Secondary structure and disorder prediction

		1	.	.	.	.	.	.	.	.	10	.	.	.	.	.	.	.	.	.	20	.	.	.	.	.	.	.	.	.	30	.	.	.	.	.	.	.	.	.	40	.	.	.	.	.	.	.	.	.	50	.	.	.	.	.	.	.	.	.	60
Sequence		M	P	V	K	E	Q	G	F	S	L	L	E	V	L	I	A	M	A	I	S	S	V	L	L	L	G	A	A	R	F	L	P	A	L	Q	R	E	S	L	T	S	T	R	K	L	A	L	E	D	E	I	W	L	R	V	F	T	V	A	K
Secondary structure
SS confidence
Disorder		?	?	?	?	?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	70	.	.	.	.	.	.	.	.	.	80	.	.	.	.	.	.	.	.	.	90	.	.	.	.	.	.	.	.	.	100	.	.	.	.	.	.	.	.	.	110	.	.	.	.	.	.	.	.	.	120
Sequence		H	L	Q	R	A	G	Y	C	H	G	I	C	T	G	E	G	L	E	I	V	G	Q	G	D	C	V	I	V	Q	W	D	A	N	S	N	G	I	W	D	R	E	P	V	K	E	S	D	Q	I	G	F	R	L	K	E	H	V	L	E	T
Secondary structure
SS confidence
Disorder									?	?	?		?																							?	?	?	?	?	?	?	?	?	?		?										?
Disorder confidence
		.	.	.	.	.	.	.	.	.	130	.	.	.	.	.	.	.	.	.	140	.	.	.	.	.	.	.	.	.	150	.	.	.	.	.	.	.	.	.	160	.	.	.	.	.	.	.	.	.	170	.	.	.	.	.	.	.	.	.	180
Sequence		L	R	G	A	T	S	C	E	G	K	G	W	D	K	V	T	N	P	D	A	I	I	I	D	T	F	Q	V	V	R	Q	D	V	S	G	F	S	P	V	L	T	V	N	M	R	A	A	S	K	S	E	P	Q	T	V	V	N	A	S	Y
Secondary structure
SS confidence
Disorder					?	?		?	?			?								?												?	?	?	?	?	?	?										?					?
Disorder confidence
		.	.	.	.	.	.	.
Sequence		S	V	T	G	F	N	L
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: 40 - 176 Aligned: 132 Modelled: 137 Confidence: 98.4% Identity: 13% Fold: Pili subunits Superfamily: Pili subunits Family: EpsJ-like Phyre2 PDB 3ci0 chain J domain 1 Region: 48 - 175 Aligned: 124 Modelled: 126 Confidence: 98.4% Identity: 11% Fold: Pili subunits Superfamily: Pili subunits Family: EpsJ-like Phyre2 PDB 3sok chain B Region: 8 - 57 Aligned: 50 Modelled: 50 Confidence: 98.3% Identity: 18% 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: 98.2% Identity: 17% Fold: Pili subunits Superfamily: Pili subunits Family: Pilin Phyre2 PDB 2pil chain A Region: 9 - 61 Aligned: 53 Modelled: 53 Confidence: 98.0% Identity: 21% Fold: Pili subunits Superfamily: Pili subunits Family: Pilin Phyre2 PDB 3nje chain A Region: 43 - 175 Aligned: 119 Modelled: 133 Confidence: 97.9% Identity: 13% 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 2gc9 chain A domain 1 Region: 83 - 164 Aligned: 69 Modelled: 80 Confidence: 38.0% Identity: 16% Fold: Lipocalins Superfamily: Lipocalins Family: Phenolic acid decarboxylase (PAD) Phyre2 PDB 4a18 chain U Region: 6 - 16 Aligned: 11 Modelled: 11 Confidence: 29.4% 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: 6 - 16 Aligned: 11 Modelled: 11 Confidence: 27.7% 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 3nad chain B Region: 83 - 164 Aligned: 69 Modelled: 82 Confidence: 23.8% Identity: 17% PDB header:lyase Chain: B: PDB Molecule:ferulate decarboxylase; PDBTitle: crystal structure of phenolic acid decarboxylase from bacillus pumilus2 ui-670 Phyre2 PDB 3nx2 chain B Region: 83 - 164 Aligned: 69 Modelled: 82 Confidence: 13.8% Identity: 22% PDB header:lyase Chain: B: PDB Molecule:ferulic acid decarboxylase; PDBTitle: enterobacter sp. px6-4 ferulic acid decarboxylase in complex with2 substrate analogues Phyre2 PDB 3alz chain B Region: 95 - 146 Aligned: 50 Modelled: 52 Confidence: 12.1% Identity: 20% PDB header:viral protein/membrane protein Chain: B: PDB Molecule:cdw150; PDBTitle: crystal structure of the measles virus hemagglutinin bound to its2 cellular receptor slam (form i) Phyre2 PDB 2kb1 chain A Region: 8 - 39 Aligned: 32 Modelled: 32 Confidence: 11.5% Identity: 6% 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 1r3j chain C Region: 5 - 40 Aligned: 36 Modelled: 36 Confidence: 10.7% Identity: 6% Fold: Voltage-gated potassium channels Superfamily: Voltage-gated potassium channels Family: Voltage-gated potassium channels Phyre2 PDB 3lw5 chain K Region: 7 - 23 Aligned: 17 Modelled: 17 Confidence: 9.8% Identity: 24% PDB header:photosynthesis Chain: K: PDB Molecule:photosystem i reaction center subunit x psak; PDBTitle: improved model of plant photosystem i Phyre2 PDB 1jb0 chain K Region: 4 - 28 Aligned: 25 Modelled: 25 Confidence: 7.9% Identity: 28% Fold: Photosystem I reaction center subunit X, PsaK Superfamily: Photosystem I reaction center subunit X, PsaK Family: Photosystem I reaction center subunit X, PsaK Phyre2 PDB 1jb0 chain K Region: 4 - 28 Aligned: 25 Modelled: 25 Confidence: 7.9% Identity: 28% 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 PDB 2hgk chain A domain 1 Region: 48 - 86 Aligned: 39 Modelled: 39 Confidence: 7.6% Identity: 10% Fold: Bromodomain-like Superfamily: YqcC-like Family: YqcC-like Phyre2 PDB 2axt chain H domain 1 Region: 13 - 33 Aligned: 21 Modelled: 21 Confidence: 6.7% Identity: 19% Fold: Single transmembrane helix Superfamily: Photosystem II 10 kDa phosphoprotein PsbH Family: PsbH-like Phyre2 PDB 2wsf chain G Region: 7 - 14 Aligned: 8 Modelled: 8 Confidence: 6.5% Identity: 50% PDB header:photosynthesis Chain: G: PDB Molecule:photosystem i reaction center subunit v, PDBTitle: improved model of plant photosystem i Phyre2 1 d2retb1 2 d3ci0j1 3 c3sokB_ 4 d1oqwa_ 5 d2pila_ 6 c3njeA_ 7 d2gc9a1 8 c4a18U_ 9 c3u5eL_ 10 c3nadB_ 11 c3nx2B_ 12 c3alzB_ 13 c2kb1A_ 14 d1r3jc_ 15 c3lw5K_ 16 d1jb0k_ 17 c1jb0K_ 18 d2hgka1 19 d2axth1 20 c2wsfG_

Detailed template information

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

1 d2retb1 98.4 13 Fold:Pili subunits Superfamily:Pili subunits Family:EpsJ-like 2 d3ci0j1 98.4 11 Fold:Pili subunits Superfamily:Pili subunits Family:EpsJ-like 3 c3sokB_ 98.3 18 PDB header:cell adhesion Chain: B: PDB Molecule:fimbrial protein; PDBTitle: dichelobacter nodosus pilin fima 4 d1oqwa_ 98.2 17 Fold:Pili subunits Superfamily:Pili subunits Family:Pilin 5 d2pila_ 98.0 21 Fold:Pili subunits Superfamily:Pili subunits Family:Pilin 6 c3njeA_ 97.9 13 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 7 d2gc9a1 38.0 16 Fold:Lipocalins Superfamily:Lipocalins Family:Phenolic acid decarboxylase (PAD) 8 c4a18U_ 29.4 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 9 c3u5eL_ 27.7 55 PDB header:ribosome Chain: L: PDB Molecule:60s ribosomal protein l13-a; PDBTitle: the structure of the eukaryotic ribosome at 3.0 resolution 10 c3nadB_ 23.8 17 PDB header:lyase Chain: B: PDB Molecule:ferulate decarboxylase; PDBTitle: crystal structure of phenolic acid decarboxylase from bacillus pumilus2 ui-670 11 c3nx2B_ 13.8 22 PDB header:lyase Chain: B: PDB Molecule:ferulic acid decarboxylase; PDBTitle: enterobacter sp. px6-4 ferulic acid decarboxylase in complex with2 substrate analogues 12 c3alzB_ 12.1 20 PDB header:viral protein/membrane protein Chain: B: PDB Molecule:cdw150; PDBTitle: crystal structure of the measles virus hemagglutinin bound to its2 cellular receptor slam (form i) 13 c2kb1A_ 11.5 6 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 14 d1r3jc_ 10.7 6 Fold:Voltage-gated potassium channels Superfamily:Voltage-gated potassium channels Family:Voltage-gated potassium channels 15 c3lw5K_ 9.8 24 PDB header:photosynthesis Chain: K: PDB Molecule:photosystem i reaction center subunit x psak; PDBTitle: improved model of plant photosystem i 16 d1jb0k_ 7.9 28 Fold:Photosystem I reaction center subunit X, PsaK Superfamily:Photosystem I reaction center subunit X, PsaK Family:Photosystem I reaction center subunit X, PsaK 17 c1jb0K_ 7.9 28 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 18 d2hgka1 7.6 10 Fold:Bromodomain-like Superfamily:YqcC-like Family:YqcC-like 19 d2axth1 6.7 19 Fold:Single transmembrane helix Superfamily:Photosystem II 10 kDa phosphoprotein PsbH Family:PsbH-like 20 c2wsfG_ 6.5 50 PDB header:photosynthesis Chain: G: PDB Molecule:photosystem i reaction center subunit v, PDBTitle: improved model of plant photosystem i

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