Secondary structure and disorder prediction

		1	.	.	.	.	.	.	.	.	10	.	.	.	.	.	.	.	.	.	20	.	.	.	.	.	.	.	.	.	30	.	.	.	.	.	.	.	.	.	40	.	.	.	.	.	.	.	.	.	50	.	.	.	.	.	.	.	.	.	60
Sequence		M	V	L	W	Q	S	D	L	R	V	S	W	R	A	Q	W	L	S	L	L	I	H	G	L	V	A	A	V	I	L	L	M	P	W	P	L	S	Y	T	P	L	W	M	V	L	L	S	L	V	V	F	D	C	V	R	S	Q	R	R	I
Secondary structure
SS confidence
Disorder		?	?	?	?	?	?																																																						?
Disorder confidence
		.	.	.	.	.	.	.	.	.	70	.	.	.	.	.	.	.	.	.	80	.	.	.	.	.	.	.	.	.	90	.	.	.	.	.	.	.	.	.	100	.	.	.	.	.	.	.	.	.	110	.	.	.	.	.	.	.	.	.	120
Sequence		N	A	R	Q	G	E	I	R	L	L	M	D	G	R	L	R	W	Q	G	Q	E	W	S	I	V	K	A	P	W	M	I	K	S	G	M	M	L	R	L	R	S	D	G	G	K	R	Q	H	L	W	L	A	A	D	S	M	D	E	A	E
Secondary structure
SS confidence
Disorder		?	?	?	?														?																								?		?
Disorder confidence
		.	.	.	.	.	.	.	.	.	130	.	.	.	.	.
Sequence		W	R	D	L	R	R	I	L	L	Q	Q	E	T	Q	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 1cks chain A Region: 116 - 124 Aligned: 9 Modelled: 9 Confidence: 35.9% Identity: 67% Fold: Cell cycle regulatory proteins Superfamily: Cell cycle regulatory proteins Family: Cell cycle regulatory proteins Phyre2 PDB 2ast chain C domain 1 Region: 116 - 124 Aligned: 9 Modelled: 9 Confidence: 35.1% Identity: 67% Fold: Cell cycle regulatory proteins Superfamily: Cell cycle regulatory proteins Family: Cell cycle regulatory proteins Phyre2 PDB 1puc chain A Region: 116 - 124 Aligned: 9 Modelled: 9 Confidence: 33.3% Identity: 56% Fold: Cell cycle regulatory proteins Superfamily: Cell cycle regulatory proteins Family: Cell cycle regulatory proteins Phyre2 PDB 1qb3 chain B Region: 116 - 124 Aligned: 9 Modelled: 9 Confidence: 31.5% Identity: 56% PDB header:cell cycle Chain: B: PDB Molecule:cyclin-dependent kinases regulatory subunit; PDBTitle: crystal structure of the cell cycle regulatory protein cks1 Phyre2 PDB 1qb3 chain A Region: 116 - 124 Aligned: 9 Modelled: 9 Confidence: 30.6% Identity: 56% Fold: Cell cycle regulatory proteins Superfamily: Cell cycle regulatory proteins Family: Cell cycle regulatory proteins Phyre2 PDB 2nvn chain A domain 1 Region: 117 - 134 Aligned: 18 Modelled: 18 Confidence: 10.4% Identity: 28% Fold: ssDNA-binding transcriptional regulator domain Superfamily: ssDNA-binding transcriptional regulator domain Family: PMN2A0962/syc2379c-like Phyre2 PDB 2it9 chain A domain 1 Region: 117 - 134 Aligned: 18 Modelled: 18 Confidence: 9.7% Identity: 28% Fold: ssDNA-binding transcriptional regulator domain Superfamily: ssDNA-binding transcriptional regulator domain Family: PMN2A0962/syc2379c-like Phyre2 PDB 1wq6 chain A Region: 118 - 128 Aligned: 11 Modelled: 11 Confidence: 8.0% Identity: 36% PDB header:oncoprotein Chain: A: PDB Molecule:aml1-eto; PDBTitle: the tetramer structure of the nervy homolgy two (nhr2) domain of aml1-2 eto is critical for aml1-eto's activity Phyre2 PDB 1na6 chain A domain 1 Region: 92 - 120 Aligned: 29 Modelled: 29 Confidence: 7.7% Identity: 28% Fold: DNA-binding pseudobarrel domain Superfamily: DNA-binding pseudobarrel domain Family: Type II restriction endonuclease effector domain Phyre2 PDB 3cx5 chain C domain 1 Region: 15 - 57 Aligned: 43 Modelled: 43 Confidence: 6.3% Identity: 16% Fold: a domain/subunit of cytochrome bc1 complex (Ubiquinol-cytochrome c reductase) Superfamily: a domain/subunit of cytochrome bc1 complex (Ubiquinol-cytochrome c reductase) Family: a domain/subunit of cytochrome bc1 complex (Ubiquinol-cytochrome c reductase) Phyre2 PDB 1d1d chain A domain 1 Region: 49 - 59 Aligned: 11 Modelled: 11 Confidence: 5.3% Identity: 36% Fold: Acyl carrier protein-like Superfamily: Retrovirus capsid dimerization domain-like Family: Retrovirus capsid protein C-terminal domain Phyre2 PDB 1in1 chain A Region: 50 - 58 Aligned: 9 Modelled: 9 Confidence: 5.3% Identity: 33% Fold: BRCT domain Superfamily: BRCT domain Family: DNA ligase Phyre2 PDB 1z9e chain A Region: 52 - 66 Aligned: 15 Modelled: 15 Confidence: 5.3% Identity: 7% PDB header:protein binding/transcription Chain: A: PDB Molecule:pc4 and sfrs1 interacting protein 2; PDBTitle: solution structure of the hiv-1 integrase-binding domain in2 ledgf/p75 Phyre2 PDB 3c8i chain A Region: 112 - 133 Aligned: 22 Modelled: 22 Confidence: 5.1% Identity: 18% PDB header:membrane protein Chain: A: PDB Molecule:putative membrane protein; PDBTitle: crystal structure of a putative membrane protein from corynebacterium2 diphtheriae Phyre2 1 d1cksa_ 2 d2astc1 3 d1puca_ 4 c1qb3B_ 5 d1qb3a_ 6 d2nvna1 7 d2it9a1 8 c1wq6A_ 9 d1na6a1 10 d3cx5c1 11 d1d1da1 12 d1in1a_ 13 c1z9eA_ 14 c3c8iA_

Detailed template information

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

1 d1cksa_ 35.9 67 Fold:Cell cycle regulatory proteins Superfamily:Cell cycle regulatory proteins Family:Cell cycle regulatory proteins 2 d2astc1 35.1 67 Fold:Cell cycle regulatory proteins Superfamily:Cell cycle regulatory proteins Family:Cell cycle regulatory proteins 3 d1puca_ 33.3 56 Fold:Cell cycle regulatory proteins Superfamily:Cell cycle regulatory proteins Family:Cell cycle regulatory proteins 4 c1qb3B_ 31.5 56 PDB header:cell cycle Chain: B: PDB Molecule:cyclin-dependent kinases regulatory subunit; PDBTitle: crystal structure of the cell cycle regulatory protein cks1 5 d1qb3a_ 30.6 56 Fold:Cell cycle regulatory proteins Superfamily:Cell cycle regulatory proteins Family:Cell cycle regulatory proteins 6 d2nvna1 10.4 28 Fold:ssDNA-binding transcriptional regulator domain Superfamily:ssDNA-binding transcriptional regulator domain Family:PMN2A0962/syc2379c-like 7 d2it9a1 9.7 28 Fold:ssDNA-binding transcriptional regulator domain Superfamily:ssDNA-binding transcriptional regulator domain Family:PMN2A0962/syc2379c-like 8 c1wq6A_ 8.0 36 PDB header:oncoprotein Chain: A: PDB Molecule:aml1-eto; PDBTitle: the tetramer structure of the nervy homolgy two (nhr2) domain of aml1-2 eto is critical for aml1-eto's activity 9 d1na6a1 7.7 28 Fold:DNA-binding pseudobarrel domain Superfamily:DNA-binding pseudobarrel domain Family:Type II restriction endonuclease effector domain 10 d3cx5c1 6.3 16 Fold:a domain/subunit of cytochrome bc1 complex (Ubiquinol-cytochrome c reductase) Superfamily:a domain/subunit of cytochrome bc1 complex (Ubiquinol-cytochrome c reductase) Family:a domain/subunit of cytochrome bc1 complex (Ubiquinol-cytochrome c reductase) 11 d1d1da1 5.3 36 Fold:Acyl carrier protein-like Superfamily:Retrovirus capsid dimerization domain-like Family:Retrovirus capsid protein C-terminal domain 12 d1in1a_ 5.3 33 Fold:BRCT domain Superfamily:BRCT domain Family:DNA ligase 13 c1z9eA_ 5.3 7 PDB header:protein binding/transcription Chain: A: PDB Molecule:pc4 and sfrs1 interacting protein 2; PDBTitle: solution structure of the hiv-1 integrase-binding domain in2 ledgf/p75 14 c3c8iA_ 5.1 18 PDB header:membrane protein Chain: A: PDB Molecule:putative membrane protein; PDBTitle: crystal structure of a putative membrane protein from corynebacterium2 diphtheriae

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