Email l.a.kelley@imperial.ac.uk Description P0A0I4 Date Tue Jul 17 17:05:06 BST 2012 Unique Job ID d62902ff64f127ca

Summary

Top model

Image coloured by rainbow N → C terminus Close Jmol

Model (left) based on template c2akhZ_ Top template information PDB header:protein transport Chain: Z: PDB Molecule:preprotein translocase sece subunit; PDBTitle: normal mode-based flexible fitted coordinates of a non-2 translocating secyeg protein-conducting channel into the3 cryo-em map of a secyeg-nascent chain-70s ribosome complex4 from e. coli Confidence and coverage Confidence: 99.8% Coverage: 97% 58 residues ( 97% of your sequence) have been modelled with 99.8% confidence by the single highest scoring template. 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 2akh chain Z Region: 3 - 60 Aligned: 58 Modelled: 58 Confidence: 99.8% Identity: 24% PDB header:protein transport Chain: Z: PDB Molecule:preprotein translocase sece subunit; PDBTitle: normal mode-based flexible fitted coordinates of a non-2 translocating secyeg protein-conducting channel into the3 cryo-em map of a secyeg-nascent chain-70s ribosome complex4 from e. coli Phyre2 PDB 3din chain D Region: 10 - 60 Aligned: 51 Modelled: 51 Confidence: 99.8% Identity: 27% PDB header:membrane protein, protein transport Chain: D: PDB Molecule:preprotein translocase subunit sece; PDBTitle: crystal structure of the protein-translocation complex formed by the2 secy channel and the seca atpase Phyre2 PDB 2zjs chain E Region: 12 - 56 Aligned: 45 Modelled: 45 Confidence: 98.9% Identity: 22% PDB header:protein transport/immune system Chain: E: PDB Molecule:preprotein translocase sece subunit; PDBTitle: crystal structure of secye translocon from thermus thermophilus with a2 fab fragment Phyre2 PDB 3dl8 chain D Region: 28 - 60 Aligned: 33 Modelled: 33 Confidence: 96.9% Identity: 24% PDB header:protein transport Chain: D: PDB Molecule:sece; PDBTitle: structure of the complex of aquifex aeolicus secyeg and2 bacillus subtilis seca Phyre2 PDB 1rhz chain B Region: 2 - 58 Aligned: 57 Modelled: 57 Confidence: 94.4% Identity: 16% Fold: Single transmembrane helix Superfamily: Preprotein translocase SecE subunit Family: Preprotein translocase SecE subunit Phyre2 PDB 2wwb chain B Region: 1 - 60 Aligned: 60 Modelled: 60 Confidence: 93.9% Identity: 13% PDB header:ribosome Chain: B: PDB Molecule:protein transport protein sec61 subunit gamma; PDBTitle: cryo-em structure of the mammalian sec61 complex bound to the2 actively translating wheat germ 80s ribosome Phyre2 PDB 2ww9 chain B Region: 1 - 58 Aligned: 58 Modelled: 58 Confidence: 93.4% Identity: 17% PDB header:ribosome Chain: B: PDB Molecule:protein transport protein sss1; PDBTitle: cryo-em structure of the active yeast ssh1 complex bound to the2 yeast 80s ribosome Phyre2 PDB 1rh5 chain B Region: 5 - 58 Aligned: 54 Modelled: 54 Confidence: 70.9% Identity: 17% Fold: Single transmembrane helix Superfamily: Preprotein translocase SecE subunit Family: Preprotein translocase SecE subunit Phyre2 PDB 3mp7 chain B Region: 4 - 51 Aligned: 48 Modelled: 48 Confidence: 61.4% Identity: 17% PDB header:protein transport Chain: B: PDB Molecule:preprotein translocase subunit sece; PDBTitle: lateral opening of a translocon upon entry of protein suggests the2 mechanism of insertion into membranes Phyre2 PDB 1yq3 chain C Region: 22 - 47 Aligned: 26 Modelled: 26 Confidence: 28.6% Identity: 12% PDB header:oxidoreductase Chain: C: PDB Molecule:succinate dehydrogenase cytochrome b, large subunit; PDBTitle: avian respiratory complex ii with oxaloacetate and ubiquinone Phyre2 PDB 2ehb chain D Region: 5 - 20 Aligned: 16 Modelled: 16 Confidence: 15.6% Identity: 31% PDB header:signalling protein/transferase Chain: D: PDB Molecule:cbl-interacting serine/threonine-protein kinase 24; PDBTitle: the structure of the c-terminal domain of the protein kinase atsos22 bound to the calcium sensor atsos3 Phyre2 PDB 1v0d chain A Region: 2 - 28 Aligned: 27 Modelled: 27 Confidence: 14.3% Identity: 11% Fold: His-Me finger endonucleases Superfamily: His-Me finger endonucleases Family: Caspase-activated DNase, CAD (DffB, DFF40) Phyre2 PDB 1v0d chain A Region: 2 - 28 Aligned: 27 Modelled: 27 Confidence: 14.3% Identity: 11% PDB header:hydrolase Chain: A: PDB Molecule:dna fragmentation factor 40 kda subunit; PDBTitle: crystal structure of caspase-activated dnase (cad) Phyre2 PDB 3fwb chain B Region: 2 - 24 Aligned: 23 Modelled: 23 Confidence: 12.4% Identity: 13% PDB header:cell cycle, transcription Chain: B: PDB Molecule:nuclear mrna export protein sac3; PDBTitle: sac3:sus1:cdc31 complex Phyre2 PDB 1qop chain A Region: 1 - 29 Aligned: 29 Modelled: 29 Confidence: 11.6% Identity: 24% Fold: TIM beta/alpha-barrel Superfamily: Ribulose-phoshate binding barrel Family: Tryptophan biosynthesis enzymes Phyre2 PDB 1jy1 chain A domain 2 Region: 17 - 29 Aligned: 13 Modelled: 13 Confidence: 11.2% Identity: 15% Fold: Phospholipase D/nuclease Superfamily: Phospholipase D/nuclease Family: Tyrosyl-DNA phosphodiesterase TDP1 Phyre2 PDB 2ekc chain A Region: 1 - 29 Aligned: 29 Modelled: 28 Confidence: 8.9% Identity: 31% PDB header:lyase Chain: A: PDB Molecule:tryptophan synthase alpha chain; PDBTitle: structural study of project id aq_1548 from aquifex aeolicus vf5 Phyre2 PDB 1xcf chain A Region: 1 - 28 Aligned: 28 Modelled: 28 Confidence: 8.3% Identity: 32% Fold: TIM beta/alpha-barrel Superfamily: Ribulose-phoshate binding barrel Family: Tryptophan biosynthesis enzymes Phyre2 PDB 3sq3 chain C Region: 17 - 29 Aligned: 13 Modelled: 13 Confidence: 8.0% Identity: 23% PDB header:hydrolase Chain: C: PDB Molecule:tyrosyl-dna phosphodiesterase 1; PDBTitle: crystal structure analysis of the yeast tyrosyl-dna phosphodiesterase2 h182a mutant Phyre2 PDB 2ysk chain A Region: 2 - 34 Aligned: 30 Modelled: 33 Confidence: 7.8% Identity: 13% PDB header:structural genomics, unknown function Chain: A: PDB Molecule:hypothetical protein ttha1432; PDBTitle: crystal structure of a hypothetical protein ttha1432 from thermus2 thermophilus Phyre2 1 c2akhZ_ 2 c3dinD_ 3 c2zjsE_ 4 c3dl8D_ 5 d1rhzb_ 6 c2wwbB_ 7 c2ww9B_ 8 d1rh5b_ 9 c3mp7B_ 10 c1yq3C_ 11 c2ehbD_ 12 d1v0da_ 13 c1v0dA_ 14 c3fwbB_ 15 d1qopa_ 16 d1jy1a2 17 c2ekcA_ 18 d1xcfa_ 19 c3sq3C_ 20 c2yskA_ 21 22 23 24 25 26

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