Email l.a.kelley@imperial.ac.uk Description Q96PG8 Date Wed May 9 17:36:55 BST 2012 Unique Job ID 61140126926bc642

Summary

Top model

Image coloured by rainbow N → C terminus Close Jmol

Model (left) based on template c3fqmA_ Top template information PDB header:metal binding protein Chain: A: PDB Molecule:non-structural protein 5a; PDBTitle: crystal structure of a novel dimeric form of hcv ns5a domain i protein Confidence and coverage Confidence: 44.5% Coverage: 21% 21 residues ( 21% of your sequence) have been modelled with 44.5% 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. Warning: 54% of your sequence is predicted disordered. Disordered regions cannot be meaningfully predicted. 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 3fqm chain A Region: 4 - 24 Aligned: 21 Modelled: 21 Confidence: 44.5% Identity: 48% PDB header:metal binding protein Chain: A: PDB Molecule:non-structural protein 5a; PDBTitle: crystal structure of a novel dimeric form of hcv ns5a domain i protein Phyre2 PDB 2i9w chain A domain 2 Region: 7 - 25 Aligned: 19 Modelled: 19 Confidence: 33.5% Identity: 42% Fold: Sec-C motif Superfamily: Sec-C motif Family: Sec-C motif Phyre2 PDB 2x2z chain E Region: 3 - 40 Aligned: 33 Modelled: 38 Confidence: 20.0% Identity: 36% PDB header:membrane protein Chain: E: PDB Molecule:apical membrane antigen 1, putative; PDBTitle: crystal structure ama1 from toxoplasma gondii Phyre2 PDB 1miq chain A Region: 1 - 31 Aligned: 31 Modelled: 31 Confidence: 17.4% Identity: 19% Fold: Acid proteases Superfamily: Acid proteases Family: Pepsin-like Phyre2 PDB 2y8r chain D Region: 3 - 40 Aligned: 33 Modelled: 38 Confidence: 16.9% Identity: 36% PDB header:membrane protein Chain: D: PDB Molecule:apical membrane antigen, putative; PDBTitle: crystal structure of apo ama1 mutant (tyr230ala) from2 toxoplasma gondii Phyre2 PDB 1dpj chain A Region: 1 - 30 Aligned: 30 Modelled: 30 Confidence: 15.7% Identity: 23% Fold: Acid proteases Superfamily: Acid proteases Family: Pepsin-like Phyre2 PDB 2apr chain A Region: 1 - 29 Aligned: 29 Modelled: 29 Confidence: 15.3% Identity: 14% Fold: Acid proteases Superfamily: Acid proteases Family: Pepsin-like Phyre2 PDB 1qs8 chain A Region: 2 - 29 Aligned: 28 Modelled: 28 Confidence: 14.6% Identity: 21% Fold: Acid proteases Superfamily: Acid proteases Family: Pepsin-like Phyre2 PDB 1wkr chain A Region: 2 - 29 Aligned: 28 Modelled: 28 Confidence: 13.6% Identity: 29% Fold: Acid proteases Superfamily: Acid proteases Family: Pepsin-like Phyre2 PDB 1qxf chain A Region: 14 - 31 Aligned: 18 Modelled: 18 Confidence: 12.6% Identity: 39% Fold: Rubredoxin-like Superfamily: Zn-binding ribosomal proteins Family: Ribosomal protein S27e Phyre2 PDB 3iz6 chain X Region: 20 - 31 Aligned: 12 Modelled: 12 Confidence: 11.6% Identity: 50% PDB header:ribosome Chain: X: PDB Molecule:40s ribosomal protein s27 (s27e); PDBTitle: localization of the small subunit ribosomal proteins into a 5.5 a2 cryo-em map of triticum aestivum translating 80s ribosome Phyre2 PDB 4pep chain A Region: 1 - 29 Aligned: 29 Modelled: 29 Confidence: 10.9% Identity: 31% Fold: Acid proteases Superfamily: Acid proteases Family: Pepsin-like Phyre2 PDB 2xzm chain 6 Region: 20 - 31 Aligned: 12 Modelled: 12 Confidence: 10.4% Identity: 17% PDB header:ribosome Chain: 6: PDB Molecule:rps27e; PDBTitle: crystal structure of the eukaryotic 40s ribosomal2 subunit in complex with initiation factor 1. this file3 contains the 40s subunit and initiation factor for4 molecule 1 Phyre2 PDB 1pfz chain A Region: 1 - 30 Aligned: 30 Modelled: 30 Confidence: 10.3% Identity: 20% Fold: Acid proteases Superfamily: Acid proteases Family: Pepsin-like Phyre2 PDB 2asi chain A Region: 1 - 30 Aligned: 30 Modelled: 30 Confidence: 10.1% Identity: 27% Fold: Acid proteases Superfamily: Acid proteases Family: Pepsin-like Phyre2 PDB 3cms chain A Region: 1 - 29 Aligned: 29 Modelled: 29 Confidence: 9.8% Identity: 28% Fold: Acid proteases Superfamily: Acid proteases Family: Pepsin-like Phyre2 PDB 3fnu chain A Region: 2 - 29 Aligned: 28 Modelled: 28 Confidence: 9.2% Identity: 29% PDB header:hydrolase/hydrolase inhibitor Chain: A: PDB Molecule:hap protein; PDBTitle: crystal structure of kni-10006 bound histo-aspartic protease (hap)2 from plasmodium falciparum Phyre2 PDB 1ls5 chain A Region: 1 - 31 Aligned: 31 Modelled: 31 Confidence: 8.8% Identity: 19% Fold: Acid proteases Superfamily: Acid proteases Family: Pepsin-like Phyre2 PDB 1tzs chain A Region: 1 - 29 Aligned: 29 Modelled: 29 Confidence: 8.8% Identity: 28% PDB header:hydrolase Chain: A: PDB Molecule:cathepsin e; PDBTitle: crystal structure of an activation intermediate of2 cathepsin e Phyre2 PDB 2l23 chain A Region: 18 - 40 Aligned: 23 Modelled: 23 Confidence: 8.8% Identity: 22% PDB header:transcription Chain: A: PDB Molecule:mediator of rna polymerase ii transcription subunit 25; PDBTitle: nmr structure of the acid (activator interacting domain) of the human2 mediator med25 protein Phyre2 1 c3fqmA_ 2 d2i9wa2 3 c2x2zE_ 4 d1miqa_ 5 c2y8rD_ 6 d1dpja_ 7 d2apra_ 8 d1qs8a_ 9 d1wkra_ 10 d1qxfa_ 11 c3iz6X_ 12 d4pepa_ 13 c2xzm6_ 14 d1pfza_ 15 d2asia_ 16 d3cmsa_ 17 c3fnuA_ 18 d1ls5a_ 19 c1tzsA_ 20 c2l23A_ 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35

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