Secondary structure and disorder prediction

		1	.	.	.	.	.	.	.	.	10	.	.	.	.	.	.	.	.	.	20	.	.	.	.	.	.	.	.	.	30	.	.	.	.	.	.	.	.	.	40	.	.	.	.	.	.	.	.	.	50	.	.	.	.	.	.	.	.	.	60
Sequence		M	T	T	D	N	T	N	T	T	R	N	D	S	L	V	A	R	T	D	T	W	L	Q	S	L	L	V	W	S	P	G	Q	R	D	I	I	K	T	V	A	L	V	L	M	V	L	D	H	A	N	R	I	L	H	L	D	Q	S	W	M
Secondary structure
SS confidence
Disorder		?	?	?	?	?	?	?	?	?	?	?	?	?	?				?	?						?	?	?	?	?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	70	.	.	.	.	.	.	.	.	.	80	.	.	.	.	.	.	.	.	.	90	.	.	.	.	.	.	.	.	.	100	.	.	.	.	.	.	.	.	.	110	.	.	.	.	.	.	.	.	.	120
Sequence		F	L	A	G	R	G	A	F	P	L	F	A	L	V	W	G	L	N	L	S	R	H	A	H	I	R	Q	L	A	I	N	R	L	W	G	W	A	V	F	S	Q	F	W	Y	Y	F	A	G	F	P	W	Y	E	G	N	I	L	F	A	F
Secondary structure
SS confidence
Disorder
Disorder confidence
		.	.	.	.	.	.	.	.	.	130	.	.	.	.	.	.	.	.	.	140	.	.	.	.	.	.	.	.	.	150	.	.	.	.	.	.	.	.	.	160	.	.	.	.	.	.	.	.	.	170	.	.	.	.	.	.	.	.	.	180
Sequence		A	V	A	A	Q	V	L	T	W	C	E	T	R	S	G	W	R	T	A	A	A	I	L	M	M	A	L	W	G	P	L	S	G	T	S	Y	G	I	A	G	L	L	M	L	A	V	S	H	R	L	Y	R	A	E	D	R	M	E	R	L
Secondary structure
SS confidence
Disorder																																																								?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	190	.	.	.	.	.	.	.	.	.	200	.	.	.	.	.	.	.	.	.	210	.	.	.	.	.	.	.	.	.	220	.	.	.	.	.	.	.	.	.	230	.	.	.	.	.	.	.	.	.	240
Sequence		V	L	V	A	C	L	L	A	V	I	P	A	L	N	L	A	T	S	D	A	A	A	V	A	G	L	V	M	T	V	L	T	V	G	L	V	S	C	A	G	K	L	L	S	R	F	W	P	G	D	F	F	P	T	F	Y	A	C	H	L
Secondary structure
SS confidence
Disorder																																							?	?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.
Sequence		A	V	L	G	V	L	A	L
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 2kp6 chain A Region: 28 - 37 Aligned: 10 Modelled: 10 Confidence: 25.6% Identity: 30% PDB header:structural genomics, unknown function Chain: A: PDB Molecule:uncharacterized protein; PDBTitle: solution nmr structure of protein cv0237 from2 chromobacterium violaceum. northeast structural genomics3 consortium (nesg) target cvt1 Phyre2 PDB 2hcn chain A Region: 71 - 103 Aligned: 27 Modelled: 33 Confidence: 15.8% Identity: 30% PDB header:transferase Chain: A: PDB Molecule:rna-directed rna polymerase (ns5); PDBTitle: crystal structure of rna dependent rna polymerase domain from west2 nile virus Phyre2 PDB 2j7u chain A Region: 71 - 103 Aligned: 27 Modelled: 28 Confidence: 14.2% Identity: 30% PDB header:viral protein Chain: A: PDB Molecule:rna dependent rna polymerase; PDBTitle: dengue virus ns5 rna dependent rna polymerase domain Phyre2 PDB 3lyg chain A Region: 30 - 56 Aligned: 27 Modelled: 27 Confidence: 10.6% Identity: 33% PDB header:structural genomics, unknown function Chain: A: PDB Molecule:ntf2-like protein of unknown function; PDBTitle: crystal structure of ntf2-like protein of unknown function2 (yp_270605.1) from colwellia psychrerythraea 34h at 1.61 a resolution Phyre2 PDB 1t6l chain A domain 2 Region: 34 - 40 Aligned: 7 Modelled: 7 Confidence: 9.4% Identity: 29% Fold: DNA clamp Superfamily: DNA clamp Family: DNA polymerase processivity factor Phyre2 PDB 3o59 chain X Region: 71 - 93 Aligned: 23 Modelled: 22 Confidence: 8.2% Identity: 17% PDB header:transferase Chain: X: PDB Molecule:dna polymerase ii large subunit; PDBTitle: dna polymerase d large subunit dp2(1-300) from pyrococcus horikoshii Phyre2 PDB 1j5w chain A Region: 71 - 93 Aligned: 22 Modelled: 23 Confidence: 7.6% Identity: 23% Fold: Class II aaRS and biotin synthetases Superfamily: Class II aaRS and biotin synthetases Family: Class II aminoacyl-tRNA synthetase (aaRS)-like, catalytic domain Phyre2 PDB 2hfz chain A Region: 71 - 103 Aligned: 27 Modelled: 28 Confidence: 5.6% Identity: 30% PDB header:transferase Chain: A: PDB Molecule:rna-directed rna polymerase(ns5); PDBTitle: crystal structure of rna dependent rna polymerase domain2 from west nile virus Phyre2 PDB 3rf1 chain B Region: 71 - 93 Aligned: 22 Modelled: 23 Confidence: 5.3% Identity: 18% PDB header:ligase Chain: B: PDB Molecule:glycyl-trna synthetase alpha subunit; PDBTitle: the crystal structure of glycyl-trna synthetase subunit alpha from2 campylobacter jejuni subsp. jejuni nctc 11168 Phyre2 1 c2kp6A_ 2 c2hcnA_ 3 c2j7uA_ 4 c3lygA_ 5 d1t6la2 6 c3o59X_ 7 d1j5wa_ 8 c2hfzA_ 9 c3rf1B_

Detailed template information

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

1 c2kp6A_ 25.6 30 PDB header:structural genomics, unknown function Chain: A: PDB Molecule:uncharacterized protein; PDBTitle: solution nmr structure of protein cv0237 from2 chromobacterium violaceum. northeast structural genomics3 consortium (nesg) target cvt1 2 c2hcnA_ 15.8 30 PDB header:transferase Chain: A: PDB Molecule:rna-directed rna polymerase (ns5); PDBTitle: crystal structure of rna dependent rna polymerase domain from west2 nile virus 3 c2j7uA_ 14.2 30 PDB header:viral protein Chain: A: PDB Molecule:rna dependent rna polymerase; PDBTitle: dengue virus ns5 rna dependent rna polymerase domain 4 c3lygA_ 10.6 33 PDB header:structural genomics, unknown function Chain: A: PDB Molecule:ntf2-like protein of unknown function; PDBTitle: crystal structure of ntf2-like protein of unknown function2 (yp_270605.1) from colwellia psychrerythraea 34h at 1.61 a resolution 5 d1t6la2 9.4 29 Fold:DNA clamp Superfamily:DNA clamp Family:DNA polymerase processivity factor 6 c3o59X_ 8.2 17 PDB header:transferase Chain: X: PDB Molecule:dna polymerase ii large subunit; PDBTitle: dna polymerase d large subunit dp2(1-300) from pyrococcus horikoshii 7 d1j5wa_ 7.6 23 Fold:Class II aaRS and biotin synthetases Superfamily:Class II aaRS and biotin synthetases Family:Class II aminoacyl-tRNA synthetase (aaRS)-like, catalytic domain 8 c2hfzA_ 5.6 30 PDB header:transferase Chain: A: PDB Molecule:rna-directed rna polymerase(ns5); PDBTitle: crystal structure of rna dependent rna polymerase domain2 from west nile virus 9 c3rf1B_ 5.3 18 PDB header:ligase Chain: B: PDB Molecule:glycyl-trna synthetase alpha subunit; PDBTitle: the crystal structure of glycyl-trna synthetase subunit alpha from2 campylobacter jejuni subsp. jejuni nctc 11168

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