Secondary structure and disorder prediction

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Sequence		M	S	R	V	C	Q	V	T	G	K	R	P	V	T	G	N	N	R	S	H	A	L	N	A	T	K	R	R	F	L	P	N	L	H	S	H	R	F	W	V	E	S	E	K	R	F	V	T	L	R	V	S	A	K	G	M	R	V	I	D
Secondary structure
SS confidence
Disorder		?	?	?	?	?	?	?									?
Disorder confidence
		.	.	.	.	.	.	.	.	.	70	.	.	.	.	.	.	.	.
Sequence		K	K	G	I	D	T	V	L	A	E	L	R	A	R	G	E	K	Y
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 2qam chain Z domain 1 Region: 2 - 78 Aligned: 77 Modelled: 77 Confidence: 100.0% Identity: 100% Fold: L28p-like Superfamily: L28p-like Family: Ribosomal protein L28 Phyre2 PDB 3bbo chain Y Region: 3 - 71 Aligned: 69 Modelled: 69 Confidence: 100.0% Identity: 39% PDB header:ribosome Chain: Y: PDB Molecule:ribosomal protein l28; PDBTitle: homology model for the spinach chloroplast 50s subunit2 fitted to 9.4a cryo-em map of the 70s chlororibosome Phyre2 PDB 2jz6 chain A domain 1 Region: 1 - 66 Aligned: 65 Modelled: 66 Confidence: 99.9% Identity: 31% Fold: L28p-like Superfamily: L28p-like Family: Ribosomal protein L28 Phyre2 PDB 2jl8 chain 1 Region: 3 - 61 Aligned: 57 Modelled: 57 Confidence: 99.8% Identity: 33% PDB header:ribosome Chain: 1: PDB Molecule:50s ribosomal protein l28; PDBTitle: insights into translational termination from the structure2 of rf2 bound to the ribosome (part 4 of 4).3 this file contains the 50s subunit. Phyre2 PDB 2zjr chain U domain 1 Region: 4 - 62 Aligned: 57 Modelled: 57 Confidence: 99.2% Identity: 25% Fold: L28p-like Superfamily: L28p-like Family: Ribosomal protein L28 Phyre2 PDB 2j01 chain 1 domain 1 Region: 8 - 56 Aligned: 47 Modelled: 49 Confidence: 97.7% Identity: 36% Fold: L28p-like Superfamily: L28p-like Family: Ribosomal protein L28 Phyre2 PDB 2cu8 chain A domain 1 Region: 1 - 19 Aligned: 19 Modelled: 19 Confidence: 44.6% Identity: 21% Fold: Glucocorticoid receptor-like (DNA-binding domain) Superfamily: Glucocorticoid receptor-like (DNA-binding domain) Family: LIM domain Phyre2 PDB 2k5c chain A Region: 1 - 10 Aligned: 9 Modelled: 10 Confidence: 34.9% Identity: 33% PDB header:metal binding protein Chain: A: PDB Molecule:uncharacterized protein pf0385; PDBTitle: nmr structure for pf0385 Phyre2 PDB 2uz0 chain B Region: 31 - 51 Aligned: 21 Modelled: 21 Confidence: 22.4% Identity: 10% PDB header:hydrolase Chain: B: PDB Molecule:tributyrin esterase; PDBTitle: the crystal crystal structure of the esta protein, a2 virulence factor esta protein from streptococcus pneumonia Phyre2 PDB 2yt9 chain A domain 2 Region: 5 - 10 Aligned: 6 Modelled: 6 Confidence: 14.7% Identity: 50% Fold: beta-beta-alpha zinc fingers Superfamily: beta-beta-alpha zinc fingers Family: Classic zinc finger, C2H2 Phyre2 PDB 2elr chain A Region: 5 - 11 Aligned: 7 Modelled: 7 Confidence: 14.6% Identity: 43% PDB header:transcription Chain: A: PDB Molecule:zinc finger protein 406; PDBTitle: solution structure of the 15th c2h2 zinc finger of human2 zinc finger protein 406 Phyre2 PDB 1dvp chain A Region: 2 - 62 Aligned: 60 Modelled: 61 Confidence: 14.1% Identity: 15% PDB header:transferase Chain: A: PDB Molecule:hepatocyte growth factor-regulated tyrosine PDBTitle: crystal structure of the vhs and fyve tandem domains of hrs,2 a protein involved in membrane trafficking and signal3 transduction Phyre2 PDB 3zyq chain A Region: 2 - 61 Aligned: 59 Modelled: 60 Confidence: 10.2% Identity: 14% PDB header:signaling Chain: A: PDB Molecule:hepatocyte growth factor-regulated tyrosine kinase PDBTitle: crystal structure of the tandem vhs and fyve domains of hepatocyte2 growth factor-regulated tyrosine kinase substrate (hgs-hrs) at 1.483 a resolution Phyre2 PDB 2dmd chain A domain 2 Region: 4 - 10 Aligned: 7 Modelled: 7 Confidence: 9.4% Identity: 57% Fold: beta-beta-alpha zinc fingers Superfamily: beta-beta-alpha zinc fingers Family: Classic zinc finger, C2H2 Phyre2 PDB 2c4i chain A Region: 2 - 10 Aligned: 9 Modelled: 9 Confidence: 9.1% Identity: 56% PDB header:glycoprotein Chain: A: PDB Molecule:avidin; PDBTitle: crystal structure of engineered avidin Phyre2 PDB 1ibi chain A domain 2 Region: 4 - 16 Aligned: 13 Modelled: 13 Confidence: 8.6% Identity: 23% Fold: Glucocorticoid receptor-like (DNA-binding domain) Superfamily: Glucocorticoid receptor-like (DNA-binding domain) Family: LIM domain Phyre2 PDB 2oz5 chain A Region: 54 - 70 Aligned: 17 Modelled: 17 Confidence: 7.4% Identity: 18% PDB header:structural genomics, unknown function Chain: A: PDB Molecule:phosphotyrosine protein phosphatase ptpb; PDBTitle: crystal structure of mycobacterium tuberculosis protein tyrosine2 phosphatase ptpb in complex with the specific inhibitor omts Phyre2 PDB 2jtg chain A Region: 1 - 20 Aligned: 20 Modelled: 20 Confidence: 7.4% Identity: 20% PDB header:metal binding protein Chain: A: PDB Molecule:thap domain-containing protein 1; PDBTitle: solution structure of the thap-zinc finger of thap1 Phyre2 PDB 3jyv chain N Region: 2 - 11 Aligned: 10 Modelled: 10 Confidence: 7.3% Identity: 40% PDB header:ribosome Chain: N: PDB Molecule:40s ribosomal protein s29(a); PDBTitle: structure of the 40s rrna and proteins and p/e trna for eukaryotic2 ribosome based on cryo-em map of thermomyces lanuginosus ribosome at3 8.9a resolution Phyre2 PDB 1wbi chain D Region: 2 - 10 Aligned: 9 Modelled: 9 Confidence: 7.3% Identity: 44% PDB header:avidin-related protein Chain: D: PDB Molecule:avidin-related protein 2; PDBTitle: avr2 Phyre2 1 d2qamz1 2 c3bboY_ 3 d2jz6a1 4 c2jl81_ 5 d2zjru1 6 d2j0111 7 d2cu8a1 8 c2k5cA_ 9 c2uz0B_ 10 d2yt9a2 11 c2elrA_ 12 c1dvpA_ 13 c3zyqA_ 14 d2dmda2 15 c2c4iA_ 16 d1ibia2 17 c2oz5A_ 18 c2jtgA_ 19 c3jyvN_ 20 c1wbiD_ 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38

Detailed template information

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

1 d2qamz1 100.0 100 Fold:L28p-like Superfamily:L28p-like Family:Ribosomal protein L28 2 c3bboY_ 100.0 39 PDB header:ribosome Chain: Y: PDB Molecule:ribosomal protein l28; PDBTitle: homology model for the spinach chloroplast 50s subunit2 fitted to 9.4a cryo-em map of the 70s chlororibosome 3 d2jz6a1 99.9 31 Fold:L28p-like Superfamily:L28p-like Family:Ribosomal protein L28 4 c2jl81_ 99.8 33 PDB header:ribosome Chain: 1: PDB Molecule:50s ribosomal protein l28; PDBTitle: insights into translational termination from the structure2 of rf2 bound to the ribosome (part 4 of 4).3 this file contains the 50s subunit. 5 d2zjru1 99.2 25 Fold:L28p-like Superfamily:L28p-like Family:Ribosomal protein L28 6 d2j0111 97.7 36 Fold:L28p-like Superfamily:L28p-like Family:Ribosomal protein L28 7 d2cu8a1 44.6 21 Fold:Glucocorticoid receptor-like (DNA-binding domain) Superfamily:Glucocorticoid receptor-like (DNA-binding domain) Family:LIM domain 8 c2k5cA_ 34.9 33 PDB header:metal binding protein Chain: A: PDB Molecule:uncharacterized protein pf0385; PDBTitle: nmr structure for pf0385 9 c2uz0B_ 22.4 10 PDB header:hydrolase Chain: B: PDB Molecule:tributyrin esterase; PDBTitle: the crystal crystal structure of the esta protein, a2 virulence factor esta protein from streptococcus pneumonia 10 d2yt9a2 14.7 50 Fold:beta-beta-alpha zinc fingers Superfamily:beta-beta-alpha zinc fingers Family:Classic zinc finger, C2H2 11 c2elrA_ 14.6 43 PDB header:transcription Chain: A: PDB Molecule:zinc finger protein 406; PDBTitle: solution structure of the 15th c2h2 zinc finger of human2 zinc finger protein 406 12 c1dvpA_ 14.1 15 PDB header:transferase Chain: A: PDB Molecule:hepatocyte growth factor-regulated tyrosine PDBTitle: crystal structure of the vhs and fyve tandem domains of hrs,2 a protein involved in membrane trafficking and signal3 transduction 13 c3zyqA_ 10.2 14 PDB header:signaling Chain: A: PDB Molecule:hepatocyte growth factor-regulated tyrosine kinase PDBTitle: crystal structure of the tandem vhs and fyve domains of hepatocyte2 growth factor-regulated tyrosine kinase substrate (hgs-hrs) at 1.483 a resolution 14 d2dmda2 9.4 57 Fold:beta-beta-alpha zinc fingers Superfamily:beta-beta-alpha zinc fingers Family:Classic zinc finger, C2H2 15 c2c4iA_ 9.1 56 PDB header:glycoprotein Chain: A: PDB Molecule:avidin; PDBTitle: crystal structure of engineered avidin 16 d1ibia2 8.6 23 Fold:Glucocorticoid receptor-like (DNA-binding domain) Superfamily:Glucocorticoid receptor-like (DNA-binding domain) Family:LIM domain 17 c2oz5A_ 7.4 18 PDB header:structural genomics, unknown function Chain: A: PDB Molecule:phosphotyrosine protein phosphatase ptpb; PDBTitle: crystal structure of mycobacterium tuberculosis protein tyrosine2 phosphatase ptpb in complex with the specific inhibitor omts 18 c2jtgA_ 7.4 20 PDB header:metal binding protein Chain: A: PDB Molecule:thap domain-containing protein 1; PDBTitle: solution structure of the thap-zinc finger of thap1 19 c3jyvN_ 7.3 40 PDB header:ribosome Chain: N: PDB Molecule:40s ribosomal protein s29(a); PDBTitle: structure of the 40s rrna and proteins and p/e trna for eukaryotic2 ribosome based on cryo-em map of thermomyces lanuginosus ribosome at3 8.9a resolution 20 c1wbiD_ 7.3 44 PDB header:avidin-related protein Chain: D: PDB Molecule:avidin-related protein 2; PDBTitle: avr2 21 c3iufA_ not modelled 7.0 43 PDB header:protein binding Chain: A: PDB Molecule:zinc finger protein ubi-d4; PDBTitle: crystal structure of the c2h2-type zinc finger domain of2 human ubi-d4 22 c2xznN_ not modelled 6.7 50 PDB header:ribosome Chain: N: PDB Molecule:rps29e; PDBTitle: crystal structure of the eukaryotic 40s ribosomal2 subunit in complex with initiation factor 1. this file3 contains the 40s subunit and initiation factor for4 molecule 2 23 d1dxga_ not modelled 6.7 33 Fold:Rubredoxin-like Superfamily:Rubredoxin-like Family:Desulforedoxin 24 d2fkza1 not modelled 6.6 28 Fold:Ferritin-like Superfamily:Ferritin-like Family:Ferritin 25 d1zfoa_ not modelled 6.5 33 Fold:Glucocorticoid receptor-like (DNA-binding domain) Superfamily:Glucocorticoid receptor-like (DNA-binding domain) Family:LASP-1 26 d1ywfa1 not modelled 6.5 18 Fold:(Phosphotyrosine protein) phosphatases II Superfamily:(Phosphotyrosine protein) phosphatases II Family:Mycobacterial PtpB-like 27 c2zkqn_ not modelled 6.1 50 PDB header:ribosomal protein/rna Chain: N: PDB Molecule: PDBTitle: structure of a mammalian ribosomal 40s subunit within an2 80s complex obtained by docking homology models of the rna3 and proteins into an 8.7 a cryo-em map 28 d2htna1 not modelled 6.0 19 Fold:Ferritin-like Superfamily:Ferritin-like Family:Ferritin 29 d2csha2 not modelled 5.8 30 Fold:beta-beta-alpha zinc fingers Superfamily:beta-beta-alpha zinc fingers Family:Classic zinc finger, C2H2 30 d2b8ta2 not modelled 5.7 11 Fold:Glucocorticoid receptor-like (DNA-binding domain) Superfamily:Glucocorticoid receptor-like (DNA-binding domain) Family:Type II thymidine kinase zinc finger 31 c2qm0B_ not modelled 5.6 9 PDB header:structural genomics, unknown function Chain: B: PDB Molecule:bes; PDBTitle: crystal structure of bes protein from bacillus cereus 32 d2d8ya1 not modelled 5.5 17 Fold:Glucocorticoid receptor-like (DNA-binding domain) Superfamily:Glucocorticoid receptor-like (DNA-binding domain) Family:LIM domain 33 d2cota2 not modelled 5.3 38 Fold:beta-beta-alpha zinc fingers Superfamily:beta-beta-alpha zinc fingers Family:Classic zinc finger, C2H2 34 c1ardA_ not modelled 5.3 38 PDB header:transcription regulation Chain: A: PDB Molecule:yeast transcription factor adr1; PDBTitle: structures of dna-binding mutant zinc finger domains:2 implications for dna binding 35 d2adra1 not modelled 5.2 38 Fold:beta-beta-alpha zinc fingers Superfamily:beta-beta-alpha zinc fingers Family:Classic zinc finger, C2H2 36 c3hi2C_ not modelled 5.2 25 PDB header:dna binding protein/toxin Chain: C: PDB Molecule:hth-type transcriptional regulator mqsa(ygit); PDBTitle: structure of the n-terminal domain of the e. coli antitoxin mqsa2 (ygit/b3021) in complex with the e. coli toxin mqsr (ygiu/b3022) 37 d1llmc2 not modelled 5.1 25 Fold:beta-beta-alpha zinc fingers Superfamily:beta-beta-alpha zinc fingers Family:Classic zinc finger, C2H2 38 d1dvpa2 not modelled 5.0 15 Fold:FYVE/PHD zinc finger Superfamily:FYVE/PHD zinc finger Family:FYVE, a phosphatidylinositol-3-phosphate binding domain

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