Secondary structure and disorder prediction

		1	.	.	.	.	.	.	.	.	10	.	.	.	.	.	.	.	.	.	20	.	.	.	.	.	.	.	.	.	30	.	.	.	.	.	.	.	.	.	40	.	.	.	.	.	.	.	.	.	50	.	.	.	.	.	.	.	.	.	60
Sequence		M	I	Q	K	I	N	I	L	D	S	S	Q	S	G	V	K	N	G	A	D	S	E	A	V	L	A	A	L	I	E	H	L	E	L	I	N	P	S	G	R	L	S	Q	N	T	R	S	A	M	L	Q	L	R	E	E	E	W	S	E	F
Secondary structure
SS confidence
Disorder		?	?	?	?	?	?	?			?	?	?	?	?	?	?	?	?	?																		?		?	?	?	?	?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	70	.	.	.	.	.	.	.	.	.	80	.	.	.	.	.	.	.	.	.	90	.	.	.	.	.	.	.	.	.	100	.	.	.	.	.	.	.	.	.	110	.	.	.	.	.	.	.	.	.	120
Sequence		F	F	W	L	L	N	S	L	E	C	L	D	Y	V	I	I	N	L	T	P	E	S	K	K	T	L	M	S	E	H	R	N	N	I	Q	V	A	I	D	A	L	Y	S	Q	R	R	R	K	S	P	G	D	E	S	E	T	L	T	R	R
Secondary structure
SS confidence
Disorder																														?	?														?	?	?	?	?	?	?	?	?	?	?	?	?	?	?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	130	.	.	.	.	.	.	.	.	.	140	.	.	.	.	.	.
Sequence		N	D	A	I	F	G	N	H	V	W	Q	T	F	A	Q	Y	F	P	P	G	L	E	K	P	S	V
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 3k64 chain A Region: 125 - 139 Aligned: 15 Modelled: 15 Confidence: 39.0% Identity: 33% PDB header:rna/rna binding protein Chain: A: PDB Molecule:fem-3 mrna-binding factor 2; PDBTitle: crystal structure of fbf-2/fem-3 pme complex Phyre2 PDB 3geb chain C Region: 36 - 75 Aligned: 40 Modelled: 40 Confidence: 17.4% Identity: 33% PDB header:hydrolase Chain: C: PDB Molecule:eyes absent homolog 2; PDBTitle: crystal structure of edeya2 Phyre2 PDB 1trr chain A Region: 48 - 86 Aligned: 39 Modelled: 39 Confidence: 17.3% Identity: 36% Fold: DNA/RNA-binding 3-helical bundle Superfamily: TrpR-like Family: Trp repressor, TrpR Phyre2 PDB 1f44 chain A domain 1 Region: 21 - 64 Aligned: 37 Modelled: 44 Confidence: 17.1% Identity: 19% Fold: SAM domain-like Superfamily: lambda integrase-like, N-terminal domain Family: lambda integrase-like, N-terminal domain Phyre2 PDB 3v71 chain A Region: 125 - 139 Aligned: 15 Modelled: 15 Confidence: 14.0% Identity: 27% PDB header:rna binding protein/rna Chain: A: PDB Molecule:puf (pumilio/fbf) domain-containing protein 7, confirmed by PDBTitle: crystal structure of puf-6 in complex with 5be13 rna Phyre2 PDB 2r4g chain A Region: 29 - 68 Aligned: 40 Modelled: 40 Confidence: 12.8% Identity: 5% PDB header:transferase Chain: A: PDB Molecule:telomerase reverse transcriptase; PDBTitle: the high resolution structure of the rna-binding domain of telomerase Phyre2 PDB 1a2x chain B Region: 43 - 56 Aligned: 14 Modelled: 14 Confidence: 12.3% Identity: 43% PDB header:complex (skeletal muscle/muscle protein) Chain: B: PDB Molecule:troponin i; PDBTitle: complex of troponin c with a 47 residue (1-47) fragment of2 troponin i Phyre2 PDB 2az0 chain A domain 1 Region: 82 - 146 Aligned: 63 Modelled: 65 Confidence: 12.1% Identity: 29% Fold: ROP-like Superfamily: FHV B2 protein-like Family: FHV B2 protein-like Phyre2 PDB 3k49 chain C Region: 125 - 139 Aligned: 15 Modelled: 15 Confidence: 11.4% Identity: 40% PDB header:rna binding protein / rna Chain: C: PDB Molecule:mrna-binding protein puf3; PDBTitle: puf3 rna binding domain bound to cox17 rna 3' utr recognition sequence2 site b Phyre2 PDB 1wjo chain A Region: 60 - 138 Aligned: 73 Modelled: 79 Confidence: 10.0% Identity: 12% Fold: CH domain-like Superfamily: Calponin-homology domain, CH-domain Family: Calponin-homology domain, CH-domain Phyre2 PDB 1u0j chain A Region: 52 - 63 Aligned: 12 Modelled: 12 Confidence: 9.0% Identity: 33% Fold: P-loop containing nucleoside triphosphate hydrolases Superfamily: P-loop containing nucleoside triphosphate hydrolases Family: Extended AAA-ATPase domain Phyre2 PDB 1jrj chain A Region: 51 - 67 Aligned: 17 Modelled: 17 Confidence: 9.0% Identity: 41% PDB header:hormone/growth factor Chain: A: PDB Molecule:exendin-4; PDBTitle: solution structure of exendin-4 in 30-vol% trifluoroethanol Phyre2 PDB 1ity chain A Region: 105 - 140 Aligned: 36 Modelled: 36 Confidence: 8.9% Identity: 17% Fold: DNA/RNA-binding 3-helical bundle Superfamily: Homeodomain-like Family: DNA-binding domain of telomeric protein Phyre2 PDB 3vub chain A Region: 88 - 103 Aligned: 16 Modelled: 16 Confidence: 8.6% Identity: 31% Fold: SH3-like barrel Superfamily: Cell growth inhibitor/plasmid maintenance toxic component Family: CcdB Phyre2 PDB 2end chain A Region: 76 - 112 Aligned: 37 Modelled: 37 Confidence: 8.3% Identity: 32% Fold: T4 endonuclease V Superfamily: T4 endonuclease V Family: T4 endonuclease V Phyre2 PDB 1mxa chain A domain 2 Region: 34 - 41 Aligned: 8 Modelled: 8 Confidence: 7.4% Identity: 63% Fold: S-adenosylmethionine synthetase Superfamily: S-adenosylmethionine synthetase Family: S-adenosylmethionine synthetase Phyre2 PDB 1a8d chain A domain 2 Region: 106 - 125 Aligned: 20 Modelled: 20 Confidence: 6.9% Identity: 25% Fold: beta-Trefoil Superfamily: STI-like Family: Clostridium neurotoxins, C-terminal domain Phyre2 PDB 3jrz chain A Region: 88 - 103 Aligned: 16 Modelled: 16 Confidence: 6.8% Identity: 50% PDB header:toxin Chain: A: PDB Molecule:ccdb; PDBTitle: ccdbvfi-formii-ph5.6 Phyre2 PDB 1jhg chain A Region: 48 - 67 Aligned: 20 Modelled: 20 Confidence: 6.8% Identity: 40% Fold: DNA/RNA-binding 3-helical bundle Superfamily: TrpR-like Family: Trp repressor, TrpR Phyre2 PDB 1d0r chain A Region: 51 - 67 Aligned: 17 Modelled: 17 Confidence: 6.7% Identity: 29% PDB header:hormone/growth factor Chain: A: PDB Molecule:glucagon-like peptide-1-(7-36)-amide; PDBTitle: solution structure of glucagon-like peptide-1-(7-36)-amide2 in trifluoroethanol/water Phyre2 1 c3k64A_ 2 c3gebC_ 3 d1trra_ 4 d1f44a1 5 c3v71A_ 6 c2r4gA_ 7 c1a2xB_ 8 d2az0a1 9 c3k49C_ 10 d1wjoa_ 11 d1u0ja_ 12 c1jrjA_ 13 d1itya_ 14 d3vuba_ 15 d2enda_ 16 d1mxaa2 17 d1a8da2 18 c3jrzA_ 19 d1jhga_ 20 c1d0rA_ 21 22 23 24 25 26 27

Detailed template information

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

1 c3k64A_ 39.0 33 PDB header:rna/rna binding protein Chain: A: PDB Molecule:fem-3 mrna-binding factor 2; PDBTitle: crystal structure of fbf-2/fem-3 pme complex 2 c3gebC_ 17.4 33 PDB header:hydrolase Chain: C: PDB Molecule:eyes absent homolog 2; PDBTitle: crystal structure of edeya2 3 d1trra_ 17.3 36 Fold:DNA/RNA-binding 3-helical bundle Superfamily:TrpR-like Family:Trp repressor, TrpR 4 d1f44a1 17.1 19 Fold:SAM domain-like Superfamily:lambda integrase-like, N-terminal domain Family:lambda integrase-like, N-terminal domain 5 c3v71A_ 14.0 27 PDB header:rna binding protein/rna Chain: A: PDB Molecule:puf (pumilio/fbf) domain-containing protein 7, confirmed by PDBTitle: crystal structure of puf-6 in complex with 5be13 rna 6 c2r4gA_ 12.8 5 PDB header:transferase Chain: A: PDB Molecule:telomerase reverse transcriptase; PDBTitle: the high resolution structure of the rna-binding domain of telomerase 7 c1a2xB_ 12.3 43 PDB header:complex (skeletal muscle/muscle protein) Chain: B: PDB Molecule:troponin i; PDBTitle: complex of troponin c with a 47 residue (1-47) fragment of2 troponin i 8 d2az0a1 12.1 29 Fold:ROP-like Superfamily:FHV B2 protein-like Family:FHV B2 protein-like 9 c3k49C_ 11.4 40 PDB header:rna binding protein / rna Chain: C: PDB Molecule:mrna-binding protein puf3; PDBTitle: puf3 rna binding domain bound to cox17 rna 3' utr recognition sequence2 site b 10 d1wjoa_ 10.0 12 Fold:CH domain-like Superfamily:Calponin-homology domain, CH-domain Family:Calponin-homology domain, CH-domain 11 d1u0ja_ 9.0 33 Fold:P-loop containing nucleoside triphosphate hydrolases Superfamily:P-loop containing nucleoside triphosphate hydrolases Family:Extended AAA-ATPase domain 12 c1jrjA_ 9.0 41 PDB header:hormone/growth factor Chain: A: PDB Molecule:exendin-4; PDBTitle: solution structure of exendin-4 in 30-vol% trifluoroethanol 13 d1itya_ 8.9 17 Fold:DNA/RNA-binding 3-helical bundle Superfamily:Homeodomain-like Family:DNA-binding domain of telomeric protein 14 d3vuba_ 8.6 31 Fold:SH3-like barrel Superfamily:Cell growth inhibitor/plasmid maintenance toxic component Family:CcdB 15 d2enda_ 8.3 32 Fold:T4 endonuclease V Superfamily:T4 endonuclease V Family:T4 endonuclease V 16 d1mxaa2 7.4 63 Fold:S-adenosylmethionine synthetase Superfamily:S-adenosylmethionine synthetase Family:S-adenosylmethionine synthetase 17 d1a8da2 6.9 25 Fold:beta-Trefoil Superfamily:STI-like Family:Clostridium neurotoxins, C-terminal domain 18 c3jrzA_ 6.8 50 PDB header:toxin Chain: A: PDB Molecule:ccdb; PDBTitle: ccdbvfi-formii-ph5.6 19 d1jhga_ 6.8 40 Fold:DNA/RNA-binding 3-helical bundle Superfamily:TrpR-like Family:Trp repressor, TrpR 20 c1d0rA_ 6.7 29 PDB header:hormone/growth factor Chain: A: PDB Molecule:glucagon-like peptide-1-(7-36)-amide; PDBTitle: solution structure of glucagon-like peptide-1-(7-36)-amide2 in trifluoroethanol/water 21 d1v92a_ not modelled 6.7 10 Fold:RuvA C-terminal domain-like Superfamily:UBA-like Family:TAP-C domain-like 22 d2p02a2 not modelled 6.7 50 Fold:S-adenosylmethionine synthetase Superfamily:S-adenosylmethionine synthetase Family:S-adenosylmethionine synthetase 23 d1qm4a2 not modelled 6.6 50 Fold:S-adenosylmethionine synthetase Superfamily:S-adenosylmethionine synthetase Family:S-adenosylmethionine synthetase 24 c3sviA_ not modelled 6.4 30 PDB header:signaling protein Chain: A: PDB Molecule:type iii effector hopab2; PDBTitle: structure of the pto-binding domain of hoppmal generated by limited2 thermolysin digestion 25 c2rmrA_ not modelled 6.0 21 PDB header:transcription Chain: A: PDB Molecule:paired amphipathic helix protein sin3a; PDBTitle: solution structure of msin3a pah1 domain 26 d1eyea_ not modelled 6.0 38 Fold:TIM beta/alpha-barrel Superfamily:Dihydropteroate synthetase-like Family:Dihydropteroate synthetase 27 c2dhyA_ not modelled 5.4 11 PDB header:immune system Chain: A: PDB Molecule:cue domain-containing protein 1; PDBTitle: solution structure of the cue domain in the human cue2 domain containing protein 1 (cuedc1)

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