Secondary structure and disorder prediction

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Sequence		M	R	I	G	I	I	F	P	V	V	I	F	I	T	A	V	V	F	L	A	W	F	F	I	G	G	Y	A	A	P	G	A
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 2axt chain L Region: 11 - 23 Aligned: 13 Modelled: 13 Confidence: 31.6% Identity: 38% PDB header:electron transport Chain: L: PDB Molecule:photosystem ii reaction center l protein; PDBTitle: crystal structure of photosystem ii from thermosynechococcus elongatus Phyre2 PDB 3kzi chain L Region: 11 - 23 Aligned: 13 Modelled: 13 Confidence: 31.6% Identity: 38% PDB header:electron transport Chain: L: PDB Molecule:photosystem ii reaction center protein l; PDBTitle: crystal structure of monomeric form of cyanobacterial photosystem ii Phyre2 PDB 3a0b chain L Region: 11 - 23 Aligned: 13 Modelled: 13 Confidence: 31.6% Identity: 38% PDB header:electron transport Chain: L: PDB Molecule:photosystem ii reaction center protein l; PDBTitle: crystal structure of br-substituted photosystem ii complex Phyre2 PDB 3prr chain L Region: 11 - 23 Aligned: 13 Modelled: 13 Confidence: 31.6% Identity: 38% PDB header:photosynthesis Chain: L: PDB Molecule:photosystem ii reaction center protein l; PDBTitle: crystal structure of cyanobacterial photosystem ii in complex with2 terbutryn (part 2 of 2). this file contains second monomer of psii3 dimer Phyre2 PDB 3arc chain L Region: 11 - 23 Aligned: 13 Modelled: 13 Confidence: 31.6% Identity: 38% PDB header:electron transport, photosynthesis Chain: L: PDB Molecule:photosystem ii reaction center protein l; PDBTitle: crystal structure of oxygen-evolving photosystem ii at 1.9 angstrom2 resolution Phyre2 PDB 1s5l chain L Region: 11 - 23 Aligned: 13 Modelled: 13 Confidence: 31.6% Identity: 38% PDB header:photosynthesis Chain: L: PDB Molecule:photosystem ii reaction center l protein; PDBTitle: architecture of the photosynthetic oxygen evolving center Phyre2 PDB 3a0b chain L Region: 11 - 23 Aligned: 13 Modelled: 13 Confidence: 31.6% Identity: 38% PDB header:electron transport Chain: L: PDB Molecule:photosystem ii reaction center protein l; PDBTitle: crystal structure of br-substituted photosystem ii complex Phyre2 PDB 1s5l chain L Region: 11 - 23 Aligned: 13 Modelled: 13 Confidence: 31.6% Identity: 38% PDB header:photosynthesis Chain: L: PDB Molecule:photosystem ii reaction center l protein; PDBTitle: architecture of the photosynthetic oxygen evolving center Phyre2 PDB 2axt chain L Region: 11 - 23 Aligned: 13 Modelled: 13 Confidence: 31.6% Identity: 38% PDB header:electron transport Chain: L: PDB Molecule:photosystem ii reaction center l protein; PDBTitle: crystal structure of photosystem ii from thermosynechococcus elongatus Phyre2 PDB 3bz1 chain L Region: 11 - 23 Aligned: 13 Modelled: 13 Confidence: 31.6% Identity: 38% PDB header:electron transport Chain: L: PDB Molecule:photosystem ii reaction center protein l; PDBTitle: crystal structure of cyanobacterial photosystem ii (part 12 of 2). this file contains first monomer of psii dimer Phyre2 PDB 3prq chain L Region: 11 - 23 Aligned: 13 Modelled: 13 Confidence: 31.6% Identity: 38% PDB header:photosynthesis Chain: L: PDB Molecule:photosystem ii reaction center protein l; PDBTitle: crystal structure of cyanobacterial photosystem ii in complex with2 terbutryn (part 1 of 2). this file contains first monomer of psii3 dimer Phyre2 PDB 3bz2 chain L Region: 11 - 23 Aligned: 13 Modelled: 13 Confidence: 31.6% Identity: 38% PDB header:electron transport Chain: L: PDB Molecule:photosystem ii reaction center protein l; PDBTitle: crystal structure of cyanobacterial photosystem ii (part 22 of 2). this file contains second monomer of psii dimer Phyre2 PDB 2axt chain L domain 1 Region: 11 - 23 Aligned: 13 Modelled: 13 Confidence: 31.6% Identity: 38% Fold: Single transmembrane helix Superfamily: Photosystem II reaction center protein L, PsbL Family: PsbL-like Phyre2 PDB 3bz1 chain Y Region: 3 - 16 Aligned: 14 Modelled: 14 Confidence: 23.1% Identity: 57% PDB header:electron transport Chain: Y: PDB Molecule:photosystem ii protein y; PDBTitle: crystal structure of cyanobacterial photosystem ii (part 12 of 2). this file contains first monomer of psii dimer Phyre2 PDB 3a0h chain Y Region: 3 - 16 Aligned: 14 Modelled: 14 Confidence: 23.1% Identity: 57% PDB header:electron transport Chain: Y: PDB Molecule:photosystem ii reaction center protein ycf12; PDBTitle: crystal structure of i-substituted photosystem ii complex Phyre2 PDB 3a0h chain Y Region: 3 - 16 Aligned: 14 Modelled: 14 Confidence: 23.1% Identity: 57% PDB header:electron transport Chain: Y: PDB Molecule:photosystem ii reaction center protein ycf12; PDBTitle: crystal structure of i-substituted photosystem ii complex Phyre2 PDB 3arc chain Y Region: 3 - 16 Aligned: 14 Modelled: 14 Confidence: 22.1% Identity: 57% PDB header:electron transport, photosynthesis Chain: Y: PDB Molecule:protein ycf12; PDBTitle: crystal structure of oxygen-evolving photosystem ii at 1.9 angstrom2 resolution Phyre2 PDB 3arc chain Y Region: 3 - 16 Aligned: 14 Modelled: 14 Confidence: 22.1% Identity: 57% PDB header:electron transport, photosynthesis Chain: Y: PDB Molecule:protein ycf12; PDBTitle: crystal structure of oxygen-evolving photosystem ii at 1.9 angstrom2 resolution Phyre2 PDB 3arc chain L Region: 9 - 23 Aligned: 15 Modelled: 15 Confidence: 22.0% Identity: 33% PDB header:electron transport, photosynthesis Chain: L: PDB Molecule:photosystem ii reaction center protein l; PDBTitle: crystal structure of oxygen-evolving photosystem ii at 1.9 angstrom2 resolution Phyre2 PDB 3a0h chain L Region: 11 - 23 Aligned: 13 Modelled: 13 Confidence: 21.8% Identity: 38% PDB header:electron transport Chain: L: PDB Molecule:photosystem ii reaction center protein l; PDBTitle: crystal structure of i-substituted photosystem ii complex Phyre2 1 c2axtl_ 2 c3kziL_ 3 c3a0bL_ 4 c3prrL_ 5 c3arcL_ 6 c1s5lL_ 7 c3a0bl_ 8 c1s5ll_ 9 c2axtL_ 10 c3bz1L_ 11 c3prqL_ 12 c3bz2L_ 13 d2axtl1 14 c3bz1y_ 15 c3a0hY_ 16 c3a0hy_ 17 c3arcY_ 18 c3arcy_ 19 c3arcl_ 20 c3a0hl_ 21 22 23

Detailed template information

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

1 c2axtl_ 31.6 38 PDB header:electron transport Chain: L: PDB Molecule:photosystem ii reaction center l protein; PDBTitle: crystal structure of photosystem ii from thermosynechococcus elongatus 2 c3kziL_ 31.6 38 PDB header:electron transport Chain: L: PDB Molecule:photosystem ii reaction center protein l; PDBTitle: crystal structure of monomeric form of cyanobacterial photosystem ii 3 c3a0bL_ 31.6 38 PDB header:electron transport Chain: L: PDB Molecule:photosystem ii reaction center protein l; PDBTitle: crystal structure of br-substituted photosystem ii complex 4 c3prrL_ 31.6 38 PDB header:photosynthesis Chain: L: PDB Molecule:photosystem ii reaction center protein l; PDBTitle: crystal structure of cyanobacterial photosystem ii in complex with2 terbutryn (part 2 of 2). this file contains second monomer of psii3 dimer 5 c3arcL_ 31.6 38 PDB header:electron transport, photosynthesis Chain: L: PDB Molecule:photosystem ii reaction center protein l; PDBTitle: crystal structure of oxygen-evolving photosystem ii at 1.9 angstrom2 resolution 6 c1s5lL_ 31.6 38 PDB header:photosynthesis Chain: L: PDB Molecule:photosystem ii reaction center l protein; PDBTitle: architecture of the photosynthetic oxygen evolving center 7 c3a0bl_ 31.6 38 PDB header:electron transport Chain: L: PDB Molecule:photosystem ii reaction center protein l; PDBTitle: crystal structure of br-substituted photosystem ii complex 8 c1s5ll_ 31.6 38 PDB header:photosynthesis Chain: L: PDB Molecule:photosystem ii reaction center l protein; PDBTitle: architecture of the photosynthetic oxygen evolving center 9 c2axtL_ 31.6 38 PDB header:electron transport Chain: L: PDB Molecule:photosystem ii reaction center l protein; PDBTitle: crystal structure of photosystem ii from thermosynechococcus elongatus 10 c3bz1L_ 31.6 38 PDB header:electron transport Chain: L: PDB Molecule:photosystem ii reaction center protein l; PDBTitle: crystal structure of cyanobacterial photosystem ii (part 12 of 2). this file contains first monomer of psii dimer 11 c3prqL_ 31.6 38 PDB header:photosynthesis Chain: L: PDB Molecule:photosystem ii reaction center protein l; PDBTitle: crystal structure of cyanobacterial photosystem ii in complex with2 terbutryn (part 1 of 2). this file contains first monomer of psii3 dimer 12 c3bz2L_ 31.6 38 PDB header:electron transport Chain: L: PDB Molecule:photosystem ii reaction center protein l; PDBTitle: crystal structure of cyanobacterial photosystem ii (part 22 of 2). this file contains second monomer of psii dimer 13 d2axtl1 31.6 38 Fold:Single transmembrane helix Superfamily:Photosystem II reaction center protein L, PsbL Family:PsbL-like 14 c3bz1y_ 23.1 57 PDB header:electron transport Chain: Y: PDB Molecule:photosystem ii protein y; PDBTitle: crystal structure of cyanobacterial photosystem ii (part 12 of 2). this file contains first monomer of psii dimer 15 c3a0hY_ 23.1 57 PDB header:electron transport Chain: Y: PDB Molecule:photosystem ii reaction center protein ycf12; PDBTitle: crystal structure of i-substituted photosystem ii complex 16 c3a0hy_ 23.1 57 PDB header:electron transport Chain: Y: PDB Molecule:photosystem ii reaction center protein ycf12; PDBTitle: crystal structure of i-substituted photosystem ii complex 17 c3arcY_ 22.1 57 PDB header:electron transport, photosynthesis Chain: Y: PDB Molecule:protein ycf12; PDBTitle: crystal structure of oxygen-evolving photosystem ii at 1.9 angstrom2 resolution 18 c3arcy_ 22.1 57 PDB header:electron transport, photosynthesis Chain: Y: PDB Molecule:protein ycf12; PDBTitle: crystal structure of oxygen-evolving photosystem ii at 1.9 angstrom2 resolution 19 c3arcl_ 22.0 33 PDB header:electron transport, photosynthesis Chain: L: PDB Molecule:photosystem ii reaction center protein l; PDBTitle: crystal structure of oxygen-evolving photosystem ii at 1.9 angstrom2 resolution 20 c3a0hl_ 21.8 38 PDB header:electron transport Chain: L: PDB Molecule:photosystem ii reaction center protein l; PDBTitle: crystal structure of i-substituted photosystem ii complex 21 c3a0hL_ not modelled 21.8 38 PDB header:electron transport Chain: L: PDB Molecule:photosystem ii reaction center protein l; PDBTitle: crystal structure of i-substituted photosystem ii complex 22 c3a0by_ not modelled 17.3 57 PDB header:electron transport Chain: Y: PDB Molecule:photosystem ii reaction center protein ycf12; PDBTitle: crystal structure of br-substituted photosystem ii complex 23 c3a0bY_ not modelled 15.6 57 PDB header:electron transport Chain: Y: PDB Molecule:photosystem ii reaction center protein ycf12; PDBTitle: crystal structure of br-substituted photosystem ii complex

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