Secondary structure and disorder prediction

		1	.	.	.	.	.	.	.	.	10	.	.	.	.	.	.	.	.	.	20	.	.	.	.	.	.	.	.	.	30	.	.	.	.	.	.	.	.	.	40	.	.	.	.	.	.	.	.	.	50	.	.	.	.	.	.	.	.	.	60
Sequence		M	I	N	R	Q	Q	G	F	T	L	L	E	V	M	A	A	L	A	I	F	S	M	L	S	V	L	A	F	M	I	F	S	Q	A	S	E	L	H	Q	R	S	Q	K	E	I	Q	Q	F	N	Q	L	Q	R	T	I	T	I	L	D	N
Secondary structure
SS confidence
Disorder		?	?	?	?	?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	70	.	.	.	.	.	.	.	.	.	80	.	.	.	.	.	.	.	.	.	90	.	.	.	.	.	.	.	.	.	100	.	.	.	.	.	.	.	.	.	110	.	.	.	.	.	.	.	.	.	120
Sequence		D	L	L	Q	L	V	A	R	R	N	R	S	T	D	K	I	M	V	L	G	E	E	A	I	F	T	T	Q	S	R	D	P	L	A	P	L	S	E	A	Q	T	L	L	T	V	H	W	Y	L	R	N	H	T	L	Y	R	A	V	R	T
Secondary structure
SS confidence
Disorder																			?			?	?								?	?	?	?	?	?	?	?	?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	130	.	.	.	.	.	.	.	.	.	140	.	.	.	.	.	.	.	.	.	150	.	.	.	.	.	.	.	.	.	160	.	.	.	.	.	.	.	.	.	170	.	.	.	.	.	.	.	.	.	180
Sequence		S	V	D	G	R	K	D	Q	P	A	Q	A	M	L	E	H	V	E	S	F	L	L	E	S	N	S	G	E	S	Q	E	L	P	L	S	V	T	L	H	L	Q	T	Q	Q	Y	G	G	L	Q	R	R	F	A	L	P	E	Q	L	A	R
Secondary structure
SS confidence
Disorder				?	?	?	?	?	?																			?		?																												?	?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	190	.	.	.	.	.
Sequence		E	E	S	P	A	Q	T	Q	A	G	N	N	N	H	E
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 B domain 1 Region: 39 - 181 Aligned: 143 Modelled: 143 Confidence: 100.0% Identity: 20% Fold: Pili subunits Superfamily: Pili subunits Family: EpsJ-like Phyre2 PDB 3ci0 chain J domain 1 Region: 46 - 177 Aligned: 132 Modelled: 121 Confidence: 100.0% Identity: 24% Fold: Pili subunits Superfamily: Pili subunits Family: EpsJ-like Phyre2 PDB 3nje chain A Region: 42 - 181 Aligned: 131 Modelled: 140 Confidence: 99.9% Identity: 31% PDB header:protein transport Chain: A: PDB Molecule:general secretion pathway protein j; PDBTitle: structure of the minor pseudopilin xcpw from the pseudomonas2 aeruginosa type ii secretion system Phyre2 PDB 3sok chain B Region: 8 - 58 Aligned: 51 Modelled: 51 Confidence: 98.7% Identity: 24% PDB header:cell adhesion Chain: B: PDB Molecule:fimbrial protein; PDBTitle: dichelobacter nodosus pilin fima Phyre2 PDB 1oqw chain A Region: 8 - 60 Aligned: 53 Modelled: 53 Confidence: 98.7% Identity: 19% Fold: Pili subunits Superfamily: Pili subunits Family: Pilin Phyre2 PDB 2pil chain A Region: 9 - 61 Aligned: 52 Modelled: 53 Confidence: 98.5% Identity: 21% Fold: Pili subunits Superfamily: Pili subunits Family: Pilin Phyre2 PDB 4a18 chain U Region: 6 - 16 Aligned: 11 Modelled: 11 Confidence: 37.9% Identity: 64% 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 1f6g chain A Region: 8 - 68 Aligned: 60 Modelled: 61 Confidence: 37.6% Identity: 13% Fold: Voltage-gated potassium channels Superfamily: Voltage-gated potassium channels Family: Voltage-gated potassium channels Phyre2 PDB 3u5e chain L Region: 6 - 16 Aligned: 11 Modelled: 11 Confidence: 35.4% Identity: 73% 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 3lw5 chain K Region: 3 - 24 Aligned: 22 Modelled: 22 Confidence: 22.7% Identity: 23% PDB header:photosynthesis Chain: K: PDB Molecule:photosystem i reaction center subunit x psak; PDBTitle: improved model of plant photosystem i Phyre2 PDB 2knc chain B Region: 13 - 50 Aligned: 38 Modelled: 38 Confidence: 19.1% Identity: 13% PDB header:cell adhesion Chain: B: PDB Molecule:integrin beta-3; PDBTitle: platelet integrin alfaiib-beta3 transmembrane-cytoplasmic2 heterocomplex Phyre2 PDB 2kb1 chain A Region: 8 - 39 Aligned: 32 Modelled: 32 Confidence: 18.1% Identity: 13% 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 PDB 2wsf chain G Region: 3 - 14 Aligned: 12 Modelled: 12 Confidence: 16.8% Identity: 33% PDB header:photosynthesis Chain: G: PDB Molecule:photosystem i reaction center subunit v, PDBTitle: improved model of plant photosystem i Phyre2 PDB 1r3j chain C Region: 5 - 40 Aligned: 36 Modelled: 36 Confidence: 15.3% Identity: 8% Fold: Voltage-gated potassium channels Superfamily: Voltage-gated potassium channels Family: Voltage-gated potassium channels Phyre2 PDB 2axt chain Z domain 1 Region: 13 - 45 Aligned: 33 Modelled: 33 Confidence: 14.9% Identity: 27% Fold: Transmembrane helix hairpin Superfamily: PsbZ-like Family: PsbZ-like Phyre2 PDB 2o01 chain G Region: 7 - 14 Aligned: 8 Modelled: 8 Confidence: 12.0% 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 1pgs chain A domain 1 Region: 142 - 161 Aligned: 20 Modelled: 20 Confidence: 11.8% Identity: 10% Fold: Nucleoplasmin-like/VP (viral coat and capsid proteins) Superfamily: PHM/PNGase F Family: Glycosyl-asparaginase Phyre2 PDB 2kpe chain A Region: 15 - 39 Aligned: 25 Modelled: 25 Confidence: 8.8% Identity: 16% PDB header:membrane protein Chain: A: PDB Molecule:glycophorin-a; PDBTitle: refined structure of glycophorin a transmembrane segment dimer in dpc2 micelles Phyre2 PDB 2kpe chain B Region: 15 - 39 Aligned: 25 Modelled: 25 Confidence: 8.8% Identity: 16% PDB header:membrane protein Chain: B: PDB Molecule:glycophorin-a; PDBTitle: refined structure of glycophorin a transmembrane segment dimer in dpc2 micelles Phyre2 PDB 1jb0 chain K Region: 2 - 27 Aligned: 26 Modelled: 26 Confidence: 8.3% Identity: 19% PDB header:photosynthesis Chain: K: PDB Molecule:photosystem 1 reaction centre subunit x; PDBTitle: crystal structure of photosystem i: a photosynthetic reaction center2 and core antenna system from cyanobacteria Phyre2 1 d2retb1 2 d3ci0j1 3 c3njeA_ 4 c3sokB_ 5 d1oqwa_ 6 d2pila_ 7 c4a18U_ 8 d1f6ga_ 9 c3u5eL_ 10 c3lw5K_ 11 c2kncB_ 12 c2kb1A_ 13 c2wsfG_ 14 d1r3jc_ 15 d2axtz1 16 c2o01G_ 17 d1pgsa1 18 c2kpeA_ 19 c2kpeB_ 20 c1jb0K_ 21 22 23 24

Detailed template information

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

1 d2retb1 100.0 20 Fold:Pili subunits Superfamily:Pili subunits Family:EpsJ-like 2 d3ci0j1 100.0 24 Fold:Pili subunits Superfamily:Pili subunits Family:EpsJ-like 3 c3njeA_ 99.9 31 PDB header:protein transport Chain: A: PDB Molecule:general secretion pathway protein j; PDBTitle: structure of the minor pseudopilin xcpw from the pseudomonas2 aeruginosa type ii secretion system 4 c3sokB_ 98.7 24 PDB header:cell adhesion Chain: B: PDB Molecule:fimbrial protein; PDBTitle: dichelobacter nodosus pilin fima 5 d1oqwa_ 98.7 19 Fold:Pili subunits Superfamily:Pili subunits Family:Pilin 6 d2pila_ 98.5 21 Fold:Pili subunits Superfamily:Pili subunits Family:Pilin 7 c4a18U_ 37.9 64 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 d1f6ga_ 37.6 13 Fold:Voltage-gated potassium channels Superfamily:Voltage-gated potassium channels Family:Voltage-gated potassium channels 9 c3u5eL_ 35.4 73 PDB header:ribosome Chain: L: PDB Molecule:60s ribosomal protein l13-a; PDBTitle: the structure of the eukaryotic ribosome at 3.0 resolution 10 c3lw5K_ 22.7 23 PDB header:photosynthesis Chain: K: PDB Molecule:photosystem i reaction center subunit x psak; PDBTitle: improved model of plant photosystem i 11 c2kncB_ 19.1 13 PDB header:cell adhesion Chain: B: PDB Molecule:integrin beta-3; PDBTitle: platelet integrin alfaiib-beta3 transmembrane-cytoplasmic2 heterocomplex 12 c2kb1A_ 18.1 13 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 13 c2wsfG_ 16.8 33 PDB header:photosynthesis Chain: G: PDB Molecule:photosystem i reaction center subunit v, PDBTitle: improved model of plant photosystem i 14 d1r3jc_ 15.3 8 Fold:Voltage-gated potassium channels Superfamily:Voltage-gated potassium channels Family:Voltage-gated potassium channels 15 d2axtz1 14.9 27 Fold:Transmembrane helix hairpin Superfamily:PsbZ-like Family:PsbZ-like 16 c2o01G_ 12.0 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 17 d1pgsa1 11.8 10 Fold:Nucleoplasmin-like/VP (viral coat and capsid proteins) Superfamily:PHM/PNGase F Family:Glycosyl-asparaginase 18 c2kpeA_ 8.8 16 PDB header:membrane protein Chain: A: PDB Molecule:glycophorin-a; PDBTitle: refined structure of glycophorin a transmembrane segment dimer in dpc2 micelles 19 c2kpeB_ 8.8 16 PDB header:membrane protein Chain: B: PDB Molecule:glycophorin-a; PDBTitle: refined structure of glycophorin a transmembrane segment dimer in dpc2 micelles 20 c1jb0K_ 8.3 19 PDB header:photosynthesis Chain: K: PDB Molecule:photosystem 1 reaction centre subunit x; PDBTitle: crystal structure of photosystem i: a photosynthetic reaction center2 and core antenna system from cyanobacteria 21 d1jb0k_ not modelled 8.3 19 Fold:Photosystem I reaction center subunit X, PsaK Superfamily:Photosystem I reaction center subunit X, PsaK Family:Photosystem I reaction center subunit X, PsaK 22 c2wscK_ not modelled 8.1 33 PDB header:photosynthesis Chain: K: PDB Molecule:photosystem i reaction center subunit psak, PDBTitle: improved model of plant photosystem i 23 c2h7vD_ not modelled 7.2 23 PDB header:signaling protein Chain: D: PDB Molecule:protein kinase ypka; PDBTitle: co-crystal structure of ypka-rac1 24 c1nhlA_ not modelled 5.9 12 PDB header:protein transport Chain: A: PDB Molecule:synaptosomal-associated protein 23; PDBTitle: snap-23n structure

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