Secondary structure and disorder prediction

		1	.	.	.	.	.	.	.	.	10	.	.	.	.	.	.	.	.	.	20	.	.	.	.	.	.	.	.	.	30	.	.	.	.	.	.	.	.	.	40	.	.	.	.	.	.	.	.	.	50	.	.	.	.	.	.	.	.	.	60
Sequence		M	N	N	S	N	N	L	D	Y	F	T	L	Y	I	I	F	S	I	A	F	M	L	I	T	L	L	V	I	L	I	A	K	P	S	T	G	L	G	E	V	L	V	T	I	N	L	L	N	A	L	V	W	L	A	I	N	L	V	N	R
Secondary structure
SS confidence
Disorder		?	?	?	?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	70	.	.
Sequence		L	R	E	R	L	V	N	H	R	D	Q	Q
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 2l23 chain A Region: 56 - 72 Aligned: 17 Modelled: 17 Confidence: 17.1% Identity: 35% PDB header:transcription Chain: A: PDB Molecule:mediator of rna polymerase ii transcription subunit 25; PDBTitle: nmr structure of the acid (activator interacting domain) of the human2 mediator med25 protein Phyre2 PDB 3lmm chain A Region: 61 - 72 Aligned: 12 Modelled: 12 Confidence: 8.0% Identity: 50% PDB header:structural genomics, unknown function Chain: A: PDB Molecule:uncharacterized protein; PDBTitle: crystal structure of the dip2311 protein from2 corynebacterium diphtheriae, northeast structural genomics3 consortium target cdr35 Phyre2 PDB 1f7u chain A domain 3 Region: 4 - 14 Aligned: 11 Modelled: 11 Confidence: 7.7% Identity: 36% Fold: RRF/tRNA synthetase additional domain-like Superfamily: Arginyl-tRNA synthetase (ArgRS), N-terminal 'additional' domain Family: Arginyl-tRNA synthetase (ArgRS), N-terminal 'additional' domain Phyre2 PDB 3pcq chain X Region: 35 - 55 Aligned: 21 Modelled: 21 Confidence: 7.0% Identity: 33% PDB header:photosynthesis Chain: X: PDB Molecule:photosystem i 4.8k protein; PDBTitle: femtosecond x-ray protein nanocrystallography Phyre2 PDB 1qf9 chain A Region: 1 - 36 Aligned: 18 Modelled: 18 Confidence: 6.5% Identity: 28% Fold: P-loop containing nucleoside triphosphate hydrolases Superfamily: P-loop containing nucleoside triphosphate hydrolases Family: Nucleotide and nucleoside kinases Phyre2 PDB 1yj5 chain A domain 2 Region: 26 - 36 Aligned: 11 Modelled: 11 Confidence: 5.4% Identity: 27% Fold: P-loop containing nucleoside triphosphate hydrolases Superfamily: P-loop containing nucleoside triphosphate hydrolases Family: Nucleotide and nucleoside kinases Phyre2 PDB 2l3n chain A Region: 57 - 71 Aligned: 15 Modelled: 15 Confidence: 5.0% Identity: 47% PDB header:dna binding protein Chain: A: PDB Molecule:dna-binding protein rap1, telomere length regulator taz1; PDBTitle: solution structure of rap1-taz1 fusion protein Phyre2 1 c2l23A_ 2 c3lmmA_ 3 d1f7ua3 4 c3pcqX_ 5 d1qf9a_ 6 d1yj5a2 7 c2l3nA_

Detailed template information

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

1 c2l23A_ 17.1 35 PDB header:transcription Chain: A: PDB Molecule:mediator of rna polymerase ii transcription subunit 25; PDBTitle: nmr structure of the acid (activator interacting domain) of the human2 mediator med25 protein 2 c3lmmA_ 8.0 50 PDB header:structural genomics, unknown function Chain: A: PDB Molecule:uncharacterized protein; PDBTitle: crystal structure of the dip2311 protein from2 corynebacterium diphtheriae, northeast structural genomics3 consortium target cdr35 3 d1f7ua3 7.7 36 Fold:RRF/tRNA synthetase additional domain-like Superfamily:Arginyl-tRNA synthetase (ArgRS), N-terminal 'additional' domain Family:Arginyl-tRNA synthetase (ArgRS), N-terminal 'additional' domain 4 c3pcqX_ 7.0 33 PDB header:photosynthesis Chain: X: PDB Molecule:photosystem i 4.8k protein; PDBTitle: femtosecond x-ray protein nanocrystallography 5 d1qf9a_ 6.5 28 Fold:P-loop containing nucleoside triphosphate hydrolases Superfamily:P-loop containing nucleoside triphosphate hydrolases Family:Nucleotide and nucleoside kinases 6 d1yj5a2 5.4 27 Fold:P-loop containing nucleoside triphosphate hydrolases Superfamily:P-loop containing nucleoside triphosphate hydrolases Family:Nucleotide and nucleoside kinases 7 c2l3nA_ 5.0 47 PDB header:dna binding protein Chain: A: PDB Molecule:dna-binding protein rap1, telomere length regulator taz1; PDBTitle: solution structure of rap1-taz1 fusion protein

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

---

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