Email l.a.kelley@imperial.ac.uk Description C6Y4C1 Date Sun Jul 8 11:45:08 BST 2012 Unique Job ID 5337bd441a2d6535

Summary

Top model

Image coloured by rainbow N → C terminus Close Jmol

Model (left) based on template c1l4aE_ Top template information PDB header:endocytosis/exocytosis Chain: E: PDB Molecule:synaphin a; PDBTitle: x-ray structure of the neuronal complexin/snare complex2 from the squid loligo pealei Confidence and coverage Confidence: 24.6% Coverage: 17% 15 residues ( 17% of your sequence) have been modelled with 24.6% 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 1l4a chain E Region: 24 - 38 Aligned: 15 Modelled: 15 Confidence: 24.6% Identity: 33% PDB header:endocytosis/exocytosis Chain: E: PDB Molecule:synaphin a; PDBTitle: x-ray structure of the neuronal complexin/snare complex2 from the squid loligo pealei Phyre2 PDB 1kil chain E Region: 24 - 38 Aligned: 15 Modelled: 15 Confidence: 21.3% Identity: 33% PDB header:membrane protein Chain: E: PDB Molecule:complexin i snare-complex binding region; PDBTitle: three-dimensional structure of the complexin/snare complex Phyre2 PDB 3rl0 chain J Region: 24 - 38 Aligned: 15 Modelled: 15 Confidence: 18.4% Identity: 27% PDB header:membrane protein/exocytosis Chain: J: PDB Molecule:syntaxin-1a; PDBTitle: truncated snare complex with complexin (p1) Phyre2 PDB 3bhp chain A Region: 53 - 67 Aligned: 15 Modelled: 15 Confidence: 18.1% Identity: 40% PDB header:structural genomics, unknown function Chain: A: PDB Molecule:upf0291 protein ynzc; PDBTitle: crystal structure of upf0291 protein ynzc from bacillus2 subtilis at resolution 2.0 a. northeast structural3 genomics consortium target sr384 Phyre2 PDB 1dxz chain A Region: 6 - 23 Aligned: 18 Modelled: 18 Confidence: 15.4% Identity: 17% PDB header:transmembrane protein Chain: A: PDB Molecule:acetylcholine receptor protein, alpha chain; PDBTitle: m2 transmembrane segment of alpha-subunit of nicotinic2 acetylcholine receptor from torpedo californica, nmr, 203 structures Phyre2 PDB 2jvd chain A Region: 53 - 67 Aligned: 15 Modelled: 15 Confidence: 14.1% Identity: 40% PDB header:structural genomics, unknown function Chain: A: PDB Molecule:upf0291 protein ynzc; PDBTitle: solution nmr structure of the folded n-terminal fragment of2 upf0291 protein ynzc from bacillus subtilis. northeast3 structural genomics target sr384-1-46 Phyre2 PDB 1u58 chain A domain 2 Region: 50 - 81 Aligned: 32 Modelled: 32 Confidence: 13.0% Identity: 16% Fold: MHC antigen-recognition domain Superfamily: MHC antigen-recognition domain Family: MHC antigen-recognition domain Phyre2 PDB 2hep chain A Region: 53 - 67 Aligned: 15 Modelled: 15 Confidence: 10.8% Identity: 40% PDB header:structural genomics, unknown function Chain: A: PDB Molecule:upf0291 protein ynzc; PDBTitle: solution nmr structure of the upf0291 protein ynzc from2 bacillus subtilis. northeast structural genomics target3 sr384. Phyre2 PDB 2hep chain A domain 1 Region: 53 - 67 Aligned: 15 Modelled: 15 Confidence: 10.8% Identity: 40% Fold: Long alpha-hairpin Superfamily: YnzC-like Family: YznC-like Phyre2 PDB 1vry chain A Region: 4 - 22 Aligned: 19 Modelled: 19 Confidence: 9.9% Identity: 5% PDB header:membrane protein Chain: A: PDB Molecule:glycine receptor alpha-1 chain; PDBTitle: second and third transmembrane domains of the alpha-12 subunit of human glycine receptor Phyre2 PDB 1gak chain A Region: 22 - 44 Aligned: 23 Modelled: 23 Confidence: 9.3% Identity: 22% Fold: Fertilization protein Superfamily: Fertilization protein Family: Fertilization protein Phyre2 PDB 3t98 chain A Region: 24 - 42 Aligned: 19 Modelled: 19 Confidence: 9.0% Identity: 32% PDB header:protein transport Chain: A: PDB Molecule:nuclear pore complex protein nup54; PDBTitle: molecular architecture of the transport channel of the nuclear pore2 complex: nup54/nup58 Phyre2 PDB 1b9x chain C Region: 36 - 58 Aligned: 23 Modelled: 23 Confidence: 8.6% Identity: 17% PDB header:signaling protein Chain: C: PDB Molecule:protein (phosducin); PDBTitle: structural analysis of phosducin and its phosphorylation-2 regulated interaction with transducin Phyre2 PDB 1wgn chain A Region: 35 - 55 Aligned: 21 Modelled: 21 Confidence: 7.2% Identity: 19% Fold: RuvA C-terminal domain-like Superfamily: UBA-like Family: UBA domain Phyre2 PDB 3cyo chain A Region: 19 - 57 Aligned: 39 Modelled: 39 Confidence: 7.2% Identity: 10% PDB header:viral protein Chain: A: PDB Molecule:transmembrane protein; PDBTitle: structure of a longer thermalstable core domain of hiv-12 gp41 containing the enfuvirtide resistance mutation n43d3 and complementary mutation e137k Phyre2 PDB 1v54 chain D Region: 6 - 24 Aligned: 19 Modelled: 19 Confidence: 7.1% Identity: 16% Fold: Single transmembrane helix Superfamily: Mitochondrial cytochrome c oxidase subunit IV Family: Mitochondrial cytochrome c oxidase subunit IV Phyre2 PDB 1gyg chain A Region: 4 - 23 Aligned: 20 Modelled: 20 Confidence: 6.5% Identity: 15% PDB header:hydrolase Chain: A: PDB Molecule:phospholipase c; PDBTitle: r32 closed form of alpha-toxin from clostridium perfringens2 strain cer89l43 Phyre2 PDB 1oed chain E Region: 2 - 23 Aligned: 22 Modelled: 22 Confidence: 6.4% Identity: 9% Fold: Neurotransmitter-gated ion-channel transmembrane pore Superfamily: Neurotransmitter-gated ion-channel transmembrane pore Family: Neurotransmitter-gated ion-channel transmembrane pore Phyre2 PDB 1v54 chain I Region: 6 - 47 Aligned: 42 Modelled: 42 Confidence: 6.3% Identity: 31% Fold: Single transmembrane helix Superfamily: Mitochondrial cytochrome c oxidase subunit VIc Family: Mitochondrial cytochrome c oxidase subunit VIc Phyre2 PDB 2trc chain P Region: 36 - 44 Aligned: 9 Modelled: 9 Confidence: 5.8% Identity: 33% Fold: Thioredoxin fold Superfamily: Thioredoxin-like Family: Phosducin Phyre2 1 c1l4aE_ 2 c1kilE_ 3 c3rl0j_ 4 c3bhpA_ 5 c1dxzA_ 6 c2jvdA_ 7 d1u58a2 8 c2hepA_ 9 d2hepa1 10 c1vryA_ 11 d1gaka_ 12 c3t98A_ 13 c1b9xC_ 14 d1wgna_ 15 c3cyoA_ 16 d1v54d_ 17 c1gygA_ 18 d1oede_ 19 d1v54i_ 20 d2trcp_ 21 22 23 24 25

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