Secondary structure and disorder prediction

		1	.	.	.	.	.	.	.	.	10	.	.	.	.	.	.	.	.	.	20	.	.	.	.	.	.	.	.	.	30	.	.	.	.	.	.	.	.	.	40	.	.	.	.	.	.	.	.	.	50	.	.	.	.	.	.	.	.	.	60
Sequence		M	R	L	S	L	P	R	L	K	M	P	R	L	P	G	F	S	I	L	V	W	I	S	T	A	L	K	G	W	V	M	G	S	R	E	K	D	T	D	S	L	I	M	Y	D	R	T	L	L	W	L	T	F	G	L	A	A	I	G	F
Secondary structure
SS confidence
Disorder		?	?	?	?	?	?	?	?	?	?	?	?	?	?	?																			?	?	?	?	?	?		?
Disorder confidence
		.	.	.	.	.	.	.	.	.	70	.	.	.	.	.	.	.	.	.	80	.	.	.	.	.	.	.	.	.	90	.	.	.	.	.	.	.	.	.	100	.	.	.	.	.	.	.	.	.	110	.	.	.	.	.	.	.	.	.	120
Sequence		I	M	V	T	S	A	S	M	P	I	G	Q	R	L	T	N	D	P	F	F	F	A	K	R	D	G	V	Y	L	I	L	A	F	I	L	A	I	I	T	L	R	L	P	M	E	F	W	Q	R	Y	S	A	T	M	L	L	G	S	I	I
Secondary structure
SS confidence
Disorder							?	?	?	?	?			?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	130	.	.	.	.	.	.	.	.	.	140	.	.	.	.	.	.	.	.	.	150	.	.	.	.	.	.	.	.	.	160	.	.	.	.	.	.	.	.	.	170	.	.	.	.	.	.	.	.	.	180
Sequence		L	L	M	I	V	L	V	V	G	S	S	V	K	G	A	S	R	W	I	D	L	G	L	L	R	I	Q	P	A	E	L	T	K	L	S	L	F	C	Y	I	A	N	Y	L	V	R	K	G	D	E	V	R	N	N	L	R	G	F	L	K
Secondary structure
SS confidence
Disorder								?	?	?	?	?																																						?	?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	190	.	.	.	.	.	.	.	.	.	200	.	.	.	.	.	.	.	.	.	210	.	.	.	.	.	.	.	.	.	220	.	.	.	.	.	.	.	.	.	230	.	.	.	.	.	.	.	.	.	240
Sequence		P	M	G	V	I	L	V	L	A	V	L	L	L	A	Q	P	D	L	G	T	V	V	V	L	F	V	T	T	L	A	M	L	F	L	A	G	A	K	L	W	Q	F	I	A	I	I	G	M	G	I	S	A	V	V	L	L	I	L	A	E
Secondary structure
SS confidence
Disorder
Disorder confidence
		.	.	.	.	.	.	.	.	.	250	.	.	.	.	.	.	.	.	.	260	.	.	.	.	.	.	.	.	.	270	.	.	.	.	.	.	.	.	.	280	.	.	.	.	.	.	.	.	.	290	.	.	.	.	.	.	.	.	.	300
Sequence		P	Y	R	I	R	R	V	T	A	F	W	N	P	W	E	D	P	F	G	S	G	Y	Q	L	T	Q	S	L	M	A	F	G	R	G	E	L	W	G	Q	G	L	G	N	S	V	Q	K	L	E	Y	L	P	E	A	H	T	D	F	I	F
Secondary structure
SS confidence
Disorder																																														?
Disorder confidence
		.	.	.	.	.	.	.	.	.	310	.	.	.	.	.	.	.	.	.	320	.	.	.	.	.	.	.	.	.	330	.	.	.	.	.	.	.	.	.	340	.	.	.	.	.	.	.	.	.	350	.	.	.	.	.	.	.	.	.	360
Sequence		A	I	I	G	E	E	L	G	Y	V	G	V	V	L	A	L	L	M	V	F	F	V	A	F	R	A	M	S	I	G	R	K	A	L	E	I	D	H	R	F	S	G	F	L	A	C	S	I	G	I	W	F	S	F	Q	A	L	V	N	V
Secondary structure
SS confidence
Disorder																																					?
Disorder confidence
		.	.	.	.	.	.	.	.	.	370	.	.	.	.	.	.	.	.	.	380	.	.	.	.	.	.	.	.	.	390	.	.	.	.	.	.	.	.	.	400	.	.	.	.	.	.	.	.	.	410	.	.	.	.
Sequence		G	A	A	A	G	M	L	P	T	K	G	L	T	L	P	L	I	S	Y	G	G	S	S	L	L	I	M	S	T	A	I	M	M	L	L	R	I	D	Y	E	T	R	L	E	K	A	Q	A	F	V	R	G	S	R
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 2aki chain Y Region: 337 - 412 Aligned: 65 Modelled: 76 Confidence: 37.6% Identity: 14% PDB header:protein transport Chain: Y: PDB Molecule:preprotein translocase secy subunit; PDBTitle: normal mode-based flexible fitted coordinates of a2 translocating secyeg protein-conducting channel into the3 cryo-em map of a secyeg-nascent chain-70s ribosome complex4 from e. coli Phyre2 PDB 3dl8 chain H Region: 337 - 412 Aligned: 65 Modelled: 76 Confidence: 28.5% Identity: 9% PDB header:protein transport Chain: H: PDB Molecule:preprotein translocase subunit secy; PDBTitle: structure of the complex of aquifex aeolicus secyeg and2 bacillus subtilis seca Phyre2 PDB 2aze chain A domain 1 Region: 368 - 377 Aligned: 10 Modelled: 10 Confidence: 27.4% Identity: 40% Fold: E2F-DP heterodimerization region Superfamily: E2F-DP heterodimerization region Family: DP dimerization segment Phyre2 PDB 2knc chain B Region: 307 - 343 Aligned: 33 Modelled: 37 Confidence: 22.9% Identity: 15% PDB header:cell adhesion Chain: B: PDB Molecule:integrin beta-3; PDBTitle: platelet integrin alfaiib-beta3 transmembrane-cytoplasmic2 heterocomplex Phyre2 PDB 3j01 chain A Region: 337 - 412 Aligned: 65 Modelled: 76 Confidence: 21.6% Identity: 11% PDB header:ribosome/ribosomal protein Chain: A: PDB Molecule:preprotein translocase secy subunit; PDBTitle: structure of the ribosome-secye complex in the membrane environment Phyre2 PDB 2klu chain A Region: 373 - 410 Aligned: 38 Modelled: 38 Confidence: 17.3% Identity: 18% PDB header:immune system, membrane protein Chain: A: PDB Molecule:t-cell surface glycoprotein cd4; PDBTitle: nmr structure of the transmembrane and cytoplasmic domains2 of human cd4 Phyre2 PDB 2gdw chain A domain 1 Region: 363 - 387 Aligned: 24 Modelled: 25 Confidence: 14.0% Identity: 29% Fold: Acyl carrier protein-like Superfamily: ACP-like Family: Peptidyl carrier domain Phyre2 PDB 3din chain F Region: 337 - 412 Aligned: 65 Modelled: 76 Confidence: 12.4% Identity: 14% PDB header:membrane protein, protein transport Chain: F: PDB Molecule:preprotein translocase subunit secy; PDBTitle: crystal structure of the protein-translocation complex formed by the2 secy channel and the seca atpase Phyre2 PDB 2png chain A domain 1 Region: 360 - 387 Aligned: 28 Modelled: 28 Confidence: 10.9% Identity: 29% Fold: Acyl carrier protein-like Superfamily: ACP-like Family: Acyl-carrier protein (ACP) Phyre2 PDB 1iwg chain A domain 8 Region: 349 - 411 Aligned: 63 Modelled: 63 Confidence: 7.5% Identity: 16% Fold: Multidrug efflux transporter AcrB transmembrane domain Superfamily: Multidrug efflux transporter AcrB transmembrane domain Family: Multidrug efflux transporter AcrB transmembrane domain Phyre2 PDB 2ywx chain A Region: 367 - 389 Aligned: 22 Modelled: 23 Confidence: 5.6% Identity: 18% PDB header:lyase Chain: A: PDB Molecule:phosphoribosylaminoimidazole carboxylase catalytic subunit; PDBTitle: crystal structure of phosphoribosylaminoimidazole carboxylase2 catalytic subunit from methanocaldococcus jannaschii Phyre2 PDB 2cq8 chain A Region: 363 - 390 Aligned: 28 Modelled: 28 Confidence: 5.3% Identity: 7% PDB header:oxidoreductase Chain: A: PDB Molecule:10-formyltetrahydrofolate dehydrogenase; PDBTitle: solution structure of rsgi ruh-033, a pp-binding domain of2 10-fthfdh from human cdna Phyre2 PDB 1ar1 chain B Region: 43 - 110 Aligned: 68 Modelled: 68 Confidence: 5.0% Identity: 4% PDB header:complex (oxidoreductase/antibody) Chain: B: PDB Molecule:cytochrome c oxidase; PDBTitle: structure at 2.7 angstrom resolution of the paracoccus2 denitrificans two-subunit cytochrome c oxidase complexed3 with an antibody fv fragment Phyre2 1 c2akiY_ 2 c3dl8H_ 3 d2azea1 4 c2kncB_ 5 c3j01A_ 6 c2kluA_ 7 d2gdwa1 8 c3dinF_ 9 d2pnga1 10 d1iwga8 11 c2ywxA_ 12 c2cq8A_ 13 c1ar1B_

Detailed template information

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

1 c2akiY_ 37.6 14 PDB header:protein transport Chain: Y: PDB Molecule:preprotein translocase secy subunit; PDBTitle: normal mode-based flexible fitted coordinates of a2 translocating secyeg protein-conducting channel into the3 cryo-em map of a secyeg-nascent chain-70s ribosome complex4 from e. coli 2 c3dl8H_ 28.5 9 PDB header:protein transport Chain: H: PDB Molecule:preprotein translocase subunit secy; PDBTitle: structure of the complex of aquifex aeolicus secyeg and2 bacillus subtilis seca 3 d2azea1 27.4 40 Fold:E2F-DP heterodimerization region Superfamily:E2F-DP heterodimerization region Family:DP dimerization segment 4 c2kncB_ 22.9 15 PDB header:cell adhesion Chain: B: PDB Molecule:integrin beta-3; PDBTitle: platelet integrin alfaiib-beta3 transmembrane-cytoplasmic2 heterocomplex 5 c3j01A_ 21.6 11 PDB header:ribosome/ribosomal protein Chain: A: PDB Molecule:preprotein translocase secy subunit; PDBTitle: structure of the ribosome-secye complex in the membrane environment 6 c2kluA_ 17.3 18 PDB header:immune system, membrane protein Chain: A: PDB Molecule:t-cell surface glycoprotein cd4; PDBTitle: nmr structure of the transmembrane and cytoplasmic domains2 of human cd4 7 d2gdwa1 14.0 29 Fold:Acyl carrier protein-like Superfamily:ACP-like Family:Peptidyl carrier domain 8 c3dinF_ 12.4 14 PDB header:membrane protein, protein transport Chain: F: PDB Molecule:preprotein translocase subunit secy; PDBTitle: crystal structure of the protein-translocation complex formed by the2 secy channel and the seca atpase 9 d2pnga1 10.9 29 Fold:Acyl carrier protein-like Superfamily:ACP-like Family:Acyl-carrier protein (ACP) 10 d1iwga8 7.5 16 Fold:Multidrug efflux transporter AcrB transmembrane domain Superfamily:Multidrug efflux transporter AcrB transmembrane domain Family:Multidrug efflux transporter AcrB transmembrane domain 11 c2ywxA_ 5.6 18 PDB header:lyase Chain: A: PDB Molecule:phosphoribosylaminoimidazole carboxylase catalytic subunit; PDBTitle: crystal structure of phosphoribosylaminoimidazole carboxylase2 catalytic subunit from methanocaldococcus jannaschii 12 c2cq8A_ 5.3 7 PDB header:oxidoreductase Chain: A: PDB Molecule:10-formyltetrahydrofolate dehydrogenase; PDBTitle: solution structure of rsgi ruh-033, a pp-binding domain of2 10-fthfdh from human cdna 13 c1ar1B_ 5.0 4 PDB header:complex (oxidoreductase/antibody) Chain: B: PDB Molecule:cytochrome c oxidase; PDBTitle: structure at 2.7 angstrom resolution of the paracoccus2 denitrificans two-subunit cytochrome c oxidase complexed3 with an antibody fv fragment

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