E	L	L	S	G	H	Y	Q	P	L	P	A	R	R	V	Y	I	P	K	S	N	G	K	L	R	P	L	G	I	P	A	L	R	D	R	I	V	Q	R	A	M	L	M	A	M	E	P	I	W	E	S
Secondary structure
SS confidence
Disorder															?
Disorder confidence
		.	.	.	.	.	.	.	.	.	130	.	.	.	.	.	.	.	.	.	140	.	.	.	.	.	.	.	.	.	150	.	.	.	.	.	.	.	.	.	160	.	.	.	.	.	.	.	.	.	170	.	.	.	.	.	.	.	.	.	180
Sequence		D	F	H	T	L	S	Y	G	F	R	P	E	R	S	V	H	H	A	I	R	T	V	K	L	Q	L	T	D	C	G	E	T	R	G	R	W	V	I	E	G	D	L	S	S	Y	F	D	T	V	H	H	R	L	L	M	K	A	V	R	R
Secondary structure
SS confidence
Disorder
Disorder confidence
		.	.	.	.	.	.	.	.	.	190	.	.	.	.	.	.	.	.	.	200	.	.	.	.	.	.	.	.	.	210	.	.	.	.	.	.	.	.	.	220	.	.	.	.	.	.	.	.	.	230	.	.	.	.	.	.	.	.	.	240
Sequence		R	I	S	D	A	R	F	M	T	L	L	W	K	T	I	K	A	G	H	I	D	V	G	L	F	R	A	A	S	E	G	V	P	Q	G	G	V	I	S	P	L	L	S	N	I	M	L	N	E	F	D	Q	Y	L	H	E	R	Y	L	S
Secondary structure
SS confidence
Disorder																		?																																									?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	250	.	.	.	.	.	.	.	.	.	260	.	.	.	.	.	.	.	.	.	270	.	.	.	.	.	.	.	.	.	280	.	.	.	.	.	.	.	.	.	290	.	.	.	.	.	.	.	.	.	300
Sequence		G	K	A	R	K	D	R	W	Y	W	N	N	S	I	Q	R	G	R	S	T	A	V	R	E	N	W	Q	W	K	P	A	V	A	Y	C	R	Y	A	D	D	F	V	L	I	V	K	G	T	K	A	Q	V	E	A	I	R	E	E	C	R
Secondary structure
SS confidence
Disorder		?	?	?	?	?						?	?	?	?	?	?	?	?	?	?	?	?	?	?	?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	310	.	.	.	.	.	.	.	.	.	320	.	.	.	.	.	.	.	.	.	330	.	.	.	.	.	.	.	.	.	340	.	.	.	.	.	.	.	.	.	350	.	.	.	.	.	.	.	.	.	360
Sequence		G	V	L	E	G	S	L	K	L	R	L	N	M	D	K	T	K	I	P	H	V	N	D	G	F	I	F	L	G	H	R	L	I	R	K	R	S	R	Y	G	E	M	R	V	V	S	T	I	P	Q	E	K	A	R	N	F	A	A	S	L
Secondary structure
SS confidence
Disorder																																			?	?				?	?	?	?				?	?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	370	.	.	.	.	.	.
Sequence		T	A	L	L	W	K	V	R	I	S	G	E	I	L	L	G
Secondary structure
SS confidence
Disorder										?	?	?	?	?	?	?	?
Disorder confidence

Confidence Key
High(9)											Low (0)

?	Disordered
	Alpha helix
	Beta strand

Domain analysis

Hover over an aligned region to see model and summary info

Please note, only up to the top 20 hits are modelled to reduce computer load

Rank Aligned region

PDB 3du6 chain A Region: 53 - 333 Aligned: 230 Modelled: 243 Confidence: 99.9% Identity: 16% PDB header:transferase Chain: A: PDB Molecule:telomerase reverse transcriptase; PDBTitle: structure of the catalytic subunit of telomerase, tert Phyre2 PDB 1rth chain A Region: 57 - 336 Aligned: 204 Modelled: 208 Confidence: 99.5% Identity: 20% PDB header:nucleotidyltransferase Chain: A: PDB Molecule:hiv-1 reverse transcriptase; PDBTitle: high resolution structures of hiv-1 rt from four rt-2 inhibitor complexes Phyre2 PDB 1mu2 chain A Region: 153 - 332 Aligned: 124 Modelled: 128 Confidence: 99.2% Identity: 19% PDB header:transferase Chain: A: PDB Molecule:hiv-2 rt; PDBTitle: crystal structure of hiv-2 reverse transcriptase Phyre2 PDB 2opq chain A Region: 153 - 338 Aligned: 139 Modelled: 155 Confidence: 98.9% Identity: 20% PDB header:transferase Chain: A: PDB Molecule:reverse transcriptase/ribonuclease h; PDBTitle: crystal structure of l100i mutant hiv-1 reverse2 transcriptase in complex with gw420867x. Phyre2 PDB 1xr7 chain A Region: 91 - 350 Aligned: 222 Modelled: 235 Confidence: 98.7% Identity: 16% Fold: DNA/RNA polymerases Superfamily: DNA/RNA polymerases Family: RNA-dependent RNA-polymerase Phyre2 PDB 2zd1 chain B domain 1 Region: 57 - 338 Aligned: 194 Modelled: 195 Confidence: 98.7% Identity: 21% Fold: DNA/RNA polymerases Superfamily: DNA/RNA polymerases Family: Reverse transcriptase Phyre2 PDB 1u09 chain A Region: 91 - 336 Aligned: 209 Modelled: 221 Confidence: 98.7% Identity: 16% Fold: DNA/RNA polymerases Superfamily: DNA/RNA polymerases Family: RNA-dependent RNA-polymerase Phyre2 PDB 3n6m chain A Region: 91 - 350 Aligned: 221 Modelled: 235 Confidence: 98.7% Identity: 15% PDB header:transferase Chain: A: PDB Molecule:rna-dependent rna polymerase; PDBTitle: crystal structure of ev71 rdrp in complex with gtp Phyre2 PDB 1mu2 chain A domain 2 Region: 152 - 338 Aligned: 131 Modelled: 135 Confidence: 98.7% Identity: 18% Fold: DNA/RNA polymerases Superfamily: DNA/RNA polymerases Family: Reverse transcriptase Phyre2 PDB 1xr6 chain A Region: 91 - 350 Aligned: 222 Modelled: 235 Confidence: 98.6% Identity: 15% Fold: DNA/RNA polymerases Superfamily: DNA/RNA polymerases Family: RNA-dependent RNA-polymerase Phyre2 PDB 1ra6 chain A Region: 91 - 350 Aligned: 217 Modelled: 236 Confidence: 98.5% Identity: 13% Fold: DNA/RNA polymerases Superfamily: DNA/RNA polymerases Family: RNA-dependent RNA-polymerase Phyre2 PDB 1ztw chain A domain 1 Region: 212 - 337 Aligned: 91 Modelled: 95 Confidence: 98.5% Identity: 24% Fold: DNA/RNA polymerases Superfamily: DNA/RNA polymerases Family: Reverse transcriptase Phyre2 PDB 1khv chain A Region: 30 - 336 Aligned: 276 Modelled: 288 Confidence: 98.5% Identity: 16% Fold: DNA/RNA polymerases Superfamily: DNA/RNA polymerases Family: RNA-dependent RNA-polymerase Phyre2 PDB 2ijd chain 1 Region: 91 - 350 Aligned: 220 Modelled: 235 Confidence: 98.3% Identity: 13% PDB header:hydrolase, transferase Chain: 1: PDB Molecule:picornain 3c, rna-directed rna polymerase; PDBTitle: crystal structure of the poliovirus precursor protein 3cd Phyre2 PDB 3kk1 chain B Region: 57 - 329 Aligned: 194 Modelled: 201 Confidence: 98.3% Identity: 18% PDB header:transferase/dna Chain: B: PDB Molecule:reverse transcriptase p51 subunit; PDBTitle: hiv-1 reverse transcriptase-dna complex with nuceotide inhibitor gs-2 9148-diphosphate bound in nucleotide site Phyre2 PDB 1xr5 chain A Region: 91 - 350 Aligned: 219 Modelled: 235 Confidence: 98.3% Identity: 15% Fold: DNA/RNA polymerases Superfamily: DNA/RNA polymerases Family: RNA-dependent RNA-polymerase Phyre2 PDB 2uut chain A Region: 91 - 336 Aligned: 209 Modelled: 228 Confidence: 98.1% Identity: 14% PDB header:hydrolase Chain: A: PDB Molecule:rna-directed rna polymerase; PDBTitle: the 2.4 angstrom resolution structure of the d346g mutant2 of the sapporo virus rdrp polymerase Phyre2 PDB 3nah chain C Region: 91 - 336 Aligned: 211 Modelled: 224 Confidence: 98.1% Identity: 16% PDB header:transferase Chain: C: PDB Molecule:rna dependent rna polymerase; PDBTitle: crystal structures and functional analysis of murine norovirus rna-2 dependent rna polymerase Phyre2 PDB 1sh0 chain A Region: 60 - 336 Aligned: 242 Modelled: 255 Confidence: 97.9% Identity: 17% Fold: DNA/RNA polymerases Superfamily: DNA/RNA polymerases Family: RNA-dependent RNA-polymerase Phyre2 PDB 2b43 chain D Region: 60 - 336 Aligned: 240 Modelled: 255 Confidence: 97.9% Identity: 15% PDB header:viral protein Chain: D: PDB Molecule:non-structural polyprotein; PDBTitle: crystal structure of the norwalk virus rna dependent rna polymerase2 from strain hu/nlv/dresden174/1997/ge Phyre2 1 c3du6A_ 2 c1rthA_ 3 c1mu2A_ 4 c2opqA_ 5 d1xr7a_ 6 d2zd1b1 7 d1u09a_ 8 c3n6mA_ 9 d1mu2a2 10 d1xr6a_ 11 d1ra6a_ 12 d1ztwa1 13 d1khva_ 14 c2ijd1_ 15 c3kk1B_ 16 d1xr5a_ 17 c2uutA_ 18 c3nahC_ 19 d1sh0a_ 20 c2b43D_ 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35

Detailed template information

# Template Alignment Coverage 3D Model Confidence % i.d. Template Information

1 c3du6A_ 99.9 16 PDB header:transferase Chain: A: PDB Molecule:telomerase reverse transcriptase; PDBTitle: structure of the catalytic subunit of telomerase, tert 2 c1rthA_ 99.5 20 PDB header:nucleotidyltransferase Chain: A: PDB Molecule:hiv-1 reverse transcriptase; PDBTitle: high resolution structures of hiv-1 rt from four rt-2 inhibitor complexes 3 c1mu2A_ 99.2 19 PDB header:transferase Chain: A: PDB Molecule:hiv-2 rt; PDBTitle: crystal structure of hiv-2 reverse transcriptase 4 c2opqA_ 98.9 20 PDB header:transferase Chain: A: PDB Molecule:reverse transcriptase/ribonuclease h; PDBTitle: crystal structure of l100i mutant hiv-1 reverse2 transcriptase in complex with gw420867x. 5 d1xr7a_ 98.7 16 Fold:DNA/RNA polymerases Superfamily:DNA/RNA polymerases Family:RNA-dependent RNA-polymerase 6 d2zd1b1 98.7 21 Fold:DNA/RNA polymerases Superfamily:DNA/RNA polymerases Family:Reverse transcriptase 7 d1u09a_ 98.7 16 Fold:DNA/RNA polymerases Superfamily:DNA/RNA polymerases Family:RNA-dependent RNA-polymerase 8 c3n6mA_ 98.7 15 PDB header:transferase Chain: A: PDB Molecule:rna-dependent rna polymerase; PDBTitle: crystal structure of ev71 rdrp in complex with gtp 9 d1mu2a2 98.7 18 Fold:DNA/RNA polymerases Superfamily:DNA/RNA polymerases Family:Reverse transcriptase 10 d1xr6a_ 98.6 15 Fold:DNA/RNA polymerases Superfamily:DNA/RNA polymerases Family:RNA-dependent RNA-polymerase 11 d1ra6a_ 98.5 13 Fold:DNA/RNA polymerases Superfamily:DNA/RNA polymerases Family:RNA-dependent RNA-polymerase 12 d1ztwa1 98.5 24 Fold:DNA/RNA polymerases Superfamily:DNA/RNA polymerases Family:Reverse transcriptase 13 d1khva_ 98.5 16 Fold:DNA/RNA polymerases Superfamily:DNA/RNA polymerases Family:RNA-dependent RNA-polymerase 14 c2ijd1_ 98.3 13 PDB header:hydrolase, transferase Chain: 1: PDB Molecule:picornain 3c, rna-directed rna polymerase; PDBTitle: crystal structure of the poliovirus precursor protein 3cd 15 c3kk1B_ 98.3 18 PDB header:transferase/dna Chain: B: PDB Molecule:reverse transcriptase p51 subunit; PDBTitle: hiv-1 reverse transcriptase-dna complex with nuceotide inhibitor gs-2 9148-diphosphate bound in nucleotide site 16 d1xr5a_ 98.3 15 Fold:DNA/RNA polymerases Superfamily:DNA/RNA polymerases Family:RNA-dependent RNA-polymerase 17 c2uutA_ 98.1 14 PDB header:hydrolase Chain: A: PDB Molecule:rna-directed rna polymerase; PDBTitle: the 2.4 angstrom resolution structure of the d346g mutant2 of the sapporo virus rdrp polymerase 18 c3nahC_ 98.1 16 PDB header:transferase Chain: C: PDB Molecule:rna dependent rna polymerase; PDBTitle: crystal structures and functional analysis of murine norovirus rna-2 dependent rna polymerase 19 d1sh0a_ 97.9 17 Fold:DNA/RNA polymerases Superfamily:DNA/RNA polymerases Family:RNA-dependent RNA-polymerase 20 c2b43D_ 97.9 15 PDB header:viral protein Chain: D: PDB Molecule:non-structural polyprotein; PDBTitle: crystal structure of the norwalk virus rna dependent rna polymerase2 from strain hu/nlv/dresden174/1997/ge 21 d1rw3a_ not modelled 97.3 19 Fold:DNA/RNA polymerases Superfamily:DNA/RNA polymerases Family:Reverse transcriptase 22 d1hara_ not modelled 96.5 23 Fold:DNA/RNA polymerases Superfamily:DNA/RNA polymerases Family:Reverse transcriptase 23 d1raja_ not modelled 93.9 14 Fold:DNA/RNA polymerases Superfamily:DNA/RNA polymerases Family:RNA-dependent RNA-polymerase 24 c3mmpG_ not modelled 88.7 16 PDB header:transferase Chain: G: PDB Molecule:rna-directed rna polymerase beta chain; PDBTitle: structure of the qb replicase, an rna-dependent rna polymerase2 consisting of viral and host proteins 25 c3agqA_ not modelled 72.6 17 PDB header:translation,transferase Chain: A: PDB Molecule:elongation factor ts, elongation factor tu 1, linker, q PDBTitle: structure of viral polymerase form ii 26 d1nb4a_ not modelled 71.3 15 Fold:DNA/RNA polymerases Superfamily:DNA/RNA polymerases Family:RNA-dependent RNA-polymerase 27 d1gx5a_ not modelled 41.9 17 Fold:DNA/RNA polymerases Superfamily:DNA/RNA polymerases Family:RNA-dependent RNA-polymerase 28 c1nh2D_ not modelled 35.3 23 PDB header:transcription/dna Chain: D: PDB Molecule:transcription initiation factor iia small chain; PDBTitle: crystal structure of a yeast tfiia/tbp/dna complex 29 c1nvpD_ not modelled 33.2 19 PDB header:transcription/dna Chain: D: PDB Molecule:transcription initiation factor iia gamma chain; PDBTitle: human tfiia/tbp/dna complex 30 d1c0aa2 not modelled 15.8 19 Fold:DCoH-like Superfamily:GAD domain-like Family:GAD domain 31 d1l0wa2 not modelled 14.3 22 Fold:DCoH-like Superfamily:GAD domain-like Family:GAD domain 32 d1nh2d1 not modelled 11.2 26 Fold:Transcription factor IIA (TFIIA), alpha-helical domain Superfamily:Transcription factor IIA (TFIIA), alpha-helical domain Family:Transcription factor IIA (TFIIA), alpha-helical domain 33 d1nvpd1 not modelled 9.5 25 Fold:Transcription factor IIA (TFIIA), alpha-helical domain Superfamily:Transcription factor IIA (TFIIA), alpha-helical domain Family:Transcription factor IIA (TFIIA), alpha-helical domain 34 d1p9ya_ not modelled 7.3 14 Fold:Ribosome binding domain-like Superfamily:Trigger factor ribosome-binding domain Family:Trigger factor ribosome-binding domain 35 d1w26a2 not modelled 6.3 21 Fold:Ribosome binding domain-like Superfamily:Trigger factor ribosome-binding domain Family:Trigger factor ribosome-binding domain

Binding site prediction

Due to computational demand, binding site predictions are not run for batch jobs

If you want to predict binding sites, please manually submit your model of choice to 3DLigandSite

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Phyre is for academic use only

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]
If you use the binding site predictions from 3DLigandSite, please also cite:
3DLigandSite: predicting ligand-binding sites using similar structures.
Wass MN, Kelley LA and Sternberg MJ Nucleic Acids Research 38, W469-73 (2010) [PubMed]
© Structural Bioinformatics Group Imperial College London Lawrence Kelley, Benjamin Jefferys Disclaimer Terms and Conditions	Component software Template detection: HHpred 1.51 Secondary structure prediction: Psi-pred 2.5 Disorder prediction: Disopred 2.4 Transmembrane prediction: Memsat_SVM Multi-template modelling and ab initio: Poing 1.0