Secondary structure and disorder prediction

		1	.	.	.	.	.	.	.	.	10	.	.	.	.	.	.	.	.	.	20	.	.	.	.	.	.	.	.	.	30	.	.	.	.	.	.	.	.	.	40	.	.	.	.	.	.	.	.	.	50	.	.	.	.	.	.	.	.	.	60
Sequence		M	K	H	P	L	E	T	L	T	T	A	A	G	I	L	L	M	A	F	L	S	C	L	L	L	P	A	P	A	L	G	L	A	L	A	Q	K	L	V	T	M	F	H	L	M	D	L	S	Q	L	Y	T	L	L	F	C	L	W	F	L
Secondary structure
SS confidence
Disorder		?	?	?																									?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	70	.	.	.	.	.	.	.	.	.	80	.	.
Sequence		V	L	G	A	I	E	Y	F	V	L	R	F	I	W	R	R	W	F	S	L	A	D
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 1vry chain A Region: 53 - 75 Aligned: 23 Modelled: 23 Confidence: 37.3% Identity: 35% PDB header:membrane protein Chain: A: PDB Molecule:glycine receptor alpha-1 chain; PDBTitle: second and third transmembrane domains of the alpha-12 subunit of human glycine receptor Phyre2 PDB 1lgh chain B Region: 64 - 78 Aligned: 15 Modelled: 15 Confidence: 29.6% Identity: 40% Fold: Light-harvesting complex subunits Superfamily: Light-harvesting complex subunits Family: Light-harvesting complex subunits Phyre2 PDB 1eys chain H Region: 43 - 62 Aligned: 20 Modelled: 20 Confidence: 19.7% Identity: 35% PDB header:electron transport Chain: H: PDB Molecule:photosynthetic reaction center; PDBTitle: crystal structure of photosynthetic reaction center from a2 thermophilic bacterium, thermochromatium tepidum Phyre2 PDB 1ho8 chain A Region: 50 - 60 Aligned: 11 Modelled: 11 Confidence: 19.4% Identity: 36% Fold: alpha-alpha superhelix Superfamily: ARM repeat Family: Regulatory subunit H of the V-type ATPase Phyre2 PDB 1jo5 chain A Region: 64 - 78 Aligned: 15 Modelled: 15 Confidence: 19.3% Identity: 47% Fold: Light-harvesting complex subunits Superfamily: Light-harvesting complex subunits Family: Light-harvesting complex subunits Phyre2 PDB 1eys chain H domain 2 Region: 43 - 68 Aligned: 24 Modelled: 26 Confidence: 14.3% Identity: 29% Fold: Single transmembrane helix Superfamily: Photosystem II reaction centre subunit H, transmembrane region Family: Photosystem II reaction centre subunit H, transmembrane region Phyre2 PDB 1ppj chain C domain 1 Region: 47 - 72 Aligned: 26 Modelled: 26 Confidence: 13.7% Identity: 42% Fold: a domain/subunit of cytochrome bc1 complex (Ubiquinol-cytochrome c reductase) Superfamily: a domain/subunit of cytochrome bc1 complex (Ubiquinol-cytochrome c reductase) Family: a domain/subunit of cytochrome bc1 complex (Ubiquinol-cytochrome c reductase) Phyre2 PDB 1m98 chain A domain 1 Region: 35 - 54 Aligned: 20 Modelled: 20 Confidence: 10.0% Identity: 25% Fold: Orange carotenoid protein, N-terminal domain Superfamily: Orange carotenoid protein, N-terminal domain Family: Orange carotenoid protein, N-terminal domain Phyre2 PDB 3d1d chain C Region: 43 - 55 Aligned: 13 Modelled: 13 Confidence: 8.7% Identity: 46% PDB header:nuclear protein Chain: C: PDB Molecule:rna-induced transcriptional silencing complex PDBTitle: hexagonal crystal structure of tas3 c-terminal alpha motif Phyre2 PDB 2ww9 chain B Region: 59 - 69 Aligned: 11 Modelled: 11 Confidence: 7.9% Identity: 36% PDB header:ribosome Chain: B: PDB Molecule:protein transport protein sss1; PDBTitle: cryo-em structure of the active yeast ssh1 complex bound to the2 yeast 80s ribosome Phyre2 PDB 1wrg chain A Region: 57 - 78 Aligned: 22 Modelled: 22 Confidence: 7.7% Identity: 27% PDB header:membrane protein Chain: A: PDB Molecule:light-harvesting protein b-880, beta chain; PDBTitle: light-harvesting complex 1 beta subunit from wild-type2 rhodospirillum rubrum Phyre2 PDB 2knc chain A Region: 12 - 24 Aligned: 13 Modelled: 13 Confidence: 7.2% Identity: 31% PDB header:cell adhesion Chain: A: PDB Molecule:integrin alpha-iib; PDBTitle: platelet integrin alfaiib-beta3 transmembrane-cytoplasmic2 heterocomplex Phyre2 PDB 1fqv chain A domain 1 Region: 15 - 26 Aligned: 12 Modelled: 12 Confidence: 6.1% Identity: 58% Fold: F-box domain Superfamily: F-box domain Family: F-box domain Phyre2 1 c1vryA_ 2 d1lghb_ 3 c1eysH_ 4 d1ho8a_ 5 d1jo5a_ 6 d1eysh2 7 d1ppjc1 8 d1m98a1 9 c3d1dC_ 10 c2ww9B_ 11 c1wrgA_ 12 c2kncA_ 13 d1fqva1

Detailed template information

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

1 c1vryA_ 37.3 35 PDB header:membrane protein Chain: A: PDB Molecule:glycine receptor alpha-1 chain; PDBTitle: second and third transmembrane domains of the alpha-12 subunit of human glycine receptor 2 d1lghb_ 29.6 40 Fold:Light-harvesting complex subunits Superfamily:Light-harvesting complex subunits Family:Light-harvesting complex subunits 3 c1eysH_ 19.7 35 PDB header:electron transport Chain: H: PDB Molecule:photosynthetic reaction center; PDBTitle: crystal structure of photosynthetic reaction center from a2 thermophilic bacterium, thermochromatium tepidum 4 d1ho8a_ 19.4 36 Fold:alpha-alpha superhelix Superfamily:ARM repeat Family:Regulatory subunit H of the V-type ATPase 5 d1jo5a_ 19.3 47 Fold:Light-harvesting complex subunits Superfamily:Light-harvesting complex subunits Family:Light-harvesting complex subunits 6 d1eysh2 14.3 29 Fold:Single transmembrane helix Superfamily:Photosystem II reaction centre subunit H, transmembrane region Family:Photosystem II reaction centre subunit H, transmembrane region 7 d1ppjc1 13.7 42 Fold:a domain/subunit of cytochrome bc1 complex (Ubiquinol-cytochrome c reductase) Superfamily:a domain/subunit of cytochrome bc1 complex (Ubiquinol-cytochrome c reductase) Family:a domain/subunit of cytochrome bc1 complex (Ubiquinol-cytochrome c reductase) 8 d1m98a1 10.0 25 Fold:Orange carotenoid protein, N-terminal domain Superfamily:Orange carotenoid protein, N-terminal domain Family:Orange carotenoid protein, N-terminal domain 9 c3d1dC_ 8.7 46 PDB header:nuclear protein Chain: C: PDB Molecule:rna-induced transcriptional silencing complex PDBTitle: hexagonal crystal structure of tas3 c-terminal alpha motif 10 c2ww9B_ 7.9 36 PDB header:ribosome Chain: B: PDB Molecule:protein transport protein sss1; PDBTitle: cryo-em structure of the active yeast ssh1 complex bound to the2 yeast 80s ribosome 11 c1wrgA_ 7.7 27 PDB header:membrane protein Chain: A: PDB Molecule:light-harvesting protein b-880, beta chain; PDBTitle: light-harvesting complex 1 beta subunit from wild-type2 rhodospirillum rubrum 12 c2kncA_ 7.2 31 PDB header:cell adhesion Chain: A: PDB Molecule:integrin alpha-iib; PDBTitle: platelet integrin alfaiib-beta3 transmembrane-cytoplasmic2 heterocomplex 13 d1fqva1 6.1 58 Fold:F-box domain Superfamily:F-box domain Family:F-box 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