Secondary structure and disorder prediction

		1	.	.	.	.	.	.	.	.	10	.	.	.	.	.	.	.	.	.	20	.	.	.	.	.	.	.	.	.	30	.	.	.	.	.	.	.	.	.	40	.	.	.	.	.	.	.	.	.	50	.	.	.	.	.	.	.	.	.	60
Sequence		M	V	C	F	L	I	Y	I	T	L	L	F	I	Q	R	V	Y	F	I	S	S	E	K	K	L	T	I	H	I	V	Q	M	F	Q	L	L	S	Q	A	F	Y	N	L	K	M	F	L	M	M	D	M	L	G	V	G	D	A	I	N	I
Secondary structure
SS confidence
Disorder		?	?																																																										?
Disorder confidence
		.	.	.	.	.	.	.	.	.	70
Sequence		N	T	N	K	N	I	R	Q	V	C
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 1m9f chain D Region: 22 - 53 Aligned: 32 Modelled: 32 Confidence: 35.7% Identity: 25% Fold: Retrovirus capsid protein, N-terminal core domain Superfamily: Retrovirus capsid protein, N-terminal core domain Family: Retrovirus capsid protein, N-terminal core domain Phyre2 PDB 1m9d chain C Region: 22 - 53 Aligned: 32 Modelled: 32 Confidence: 25.3% Identity: 25% Fold: Retrovirus capsid protein, N-terminal core domain Superfamily: Retrovirus capsid protein, N-terminal core domain Family: Retrovirus capsid protein, N-terminal core domain Phyre2 PDB 2wlv chain A Region: 22 - 53 Aligned: 32 Modelled: 32 Confidence: 24.4% Identity: 31% PDB header:virus protein Chain: A: PDB Molecule:gag polyprotein; PDBTitle: structure of the n-terminal capsid domain of hiv-2 Phyre2 PDB 2pxr chain C domain 1 Region: 22 - 53 Aligned: 32 Modelled: 32 Confidence: 20.6% Identity: 25% Fold: Retrovirus capsid protein, N-terminal core domain Superfamily: Retrovirus capsid protein, N-terminal core domain Family: Retrovirus capsid protein, N-terminal core domain Phyre2 PDB 2eia chain A domain 2 Region: 22 - 53 Aligned: 32 Modelled: 32 Confidence: 20.2% Identity: 19% Fold: Retrovirus capsid protein, N-terminal core domain Superfamily: Retrovirus capsid protein, N-terminal core domain Family: Retrovirus capsid protein, N-terminal core domain Phyre2 PDB 1l6n chain A Region: 22 - 53 Aligned: 32 Modelled: 32 Confidence: 17.0% Identity: 25% PDB header:viral protein Chain: A: PDB Molecule:gag polyprotein; PDBTitle: structure of the n-terminal 283-residue fragment of the hiv-2 1 gag polyprotein Phyre2 PDB 2xgv chain A Region: 22 - 53 Aligned: 32 Modelled: 32 Confidence: 7.2% Identity: 22% PDB header:viral protein Chain: A: PDB Molecule:psiv capsid n-terminal domain; PDBTitle: structure of the n-terminal domain of capsid protein from2 rabbit endogenous lentivirus (relik) Phyre2 PDB 1q08 chain A Region: 13 - 37 Aligned: 25 Modelled: 25 Confidence: 6.7% Identity: 32% Fold: Putative DNA-binding domain Superfamily: Putative DNA-binding domain Family: DNA-binding N-terminal domain of transcription activators Phyre2 1 d1m9fd_ 2 d1m9dc_ 3 c2wlvA_ 4 d2pxrc1 5 d2eiaa2 6 c1l6nA_ 7 c2xgvA_ 8 d1q08a_

Detailed template information

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

1 d1m9fd_ 35.7 25 Fold:Retrovirus capsid protein, N-terminal core domain Superfamily:Retrovirus capsid protein, N-terminal core domain Family:Retrovirus capsid protein, N-terminal core domain 2 d1m9dc_ 25.3 25 Fold:Retrovirus capsid protein, N-terminal core domain Superfamily:Retrovirus capsid protein, N-terminal core domain Family:Retrovirus capsid protein, N-terminal core domain 3 c2wlvA_ 24.4 31 PDB header:virus protein Chain: A: PDB Molecule:gag polyprotein; PDBTitle: structure of the n-terminal capsid domain of hiv-2 4 d2pxrc1 20.6 25 Fold:Retrovirus capsid protein, N-terminal core domain Superfamily:Retrovirus capsid protein, N-terminal core domain Family:Retrovirus capsid protein, N-terminal core domain 5 d2eiaa2 20.2 19 Fold:Retrovirus capsid protein, N-terminal core domain Superfamily:Retrovirus capsid protein, N-terminal core domain Family:Retrovirus capsid protein, N-terminal core domain 6 c1l6nA_ 17.0 25 PDB header:viral protein Chain: A: PDB Molecule:gag polyprotein; PDBTitle: structure of the n-terminal 283-residue fragment of the hiv-2 1 gag polyprotein 7 c2xgvA_ 7.2 22 PDB header:viral protein Chain: A: PDB Molecule:psiv capsid n-terminal domain; PDBTitle: structure of the n-terminal domain of capsid protein from2 rabbit endogenous lentivirus (relik) 8 d1q08a_ 6.7 32 Fold:Putative DNA-binding domain Superfamily:Putative DNA-binding domain Family:DNA-binding N-terminal domain of transcription activators

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