Secondary structure and disorder prediction

		1	.	.	.	.	.	.	.	.	10	.	.	.	.	.	.	.	.	.	20	.	.	.	.	.	.	.	.	.	30	.	.	.	.	.	.	.	.	.	40	.	.	.	.	.	.	.	.	.	50	.	.	.	.	.	.	.	.	.	60
Sequence		M	F	K	F	L	V	L	T	L	G	I	I	S	C	Q	A	Y	A	E	D	T	V	I	V	N	D	H	D	I	S	A	I	K	D	C	W	Q	K	N	S	D	D	D	T	D	V	N	V	I	K	S	C	L	R	Q	E	Y	N	L	V
Secondary structure
SS confidence
Disorder		?												?	?	?	?	?	?						?																	?			?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	70	.	.	.	.	.	.	.	.	.	80	.	.	.	.	.	.	.	.	.	90	.	.	.	.	.	.	.	.	.	100	.	.	.	.	.	.	.	.	.	110	.	.	.	.	.	.	.	.	.	120
Sequence		D	A	Q	L	N	K	A	Y	G	E	A	Y	R	Y	I	E	Q	V	P	R	T	G	V	K	K	P	D	T	E	Q	L	N	L	L	K	K	S	Q	R	A	W	L	D	F	R	D	K	E	C	E	L	I	L	S	N	E	D	V	Q	D
Secondary structure
SS confidence
Disorder																	?	?	?	?	?	?	?	?	?	?	?	?	?																											?	?	?	?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	130	.	.	.	.	.	.	.	.	.	140	.	.	.	.	.	.	.	.	.	150	.	.	.	.	.	.	.	.	.	160	.	.
Sequence		L	S	D	P	Y	S	E	S	E	W	L	S	C	M	I	I	Q	T	N	T	R	T	R	Q	L	Q	L	Y	R	N	S	E	D	F	Y	P	S	P	L	T	R	G
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 3gi7 chain A Region: 42 - 152 Aligned: 103 Modelled: 111 Confidence: 99.9% Identity: 15% PDB header:unknown function Chain: A: PDB Molecule:secreted protein of unknown function duf1311; PDBTitle: crystal structure of a duf1311 family protein (pp0307) from2 pseudomonas putida kt2440 at 1.85 a resolution Phyre2 PDB 1n4c chain A Region: 61 - 113 Aligned: 52 Modelled: 53 Confidence: 12.2% Identity: 13% Fold: Long alpha-hairpin Superfamily: Chaperone J-domain Family: Chaperone J-domain Phyre2 PDB 1zxa chain B Region: 134 - 161 Aligned: 28 Modelled: 28 Confidence: 10.9% Identity: 14% PDB header:transferase Chain: B: PDB Molecule:cgmp-dependent protein kinase 1, alpha isozyme; PDBTitle: solution structure of the coiled-coil domain of cgmp-2 dependent protein kinase ia Phyre2 PDB 1pm6 chain A Region: 142 - 162 Aligned: 21 Modelled: 21 Confidence: 9.2% Identity: 14% Fold: Putative DNA-binding domain Superfamily: Putative DNA-binding domain Family: Excisionase-like Phyre2 PDB 2rkh chain A Region: 88 - 149 Aligned: 52 Modelled: 62 Confidence: 9.2% Identity: 19% PDB header:transcription Chain: A: PDB Molecule:putative apha-like transcription factor; PDBTitle: crystal structure of a putative apha-like transcription factor2 (zp_00208345.1) from magnetospirillum magnetotacticum ms-1 at 2.00 a3 resolution Phyre2 PDB 2noc chain A domain 1 Region: 3 - 26 Aligned: 24 Modelled: 24 Confidence: 6.6% Identity: 21% Fold: Dodecin subunit-like Superfamily: YdgH-like Family: YdgH-like Phyre2 PDB 1rh6 chain A Region: 142 - 162 Aligned: 21 Modelled: 21 Confidence: 6.5% Identity: 14% Fold: Putative DNA-binding domain Superfamily: Putative DNA-binding domain Family: Excisionase-like Phyre2 PDB 2jrm chain A Region: 105 - 155 Aligned: 46 Modelled: 51 Confidence: 5.5% Identity: 22% PDB header:structural genomics, unknown function Chain: A: PDB Molecule:ribosome modulation factor; PDBTitle: solution nmr structure of ribosome modulation factor vp1593 from2 vibrio parahaemolyticus. northeast structural genomics target vpr55 Phyre2 PDB 2dn9 chain A Region: 61 - 123 Aligned: 59 Modelled: 63 Confidence: 5.2% Identity: 14% PDB header:apoptosis, chaperone Chain: A: PDB Molecule:dnaj homolog subfamily a member 3; PDBTitle: solution structure of j-domain from the dnaj homolog, human2 tid1 protein Phyre2 1 c3gi7A_ 2 d1n4ca_ 3 c1zxaB_ 4 d1pm6a_ 5 c2rkhA_ 6 d2noca1 7 d1rh6a_ 8 c2jrmA_ 9 c2dn9A_

Detailed template information

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

1 c3gi7A_ 99.9 15 PDB header:unknown function Chain: A: PDB Molecule:secreted protein of unknown function duf1311; PDBTitle: crystal structure of a duf1311 family protein (pp0307) from2 pseudomonas putida kt2440 at 1.85 a resolution 2 d1n4ca_ 12.2 13 Fold:Long alpha-hairpin Superfamily:Chaperone J-domain Family:Chaperone J-domain 3 c1zxaB_ 10.9 14 PDB header:transferase Chain: B: PDB Molecule:cgmp-dependent protein kinase 1, alpha isozyme; PDBTitle: solution structure of the coiled-coil domain of cgmp-2 dependent protein kinase ia 4 d1pm6a_ 9.2 14 Fold:Putative DNA-binding domain Superfamily:Putative DNA-binding domain Family:Excisionase-like 5 c2rkhA_ 9.2 19 PDB header:transcription Chain: A: PDB Molecule:putative apha-like transcription factor; PDBTitle: crystal structure of a putative apha-like transcription factor2 (zp_00208345.1) from magnetospirillum magnetotacticum ms-1 at 2.00 a3 resolution 6 d2noca1 6.6 21 Fold:Dodecin subunit-like Superfamily:YdgH-like Family:YdgH-like 7 d1rh6a_ 6.5 14 Fold:Putative DNA-binding domain Superfamily:Putative DNA-binding domain Family:Excisionase-like 8 c2jrmA_ 5.5 22 PDB header:structural genomics, unknown function Chain: A: PDB Molecule:ribosome modulation factor; PDBTitle: solution nmr structure of ribosome modulation factor vp1593 from2 vibrio parahaemolyticus. northeast structural genomics target vpr55 9 c2dn9A_ 5.2 14 PDB header:apoptosis, chaperone Chain: A: PDB Molecule:dnaj homolog subfamily a member 3; PDBTitle: solution structure of j-domain from the dnaj homolog, human2 tid1 protein

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