Secondary structure and disorder prediction

		1	.	.	.	.	.	.	.	.	10	.	.	.	.	.	.	.	.	.	20	.	.	.	.	.	.	.	.	.	30	.	.	.	.	.	.	.	.	.	40	.	.	.	.	.	.	.	.	.	50	.	.	.	.	.	.	.	.	.	60
Sequence		M	K	Q	E	V	E	K	W	R	P	F	G	H	P	D	G	D	I	R	D	L	S	F	L	D	A	H	Q	A	V	Y	V	Q	H	H	E	G	K	E	P	L	E	Y	R	F	W	V	T	Y	S	L	H	C	F	T	K	D	Y	E	H
Secondary structure
SS confidence
Disorder		?	?	?	?	?	?	?																												?	?	?	?	?	?																	?	?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	70	.	.	.	.	.	.	.	.	.	80	.	.	.	.	.	.	.	.	.	90	.	.	.	.	.	.	.	.	.	100	.	.	.	.	.	.	.	.	.	110	.	.	.	.	.	.	.	.	.	120
Sequence		Q	T	N	E	E	K	Q	S	L	M	Y	H	A	P	K	E	S	R	P	F	C	Q	H	R	Y	N	L	A	R	T	H	L	K	R	T	I	L	A	L	P	E	S	N	V	I	H	A	G	Y	G	S	Y	A	V	I	E	V	D	L	D
Secondary structure
SS confidence
Disorder		?	?	?	?	?	?	?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	130	.	.	.	.	.	.	.	.	.	140	.	.	.	.	.	.	.	.	.	150	.	.	.	.	.	.	.	.	.	160	.	.	.	.	.	.	.	.	.	170	.	.	.	.	.	.	.	.	.
Sequence		G	G	D	K	A	F	Y	F	V	A	F	R	A	F	R	E	K	K	K	L	R	L	H	V	T	S	A	Y	P	I	S	E	K	Q	K	G	K	S	V	K	F	F	T	I	A	Y	N	L	L	R	N	K	Q	L	P	Q	P	S	K
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 1kl9 chain A domain 1 Region: 81 - 97 Aligned: 16 Modelled: 17 Confidence: 37.4% Identity: 13% Fold: SAM domain-like Superfamily: eIF2alpha middle domain-like Family: eIF2alpha middle domain-like Phyre2 PDB 1q46 chain A domain 1 Region: 81 - 101 Aligned: 20 Modelled: 21 Confidence: 27.2% Identity: 20% Fold: SAM domain-like Superfamily: eIF2alpha middle domain-like Family: eIF2alpha middle domain-like Phyre2 PDB 2vty chain A Region: 84 - 103 Aligned: 20 Modelled: 20 Confidence: 18.8% Identity: 25% PDB header:apoptosis Chain: A: PDB Molecule:protein f1; PDBTitle: vaccinia virus anti-apoptotic f1l is a novel bcl-2-like2 domain swapped dimer Phyre2 PDB 1u84 chain A Region: 1 - 20 Aligned: 19 Modelled: 20 Confidence: 12.7% Identity: 26% Fold: YugE-like Superfamily: YugE-like Family: YugE-like Phyre2 PDB 1fcd chain A domain 3 Region: 48 - 55 Aligned: 8 Modelled: 8 Confidence: 9.4% Identity: 25% Fold: CO dehydrogenase flavoprotein C-domain-like Superfamily: FAD/NAD-linked reductases, dimerisation (C-terminal) domain Family: FAD/NAD-linked reductases, dimerisation (C-terminal) domain Phyre2 PDB 3doa chain A Region: 123 - 174 Aligned: 51 Modelled: 51 Confidence: 7.5% Identity: 14% PDB header:protein binding Chain: A: PDB Molecule:fibrinogen binding protein; PDBTitle: the crystal structure of the fibrinogen binding protein from2 staphylococcus aureus Phyre2 PDB 2q8a chain A Region: 130 - 163 Aligned: 34 Modelled: 34 Confidence: 7.4% Identity: 12% PDB header:immune system Chain: A: PDB Molecule:apical membrane antigen 1; PDBTitle: structure of the malaria antigen ama1 in complex with a growth-2 inhibitory antibody Phyre2 PDB 1sqw chain A domain 1 Region: 43 - 68 Aligned: 26 Modelled: 26 Confidence: 7.0% Identity: 23% Fold: PUA domain-like Superfamily: PUA domain-like Family: PUA domain Phyre2 PDB 1cz5 chain A domain 1 Region: 135 - 151 Aligned: 17 Modelled: 17 Confidence: 6.1% Identity: 18% Fold: Double psi beta-barrel Superfamily: ADC-like Family: Cdc48 N-terminal domain-like Phyre2 PDB 1mv8 chain A domain 1 Region: 49 - 58 Aligned: 10 Modelled: 10 Confidence: 5.9% Identity: 30% Fold: 6-phosphogluconate dehydrogenase C-terminal domain-like Superfamily: 6-phosphogluconate dehydrogenase C-terminal domain-like Family: UDP-glucose/GDP-mannose dehydrogenase dimerisation domain Phyre2 PDB 1dzf chain A domain 2 Region: 82 - 130 Aligned: 49 Modelled: 49 Confidence: 5.7% Identity: 24% Fold: RPB5-like RNA polymerase subunit Superfamily: RPB5-like RNA polymerase subunit Family: RPB5 Phyre2 PDB 1tp6 chain A Region: 12 - 45 Aligned: 31 Modelled: 34 Confidence: 5.6% Identity: 16% Fold: Cystatin-like Superfamily: NTF2-like Family: PA1314-like Phyre2 PDB 1z67 chain A domain 1 Region: 86 - 104 Aligned: 18 Modelled: 19 Confidence: 5.6% Identity: 44% Fold: YidB-like Superfamily: YidB-like Family: YidB-like Phyre2 1 d1kl9a1 2 d1q46a1 3 c2vtyA_ 4 d1u84a_ 5 d1fcda3 6 c3doaA_ 7 c2q8aA_ 8 d1sqwa1 9 d1cz5a1 10 d1mv8a1 11 d1dzfa2 12 d1tp6a_ 13 d1z67a1

Detailed template information

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

1 d1kl9a1 37.4 13 Fold:SAM domain-like Superfamily:eIF2alpha middle domain-like Family:eIF2alpha middle domain-like 2 d1q46a1 27.2 20 Fold:SAM domain-like Superfamily:eIF2alpha middle domain-like Family:eIF2alpha middle domain-like 3 c2vtyA_ 18.8 25 PDB header:apoptosis Chain: A: PDB Molecule:protein f1; PDBTitle: vaccinia virus anti-apoptotic f1l is a novel bcl-2-like2 domain swapped dimer 4 d1u84a_ 12.7 26 Fold:YugE-like Superfamily:YugE-like Family:YugE-like 5 d1fcda3 9.4 25 Fold:CO dehydrogenase flavoprotein C-domain-like Superfamily:FAD/NAD-linked reductases, dimerisation (C-terminal) domain Family:FAD/NAD-linked reductases, dimerisation (C-terminal) domain 6 c3doaA_ 7.5 14 PDB header:protein binding Chain: A: PDB Molecule:fibrinogen binding protein; PDBTitle: the crystal structure of the fibrinogen binding protein from2 staphylococcus aureus 7 c2q8aA_ 7.4 12 PDB header:immune system Chain: A: PDB Molecule:apical membrane antigen 1; PDBTitle: structure of the malaria antigen ama1 in complex with a growth-2 inhibitory antibody 8 d1sqwa1 7.0 23 Fold:PUA domain-like Superfamily:PUA domain-like Family:PUA domain 9 d1cz5a1 6.1 18 Fold:Double psi beta-barrel Superfamily:ADC-like Family:Cdc48 N-terminal domain-like 10 d1mv8a1 5.9 30 Fold:6-phosphogluconate dehydrogenase C-terminal domain-like Superfamily:6-phosphogluconate dehydrogenase C-terminal domain-like Family:UDP-glucose/GDP-mannose dehydrogenase dimerisation domain 11 d1dzfa2 5.7 24 Fold:RPB5-like RNA polymerase subunit Superfamily:RPB5-like RNA polymerase subunit Family:RPB5 12 d1tp6a_ 5.6 16 Fold:Cystatin-like Superfamily:NTF2-like Family:PA1314-like 13 d1z67a1 5.6 44 Fold:YidB-like Superfamily:YidB-like Family:YidB-like

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