Secondary structure and disorder prediction

		1	.	.	.	.	.	.	.	.	10	.	.	.	.	.	.	.	.	.	20	.	.	.	.	.	.	.	.	.	30	.	.	.	.	.	.	.	.	.	40	.	.	.	.	.	.	.	.	.	50	.	.	.	.	.	.	.	.	.	60
Sequence		M	K	I	I	T	R	G	E	A	M	R	I	H	Q	Q	H	P	T	S	R	L	F	P	F	C	T	G	K	Y	R	W	H	G	S	A	E	A	Y	T	G	R	E	V	Q	D	I	P	G	V	L	A	V	F	A	E	R	R	K	D	S
Secondary structure
SS confidence
Disorder		?	?	?	?	?	?	?				?	?	?																					?	?		?																							?
Disorder confidence
		.	.	.	.	.	.	.	.	.	70	.	.	.
Sequence		F	G	P	Y	V	R	L	M	S	V	T	L	N
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 3pa8 chain A Region: 9 - 72 Aligned: 64 Modelled: 64 Confidence: 25.7% Identity: 20% PDB header:toxin/peptide inhibitor Chain: A: PDB Molecule:toxin b; PDBTitle: structure of the c. difficile tcdb cysteine protease domain in complex2 with a peptide inhibitor Phyre2 PDB 2zjr chain K domain 1 Region: 41 - 68 Aligned: 28 Modelled: 28 Confidence: 16.6% Identity: 18% Fold: Prokaryotic ribosomal protein L17 Superfamily: Prokaryotic ribosomal protein L17 Family: Prokaryotic ribosomal protein L17 Phyre2 PDB 2cqm chain A domain 1 Region: 42 - 68 Aligned: 27 Modelled: 27 Confidence: 14.6% Identity: 41% Fold: Prokaryotic ribosomal protein L17 Superfamily: Prokaryotic ribosomal protein L17 Family: Prokaryotic ribosomal protein L17 Phyre2 PDB 1tif chain A Region: 1 - 31 Aligned: 30 Modelled: 31 Confidence: 12.8% Identity: 33% Fold: beta-Grasp (ubiquitin-like) Superfamily: Translation initiation factor IF3, N-terminal domain Family: Translation initiation factor IF3, N-terminal domain Phyre2 PDB 1bnl chain A Region: 21 - 39 Aligned: 19 Modelled: 19 Confidence: 10.6% Identity: 32% Fold: C-type lectin-like Superfamily: C-type lectin-like Family: Endostatin Phyre2 PDB 1gd8 chain A Region: 41 - 70 Aligned: 30 Modelled: 30 Confidence: 9.6% Identity: 23% Fold: Prokaryotic ribosomal protein L17 Superfamily: Prokaryotic ribosomal protein L17 Family: Prokaryotic ribosomal protein L17 Phyre2 PDB 2jya chain A Region: 31 - 57 Aligned: 27 Modelled: 27 Confidence: 9.0% Identity: 11% PDB header:structural genomics, unknown function Chain: A: PDB Molecule:uncharacterized protein atu1810; PDBTitle: nmr solution structure of protein atu1810 from agrobacterium2 tumefaciens. northeast structural genomics consortium target atr23,3 ontario centre for structural proteomics target atc1776 Phyre2 PDB 1m9s chain A domain 3 Region: 23 - 44 Aligned: 22 Modelled: 22 Confidence: 8.2% Identity: 18% Fold: SH3-like barrel Superfamily: Prokaryotic SH3-related domain Family: GW domain Phyre2 PDB 3bbo chain P Region: 41 - 68 Aligned: 28 Modelled: 28 Confidence: 8.2% Identity: 25% PDB header:ribosome Chain: P: PDB Molecule:ribosomal protein l17; PDBTitle: homology model for the spinach chloroplast 50s subunit2 fitted to 9.4a cryo-em map of the 70s chlororibosome Phyre2 PDB 1koe chain A Region: 23 - 39 Aligned: 17 Modelled: 17 Confidence: 8.1% Identity: 35% Fold: C-type lectin-like Superfamily: C-type lectin-like Family: Endostatin Phyre2 PDB 2qam chain N domain 1 Region: 41 - 68 Aligned: 28 Modelled: 28 Confidence: 7.3% Identity: 18% Fold: Prokaryotic ribosomal protein L17 Superfamily: Prokaryotic ribosomal protein L17 Family: Prokaryotic ribosomal protein L17 Phyre2 PDB 1hd2 chain A Region: 25 - 51 Aligned: 27 Modelled: 27 Confidence: 7.0% Identity: 15% Fold: Thioredoxin fold Superfamily: Thioredoxin-like Family: Glutathione peroxidase-like Phyre2 PDB 1ztx chain E domain 1 Region: 22 - 37 Aligned: 16 Modelled: 16 Confidence: 6.6% Identity: 13% Fold: Immunoglobulin-like beta-sandwich Superfamily: E set domains Family: Class II viral fusion proteins C-terminal domain Phyre2 PDB 2bh1 chain A domain 1 Region: 2 - 30 Aligned: 29 Modelled: 29 Confidence: 6.1% Identity: 21% Fold: Ribonuclease H-like motif Superfamily: Actin-like ATPase domain Family: Cyto-EpsL domain Phyre2 PDB 2q79 chain A domain 1 Region: 11 - 35 Aligned: 22 Modelled: 25 Confidence: 6.1% Identity: 27% Fold: Ferredoxin-like Superfamily: Viral DNA-binding domain Family: Viral DNA-binding domain Phyre2 PDB 2j01 chain S domain 1 Region: 24 - 38 Aligned: 15 Modelled: 15 Confidence: 5.9% Identity: 40% Fold: Ribonuclease H-like motif Superfamily: Translational machinery components Family: Ribosomal protein L18 and S11 Phyre2 PDB 2jz8 chain A Region: 23 - 37 Aligned: 15 Modelled: 15 Confidence: 5.3% Identity: 33% PDB header:structural genomics, unknown function Chain: A: PDB Molecule:uncharacterized protein bh09830; PDBTitle: solution nmr structure of bh09830 from bartonella henselae2 modeled with one zn+2 bound. northeast structural genomics3 consortium target bnr55 Phyre2 1 c3pa8A_ 2 d2zjrk1 3 d2cqma1 4 d1tifa_ 5 d1bnla_ 6 d1gd8a_ 7 c2jyaA_ 8 d1m9sa3 9 c3bboP_ 10 d1koea_ 11 d2qamn1 12 d1hd2a_ 13 d1ztxe1 14 d2bh1a1 15 d2q79a1 16 d2j01s1 17 c2jz8A_

Detailed template information

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

1 c3pa8A_ 25.7 20 PDB header:toxin/peptide inhibitor Chain: A: PDB Molecule:toxin b; PDBTitle: structure of the c. difficile tcdb cysteine protease domain in complex2 with a peptide inhibitor 2 d2zjrk1 16.6 18 Fold:Prokaryotic ribosomal protein L17 Superfamily:Prokaryotic ribosomal protein L17 Family:Prokaryotic ribosomal protein L17 3 d2cqma1 14.6 41 Fold:Prokaryotic ribosomal protein L17 Superfamily:Prokaryotic ribosomal protein L17 Family:Prokaryotic ribosomal protein L17 4 d1tifa_ 12.8 33 Fold:beta-Grasp (ubiquitin-like) Superfamily:Translation initiation factor IF3, N-terminal domain Family:Translation initiation factor IF3, N-terminal domain 5 d1bnla_ 10.6 32 Fold:C-type lectin-like Superfamily:C-type lectin-like Family:Endostatin 6 d1gd8a_ 9.6 23 Fold:Prokaryotic ribosomal protein L17 Superfamily:Prokaryotic ribosomal protein L17 Family:Prokaryotic ribosomal protein L17 7 c2jyaA_ 9.0 11 PDB header:structural genomics, unknown function Chain: A: PDB Molecule:uncharacterized protein atu1810; PDBTitle: nmr solution structure of protein atu1810 from agrobacterium2 tumefaciens. northeast structural genomics consortium target atr23,3 ontario centre for structural proteomics target atc1776 8 d1m9sa3 8.2 18 Fold:SH3-like barrel Superfamily:Prokaryotic SH3-related domain Family:GW domain 9 c3bboP_ 8.2 25 PDB header:ribosome Chain: P: PDB Molecule:ribosomal protein l17; PDBTitle: homology model for the spinach chloroplast 50s subunit2 fitted to 9.4a cryo-em map of the 70s chlororibosome 10 d1koea_ 8.1 35 Fold:C-type lectin-like Superfamily:C-type lectin-like Family:Endostatin 11 d2qamn1 7.3 18 Fold:Prokaryotic ribosomal protein L17 Superfamily:Prokaryotic ribosomal protein L17 Family:Prokaryotic ribosomal protein L17 12 d1hd2a_ 7.0 15 Fold:Thioredoxin fold Superfamily:Thioredoxin-like Family:Glutathione peroxidase-like 13 d1ztxe1 6.6 13 Fold:Immunoglobulin-like beta-sandwich Superfamily:E set domains Family:Class II viral fusion proteins C-terminal domain 14 d2bh1a1 6.1 21 Fold:Ribonuclease H-like motif Superfamily:Actin-like ATPase domain Family:Cyto-EpsL domain 15 d2q79a1 6.1 27 Fold:Ferredoxin-like Superfamily:Viral DNA-binding domain Family:Viral DNA-binding domain 16 d2j01s1 5.9 40 Fold:Ribonuclease H-like motif Superfamily:Translational machinery components Family:Ribosomal protein L18 and S11 17 c2jz8A_ 5.3 33 PDB header:structural genomics, unknown function Chain: A: PDB Molecule:uncharacterized protein bh09830; PDBTitle: solution nmr structure of bh09830 from bartonella henselae2 modeled with one zn+2 bound. northeast structural genomics3 consortium target bnr55

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