Email l.a.kelley@imperial.ac.uk Description A6X995 Date Sun Jul 8 11:45:04 BST 2012 Unique Job ID 614868f70328ece6

Summary

Top model

Image coloured by rainbow N → C terminus Close Jmol

Model (left) based on template c2i2jA_ Top template information PDB header:signaling protein Chain: A: PDB Molecule:signaling peptide ua159sp; PDBTitle: nmr structure of ua159sp in tfe Confidence and coverage Confidence: 9.0% Coverage: 12% 5 residues ( 12% of your sequence) have been modelled with 9.0% confidence by the single highest scoring template. You may wish to submit your sequence to Phyrealarm. This will automatically scan your sequence every week for new potential templates as they appear in the Phyre2 library. Please note: You must be registered and logged in to use Phyrealarm. 3D viewing Interactive 3D view in Jmol

Sequence analysis

Secondary structure and disorder prediction

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 2i2j chain A Region: 11 - 15 Aligned: 5 Modelled: 5 Confidence: 9.0% Identity: 100% PDB header:signaling protein Chain: A: PDB Molecule:signaling peptide ua159sp; PDBTitle: nmr structure of ua159sp in tfe Phyre2 PDB 3arc chain T Region: 34 - 41 Aligned: 8 Modelled: 8 Confidence: 8.9% Identity: 63% 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 4fao chain I Region: 23 - 32 Aligned: 10 Modelled: 10 Confidence: 7.7% Identity: 50% PDB header:signaling protein/signaling protein Chain: I: PDB Molecule:serine/threonine-protein kinase receptor r3; PDBTitle: specificity and structure of a high affinity activin-like 1 (alk1)2 signaling complex Phyre2 PDB 3a0b chain T Region: 34 - 41 Aligned: 8 Modelled: 8 Confidence: 7.5% Identity: 63% 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 1xrd chain A domain 1 Region: 3 - 21 Aligned: 19 Modelled: 19 Confidence: 6.8% Identity: 21% Fold: Light-harvesting complex subunits Superfamily: Light-harvesting complex subunits Family: Light-harvesting complex subunits Phyre2 PDB 2axt chain T domain 1 Region: 34 - 41 Aligned: 8 Modelled: 8 Confidence: 6.4% Identity: 63% Fold: Single transmembrane helix Superfamily: Photosystem II reaction center protein T, PsbT Family: PsbT-like Phyre2 PDB 3arc chain T Region: 34 - 41 Aligned: 8 Modelled: 8 Confidence: 6.4% Identity: 63% 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 3a0h chain T Region: 34 - 41 Aligned: 8 Modelled: 8 Confidence: 6.4% Identity: 63% 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 3a0h chain T Region: 34 - 41 Aligned: 8 Modelled: 8 Confidence: 6.4% Identity: 63% 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 2axt chain T Region: 34 - 41 Aligned: 8 Modelled: 8 Confidence: 6.4% Identity: 63% 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: 34 - 41 Aligned: 8 Modelled: 8 Confidence: 6.4% Identity: 63% 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 Region: 34 - 41 Aligned: 8 Modelled: 8 Confidence: 6.4% Identity: 63% 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 3kzi chain T Region: 34 - 41 Aligned: 8 Modelled: 8 Confidence: 6.4% Identity: 63% 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 PDB 1s5l chain T Region: 34 - 41 Aligned: 8 Modelled: 8 Confidence: 6.3% Identity: 63% PDB header:photosynthesis Chain: T: PDB Molecule:photosystem ii psbt protein; PDBTitle: architecture of the photosynthetic oxygen evolving center Phyre2 PDB 1s5l chain T Region: 34 - 41 Aligned: 8 Modelled: 8 Confidence: 6.3% Identity: 63% PDB header:photosynthesis Chain: T: PDB Molecule:photosystem ii psbt protein; PDBTitle: architecture of the photosynthetic oxygen evolving center Phyre2 PDB 4fby chain T Region: 34 - 41 Aligned: 8 Modelled: 8 Confidence: 6.2% Identity: 63% PDB header:photosynthesis Chain: T: PDB Molecule:photosystem ii reaction center protein t; PDBTitle: fs x-ray diffraction of photosystem ii Phyre2 PDB 3prq chain T Region: 34 - 41 Aligned: 8 Modelled: 8 Confidence: 6.2% Identity: 63% PDB header:photosynthesis Chain: T: PDB Molecule:photosystem ii reaction center protein t; 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 3prr chain T Region: 34 - 41 Aligned: 8 Modelled: 8 Confidence: 6.2% Identity: 63% PDB header:photosynthesis Chain: T: PDB Molecule:photosystem ii reaction center protein t; 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 3bz2 chain T Region: 34 - 41 Aligned: 8 Modelled: 8 Confidence: 6.2% Identity: 63% PDB header:electron transport Chain: T: PDB Molecule:photosystem ii reaction center protein t; PDBTitle: crystal structure of cyanobacterial photosystem ii (part 2 of 2). this2 file contains second monomer of psii dimer Phyre2 PDB 3bz1 chain T Region: 34 - 41 Aligned: 8 Modelled: 8 Confidence: 6.2% Identity: 63% PDB header:electron transport Chain: T: PDB Molecule:photosystem ii reaction center protein t; PDBTitle: crystal structure of cyanobacterial photosystem ii (part 1 of 2). this2 file contains first monomer of psii dimer Phyre2 1 c2i2jA_ 2 c3arct_ 3 c4faoI_ 4 c3a0bT_ 5 d1xrda1 6 d2axtt1 7 c3arcT_ 8 c3a0hT_ 9 c3a0ht_ 10 c2axtt_ 11 c3a0bt_ 12 c2axtT_ 13 c3kziT_ 14 c1s5lt_ 15 c1s5lT_ 16 c4fbyT_ 17 c3prqT_ 18 c3prrT_ 19 c3bz2T_ 20 c3bz1T_ 21 22 23

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

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