Secondary structure and disorder prediction

		1	.	.	.	.	.	.	.	.	10	.	.	.	.	.	.	.	.	.	20	.	.	.	.	.	.	.	.	.	30	.	.	.	.	.	.	.	.	.	40	.	.	.	.	.	.	.	.	.	50	.	.	.	.	.
Sequence		M	K	K	L	T	D	K	Q	K	S	R	L	W	E	L	Q	R	N	R	N	F	Q	A	S	R	R	L	E	G	V	E	M	P	L	V	T	L	T	A	A	E	A	L	A	R	L	E	E	L	R	S	H	Y	E	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 3aei chain A Region: 34 - 55 Aligned: 22 Modelled: 22 Confidence: 12.0% Identity: 41% PDB header:chaperone Chain: A: PDB Molecule:prefoldin beta subunit 2; PDBTitle: crystal structure of the prefoldin beta2 subunit from thermococcus2 strain ks-1 Phyre2 PDB 3dom chain C Region: 11 - 19 Aligned: 9 Modelled: 9 Confidence: 9.2% Identity: 56% PDB header:transcription Chain: C: PDB Molecule:rna polymerase ii transcription factor b subunit 2; PDBTitle: crystal structure of the complex between tfb5 and the c-terminal2 domain of tfb2 Phyre2 PDB 2wb1 chain J Region: 37 - 55 Aligned: 19 Modelled: 19 Confidence: 8.7% Identity: 26% PDB header:transcription Chain: J: PDB Molecule:dna-directed rna polymerase rpo13 subunit; PDBTitle: the complete structure of the archaeal 13-subunit dna-2 directed rna polymerase Phyre2 PDB 2kwh chain A Region: 5 - 17 Aligned: 13 Modelled: 13 Confidence: 8.0% Identity: 46% PDB header:transport protein Chain: A: PDB Molecule:rala-binding protein 1; PDBTitle: ral binding domain of rlip76 (ralbp1) Phyre2 PDB 2wb1 chain Q Region: 37 - 54 Aligned: 18 Modelled: 18 Confidence: 7.7% Identity: 28% PDB header:transcription Chain: Q: PDB Molecule:dna-directed rna polymerase rpo13 subunit; PDBTitle: the complete structure of the archaeal 13-subunit dna-2 directed rna polymerase Phyre2 PDB 2cmp chain A Region: 3 - 14 Aligned: 12 Modelled: 12 Confidence: 5.8% Identity: 42% PDB header:terminase Chain: A: PDB Molecule:terminase small subunit; PDBTitle: crystal structure of the dna binding domain of g1p small2 terminase subunit from bacteriophage sf6 Phyre2 1 c3aeiA_ 2 c3domC_ 3 c2wb1J_ 4 c2kwhA_ 5 c2wb1Q_ 6 c2cmpA_

Detailed template information

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

1 c3aeiA_ 12.0 41 PDB header:chaperone Chain: A: PDB Molecule:prefoldin beta subunit 2; PDBTitle: crystal structure of the prefoldin beta2 subunit from thermococcus2 strain ks-1 2 c3domC_ 9.2 56 PDB header:transcription Chain: C: PDB Molecule:rna polymerase ii transcription factor b subunit 2; PDBTitle: crystal structure of the complex between tfb5 and the c-terminal2 domain of tfb2 3 c2wb1J_ 8.7 26 PDB header:transcription Chain: J: PDB Molecule:dna-directed rna polymerase rpo13 subunit; PDBTitle: the complete structure of the archaeal 13-subunit dna-2 directed rna polymerase 4 c2kwhA_ 8.0 46 PDB header:transport protein Chain: A: PDB Molecule:rala-binding protein 1; PDBTitle: ral binding domain of rlip76 (ralbp1) 5 c2wb1Q_ 7.7 28 PDB header:transcription Chain: Q: PDB Molecule:dna-directed rna polymerase rpo13 subunit; PDBTitle: the complete structure of the archaeal 13-subunit dna-2 directed rna polymerase 6 c2cmpA_ 5.8 42 PDB header:terminase Chain: A: PDB Molecule:terminase small subunit; PDBTitle: crystal structure of the dna binding domain of g1p small2 terminase subunit from bacteriophage sf6

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