Secondary structure and disorder prediction

		1	.	.	.	.	.	.	.	.	10	.	.	.	.	.	.	.	.	.	20	.	.	.	.	.	.	.	.	.	30	.	.	.	.	.	.	.	.	.	40	.	.	.	.	.	.	.	.	.	50	.	.	.	.	.	.	.	.	.	60
Sequence		M	R	N	K	L	S	F	D	L	Q	L	S	A	R	K	A	A	I	A	E	R	I	A	A	H	K	I	A	R	S	K	V	S	V	F	L	M	A	M	S	A	G	V	F	M	A	I	G	F	T	F	Y	L	S	V	I	A	D	A	P
Secondary structure
SS confidence
Disorder		?	?	?	?	?	?	?	?																																																	?			?
Disorder confidence
		.	.	.	.	.	.	.	.	.	70	.	.	.	.	.	.	.	.	.	80	.	.	.	.	.	.	.	.	.	90	.	.	.	.	.	.	.	.	.	100	.	.	.	.	.	.	.	.	.	110	.	.	.	.	.	.	.	.	.	120
Sequence		S	S	Q	A	L	T	H	L	V	G	G	L	C	F	T	L	G	F	I	L	L	A	V	C	G	T	S	L	F	T	S	S	V	M	T	V	M	A	K	S	R	G	V	I	S	W	R	T	W	L	I	N	A	L	L	V	A	C	G	N
Secondary structure
SS confidence
Disorder
Disorder confidence
		.	.	.	.	.	.	.	.	.	130	.	.	.	.	.	.	.	.	.	140	.	.	.	.	.	.	.	.	.	150	.	.	.	.	.	.	.	.	.	160	.	.	.	.	.	.	.	.	.	170	.	.	.	.	.	.	.	.	.	180
Sequence		L	A	G	I	A	C	F	S	L	L	I	W	F	S	G	L	V	M	S	E	N	A	M	W	G	V	A	V	L	H	C	A	E	G	K	M	H	H	T	F	T	E	S	V	S	L	G	I	M	C	N	L	M	V	C	L	A	L	W	M
Secondary structure
SS confidence
Disorder																	?			?		?
Disorder confidence
		.	.	.	.	.	.	.	.	.	190	.	.	.	.	.	.	.	.	.	200	.	.	.	.	.	.	.	.	.	210	.	.	.	.	.	.	.	.	.	220	.	.	.	.	.	.	.	.	.	230	.	.	.	.	.	.	.	.	.	240
Sequence		S	Y	C	G	R	S	L	C	D	K	I	V	A	M	I	L	P	I	T	L	F	V	A	S	G	F	E	H	C	I	A	N	L	F	V	I	P	F	A	I	A	I	R	H	F	A	P	P	P	F	W	Q	L	A	H	S	S	A	D	N
Secondary structure
SS confidence
Disorder		?		?	?																																							?														?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	250	.	.	.	.	.	.	.	.	.	260	.	.	.	.	.	.	.	.	.	270	.	.	.	.	.	.	.	.	.	280	.	.
Sequence		F	P	A	L	T	V	S	H	F	I	T	A	N	L	L	P	V	M	L	G	N	I	I	G	G	A	V	L	V	S	M	C	Y	R	A	I	Y	L	R	Q	E	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 3klz chain E Region: 24 - 279 Aligned: 256 Modelled: 256 Confidence: 100.0% Identity: 43% PDB header:membrane protein Chain: E: PDB Molecule:putative formate transporter 1; PDBTitle: pentameric formate channel with formate bound Phyre2 PDB 3kcv chain G Region: 29 - 279 Aligned: 251 Modelled: 251 Confidence: 100.0% Identity: 53% PDB header:transport protein Chain: G: PDB Molecule:probable formate transporter 1; PDBTitle: structure of formate channel Phyre2 PDB 1rc2 chain A Region: 32 - 281 Aligned: 224 Modelled: 232 Confidence: 92.4% Identity: 9% Fold: Aquaporin-like Superfamily: Aquaporin-like Family: Aquaporin-like Phyre2 PDB 3llq chain B Region: 28 - 279 Aligned: 224 Modelled: 234 Confidence: 90.7% Identity: 10% PDB header:membrane protein Chain: B: PDB Molecule:aquaporin z 2; PDBTitle: aquaporin structure from plant pathogen agrobacterium tumerfaciens Phyre2 PDB 1fx8 chain A Region: 30 - 280 Aligned: 218 Modelled: 224 Confidence: 88.8% Identity: 18% Fold: Aquaporin-like Superfamily: Aquaporin-like Family: Aquaporin-like Phyre2 PDB 1lda chain A Region: 30 - 280 Aligned: 218 Modelled: 224 Confidence: 88.8% Identity: 18% PDB header:transport protein Chain: A: PDB Molecule:glycerol uptake facilitator protein; PDBTitle: crystal structure of the e. coli glycerol facilitator (glpf) without2 substrate glycerol Phyre2 PDB 2d57 chain A Region: 28 - 209 Aligned: 172 Modelled: 182 Confidence: 77.7% Identity: 10% PDB header:transport protein Chain: A: PDB Molecule:aquaporin-4; PDBTitle: double layered 2d crystal structure of aquaporin-4 (aqp4m23) at 3.2 a2 resolution by electron crystallography Phyre2 PDB 3gd8 chain A Region: 29 - 209 Aligned: 171 Modelled: 181 Confidence: 76.0% Identity: 11% PDB header:membrane protein Chain: A: PDB Molecule:aquaporin-4; PDBTitle: crystal structure of human aquaporin 4 at 1.8 and its mechanism of2 conductance Phyre2 PDB 1j4n chain A Region: 27 - 282 Aligned: 220 Modelled: 222 Confidence: 73.4% Identity: 15% Fold: Aquaporin-like Superfamily: Aquaporin-like Family: Aquaporin-like Phyre2 PDB 2w2e chain A Region: 28 - 204 Aligned: 164 Modelled: 164 Confidence: 71.1% Identity: 16% PDB header:membrane protein Chain: A: PDB Molecule:aquaporin; PDBTitle: 1.15 angstrom crystal structure of p.pastoris aquaporin,2 aqy1, in a closed conformation at ph 3.5 Phyre2 PDB 3iyz chain A Region: 28 - 277 Aligned: 212 Modelled: 225 Confidence: 67.9% Identity: 13% PDB header:transport protein Chain: A: PDB Molecule:aquaporin-4; PDBTitle: structure of aquaporin-4 s180d mutant at 10.0 a resolution from2 electron micrograph Phyre2 PDB 1ymg chain A domain 1 Region: 44 - 282 Aligned: 204 Modelled: 215 Confidence: 57.2% Identity: 14% Fold: Aquaporin-like Superfamily: Aquaporin-like Family: Aquaporin-like Phyre2 PDB 1ymg chain A Region: 44 - 282 Aligned: 204 Modelled: 215 Confidence: 57.2% 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 2b5f chain D Region: 28 - 276 Aligned: 216 Modelled: 226 Confidence: 49.4% Identity: 9% PDB header:transport protein,membrane protein Chain: D: PDB Molecule:aquaporin; PDBTitle: crystal structure of the spinach aquaporin sopip2;1 in an2 open conformation to 3.9 resolution Phyre2 PDB 1h6i chain A Region: 31 - 206 Aligned: 166 Modelled: 166 Confidence: 38.2% Identity: 13% Fold: Aquaporin-like Superfamily: Aquaporin-like Family: Aquaporin-like Phyre2 PDB 3d9s chain B Region: 33 - 282 Aligned: 214 Modelled: 232 Confidence: 35.6% Identity: 15% PDB header:membrane protein Chain: B: PDB Molecule:aquaporin-5; PDBTitle: human aquaporin 5 (aqp5) - high resolution x-ray structure Phyre2 PDB 2f2b chain A Region: 30 - 204 Aligned: 167 Modelled: 175 Confidence: 32.0% Identity: 11% PDB header:membrane protein Chain: A: PDB Molecule:aquaporin aqpm; PDBTitle: crystal structure of integral membrane protein aquaporin aqpm at 1.68a2 resolution Phyre2 PDB 1c17 chain M Region: 258 - 275 Aligned: 18 Modelled: 18 Confidence: 21.4% Identity: 17% Fold: F1F0 ATP synthase subunit A Superfamily: F1F0 ATP synthase subunit A Family: F1F0 ATP synthase subunit A Phyre2 PDB 3c02 chain A Region: 30 - 278 Aligned: 232 Modelled: 244 Confidence: 17.5% Identity: 9% PDB header:membrane protein Chain: A: PDB Molecule:aquaglyceroporin; PDBTitle: x-ray structure of the aquaglyceroporin from plasmodium falciparum Phyre2 PDB 2jy0 chain A Region: 264 - 273 Aligned: 10 Modelled: 10 Confidence: 11.4% Identity: 50% PDB header:membrane protein, viral protein Chain: A: PDB Molecule:protease ns2-3; PDBTitle: solution nmr structure of hcv ns2 protein, membrane segment2 (1-27) Phyre2 1 c3klzE_ 2 c3kcvG_ 3 d1rc2a_ 4 c3llqB_ 5 d1fx8a_ 6 c1ldaA_ 7 c2d57A_ 8 c3gd8A_ 9 d1j4na_ 10 c2w2eA_ 11 c3iyzA_ 12 d1ymga1 13 c1ymgA_ 14 c2b5fD_ 15 d1h6ia_ 16 c3d9sB_ 17 c2f2bA_ 18 d1c17m_ 19 c3c02A_ 20 c2jy0A_ 21 22 23 24 25 26 27 28

Detailed template information

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

1 c3klzE_ 100.0 43 PDB header:membrane protein Chain: E: PDB Molecule:putative formate transporter 1; PDBTitle: pentameric formate channel with formate bound 2 c3kcvG_ 100.0 53 PDB header:transport protein Chain: G: PDB Molecule:probable formate transporter 1; PDBTitle: structure of formate channel 3 d1rc2a_ 92.4 9 Fold:Aquaporin-like Superfamily:Aquaporin-like Family:Aquaporin-like 4 c3llqB_ 90.7 10 PDB header:membrane protein Chain: B: PDB Molecule:aquaporin z 2; PDBTitle: aquaporin structure from plant pathogen agrobacterium tumerfaciens 5 d1fx8a_ 88.8 18 Fold:Aquaporin-like Superfamily:Aquaporin-like Family:Aquaporin-like 6 c1ldaA_ 88.8 18 PDB header:transport protein Chain: A: PDB Molecule:glycerol uptake facilitator protein; PDBTitle: crystal structure of the e. coli glycerol facilitator (glpf) without2 substrate glycerol 7 c2d57A_ 77.7 10 PDB header:transport protein Chain: A: PDB Molecule:aquaporin-4; PDBTitle: double layered 2d crystal structure of aquaporin-4 (aqp4m23) at 3.2 a2 resolution by electron crystallography 8 c3gd8A_ 76.0 11 PDB header:membrane protein Chain: A: PDB Molecule:aquaporin-4; PDBTitle: crystal structure of human aquaporin 4 at 1.8 and its mechanism of2 conductance 9 d1j4na_ 73.4 15 Fold:Aquaporin-like Superfamily:Aquaporin-like Family:Aquaporin-like 10 c2w2eA_ 71.1 16 PDB header:membrane protein Chain: A: PDB Molecule:aquaporin; PDBTitle: 1.15 angstrom crystal structure of p.pastoris aquaporin,2 aqy1, in a closed conformation at ph 3.5 11 c3iyzA_ 67.9 13 PDB header:transport protein Chain: A: PDB Molecule:aquaporin-4; PDBTitle: structure of aquaporin-4 s180d mutant at 10.0 a resolution from2 electron micrograph 12 d1ymga1 57.2 14 Fold:Aquaporin-like Superfamily:Aquaporin-like Family:Aquaporin-like 13 c1ymgA_ 57.2 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 14 c2b5fD_ 49.4 9 PDB header:transport protein,membrane protein Chain: D: PDB Molecule:aquaporin; PDBTitle: crystal structure of the spinach aquaporin sopip2;1 in an2 open conformation to 3.9 resolution 15 d1h6ia_ 38.2 13 Fold:Aquaporin-like Superfamily:Aquaporin-like Family:Aquaporin-like 16 c3d9sB_ 35.6 15 PDB header:membrane protein Chain: B: PDB Molecule:aquaporin-5; PDBTitle: human aquaporin 5 (aqp5) - high resolution x-ray structure 17 c2f2bA_ 32.0 11 PDB header:membrane protein Chain: A: PDB Molecule:aquaporin aqpm; PDBTitle: crystal structure of integral membrane protein aquaporin aqpm at 1.68a2 resolution 18 d1c17m_ 21.4 17 Fold:F1F0 ATP synthase subunit A Superfamily:F1F0 ATP synthase subunit A Family:F1F0 ATP synthase subunit A 19 c3c02A_ 17.5 9 PDB header:membrane protein Chain: A: PDB Molecule:aquaglyceroporin; PDBTitle: x-ray structure of the aquaglyceroporin from plasmodium falciparum 20 c2jy0A_ 11.4 50 PDB header:membrane protein, viral protein Chain: A: PDB Molecule:protease ns2-3; PDBTitle: solution nmr structure of hcv ns2 protein, membrane segment2 (1-27) 21 d2c1wa1 not modelled 10.6 67 Fold:EndoU-like Superfamily:EndoU-like Family:Eukaryotic EndoU ribonuclease 22 d2foka2 not modelled 8.7 10 Fold:DNA/RNA-binding 3-helical bundle Superfamily:"Winged helix" DNA-binding domain Family:Restriction endonuclease FokI, N-terminal (recognition) domain 23 c2kncA_ not modelled 6.9 21 PDB header:cell adhesion Chain: A: PDB Molecule:integrin alpha-iib; PDBTitle: platelet integrin alfaiib-beta3 transmembrane-cytoplasmic2 heterocomplex 24 c3if8B_ not modelled 6.3 11 PDB header:cell cycle Chain: B: PDB Molecule:protein zwilch homolog; PDBTitle: crystal structure of zwilch, a member of the rzz kinetochore complex 25 c2h3oA_ not modelled 5.9 19 PDB header:membrane protein Chain: A: PDB Molecule:merf; PDBTitle: structure of merft, a membrane protein with two trans-2 membrane helices 26 c2voyG_ not modelled 5.8 39 PDB header:hydrolase Chain: G: PDB Molecule:sarcoplasmic/endoplasmic reticulum calcium PDBTitle: cryoem model of copa, the copper transporting atpase from2 archaeoglobus fulgidus 27 c2kncB_ not modelled 5.8 21 PDB header:cell adhesion Chain: B: PDB Molecule:integrin beta-3; PDBTitle: platelet integrin alfaiib-beta3 transmembrane-cytoplasmic2 heterocomplex 28 d1o5wa1 not modelled 5.7 25 Fold:FAD/NAD(P)-binding domain Superfamily:FAD/NAD(P)-binding domain Family:FAD-linked reductases, N-terminal domain

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