Secondary structure and disorder prediction

		1	.	.	.	.	.	.	.	.	10	.	.	.	.	.	.	.	.	.	20	.	.	.	.	.	.	.	.	.	30	.	.	.	.	.	.	.	.	.	40	.	.	.	.	.	.	.	.	.	50	.	.	.	.	.	.	.	.	.	60
Sequence		M	N	L	W	Q	Q	N	Y	D	P	A	G	N	I	W	L	S	S	L	I	A	S	L	P	I	L	F	F	F	F	A	L	I	K	L	K	L	K	G	Y	V	A	A	S	W	T	V	A	I	A	L	A	V	A	L	L	F	Y	K	M
Secondary structure
SS confidence
Disorder		?	?	?	?	?	?	?																												?	?		?
Disorder confidence
		.	.	.	.	.	.	.	.	.	70	.	.	.	.	.	.	.	.	.	80	.	.	.	.	.	.	.	.	.	90	.	.	.	.	.	.	.	.	.	100	.	.	.	.	.	.	.	.	.	110	.	.	.	.	.	.	.	.	.	120
Sequence		P	V	A	N	A	L	A	S	V	V	Y	G	F	F	Y	G	L	W	P	I	A	W	I	I	I	A	A	V	F	V	Y	K	I	S	V	K	T	G	Q	F	D	I	I	R	S	S	I	L	S	I	T	P	D	Q	R	L	Q	M	L	I
Secondary structure
SS confidence
Disorder
Disorder confidence
		.	.	.	.	.	.	.	.	.	130	.	.	.	.	.	.	.	.	.	140	.	.	.	.	.	.	.	.	.	150	.	.	.	.	.	.	.	.	.	160	.	.	.	.	.	.	.	.	.	170	.	.	.	.	.	.	.	.	.	180
Sequence		V	G	F	C	F	G	A	F	L	E	G	A	A	G	F	G	A	P	V	A	I	T	A	A	L	L	V	G	L	G	F	K	P	L	Y	A	A	G	L	C	L	I	V	N	T	A	P	V	A	F	G	A	M	G	I	P	I	L	V	A
Secondary structure
SS confidence
Disorder
Disorder confidence
		.	.	.	.	.	.	.	.	.	190	.	.	.	.	.	.	.	.	.	200	.	.	.	.	.	.	.	.	.	210	.	.	.	.	.	.	.	.	.	220	.	.	.	.	.	.	.	.	.	230	.	.	.	.	.	.	.	.	.	240
Sequence		G	Q	V	T	G	I	D	S	F	E	I	G	Q	M	V	G	R	Q	L	P	F	M	T	I	I	V	L	F	W	I	M	A	I	M	D	G	W	R	G	I	K	E	T	W	P	A	V	V	V	A	G	G	S	F	A	I	A	Q	Y	L
Secondary structure
SS confidence
Disorder			?		?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	250	.	.	.	.	.	.	.	.	.	260	.	.	.	.	.	.	.	.	.	270	.	.	.	.	.	.	.	.	.	280	.	.	.	.	.	.	.	.	.	290	.	.	.	.	.	.	.	.	.	300
Sequence		S	S	N	F	I	G	P	E	L	P	D	I	I	S	S	L	V	S	L	L	C	L	T	L	F	L	K	R	W	Q	P	V	R	V	F	R	F	G	D	L	G	A	S	Q	V	D	M	T	L	A	H	T	G	Y	T	A	G	Q	V	L
Secondary structure
SS confidence
Disorder																																			?		?	?	?	?	?	?	?	?	?	?	?	?	?	?	?	?	?	?	?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	310	.	.	.	.	.	.	.	.	.	320	.	.	.	.	.	.	.	.	.	330	.	.	.	.	.	.	.	.	.	340	.	.	.	.	.	.	.	.	.	350	.	.	.	.	.	.	.	.	.	360
Sequence		R	A	W	T	P	F	L	F	L	T	A	T	V	T	L	W	S	I	P	P	F	K	A	L	F	A	S	G	G	A	L	Y	E	W	V	I	N	I	P	V	P	Y	L	D	K	L	V	A	R	M	P	P	V	V	S	E	A	T	A	Y
Secondary structure
SS confidence
Disorder																			?		?	?	?	?	?	?	?	?	?		?	?	?									?				?	?	?	?	?	?	?	?	?	?	?	?	?	?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	370	.	.	.	.	.	.	.	.	.	380	.	.	.	.	.	.	.	.	.	390	.	.	.	.	.	.	.	.	.	400	.	.	.	.	.	.	.	.	.	410	.	.	.	.	.	.	.	.	.	420
Sequence		A	A	V	F	K	F	D	W	F	S	A	T	G	T	A	I	L	F	A	A	L	L	S	I	V	W	L	K	M	K	P	S	D	A	I	S	T	F	G	S	T	L	K	E	L	A	L	P	I	Y	S	I	G	M	V	L	A	F	A	F
Secondary structure
SS confidence
Disorder		?																												?
Disorder confidence
		.	.	.	.	.	.	.	.	.	430	.	.	.	.	.	.	.	.	.	440	.	.	.	.	.	.	.	.	.	450	.	.	.	.	.	.	.	.	.	460	.	.	.	.	.	.	.	.	.	470	.	.	.	.	.	.	.	.	.	480
Sequence		I	S	N	Y	S	G	L	S	S	T	L	A	L	A	L	A	H	T	G	H	A	F	T	F	F	S	P	F	L	G	W	L	G	V	F	L	T	G	S	D	T	S	S	N	A	L	F	A	A	L	Q	A	T	A	A	Q	Q	I	G	V
Secondary structure
SS confidence
Disorder				?			?																																																				?
Disorder confidence
		.	.	.	.	.	.	.	.	.	490	.	.	.	.	.	.	.	.	.	500	.	.	.	.	.	.	.	.	.	510	.	.	.	.	.	.	.	.	.	520	.	.	.	.	.	.	.	.	.	530	.	.	.	.	.	.	.	.	.	540
Sequence		S	D	L	L	L	V	A	A	N	T	T	G	G	V	T	G	K	M	I	S	P	Q	S	I	A	I	A	C	A	A	V	G	L	V	G	K	E	S	D	L	F	R	F	T	V	K	H	S	L	I	F	T	C	I	V	G	V	I	T	T
Secondary structure
SS confidence
Disorder
Disorder confidence
		.	.	.	.	.	.	.	.	.	550	.
Sequence		L	Q	A	Y	V	L	T	W	M	I	P
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 1z96 chain A domain 1 Region: 146 - 164 Aligned: 19 Modelled: 19 Confidence: 25.2% Identity: 47% Fold: RuvA C-terminal domain-like Superfamily: UBA-like Family: UBA domain Phyre2 PDB 1cuk chain A domain 1 Region: 146 - 156 Aligned: 11 Modelled: 11 Confidence: 17.3% Identity: 64% Fold: RuvA C-terminal domain-like Superfamily: DNA helicase RuvA subunit, C-terminal domain Family: DNA helicase RuvA subunit, C-terminal domain Phyre2 PDB 2axt chain K domain 1 Region: 10 - 40 Aligned: 31 Modelled: 31 Confidence: 16.5% Identity: 16% Fold: Single transmembrane helix Superfamily: Photosystem II reaction center protein K, PsbK Family: PsbK-like Phyre2 PDB 2lbg chain A Region: 447 - 462 Aligned: 16 Modelled: 16 Confidence: 15.6% Identity: 38% PDB header:membrane protein Chain: A: PDB Molecule:major prion protein; PDBTitle: structure of the chr of the prion protein in dpc micelles Phyre2 PDB 3eh4 chain A Region: 14 - 336 Aligned: 313 Modelled: 318 Confidence: 14.5% Identity: 13% PDB header:oxidoreductase Chain: A: PDB Molecule:cytochrome c oxidase subunit 1; PDBTitle: structure of the reduced form of cytochrome ba3 oxidase from thermus2 thermophilus Phyre2 PDB 1xme chain A domain 1 Region: 18 - 336 Aligned: 309 Modelled: 314 Confidence: 13.6% Identity: 13% Fold: Cytochrome c oxidase subunit I-like Superfamily: Cytochrome c oxidase subunit I-like Family: Cytochrome c oxidase subunit I-like Phyre2 PDB 3a0b chain K Region: 10 - 40 Aligned: 31 Modelled: 31 Confidence: 10.6% Identity: 16% PDB header:electron transport Chain: K: PDB Molecule:photosystem ii reaction center protein k; PDBTitle: crystal structure of br-substituted photosystem ii complex Phyre2 PDB 3orc chain A Region: 471 - 485 Aligned: 15 Modelled: 15 Confidence: 8.4% Identity: 27% Fold: lambda repressor-like DNA-binding domains Superfamily: lambda repressor-like DNA-binding domains Family: Phage repressors Phyre2 PDB 2knc chain A Region: 249 - 284 Aligned: 36 Modelled: 36 Confidence: 7.3% Identity: 19% PDB header:cell adhesion Chain: A: PDB Molecule:integrin alpha-iib; PDBTitle: platelet integrin alfaiib-beta3 transmembrane-cytoplasmic2 heterocomplex Phyre2 PDB 3a0b chain K Region: 10 - 40 Aligned: 31 Modelled: 31 Confidence: 6.6% Identity: 16% PDB header:electron transport Chain: K: PDB Molecule:photosystem ii reaction center protein k; PDBTitle: crystal structure of br-substituted photosystem ii complex Phyre2 PDB 1y60 chain A Region: 458 - 478 Aligned: 21 Modelled: 21 Confidence: 6.3% Identity: 14% Fold: Ribosomal protein S5 domain 2-like Superfamily: Ribosomal protein S5 domain 2-like Family: Formaldehyde-activating enzyme, FAE Phyre2 PDB 3a0h chain K Region: 16 - 40 Aligned: 25 Modelled: 25 Confidence: 6.2% Identity: 16% PDB header:electron transport Chain: K: PDB Molecule:photosystem ii reaction center protein k; PDBTitle: crystal structure of i-substituted photosystem ii complex Phyre2 PDB 1ej5 chain A Region: 89 - 113 Aligned: 25 Modelled: 25 Confidence: 5.8% Identity: 12% Fold: Wiscott-Aldrich syndrome protein, WASP, C-terminal domain Superfamily: Wiscott-Aldrich syndrome protein, WASP, C-terminal domain Family: Wiscott-Aldrich syndrome protein, WASP, C-terminal domain Phyre2 PDB 2z3x chain C Region: 469 - 499 Aligned: 31 Modelled: 31 Confidence: 5.7% Identity: 19% PDB header:dna binding protein/dna Chain: C: PDB Molecule:small, acid-soluble spore protein c; PDBTitle: structure of a protein-dna complex essential for dna2 protection in spore of bacillus species Phyre2 1 d1z96a1 2 d1cuka1 3 d2axtk1 4 c2lbgA_ 5 c3eh4A_ 6 d1xmea1 7 c3a0bK_ 8 d3orca_ 9 c2kncA_ 10 c3a0bk_ 11 d1y60a_ 12 c3a0hk_ 13 d1ej5a_ 14 c2z3xC_

Detailed template information

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

1 d1z96a1 25.2 47 Fold:RuvA C-terminal domain-like Superfamily:UBA-like Family:UBA domain 2 d1cuka1 17.3 64 Fold:RuvA C-terminal domain-like Superfamily:DNA helicase RuvA subunit, C-terminal domain Family:DNA helicase RuvA subunit, C-terminal domain 3 d2axtk1 16.5 16 Fold:Single transmembrane helix Superfamily:Photosystem II reaction center protein K, PsbK Family:PsbK-like 4 c2lbgA_ 15.6 38 PDB header:membrane protein Chain: A: PDB Molecule:major prion protein; PDBTitle: structure of the chr of the prion protein in dpc micelles 5 c3eh4A_ 14.5 13 PDB header:oxidoreductase Chain: A: PDB Molecule:cytochrome c oxidase subunit 1; PDBTitle: structure of the reduced form of cytochrome ba3 oxidase from thermus2 thermophilus 6 d1xmea1 13.6 13 Fold:Cytochrome c oxidase subunit I-like Superfamily:Cytochrome c oxidase subunit I-like Family:Cytochrome c oxidase subunit I-like 7 c3a0bK_ 10.6 16 PDB header:electron transport Chain: K: PDB Molecule:photosystem ii reaction center protein k; PDBTitle: crystal structure of br-substituted photosystem ii complex 8 d3orca_ 8.4 27 Fold:lambda repressor-like DNA-binding domains Superfamily:lambda repressor-like DNA-binding domains Family:Phage repressors 9 c2kncA_ 7.3 19 PDB header:cell adhesion Chain: A: PDB Molecule:integrin alpha-iib; PDBTitle: platelet integrin alfaiib-beta3 transmembrane-cytoplasmic2 heterocomplex 10 c3a0bk_ 6.6 16 PDB header:electron transport Chain: K: PDB Molecule:photosystem ii reaction center protein k; PDBTitle: crystal structure of br-substituted photosystem ii complex 11 d1y60a_ 6.3 14 Fold:Ribosomal protein S5 domain 2-like Superfamily:Ribosomal protein S5 domain 2-like Family:Formaldehyde-activating enzyme, FAE 12 c3a0hk_ 6.2 16 PDB header:electron transport Chain: K: PDB Molecule:photosystem ii reaction center protein k; PDBTitle: crystal structure of i-substituted photosystem ii complex 13 d1ej5a_ 5.8 12 Fold:Wiscott-Aldrich syndrome protein, WASP, C-terminal domain Superfamily:Wiscott-Aldrich syndrome protein, WASP, C-terminal domain Family:Wiscott-Aldrich syndrome protein, WASP, C-terminal domain 14 c2z3xC_ 5.7 19 PDB header:dna binding protein/dna Chain: C: PDB Molecule:small, acid-soluble spore protein c; PDBTitle: structure of a protein-dna complex essential for dna2 protection in spore of bacillus species

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