Secondary structure and disorder prediction

		1	.	.	.	.	.	.	.	.	10	.	.	.	.	.	.	.	.	.	20	.	.	.	.	.	.	.	.	.	30	.	.	.	.	.	.	.	.	.	40	.	.	.	.	.	.	.	.	.	50	.	.	.	.	.	.	.	.	.	60
Sequence		M	S	T	S	I	R	I	C	S	Y	L	L	L	P	L	I	Y	L	L	V	N	V	K	I	A	Q	L	G	E	S	F	P	I	T	I	V	T	F	L	P	V	L	L	L	L	F	L	E	R	I	S	V	K	K	L	M	I	A	L	G
Secondary structure
SS confidence
Disorder		?	?	?	?	?		?
Disorder confidence
		.	.	.	.	.	.	.	.	.	70	.	.	.	.	.	.	.	.	.	80	.	.	.	.	.	.	.	.	.	90	.	.	.	.	.	.	.	.	.	100	.	.	.	.	.	.	.	.	.	110	.	.	.	.	.	.	.	.	.	120
Sequence		I	G	A	G	L	T	A	F	N	Y	L	F	G	Q	S	L	D	A	S	K	Y	V	T	S	T	M	L	F	V	Y	I	V	I	I	I	G	M	V	W	S	I	R	F	K	T	I	S	P	H	N	H	R	K	I	L	R	F	F	Y	L
Secondary structure
SS confidence
Disorder
Disorder confidence
		.	.	.	.	.	.	.	.	.	130	.	.	.	.	.	.	.	.	.	140	.	.	.	.	.	.	.	.	.	150	.	.	.	.	.	.	.	.	.	160	.	.	.	.	.	.	.	.	.	170	.	.	.	.	.	.	.	.	.	180
Sequence		V	V	G	L	V	V	A	L	A	A	V	E	M	A	Q	I	I	L	T	G	G	S	S	I	M	E	S	I	S	K	Y	L	I	Y	S	N	S	Y	V	L	N	F	I	K	F	G	G	K	R	T	T	A	L	Y	F	E	P	A	F	F
Secondary structure
SS confidence
Disorder
Disorder confidence
		.	.	.	.	.	.	.	.	.	190	.	.	.	.	.	.	.	.	.	200	.	.	.	.	.	.	.	.	.	210	.	.	.	.	.	.	.	.	.	220	.	.	.	.	.	.	.	.	.	230	.	.	.	.	.	.	.	.	.	240
Sequence		A	L	A	L	I	S	I	W	L	S	I	K	Q	F	G	I	K	T	P	K	T	D	A	M	I	L	A	G	I	I	L	S	G	S	F	S	G	V	M	T	F	I	L	F	Y	L	L	E	W	A	F	Q	Y	L	N	K	E	A	I	K
Secondary structure
SS confidence
Disorder																															?																														?
Disorder confidence
		.	.	.	.	.	.	.	.	.	250	.	.	.	.	.	.	.	.	.	260	.	.	.	.	.	.	.	.	.	270	.	.	.	.	.	.	.	.	.	280	.	.	.	.	.	.	.	.	.	290	.	.	.	.	.	.	.	.	.	300
Sequence		K	K	L	P	L	A	L	I	S	L	A	V	F	L	V	G	V	V	I	A	F	P	Y	I	S	T	R	L	G	D	L	G	T	E	G	S	S	S	Y	Y	R	I	V	G	P	L	V	M	V	G	Y	S	L	T	H	I	D	G	V	V
Secondary structure
SS confidence
Disorder		?		?	?	?																									?	?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	310	.	.	.	.	.	.	.	.	.	320	.	.	.	.	.	.	.	.	.	330	.	.	.	.	.	.	.	.	.	340	.	.	.	.	.	.	.	.	.	350	.	.	.	.	.	.	.	.	.	360
Sequence		R	F	G	S	L	Y	E	Y	V	A	S	F	G	I	F	N	G	A	D	V	G	K	T	I	D	N	G	L	Y	L	L	I	I	Y	F	S	W	F	A	V	F	L	S	L	W	Y	M	G	K	V	I	K	M	M	I	N	A	F	G	D
Secondary structure
SS confidence
Disorder																																																									?
Disorder confidence
		.	.	.	.	.	.	.	.	.	370	.	.	.	.	.	.	.	.	.	380	.	.	.	.	.	.	.	.	.	390	.	.	.	.	.	.	.	.	.	400	.	.	.	.	.
Sequence		N	R	N	F	R	V	Q	L	Y	L	F	T	P	V	S	L	F	F	T	G	S	I	F	S	P	E	Y	A	F	L	I	V	C	P	F	I	L	R	K	A	L	N	I	T	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 3cz6 chain A Region: 142 - 208 Aligned: 47 Modelled: 47 Confidence: 14.6% Identity: 28% PDB header:protein binding Chain: A: PDB Molecule:dna-binding protein rap1; PDBTitle: crystal structure of the rap1 c-terminus Phyre2 PDB 2qqh chain A Region: 296 - 329 Aligned: 28 Modelled: 34 Confidence: 12.6% Identity: 25% PDB header:immune system, membrane protein Chain: A: PDB Molecule:complement component c8 alpha chain; PDBTitle: structure of c8a-macpf reveals mechanism of membrane attack2 in complement immune defense Phyre2 PDB 1bg6 chain A domain 1 Region: 192 - 213 Aligned: 22 Modelled: 22 Confidence: 12.1% Identity: 23% Fold: 6-phosphogluconate dehydrogenase C-terminal domain-like Superfamily: 6-phosphogluconate dehydrogenase C-terminal domain-like Family: N-(1-D-carboxylethyl)-L-norvaline dehydrogenase Phyre2 PDB 1es9 chain A Region: 286 - 331 Aligned: 44 Modelled: 46 Confidence: 9.8% Identity: 20% Fold: Flavodoxin-like Superfamily: SGNH hydrolase Family: Acetylhydrolase Phyre2 PDB 3h0g chain E Region: 272 - 284 Aligned: 13 Modelled: 13 Confidence: 7.6% Identity: 38% PDB header:transcription Chain: E: PDB Molecule:dna-directed rna polymerases i, ii, and iii PDBTitle: rna polymerase ii from schizosaccharomyces pombe Phyre2 PDB 1dzf chain A domain 2 Region: 273 - 283 Aligned: 11 Modelled: 11 Confidence: 7.4% Identity: 45% Fold: RPB5-like RNA polymerase subunit Superfamily: RPB5-like RNA polymerase subunit Family: RPB5 Phyre2 PDB 1n8i chain A Region: 301 - 325 Aligned: 25 Modelled: 25 Confidence: 7.3% Identity: 36% Fold: TIM beta/alpha-barrel Superfamily: Malate synthase G Family: Malate synthase G Phyre2 PDB 2f22 chain A domain 1 Region: 189 - 200 Aligned: 12 Modelled: 12 Confidence: 6.6% Identity: 50% Fold: DinB/YfiT-like putative metalloenzymes Superfamily: DinB/YfiT-like putative metalloenzymes Family: DinB-like Phyre2 PDB 1hmj chain A Region: 273 - 283 Aligned: 11 Modelled: 11 Confidence: 6.3% Identity: 55% Fold: RPB5-like RNA polymerase subunit Superfamily: RPB5-like RNA polymerase subunit Family: RPB5 Phyre2 PDB 2lbf chain A Region: 2 - 64 Aligned: 63 Modelled: 63 Confidence: 5.6% Identity: 29% PDB header:ribosomal protein Chain: A: PDB Molecule:60s acidic ribosomal protein p1; PDBTitle: solution structure of the dimerization domain of human ribosomal2 protein p1/p2 heterodimer Phyre2 PDB 2axt chain A domain 1 Region: 333 - 385 Aligned: 51 Modelled: 53 Confidence: 5.4% Identity: 24% Fold: Bacterial photosystem II reaction centre, L and M subunits Superfamily: Bacterial photosystem II reaction centre, L and M subunits Family: Bacterial photosystem II reaction centre, L and M subunits Phyre2 1 c3cz6A_ 2 c2qqhA_ 3 d1bg6a1 4 d1es9a_ 5 c3h0gE_ 6 d1dzfa2 7 d1n8ia_ 8 d2f22a1 9 d1hmja_ 10 c2lbfA_ 11 d2axta1

Detailed template information

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

1 c3cz6A_ 14.6 28 PDB header:protein binding Chain: A: PDB Molecule:dna-binding protein rap1; PDBTitle: crystal structure of the rap1 c-terminus 2 c2qqhA_ 12.6 25 PDB header:immune system, membrane protein Chain: A: PDB Molecule:complement component c8 alpha chain; PDBTitle: structure of c8a-macpf reveals mechanism of membrane attack2 in complement immune defense 3 d1bg6a1 12.1 23 Fold:6-phosphogluconate dehydrogenase C-terminal domain-like Superfamily:6-phosphogluconate dehydrogenase C-terminal domain-like Family:N-(1-D-carboxylethyl)-L-norvaline dehydrogenase 4 d1es9a_ 9.8 20 Fold:Flavodoxin-like Superfamily:SGNH hydrolase Family:Acetylhydrolase 5 c3h0gE_ 7.6 38 PDB header:transcription Chain: E: PDB Molecule:dna-directed rna polymerases i, ii, and iii PDBTitle: rna polymerase ii from schizosaccharomyces pombe 6 d1dzfa2 7.4 45 Fold:RPB5-like RNA polymerase subunit Superfamily:RPB5-like RNA polymerase subunit Family:RPB5 7 d1n8ia_ 7.3 36 Fold:TIM beta/alpha-barrel Superfamily:Malate synthase G Family:Malate synthase G 8 d2f22a1 6.6 50 Fold:DinB/YfiT-like putative metalloenzymes Superfamily:DinB/YfiT-like putative metalloenzymes Family:DinB-like 9 d1hmja_ 6.3 55 Fold:RPB5-like RNA polymerase subunit Superfamily:RPB5-like RNA polymerase subunit Family:RPB5 10 c2lbfA_ 5.6 29 PDB header:ribosomal protein Chain: A: PDB Molecule:60s acidic ribosomal protein p1; PDBTitle: solution structure of the dimerization domain of human ribosomal2 protein p1/p2 heterodimer 11 d2axta1 5.4 24 Fold:Bacterial photosystem II reaction centre, L and M subunits Superfamily:Bacterial photosystem II reaction centre, L and M subunits Family:Bacterial photosystem II reaction centre, L and M subunits

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