Secondary structure and disorder prediction

		1	.	.	.	.	.	.	.	.	10	.	.	.	.	.	.	.	.	.	20	.	.	.	.	.	.	.	.	.	30	.	.	.	.	.	.	.	.	.	40	.	.	.	.	.	.	.	.	.	50	.	.	.	.	.	.	.	.	.	60
Sequence		M	A	R	V	T	V	Q	D	A	V	E	K	I	G	N	R	F	D	L	V	L	V	A	A	R	R	A	R	Q	M	Q	V	G	G	K	D	P	L	V	P	E	E	N	D	K	T	T	V	I	A	L	R	E	I	E	E	G	L	I	N
Secondary structure
SS confidence
Disorder		?	?	?	?																												?	?	?	?			?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	70	.	.	.	.	.	.	.	.	.	80	.	.	.	.	.	.	.	.	.	90	.
Sequence		N	Q	I	L	D	V	R	E	R	Q	E	Q	Q	E	Q	E	A	A	E	L	Q	A	V	T	A	I	A	E	G	R	R
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 3iyd chain E Region: 2 - 91 Aligned: 90 Modelled: 90 Confidence: 100.0% Identity: 100% PDB header:transcription/dna Chain: E: PDB Molecule:dna-directed rna polymerase subunit omega; PDBTitle: three-dimensional em structure of an intact activator-dependent2 transcription initiation complex Phyre2 PDB 1ynj chain K domain 1 Region: 1 - 60 Aligned: 60 Modelled: 60 Confidence: 98.2% Identity: 28% Fold: RPB6/omega subunit-like Superfamily: RPB6/omega subunit-like Family: RNA polymerase omega subunit Phyre2 PDB 1smy chain E Region: 2 - 60 Aligned: 59 Modelled: 59 Confidence: 98.1% Identity: 25% Fold: RPB6/omega subunit-like Superfamily: RPB6/omega subunit-like Family: RNA polymerase omega subunit Phyre2 PDB 1twc chain F Region: 15 - 60 Aligned: 45 Modelled: 46 Confidence: 97.0% Identity: 22% PDB header:transcription Chain: F: PDB Molecule:dna-directed rna polymerases i, ii, and iii 23 PDBTitle: rna polymerase ii complexed with gtp Phyre2 PDB 1twf chain F Region: 15 - 60 Aligned: 45 Modelled: 46 Confidence: 97.0% Identity: 22% Fold: RPB6/omega subunit-like Superfamily: RPB6/omega subunit-like Family: RPB6 Phyre2 PDB 1qkl chain A Region: 15 - 60 Aligned: 45 Modelled: 46 Confidence: 96.9% Identity: 22% Fold: RPB6/omega subunit-like Superfamily: RPB6/omega subunit-like Family: RPB6 Phyre2 PDB 3h0g chain F Region: 15 - 60 Aligned: 45 Modelled: 46 Confidence: 96.9% Identity: 22% PDB header:transcription Chain: F: PDB Molecule:dna-directed rna polymerases i, ii, and iii PDBTitle: rna polymerase ii from schizosaccharomyces pombe Phyre2 PDB 2pmz chain W Region: 15 - 60 Aligned: 45 Modelled: 46 Confidence: 96.8% Identity: 27% PDB header:translation, transferase Chain: W: PDB Molecule:dna-directed rna polymerase subunit k; PDBTitle: archaeal rna polymerase from sulfolobus solfataricus Phyre2 PDB 1hul chain A Region: 18 - 57 Aligned: 38 Modelled: 40 Confidence: 17.7% Identity: 21% Fold: 4-helical cytokines Superfamily: 4-helical cytokines Family: Short-chain cytokines Phyre2 PDB 2kxh chain B Region: 23 - 30 Aligned: 8 Modelled: 8 Confidence: 14.8% Identity: 63% PDB header:protein binding Chain: B: PDB Molecule:peptide of far upstream element-binding protein 1; PDBTitle: solution structure of the first two rrm domains of fir in the complex2 with fbp nbox peptide Phyre2 PDB 1id3 chain A Region: 41 - 54 Aligned: 14 Modelled: 14 Confidence: 13.5% Identity: 43% Fold: Histone-fold Superfamily: Histone-fold Family: Nucleosome core histones Phyre2 PDB 1ysh chain E Region: 14 - 31 Aligned: 18 Modelled: 18 Confidence: 11.8% Identity: 33% PDB header:structural protein/rna Chain: E: PDB Molecule:40s ribosomal protein s13; PDBTitle: localization and dynamic behavior of ribosomal protein l30e Phyre2 PDB 1tzy chain C Region: 45 - 54 Aligned: 10 Modelled: 10 Confidence: 7.5% Identity: 50% Fold: Histone-fold Superfamily: Histone-fold Family: Nucleosome core histones Phyre2 PDB 1p3i chain E Region: 41 - 54 Aligned: 14 Modelled: 14 Confidence: 6.6% Identity: 36% Fold: Histone-fold Superfamily: Histone-fold Family: Nucleosome core histones Phyre2 PDB 3ci9 chain B Region: 6 - 18 Aligned: 13 Modelled: 13 Confidence: 6.5% Identity: 23% PDB header:transcription Chain: B: PDB Molecule:heat shock factor-binding protein 1; PDBTitle: crystal structure of the human hsbp1 Phyre2 1 c3iydE_ 2 d1ynjk1 3 d1smye_ 4 c1twcF_ 5 d1twff_ 6 d1qkla_ 7 c3h0gF_ 8 c2pmzW_ 9 d1hula_ 10 c2kxhB_ 11 d1id3a_ 12 c1yshE_ 13 d1tzyc_ 14 d1p3ie_ 15 c3ci9B_

Detailed template information

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

1 c3iydE_ 100.0 100 PDB header:transcription/dna Chain: E: PDB Molecule:dna-directed rna polymerase subunit omega; PDBTitle: three-dimensional em structure of an intact activator-dependent2 transcription initiation complex 2 d1ynjk1 98.2 28 Fold:RPB6/omega subunit-like Superfamily:RPB6/omega subunit-like Family:RNA polymerase omega subunit 3 d1smye_ 98.1 25 Fold:RPB6/omega subunit-like Superfamily:RPB6/omega subunit-like Family:RNA polymerase omega subunit 4 c1twcF_ 97.0 22 PDB header:transcription Chain: F: PDB Molecule:dna-directed rna polymerases i, ii, and iii 23 PDBTitle: rna polymerase ii complexed with gtp 5 d1twff_ 97.0 22 Fold:RPB6/omega subunit-like Superfamily:RPB6/omega subunit-like Family:RPB6 6 d1qkla_ 96.9 22 Fold:RPB6/omega subunit-like Superfamily:RPB6/omega subunit-like Family:RPB6 7 c3h0gF_ 96.9 22 PDB header:transcription Chain: F: PDB Molecule:dna-directed rna polymerases i, ii, and iii PDBTitle: rna polymerase ii from schizosaccharomyces pombe 8 c2pmzW_ 96.8 27 PDB header:translation, transferase Chain: W: PDB Molecule:dna-directed rna polymerase subunit k; PDBTitle: archaeal rna polymerase from sulfolobus solfataricus 9 d1hula_ 17.7 21 Fold:4-helical cytokines Superfamily:4-helical cytokines Family:Short-chain cytokines 10 c2kxhB_ 14.8 63 PDB header:protein binding Chain: B: PDB Molecule:peptide of far upstream element-binding protein 1; PDBTitle: solution structure of the first two rrm domains of fir in the complex2 with fbp nbox peptide 11 d1id3a_ 13.5 43 Fold:Histone-fold Superfamily:Histone-fold Family:Nucleosome core histones 12 c1yshE_ 11.8 33 PDB header:structural protein/rna Chain: E: PDB Molecule:40s ribosomal protein s13; PDBTitle: localization and dynamic behavior of ribosomal protein l30e 13 d1tzyc_ 7.5 50 Fold:Histone-fold Superfamily:Histone-fold Family:Nucleosome core histones 14 d1p3ie_ 6.6 36 Fold:Histone-fold Superfamily:Histone-fold Family:Nucleosome core histones 15 c3ci9B_ 6.5 23 PDB header:transcription Chain: B: PDB Molecule:heat shock factor-binding protein 1; PDBTitle: crystal structure of the human hsbp1

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