Email l.a.kelley@imperial.ac.uk Description O75012 Date Mon Jul 2 19:10:23 BST 2012 Unique Job ID 1312447d8ae6db08

Summary

Top model

Image coloured by rainbow N → C terminus Close Jmol

Model (left) based on template c1ei0A_ Top template information PDB header:cell cycle Chain: A: PDB Molecule:p8mtcp1; PDBTitle: nmr structure of the alpha-helical hairpin of p8mtcp1 Confidence and coverage Confidence: 90.9% Coverage: 38% 36 residues ( 38% of your sequence) have been modelled with 90.9% 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. Warning: 57% 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 1ei0 chain A Region: 29 - 64 Aligned: 36 Modelled: 36 Confidence: 90.9% Identity: 22% PDB header:cell cycle Chain: A: PDB Molecule:p8mtcp1; PDBTitle: nmr structure of the alpha-helical hairpin of p8mtcp1 Phyre2 PDB 2hp8 chain A Region: 29 - 61 Aligned: 33 Modelled: 33 Confidence: 85.9% Identity: 24% Fold: Cysteine alpha-hairpin motif Superfamily: Cysteine alpha-hairpin motif Family: p8-MTCP1 Phyre2 PDB 2k3j chain A Region: 27 - 66 Aligned: 40 Modelled: 40 Confidence: 78.3% Identity: 10% PDB header:oxidoreductase Chain: A: PDB Molecule:mitochondrial intermembrane space import and PDBTitle: the solution structure of human mia40 Phyre2 PDB 1u97 chain A Region: 30 - 64 Aligned: 35 Modelled: 35 Confidence: 76.8% Identity: 23% Fold: Cysteine alpha-hairpin motif Superfamily: Cysteine alpha-hairpin motif Family: COX17-like Phyre2 PDB 2rnb chain A Region: 30 - 64 Aligned: 33 Modelled: 35 Confidence: 58.2% Identity: 21% PDB header:metal transport Chain: A: PDB Molecule:cytochrome c oxidase copper chaperone; PDBTitle: solution structure of human cu(i)cox17 Phyre2 PDB 2db7 chain A domain 1 Region: 30 - 64 Aligned: 35 Modelled: 35 Confidence: 44.1% Identity: 23% Fold: Orange domain-like Superfamily: Orange domain-like Family: Hairy Orange domain Phyre2 PDB 3qp5 chain C Region: 74 - 89 Aligned: 16 Modelled: 16 Confidence: 36.1% Identity: 13% PDB header:transcription Chain: C: PDB Molecule:cvir transcriptional regulator; PDBTitle: crystal structure of cvir bound to antagonist chlorolactone (cl) Phyre2 PDB 1yio chain A domain 1 Region: 48 - 89 Aligned: 42 Modelled: 42 Confidence: 29.4% Identity: 2% Fold: DNA/RNA-binding 3-helical bundle Superfamily: C-terminal effector domain of the bipartite response regulators Family: GerE-like (LuxR/UhpA family of transcriptional regulators) Phyre2 PDB 1h0m chain D Region: 74 - 89 Aligned: 16 Modelled: 16 Confidence: 28.5% Identity: 6% PDB header:transcription/dna Chain: D: PDB Molecule:transcriptional activator protein trar; PDBTitle: three-dimensional structure of the quorum sensing protein2 trar bound to its autoinducer and to its target dna Phyre2 PDB 1zlj chain E Region: 76 - 89 Aligned: 14 Modelled: 14 Confidence: 28.2% Identity: 14% PDB header:transcription Chain: E: PDB Molecule:dormancy survival regulator; PDBTitle: crystal structure of the mycobacterium tuberculosis hypoxic2 response regulator dosr c-terminal domain Phyre2 PDB 2q0o chain A Region: 74 - 89 Aligned: 16 Modelled: 16 Confidence: 26.5% Identity: 0% PDB header:transcription Chain: A: PDB Molecule:probable transcriptional activator protein trar; PDBTitle: crystal structure of an anti-activation complex in bacterial quorum2 sensing Phyre2 PDB 1ppj chain H Region: 17 - 40 Aligned: 22 Modelled: 24 Confidence: 24.4% Identity: 18% Fold: Non-heme 11 kDa protein of cytochrome bc1 complex (Ubiquinol-cytochrome c reductase) Superfamily: Non-heme 11 kDa protein of cytochrome bc1 complex (Ubiquinol-cytochrome c reductase) Family: Non-heme 11 kDa protein of cytochrome bc1 complex (Ubiquinol-cytochrome c reductase) Phyre2 PDB 1fse chain A Region: 74 - 89 Aligned: 16 Modelled: 16 Confidence: 23.1% Identity: 6% Fold: DNA/RNA-binding 3-helical bundle Superfamily: C-terminal effector domain of the bipartite response regulators Family: GerE-like (LuxR/UhpA family of transcriptional regulators) Phyre2 PDB 1a04 chain A domain 1 Region: 48 - 90 Aligned: 43 Modelled: 43 Confidence: 21.6% Identity: 9% Fold: DNA/RNA-binding 3-helical bundle Superfamily: C-terminal effector domain of the bipartite response regulators Family: GerE-like (LuxR/UhpA family of transcriptional regulators) Phyre2 PDB 1l0l chain H Region: 17 - 40 Aligned: 22 Modelled: 24 Confidence: 20.6% Identity: 18% Fold: Non-heme 11 kDa protein of cytochrome bc1 complex (Ubiquinol-cytochrome c reductase) Superfamily: Non-heme 11 kDa protein of cytochrome bc1 complex (Ubiquinol-cytochrome c reductase) Family: Non-heme 11 kDa protein of cytochrome bc1 complex (Ubiquinol-cytochrome c reductase) Phyre2 PDB 3szt chain B Region: 74 - 89 Aligned: 16 Modelled: 16 Confidence: 20.6% Identity: 6% PDB header:transcription Chain: B: PDB Molecule:quorum-sensing control repressor; PDBTitle: quorum sensing control repressor, qscr, bound to n-3-oxo-dodecanoyl-l-2 homoserine lactone Phyre2 PDB 2jpc chain A Region: 52 - 89 Aligned: 38 Modelled: 38 Confidence: 19.9% Identity: 3% PDB header:dna binding protein Chain: A: PDB Molecule:ssrb; PDBTitle: ssrb dna binding protein Phyre2 PDB 1p4w chain A Region: 76 - 89 Aligned: 14 Modelled: 14 Confidence: 18.2% Identity: 7% Fold: DNA/RNA-binding 3-helical bundle Superfamily: C-terminal effector domain of the bipartite response regulators Family: GerE-like (LuxR/UhpA family of transcriptional regulators) Phyre2 PDB 3u1d chain A Region: 73 - 88 Aligned: 16 Modelled: 16 Confidence: 17.2% Identity: 38% PDB header:structural genomics, unknown function Chain: A: PDB Molecule:uncharacterized protein; PDBTitle: the structure of a protein with a gntr superfamily winged-helix-turn-2 helix domain from halomicrobium mukohataei. Phyre2 PDB 3clo chain C Region: 74 - 89 Aligned: 16 Modelled: 16 Confidence: 16.8% Identity: 13% PDB header:transcription regulator Chain: C: PDB Molecule:transcriptional regulator; PDBTitle: crystal structure of putative transcriptional regulator containing a2 luxr dna binding domain (np_811094.1) from bacteroides3 thetaiotaomicron vpi-5482 at 2.04 a resolution Phyre2 1 c1ei0A_ 2 d2hp8a_ 3 c2k3jA_ 4 d1u97a_ 5 c2rnbA_ 6 d2db7a1 7 c3qp5C_ 8 d1yioa1 9 c1h0mD_ 10 c1zljE_ 11 c2q0oA_ 12 d1ppjh_ 13 d1fsea_ 14 d1a04a1 15 d1l0lh_ 16 c3sztB_ 17 c2jpcA_ 18 d1p4wa_ 19 c3u1dA_ 20 c3cloC_ 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69

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