Email l.a.kelley@imperial.ac.uk Description O13549 Date Mon Jul 2 19:10:13 BST 2012 Unique Job ID c0859467eb56c437

Summary

Top model

Image coloured by rainbow N → C terminus Close Jmol

Model (left) based on template d1gaka_ Top template information Fold:Fertilization protein Superfamily:Fertilization protein Family:Fertilization protein Confidence and coverage Confidence: 38.0% Coverage: 52% 56 residues ( 52% of your sequence) have been modelled with 38.0% 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 1gak chain A Region: 3 - 58 Aligned: 56 Modelled: 56 Confidence: 38.0% Identity: 32% Fold: Fertilization protein Superfamily: Fertilization protein Family: Fertilization protein Phyre2 PDB 2vxd chain A Region: 22 - 47 Aligned: 26 Modelled: 26 Confidence: 27.7% Identity: 42% PDB header:nuclear protein Chain: A: PDB Molecule:nucleophosmin; PDBTitle: the structure of the c-terminal domain of nucleophosmin Phyre2 PDB 1qp6 chain B Region: 39 - 51 Aligned: 13 Modelled: 13 Confidence: 21.8% Identity: 54% PDB header:de novo protein Chain: B: PDB Molecule:protein (alpha2d); PDBTitle: solution structure of alpha2d Phyre2 PDB 2llh chain A Region: 22 - 47 Aligned: 26 Modelled: 26 Confidence: 17.8% Identity: 42% PDB header:dna binding protein, chaperone Chain: A: PDB Molecule:nucleophosmin; PDBTitle: nmr structure of npm1_c70 Phyre2 PDB 2kne chain B Region: 70 - 86 Aligned: 17 Modelled: 17 Confidence: 14.7% Identity: 35% PDB header:metal transport Chain: B: PDB Molecule:atpase, ca++ transporting, plasma membrane 4; PDBTitle: calmodulin wraps around its binding domain in the plasma2 membrane ca2+ pump anchored by a novel 18-1 motif Phyre2 PDB 3vie chain F Region: 14 - 35 Aligned: 22 Modelled: 22 Confidence: 9.8% Identity: 27% PDB header:viral protein/antiviral protein Chain: F: PDB Molecule:sifuvirtide; PDBTitle: hiv-gp41 fusion inhibitor sifuvirtide Phyre2 PDB 3uc2 chain A Region: 96 - 107 Aligned: 12 Modelled: 12 Confidence: 7.2% Identity: 25% PDB header:structural genomics, unknown function Chain: A: PDB Molecule:hypothetical protein with immunoglobulin-like fold; PDBTitle: crystal structure of a hypothetical protein with immunoglobulin-like2 fold (pa0388) from pseudomonas aeruginosa pao1 at 2.09 a resolution Phyre2 PDB 1m9f chain D Region: 75 - 89 Aligned: 15 Modelled: 15 Confidence: 7.2% Identity: 40% Fold: Retrovirus capsid protein, N-terminal core domain Superfamily: Retrovirus capsid protein, N-terminal core domain Family: Retrovirus capsid protein, N-terminal core domain Phyre2 PDB 1fav chain C Region: 15 - 35 Aligned: 21 Modelled: 21 Confidence: 6.8% Identity: 29% PDB header:viral protein Chain: C: PDB Molecule:protein (transmembrane glycoprotein); PDBTitle: the structure of an hiv-1 specific cell entry inhibitor in complex2 with the hiv-1 gp41 trimeric core Phyre2 PDB 1yf2 chain A domain 1 Region: 47 - 65 Aligned: 19 Modelled: 19 Confidence: 6.2% Identity: 21% Fold: DNA methylase specificity domain Superfamily: DNA methylase specificity domain Family: Type I restriction modification DNA specificity domain Phyre2 PDB 2eia chain A domain 2 Region: 75 - 89 Aligned: 15 Modelled: 15 Confidence: 6.2% Identity: 20% Fold: Retrovirus capsid protein, N-terminal core domain Superfamily: Retrovirus capsid protein, N-terminal core domain Family: Retrovirus capsid protein, N-terminal core domain Phyre2 PDB 1lj2 chain D Region: 27 - 32 Aligned: 6 Modelled: 6 Confidence: 6.2% Identity: 100% PDB header:viral protein/ translation Chain: D: PDB Molecule:eukaryotic protein synthesis initiation factor; PDBTitle: recognition of eif4g by rotavirus nsp3 reveals a basis for2 mrna circularization Phyre2 PDB 1m9d chain C Region: 75 - 89 Aligned: 15 Modelled: 15 Confidence: 5.9% Identity: 40% Fold: Retrovirus capsid protein, N-terminal core domain Superfamily: Retrovirus capsid protein, N-terminal core domain Family: Retrovirus capsid protein, N-terminal core domain Phyre2 PDB 1l6n chain A Region: 75 - 89 Aligned: 15 Modelled: 15 Confidence: 5.8% Identity: 40% PDB header:viral protein Chain: A: PDB Molecule:gag polyprotein; PDBTitle: structure of the n-terminal 283-residue fragment of the hiv-2 1 gag polyprotein Phyre2 PDB 2o8g chain J Region: 62 - 75 Aligned: 14 Modelled: 14 Confidence: 5.3% Identity: 50% PDB header:hydrolase/inhibitor Chain: J: PDB Molecule:protein phosphatase inhibitor 2; PDBTitle: rat pp1c gamma complexed with mouse inhibitor-2 Phyre2 1 d1gaka_ 2 c2vxdA_ 3 c1qp6B_ 4 c2llhA_ 5 c2kneB_ 6 c3vieF_ 7 c3uc2A_ 8 d1m9fd_ 9 c1favC_ 10 d1yf2a1 11 d2eiaa2 12 c1lj2D_ 13 d1m9dc_ 14 c1l6nA_ 15 c2o8gJ_

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