Secondary structure and disorder prediction

		1	.	.	.	.	.	.	.	.	10	.	.	.	.	.	.	.	.	.	20	.	.	.	.	.	.	.	.	.	30	.	.	.	.	.	.	.	.	.	40	.	.	.	.	.	.	.	.	.	50	.	.	.	.	.	.	.	.	.	60
Sequence		M	N	E	L	V	Q	I	L	K	N	T	R	Q	H	L	M	T	G	V	S	H	M	I	P	F	V	V	S	G	G	I	L	L	A	V	S	V	M	L	Y	G	K	G	A	V	P	D	A	V	A	D	P	N	L	K	K	L	F	D	I
Secondary structure
SS confidence
Disorder		?	?	?	?	?																																					?	?		?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	70	.	.	.	.	.	.	.	.	.	80	.	.	.	.	.	.	.	.	.	90	.	.	.	.	.	.	.	.	.	100	.	.	.	.	.	.	.	.	.	110	.	.	.	.	.	.	.	.	.	120
Sequence		G	V	A	G	L	T	L	M	V	P	F	L	A	A	Y	I	G	Y	S	I	A	E	R	S	A	L	A	P	C	A	I	G	A	W	V	G	N	S	F	G	A	G	F	F	G	A	L	I	A	G	I	I	G	G	I	V	V	H	Y	L
Secondary structure
SS confidence
Disorder																																							?	?	?	?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	130	.	.	.	.	.	.	.	.	.	140	.	.	.	.	.	.	.	.	.	150	.	.	.	.	.	.	.	.	.	160	.	.	.	.	.	.	.	.	.	170	.	.	.	.	.	.	.	.	.	180
Sequence		K	K	I	P	V	H	K	V	L	R	S	V	M	P	I	F	I	I	P	I	V	G	T	L	I	T	A	G	I	M	M	W	G	L	G	E	P	V	G	A	L	T	N	S	L	T	Q	W	L	Q	G	M	Q	Q	G	S	I	V	M	L
Secondary structure
SS confidence
Disorder								?
Disorder confidence
		.	.	.	.	.	.	.	.	.	190	.	.	.	.	.	.	.	.	.	200	.	.	.	.	.	.	.	.	.	210	.	.	.	.	.	.	.	.	.	220	.	.	.	.	.	.	.	.	.	230	.	.	.	.	.	.	.	.	.	240
Sequence		A	V	I	M	G	L	M	L	A	F	D	M	G	G	P	V	N	K	V	A	Y	A	F	M	L	I	C	V	A	Q	G	V	Y	T	V	V	A	I	A	A	V	G	I	C	I	P	P	L	G	M	G	L	A	T	L	I	G	R	K	N
Secondary structure
SS confidence
Disorder																																?												?																?
Disorder confidence
		.	.	.	.	.	.	.	.	.	250	.	.	.	.	.	.	.	.	.	260	.	.	.	.	.	.	.	.	.	270	.	.	.	.	.	.	.	.	.	280	.	.	.	.	.	.	.	.	.	290	.	.	.	.	.	.	.	.	.	300
Sequence		F	S	A	E	E	R	E	T	G	K	A	A	L	V	M	G	C	V	G	V	T	E	G	A	I	P	F	A	A	A	D	P	L	R	V	I	P	S	I	M	V	G	S	V	C	G	A	V	T	A	A	L	V	G	A	Q	C	Y	A	G
Secondary structure
SS confidence
Disorder									?	?	?	?																																												?	?	?	?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	310	.	.	.	.	.	.	.	.	.	320	.	.	.	.	.	.	.	.	.	330	.	.	.	.	.	.	.	.	.	340	.	.	.	.	.	.	.	.	.	350	.	.	.	.	.	.	.	.	.
Sequence		W	G	G	L	I	V	L	P	V	V	E	G	K	L	G	Y	I	A	A	V	A	V	G	A	V	V	T	A	V	C	V	N	V	L	K	S	L	A	R	K	N	G	S	S	T	D	E	K	E	D	D	L	D	L	D	F	E	I	N
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 3qnq chain D Region: 2 - 353 Aligned: 350 Modelled: 352 Confidence: 100.0% Identity: 17% 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 2b2h chain A Region: 191 - 353 Aligned: 162 Modelled: 163 Confidence: 82.0% Identity: 14% PDB header:transport protein Chain: A: PDB Molecule:ammonium transporter; PDBTitle: ammonium transporter amt-1 from a. fulgidus (as) Phyre2 PDB 3hd6 chain A Region: 209 - 357 Aligned: 145 Modelled: 149 Confidence: 79.5% Identity: 16% PDB header:membrane protein, transport protein Chain: A: PDB Molecule:ammonium transporter rh type c; PDBTitle: crystal structure of the human rhesus glycoprotein rhcg Phyre2 PDB 2knc chain A Region: 312 - 355 Aligned: 44 Modelled: 44 Confidence: 76.3% Identity: 14% PDB header:cell adhesion Chain: A: PDB Molecule:integrin alpha-iib; PDBTitle: platelet integrin alfaiib-beta3 transmembrane-cytoplasmic2 heterocomplex Phyre2 PDB 3b9y chain A Region: 191 - 355 Aligned: 162 Modelled: 165 Confidence: 66.2% Identity: 12% PDB header:transport protein Chain: A: PDB Molecule:ammonium transporter family rh-like protein; PDBTitle: crystal structure of the nitrosomonas europaea rh protein Phyre2 PDB 2jln chain A Region: 321 - 357 Aligned: 37 Modelled: 37 Confidence: 42.6% Identity: 11% PDB header:membrane protein Chain: A: PDB Molecule:mhp1; PDBTitle: structure of mhp1, a nucleobase-cation-symport-1 family2 transporter Phyre2 PDB 1j4n chain A Region: 103 - 352 Aligned: 222 Modelled: 222 Confidence: 42.2% Identity: 10% Fold: Aquaporin-like Superfamily: Aquaporin-like Family: Aquaporin-like Phyre2 PDB 2oar chain A domain 1 Region: 312 - 353 Aligned: 42 Modelled: 42 Confidence: 26.6% Identity: 2% Fold: Gated mechanosensitive channel Superfamily: Gated mechanosensitive channel Family: Gated mechanosensitive channel Phyre2 PDB 3d9s chain B Region: 137 - 357 Aligned: 193 Modelled: 197 Confidence: 18.2% Identity: 15% PDB header:membrane protein Chain: B: PDB Molecule:aquaporin-5; PDBTitle: human aquaporin 5 (aqp5) - high resolution x-ray structure Phyre2 PDB 1fft chain B domain 2 Region: 313 - 358 Aligned: 46 Modelled: 46 Confidence: 14.6% Identity: 9% Fold: Transmembrane helix hairpin Superfamily: Cytochrome c oxidase subunit II-like, transmembrane region Family: Cytochrome c oxidase subunit II-like, transmembrane region Phyre2 PDB 3dtu chain B domain 2 Region: 312 - 355 Aligned: 44 Modelled: 44 Confidence: 13.5% Identity: 11% Fold: Transmembrane helix hairpin Superfamily: Cytochrome c oxidase subunit II-like, transmembrane region Family: Cytochrome c oxidase subunit II-like, transmembrane region Phyre2 PDB 1ymg chain A Region: 177 - 353 Aligned: 149 Modelled: 152 Confidence: 13.2% Identity: 14% PDB header:membrane protein Chain: A: PDB Molecule:lens fiber major intrinsic protein; PDBTitle: the channel architecture of aquaporin o at 2.2 angstrom resolution Phyre2 PDB 1ymg chain A domain 1 Region: 177 - 353 Aligned: 149 Modelled: 152 Confidence: 13.2% Identity: 14% Fold: Aquaporin-like Superfamily: Aquaporin-like Family: Aquaporin-like Phyre2 PDB 3ehb chain B domain 2 Region: 312 - 355 Aligned: 44 Modelled: 44 Confidence: 11.0% Identity: 9% Fold: Transmembrane helix hairpin Superfamily: Cytochrome c oxidase subunit II-like, transmembrane region Family: Cytochrome c oxidase subunit II-like, transmembrane region Phyre2 PDB 2oar chain A Region: 279 - 353 Aligned: 75 Modelled: 75 Confidence: 7.1% Identity: 9% PDB header:membrane protein Chain: A: PDB Molecule:large-conductance mechanosensitive channel; PDBTitle: mechanosensitive channel of large conductance (mscl) Phyre2 PDB 2ket chain A Region: 2 - 26 Aligned: 21 Modelled: 25 Confidence: 6.9% Identity: 24% PDB header:antibiotic Chain: A: PDB Molecule:cathelicidin-6; PDBTitle: solution structure of bmap-27 Phyre2 PDB 2ht2 chain B Region: 108 - 351 Aligned: 228 Modelled: 229 Confidence: 6.1% Identity: 9% PDB header:membrane protein Chain: B: PDB Molecule:h(+)/cl(-) exchange transporter clca; PDBTitle: structure of the escherichia coli clc chloride channel2 y445h mutant and fab complex Phyre2 PDB 1qle chain B Region: 312 - 356 Aligned: 45 Modelled: 45 Confidence: 5.9% Identity: 9% PDB header:oxidoreductase/immune system Chain: B: PDB Molecule:cytochrome c oxidase polypeptide ii; PDBTitle: cryo-structure of the paracoccus denitrificans four-subunit2 cytochrome c oxidase in the completely oxidized state3 complexed with an antibody fv fragment Phyre2 1 c3qnqD_ 2 c2b2hA_ 3 c3hd6A_ 4 c2kncA_ 5 c3b9yA_ 6 c2jlnA_ 7 d1j4na_ 8 d2oara1 9 c3d9sB_ 10 d1fftb2 11 d3dtub2 12 c1ymgA_ 13 d1ymga1 14 d3ehbb2 15 c2oarA_ 16 c2ketA_ 17 c2ht2B_ 18 c1qleB_

Detailed template information

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

1 c3qnqD_ 100.0 17 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 2 c2b2hA_ 82.0 14 PDB header:transport protein Chain: A: PDB Molecule:ammonium transporter; PDBTitle: ammonium transporter amt-1 from a. fulgidus (as) 3 c3hd6A_ 79.5 16 PDB header:membrane protein, transport protein Chain: A: PDB Molecule:ammonium transporter rh type c; PDBTitle: crystal structure of the human rhesus glycoprotein rhcg 4 c2kncA_ 76.3 14 PDB header:cell adhesion Chain: A: PDB Molecule:integrin alpha-iib; PDBTitle: platelet integrin alfaiib-beta3 transmembrane-cytoplasmic2 heterocomplex 5 c3b9yA_ 66.2 12 PDB header:transport protein Chain: A: PDB Molecule:ammonium transporter family rh-like protein; PDBTitle: crystal structure of the nitrosomonas europaea rh protein 6 c2jlnA_ 42.6 11 PDB header:membrane protein Chain: A: PDB Molecule:mhp1; PDBTitle: structure of mhp1, a nucleobase-cation-symport-1 family2 transporter 7 d1j4na_ 42.2 10 Fold:Aquaporin-like Superfamily:Aquaporin-like Family:Aquaporin-like 8 d2oara1 26.6 2 Fold:Gated mechanosensitive channel Superfamily:Gated mechanosensitive channel Family:Gated mechanosensitive channel 9 c3d9sB_ 18.2 15 PDB header:membrane protein Chain: B: PDB Molecule:aquaporin-5; PDBTitle: human aquaporin 5 (aqp5) - high resolution x-ray structure 10 d1fftb2 14.6 9 Fold:Transmembrane helix hairpin Superfamily:Cytochrome c oxidase subunit II-like, transmembrane region Family:Cytochrome c oxidase subunit II-like, transmembrane region 11 d3dtub2 13.5 11 Fold:Transmembrane helix hairpin Superfamily:Cytochrome c oxidase subunit II-like, transmembrane region Family:Cytochrome c oxidase subunit II-like, transmembrane region 12 c1ymgA_ 13.2 14 PDB header:membrane protein Chain: A: PDB Molecule:lens fiber major intrinsic protein; PDBTitle: the channel architecture of aquaporin o at 2.2 angstrom resolution 13 d1ymga1 13.2 14 Fold:Aquaporin-like Superfamily:Aquaporin-like Family:Aquaporin-like 14 d3ehbb2 11.0 9 Fold:Transmembrane helix hairpin Superfamily:Cytochrome c oxidase subunit II-like, transmembrane region Family:Cytochrome c oxidase subunit II-like, transmembrane region 15 c2oarA_ 7.1 9 PDB header:membrane protein Chain: A: PDB Molecule:large-conductance mechanosensitive channel; PDBTitle: mechanosensitive channel of large conductance (mscl) 16 c2ketA_ 6.9 24 PDB header:antibiotic Chain: A: PDB Molecule:cathelicidin-6; PDBTitle: solution structure of bmap-27 17 c2ht2B_ 6.1 9 PDB header:membrane protein Chain: B: PDB Molecule:h(+)/cl(-) exchange transporter clca; PDBTitle: structure of the escherichia coli clc chloride channel2 y445h mutant and fab complex 18 c1qleB_ 5.9 9 PDB header:oxidoreductase/immune system Chain: B: PDB Molecule:cytochrome c oxidase polypeptide ii; PDBTitle: cryo-structure of the paracoccus denitrificans four-subunit2 cytochrome c oxidase in the completely oxidized state3 complexed 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