Secondary structure and disorder prediction

		1	.	.	.	.	.	.	.	.	10	.	.	.	.	.	.	.	.	.	20	.	.	.	.	.	.	.	.	.	30	.	.	.	.	.	.	.	.	.	40	.	.	.	.	.	.	.	.	.	50	.	.	.	.	.	.	.	.	.	60
Sequence		M	R	R	W	I	S	Q	N	N	I	R	L	P	R	G	A	F	F	I	S	A	L	F	F	F	N	A	V	C	I	V	S	D	N	L	L	I	I	E	S	F	G	E	M	A	Y	N	I	S	Y	L	T	R	V	P	G	T	N	T	L
Secondary structure
SS confidence
Disorder		?	?	?	?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	70	.	.	.	.	.	.
Sequence		L	A	C	C	C	L	L	R	P	E	E	V	N	S	E	Y
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 2z1d chain A Region: 36 - 62 Aligned: 20 Modelled: 27 Confidence: 11.9% Identity: 30% PDB header:metal binding protein Chain: A: PDB Molecule:hydrogenase expression/formation protein hypd; PDBTitle: crystal structure of [nife] hydrogenase maturation protein, hypd from2 thermococcus kodakaraensis Phyre2 PDB 1fjr chain A Region: 36 - 69 Aligned: 34 Modelled: 34 Confidence: 8.0% Identity: 24% Fold: Methuselah ectodomain Superfamily: Methuselah ectodomain Family: Methuselah ectodomain Phyre2 PDB 1icl chain A Region: 46 - 60 Aligned: 15 Modelled: 15 Confidence: 6.0% Identity: 47% PDB header:de novo protein Chain: A: PDB Molecule:th1ox; PDBTitle: solution structure of designed beta-sheet mini-protein th1ox Phyre2 PDB 3arc chain T Region: 19 - 25 Aligned: 7 Modelled: 7 Confidence: 5.0% Identity: 86% 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 2axt chain T Region: 19 - 25 Aligned: 7 Modelled: 7 Confidence: 5.0% Identity: 86% PDB header:electron transport Chain: T: PDB Molecule:photosystem ii reaction center t protein; PDBTitle: crystal structure of photosystem ii from thermosynechococcus elongatus Phyre2 PDB 2axt chain T Region: 19 - 25 Aligned: 7 Modelled: 7 Confidence: 5.0% Identity: 86% PDB header:electron transport Chain: T: PDB Molecule:photosystem ii reaction center t protein; PDBTitle: crystal structure of photosystem ii from thermosynechococcus elongatus Phyre2 PDB 3a0b chain T Region: 19 - 25 Aligned: 7 Modelled: 7 Confidence: 5.0% Identity: 86% 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 2axt chain T domain 1 Region: 19 - 25 Aligned: 7 Modelled: 7 Confidence: 5.0% Identity: 86% Fold: Single transmembrane helix Superfamily: Photosystem II reaction center protein T, PsbT Family: PsbT-like Phyre2 PDB 3a0h chain T Region: 19 - 25 Aligned: 7 Modelled: 7 Confidence: 5.0% Identity: 86% PDB header:electron transport Chain: T: PDB Molecule:photosystem ii reaction center protein t; PDBTitle: crystal structure of i-substituted photosystem ii complex Phyre2 PDB 3kzi chain T Region: 19 - 25 Aligned: 7 Modelled: 7 Confidence: 5.0% Identity: 86% PDB header:electron transport Chain: T: PDB Molecule:photosystem ii reaction center protein t; PDBTitle: crystal structure of monomeric form of cyanobacterial photosystem ii Phyre2 1 c2z1dA_ 2 d1fjra_ 3 c1iclA_ 4 c3arcT_ 5 c2axtt_ 6 c2axtT_ 7 c3a0bt_ 8 d2axtt1 9 c3a0hT_ 10 c3kziT_

Detailed template information

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

1 c2z1dA_ 11.9 30 PDB header:metal binding protein Chain: A: PDB Molecule:hydrogenase expression/formation protein hypd; PDBTitle: crystal structure of [nife] hydrogenase maturation protein, hypd from2 thermococcus kodakaraensis 2 d1fjra_ 8.0 24 Fold:Methuselah ectodomain Superfamily:Methuselah ectodomain Family:Methuselah ectodomain 3 c1iclA_ 6.0 47 PDB header:de novo protein Chain: A: PDB Molecule:th1ox; PDBTitle: solution structure of designed beta-sheet mini-protein th1ox 4 c3arcT_ 5.0 86 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 5 c2axtt_ 5.0 86 PDB header:electron transport Chain: T: PDB Molecule:photosystem ii reaction center t protein; PDBTitle: crystal structure of photosystem ii from thermosynechococcus elongatus 6 c2axtT_ 5.0 86 PDB header:electron transport Chain: T: PDB Molecule:photosystem ii reaction center t protein; PDBTitle: crystal structure of photosystem ii from thermosynechococcus elongatus 7 c3a0bt_ 5.0 86 PDB header:electron transport Chain: T: PDB Molecule:photosystem ii reaction center protein t; PDBTitle: crystal structure of br-substituted photosystem ii complex 8 d2axtt1 5.0 86 Fold:Single transmembrane helix Superfamily:Photosystem II reaction center protein T, PsbT Family:PsbT-like 9 c3a0hT_ 5.0 86 PDB header:electron transport Chain: T: PDB Molecule:photosystem ii reaction center protein t; PDBTitle: crystal structure of i-substituted photosystem ii complex 10 c3kziT_ 5.0 86 PDB header:electron transport Chain: T: PDB Molecule:photosystem ii reaction center protein t; PDBTitle: crystal structure of monomeric form of cyanobacterial photosystem ii

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