Secondary structure and disorder prediction

		1	.	.	.	.	.	.	.	.	10	.	.	.	.	.	.	.	.	.	20	.	.	.	.	.	.	.	.	.	30	.	.	.	.	.	.	.	.	.	40	.	.	.	.	.	.	.	.	.	50	.	.	.	.	.	.	.	.	.	60
Sequence		M	N	Q	Q	R	G	F	T	L	L	E	M	M	L	V	L	A	L	V	A	I	T	A	S	V	V	L	F	T	Y	G	R	E	D	V	A	S	T	R	A	R	E	T	A	A	R	F	T	A	A	L	E	L	A	I	D	R	A	T	L
Secondary structure
SS confidence
Disorder		?	?	?	?	?	?	?																					?	?	?	?	?	?	?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	70	.	.	.	.	.	.	.	.	.	80	.	.	.	.	.	.	.	.	.	90	.	.	.	.	.	.	.	.	.	100	.	.	.	.	.	.	.	.	.	110	.	.	.	.	.	.	.	.	.	120
Sequence		S	G	Q	P	V	G	I	H	F	S	D	S	A	W	R	I	M	V	P	G	K	T	P	S	A	W	R	W	V	P	L	Q	E	D	A	A	D	E	S	Q	N	D	W	D	E	E	L	S	I	H	L	Q	P	F	K	P	D	D	S	N
Secondary structure
SS confidence
Disorder																																		?		?		?	?	?	?	?	?	?	?	?	?	?	?	?	?	?	?	?	?	?	?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	130	.	.	.	.	.	.	.	.	.	140	.	.	.	.	.	.	.	.	.	150	.	.	.	.	.	.	.	.	.	160	.	.	.	.	.	.	.	.	.
Sequence		Q	P	Q	V	V	I	L	A	D	G	Q	I	T	P	F	S	L	L	M	A	N	A	G	T	G	E	P	L	L	T	L	V	C	S	G	S	W	P	L	D	Q	T	L	A	R	D	T	R	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 2knq chain A Region: 28 - 169 Aligned: 142 Modelled: 142 Confidence: 99.9% Identity: 98% PDB header:protein transport Chain: A: PDB Molecule:general secretion pathway protein h; PDBTitle: solution structure of e.coli gsph Phyre2 PDB 2qv8 chain B Region: 39 - 160 Aligned: 116 Modelled: 122 Confidence: 99.5% Identity: 22% PDB header:transport protein Chain: B: PDB Molecule:general secretion pathway protein h; PDBTitle: structure of the minor pseudopilin epsh from the type 2 secretion2 system of vibrio cholerae Phyre2 PDB 1oqw chain A Region: 7 - 156 Aligned: 132 Modelled: 134 Confidence: 99.4% Identity: 17% Fold: Pili subunits Superfamily: Pili subunits Family: Pilin Phyre2 PDB 3sok chain B Region: 7 - 86 Aligned: 79 Modelled: 80 Confidence: 99.4% Identity: 20% PDB header:cell adhesion Chain: B: PDB Molecule:fimbrial protein; PDBTitle: dichelobacter nodosus pilin fima Phyre2 PDB 2pil chain A Region: 8 - 65 Aligned: 56 Modelled: 58 Confidence: 99.2% Identity: 27% Fold: Pili subunits Superfamily: Pili subunits Family: Pilin Phyre2 PDB 4a18 chain U Region: 5 - 15 Aligned: 11 Modelled: 11 Confidence: 34.7% Identity: 55% PDB header:ribosome Chain: U: PDB Molecule:rpl13; PDBTitle: t.thermophila 60s ribosomal subunit in complex with initiation2 factor 6. this file contains 26s rrna and proteins of molecule 1 Phyre2 PDB 3u5e chain L Region: 5 - 15 Aligned: 11 Modelled: 11 Confidence: 33.1% Identity: 55% PDB header:ribosome Chain: L: PDB Molecule:60s ribosomal protein l13-a; PDBTitle: the structure of the eukaryotic ribosome at 3.0 resolution Phyre2 PDB 3dtu chain B domain 2 Region: 2 - 30 Aligned: 29 Modelled: 29 Confidence: 15.9% Identity: 21% Fold: Transmembrane helix hairpin Superfamily: Cytochrome c oxidase subunit II-like, transmembrane region Family: Cytochrome c oxidase subunit II-like, transmembrane region Phyre2 PDB 2ii8 chain F Region: 123 - 152 Aligned: 30 Modelled: 30 Confidence: 14.5% Identity: 23% PDB header:signaling protein Chain: F: PDB Molecule:anabaena sensory rhodopsin transducer protein; PDBTitle: anabaena sensory rhodopsin transducer Phyre2 PDB 1v54 chain B domain 2 Region: 2 - 30 Aligned: 29 Modelled: 29 Confidence: 14.4% Identity: 10% Fold: Transmembrane helix hairpin Superfamily: Cytochrome c oxidase subunit II-like, transmembrane region Family: Cytochrome c oxidase subunit II-like, transmembrane region Phyre2 PDB 3ehb chain B domain 2 Region: 8 - 30 Aligned: 23 Modelled: 23 Confidence: 12.6% Identity: 26% Fold: Transmembrane helix hairpin Superfamily: Cytochrome c oxidase subunit II-like, transmembrane region Family: Cytochrome c oxidase subunit II-like, transmembrane region Phyre2 PDB 2wsf chain G Region: 5 - 13 Aligned: 9 Modelled: 9 Confidence: 11.5% Identity: 22% PDB header:photosynthesis Chain: G: PDB Molecule:photosystem i reaction center subunit v, PDBTitle: improved model of plant photosystem i Phyre2 PDB 2kxe chain A Region: 7 - 13 Aligned: 7 Modelled: 7 Confidence: 9.7% Identity: 43% PDB header:transferase Chain: A: PDB Molecule:dna polymerase ii small subunit; PDBTitle: n-terminal domain of the dp1 subunit of an archaeal d-family dna2 polymerase Phyre2 PDB 1jb0 chain K Region: 2 - 30 Aligned: 29 Modelled: 29 Confidence: 9.6% Identity: 17% PDB header:photosynthesis Chain: K: PDB Molecule:photosystem 1 reaction centre subunit x; PDBTitle: crystal structure of photosystem i: a photosynthetic reaction center2 and core antenna system from cyanobacteria Phyre2 PDB 1jb0 chain K Region: 2 - 30 Aligned: 29 Modelled: 29 Confidence: 9.6% Identity: 17% Fold: Photosystem I reaction center subunit X, PsaK Superfamily: Photosystem I reaction center subunit X, PsaK Family: Photosystem I reaction center subunit X, PsaK Phyre2 PDB 1afo chain B Region: 11 - 25 Aligned: 15 Modelled: 15 Confidence: 9.4% Identity: 27% PDB header:integral membrane protein Chain: B: PDB Molecule:glycophorin a; PDBTitle: dimeric transmembrane domain of human glycophorin a, nmr,2 20 structures Phyre2 PDB 1qle chain B Region: 2 - 30 Aligned: 29 Modelled: 29 Confidence: 8.6% Identity: 21% 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 PDB 1ar1 chain B Region: 2 - 30 Aligned: 29 Modelled: 29 Confidence: 8.6% Identity: 21% PDB header:complex (oxidoreductase/antibody) Chain: B: PDB Molecule:cytochrome c oxidase; PDBTitle: structure at 2.7 angstrom resolution of the paracoccus2 denitrificans two-subunit cytochrome c oxidase complexed3 with an antibody fv fragment Phyre2 PDB 2kb1 chain A Region: 7 - 38 Aligned: 32 Modelled: 32 Confidence: 8.2% Identity: 9% PDB header:membrane protein Chain: A: PDB Molecule:wsk3; PDBTitle: nmr studies of a channel protein without membrane:2 structure and dynamics of water-solubilized kcsa Phyre2 PDB 3lw5 chain K Region: 5 - 32 Aligned: 28 Modelled: 28 Confidence: 7.4% Identity: 21% PDB header:photosynthesis Chain: K: PDB Molecule:photosystem i reaction center subunit x psak; PDBTitle: improved model of plant photosystem i Phyre2 1 c2knqA_ 2 c2qv8B_ 3 d1oqwa_ 4 c3sokB_ 5 d2pila_ 6 c4a18U_ 7 c3u5eL_ 8 d3dtub2 9 c2ii8F_ 10 d1v54b2 11 d3ehbb2 12 c2wsfG_ 13 c2kxeA_ 14 c1jb0K_ 15 d1jb0k_ 16 c1afoB_ 17 c1qleB_ 18 c1ar1B_ 19 c2kb1A_ 20 c3lw5K_ 21

Detailed template information

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

1 c2knqA_ 99.9 98 PDB header:protein transport Chain: A: PDB Molecule:general secretion pathway protein h; PDBTitle: solution structure of e.coli gsph 2 c2qv8B_ 99.5 22 PDB header:transport protein Chain: B: PDB Molecule:general secretion pathway protein h; PDBTitle: structure of the minor pseudopilin epsh from the type 2 secretion2 system of vibrio cholerae 3 d1oqwa_ 99.4 17 Fold:Pili subunits Superfamily:Pili subunits Family:Pilin 4 c3sokB_ 99.4 20 PDB header:cell adhesion Chain: B: PDB Molecule:fimbrial protein; PDBTitle: dichelobacter nodosus pilin fima 5 d2pila_ 99.2 27 Fold:Pili subunits Superfamily:Pili subunits Family:Pilin 6 c4a18U_ 34.7 55 PDB header:ribosome Chain: U: PDB Molecule:rpl13; PDBTitle: t.thermophila 60s ribosomal subunit in complex with initiation2 factor 6. this file contains 26s rrna and proteins of molecule 1 7 c3u5eL_ 33.1 55 PDB header:ribosome Chain: L: PDB Molecule:60s ribosomal protein l13-a; PDBTitle: the structure of the eukaryotic ribosome at 3.0 resolution 8 d3dtub2 15.9 21 Fold:Transmembrane helix hairpin Superfamily:Cytochrome c oxidase subunit II-like, transmembrane region Family:Cytochrome c oxidase subunit II-like, transmembrane region 9 c2ii8F_ 14.5 23 PDB header:signaling protein Chain: F: PDB Molecule:anabaena sensory rhodopsin transducer protein; PDBTitle: anabaena sensory rhodopsin transducer 10 d1v54b2 14.4 10 Fold:Transmembrane helix hairpin Superfamily:Cytochrome c oxidase subunit II-like, transmembrane region Family:Cytochrome c oxidase subunit II-like, transmembrane region 11 d3ehbb2 12.6 26 Fold:Transmembrane helix hairpin Superfamily:Cytochrome c oxidase subunit II-like, transmembrane region Family:Cytochrome c oxidase subunit II-like, transmembrane region 12 c2wsfG_ 11.5 22 PDB header:photosynthesis Chain: G: PDB Molecule:photosystem i reaction center subunit v, PDBTitle: improved model of plant photosystem i 13 c2kxeA_ 9.7 43 PDB header:transferase Chain: A: PDB Molecule:dna polymerase ii small subunit; PDBTitle: n-terminal domain of the dp1 subunit of an archaeal d-family dna2 polymerase 14 c1jb0K_ 9.6 17 PDB header:photosynthesis Chain: K: PDB Molecule:photosystem 1 reaction centre subunit x; PDBTitle: crystal structure of photosystem i: a photosynthetic reaction center2 and core antenna system from cyanobacteria 15 d1jb0k_ 9.6 17 Fold:Photosystem I reaction center subunit X, PsaK Superfamily:Photosystem I reaction center subunit X, PsaK Family:Photosystem I reaction center subunit X, PsaK 16 c1afoB_ 9.4 27 PDB header:integral membrane protein Chain: B: PDB Molecule:glycophorin a; PDBTitle: dimeric transmembrane domain of human glycophorin a, nmr,2 20 structures 17 c1qleB_ 8.6 21 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 18 c1ar1B_ 8.6 21 PDB header:complex (oxidoreductase/antibody) Chain: B: PDB Molecule:cytochrome c oxidase; PDBTitle: structure at 2.7 angstrom resolution of the paracoccus2 denitrificans two-subunit cytochrome c oxidase complexed3 with an antibody fv fragment 19 c2kb1A_ 8.2 9 PDB header:membrane protein Chain: A: PDB Molecule:wsk3; PDBTitle: nmr studies of a channel protein without membrane:2 structure and dynamics of water-solubilized kcsa 20 c3lw5K_ 7.4 21 PDB header:photosynthesis Chain: K: PDB Molecule:photosystem i reaction center subunit x psak; PDBTitle: improved model of plant photosystem i 21 c2o01G_ not modelled 6.6 25 PDB header:photosynthesis Chain: G: PDB Molecule:photosystem i reaction center subunit v, PDBTitle: the structure of a plant photosystem i supercomplex at 3.42 angstrom resolution

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