Secondary structure and disorder prediction

		1	.	.	.	.	.	.	.	.	10	.	.	.	.	.	.	.	.	.	20	.	.	.	.	.	.	.	.	.	30	.	.	.	.	.	.	.	.	.	40	.	.	.	.	.	.	.	.	.	50	.	.	.	.	.	.	.	.	.	60
Sequence		M	I	D	Y	K	K	N	L	L	F	I	L	V	F	I	S	G	F	I	L	F	T	V	Y	S	Y	T	A	E	K	M	I	Y	N	E	T	C	T	A	N	W	V	I	F	N	D	Q	G	R	A	N	L	T	I	D	F	M	Y	N	K
Secondary structure
SS confidence
Disorder		?	?	?	?	?	?																			?					?	?	?		?
Disorder confidence
		.	.	.	.	.	.	.	.	.	70	.	.	.	.	.	.	.	.	.	80	.	.	.	.	.	.	.	.	.	90	.	.	.	.	.	.	.	.	.	100	.	.	.	.	.	.	.	.	.	110	.	.	.	.	.	.	.	.	.	120
Sequence		K	N	K	T	G	T	V	A	L	S	G	T	W	Q	Q	G	N	R	E	S	K	S	I	R	R	N	I	E	Y	T	W	I	E	N	Y	D	T	A	H	L	T	S	K	K	V	N	K	F	E	I	M	D	Q	V	D	D	D	R	L	A
Secondary structure
SS confidence
Disorder																			?	?	?	?																												?	?	?	?	?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	130	.	.	.	.	.	.	.	.	.	140	.	.	.	.	.	.	.	.	.	150	.	.	.	.	.	.	.	.	.	160
Sequence		Q	L	I	P	D	F	Y	V	F	P	E	K	S	V	S	Y	N	I	L	K	Q	G	K	H	A	F	I	L	S	I	G	N	R	A	I	M	H	C	A	R
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 2gmq chain A domain 1 Region: 128 - 157 Aligned: 29 Modelled: 30 Confidence: 16.3% Identity: 10% Fold: PUA domain-like Superfamily: PUA domain-like Family: PrgU-like Phyre2 PDB 8tfv chain A Region: 149 - 160 Aligned: 12 Modelled: 12 Confidence: 14.6% Identity: 33% PDB header:antimicrobial Chain: A: PDB Molecule:protein (thanatin); PDBTitle: insect defense peptide Phyre2 PDB 1cid chain A domain 1 Region: 42 - 91 Aligned: 46 Modelled: 50 Confidence: 13.4% Identity: 13% Fold: Immunoglobulin-like beta-sandwich Superfamily: Immunoglobulin Family: V set domains (antibody variable domain-like) Phyre2 PDB 1q6w chain A Region: 32 - 74 Aligned: 43 Modelled: 43 Confidence: 11.3% Identity: 16% Fold: Thioesterase/thiol ester dehydrase-isomerase Superfamily: Thioesterase/thiol ester dehydrase-isomerase Family: MaoC-like Phyre2 PDB 1cid chain A Region: 42 - 115 Aligned: 69 Modelled: 74 Confidence: 10.6% Identity: 14% PDB header:t-cell surface glycoprotein Chain: A: PDB Molecule:t cell surface glycoprotein cd4; PDBTitle: crystal structure of domains 3 & 4 of rat cd4 and their2 relationship to the nh2-terminal domains Phyre2 PDB 1ppj chain D domain 2 Region: 3 - 24 Aligned: 22 Modelled: 22 Confidence: 9.7% Identity: 27% Fold: Single transmembrane helix Superfamily: Cytochrome c1 subunit of cytochrome bc1 complex (Ubiquinol-cytochrome c reductase), transmembrane anchor Family: Cytochrome c1 subunit of cytochrome bc1 complex (Ubiquinol-cytochrome c reductase), transmembrane anchor Phyre2 PDB 1azp chain A Region: 78 - 95 Aligned: 18 Modelled: 18 Confidence: 8.6% Identity: 11% Fold: SH3-like barrel Superfamily: Chromo domain-like Family: "Histone-like" proteins from archaea Phyre2 PDB 3cx5 chain D domain 2 Region: 3 - 24 Aligned: 22 Modelled: 22 Confidence: 7.9% Identity: 23% Fold: Single transmembrane helix Superfamily: Cytochrome c1 subunit of cytochrome bc1 complex (Ubiquinol-cytochrome c reductase), transmembrane anchor Family: Cytochrome c1 subunit of cytochrome bc1 complex (Ubiquinol-cytochrome c reductase), transmembrane anchor Phyre2 PDB 3if8 chain A Region: 151 - 160 Aligned: 10 Modelled: 10 Confidence: 6.2% Identity: 10% PDB header:cell cycle Chain: A: PDB Molecule:protein zwilch homolog; PDBTitle: crystal structure of zwilch, a member of the rzz kinetochore complex Phyre2 PDB 2bo9 chain B Region: 30 - 57 Aligned: 28 Modelled: 28 Confidence: 5.7% Identity: 14% PDB header:hydrolase Chain: B: PDB Molecule:human latexin; PDBTitle: human carboxypeptidase a4 in complex with human latexin. Phyre2 PDB 1qcs chain A domain 1 Region: 101 - 154 Aligned: 50 Modelled: 51 Confidence: 5.7% Identity: 12% Fold: Double psi beta-barrel Superfamily: ADC-like Family: Cdc48 N-terminal domain-like Phyre2 PDB 3arc chain T Region: 8 - 25 Aligned: 18 Modelled: 18 Confidence: 5.6% Identity: 22% PDB header:electron transport, photosynthesis Chain: T: PDB Molecule:photosystem ii reaction center protein t; PDBTitle: crystal structure of oxygen-evolving photosystem ii at 1.9 angstrom2 resolution Phyre2 PDB 3a0b chain T Region: 8 - 25 Aligned: 18 Modelled: 18 Confidence: 5.6% Identity: 22% PDB header:electron transport Chain: T: PDB Molecule:photosystem ii reaction center protein t; PDBTitle: crystal structure of br-substituted photosystem ii complex Phyre2 PDB 2j7a chain C Region: 9 - 37 Aligned: 29 Modelled: 29 Confidence: 5.1% Identity: 10% PDB header:oxidoreductase Chain: C: PDB Molecule:cytochrome c quinol dehydrogenase nrfh; PDBTitle: crystal structure of cytochrome c nitrite reductase nrfha2 complex from desulfovibrio vulgaris Phyre2 1 d2gmqa1 2 c8tfvA_ 3 d1cida1 4 d1q6wa_ 5 c1cidA_ 6 d1ppjd2 7 d1azpa_ 8 d3cx5d2 9 c3if8A_ 10 c2bo9B_ 11 d1qcsa1 12 c3arct_ 13 c3a0bT_ 14 c2j7aC_

Detailed template information

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

1 d2gmqa1 16.3 10 Fold:PUA domain-like Superfamily:PUA domain-like Family:PrgU-like 2 c8tfvA_ 14.6 33 PDB header:antimicrobial Chain: A: PDB Molecule:protein (thanatin); PDBTitle: insect defense peptide 3 d1cida1 13.4 13 Fold:Immunoglobulin-like beta-sandwich Superfamily:Immunoglobulin Family:V set domains (antibody variable domain-like) 4 d1q6wa_ 11.3 16 Fold:Thioesterase/thiol ester dehydrase-isomerase Superfamily:Thioesterase/thiol ester dehydrase-isomerase Family:MaoC-like 5 c1cidA_ 10.6 14 PDB header:t-cell surface glycoprotein Chain: A: PDB Molecule:t cell surface glycoprotein cd4; PDBTitle: crystal structure of domains 3 & 4 of rat cd4 and their2 relationship to the nh2-terminal domains 6 d1ppjd2 9.7 27 Fold:Single transmembrane helix Superfamily:Cytochrome c1 subunit of cytochrome bc1 complex (Ubiquinol-cytochrome c reductase), transmembrane anchor Family:Cytochrome c1 subunit of cytochrome bc1 complex (Ubiquinol-cytochrome c reductase), transmembrane anchor 7 d1azpa_ 8.6 11 Fold:SH3-like barrel Superfamily:Chromo domain-like Family:"Histone-like" proteins from archaea 8 d3cx5d2 7.9 23 Fold:Single transmembrane helix Superfamily:Cytochrome c1 subunit of cytochrome bc1 complex (Ubiquinol-cytochrome c reductase), transmembrane anchor Family:Cytochrome c1 subunit of cytochrome bc1 complex (Ubiquinol-cytochrome c reductase), transmembrane anchor 9 c3if8A_ 6.2 10 PDB header:cell cycle Chain: A: PDB Molecule:protein zwilch homolog; PDBTitle: crystal structure of zwilch, a member of the rzz kinetochore complex 10 c2bo9B_ 5.7 14 PDB header:hydrolase Chain: B: PDB Molecule:human latexin; PDBTitle: human carboxypeptidase a4 in complex with human latexin. 11 d1qcsa1 5.7 12 Fold:Double psi beta-barrel Superfamily:ADC-like Family:Cdc48 N-terminal domain-like 12 c3arct_ 5.6 22 PDB header:electron transport, photosynthesis Chain: T: PDB Molecule:photosystem ii reaction center protein t; PDBTitle: crystal structure of oxygen-evolving photosystem ii at 1.9 angstrom2 resolution 13 c3a0bT_ 5.6 22 PDB header:electron transport Chain: T: PDB Molecule:photosystem ii reaction center protein t; PDBTitle: crystal structure of br-substituted photosystem ii complex 14 c2j7aC_ 5.1 10 PDB header:oxidoreductase Chain: C: PDB Molecule:cytochrome c quinol dehydrogenase nrfh; PDBTitle: crystal structure of cytochrome c nitrite reductase nrfha2 complex from desulfovibrio vulgaris

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