Secondary structure and disorder prediction

		1	.	.	.	.	.	.	.	.	10	.	.	.	.	.	.	.	.	.	20	.	.	.	.	.	.	.	.	.	30	.	.	.	.	.	.	.	.	.	40	.	.	.	.	.	.	.	.	.	50	.	.	.	.	.	.	.	.	.	60
Sequence		M	F	A	L	V	L	F	V	C	Y	L	D	G	G	C	E	D	I	V	V	D	V	Y	N	T	E	Q	Q	C	L	Y	S	M	S	D	Q	R	I	R	Q	G	G	C	F	P	I	E	D	F	I	D	G	F	W	R	P	A	Q	E	Y
Secondary structure
SS confidence
Disorder		?																																																											?
Disorder confidence
		.	.	.
Sequence		G	D	F
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 1eoq chain A Region: 38 - 58 Aligned: 21 Modelled: 21 Confidence: 33.6% Identity: 24% Fold: Acyl carrier protein-like Superfamily: Retrovirus capsid dimerization domain-like Family: Retrovirus capsid protein C-terminal domain Phyre2 PDB 1a8o chain A Region: 38 - 58 Aligned: 21 Modelled: 21 Confidence: 31.5% Identity: 38% Fold: Acyl carrier protein-like Superfamily: Retrovirus capsid dimerization domain-like Family: Retrovirus capsid protein C-terminal domain Phyre2 PDB 1qrj chain B domain 1 Region: 34 - 58 Aligned: 25 Modelled: 25 Confidence: 31.2% Identity: 24% Fold: Acyl carrier protein-like Superfamily: Retrovirus capsid dimerization domain-like Family: Retrovirus capsid protein C-terminal domain Phyre2 PDB 2eia chain A domain 1 Region: 34 - 59 Aligned: 26 Modelled: 26 Confidence: 27.4% Identity: 31% Fold: Acyl carrier protein-like Superfamily: Retrovirus capsid dimerization domain-like Family: Retrovirus capsid protein C-terminal domain Phyre2 PDB 1baj chain A Region: 34 - 58 Aligned: 25 Modelled: 25 Confidence: 23.6% Identity: 36% PDB header:viral protein Chain: A: PDB Molecule:gag polyprotein; PDBTitle: hiv-1 capsid protein c-terminal fragment plus gag p2 domain Phyre2 PDB 2k1c chain A Region: 34 - 53 Aligned: 20 Modelled: 20 Confidence: 21.7% Identity: 45% PDB header:hydrolase/hydrolase inhibitor Chain: A: PDB Molecule:capsid protein p24; PDBTitle: nmr structure of the c-terminal domain of hiv-1 capsid in complex with2 peptide inhibitor Phyre2 PDB 3dik chain A Region: 38 - 58 Aligned: 21 Modelled: 21 Confidence: 14.5% Identity: 38% PDB header:viral protein Chain: A: PDB Molecule:capsid protein p24; PDBTitle: pseudo-atomic model of the hiv-1 ca hexameric lattice Phyre2 PDB 1bmx chain A Region: 38 - 54 Aligned: 17 Modelled: 17 Confidence: 13.7% Identity: 47% PDB header:viral protein Chain: A: PDB Molecule:human immunodeficiency virus type 1 capsid; PDBTitle: hiv-1 capsid protein major homology region peptide analog,2 nmr, 8 structures Phyre2 PDB 3gv2 chain E Region: 34 - 58 Aligned: 25 Modelled: 25 Confidence: 13.7% Identity: 36% PDB header:viral protein Chain: E: PDB Molecule:fusion protein consisting of capsid protein p24, PDBTitle: x-ray structure of hexameric hiv-1 ca Phyre2 PDB 1pzr chain A Region: 30 - 41 Aligned: 12 Modelled: 12 Confidence: 12.6% Identity: 58% Fold: HLH-like Superfamily: Docking domain B of the erythromycin polyketide synthase (DEBS) Family: Docking domain B of the erythromycin polyketide synthase (DEBS) Phyre2 PDB 1eia chain A Region: 34 - 58 Aligned: 25 Modelled: 25 Confidence: 11.5% Identity: 32% PDB header:viral protein Chain: A: PDB Molecule:eiav capsid protein p26; PDBTitle: x-ray crystal structure of equine infectious anemia virus2 (eiav) capsid protein p26 Phyre2 PDB 1d1d chain A Region: 38 - 58 Aligned: 21 Modelled: 21 Confidence: 9.6% Identity: 24% PDB header:viral protein Chain: A: PDB Molecule:protein (capsid protein); PDBTitle: nmr solution structure of the capsid protein from rous2 sarcoma virus Phyre2 PDB 2x8q chain A Region: 38 - 53 Aligned: 16 Modelled: 16 Confidence: 6.8% Identity: 31% PDB header:virus Chain: A: PDB Molecule:capsid protein p27; PDBTitle: cryo-em 3d model of the icosahedral particle2 composed of rous sarcoma virus capsid protein pentamers Phyre2 PDB 3kev chain A Region: 15 - 53 Aligned: 36 Modelled: 39 Confidence: 5.7% Identity: 25% PDB header:structural genomics, unknown function Chain: A: PDB Molecule:galieria sulfuraria dcun1 domain-containing protein; PDBTitle: x-ray crystal structure of a dcun1 domain-containing protein from2 galdieria sulfuraria Phyre2 1 d1eoqa_ 2 d1a8oa_ 3 d1qrjb1 4 d2eiaa1 5 c1bajA_ 6 c2k1cA_ 7 c3dikA_ 8 c1bmxA_ 9 c3gv2E_ 10 d1pzra_ 11 c1eiaA_ 12 c1d1dA_ 13 c2x8qA_ 14 c3kevA_

Detailed template information

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

1 d1eoqa_ 33.6 24 Fold:Acyl carrier protein-like Superfamily:Retrovirus capsid dimerization domain-like Family:Retrovirus capsid protein C-terminal domain 2 d1a8oa_ 31.5 38 Fold:Acyl carrier protein-like Superfamily:Retrovirus capsid dimerization domain-like Family:Retrovirus capsid protein C-terminal domain 3 d1qrjb1 31.2 24 Fold:Acyl carrier protein-like Superfamily:Retrovirus capsid dimerization domain-like Family:Retrovirus capsid protein C-terminal domain 4 d2eiaa1 27.4 31 Fold:Acyl carrier protein-like Superfamily:Retrovirus capsid dimerization domain-like Family:Retrovirus capsid protein C-terminal domain 5 c1bajA_ 23.6 36 PDB header:viral protein Chain: A: PDB Molecule:gag polyprotein; PDBTitle: hiv-1 capsid protein c-terminal fragment plus gag p2 domain 6 c2k1cA_ 21.7 45 PDB header:hydrolase/hydrolase inhibitor Chain: A: PDB Molecule:capsid protein p24; PDBTitle: nmr structure of the c-terminal domain of hiv-1 capsid in complex with2 peptide inhibitor 7 c3dikA_ 14.5 38 PDB header:viral protein Chain: A: PDB Molecule:capsid protein p24; PDBTitle: pseudo-atomic model of the hiv-1 ca hexameric lattice 8 c1bmxA_ 13.7 47 PDB header:viral protein Chain: A: PDB Molecule:human immunodeficiency virus type 1 capsid; PDBTitle: hiv-1 capsid protein major homology region peptide analog,2 nmr, 8 structures 9 c3gv2E_ 13.7 36 PDB header:viral protein Chain: E: PDB Molecule:fusion protein consisting of capsid protein p24, PDBTitle: x-ray structure of hexameric hiv-1 ca 10 d1pzra_ 12.6 58 Fold:HLH-like Superfamily:Docking domain B of the erythromycin polyketide synthase (DEBS) Family:Docking domain B of the erythromycin polyketide synthase (DEBS) 11 c1eiaA_ 11.5 32 PDB header:viral protein Chain: A: PDB Molecule:eiav capsid protein p26; PDBTitle: x-ray crystal structure of equine infectious anemia virus2 (eiav) capsid protein p26 12 c1d1dA_ 9.6 24 PDB header:viral protein Chain: A: PDB Molecule:protein (capsid protein); PDBTitle: nmr solution structure of the capsid protein from rous2 sarcoma virus 13 c2x8qA_ 6.8 31 PDB header:virus Chain: A: PDB Molecule:capsid protein p27; PDBTitle: cryo-em 3d model of the icosahedral particle2 composed of rous sarcoma virus capsid protein pentamers 14 c3kevA_ 5.7 25 PDB header:structural genomics, unknown function Chain: A: PDB Molecule:galieria sulfuraria dcun1 domain-containing protein; PDBTitle: x-ray crystal structure of a dcun1 domain-containing protein from2 galdieria sulfuraria

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