Secondary structure and disorder prediction

		1	.	.	.	.	.	.	.	.	10	.	.	.	.	.	.	.	.	.	20	.	.	.	.	.	.	.	.	.	30	.	.	.	.	.	.	.	.	.	40	.	.	.	.	.	.	.	.	.	50	.	.	.	.	.	.	.	.	.	60
Sequence		M	K	T	Q	R	G	Y	T	L	I	E	T	L	V	A	M	L	I	L	V	M	L	S	A	S	G	L	Y	G	W	Q	Y	W	Q	Q	S	Q	R	L	W	Q	T	A	S	Q	A	R	D	Y	L	L	Y	L	R	E	D	A	N	W	H
Secondary structure
SS confidence
Disorder		?	?	?	?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	70	.	.	.	.	.	.	.	.	.	80	.	.	.	.	.	.	.	.	.	90	.	.	.	.	.	.	.	.	.	100	.	.	.	.	.	.	.	.	.	110	.	.	.	.	.	.	.	.	.	120
Sequence		N	R	D	H	S	I	S	V	I	R	E	G	T	L	W	C	L	V	S	S	A	A	G	A	N	T	C	H	G	S	S	P	L	V	F	V	P	R	W	P	E	V	E	M	S	D	L	T	P	S	L	A	F	F	G	L	R	N	T	A
Secondary structure
SS confidence
Disorder														?									?	?	?	?	?	?	?		?	?	?			?	?	?	?			?	?			?	?	?	?	?					?	?	?		?
Disorder confidence
		.	.	.	.	.	.	.	.	.	130	.	.	.	.	.	.	.	.	.	140	.	.	.	.	.	.	.	.	.	150	.	.	.	.	.	.
Sequence		W	A	G	H	I	R	F	K	N	S	T	G	E	W	W	L	V	V	S	P	W	G	R	L	R	L	C	Q	Q	G	E	T	E	G	C	L
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 3sok chain B Region: 7 - 90 Aligned: 84 Modelled: 84 Confidence: 99.5% Identity: 11% PDB header:cell adhesion Chain: B: PDB Molecule:fimbrial protein; PDBTitle: dichelobacter nodosus pilin fima Phyre2 PDB 1oqw chain A Region: 7 - 132 Aligned: 123 Modelled: 126 Confidence: 99.5% Identity: 15% Fold: Pili subunits Superfamily: Pili subunits Family: Pilin Phyre2 PDB 2pil chain A Region: 8 - 62 Aligned: 55 Modelled: 55 Confidence: 99.3% Identity: 22% Fold: Pili subunits Superfamily: Pili subunits Family: Pilin Phyre2 PDB 2qv8 chain B Region: 38 - 151 Aligned: 113 Modelled: 112 Confidence: 98.3% Identity: 18% 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 2knq chain A Region: 35 - 146 Aligned: 111 Modelled: 112 Confidence: 97.3% Identity: 14% PDB header:protein transport Chain: A: PDB Molecule:general secretion pathway protein h; PDBTitle: solution structure of e.coli gsph Phyre2 PDB 4a18 chain U Region: 5 - 15 Aligned: 11 Modelled: 11 Confidence: 32.3% 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: 31.3% 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 2knc chain B Region: 12 - 49 Aligned: 38 Modelled: 38 Confidence: 16.3% Identity: 5% PDB header:cell adhesion Chain: B: PDB Molecule:integrin beta-3; PDBTitle: platelet integrin alfaiib-beta3 transmembrane-cytoplasmic2 heterocomplex Phyre2 PDB 3ehb chain B domain 2 Region: 8 - 38 Aligned: 31 Modelled: 31 Confidence: 13.1% 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 2kxe chain A Region: 7 - 13 Aligned: 7 Modelled: 7 Confidence: 12.7% 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 1fft chain B domain 2 Region: 2 - 35 Aligned: 34 Modelled: 34 Confidence: 12.4% 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 1ybx chain A Region: 124 - 145 Aligned: 22 Modelled: 22 Confidence: 12.4% Identity: 9% PDB header:structural genomics, unknown function Chain: A: PDB Molecule:conserved hypothetical protein; PDBTitle: conserved hypothetical protein cth-383 from clostridium thermocellum Phyre2 PDB 2vnv chain C Region: 101 - 143 Aligned: 43 Modelled: 43 Confidence: 11.6% Identity: 16% PDB header:sugar-binding protein Chain: C: PDB Molecule:bcla; PDBTitle: crystal structure of bcla lectin from burkholderia2 cenocepacia in complex with alpha-methyl-mannoside at 1.73 angstrom resolution Phyre2 PDB 1m56 chain D Region: 14 - 29 Aligned: 16 Modelled: 16 Confidence: 10.4% Identity: 25% Fold: Single transmembrane helix Superfamily: Bacterial aa3 type cytochrome c oxidase subunit IV Family: Bacterial aa3 type cytochrome c oxidase subunit IV Phyre2 PDB 1pug chain A Region: 124 - 145 Aligned: 22 Modelled: 22 Confidence: 10.0% Identity: 9% Fold: YbaB-like Superfamily: YbaB-like Family: YbaB-like Phyre2 PDB 1j8b chain A Region: 124 - 145 Aligned: 22 Modelled: 22 Confidence: 9.8% Identity: 9% Fold: YbaB-like Superfamily: YbaB-like Family: YbaB-like Phyre2 PDB 1qle chain B Region: 2 - 38 Aligned: 37 Modelled: 37 Confidence: 9.5% Identity: 22% 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 - 38 Aligned: 37 Modelled: 37 Confidence: 9.5% Identity: 22% 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: 5 - 38 Aligned: 34 Modelled: 34 Confidence: 9.0% 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 2ljc chain A Region: 12 - 26 Aligned: 15 Modelled: 15 Confidence: 8.2% Identity: 27% PDB header:transport protein/inhibitor Chain: A: PDB Molecule:m2 protein, bm2 protein chimera; PDBTitle: structure of the influenza am2-bm2 chimeric channel bound to2 rimantadine Phyre2 1 c3sokB_ 2 d1oqwa_ 3 d2pila_ 4 c2qv8B_ 5 c2knqA_ 6 c4a18U_ 7 c3u5eL_ 8 c2kncB_ 9 d3ehbb2 10 c2kxeA_ 11 d1fftb2 12 c1ybxA_ 13 c2vnvC_ 14 d1m56d_ 15 d1puga_ 16 d1j8ba_ 17 c1qleB_ 18 c1ar1B_ 19 c2kb1A_ 20 c2ljcA_ 21 22 23 24 25 26 27 28 29 30 31 32 33

Detailed template information

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

1 c3sokB_ 99.5 11 PDB header:cell adhesion Chain: B: PDB Molecule:fimbrial protein; PDBTitle: dichelobacter nodosus pilin fima 2 d1oqwa_ 99.5 15 Fold:Pili subunits Superfamily:Pili subunits Family:Pilin 3 d2pila_ 99.3 22 Fold:Pili subunits Superfamily:Pili subunits Family:Pilin 4 c2qv8B_ 98.3 18 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 5 c2knqA_ 97.3 14 PDB header:protein transport Chain: A: PDB Molecule:general secretion pathway protein h; PDBTitle: solution structure of e.coli gsph 6 c4a18U_ 32.3 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_ 31.3 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 c2kncB_ 16.3 5 PDB header:cell adhesion Chain: B: PDB Molecule:integrin beta-3; PDBTitle: platelet integrin alfaiib-beta3 transmembrane-cytoplasmic2 heterocomplex 9 d3ehbb2 13.1 26 Fold:Transmembrane helix hairpin Superfamily:Cytochrome c oxidase subunit II-like, transmembrane region Family:Cytochrome c oxidase subunit II-like, transmembrane region 10 c2kxeA_ 12.7 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 11 d1fftb2 12.4 9 Fold:Transmembrane helix hairpin Superfamily:Cytochrome c oxidase subunit II-like, transmembrane region Family:Cytochrome c oxidase subunit II-like, transmembrane region 12 c1ybxA_ 12.4 9 PDB header:structural genomics, unknown function Chain: A: PDB Molecule:conserved hypothetical protein; PDBTitle: conserved hypothetical protein cth-383 from clostridium thermocellum 13 c2vnvC_ 11.6 16 PDB header:sugar-binding protein Chain: C: PDB Molecule:bcla; PDBTitle: crystal structure of bcla lectin from burkholderia2 cenocepacia in complex with alpha-methyl-mannoside at 1.73 angstrom resolution 14 d1m56d_ 10.4 25 Fold:Single transmembrane helix Superfamily:Bacterial aa3 type cytochrome c oxidase subunit IV Family:Bacterial aa3 type cytochrome c oxidase subunit IV 15 d1puga_ 10.0 9 Fold:YbaB-like Superfamily:YbaB-like Family:YbaB-like 16 d1j8ba_ 9.8 9 Fold:YbaB-like Superfamily:YbaB-like Family:YbaB-like 17 c1qleB_ 9.5 22 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_ 9.5 22 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_ 9.0 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 c2ljcA_ 8.2 27 PDB header:transport protein/inhibitor Chain: A: PDB Molecule:m2 protein, bm2 protein chimera; PDBTitle: structure of the influenza am2-bm2 chimeric channel bound to2 rimantadine 21 c2kadC_ not modelled 7.9 27 PDB header:membrane protein Chain: C: PDB Molecule:transmembrane peptide of matrix protein 2; PDBTitle: magic-angle-spinning solid-state nmr structure of influenza2 a m2 transmembrane domain 22 c2kadA_ not modelled 7.9 27 PDB header:membrane protein Chain: A: PDB Molecule:transmembrane peptide of matrix protein 2; PDBTitle: magic-angle-spinning solid-state nmr structure of influenza2 a m2 transmembrane domain 23 c2kadD_ not modelled 7.9 27 PDB header:membrane protein Chain: D: PDB Molecule:transmembrane peptide of matrix protein 2; PDBTitle: magic-angle-spinning solid-state nmr structure of influenza2 a m2 transmembrane domain 24 c2kadB_ not modelled 7.9 27 PDB header:membrane protein Chain: B: PDB Molecule:transmembrane peptide of matrix protein 2; PDBTitle: magic-angle-spinning solid-state nmr structure of influenza2 a m2 transmembrane domain 25 c2boiA_ not modelled 7.6 24 PDB header:lectin Chain: A: PDB Molecule:cv-iil lectin; PDBTitle: 1.1a structure of chromobacterium violaceum lectin cv2l in2 complex with alpha-methyl-fucoside 26 d3dtub2 not modelled 7.6 16 Fold:Transmembrane helix hairpin Superfamily:Cytochrome c oxidase subunit II-like, transmembrane region Family:Cytochrome c oxidase subunit II-like, transmembrane region 27 c1bttA_ not modelled 7.5 27 PDB header:transmembrane protein Chain: A: PDB Molecule:band 3 anion transport protein; PDBTitle: the solution structures of the first and second2 transmembrane-spanning segments of band 3 28 c1btsA_ not modelled 7.5 27 PDB header:transmembrane protein Chain: A: PDB Molecule:band 3 anion transport protein; PDBTitle: the solution structures of the first and second2 transmembrane-spanning segments of band 3 29 c2hg5D_ not modelled 7.0 11 PDB header:membrane protein Chain: D: PDB Molecule:kcsa channel; PDBTitle: cs+ complex of a k channel with an amide to ester substitution in the2 selectivity filter 30 d1uzva_ not modelled 6.5 24 Fold:Calcium-mediated lectin Superfamily:Calcium-mediated lectin Family:Calcium-mediated lectin 31 d1v54b2 not modelled 6.1 14 Fold:Transmembrane helix hairpin Superfamily:Cytochrome c oxidase subunit II-like, transmembrane region Family:Cytochrome c oxidase subunit II-like, transmembrane region 32 c2o01G_ not modelled 5.8 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 33 d1r3jc_ not modelled 5.8 12 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

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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