Secondary structure and disorder prediction

		1	.	.	.	.	.	.	.	.	10	.	.	.	.	.	.	.	.	.	20	.	.	.	.	.	.	.	.	.	30	.	.	.	.	.	.	.	.	.	40	.	.	.	.	.	.	.	.	.	50	.	.	.	.	.	.	.	.	.	60
Sequence		M	A	L	P	R	I	T	Q	K	E	M	T	E	R	E	Q	R	E	L	K	T	L	L	D	R	A	R	I	A	H	G	R	V	L	T	N	S	E	T	N	S	I	K	K	D	Y	I	D	K	L	M	V	E	R	E	A	E	A	K	K
Secondary structure
SS confidence
Disorder		?	?	?	?		?	?				?	?																			?			?		?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	70	.	.	.	.	.	.	.	.	.	80	.	.	.	.	.	.	.	.	.	90
Sequence		A	R	Q	L	K	K	K	Q	A	Y	K	P	D	P	E	A	S	F	S	W	S	A	N	T	S	T	R	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 1jjc chain B domain 4 Region: 29 - 50 Aligned: 22 Modelled: 22 Confidence: 15.3% Identity: 18% Fold: Ferredoxin-like Superfamily: Anticodon-binding domain of PheRS Family: Anticodon-binding domain of PheRS Phyre2 PDB 2owl chain A Region: 16 - 51 Aligned: 36 Modelled: 36 Confidence: 13.2% Identity: 19% PDB header:recombination Chain: A: PDB Molecule:recombination-associated protein rdgc; PDBTitle: crystal structure of e. coli rdgc Phyre2 PDB 1usd chain A Region: 38 - 53 Aligned: 16 Modelled: 16 Confidence: 12.3% Identity: 25% PDB header:signaling protein Chain: A: PDB Molecule:vasodilator-stimulated phosphoprotein; PDBTitle: human vasp tetramerisation domain l352m Phyre2 PDB 1ygm chain A Region: 22 - 47 Aligned: 26 Modelled: 26 Confidence: 11.7% Identity: 31% PDB header:membrane protein Chain: A: PDB Molecule:hypothetical protein bsu31320; PDBTitle: nmr structure of mistic Phyre2 PDB 1b7y chain B domain 4 Region: 29 - 51 Aligned: 23 Modelled: 23 Confidence: 10.6% Identity: 17% Fold: Ferredoxin-like Superfamily: Anticodon-binding domain of PheRS Family: Anticodon-binding domain of PheRS Phyre2 PDB 2zc2 chain A Region: 21 - 46 Aligned: 26 Modelled: 26 Confidence: 9.5% Identity: 23% PDB header:replication Chain: A: PDB Molecule:dnad-like replication protein; PDBTitle: crystal structure of dnad-like replication protein from2 streptococcus mutans ua159, gi 24377835, residues 127-199 Phyre2 PDB 1pu1 chain A Region: 1 - 13 Aligned: 13 Modelled: 13 Confidence: 9.0% Identity: 31% Fold: Hypothetical protein MTH677 Superfamily: Hypothetical protein MTH677 Family: Hypothetical protein MTH677 Phyre2 PDB 2r18 chain A Region: 53 - 88 Aligned: 35 Modelled: 36 Confidence: 6.9% Identity: 29% PDB header:viral protein Chain: A: PDB Molecule:capsid assembly protein vp3; PDBTitle: structural insights into the multifunctional protein vp3 of2 birnaviruses Phyre2 PDB 2of5 chain K Region: 11 - 46 Aligned: 36 Modelled: 36 Confidence: 6.2% Identity: 17% PDB header:apoptosis Chain: K: PDB Molecule:leucine-rich repeat and death domain-containing PDBTitle: oligomeric death domain complex Phyre2 PDB 3bdn chain B Region: 6 - 31 Aligned: 24 Modelled: 26 Confidence: 6.1% Identity: 25% PDB header:transcription/dna Chain: B: PDB Molecule:lambda repressor; PDBTitle: crystal structure of the lambda repressor Phyre2 PDB 3cmq chain A Region: 29 - 51 Aligned: 23 Modelled: 23 Confidence: 5.5% Identity: 17% PDB header:ligase Chain: A: PDB Molecule:phenylalanyl-trna synthetase, mitochondrial; PDBTitle: crystal structure of human mitochondrial phenylalanine trna2 synthetase Phyre2 PDB 2cb2 chain A domain 1 Region: 24 - 50 Aligned: 27 Modelled: 27 Confidence: 5.5% Identity: 30% Fold: Ferredoxin-like Superfamily: Dimeric alpha+beta barrel Family: SOR-like Phyre2 PDB 2gid chain P Region: 74 - 82 Aligned: 9 Modelled: 9 Confidence: 5.3% Identity: 33% PDB header:translation Chain: P: PDB Molecule:mitochondrial rna-binding protein 2; PDBTitle: crystal structures of trypanosoma bruciei mrp1/mrp2 Phyre2 PDB 2owy chain B Region: 16 - 51 Aligned: 36 Modelled: 36 Confidence: 5.2% Identity: 19% PDB header:dna binding protein Chain: B: PDB Molecule:recombination-associated protein rdgc; PDBTitle: the recombination-associated protein rdgc adopts a novel toroidal2 architecture for dna binding Phyre2 PDB 1a7g chain E Region: 62 - 89 Aligned: 27 Modelled: 28 Confidence: 5.1% Identity: 22% Fold: Ferredoxin-like Superfamily: Viral DNA-binding domain Family: Viral DNA-binding domain Phyre2 PDB 3t97 chain A Region: 10 - 25 Aligned: 16 Modelled: 16 Confidence: 5.1% Identity: 31% PDB header:protein transport Chain: A: PDB Molecule:nuclear pore glycoprotein p62; PDBTitle: molecular architecture of the transport channel of the nuclear pore2 complex: nup62/nup54 Phyre2 1 d1jjcb4 2 c2owlA_ 3 c1usdA_ 4 c1ygmA_ 5 d1b7yb4 6 c2zc2A_ 7 d1pu1a_ 8 c2r18A_ 9 c2of5K_ 10 c3bdnB_ 11 c3cmqA_ 12 d2cb2a1 13 c2gidP_ 14 c2owyB_ 15 d1a7ge_ 16 c3t97A_

Detailed template information

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

1 d1jjcb4 15.3 18 Fold:Ferredoxin-like Superfamily:Anticodon-binding domain of PheRS Family:Anticodon-binding domain of PheRS 2 c2owlA_ 13.2 19 PDB header:recombination Chain: A: PDB Molecule:recombination-associated protein rdgc; PDBTitle: crystal structure of e. coli rdgc 3 c1usdA_ 12.3 25 PDB header:signaling protein Chain: A: PDB Molecule:vasodilator-stimulated phosphoprotein; PDBTitle: human vasp tetramerisation domain l352m 4 c1ygmA_ 11.7 31 PDB header:membrane protein Chain: A: PDB Molecule:hypothetical protein bsu31320; PDBTitle: nmr structure of mistic 5 d1b7yb4 10.6 17 Fold:Ferredoxin-like Superfamily:Anticodon-binding domain of PheRS Family:Anticodon-binding domain of PheRS 6 c2zc2A_ 9.5 23 PDB header:replication Chain: A: PDB Molecule:dnad-like replication protein; PDBTitle: crystal structure of dnad-like replication protein from2 streptococcus mutans ua159, gi 24377835, residues 127-199 7 d1pu1a_ 9.0 31 Fold:Hypothetical protein MTH677 Superfamily:Hypothetical protein MTH677 Family:Hypothetical protein MTH677 8 c2r18A_ 6.9 29 PDB header:viral protein Chain: A: PDB Molecule:capsid assembly protein vp3; PDBTitle: structural insights into the multifunctional protein vp3 of2 birnaviruses 9 c2of5K_ 6.2 17 PDB header:apoptosis Chain: K: PDB Molecule:leucine-rich repeat and death domain-containing PDBTitle: oligomeric death domain complex 10 c3bdnB_ 6.1 25 PDB header:transcription/dna Chain: B: PDB Molecule:lambda repressor; PDBTitle: crystal structure of the lambda repressor 11 c3cmqA_ 5.5 17 PDB header:ligase Chain: A: PDB Molecule:phenylalanyl-trna synthetase, mitochondrial; PDBTitle: crystal structure of human mitochondrial phenylalanine trna2 synthetase 12 d2cb2a1 5.5 30 Fold:Ferredoxin-like Superfamily:Dimeric alpha+beta barrel Family:SOR-like 13 c2gidP_ 5.3 33 PDB header:translation Chain: P: PDB Molecule:mitochondrial rna-binding protein 2; PDBTitle: crystal structures of trypanosoma bruciei mrp1/mrp2 14 c2owyB_ 5.2 19 PDB header:dna binding protein Chain: B: PDB Molecule:recombination-associated protein rdgc; PDBTitle: the recombination-associated protein rdgc adopts a novel toroidal2 architecture for dna binding 15 d1a7ge_ 5.1 22 Fold:Ferredoxin-like Superfamily:Viral DNA-binding domain Family:Viral DNA-binding domain 16 c3t97A_ 5.1 31 PDB header:protein transport Chain: A: PDB Molecule:nuclear pore glycoprotein p62; PDBTitle: molecular architecture of the transport channel of the nuclear pore2 complex: nup62/nup54

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