Email l.a.kelley@imperial.ac.uk Description O60200 Date Mon Jul 2 19:10:23 BST 2012 Unique Job ID 44205535b421e5f2

Summary

Top model

Image coloured by rainbow N → C terminus Close Jmol

Model (left) based on template d1l0lh_ Top template information 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) Confidence and coverage Confidence: 84.9% Coverage: 59% 51 residues ( 59% of your sequence) have been modelled with 84.9% 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. 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 1l0l chain H Region: 10 - 65 Aligned: 51 Modelled: 56 Confidence: 84.9% Identity: 10% 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 1ppj chain H Region: 10 - 65 Aligned: 51 Modelled: 56 Confidence: 83.2% Identity: 10% 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 3cx5 chain F Region: 10 - 65 Aligned: 55 Modelled: 56 Confidence: 82.4% Identity: 13% PDB header:oxidoreductase Chain: F: PDB Molecule:cytochrome b-c1 complex subunit 6; PDBTitle: structure of complex iii with bound cytochrome c in reduced2 state and definition of a minimal core interface for3 electron transfer. Phyre2 PDB 3cx5 chain F domain 1 Region: 10 - 65 Aligned: 55 Modelled: 56 Confidence: 82.4% Identity: 13% 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 1u97 chain A Region: 13 - 55 Aligned: 35 Modelled: 36 Confidence: 67.0% Identity: 29% Fold: Cysteine alpha-hairpin motif Superfamily: Cysteine alpha-hairpin motif Family: COX17-like Phyre2 PDB 2rnb chain A Region: 13 - 54 Aligned: 32 Modelled: 39 Confidence: 65.0% Identity: 38% PDB header:metal transport Chain: A: PDB Molecule:cytochrome c oxidase copper chaperone; PDBTitle: solution structure of human cu(i)cox17 Phyre2 PDB 2k3j chain A Region: 24 - 55 Aligned: 32 Modelled: 32 Confidence: 60.3% Identity: 19% PDB header:oxidoreductase Chain: A: PDB Molecule:mitochondrial intermembrane space import and PDBTitle: the solution structure of human mia40 Phyre2 PDB 2q00 chain B Region: 29 - 72 Aligned: 43 Modelled: 44 Confidence: 42.8% Identity: 21% PDB header:structural genomics, unknown function Chain: B: PDB Molecule:orf c02003 protein; PDBTitle: crystal structure of the p95883_sulso protein from2 sulfolobus solfataricus. nesg target ssr10. Phyre2 PDB 2p22 chain D Region: 24 - 33 Aligned: 10 Modelled: 10 Confidence: 27.5% Identity: 50% PDB header:transport protein Chain: D: PDB Molecule:hypothetical 12.0 kda protein in ade3-ser2 PDBTitle: structure of the yeast escrt-i heterotetramer core Phyre2 PDB 2nn6 chain B domain 2 Region: 42 - 62 Aligned: 21 Modelled: 21 Confidence: 17.0% Identity: 10% Fold: Ribonuclease PH domain 2-like Superfamily: Ribonuclease PH domain 2-like Family: Ribonuclease PH domain 2-like Phyre2 PDB 2jod chain A domain 1 Region: 5 - 26 Aligned: 21 Modelled: 22 Confidence: 15.7% Identity: 14% Fold: Hormone receptor domain Superfamily: Hormone receptor domain Family: Hormone receptor domain Phyre2 PDB 2nn6 chain F domain 2 Region: 42 - 62 Aligned: 21 Modelled: 21 Confidence: 13.9% Identity: 14% Fold: Ribonuclease PH domain 2-like Superfamily: Ribonuclease PH domain 2-like Family: Ribonuclease PH domain 2-like Phyre2 PDB 1c55 chain A Region: 6 - 27 Aligned: 22 Modelled: 22 Confidence: 12.2% Identity: 27% Fold: Knottins (small inhibitors, toxins, lectins) Superfamily: Scorpion toxin-like Family: Short-chain scorpion toxins Phyre2 PDB 4ab7 chain C Region: 25 - 59 Aligned: 32 Modelled: 35 Confidence: 11.4% Identity: 9% PDB header:transferase Chain: C: PDB Molecule:protein arg5,6, mitochondrial; PDBTitle: crystal structure of a tetrameric acetylglutamate kinase2 from saccharomyces cerevisiae complexed with its substrate3 n-acetylglutamate Phyre2 PDB 3fyb chain A Region: 22 - 30 Aligned: 9 Modelled: 7 Confidence: 10.0% Identity: 33% PDB header:structural genomics, unknown function Chain: A: PDB Molecule:protein of unknown function (duf1244); PDBTitle: crystal structure of a protein of unknown function (duf1244) from2 alcanivorax borkumensis Phyre2 PDB 2o35 chain A Region: 22 - 30 Aligned: 9 Modelled: 9 Confidence: 9.8% Identity: 44% PDB header:structural genomics, unknown function Chain: A: PDB Molecule:hypothetical protein duf1244; PDBTitle: protein of unknown function (duf1244) from sinorhizobium meliloti Phyre2 PDB 2o35 chain A domain 1 Region: 22 - 30 Aligned: 9 Modelled: 9 Confidence: 9.8% Identity: 44% Fold: SMc04008-like Superfamily: SMc04008-like Family: SMc04008-like Phyre2 PDB 1wgn chain A Region: 51 - 61 Aligned: 11 Modelled: 11 Confidence: 8.8% Identity: 45% Fold: RuvA C-terminal domain-like Superfamily: UBA-like Family: UBA domain Phyre2 PDB 1b33 chain N Region: 24 - 30 Aligned: 7 Modelled: 7 Confidence: 7.3% Identity: 29% Fold: Allophycocyanin linker chain (domain) Superfamily: Allophycocyanin linker chain (domain) Family: Allophycocyanin linker chain (domain) Phyre2 PDB 3fdq chain B Region: 30 - 66 Aligned: 37 Modelled: 37 Confidence: 7.2% Identity: 16% PDB header:dna binding protein/dna Chain: B: PDB Molecule:motility gene repressor mogr; PDBTitle: recognition of at-rich dna binding sites by the mogr2 repressor Phyre2 1 d1l0lh_ 2 d1ppjh_ 3 c3cx5F_ 4 d3cx5f1 5 d1u97a_ 6 c2rnbA_ 7 c2k3jA_ 8 c2q00B_ 9 c2p22D_ 10 d2nn6b2 11 d2joda1 12 d2nn6f2 13 d1c55a_ 14 c4ab7C_ 15 c3fybA_ 16 c2o35A_ 17 d2o35a1 18 d1wgna_ 19 d1b33n_ 20 c3fdqB_ 21 22 23 24 25 26 27 28 29 30 31

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