Secondary structure and disorder prediction

		1	.	.	.	.	.	.	.	.	10	.	.	.	.	.	.	.	.	.	20	.	.	.	.	.	.	.	.	.	30	.	.	.	.	.	.	.	.	.	40	.	.	.	.	.	.	.	.	.	50	.	.	.	.	.	.	.	.	.	60
Sequence		M	A	V	Q	L	F	K	T	L	L	N	Q	I	P	L	L	S	S	L	Q	S	G	T	L	P	L	F	G	Y	S	G	W	G	R	P	M	K	K	A	H	T	G	E	S	G	L	K	W	E	A	K	D	S	S	K	L	I	G	N	K
Secondary structure
SS confidence
Disorder		?	?													?	?	?		?																			?	?	?	?	?	?	?	?				?		?			?		?	?	?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	70	.	.	.	.	.	.	.	.	.	80	.
Sequence		D	H	A	L	R	G	L	S	S	P	M	A	V	I	R	Q	I	R	L	I	T
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 2haf chain A domain 1 Region: 26 - 33 Aligned: 8 Modelled: 8 Confidence: 20.0% Identity: 63% Fold: VC0467-like Superfamily: VC0467-like Family: VC0467-like Phyre2 PDB 2aj2 chain A Region: 26 - 33 Aligned: 8 Modelled: 8 Confidence: 17.7% Identity: 63% PDB header:unknown function Chain: A: PDB Molecule:hypothetical upf0301 protein vc0467; PDBTitle: x-ray crystal structure of protein vc0467 from vibrio2 cholerae. northeast structural genomics consortium target3 vcr8. Phyre2 PDB 2do8 chain A domain 1 Region: 26 - 33 Aligned: 8 Modelled: 8 Confidence: 16.5% Identity: 38% Fold: VC0467-like Superfamily: VC0467-like Family: VC0467-like Phyre2 PDB 2gs5 chain A domain 1 Region: 26 - 33 Aligned: 8 Modelled: 8 Confidence: 15.7% Identity: 25% Fold: VC0467-like Superfamily: VC0467-like Family: VC0467-like Phyre2 PDB 2ew0 chain A domain 1 Region: 26 - 33 Aligned: 8 Modelled: 8 Confidence: 13.2% Identity: 50% Fold: VC0467-like Superfamily: VC0467-like Family: VC0467-like Phyre2 PDB 2gzo chain A domain 1 Region: 26 - 33 Aligned: 8 Modelled: 8 Confidence: 12.7% Identity: 50% Fold: VC0467-like Superfamily: VC0467-like Family: VC0467-like Phyre2 PDB 2g7h chain A Region: 13 - 60 Aligned: 40 Modelled: 45 Confidence: 12.3% Identity: 33% PDB header:transferase Chain: A: PDB Molecule:methylated-dna--protein-cysteine PDBTitle: structure of an o6-methylguanine dna methyltransferase from2 methanococcus jannaschii (mj1529) Phyre2 PDB 3izb chain T Region: 53 - 63 Aligned: 11 Modelled: 11 Confidence: 11.9% Identity: 36% PDB header:ribosome Chain: T: PDB Molecule:40s ribosomal protein rps21 (s21e); PDBTitle: localization of the small subunit ribosomal proteins into a 6.1 a2 cryo-em map of saccharomyces cerevisiae translating 80s ribosome Phyre2 PDB 1jdq chain A Region: 40 - 75 Aligned: 36 Modelled: 36 Confidence: 9.4% Identity: 25% Fold: IF3-like Superfamily: SirA-like Family: SirA-like Phyre2 PDB 1kn0 chain A Region: 26 - 32 Aligned: 7 Modelled: 7 Confidence: 5.6% Identity: 71% Fold: dsRBD-like Superfamily: dsRNA-binding domain-like Family: The homologous-pairing domain of Rad52 recombinase Phyre2 PDB 3iz6 chain T Region: 53 - 63 Aligned: 11 Modelled: 11 Confidence: 5.6% Identity: 45% PDB header:ribosome Chain: T: PDB Molecule:40s ribosomal protein s21 (s21e); PDBTitle: localization of the small subunit ribosomal proteins into a 5.5 a2 cryo-em map of triticum aestivum translating 80s ribosome Phyre2 PDB 1yvr chain A domain 1 Region: 30 - 39 Aligned: 10 Modelled: 10 Confidence: 5.5% Identity: 50% Fold: alpha-alpha superhelix Superfamily: TROVE domain-like Family: TROVE domain-like Phyre2 1 d2hafa1 2 c2aj2A_ 3 d2do8a1 4 d2gs5a1 5 d2ew0a1 6 d2gzoa1 7 c2g7hA_ 8 c3izbT_ 9 d1jdqa_ 10 d1kn0a_ 11 c3iz6T_ 12 d1yvra1

Detailed template information

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

1 d2hafa1 20.0 63 Fold:VC0467-like Superfamily:VC0467-like Family:VC0467-like 2 c2aj2A_ 17.7 63 PDB header:unknown function Chain: A: PDB Molecule:hypothetical upf0301 protein vc0467; PDBTitle: x-ray crystal structure of protein vc0467 from vibrio2 cholerae. northeast structural genomics consortium target3 vcr8. 3 d2do8a1 16.5 38 Fold:VC0467-like Superfamily:VC0467-like Family:VC0467-like 4 d2gs5a1 15.7 25 Fold:VC0467-like Superfamily:VC0467-like Family:VC0467-like 5 d2ew0a1 13.2 50 Fold:VC0467-like Superfamily:VC0467-like Family:VC0467-like 6 d2gzoa1 12.7 50 Fold:VC0467-like Superfamily:VC0467-like Family:VC0467-like 7 c2g7hA_ 12.3 33 PDB header:transferase Chain: A: PDB Molecule:methylated-dna--protein-cysteine PDBTitle: structure of an o6-methylguanine dna methyltransferase from2 methanococcus jannaschii (mj1529) 8 c3izbT_ 11.9 36 PDB header:ribosome Chain: T: PDB Molecule:40s ribosomal protein rps21 (s21e); PDBTitle: localization of the small subunit ribosomal proteins into a 6.1 a2 cryo-em map of saccharomyces cerevisiae translating 80s ribosome 9 d1jdqa_ 9.4 25 Fold:IF3-like Superfamily:SirA-like Family:SirA-like 10 d1kn0a_ 5.6 71 Fold:dsRBD-like Superfamily:dsRNA-binding domain-like Family:The homologous-pairing domain of Rad52 recombinase 11 c3iz6T_ 5.6 45 PDB header:ribosome Chain: T: PDB Molecule:40s ribosomal protein s21 (s21e); PDBTitle: localization of the small subunit ribosomal proteins into a 5.5 a2 cryo-em map of triticum aestivum translating 80s ribosome 12 d1yvra1 5.5 50 Fold:alpha-alpha superhelix Superfamily:TROVE domain-like Family:TROVE domain-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