Secondary structure and disorder prediction

		1	.	.	.	.	.	.	.	.	10	.	.	.	.	.	.	.	.	.	20	.	.	.	.	.	.	.	.	.	30	.	.	.	.	.	.	.	.	.	40	.	.	.	.	.	.	.	.	.	50	.	.	.	.	.	.	.	.	.	60
Sequence		M	N	K	Q	S	G	M	T	L	L	E	V	L	L	A	M	S	I	F	T	A	V	A	L	T	L	M	S	S	M	Q	G	Q	R	N	A	I	E	R	M	R	N	E	T	L	A	L	W	I	A	D	N	Q	L	Q	S	Q	D	S	F
Secondary structure
SS confidence
Disorder		?	?	?	?	?	?																																																				?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	70	.	.	.	.	.	.	.	.	.	80	.	.	.	.	.	.	.	.	.	90	.	.	.	.	.	.	.	.	.	100	.	.	.	.	.	.	.	.	.	110	.	.	.	.	.	.	.	.	.	120
Sequence		G	E	E	N	T	S	S	S	G	K	E	L	I	N	G	E	E	W	N	W	R	S	D	I	H	S	S	K	D	G	T	L	L	E	R	T	I	T	V	T	L	P	S	G	Q	T	T	S	L	T	R	Y	Q	S	I	D	N	K	S	G
Secondary structure
SS confidence
Disorder		?	?	?	?	?	?	?	?	?	?	?	?														?	?	?	?	?													?	?	?										?	?	?	?	?	?
Disorder confidence
		.	.	.	.	.
Sequence		Q	A	Q	D	D
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 2ret chain E Region: 36 - 117 Aligned: 82 Modelled: 82 Confidence: 99.7% Identity: 17% PDB header:protein transport Chain: E: PDB Molecule:pseudopilin epsi; PDBTitle: the crystal structure of a binary complex of two pseudopilins: epsi2 and epsj from the type 2 secretion system of vibrio vulnificus Phyre2 PDB 2ret chain A domain 1 Region: 36 - 115 Aligned: 80 Modelled: 80 Confidence: 99.7% Identity: 18% Fold: Pili subunits Superfamily: Pili subunits Family: GSPII I/J protein-like Phyre2 PDB 3ci0 chain I domain 1 Region: 38 - 115 Aligned: 77 Modelled: 78 Confidence: 99.6% Identity: 21% Fold: Pili subunits Superfamily: Pili subunits Family: GSPII I/J protein-like Phyre2 PDB 3sok chain B Region: 7 - 69 Aligned: 63 Modelled: 63 Confidence: 98.1% Identity: 14% PDB header:cell adhesion Chain: B: PDB Molecule:fimbrial protein; PDBTitle: dichelobacter nodosus pilin fima Phyre2 PDB 1oqw chain A Region: 7 - 112 Aligned: 102 Modelled: 106 Confidence: 98.1% Identity: 12% Fold: Pili subunits Superfamily: Pili subunits Family: Pilin Phyre2 PDB 2pil chain A Region: 8 - 66 Aligned: 59 Modelled: 59 Confidence: 97.5% Identity: 15% Fold: Pili subunits Superfamily: Pili subunits Family: Pilin Phyre2 PDB 4a18 chain U Region: 5 - 15 Aligned: 11 Modelled: 11 Confidence: 24.9% Identity: 45% PDB header:ribosome Chain: U: PDB Molecule:rpl13; PDBTitle: t.thermophila 60s ribosomal subunit in complex with initiation2 factor 6. this file contains 26s rrna and proteins of molecule 1 Phyre2 PDB 3u5e chain L Region: 5 - 15 Aligned: 11 Modelled: 11 Confidence: 23.5% Identity: 55% PDB header:ribosome Chain: L: PDB Molecule:60s ribosomal protein l13-a; PDBTitle: the structure of the eukaryotic ribosome at 3.0 resolution Phyre2 PDB 2wsf chain G Region: 2 - 13 Aligned: 12 Modelled: 12 Confidence: 20.6% Identity: 33% PDB header:photosynthesis Chain: G: PDB Molecule:photosystem i reaction center subunit v, PDBTitle: improved model of plant photosystem i Phyre2 PDB 3lw5 chain K Region: 2 - 13 Aligned: 12 Modelled: 12 Confidence: 16.6% Identity: 33% PDB header:photosynthesis Chain: K: PDB Molecule:photosystem i reaction center subunit x psak; PDBTitle: improved model of plant photosystem i Phyre2 PDB 2o01 chain G Region: 6 - 13 Aligned: 8 Modelled: 8 Confidence: 13.5% Identity: 38% PDB header:photosynthesis Chain: G: PDB Molecule:photosystem i reaction center subunit v, PDBTitle: the structure of a plant photosystem i supercomplex at 3.42 angstrom resolution Phyre2 PDB 2wsc chain K Region: 2 - 13 Aligned: 12 Modelled: 12 Confidence: 11.6% Identity: 33% PDB header:photosynthesis Chain: K: PDB Molecule:photosystem i reaction center subunit psak, PDBTitle: improved model of plant photosystem i Phyre2 PDB 2axt chain H domain 1 Region: 14 - 34 Aligned: 21 Modelled: 21 Confidence: 10.0% Identity: 14% Fold: Single transmembrane helix Superfamily: Photosystem II 10 kDa phosphoprotein PsbH Family: PsbH-like Phyre2 PDB 2k3p chain A Region: 9 - 17 Aligned: 9 Modelled: 9 Confidence: 7.5% Identity: 56% PDB header:structural protein Chain: A: PDB Molecule:tusp1; PDBTitle: solution structure of the c-terminal domain (tusp1-c) of the2 egg case silk from nephila antipodiana Phyre2 PDB 2bo9 chain B domain 1 Region: 44 - 108 Aligned: 65 Modelled: 65 Confidence: 7.3% Identity: 15% Fold: Cystatin-like Superfamily: Cystatin/monellin Family: Latexin-like Phyre2 PDB 1p58 chain F Region: 3 - 30 Aligned: 28 Modelled: 28 Confidence: 7.2% Identity: 21% PDB header:virus Chain: F: PDB Molecule:envelope protein m; PDBTitle: complex organization of dengue virus membrane proteins as revealed by2 9.5 angstrom cryo-em reconstruction Phyre2 PDB 2ko6 chain A Region: 3 - 17 Aligned: 15 Modelled: 15 Confidence: 6.9% Identity: 27% PDB header:structural genomics, unknown function Chain: A: PDB Molecule:uncharacterized protein yihd; PDBTitle: solution structure of protein sf3929 from shigella flexneri2 2a. northeast structural genomics consortium target3 sfr81/ontario center for structural proteomics target4 sf3929 Phyre2 PDB 2kb1 chain A Region: 7 - 38 Aligned: 32 Modelled: 32 Confidence: 6.4% Identity: 9% PDB header:membrane protein Chain: A: PDB Molecule:wsk3; PDBTitle: nmr studies of a channel protein without membrane:2 structure and dynamics of water-solubilized kcsa Phyre2 1 c2retE_ 2 d2reta1 3 d3ci0i1 4 c3sokB_ 5 d1oqwa_ 6 d2pila_ 7 c4a18U_ 8 c3u5eL_ 9 c2wsfG_ 10 c3lw5K_ 11 c2o01G_ 12 c2wscK_ 13 d2axth1 14 c2k3pA_ 15 d2bo9b1 16 c1p58F_ 17 c2ko6A_ 18 c2kb1A_

Detailed template information

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

1 c2retE_ 99.7 17 PDB header:protein transport Chain: E: PDB Molecule:pseudopilin epsi; PDBTitle: the crystal structure of a binary complex of two pseudopilins: epsi2 and epsj from the type 2 secretion system of vibrio vulnificus 2 d2reta1 99.7 18 Fold:Pili subunits Superfamily:Pili subunits Family:GSPII I/J protein-like 3 d3ci0i1 99.6 21 Fold:Pili subunits Superfamily:Pili subunits Family:GSPII I/J protein-like 4 c3sokB_ 98.1 14 PDB header:cell adhesion Chain: B: PDB Molecule:fimbrial protein; PDBTitle: dichelobacter nodosus pilin fima 5 d1oqwa_ 98.1 12 Fold:Pili subunits Superfamily:Pili subunits Family:Pilin 6 d2pila_ 97.5 15 Fold:Pili subunits Superfamily:Pili subunits Family:Pilin 7 c4a18U_ 24.9 45 PDB header:ribosome Chain: U: PDB Molecule:rpl13; PDBTitle: t.thermophila 60s ribosomal subunit in complex with initiation2 factor 6. this file contains 26s rrna and proteins of molecule 1 8 c3u5eL_ 23.5 55 PDB header:ribosome Chain: L: PDB Molecule:60s ribosomal protein l13-a; PDBTitle: the structure of the eukaryotic ribosome at 3.0 resolution 9 c2wsfG_ 20.6 33 PDB header:photosynthesis Chain: G: PDB Molecule:photosystem i reaction center subunit v, PDBTitle: improved model of plant photosystem i 10 c3lw5K_ 16.6 33 PDB header:photosynthesis Chain: K: PDB Molecule:photosystem i reaction center subunit x psak; PDBTitle: improved model of plant photosystem i 11 c2o01G_ 13.5 38 PDB header:photosynthesis Chain: G: PDB Molecule:photosystem i reaction center subunit v, PDBTitle: the structure of a plant photosystem i supercomplex at 3.42 angstrom resolution 12 c2wscK_ 11.6 33 PDB header:photosynthesis Chain: K: PDB Molecule:photosystem i reaction center subunit psak, PDBTitle: improved model of plant photosystem i 13 d2axth1 10.0 14 Fold:Single transmembrane helix Superfamily:Photosystem II 10 kDa phosphoprotein PsbH Family:PsbH-like 14 c2k3pA_ 7.5 56 PDB header:structural protein Chain: A: PDB Molecule:tusp1; PDBTitle: solution structure of the c-terminal domain (tusp1-c) of the2 egg case silk from nephila antipodiana 15 d2bo9b1 7.3 15 Fold:Cystatin-like Superfamily:Cystatin/monellin Family:Latexin-like 16 c1p58F_ 7.2 21 PDB header:virus Chain: F: PDB Molecule:envelope protein m; PDBTitle: complex organization of dengue virus membrane proteins as revealed by2 9.5 angstrom cryo-em reconstruction 17 c2ko6A_ 6.9 27 PDB header:structural genomics, unknown function Chain: A: PDB Molecule:uncharacterized protein yihd; PDBTitle: solution structure of protein sf3929 from shigella flexneri2 2a. northeast structural genomics consortium target3 sfr81/ontario center for structural proteomics target4 sf3929 18 c2kb1A_ 6.4 9 PDB header:membrane protein Chain: A: PDB Molecule:wsk3; PDBTitle: nmr studies of a channel protein without membrane:2 structure and dynamics of water-solubilized kcsa

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