Secondary structure and disorder prediction

		1	.	.	.	.	.	.	.	.	10	.	.	.	.	.	.	.	.	.	20	.	.	.	.	.	.	.	.	.	30	.	.	.	.	.	.	.	.	.	40	.	.	.	.	.	.	.	.	.	50	.	.	.	.	.	.	.	.	.	60
Sequence		M	K	R	K	N	A	S	L	L	G	N	V	L	M	G	L	G	L	V	V	M	V	V	G	V	G	Y	S	I	L	N	Q	L	P	Q	F	N	M	P	Q	Y	F	A	H	G	A	V	L	S	I	F	V	G	A	I	L	W	L	A	G
Secondary structure
SS confidence
Disorder		?	?	?	?	?	?	?																									?
Disorder confidence
		.	.	.	.	.	.	.	.	.	70	.	.	.	.	.	.	.	.	.	80	.	.	.	.	.	.	.	.	.	90	.	.
Sequence		A	R	V	G	G	H	E	Q	V	C	D	R	Y	W	W	V	R	H	Y	D	K	R	C	R	R	S	D	N	R	R	H	S
Secondary structure
SS confidence
Disorder			?		?	?	?	?																?	?	?	?	?	?	?	?	?	?
Disorder confidence

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 3hef chain B Region: 66 - 92 Aligned: 27 Modelled: 27 Confidence: 39.5% Identity: 11% PDB header:viral protein Chain: B: PDB Molecule:gene 1 protein; PDBTitle: crystal structure of the bacteriophage sf6 terminase small2 subunit Phyre2 PDB 1v54 chain J Region: 8 - 39 Aligned: 31 Modelled: 32 Confidence: 25.2% Identity: 23% Fold: Single transmembrane helix Superfamily: Mitochondrial cytochrome c oxidase subunit VIIa Family: Mitochondrial cytochrome c oxidase subunit VIIa Phyre2 PDB 2y69 chain W Region: 8 - 40 Aligned: 32 Modelled: 33 Confidence: 21.7% Identity: 22% PDB header:electron transport Chain: W: PDB Molecule:cytochrome c oxidase polypeptide 7a1; PDBTitle: bovine heart cytochrome c oxidase re-refined with molecular2 oxygen Phyre2 PDB 1ulv chain A domain 1 Region: 39 - 74 Aligned: 33 Modelled: 36 Confidence: 17.4% Identity: 30% Fold: alpha/alpha toroid Superfamily: Six-hairpin glycosidases Family: Bacterial glucoamylase C-terminal domain-like Phyre2 PDB 2qts chain A Region: 32 - 54 Aligned: 23 Modelled: 23 Confidence: 16.6% Identity: 22% PDB header:membrane protein Chain: A: PDB Molecule:acid-sensing ion channel; PDBTitle: structure of an acid-sensing ion channel 1 at 1.9 a resolution and low2 ph Phyre2 PDB 1ijd chain A Region: 34 - 56 Aligned: 23 Modelled: 23 Confidence: 15.2% Identity: 26% Fold: Light-harvesting complex subunits Superfamily: Light-harvesting complex subunits Family: Light-harvesting complex subunits Phyre2 PDB 1nkz chain A Region: 34 - 56 Aligned: 23 Modelled: 23 Confidence: 12.8% Identity: 22% Fold: Light-harvesting complex subunits Superfamily: Light-harvesting complex subunits Family: Light-harvesting complex subunits Phyre2 PDB 1h2s chain B Region: 50 - 61 Aligned: 12 Modelled: 12 Confidence: 12.6% Identity: 67% Fold: Transmembrane helix hairpin Superfamily: Htr2 transmembrane domain-like Family: Htr2 transmembrane domain-like Phyre2 PDB 1h2s chain B Region: 50 - 61 Aligned: 12 Modelled: 12 Confidence: 12.6% Identity: 67% PDB header:membrane protein Chain: B: PDB Molecule:sensory rhodopsin ii transducer; PDBTitle: molecular basis of transmenbrane signalling by sensory2 rhodopsin ii-transducer complex Phyre2 PDB 1s21 chain A Region: 61 - 77 Aligned: 17 Modelled: 17 Confidence: 11.9% Identity: 18% Fold: ADP-ribosylation Superfamily: ADP-ribosylation Family: AvrPphF ORF2, a type III effector Phyre2 PDB 1s21 chain A Region: 61 - 77 Aligned: 17 Modelled: 17 Confidence: 11.9% Identity: 18% PDB header:chaperone Chain: A: PDB Molecule:orf2; PDBTitle: crystal structure of avrpphf orf2, a type iii effector from2 p. syringae Phyre2 PDB 2j5d chain A Region: 33 - 53 Aligned: 19 Modelled: 21 Confidence: 11.5% Identity: 37% PDB header:membrane protein Chain: A: PDB Molecule:bcl2/adenovirus e1b 19 kda protein-interacting PDBTitle: nmr structure of bnip3 transmembrane domain in lipid2 bicelles Phyre2 PDB 2f95 chain B Region: 50 - 61 Aligned: 12 Modelled: 12 Confidence: 11.4% Identity: 67% PDB header:membrane protein Chain: B: PDB Molecule:sensory rhodopsin ii transducer; PDBTitle: m intermediate structure of sensory rhodopsin ii/transducer complex in2 combination with the ground state structure Phyre2 PDB 3ij4 chain A Region: 32 - 54 Aligned: 23 Modelled: 23 Confidence: 10.7% Identity: 22% PDB header:transport protein Chain: A: PDB Molecule:amiloride-sensitive cation channel 2, neuronal; PDBTitle: cesium sites in the crystal structure of a functional acid2 sensing ion channel in the desensitized state Phyre2 PDB 1q90 chain L Region: 41 - 60 Aligned: 20 Modelled: 20 Confidence: 10.4% Identity: 15% PDB header:photosynthesis Chain: L: PDB Molecule:cytochrome b6f complex subunit petl; PDBTitle: structure of the cytochrome b6f (plastohydroquinone : plastocyanin2 oxidoreductase) from chlamydomonas reinhardtii Phyre2 PDB 1q90 chain L Region: 41 - 60 Aligned: 20 Modelled: 20 Confidence: 10.4% Identity: 15% Fold: Single transmembrane helix Superfamily: PetL subunit of the cytochrome b6f complex Family: PetL subunit of the cytochrome b6f complex Phyre2 PDB 3dl8 chain D Region: 47 - 59 Aligned: 13 Modelled: 13 Confidence: 8.9% Identity: 31% PDB header:protein transport Chain: D: PDB Molecule:sece; PDBTitle: structure of the complex of aquifex aeolicus secyeg and2 bacillus subtilis seca Phyre2 PDB 3eps chain B Region: 65 - 92 Aligned: 28 Modelled: 28 Confidence: 8.9% Identity: 21% PDB header:transferase, hydrolase Chain: B: PDB Molecule:isocitrate dehydrogenase kinase/phosphatase; PDBTitle: the crystal structure of isocitrate dehydrogenase kinase/phosphatase2 from e. coli Phyre2 PDB 1t3t chain A domain 5 Region: 66 - 81 Aligned: 16 Modelled: 16 Confidence: 7.5% Identity: 19% Fold: Bacillus chorismate mutase-like Superfamily: PurM N-terminal domain-like Family: PurM N-terminal domain-like Phyre2 PDB 1cf7 chain B Region: 11 - 19 Aligned: 9 Modelled: 9 Confidence: 6.6% Identity: 44% Fold: DNA/RNA-binding 3-helical bundle Superfamily: "Winged helix" DNA-binding domain Family: Cell cycle transcription factor e2f-dp Phyre2 1 c3hefB_ 2 d1v54j_ 3 c2y69W_ 4 d1ulva1 5 c2qtsA_ 6 d1ijda_ 7 d1nkza_ 8 d1h2sb_ 9 c1h2sB_ 10 d1s21a_ 11 c1s21A_ 12 c2j5dA_ 13 c2f95B_ 14 c3ij4A_ 15 c1q90L_ 16 d1q90l_ 17 c3dl8D_ 18 c3epsB_ 19 d1t3ta5 20 d1cf7b_ 21 22 23 24

Detailed template information

# Template Alignment Coverage 3D Model Confidence % i.d. Template Information

1 c3hefB_ 39.5 11 PDB header:viral protein Chain: B: PDB Molecule:gene 1 protein; PDBTitle: crystal structure of the bacteriophage sf6 terminase small2 subunit 2 d1v54j_ 25.2 23 Fold:Single transmembrane helix Superfamily:Mitochondrial cytochrome c oxidase subunit VIIa Family:Mitochondrial cytochrome c oxidase subunit VIIa 3 c2y69W_ 21.7 22 PDB header:electron transport Chain: W: PDB Molecule:cytochrome c oxidase polypeptide 7a1; PDBTitle: bovine heart cytochrome c oxidase re-refined with molecular2 oxygen 4 d1ulva1 17.4 30 Fold:alpha/alpha toroid Superfamily:Six-hairpin glycosidases Family:Bacterial glucoamylase C-terminal domain-like 5 c2qtsA_ 16.6 22 PDB header:membrane protein Chain: A: PDB Molecule:acid-sensing ion channel; PDBTitle: structure of an acid-sensing ion channel 1 at 1.9 a resolution and low2 ph 6 d1ijda_ 15.2 26 Fold:Light-harvesting complex subunits Superfamily:Light-harvesting complex subunits Family:Light-harvesting complex subunits 7 d1nkza_ 12.8 22 Fold:Light-harvesting complex subunits Superfamily:Light-harvesting complex subunits Family:Light-harvesting complex subunits 8 d1h2sb_ 12.6 67 Fold:Transmembrane helix hairpin Superfamily:Htr2 transmembrane domain-like Family:Htr2 transmembrane domain-like 9 c1h2sB_ 12.6 67 PDB header:membrane protein Chain: B: PDB Molecule:sensory rhodopsin ii transducer; PDBTitle: molecular basis of transmenbrane signalling by sensory2 rhodopsin ii-transducer complex 10 d1s21a_ 11.9 18 Fold:ADP-ribosylation Superfamily:ADP-ribosylation Family:AvrPphF ORF2, a type III effector 11 c1s21A_ 11.9 18 PDB header:chaperone Chain: A: PDB Molecule:orf2; PDBTitle: crystal structure of avrpphf orf2, a type iii effector from2 p. syringae 12 c2j5dA_ 11.5 37 PDB header:membrane protein Chain: A: PDB Molecule:bcl2/adenovirus e1b 19 kda protein-interacting PDBTitle: nmr structure of bnip3 transmembrane domain in lipid2 bicelles 13 c2f95B_ 11.4 67 PDB header:membrane protein Chain: B: PDB Molecule:sensory rhodopsin ii transducer; PDBTitle: m intermediate structure of sensory rhodopsin ii/transducer complex in2 combination with the ground state structure 14 c3ij4A_ 10.7 22 PDB header:transport protein Chain: A: PDB Molecule:amiloride-sensitive cation channel 2, neuronal; PDBTitle: cesium sites in the crystal structure of a functional acid2 sensing ion channel in the desensitized state 15 c1q90L_ 10.4 15 PDB header:photosynthesis Chain: L: PDB Molecule:cytochrome b6f complex subunit petl; PDBTitle: structure of the cytochrome b6f (plastohydroquinone : plastocyanin2 oxidoreductase) from chlamydomonas reinhardtii 16 d1q90l_ 10.4 15 Fold:Single transmembrane helix Superfamily:PetL subunit of the cytochrome b6f complex Family:PetL subunit of the cytochrome b6f complex 17 c3dl8D_ 8.9 31 PDB header:protein transport Chain: D: PDB Molecule:sece; PDBTitle: structure of the complex of aquifex aeolicus secyeg and2 bacillus subtilis seca 18 c3epsB_ 8.9 21 PDB header:transferase, hydrolase Chain: B: PDB Molecule:isocitrate dehydrogenase kinase/phosphatase; PDBTitle: the crystal structure of isocitrate dehydrogenase kinase/phosphatase2 from e. coli 19 d1t3ta5 7.5 19 Fold:Bacillus chorismate mutase-like Superfamily:PurM N-terminal domain-like Family:PurM N-terminal domain-like 20 d1cf7b_ 6.6 44 Fold:DNA/RNA-binding 3-helical bundle Superfamily:"Winged helix" DNA-binding domain Family:Cell cycle transcription factor e2f-dp 21 c2jh9A_ not modelled 6.3 44 PDB header:viral protein Chain: A: PDB Molecule:vp4 core protein; PDBTitle: the structure of bluetongue virus vp4 reveals a2 multifunctional rna-capping production-line 22 c2ve7A_ not modelled 5.9 23 PDB header:cell cycle Chain: A: PDB Molecule:kinetochore protein hec1, kinetochore protein spc25; PDBTitle: crystal structure of a bonsai version of the human ndc802 complex 23 c1spfA_ not modelled 5.8 50 PDB header:lipoprotein(surface film) Chain: A: PDB Molecule:pulmonary surfactant-associated polypeptide c; PDBTitle: the nmr structure of the pulmonary surfactant-associated2 polypeptide sp-c in an apolar solvent contains a valyl-3 rich alpha-helix 24 c2v0xB_ not modelled 5.7 29 PDB header:cell cycle Chain: B: PDB Molecule:lamina-associated polypeptide 2 isoforms PDBTitle: the dimerization domain of lap2alpha

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

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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