Email l.a.kelley@imperial.ac.uk Description O14468 Date Mon Jul 2 19:10:22 BST 2012 Unique Job ID 0c65ad757a21c736

Summary

Top model

Image coloured by rainbow N → C terminus Close Jmol

Model (left) based on template d1xppa_ Top template information Fold:DCoH-like Superfamily:RBP11-like subunits of RNA polymerase Family:RBP11/RpoL Confidence and coverage Confidence: 38.4% Coverage: 37% 28 residues ( 37% of your sequence) have been modelled with 38.4% 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 1xpp chain A Region: 42 - 69 Aligned: 28 Modelled: 28 Confidence: 38.4% Identity: 14% Fold: DCoH-like Superfamily: RBP11-like subunits of RNA polymerase Family: RBP11/RpoL Phyre2 PDB 3pvp chain A Region: 40 - 76 Aligned: 36 Modelled: 37 Confidence: 35.9% Identity: 11% PDB header:dna binding protein/dna Chain: A: PDB Molecule:chromosomal replication initiator protein dnaa; PDBTitle: structure of mycobacterium tuberculosis dnaa-dbd in complex with box22 dna Phyre2 PDB 1m1j chain A Region: 34 - 74 Aligned: 41 Modelled: 41 Confidence: 30.4% Identity: 12% PDB header:blood clotting Chain: A: PDB Molecule:fibrinogen alpha subunit; PDBTitle: crystal structure of native chicken fibrinogen with two different2 bound ligands Phyre2 PDB 1slq chain A Region: 6 - 55 Aligned: 34 Modelled: 35 Confidence: 26.7% Identity: 26% Fold: VP4 membrane interaction domain Superfamily: VP4 membrane interaction domain Family: VP4 membrane interaction domain Phyre2 PDB 3kyp chain A Region: 46 - 76 Aligned: 31 Modelled: 31 Confidence: 21.2% Identity: 13% PDB header:chaperone Chain: A: PDB Molecule:nucleosome assembly protein; PDBTitle: crystal structure of nucleosome assembly protein s (pfnaps) from2 plasmodium falciparum Phyre2 PDB 1j1v chain A Region: 40 - 72 Aligned: 32 Modelled: 33 Confidence: 13.2% Identity: 6% Fold: DNA/RNA-binding 3-helical bundle Superfamily: TrpR-like Family: Chromosomal replication initiation factor DnaA C-terminal domain IV Phyre2 PDB 3m06 chain F Region: 30 - 76 Aligned: 44 Modelled: 47 Confidence: 13.1% Identity: 27% PDB header:protein binding Chain: F: PDB Molecule:tnf receptor-associated factor 2; PDBTitle: crystal structure of traf2 Phyre2 PDB 3gyv chain A Region: 44 - 74 Aligned: 31 Modelled: 31 Confidence: 11.6% Identity: 19% PDB header:chaperone Chain: A: PDB Molecule:nucleosome assembly protein 1, putative; PDBTitle: crystal structure of nucleosome assembly protein from plasmodium2 falciparum Phyre2 PDB 2ayu chain A domain 1 Region: 44 - 74 Aligned: 31 Modelled: 31 Confidence: 11.3% Identity: 29% Fold: NAP-like Superfamily: NAP-like Family: NAP-like Phyre2 PDB 2ayu chain A Region: 44 - 74 Aligned: 31 Modelled: 31 Confidence: 11.3% Identity: 29% PDB header:chaperone Chain: A: PDB Molecule:nucleosome assembly protein; PDBTitle: the structure of nucleosome assembly protein suggests a mechanism for2 histone binding and shuttling Phyre2 PDB 1nu9 chain C domain 1 Region: 22 - 61 Aligned: 40 Modelled: 40 Confidence: 11.2% Identity: 28% Fold: immunoglobulin/albumin-binding domain-like Superfamily: Staphylocoagulase Family: Staphylocoagulase Phyre2 PDB 3m0d chain C Region: 30 - 76 Aligned: 44 Modelled: 47 Confidence: 10.7% Identity: 27% PDB header:signaling protein Chain: C: PDB Molecule:tnf receptor-associated factor 1; PDBTitle: crystal structure of the traf1:traf2:ciap2 complex Phyre2 PDB 1nd9 chain A Region: 33 - 55 Aligned: 23 Modelled: 23 Confidence: 10.4% Identity: 30% Fold: Putative DNA-binding domain Superfamily: Putative DNA-binding domain Family: N-terminal subdomain of bacterial translation initiation factor IF2 Phyre2 PDB 2xzr chain A Region: 46 - 74 Aligned: 25 Modelled: 29 Confidence: 10.1% Identity: 44% PDB header:cell adhesion Chain: A: PDB Molecule:immunoglobulin-binding protein eibd; PDBTitle: escherichia coli immunoglobulin-binding protein eibd 391-438 fused2 to gcn4 adaptors Phyre2 PDB 2hn1 chain A Region: 34 - 76 Aligned: 43 Modelled: 43 Confidence: 9.3% Identity: 9% PDB header:metal transport Chain: A: PDB Molecule:magnesium and cobalt transporter; PDBTitle: crystal structure of a cora soluble domain from a. fulgidus in complex2 with co2+ Phyre2 PDB 2c5i chain T Region: 26 - 74 Aligned: 49 Modelled: 49 Confidence: 8.5% Identity: 20% PDB header:protein transport Chain: T: PDB Molecule:t-snare affecting a late golgi compartment PDBTitle: n-terminal domain of tlg1 complexed with n-terminus of2 vps51 in distorted conformation Phyre2 PDB 1pl5 chain A Region: 43 - 64 Aligned: 22 Modelled: 22 Confidence: 8.4% Identity: 23% PDB header:dna binding protein/transcription Chain: A: PDB Molecule:regulatory protein sir4; PDBTitle: crystal structure analysis of the sir4p c-terminal coiled2 coil Phyre2 PDB 1nyh chain A Region: 43 - 64 Aligned: 22 Modelled: 22 Confidence: 8.3% Identity: 23% PDB header:transcription repressor Chain: A: PDB Molecule:regulatory protein sir4; PDBTitle: crystal structure of the coiled-coil dimerization motif of sir4 Phyre2 PDB 1wty chain A Region: 42 - 68 Aligned: 27 Modelled: 27 Confidence: 7.8% Identity: 26% Fold: Four-helical up-and-down bundle Superfamily: Nucleotidyltransferase substrate binding subunit/domain Family: Family 1 bi-partite nucleotidyltransferase subunit Phyre2 PDB 1x8y chain A Region: 42 - 74 Aligned: 33 Modelled: 33 Confidence: 7.7% Identity: 21% PDB header:structural protein Chain: A: PDB Molecule:lamin a/c; PDBTitle: human lamin coil 2b Phyre2 1 d1xppa_ 2 c3pvpA_ 3 c1m1jA_ 4 d1slqa_ 5 c3kypA_ 6 d1j1va_ 7 c3m06F_ 8 c3gyvA_ 9 d2ayua1 10 c2ayuA_ 11 d1nu9c1 12 c3m0dC_ 13 d1nd9a_ 14 c2xzrA_ 15 c2hn1A_ 16 c2c5iT_ 17 c1pl5A_ 18 c1nyhA_ 19 d1wtya_ 20 c1x8yA_ 21 22 23 24 25 26 27 28 29

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