Secondary structure and disorder prediction

		1	.	.	.	.	.	.	.	.	10	.	.	.	.	.	.	.	.	.	20	.	.	.	.	.	.	.	.	.	30	.	.	.	.	.	.	.	.	.	40	.	.	.	.	.	.	.	.	.	50	.	.	.	.	.	.	.	.	.	60
Sequence		M	R	A	T	D	K	Q	R	G	F	T	L	L	E	I	M	V	V	I	V	I	I	G	V	L	A	S	L	V	V	P	N	L	M	G	N	K	E	K	A	D	K	Q	K	A	V	S	D	I	V	A	L	E	N	A	L	D	M	Y	K
Secondary structure
SS confidence
Disorder		?	?	?	?	?	?	?	?	?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	70	.	.	.	.	.	.	.	.	.	80	.	.	.	.	.	.	.	.	.	90	.	.	.	.	.	.	.	.	.	100	.	.	.	.	.	.	.	.	.	110	.	.	.	.	.	.	.	.	.	120
Sequence		L	D	N	H	H	Y	P	T	T	N	Q	G	L	E	S	L	V	E	A	P	T	L	P	P	L	A	A	N	Y	N	K	E	G	Y	I	K	R	L	P	A	D	P	W	G	N	D	Y	V	L	V	N	P	G	E	H	G	A	Y	D	L
Secondary structure
SS confidence
Disorder														?
Disorder confidence
		.	.	.	.	.	.	.	.	.	130	.	.	.	.	.	.	.	.	.	140	.	.	.	.	.
Sequence		L	S	A	G	P	D	G	E	M	G	T	E	D	D	I	T	N	W	G	L	S	K	K	K	K
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 1t92 chain A Region: 35 - 141 Aligned: 107 Modelled: 107 Confidence: 99.9% Identity: 64% Fold: Pili subunits Superfamily: Pili subunits Family: Pseudopilin Phyre2 PDB 2kep chain A Region: 35 - 139 Aligned: 105 Modelled: 105 Confidence: 99.9% Identity: 53% PDB header:transport protein Chain: A: PDB Molecule:general secretion pathway protein g; PDBTitle: solution structure of xcpt, the main component of the type 22 secretion system of pseudomonas aeruginosa Phyre2 PDB 3fu1 chain B Region: 35 - 142 Aligned: 107 Modelled: 108 Confidence: 99.9% Identity: 64% PDB header:protein transport Chain: B: PDB Molecule:general secretion pathway protein g; PDBTitle: crystal structure of the major pseudopilin from the type 2 secretion2 system of vibrio cholerae Phyre2 PDB 1oqw chain A Region: 10 - 142 Aligned: 122 Modelled: 133 Confidence: 99.7% Identity: 16% Fold: Pili subunits Superfamily: Pili subunits Family: Pilin Phyre2 PDB 2pil chain A Region: 11 - 143 Aligned: 133 Modelled: 133 Confidence: 99.7% Identity: 17% Fold: Pili subunits Superfamily: Pili subunits Family: Pilin Phyre2 PDB 3sok chain B Region: 10 - 71 Aligned: 62 Modelled: 62 Confidence: 99.7% Identity: 21% PDB header:cell adhesion Chain: B: PDB Molecule:fimbrial protein; PDBTitle: dichelobacter nodosus pilin fima Phyre2 PDB 1qve chain A Region: 36 - 69 Aligned: 34 Modelled: 34 Confidence: 77.7% Identity: 12% Fold: Pili subunits Superfamily: Pili subunits Family: Pilin Phyre2 PDB 1x6z chain A domain 1 Region: 36 - 70 Aligned: 35 Modelled: 35 Confidence: 68.4% Identity: 6% Fold: Pili subunits Superfamily: Pili subunits Family: Pilin Phyre2 PDB 1pby chain A domain 4 Region: 121 - 135 Aligned: 15 Modelled: 15 Confidence: 60.2% Identity: 60% Fold: Immunoglobulin-like beta-sandwich Superfamily: E set domains Family: Quinohemoprotein amine dehydrogenase A chain, domains 4 and 5 Phyre2 PDB 1pby chain A Region: 121 - 135 Aligned: 15 Modelled: 15 Confidence: 53.7% Identity: 60% PDB header:oxidoreductase Chain: A: PDB Molecule:quinohemoprotein amine dehydrogenase 60 kda PDBTitle: structure of the phenylhydrazine adduct of the2 quinohemoprotein amine dehydrogenase from paracoccus3 denitrificans at 1.7 a resolution Phyre2 PDB 4a18 chain U Region: 8 - 67 Aligned: 55 Modelled: 60 Confidence: 36.8% Identity: 20% 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 2wsf chain G Region: 1 - 16 Aligned: 16 Modelled: 16 Confidence: 31.6% Identity: 13% PDB header:photosynthesis Chain: G: PDB Molecule:photosystem i reaction center subunit v, PDBTitle: improved model of plant photosystem i Phyre2 PDB 3u5e chain L Region: 8 - 18 Aligned: 11 Modelled: 11 Confidence: 31.5% 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 1r3j chain C Region: 8 - 42 Aligned: 35 Modelled: 35 Confidence: 30.1% Identity: 11% Fold: Voltage-gated potassium channels Superfamily: Voltage-gated potassium channels Family: Voltage-gated potassium channels Phyre2 PDB 1m56 chain D Region: 17 - 30 Aligned: 14 Modelled: 14 Confidence: 27.6% Identity: 29% Fold: Single transmembrane helix Superfamily: Bacterial aa3 type cytochrome c oxidase subunit IV Family: Bacterial aa3 type cytochrome c oxidase subunit IV Phyre2 PDB 1f6g chain A Region: 10 - 58 Aligned: 49 Modelled: 49 Confidence: 27.2% Identity: 12% Fold: Voltage-gated potassium channels Superfamily: Voltage-gated potassium channels Family: Voltage-gated potassium channels Phyre2 PDB 2kb1 chain A Region: 10 - 41 Aligned: 32 Modelled: 32 Confidence: 23.3% Identity: 6% 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: 1 - 27 Aligned: 27 Modelled: 27 Confidence: 23.1% Identity: 22% PDB header:photosynthesis Chain: K: PDB Molecule:photosystem i reaction center subunit x psak; PDBTitle: improved model of plant photosystem i Phyre2 PDB 1bts chain A Region: 14 - 29 Aligned: 16 Modelled: 16 Confidence: 20.7% Identity: 25% 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 Phyre2 PDB 1btt chain A Region: 14 - 29 Aligned: 16 Modelled: 16 Confidence: 20.7% Identity: 25% 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 Phyre2 1 d1t92a_ 2 c2kepA_ 3 c3fu1B_ 4 d1oqwa_ 5 d2pila_ 6 c3sokB_ 7 d1qvea_ 8 d1x6za1 9 d1pbya4 10 c1pbyA_ 11 c4a18U_ 12 c2wsfG_ 13 c3u5eL_ 14 d1r3jc_ 15 d1m56d_ 16 d1f6ga_ 17 c2kb1A_ 18 c3lw5K_ 19 c1btsA_ 20 c1bttA_ 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65

Detailed template information

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

1 d1t92a_ 99.9 64 Fold:Pili subunits Superfamily:Pili subunits Family:Pseudopilin 2 c2kepA_ 99.9 53 PDB header:transport protein Chain: A: PDB Molecule:general secretion pathway protein g; PDBTitle: solution structure of xcpt, the main component of the type 22 secretion system of pseudomonas aeruginosa 3 c3fu1B_ 99.9 64 PDB header:protein transport Chain: B: PDB Molecule:general secretion pathway protein g; PDBTitle: crystal structure of the major pseudopilin from the type 2 secretion2 system of vibrio cholerae 4 d1oqwa_ 99.7 16 Fold:Pili subunits Superfamily:Pili subunits Family:Pilin 5 d2pila_ 99.7 17 Fold:Pili subunits Superfamily:Pili subunits Family:Pilin 6 c3sokB_ 99.7 21 PDB header:cell adhesion Chain: B: PDB Molecule:fimbrial protein; PDBTitle: dichelobacter nodosus pilin fima 7 d1qvea_ 77.7 12 Fold:Pili subunits Superfamily:Pili subunits Family:Pilin 8 d1x6za1 68.4 6 Fold:Pili subunits Superfamily:Pili subunits Family:Pilin 9 d1pbya4 60.2 60 Fold:Immunoglobulin-like beta-sandwich Superfamily:E set domains Family:Quinohemoprotein amine dehydrogenase A chain, domains 4 and 5 10 c1pbyA_ 53.7 60 PDB header:oxidoreductase Chain: A: PDB Molecule:quinohemoprotein amine dehydrogenase 60 kda PDBTitle: structure of the phenylhydrazine adduct of the2 quinohemoprotein amine dehydrogenase from paracoccus3 denitrificans at 1.7 a resolution 11 c4a18U_ 36.8 20 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 12 c2wsfG_ 31.6 13 PDB header:photosynthesis Chain: G: PDB Molecule:photosystem i reaction center subunit v, PDBTitle: improved model of plant photosystem i 13 c3u5eL_ 31.5 55 PDB header:ribosome Chain: L: PDB Molecule:60s ribosomal protein l13-a; PDBTitle: the structure of the eukaryotic ribosome at 3.0 resolution 14 d1r3jc_ 30.1 11 Fold:Voltage-gated potassium channels Superfamily:Voltage-gated potassium channels Family:Voltage-gated potassium channels 15 d1m56d_ 27.6 29 Fold:Single transmembrane helix Superfamily:Bacterial aa3 type cytochrome c oxidase subunit IV Family:Bacterial aa3 type cytochrome c oxidase subunit IV 16 d1f6ga_ 27.2 12 Fold:Voltage-gated potassium channels Superfamily:Voltage-gated potassium channels Family:Voltage-gated potassium channels 17 c2kb1A_ 23.3 6 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 18 c3lw5K_ 23.1 22 PDB header:photosynthesis Chain: K: PDB Molecule:photosystem i reaction center subunit x psak; PDBTitle: improved model of plant photosystem i 19 c1btsA_ 20.7 25 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 20 c1bttA_ 20.7 25 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 21 d3dtub2 not modelled 16.8 30 Fold:Transmembrane helix hairpin Superfamily:Cytochrome c oxidase subunit II-like, transmembrane region Family:Cytochrome c oxidase subunit II-like, transmembrane region 22 d1otsa_ not modelled 16.1 20 Fold:Clc chloride channel Superfamily:Clc chloride channel Family:Clc chloride channel 23 c3jyzA_ not modelled 15.7 0 PDB header:structural protein Chain: A: PDB Molecule:type iv pilin structural subunit; PDBTitle: crystal structure of pseudomonas aeruginosa (strain:2 pa110594) typeiv pilin in space group p41212 24 c2kxeA_ not modelled 15.1 27 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 25 c2o01G_ not modelled 14.4 13 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 26 d1oqva_ not modelled 13.7 20 Fold:Pili subunits Superfamily:Pili subunits Family:TcpA-like pilin 27 c2qksA_ not modelled 13.0 21 PDB header:metal transport Chain: A: PDB Molecule:kir3.1-prokaryotic kir channel chimera; PDBTitle: crystal structure of a kir3.1-prokaryotic kir channel chimera 28 d2a9ha1 not modelled 12.7 14 Fold:Voltage-gated potassium channels Superfamily:Voltage-gated potassium channels Family:Voltage-gated potassium channels 29 c2ljcA_ not modelled 12.5 31 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 30 c2wscK_ not modelled 10.8 31 PDB header:photosynthesis Chain: K: PDB Molecule:photosystem i reaction center subunit psak, PDBTitle: improved model of plant photosystem i 31 c1qleB_ not modelled 10.0 13 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 32 c1ar1B_ not modelled 10.0 13 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 33 c2k21A_ not modelled 9.7 10 PDB header:membrane protein Chain: A: PDB Molecule:potassium voltage-gated channel subfamily e PDBTitle: nmr structure of human kcne1 in lmpg micelles at ph 6.0 and2 40 degree c 34 c2hg5D_ not modelled 9.5 9 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 35 c1afoB_ not modelled 8.8 21 PDB header:integral membrane protein Chain: B: PDB Molecule:glycophorin a; PDBTitle: dimeric transmembrane domain of human glycophorin a, nmr,2 20 structures 36 c2j7aC_ not modelled 7.7 19 PDB header:oxidoreductase Chain: C: PDB Molecule:cytochrome c quinol dehydrogenase nrfh; PDBTitle: crystal structure of cytochrome c nitrite reductase nrfha2 complex from desulfovibrio vulgaris 37 c2jo1A_ not modelled 7.7 36 PDB header:hydrolase regulator Chain: A: PDB Molecule:phospholemman; PDBTitle: structure of the na,k-atpase regulatory protein fxyd1 in2 micelles 38 c2kadB_ not modelled 7.6 31 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 39 c2kadC_ not modelled 7.6 31 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 40 c2kadD_ not modelled 7.6 31 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 41 c2kadA_ not modelled 7.6 31 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 42 c3ifxB_ not modelled 7.5 10 PDB header:membrane protein Chain: B: PDB Molecule:voltage-gated potassium channel; PDBTitle: crystal structure of the spin-labeled kcsa mutant v48r1 43 d3ehbb2 not modelled 7.4 18 Fold:Transmembrane helix hairpin Superfamily:Cytochrome c oxidase subunit II-like, transmembrane region Family:Cytochrome c oxidase subunit II-like, transmembrane region 44 c1m57H_ not modelled 7.0 27 PDB header:oxidoreductase Chain: H: PDB Molecule:cytochrome c oxidase; PDBTitle: structure of cytochrome c oxidase from rhodobacter2 sphaeroides (eq(i-286) mutant)) 45 c2jp3A_ not modelled 7.0 21 PDB header:transcription Chain: A: PDB Molecule:fxyd domain-containing ion transport regulator 4; PDBTitle: solution structure of the human fxyd4 (chif) protein in sds2 micelles 46 c2jwaA_ not modelled 6.9 22 PDB header:transferase Chain: A: PDB Molecule:receptor tyrosine-protein kinase erbb-2; PDBTitle: erbb2 transmembrane segment dimer spatial structure 47 c2qzbB_ not modelled 6.7 47 PDB header:structural genomics, unknown function Chain: B: PDB Molecule:uncharacterized protein yfey; PDBTitle: crystal structure of the uncharacterized protein yfey from escherichia2 coli 48 c2kqtA_ not modelled 6.5 31 PDB header:transport protein Chain: A: PDB Molecule:m2 protein; PDBTitle: solid-state nmr structure of the m2 transmembrane peptide of the2 influenza a virus in dmpc lipid bilayers bound to deuterated3 amantadine 49 c1nyjB_ not modelled 6.5 31 PDB header:viral protein Chain: B: PDB Molecule:matrix protein m2; PDBTitle: the closed state structure of m2 protein h+ channel by2 solid state nmr spectroscopy 50 c2kqtC_ not modelled 6.5 31 PDB header:transport protein Chain: C: PDB Molecule:m2 protein; PDBTitle: solid-state nmr structure of the m2 transmembrane peptide of the2 influenza a virus in dmpc lipid bilayers bound to deuterated3 amantadine 51 c2kqtD_ not modelled 6.5 31 PDB header:transport protein Chain: D: PDB Molecule:m2 protein; PDBTitle: solid-state nmr structure of the m2 transmembrane peptide of the2 influenza a virus in dmpc lipid bilayers bound to deuterated3 amantadine 52 c1nyjA_ not modelled 6.5 31 PDB header:viral protein Chain: A: PDB Molecule:matrix protein m2; PDBTitle: the closed state structure of m2 protein h+ channel by2 solid state nmr spectroscopy 53 c1mp6A_ not modelled 6.5 31 PDB header:membrane protein Chain: A: PDB Molecule:matrix protein m2; PDBTitle: structure of the transmembrane region of the m2 protein h+2 channel by solid state nmr spectroscopy 54 c1nyjC_ not modelled 6.5 31 PDB header:viral protein Chain: C: PDB Molecule:matrix protein m2; PDBTitle: the closed state structure of m2 protein h+ channel by2 solid state nmr spectroscopy 55 c1nyjD_ not modelled 6.5 31 PDB header:viral protein Chain: D: PDB Molecule:matrix protein m2; PDBTitle: the closed state structure of m2 protein h+ channel by2 solid state nmr spectroscopy 56 c2kqtB_ not modelled 6.5 31 PDB header:transport protein Chain: B: PDB Molecule:m2 protein; PDBTitle: solid-state nmr structure of the m2 transmembrane peptide of the2 influenza a virus in dmpc lipid bilayers bound to deuterated3 amantadine 57 c2kncB_ not modelled 6.5 21 PDB header:cell adhesion Chain: B: PDB Molecule:integrin beta-3; PDBTitle: platelet integrin alfaiib-beta3 transmembrane-cytoplasmic2 heterocomplex 58 d1az3a_ not modelled 6.5 44 Fold:Restriction endonuclease-like Superfamily:Restriction endonuclease-like Family:Restriction endonuclease EcoRV 59 c2gs0B_ not modelled 6.4 29 PDB header:transcription Chain: B: PDB Molecule:cellular tumor antigen p53; PDBTitle: nmr structure of the complex between the ph domain of the2 tfb1 subunit from tfiih and the activation domain of p53 60 c2bnoA_ not modelled 5.7 7 PDB header:oxidoreductase Chain: A: PDB Molecule:epoxidase; PDBTitle: the structure of hydroxypropylphosphonic acid epoxidase2 from s. wedmorenis. 61 c3orgB_ not modelled 5.7 19 PDB header:transport protein Chain: B: PDB Molecule:cmclc; PDBTitle: crystal structure of a eukaryotic clc transporter 62 d1ehkb2 not modelled 5.7 28 Fold:Transmembrane helix hairpin Superfamily:Cytochrome c oxidase subunit II-like, transmembrane region Family:Cytochrome c oxidase subunit II-like, transmembrane region 63 c3jycA_ not modelled 5.7 14 PDB header:metal transport Chain: A: PDB Molecule:inward-rectifier k+ channel kir2.2; PDBTitle: crystal structure of the eukaryotic strong inward-rectifier2 k+ channel kir2.2 at 3.1 angstrom resolution 64 c2l2tA_ not modelled 5.2 21 PDB header:membrane protein Chain: A: PDB Molecule:receptor tyrosine-protein kinase erbb-4; PDBTitle: solution nmr structure of the erbb4 dimeric membrane domain 65 d1fftb2 not modelled 5.0 16 Fold:Transmembrane helix hairpin Superfamily:Cytochrome c oxidase subunit II-like, transmembrane region Family:Cytochrome c oxidase subunit II-like, transmembrane region

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