Secondary structure and disorder prediction

		1	.	.	.	.	.	.	.	.	10	.	.	.	.	.	.	.	.	.	20	.	.	.	.	.	.	.	.	.	30	.	.	.	.	.	.	.	.	.	40	.	.	.	.	.	.	.	.	.	50	.	.	.	.	.	.	.	.	.	60
Sequence		M	N	T	V	G	T	P	L	L	W	G	G	F	A	V	V	V	A	I	M	L	A	I	D	L	L	L	Q	G	R	R	G	A	H	A	M	T	M	K	Q	A	A	A	W	S	L	V	W	V	T	L	S	L	L	F	N	A	A	F	W
Secondary structure
SS confidence
Disorder		?	?	?	?	?	?																									?	?	?	?	?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	70	.	.	.	.	.	.	.	.	.	80	.	.	.	.	.	.	.	.	.	90	.	.	.	.	.	.	.	.	.	100	.	.	.	.	.	.	.	.	.	110	.	.	.	.	.	.	.	.	.	120
Sequence		W	Y	L	V	Q	T	E	G	R	A	V	A	D	P	Q	A	L	A	F	L	T	G	Y	L	I	E	K	S	L	A	V	D	N	V	F	V	W	L	M	L	F	S	Y	F	S	V	P	A	A	L	Q	R	R	V	L	V	Y	G	V	L
Secondary structure
SS confidence
Disorder						?	?	?	?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	130	.	.	.	.	.	.	.	.	.	140	.	.	.	.	.	.	.	.	.	150	.	.	.	.	.	.	.	.	.	160	.	.	.	.	.	.	.	.	.	170	.	.	.	.	.	.	.	.	.	180
Sequence		G	A	I	V	L	R	T	I	M	I	F	T	G	S	W	L	I	S	Q	F	D	W	I	L	Y	I	F	G	A	F	L	L	F	T	G	V	K	M	A	L	A	H	E	D	E	S	G	I	G	D	K	P	L	V	R	W	L	R	G	H
Secondary structure
SS confidence
Disorder																																												?	?	?	?	?	?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	190	.	.	.	.	.	.	.	.	.	200	.	.	.	.	.	.	.	.	.	210	.	.	.	.	.	.	.	.	.	220	.	.	.	.	.	.	.	.	.	230	.	.	.	.	.	.	.	.	.	240
Sequence		L	R	M	T	D	T	I	D	N	E	H	F	F	V	R	K	N	G	L	L	Y	A	T	P	L	M	L	V	L	I	L	V	E	L	S	D	V	I	F	A	V	D	S	I	P	A	I	F	A	V	T	T	D	P	F	I	V	L	T	S
Secondary structure
SS confidence
Disorder										?	?	?	?	?						?
Disorder confidence
		.	.	.	.	.	.	.	.	.	250	.	.	.	.	.	.	.	.	.	260	.	.	.	.	.	.	.	.	.	270	.	.	.	.	.	.	.	.	.	280	.	.	.	.	.	.	.	.	.	290	.	.	.	.	.	.	.	.	.	300
Sequence		N	L	F	A	I	L	G	L	R	A	M	Y	F	L	L	A	G	V	A	E	R	F	S	M	L	K	Y	G	L	A	V	I	L	V	F	I	G	I	K	M	L	I	V	D	F	Y	H	I	P	I	A	V	S	L	G	V	V	F	G	I
Secondary structure
SS confidence
Disorder
Disorder confidence
		.	.	.	.	.	.	.	.	.	310	.	.	.	.	.	.	.	.	.	320	.
Sequence		L	V	M	T	F	I	I	N	A	W	V	N	Y	R	H	D	K	Q	R	G	G
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 1yew chain I Region: 37 - 63 Aligned: 24 Modelled: 27 Confidence: 11.9% Identity: 13% PDB header:oxidoreductase, membrane protein Chain: I: PDB Molecule:particulate methane monooxygenase, b subunit; PDBTitle: crystal structure of particulate methane monooxygenase Phyre2 PDB 3rgb chain A Region: 37 - 63 Aligned: 24 Modelled: 27 Confidence: 11.9% Identity: 13% PDB header:oxidoreductase Chain: A: PDB Molecule:methane monooxygenase subunit b2; PDBTitle: crystal structure of particulate methane monooxygenase from2 methylococcus capsulatus (bath) Phyre2 PDB 1xio chain A Region: 4 - 181 Aligned: 157 Modelled: 178 Confidence: 8.9% Identity: 17% PDB header:signaling protein Chain: A: PDB Molecule:anabaena sensory rhodopsin; PDBTitle: anabaena sensory rhodopsin Phyre2 PDB 1xio chain A Region: 4 - 181 Aligned: 157 Modelled: 178 Confidence: 8.9% Identity: 17% Fold: Family A G protein-coupled receptor-like Superfamily: Family A G protein-coupled receptor-like Family: Bacteriorhodopsin-like Phyre2 PDB 1uaz chain A Region: 5 - 180 Aligned: 164 Modelled: 176 Confidence: 7.0% Identity: 10% Fold: Family A G protein-coupled receptor-like Superfamily: Family A G protein-coupled receptor-like Family: Bacteriorhodopsin-like Phyre2 PDB 1dxs chain A Region: 89 - 114 Aligned: 19 Modelled: 26 Confidence: 6.8% Identity: 21% Fold: SAM domain-like Superfamily: SAM/Pointed domain Family: SAM (sterile alpha motif) domain Phyre2 PDB 3prq chain L Region: 105 - 129 Aligned: 25 Modelled: 25 Confidence: 6.3% Identity: 32% PDB header:photosynthesis Chain: L: PDB Molecule:photosystem ii reaction center protein l; PDBTitle: crystal structure of cyanobacterial photosystem ii in complex with2 terbutryn (part 1 of 2). this file contains first monomer of psii3 dimer Phyre2 PDB 3bz1 chain L Region: 105 - 129 Aligned: 25 Modelled: 25 Confidence: 6.3% Identity: 32% PDB header:electron transport Chain: L: PDB Molecule:photosystem ii reaction center protein l; PDBTitle: crystal structure of cyanobacterial photosystem ii (part 12 of 2). this file contains first monomer of psii dimer Phyre2 PDB 3prr chain L Region: 105 - 129 Aligned: 25 Modelled: 25 Confidence: 6.3% Identity: 32% PDB header:photosynthesis Chain: L: PDB Molecule:photosystem ii reaction center protein l; PDBTitle: crystal structure of cyanobacterial photosystem ii in complex with2 terbutryn (part 2 of 2). this file contains second monomer of psii3 dimer Phyre2 PDB 1s5l chain L Region: 105 - 129 Aligned: 25 Modelled: 25 Confidence: 6.3% Identity: 32% PDB header:photosynthesis Chain: L: PDB Molecule:photosystem ii reaction center l protein; PDBTitle: architecture of the photosynthetic oxygen evolving center Phyre2 PDB 2axt chain L Region: 105 - 129 Aligned: 25 Modelled: 25 Confidence: 6.3% Identity: 32% PDB header:electron transport Chain: L: PDB Molecule:photosystem ii reaction center l protein; PDBTitle: crystal structure of photosystem ii from thermosynechococcus elongatus Phyre2 PDB 3arc chain L Region: 105 - 129 Aligned: 25 Modelled: 25 Confidence: 6.3% Identity: 32% PDB header:electron transport, photosynthesis Chain: L: PDB Molecule:photosystem ii reaction center protein l; PDBTitle: crystal structure of oxygen-evolving photosystem ii at 1.9 angstrom2 resolution Phyre2 PDB 1s5l chain L Region: 105 - 129 Aligned: 25 Modelled: 25 Confidence: 6.3% Identity: 32% PDB header:photosynthesis Chain: L: PDB Molecule:photosystem ii reaction center l protein; PDBTitle: architecture of the photosynthetic oxygen evolving center Phyre2 PDB 3bz2 chain L Region: 105 - 129 Aligned: 25 Modelled: 25 Confidence: 6.3% Identity: 32% PDB header:electron transport Chain: L: PDB Molecule:photosystem ii reaction center protein l; PDBTitle: crystal structure of cyanobacterial photosystem ii (part 22 of 2). this file contains second monomer of psii dimer Phyre2 PDB 2axt chain L Region: 105 - 129 Aligned: 25 Modelled: 25 Confidence: 6.3% Identity: 32% PDB header:electron transport Chain: L: PDB Molecule:photosystem ii reaction center l protein; PDBTitle: crystal structure of photosystem ii from thermosynechococcus elongatus Phyre2 PDB 2axt chain L domain 1 Region: 105 - 129 Aligned: 25 Modelled: 25 Confidence: 6.3% Identity: 32% Fold: Single transmembrane helix Superfamily: Photosystem II reaction center protein L, PsbL Family: PsbL-like Phyre2 PDB 3kzi chain L Region: 105 - 129 Aligned: 25 Modelled: 25 Confidence: 6.3% Identity: 32% PDB header:electron transport Chain: L: PDB Molecule:photosystem ii reaction center protein l; PDBTitle: crystal structure of monomeric form of cyanobacterial photosystem ii Phyre2 PDB 3a0h chain L Region: 105 - 129 Aligned: 25 Modelled: 25 Confidence: 6.2% Identity: 32% PDB header:electron transport Chain: L: PDB Molecule:photosystem ii reaction center protein l; PDBTitle: crystal structure of i-substituted photosystem ii complex Phyre2 PDB 3a0h chain L Region: 105 - 129 Aligned: 25 Modelled: 25 Confidence: 6.2% Identity: 32% PDB header:electron transport Chain: L: PDB Molecule:photosystem ii reaction center protein l; PDBTitle: crystal structure of i-substituted photosystem ii complex Phyre2 PDB 3a0b chain L Region: 105 - 129 Aligned: 25 Modelled: 25 Confidence: 6.2% Identity: 32% PDB header:electron transport Chain: L: PDB Molecule:photosystem ii reaction center protein l; PDBTitle: crystal structure of br-substituted photosystem ii complex Phyre2 1 c1yewI_ 2 c3rgbA_ 3 c1xioA_ 4 d1xioa_ 5 d1uaza_ 6 d1dxsa_ 7 c3prqL_ 8 c3bz1L_ 9 c3prrL_ 10 c1s5ll_ 11 c2axtl_ 12 c3arcL_ 13 c1s5lL_ 14 c3bz2L_ 15 c2axtL_ 16 d2axtl1 17 c3kziL_ 18 c3a0hl_ 19 c3a0hL_ 20 c3a0bl_ 21 22

Detailed template information

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

1 c1yewI_ 11.9 13 PDB header:oxidoreductase, membrane protein Chain: I: PDB Molecule:particulate methane monooxygenase, b subunit; PDBTitle: crystal structure of particulate methane monooxygenase 2 c3rgbA_ 11.9 13 PDB header:oxidoreductase Chain: A: PDB Molecule:methane monooxygenase subunit b2; PDBTitle: crystal structure of particulate methane monooxygenase from2 methylococcus capsulatus (bath) 3 c1xioA_ 8.9 17 PDB header:signaling protein Chain: A: PDB Molecule:anabaena sensory rhodopsin; PDBTitle: anabaena sensory rhodopsin 4 d1xioa_ 8.9 17 Fold:Family A G protein-coupled receptor-like Superfamily:Family A G protein-coupled receptor-like Family:Bacteriorhodopsin-like 5 d1uaza_ 7.0 10 Fold:Family A G protein-coupled receptor-like Superfamily:Family A G protein-coupled receptor-like Family:Bacteriorhodopsin-like 6 d1dxsa_ 6.8 21 Fold:SAM domain-like Superfamily:SAM/Pointed domain Family:SAM (sterile alpha motif) domain 7 c3prqL_ 6.3 32 PDB header:photosynthesis Chain: L: PDB Molecule:photosystem ii reaction center protein l; PDBTitle: crystal structure of cyanobacterial photosystem ii in complex with2 terbutryn (part 1 of 2). this file contains first monomer of psii3 dimer 8 c3bz1L_ 6.3 32 PDB header:electron transport Chain: L: PDB Molecule:photosystem ii reaction center protein l; PDBTitle: crystal structure of cyanobacterial photosystem ii (part 12 of 2). this file contains first monomer of psii dimer 9 c3prrL_ 6.3 32 PDB header:photosynthesis Chain: L: PDB Molecule:photosystem ii reaction center protein l; PDBTitle: crystal structure of cyanobacterial photosystem ii in complex with2 terbutryn (part 2 of 2). this file contains second monomer of psii3 dimer 10 c1s5ll_ 6.3 32 PDB header:photosynthesis Chain: L: PDB Molecule:photosystem ii reaction center l protein; PDBTitle: architecture of the photosynthetic oxygen evolving center 11 c2axtl_ 6.3 32 PDB header:electron transport Chain: L: PDB Molecule:photosystem ii reaction center l protein; PDBTitle: crystal structure of photosystem ii from thermosynechococcus elongatus 12 c3arcL_ 6.3 32 PDB header:electron transport, photosynthesis Chain: L: PDB Molecule:photosystem ii reaction center protein l; PDBTitle: crystal structure of oxygen-evolving photosystem ii at 1.9 angstrom2 resolution 13 c1s5lL_ 6.3 32 PDB header:photosynthesis Chain: L: PDB Molecule:photosystem ii reaction center l protein; PDBTitle: architecture of the photosynthetic oxygen evolving center 14 c3bz2L_ 6.3 32 PDB header:electron transport Chain: L: PDB Molecule:photosystem ii reaction center protein l; PDBTitle: crystal structure of cyanobacterial photosystem ii (part 22 of 2). this file contains second monomer of psii dimer 15 c2axtL_ 6.3 32 PDB header:electron transport Chain: L: PDB Molecule:photosystem ii reaction center l protein; PDBTitle: crystal structure of photosystem ii from thermosynechococcus elongatus 16 d2axtl1 6.3 32 Fold:Single transmembrane helix Superfamily:Photosystem II reaction center protein L, PsbL Family:PsbL-like 17 c3kziL_ 6.3 32 PDB header:electron transport Chain: L: PDB Molecule:photosystem ii reaction center protein l; PDBTitle: crystal structure of monomeric form of cyanobacterial photosystem ii 18 c3a0hl_ 6.2 32 PDB header:electron transport Chain: L: PDB Molecule:photosystem ii reaction center protein l; PDBTitle: crystal structure of i-substituted photosystem ii complex 19 c3a0hL_ 6.2 32 PDB header:electron transport Chain: L: PDB Molecule:photosystem ii reaction center protein l; PDBTitle: crystal structure of i-substituted photosystem ii complex 20 c3a0bl_ 6.2 32 PDB header:electron transport Chain: L: PDB Molecule:photosystem ii reaction center protein l; PDBTitle: crystal structure of br-substituted photosystem ii complex 21 c3arcl_ not modelled 6.2 35 PDB header:electron transport, photosynthesis Chain: L: PDB Molecule:photosystem ii reaction center protein l; PDBTitle: crystal structure of oxygen-evolving photosystem ii at 1.9 angstrom2 resolution 22 d1r3jc_ not modelled 5.9 14 Fold:Voltage-gated potassium channels Superfamily:Voltage-gated potassium channels Family:Voltage-gated potassium channels

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

Transmembrane helix prediction

Transmembrane helices have been predicted in your sequence to adopt the topology shown below

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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