Secondary structure and disorder prediction

		1	.	.	.	.	.	.	.	.	10	.	.	.	.	.	.	.	.	.	20	.	.	.	.	.	.	.	.	.	30	.	.	.	.	.	.	.	.	.	40	.	.	.	.	.	.	.	.	.	50	.	.	.	.	.	.	.	.	.	60
Sequence		M	K	L	N	F	K	G	F	F	K	A	A	G	L	F	P	L	A	L	M	L	S	G	C	I	S	Y	A	L	V	S	H	T	A	K	G	S	S	G	K	Y	Q	S	Q	S	D	T	I	T	G	L	S	Q	A	K	D	S	N	G	T
Secondary structure
SS confidence
Disorder		?	?	?	?	?																								?		?	?	?		?	?			?							?				?	?	?	?	?	?	?	?	?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	70	.	.	.	.	.	.	.	.	.	80	.	.	.	.	.	.	.	.	.	90	.	.	.	.	.	.	.	.	.	100	.	.	.	.	.	.	.	.	.	110	.	.	.	.	.	.	.	.	.	120
Sequence		K	G	Y	V	F	V	G	E	S	L	D	Y	L	I	T	D	G	A	D	D	I	V	K	M	L	N	D	P	A	L	N	R	H	N	I	Q	V	A	D	D	A	R	F	V	L	N	A	G	K	K	K	F	T	G	T	I	S	L	Y	Y
Secondary structure
SS confidence
Disorder																												?	?	?	?	?	?								?	?		?				?	?	?	?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	130	.	.	.	.	.	.	.	.	.	140	.	.	.	.	.	.	.	.	.	150	.	.	.	.	.	.	.	.	.	160	.	.	.	.	.	.	.	.	.	170	.	.	.	.	.	.	.	.	.	180
Sequence		Y	W	N	N	E	E	E	K	A	L	A	T	H	Y	G	F	A	C	G	V	Q	H	C	T	R	S	L	E	N	L	K	G	T	I	H	E	K	N	K	N	M	D	Y	S	K	V	M	A	F	Y	H	P	F	K	V	R	F	Y	E	Y
Secondary structure
SS confidence
Disorder																?							?	?	?						?	?	?						?	?	?	?	?	?	?	?	?	?	?	?											?
Disorder confidence
		.	.	.	.	.	.	.	.	.	190	.	.	.	.	.	.	.	.	.	200	.	.	.	.	.	.	.	.	.	210	.	.	.	.	.	.	.	.
Sequence		Y	S	P	R	G	I	P	D	G	V	S	A	A	L	L	P	V	T	V	T	L	D	I	I	T	A	P	L	Q	F	L	V	V	Y	A	V	N	Q
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 2k89 chain A Region: 59 - 75 Aligned: 17 Modelled: 17 Confidence: 38.7% Identity: 18% PDB header:protein binding Chain: A: PDB Molecule:phospholipase a-2-activating protein; PDBTitle: solution structure of a novel ubiquitin-binding domain from2 human plaa (pfuc, gly76-pro77 cis isomer) Phyre2 PDB 3pst chain A Region: 61 - 75 Aligned: 15 Modelled: 15 Confidence: 30.3% Identity: 33% PDB header:nuclear protein Chain: A: PDB Molecule:protein doa1; PDBTitle: crystal structure of pul and pfu(mutate) domain Phyre2 PDB 3l3f chain X Region: 61 - 75 Aligned: 15 Modelled: 15 Confidence: 27.8% Identity: 33% PDB header:protein binding Chain: X: PDB Molecule:protein doa1; PDBTitle: crystal structure of a pfu-pul domain pair of saccharomyces cerevisiae2 doa1/ufd3 Phyre2 PDB 3c0n chain A domain 1 Region: 47 - 79 Aligned: 25 Modelled: 33 Confidence: 25.9% Identity: 32% Fold: C-type lectin-like Superfamily: C-type lectin-like Family: Aerolysin/Pertussis toxin (APT) domain Phyre2 PDB 2e76 chain D Region: 3 - 29 Aligned: 27 Modelled: 27 Confidence: 18.7% Identity: 7% PDB header:photosynthesis Chain: D: PDB Molecule:cytochrome b6-f complex iron-sulfur subunit; PDBTitle: crystal structure of the cytochrome b6f complex with tridecyl-2 stigmatellin (tds) from m.laminosus Phyre2 PDB 1oe1 chain A domain 2 Region: 58 - 78 Aligned: 21 Modelled: 21 Confidence: 14.1% Identity: 19% Fold: Cupredoxin-like Superfamily: Cupredoxins Family: Multidomain cupredoxins Phyre2 PDB 2cs7 chain A domain 1 Region: 39 - 73 Aligned: 35 Modelled: 35 Confidence: 11.4% Identity: 23% Fold: IL8-like Superfamily: PhtA domain-like Family: PhtA domain-like Phyre2 PDB 2pq4 chain B Region: 1 - 18 Aligned: 18 Modelled: 18 Confidence: 10.8% Identity: 39% PDB header:chaperone/oxidoreductase Chain: B: PDB Molecule:periplasmic nitrate reductase precursor; PDBTitle: nmr solution structure of napd in complex with napa1-352 signal peptide Phyre2 PDB 1pgl chain 1 domain 1 Region: 50 - 152 Aligned: 102 Modelled: 103 Confidence: 7.0% Identity: 10% Fold: Nucleoplasmin-like/VP (viral coat and capsid proteins) Superfamily: Positive stranded ssRNA viruses Family: Comoviridae-like VP Phyre2 PDB 1hq0 chain A Region: 21 - 26 Aligned: 6 Modelled: 6 Confidence: 5.3% Identity: 67% Fold: CNF1/YfiH-like putative cysteine hydrolases Superfamily: CNF1/YfiH-like putative cysteine hydrolases Family: Type 1 cytotoxic necrotizing factor, catalytic domain Phyre2 1 c2k89A_ 2 c3pstA_ 3 c3l3fX_ 4 d3c0na1 5 c2e76D_ 6 d1oe1a2 7 d2cs7a1 8 c2pq4B_ 9 d1pgl11 10 d1hq0a_

Detailed template information

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

1 c2k89A_ 38.7 18 PDB header:protein binding Chain: A: PDB Molecule:phospholipase a-2-activating protein; PDBTitle: solution structure of a novel ubiquitin-binding domain from2 human plaa (pfuc, gly76-pro77 cis isomer) 2 c3pstA_ 30.3 33 PDB header:nuclear protein Chain: A: PDB Molecule:protein doa1; PDBTitle: crystal structure of pul and pfu(mutate) domain 3 c3l3fX_ 27.8 33 PDB header:protein binding Chain: X: PDB Molecule:protein doa1; PDBTitle: crystal structure of a pfu-pul domain pair of saccharomyces cerevisiae2 doa1/ufd3 4 d3c0na1 25.9 32 Fold:C-type lectin-like Superfamily:C-type lectin-like Family:Aerolysin/Pertussis toxin (APT) domain 5 c2e76D_ 18.7 7 PDB header:photosynthesis Chain: D: PDB Molecule:cytochrome b6-f complex iron-sulfur subunit; PDBTitle: crystal structure of the cytochrome b6f complex with tridecyl-2 stigmatellin (tds) from m.laminosus 6 d1oe1a2 14.1 19 Fold:Cupredoxin-like Superfamily:Cupredoxins Family:Multidomain cupredoxins 7 d2cs7a1 11.4 23 Fold:IL8-like Superfamily:PhtA domain-like Family:PhtA domain-like 8 c2pq4B_ 10.8 39 PDB header:chaperone/oxidoreductase Chain: B: PDB Molecule:periplasmic nitrate reductase precursor; PDBTitle: nmr solution structure of napd in complex with napa1-352 signal peptide 9 d1pgl11 7.0 10 Fold:Nucleoplasmin-like/VP (viral coat and capsid proteins) Superfamily:Positive stranded ssRNA viruses Family:Comoviridae-like VP 10 d1hq0a_ 5.3 67 Fold:CNF1/YfiH-like putative cysteine hydrolases Superfamily:CNF1/YfiH-like putative cysteine hydrolases Family:Type 1 cytotoxic necrotizing factor, catalytic 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