Secondary structure and disorder prediction

		1	.	.	.	.	.	.	.	.	10	.	.	.	.	.	.	.	.	.	20	.	.	.	.	.	.	.	.	.	30	.	.	.	.	.	.	.	.	.	40	.	.	.	.	.	.	.	.	.	50	.	.	.	.	.	.	.	.	.	60
Sequence		M	S	I	I	K	E	F	R	E	F	A	M	R	G	N	V	V	D	L	A	V	G	V	I	I	G	A	A	F	G	K	I	V	S	S	L	V	A	D	I	I	M	P	P	L	G	L	L	I	G	G	I	D	F	K	Q	F	A	V	T
Secondary structure
SS confidence
Disorder		?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	70	.	.	.	.	.	.	.	.	.	80	.	.	.	.	.	.	.	.	.	90	.	.	.	.	.	.	.	.	.	100	.	.	.	.	.	.	.	.	.	110	.	.	.	.	.	.	.	.	.	120
Sequence		L	R	D	A	Q	G	D	I	P	A	V	V	M	H	Y	G	V	F	I	Q	N	V	F	D	F	L	I	V	A	F	A	I	F	M	A	I	K	L	I	N	K	L	N	R	K	K	E	E	P	A	A	A	P	A	P	T	K	E	E	V
Secondary structure
SS confidence
Disorder																																											?	?	?	?	?	?	?	?	?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	130	.	.	.	.	.	.
Sequence		L	L	T	E	I	R	D	L	L	K	E	Q	N	N	R	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 2oar chain A Region: 3 - 133 Aligned: 124 Modelled: 124 Confidence: 100.0% Identity: 36% PDB header:membrane protein Chain: A: PDB Molecule:large-conductance mechanosensitive channel; PDBTitle: mechanosensitive channel of large conductance (mscl) Phyre2 PDB 2oar chain A domain 1 Region: 12 - 126 Aligned: 108 Modelled: 115 Confidence: 100.0% Identity: 33% Fold: Gated mechanosensitive channel Superfamily: Gated mechanosensitive channel Family: Gated mechanosensitive channel Phyre2 PDB 3hzq chain A Region: 3 - 106 Aligned: 94 Modelled: 104 Confidence: 100.0% Identity: 50% PDB header:membrane protein Chain: A: PDB Molecule:large-conductance mechanosensitive channel; PDBTitle: structure of a tetrameric mscl in an expanded intermediate2 state Phyre2 PDB 3qnq chain D Region: 32 - 114 Aligned: 83 Modelled: 83 Confidence: 82.2% Identity: 14% PDB header:membrane protein, transport protein Chain: D: PDB Molecule:pts system, cellobiose-specific iic component; PDBTitle: crystal structure of the transporter chbc, the iic component from the2 n,n'-diacetylchitobiose-specific phosphotransferase system Phyre2 PDB 1q1v chain A Region: 109 - 133 Aligned: 25 Modelled: 25 Confidence: 35.3% Identity: 28% Fold: Another 3-helical bundle Superfamily: DEK C-terminal domain Family: DEK C-terminal domain Phyre2 PDB 1vdf chain B Region: 120 - 132 Aligned: 13 Modelled: 13 Confidence: 25.8% Identity: 38% PDB header:extracellular matrix protein Chain: B: PDB Molecule:cartilage oligomeric matrix protein; PDBTitle: assembly domain of cartilage oligomeric matrix protein Phyre2 PDB 3t98 chain A Region: 118 - 134 Aligned: 17 Modelled: 17 Confidence: 18.9% Identity: 41% 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 1lm8 chain V Region: 113 - 133 Aligned: 21 Modelled: 21 Confidence: 17.8% Identity: 38% Fold: Prealbumin-like Superfamily: VHL Family: VHL Phyre2 PDB 3n53 chain B Region: 114 - 133 Aligned: 20 Modelled: 20 Confidence: 13.9% Identity: 35% PDB header:transcription Chain: B: PDB Molecule:response regulator receiver modulated diguanylate cyclase; PDBTitle: crystal structure of a response regulator receiver modulated2 diguanylate cyclase from pelobacter carbinolicus Phyre2 PDB 1sh0 chain A Region: 26 - 42 Aligned: 17 Modelled: 17 Confidence: 12.6% Identity: 12% Fold: DNA/RNA polymerases Superfamily: DNA/RNA polymerases Family: RNA-dependent RNA-polymerase Phyre2 PDB 2uut chain A Region: 26 - 42 Aligned: 17 Modelled: 17 Confidence: 11.5% Identity: 29% PDB header:hydrolase Chain: A: PDB Molecule:rna-directed rna polymerase; PDBTitle: the 2.4 angstrom resolution structure of the d346g mutant2 of the sapporo virus rdrp polymerase Phyre2 PDB 2qzj chain C Region: 113 - 134 Aligned: 22 Modelled: 22 Confidence: 11.4% Identity: 23% PDB header:transcription Chain: C: PDB Molecule:two-component response regulator; PDBTitle: crystal structure of a two-component response regulator from2 clostridium difficile Phyre2 PDB 3snx chain B Region: 95 - 132 Aligned: 38 Modelled: 36 Confidence: 10.7% Identity: 16% PDB header:sugar binding protein Chain: B: PDB Molecule:putative susd-like carbohydrate binding protein; PDBTitle: crystal structure of a putative susd-like carbohydrate binding protein2 (bt_1439) from bacteroides thetaiotaomicron vpi-5482 at 1.88 a3 resolution Phyre2 PDB 1eys chain H Region: 82 - 117 Aligned: 36 Modelled: 36 Confidence: 10.6% Identity: 19% PDB header:electron transport Chain: H: PDB Molecule:photosynthetic reaction center; PDBTitle: crystal structure of photosynthetic reaction center from a2 thermophilic bacterium, thermochromatium tepidum Phyre2 PDB 2b43 chain D Region: 26 - 42 Aligned: 17 Modelled: 17 Confidence: 10.5% Identity: 12% PDB header:viral protein Chain: D: PDB Molecule:non-structural polyprotein; PDBTitle: crystal structure of the norwalk virus rna dependent rna polymerase2 from strain hu/nlv/dresden174/1997/ge Phyre2 PDB 2rdd chain B Region: 79 - 109 Aligned: 31 Modelled: 31 Confidence: 9.8% Identity: 6% PDB header:membrane protein/transport protein Chain: B: PDB Molecule:upf0092 membrane protein yajc; PDBTitle: x-ray crystal structure of acrb in complex with a novel2 transmembrane helix. Phyre2 PDB 1khv chain A Region: 26 - 42 Aligned: 17 Modelled: 17 Confidence: 9.1% Identity: 18% Fold: DNA/RNA polymerases Superfamily: DNA/RNA polymerases Family: RNA-dependent RNA-polymerase Phyre2 PDB 2l35 chain B Region: 76 - 95 Aligned: 20 Modelled: 20 Confidence: 8.4% Identity: 15% PDB header:protein binding Chain: B: PDB Molecule:tyro protein tyrosine kinase-binding protein; PDBTitle: structure of the dap12-nkg2c transmembrane heterotrimer Phyre2 PDB 2l34 chain B Region: 76 - 95 Aligned: 20 Modelled: 20 Confidence: 8.0% Identity: 15% PDB header:protein binding Chain: B: PDB Molecule:tyro protein tyrosine kinase-binding protein; PDBTitle: structure of the dap12 transmembrane homodimer Phyre2 PDB 2l34 chain A Region: 76 - 95 Aligned: 20 Modelled: 20 Confidence: 8.0% Identity: 15% PDB header:protein binding Chain: A: PDB Molecule:tyro protein tyrosine kinase-binding protein; PDBTitle: structure of the dap12 transmembrane homodimer Phyre2 1 c2oarA_ 2 d2oara1 3 c3hzqA_ 4 c3qnqD_ 5 d1q1va_ 6 c1vdfB_ 7 c3t98A_ 8 d1lm8v_ 9 c3n53B_ 10 d1sh0a_ 11 c2uutA_ 12 c2qzjC_ 13 c3snxB_ 14 c1eysH_ 15 c2b43D_ 16 c2rddB_ 17 d1khva_ 18 c2l35B_ 19 c2l34B_ 20 c2l34A_ 21 22 23 24 25 26 27 28 29 30 31

Detailed template information

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

1 c2oarA_ 100.0 36 PDB header:membrane protein Chain: A: PDB Molecule:large-conductance mechanosensitive channel; PDBTitle: mechanosensitive channel of large conductance (mscl) 2 d2oara1 100.0 33 Fold:Gated mechanosensitive channel Superfamily:Gated mechanosensitive channel Family:Gated mechanosensitive channel 3 c3hzqA_ 100.0 50 PDB header:membrane protein Chain: A: PDB Molecule:large-conductance mechanosensitive channel; PDBTitle: structure of a tetrameric mscl in an expanded intermediate2 state 4 c3qnqD_ 82.2 14 PDB header:membrane protein, transport protein Chain: D: PDB Molecule:pts system, cellobiose-specific iic component; PDBTitle: crystal structure of the transporter chbc, the iic component from the2 n,n'-diacetylchitobiose-specific phosphotransferase system 5 d1q1va_ 35.3 28 Fold:Another 3-helical bundle Superfamily:DEK C-terminal domain Family:DEK C-terminal domain 6 c1vdfB_ 25.8 38 PDB header:extracellular matrix protein Chain: B: PDB Molecule:cartilage oligomeric matrix protein; PDBTitle: assembly domain of cartilage oligomeric matrix protein 7 c3t98A_ 18.9 41 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 8 d1lm8v_ 17.8 38 Fold:Prealbumin-like Superfamily:VHL Family:VHL 9 c3n53B_ 13.9 35 PDB header:transcription Chain: B: PDB Molecule:response regulator receiver modulated diguanylate cyclase; PDBTitle: crystal structure of a response regulator receiver modulated2 diguanylate cyclase from pelobacter carbinolicus 10 d1sh0a_ 12.6 12 Fold:DNA/RNA polymerases Superfamily:DNA/RNA polymerases Family:RNA-dependent RNA-polymerase 11 c2uutA_ 11.5 29 PDB header:hydrolase Chain: A: PDB Molecule:rna-directed rna polymerase; PDBTitle: the 2.4 angstrom resolution structure of the d346g mutant2 of the sapporo virus rdrp polymerase 12 c2qzjC_ 11.4 23 PDB header:transcription Chain: C: PDB Molecule:two-component response regulator; PDBTitle: crystal structure of a two-component response regulator from2 clostridium difficile 13 c3snxB_ 10.7 16 PDB header:sugar binding protein Chain: B: PDB Molecule:putative susd-like carbohydrate binding protein; PDBTitle: crystal structure of a putative susd-like carbohydrate binding protein2 (bt_1439) from bacteroides thetaiotaomicron vpi-5482 at 1.88 a3 resolution 14 c1eysH_ 10.6 19 PDB header:electron transport Chain: H: PDB Molecule:photosynthetic reaction center; PDBTitle: crystal structure of photosynthetic reaction center from a2 thermophilic bacterium, thermochromatium tepidum 15 c2b43D_ 10.5 12 PDB header:viral protein Chain: D: PDB Molecule:non-structural polyprotein; PDBTitle: crystal structure of the norwalk virus rna dependent rna polymerase2 from strain hu/nlv/dresden174/1997/ge 16 c2rddB_ 9.8 6 PDB header:membrane protein/transport protein Chain: B: PDB Molecule:upf0092 membrane protein yajc; PDBTitle: x-ray crystal structure of acrb in complex with a novel2 transmembrane helix. 17 d1khva_ 9.1 18 Fold:DNA/RNA polymerases Superfamily:DNA/RNA polymerases Family:RNA-dependent RNA-polymerase 18 c2l35B_ 8.4 15 PDB header:protein binding Chain: B: PDB Molecule:tyro protein tyrosine kinase-binding protein; PDBTitle: structure of the dap12-nkg2c transmembrane heterotrimer 19 c2l34B_ 8.0 15 PDB header:protein binding Chain: B: PDB Molecule:tyro protein tyrosine kinase-binding protein; PDBTitle: structure of the dap12 transmembrane homodimer 20 c2l34A_ 8.0 15 PDB header:protein binding Chain: A: PDB Molecule:tyro protein tyrosine kinase-binding protein; PDBTitle: structure of the dap12 transmembrane homodimer 21 c3p5nA_ not modelled 7.4 18 PDB header:transport protein Chain: A: PDB Molecule:riboflavin uptake protein; PDBTitle: structure and mechanism of the s component of a bacterial ecf2 transporter 22 c2jo1A_ not modelled 6.6 26 PDB header:hydrolase regulator Chain: A: PDB Molecule:phospholemman; PDBTitle: structure of the na,k-atpase regulatory protein fxyd1 in2 micelles 23 c3nahC_ not modelled 6.5 24 PDB header:transferase Chain: C: PDB Molecule:rna dependent rna polymerase; PDBTitle: crystal structures and functional analysis of murine norovirus rna-2 dependent rna polymerase 24 c2jp3A_ not modelled 6.4 16 PDB header:transcription Chain: A: PDB Molecule:fxyd domain-containing ion transport regulator 4; PDBTitle: solution structure of the human fxyd4 (chif) protein in sds2 micelles 25 d1xr6a_ not modelled 6.2 24 Fold:DNA/RNA polymerases Superfamily:DNA/RNA polymerases Family:RNA-dependent RNA-polymerase 26 c1c94B_ not modelled 6.1 36 PDB header:gene regulation Chain: B: PDB Molecule:retro-gcn4 leucine zipper; PDBTitle: reversing the sequence of the gcn4 leucine zipper does not2 affect its fold. 27 d2b3wa1 not modelled 6.0 38 Fold:YbiA-like Superfamily:YbiA-like Family:YbiA-like 28 d1u09a_ not modelled 5.8 18 Fold:DNA/RNA polymerases Superfamily:DNA/RNA polymerases Family:RNA-dependent RNA-polymerase 29 c3si5X_ not modelled 5.8 38 PDB header:cell cycle Chain: X: PDB Molecule:protein casc5; PDBTitle: kinetochore-bubr1 kinase complex 30 c2ijd1_ not modelled 5.6 24 PDB header:hydrolase, transferase Chain: 1: PDB Molecule:picornain 3c, rna-directed rna polymerase; PDBTitle: crystal structure of the poliovirus precursor protein 3cd 31 d1xdpa1 not modelled 5.5 14 Fold:Spectrin repeat-like Superfamily:PPK N-terminal domain-like Family:PPK N-terminal domain-like

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