Secondary structure and disorder prediction

		1	.	.	.	.	.	.	.	.	10	.	.	.	.	.	.	.	.	.	20	.	.	.	.	.	.	.	.	.	30	.	.	.	.	.	.	.	.	.	40	.	.	.	.	.	.	.	.	.	50	.	.	.	.	.	.	.	.	.	60
Sequence		M	S	H	D	P	Q	P	L	G	G	K	I	I	S	K	P	V	M	I	F	G	P	L	I	V	I	C	M	L	L	I	V	K	R	L	V	F	G	L	G	S	V	S	D	L	N	G	G	F	P	W	G	V	W	I	A	F	D	L	L
Secondary structure
SS confidence
Disorder		?	?	?	?	?	?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	70	.	.	.	.	.	.	.	.	.	80	.	.	.	.	.	.	.	.	.	90	.	.	.	.	.	.	.	.	.	100	.	.	.	.	.	.	.	.	.	110	.	.	.	.	.	.	.	.	.	120
Sequence		I	G	T	G	F	A	C	G	G	W	A	L	A	W	A	V	Y	V	F	N	R	G	Q	Y	H	P	L	V	R	P	A	L	L	A	S	L	F	G	Y	S	L	G	G	L	S	I	T	I	D	V	G	R	Y	W	N	L	P	Y	F	Y
Secondary structure
SS confidence
Disorder
Disorder confidence
		.	.	.	.	.	.	.	.	.	130	.	.	.	.	.	.	.	.	.	140	.	.	.	.	.	.	.	.	.	150	.	.	.	.	.	.	.	.	.	160	.	.	.	.	.	.	.	.	.	170	.	.	.	.	.	.	.	.	.	180
Sequence		I	P	G	H	F	N	V	N	S	V	L	F	E	T	A	V	C	M	T	I	Y	I	G	V	M	A	L	E	F	A	P	A	L	F	E	R	L	G	W	K	V	S	L	Q	R	L	N	K	V	M	F	F	I	I	A	L	G	A	L	L
Secondary structure
SS confidence
Disorder			?	?																																	?	?	?	?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	190	.	.	.	.	.	.	.	.	.	200	.	.	.	.	.	.	.	.	.	210	.	.	.	.	.	.	.	.	.	220	.	.	.	.	.	.	.	.	.	230	.	.	.	.	.	.	.	.	.	240
Sequence		P	T	M	H	Q	S	S	M	G	S	L	M	I	S	A	G	Y	K	V	H	P	L	W	Q	S	Y	E	M	L	P	L	F	S	L	L	T	A	F	I	M	G	F	S	I	V	I	F	E	G	S	L	V	Q	A	G	L	R	G	N	G
Secondary structure
SS confidence
Disorder																?	?		?																																					?		?	?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	250	.	.	.	.	.	.	.	.	.	260	.	.	.	.	.	.	.	.	.	270	.	.	.	.	.	.	.	.	.	280	.	.	.	.	.	.	.	.	.	290	.	.	.	.	.	.	.	.	.	300
Sequence		P	D	E	K	S	L	F	V	K	L	T	N	T	I	S	V	L	L	A	I	F	I	V	L	R	F	G	E	L	I	Y	R	D	K	L	S	L	A	F	A	G	D	F	Y	S	V	M	F	W	I	E	V	L	L	M	L	F	P	L	V
Secondary structure
SS confidence
Disorder		?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	310	.	.	.	.	.	.	.	.	.	320	.	.	.	.	.	.	.	.	.	330	.	.	.	.	.	.	.	.	.	340	.	.	.	.	.	.	.	.	.	350	.	.	.	.	.	.	.	.	.	360
Sequence		V	L	R	V	A	K	L	R	N	D	S	R	M	L	F	L	S	A	L	S	A	L	L	G	C	A	T	W	R	L	T	Y	S	L	V	A	F	N	P	G	G	G	Y	A	Y	F	P	T	W	E	E	L	L	I	S	I	G	F	V	A
Secondary structure
SS confidence
Disorder						?	?	?				?																													?
Disorder confidence
		.	.	.	.	.	.	.	.	.	370	.	.	.	.	.	.	.	.	.	380	.	.	.	.	.	.	.	.	.	390	.	.
Sequence		I	E	I	C	A	Y	I	V	L	I	R	L	L	P	I	L	P	P	L	K	Q	N	D	H	N	R	H	E	A	S	K	A
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 2vpz chain G Region: 46 - 332 Aligned: 236 Modelled: 255 Confidence: 100.0% Identity: 17% PDB header:oxidoreductase Chain: G: PDB Molecule:hypothetical membrane spanning protein; PDBTitle: polysulfide reductase native structure Phyre2 PDB 1ar1 chain A Region: 5 - 390 Aligned: 375 Modelled: 386 Confidence: 89.6% Identity: 12% Fold: Cytochrome c oxidase subunit I-like Superfamily: Cytochrome c oxidase subunit I-like Family: Cytochrome c oxidase subunit I-like Phyre2 PDB 1v54 chain A Region: 5 - 386 Aligned: 372 Modelled: 381 Confidence: 62.2% Identity: 11% Fold: Cytochrome c oxidase subunit I-like Superfamily: Cytochrome c oxidase subunit I-like Family: Cytochrome c oxidase subunit I-like Phyre2 PDB 1fft chain A Region: 5 - 388 Aligned: 374 Modelled: 375 Confidence: 61.6% Identity: 11% Fold: Cytochrome c oxidase subunit I-like Superfamily: Cytochrome c oxidase subunit I-like Family: Cytochrome c oxidase subunit I-like Phyre2 PDB 1fft chain F Region: 5 - 388 Aligned: 374 Modelled: 375 Confidence: 61.6% Identity: 11% PDB header:oxidoreductase Chain: F: PDB Molecule:ubiquinol oxidase; PDBTitle: the structure of ubiquinol oxidase from escherichia coli Phyre2 PDB 3qnq chain D Region: 313 - 388 Aligned: 76 Modelled: 76 Confidence: 48.5% Identity: 4% PDB header:membrane protein, transport protein Chain: D: PDB Molecule:pts system, cellobiose-specific iic component; PDBTitle: crystal structure of the transporter chbc, the iic component from the2 n,n'-diacetylchitobiose-specific phosphotransferase system Phyre2 PDB 1m56 chain G Region: 5 - 388 Aligned: 373 Modelled: 384 Confidence: 39.0% Identity: 12% PDB header:oxidoreductase Chain: G: PDB Molecule:cytochrome c oxidase; PDBTitle: structure of cytochrome c oxidase from rhodobactor2 sphaeroides (wild type) Phyre2 PDB 2b2h chain A Region: 218 - 391 Aligned: 173 Modelled: 174 Confidence: 10.5% Identity: 11% PDB header:transport protein Chain: A: PDB Molecule:ammonium transporter; PDBTitle: ammonium transporter amt-1 from a. fulgidus (as) Phyre2 PDB 2bbj chain B Region: 14 - 83 Aligned: 55 Modelled: 70 Confidence: 9.5% Identity: 20% PDB header:metal transport/membrane protein Chain: B: PDB Molecule:divalent cation transport-related protein; PDBTitle: crystal structure of the cora mg2+ transporter Phyre2 PDB 1vcn chain A Region: 108 - 129 Aligned: 22 Modelled: 22 Confidence: 7.7% Identity: 18% PDB header:ligase Chain: A: PDB Molecule:ctp synthetase; PDBTitle: crystal structure of t.th. hb8 ctp synthetase complex with sulfate2 anion Phyre2 PDB 1vco chain A domain 2 Region: 108 - 129 Aligned: 22 Modelled: 22 Confidence: 7.3% Identity: 18% Fold: P-loop containing nucleoside triphosphate hydrolases Superfamily: P-loop containing nucleoside triphosphate hydrolases Family: Nitrogenase iron protein-like Phyre2 PDB 1s1m chain A domain 2 Region: 108 - 129 Aligned: 22 Modelled: 22 Confidence: 6.9% Identity: 18% Fold: P-loop containing nucleoside triphosphate hydrolases Superfamily: P-loop containing nucleoside triphosphate hydrolases Family: Nitrogenase iron protein-like Phyre2 PDB 3nva chain B Region: 108 - 129 Aligned: 22 Modelled: 22 Confidence: 6.9% Identity: 18% PDB header:ligase Chain: B: PDB Molecule:ctp synthase; PDBTitle: dimeric form of ctp synthase from sulfolobus solfataricus Phyre2 PDB 1kp0 chain A domain 1 Region: 108 - 115 Aligned: 8 Modelled: 8 Confidence: 6.6% Identity: 50% Fold: Ribonuclease H-like motif Superfamily: Creatinase/prolidase N-terminal domain Family: Creatinase/prolidase N-terminal domain Phyre2 PDB 3j01 chain A Region: 218 - 392 Aligned: 174 Modelled: 175 Confidence: 5.8% Identity: 9% 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 1 c2vpzG_ 2 d1ar1a_ 3 d1v54a_ 4 d1ffta_ 5 c1fftF_ 6 c3qnqD_ 7 c1m56G_ 8 c2b2hA_ 9 c2bbjB_ 10 c1vcnA_ 11 d1vcoa2 12 d1s1ma2 13 c3nvaB_ 14 d1kp0a1 15 c3j01A_

Detailed template information

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

1 c2vpzG_ 100.0 17 PDB header:oxidoreductase Chain: G: PDB Molecule:hypothetical membrane spanning protein; PDBTitle: polysulfide reductase native structure 2 d1ar1a_ 89.6 12 Fold:Cytochrome c oxidase subunit I-like Superfamily:Cytochrome c oxidase subunit I-like Family:Cytochrome c oxidase subunit I-like 3 d1v54a_ 62.2 11 Fold:Cytochrome c oxidase subunit I-like Superfamily:Cytochrome c oxidase subunit I-like Family:Cytochrome c oxidase subunit I-like 4 d1ffta_ 61.6 11 Fold:Cytochrome c oxidase subunit I-like Superfamily:Cytochrome c oxidase subunit I-like Family:Cytochrome c oxidase subunit I-like 5 c1fftF_ 61.6 11 PDB header:oxidoreductase Chain: F: PDB Molecule:ubiquinol oxidase; PDBTitle: the structure of ubiquinol oxidase from escherichia coli 6 c3qnqD_ 48.5 4 PDB header:membrane protein, transport protein Chain: D: PDB Molecule:pts system, cellobiose-specific iic component; PDBTitle: crystal structure of the transporter chbc, the iic component from the2 n,n'-diacetylchitobiose-specific phosphotransferase system 7 c1m56G_ 39.0 12 PDB header:oxidoreductase Chain: G: PDB Molecule:cytochrome c oxidase; PDBTitle: structure of cytochrome c oxidase from rhodobactor2 sphaeroides (wild type) 8 c2b2hA_ 10.5 11 PDB header:transport protein Chain: A: PDB Molecule:ammonium transporter; PDBTitle: ammonium transporter amt-1 from a. fulgidus (as) 9 c2bbjB_ 9.5 20 PDB header:metal transport/membrane protein Chain: B: PDB Molecule:divalent cation transport-related protein; PDBTitle: crystal structure of the cora mg2+ transporter 10 c1vcnA_ 7.7 18 PDB header:ligase Chain: A: PDB Molecule:ctp synthetase; PDBTitle: crystal structure of t.th. hb8 ctp synthetase complex with sulfate2 anion 11 d1vcoa2 7.3 18 Fold:P-loop containing nucleoside triphosphate hydrolases Superfamily:P-loop containing nucleoside triphosphate hydrolases Family:Nitrogenase iron protein-like 12 d1s1ma2 6.9 18 Fold:P-loop containing nucleoside triphosphate hydrolases Superfamily:P-loop containing nucleoside triphosphate hydrolases Family:Nitrogenase iron protein-like 13 c3nvaB_ 6.9 18 PDB header:ligase Chain: B: PDB Molecule:ctp synthase; PDBTitle: dimeric form of ctp synthase from sulfolobus solfataricus 14 d1kp0a1 6.6 50 Fold:Ribonuclease H-like motif Superfamily:Creatinase/prolidase N-terminal domain Family:Creatinase/prolidase N-terminal domain 15 c3j01A_ 5.8 9 PDB header:ribosome/ribosomal protein Chain: A: PDB Molecule:preprotein translocase secy subunit; PDBTitle: structure of the ribosome-secye complex in the membrane environment

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