Secondary structure and disorder prediction

		1	.	.	.	.	.	.	.	.	10	.	.	.	.	.	.	.	.	.	20	.	.	.	.	.	.	.	.	.	30	.	.	.	.	.	.	.	.	.	40	.	.	.	.	.	.	.	.	.	50	.	.	.	.	.	.	.	.	.	60
Sequence		M	R	Q	F	I	I	S	E	N	T	M	Q	K	T	S	F	R	N	H	Q	V	K	R	F	S	S	Q	R	S	T	R	R	K	P	E	N	Q	P	T	R	V	I	L	F	N	K	P	Y	D	V	L	P	Q	F	T	D	E	A	G	R
Secondary structure
SS confidence
Disorder		?	?					?							?	?	?	?	?	?	?										?	?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	70	.	.	.	.	.	.	.	.	.	80	.	.	.	.	.	.	.	.	.	90	.	.	.	.	.	.	.	.	.	100	.	.	.	.	.	.	.	.	.	110	.	.	.	.	.	.	.	.	.	120
Sequence		K	T	L	K	E	F	I	P	V	Q	G	V	Y	A	A	G	R	L	D	R	D	S	E	G	L	L	V	L	T	N	N	G	A	L	Q	A	R	L	T	Q	P	G	K	R	T	G	K	I	Y	Y	V	Q	V	E	G	I	P	T	Q	D
Secondary structure
SS confidence
Disorder																																										?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	130	.	.	.	.	.	.	.	.	.	140	.	.	.	.	.	.	.	.	.	150	.	.	.	.	.	.	.	.	.	160	.	.	.	.	.	.	.	.	.	170	.	.	.	.	.	.	.	.	.	180
Sequence		A	L	E	A	L	R	N	G	V	T	L	N	D	G	P	T	L	P	A	G	A	E	L	V	D	E	P	A	W	L	W	P	R	N	P	P	I	R	E	R	K	S	I	P	T	S	W	L	K	I	T	L	Y	E	G	R	N	R	Q	V
Secondary structure
SS confidence
Disorder																													?	?	?	?			?		?	?	?	?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	190	.	.	.	.	.	.	.	.	.	200	.	.	.	.	.	.	.	.	.	210	.	.	.	.	.	.	.
Sequence		R	R	M	T	A	H	V	G	F	P	T	L	R	L	I	R	Y	A	M	G	D	Y	S	L	D	N	L	A	N	G	E	W	R	E	V	T	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 2oml chain A Region: 36 - 217 Aligned: 181 Modelled: 182 Confidence: 100.0% Identity: 94% PDB header:isomerase Chain: A: PDB Molecule:ribosomal large subunit pseudouridine synthase e; PDBTitle: crystal structure of e. coli pseudouridine synthase rlue Phyre2 PDB 2olw chain B Region: 38 - 217 Aligned: 179 Modelled: 180 Confidence: 100.0% Identity: 95% PDB header:isomerase Chain: B: PDB Molecule:ribosomal large subunit pseudouridine synthase e; PDBTitle: crystal structure of e. coli pseudouridine synthase rlue Phyre2 PDB 3dh3 chain C Region: 10 - 217 Aligned: 188 Modelled: 189 Confidence: 100.0% Identity: 31% PDB header:isomerase/rna Chain: C: PDB Molecule:ribosomal large subunit pseudouridine synthase f; PDBTitle: crystal structure of rluf in complex with a 22 nucleotide2 rna substrate Phyre2 PDB 1vio chain A Region: 10 - 217 Aligned: 189 Modelled: 189 Confidence: 100.0% Identity: 28% PDB header:lyase Chain: A: PDB Molecule:ribosomal small subunit pseudouridine synthase a; PDBTitle: crystal structure of pseudouridylate synthase Phyre2 PDB 1ksk chain A Region: 10 - 216 Aligned: 190 Modelled: 190 Confidence: 100.0% Identity: 32% PDB header:lyase Chain: A: PDB Molecule:ribosomal small subunit pseudouridine synthase a; PDBTitle: structure of rsua Phyre2 PDB 2gml chain A Region: 38 - 217 Aligned: 160 Modelled: 161 Confidence: 100.0% Identity: 35% PDB header:isomerase Chain: A: PDB Molecule:ribosomal large subunit pseudouridine synthase f; PDBTitle: crystal structure of catalytic domain of e.coli rluf Phyre2 PDB 1vio chain A domain 1 Region: 37 - 216 Aligned: 163 Modelled: 163 Confidence: 100.0% Identity: 29% Fold: Pseudouridine synthase Superfamily: Pseudouridine synthase Family: Pseudouridine synthase RsuA/RluD Phyre2 PDB 1ksk chain A domain 4 Region: 39 - 216 Aligned: 160 Modelled: 161 Confidence: 100.0% Identity: 36% Fold: Pseudouridine synthase Superfamily: Pseudouridine synthase Family: Pseudouridine synthase RsuA/RluD Phyre2 PDB 1v9k chain A Region: 34 - 198 Aligned: 162 Modelled: 163 Confidence: 100.0% Identity: 17% Fold: Pseudouridine synthase Superfamily: Pseudouridine synthase Family: Pseudouridine synthase RsuA/RluD Phyre2 PDB 1v9f chain A Region: 33 - 198 Aligned: 160 Modelled: 166 Confidence: 100.0% Identity: 21% PDB header:lyase Chain: A: PDB Molecule:ribosomal large subunit pseudouridine synthase d; PDBTitle: crystal structure of catalytic domain of pseudouridine2 synthase rlud from escherichia coli Phyre2 PDB 1v9f chain A Region: 33 - 198 Aligned: 160 Modelled: 166 Confidence: 100.0% Identity: 21% Fold: Pseudouridine synthase Superfamily: Pseudouridine synthase Family: Pseudouridine synthase RsuA/RluD Phyre2 PDB 1qyu chain A Region: 33 - 201 Aligned: 163 Modelled: 169 Confidence: 100.0% Identity: 20% PDB header:lyase Chain: A: PDB Molecule:ribosomal large subunit pseudouridine synthase d; PDBTitle: structure of the catalytic domain of 23s rrna pseudouridine2 synthase rlud Phyre2 PDB 2i82 chain D Region: 33 - 198 Aligned: 163 Modelled: 166 Confidence: 100.0% Identity: 20% PDB header:lyase/rna Chain: D: PDB Molecule:ribosomal large subunit pseudouridine synthase a; PDBTitle: crystal structure of pseudouridine synthase rlua: indirect2 sequence readout through protein-induced rna structure Phyre2 PDB 2apo chain A domain 2 Region: 41 - 206 Aligned: 146 Modelled: 154 Confidence: 98.8% Identity: 13% Fold: Pseudouridine synthase Superfamily: Pseudouridine synthase Family: Pseudouridine synthase II TruB Phyre2 PDB 2ey4 chain A domain 2 Region: 41 - 206 Aligned: 157 Modelled: 166 Confidence: 98.8% Identity: 17% Fold: Pseudouridine synthase Superfamily: Pseudouridine synthase Family: Pseudouridine synthase II TruB Phyre2 PDB 2ey4 chain A Region: 41 - 206 Aligned: 158 Modelled: 166 Confidence: 98.7% Identity: 15% PDB header:isomerase/biosynthetic protein Chain: A: PDB Molecule:probable trna pseudouridine synthase b; PDBTitle: crystal structure of a cbf5-nop10-gar1 complex Phyre2 PDB 1r3e chain A domain 2 Region: 41 - 212 Aligned: 164 Modelled: 170 Confidence: 98.6% Identity: 18% Fold: Pseudouridine synthase Superfamily: Pseudouridine synthase Family: Pseudouridine synthase II TruB Phyre2 PDB 2apo chain A Region: 41 - 206 Aligned: 146 Modelled: 154 Confidence: 98.6% Identity: 14% PDB header:isomerase/rna binding protein Chain: A: PDB Molecule:probable trna pseudouridine synthase b; PDBTitle: crystal structure of the methanococcus jannaschii cbf52 nop10 complex Phyre2 PDB 3uai chain A Region: 16 - 206 Aligned: 180 Modelled: 190 Confidence: 98.5% Identity: 15% PDB header:isomerase/chaperone Chain: A: PDB Molecule:h/aca ribonucleoprotein complex subunit 4; PDBTitle: structure of the shq1-cbf5-nop10-gar1 complex from saccharomyces2 cerevisiae Phyre2 PDB 1sgv chain A domain 2 Region: 41 - 206 Aligned: 150 Modelled: 166 Confidence: 98.5% Identity: 18% Fold: Pseudouridine synthase Superfamily: Pseudouridine synthase Family: Pseudouridine synthase II TruB Phyre2 1 c2omlA_ 2 c2olwB_ 3 c3dh3C_ 4 c1vioA_ 5 c1kskA_ 6 c2gmlA_ 7 d1vioa1 8 d1kska4 9 d1v9ka_ 10 c1v9fA_ 11 d1v9fa_ 12 c1qyuA_ 13 c2i82D_ 14 d2apoa2 15 d2ey4a2 16 c2ey4A_ 17 d1r3ea2 18 c2apoA_ 19 c3uaiA_ 20 d1sgva2 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

Detailed template information

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

1 c2omlA_ 100.0 94 PDB header:isomerase Chain: A: PDB Molecule:ribosomal large subunit pseudouridine synthase e; PDBTitle: crystal structure of e. coli pseudouridine synthase rlue 2 c2olwB_ 100.0 95 PDB header:isomerase Chain: B: PDB Molecule:ribosomal large subunit pseudouridine synthase e; PDBTitle: crystal structure of e. coli pseudouridine synthase rlue 3 c3dh3C_ 100.0 31 PDB header:isomerase/rna Chain: C: PDB Molecule:ribosomal large subunit pseudouridine synthase f; PDBTitle: crystal structure of rluf in complex with a 22 nucleotide2 rna substrate 4 c1vioA_ 100.0 28 PDB header:lyase Chain: A: PDB Molecule:ribosomal small subunit pseudouridine synthase a; PDBTitle: crystal structure of pseudouridylate synthase 5 c1kskA_ 100.0 32 PDB header:lyase Chain: A: PDB Molecule:ribosomal small subunit pseudouridine synthase a; PDBTitle: structure of rsua 6 c2gmlA_ 100.0 35 PDB header:isomerase Chain: A: PDB Molecule:ribosomal large subunit pseudouridine synthase f; PDBTitle: crystal structure of catalytic domain of e.coli rluf 7 d1vioa1 100.0 29 Fold:Pseudouridine synthase Superfamily:Pseudouridine synthase Family:Pseudouridine synthase RsuA/RluD 8 d1kska4 100.0 36 Fold:Pseudouridine synthase Superfamily:Pseudouridine synthase Family:Pseudouridine synthase RsuA/RluD 9 d1v9ka_ 100.0 17 Fold:Pseudouridine synthase Superfamily:Pseudouridine synthase Family:Pseudouridine synthase RsuA/RluD 10 c1v9fA_ 100.0 21 PDB header:lyase Chain: A: PDB Molecule:ribosomal large subunit pseudouridine synthase d; PDBTitle: crystal structure of catalytic domain of pseudouridine2 synthase rlud from escherichia coli 11 d1v9fa_ 100.0 21 Fold:Pseudouridine synthase Superfamily:Pseudouridine synthase Family:Pseudouridine synthase RsuA/RluD 12 c1qyuA_ 100.0 20 PDB header:lyase Chain: A: PDB Molecule:ribosomal large subunit pseudouridine synthase d; PDBTitle: structure of the catalytic domain of 23s rrna pseudouridine2 synthase rlud 13 c2i82D_ 100.0 20 PDB header:lyase/rna Chain: D: PDB Molecule:ribosomal large subunit pseudouridine synthase a; PDBTitle: crystal structure of pseudouridine synthase rlua: indirect2 sequence readout through protein-induced rna structure 14 d2apoa2 98.8 13 Fold:Pseudouridine synthase Superfamily:Pseudouridine synthase Family:Pseudouridine synthase II TruB 15 d2ey4a2 98.8 17 Fold:Pseudouridine synthase Superfamily:Pseudouridine synthase Family:Pseudouridine synthase II TruB 16 c2ey4A_ 98.7 15 PDB header:isomerase/biosynthetic protein Chain: A: PDB Molecule:probable trna pseudouridine synthase b; PDBTitle: crystal structure of a cbf5-nop10-gar1 complex 17 d1r3ea2 98.6 18 Fold:Pseudouridine synthase Superfamily:Pseudouridine synthase Family:Pseudouridine synthase II TruB 18 c2apoA_ 98.6 14 PDB header:isomerase/rna binding protein Chain: A: PDB Molecule:probable trna pseudouridine synthase b; PDBTitle: crystal structure of the methanococcus jannaschii cbf52 nop10 complex 19 c3uaiA_ 98.5 15 PDB header:isomerase/chaperone Chain: A: PDB Molecule:h/aca ribonucleoprotein complex subunit 4; PDBTitle: structure of the shq1-cbf5-nop10-gar1 complex from saccharomyces2 cerevisiae 20 d1sgva2 98.5 18 Fold:Pseudouridine synthase Superfamily:Pseudouridine synthase Family:Pseudouridine synthase II TruB 21 d1k8wa5 not modelled 98.5 20 Fold:Pseudouridine synthase Superfamily:Pseudouridine synthase Family:Pseudouridine synthase II TruB 22 c1sgvA_ not modelled 98.4 20 PDB header:lyase Chain: A: PDB Molecule:trna pseudouridine synthase b; PDBTitle: structure of trna psi55 pseudouridine synthase (trub) 23 c1k8wA_ not modelled 98.0 21 PDB header:lyase/rna Chain: A: PDB Molecule:trna pseudouridine synthase b; PDBTitle: crystal structure of the e. coli pseudouridine synthase2 trub bound to a t stem-loop rna 24 c1ze2B_ not modelled 95.4 18 PDB header:lyase/rna Chain: B: PDB Molecule:trna pseudouridine synthase b; PDBTitle: conformational change of pseudouridine 55 synthase upon its2 association with rna substrate 25 c2k6pA_ not modelled 32.2 11 PDB header:unknown function Chain: A: PDB Molecule:uncharacterized protein hp_1423; PDBTitle: solution structure of hypothetical protein, hp1423 26 c2fo1A_ not modelled 19.2 16 PDB header:gene regulation/signalling protein/dna Chain: A: PDB Molecule:lin-12 and glp-1 phenotype protein 1, isoform b; PDBTitle: crystal structure of the csl-notch-mastermind ternary2 complex bound to dna 27 d2ysca1 not modelled 13.8 45 Fold:WW domain-like Superfamily:WW domain Family:WW domain 28 d1nkga1 not modelled 12.4 14 Fold:Prealbumin-like Superfamily:Starch-binding domain-like Family:Rhamnogalacturonase B, RhgB, middle domain 29 c3cjsA_ not modelled 12.0 50 PDB header:transferase/ribosomal protein Chain: A: PDB Molecule:ribosomal protein l11 methyltransferase; PDBTitle: minimal recognition complex between prma and ribosomal protein l11 30 d2ho2a1 not modelled 11.7 42 Fold:WW domain-like Superfamily:WW domain Family:WW domain 31 c2jmzA_ not modelled 11.6 14 PDB header:unknown function Chain: A: PDB Molecule:hypothetical protein mj0781; PDBTitle: solution structure of a klba intein precursor from2 methanococcus jannaschii 32 c1f5nA_ not modelled 11.4 13 PDB header:signaling protein Chain: A: PDB Molecule:interferon-induced guanylate-binding protein 1; PDBTitle: human guanylate binding protein-1 in complex with the gtp2 analogue, gmppnp. 33 c3h7hA_ not modelled 11.2 16 PDB header:transcription Chain: A: PDB Molecule:transcription elongation factor spt4; PDBTitle: crystal structure of the human transcription elongation factor dsif,2 hspt4/hspt5 (176-273) 34 d1zhva1 not modelled 9.4 31 Fold:Ferredoxin-like Superfamily:ACT-like Family:Atu0741-like 35 c1mzwB_ not modelled 8.3 23 PDB header:isomerase Chain: B: PDB Molecule:u4/u6 snrnp 60kda protein; PDBTitle: crystal structure of a u4/u6 snrnp complex between human2 spliceosomal cyclophilin h and a u4/u6-60k peptide 36 d2hq4a1 not modelled 7.9 33 Fold:PH1570-like Superfamily:PH1570-like Family:PH1570-like 37 c2voiB_ not modelled 7.8 27 PDB header:apoptosis Chain: B: PDB Molecule:bh3-interacting domain death agonist p13; PDBTitle: structure of mouse a1 bound to the bid bh3-domain 38 c2imzA_ not modelled 6.6 14 PDB header:hydrolase Chain: A: PDB Molecule:endonuclease pi-mtui; PDBTitle: crystal structure of mtu reca intein splicing domain 39 d1t6la1 not modelled 6.4 19 Fold:DNA clamp Superfamily:DNA clamp Family:DNA polymerase processivity factor 40 c2exuA_ not modelled 6.2 16 PDB header:transcription Chain: A: PDB Molecule:transcription initiation protein spt4/spt5; PDBTitle: crystal structure of saccharomyces cerevisiae transcription elongation2 factors spt4-spt5ngn domain 41 c1tlqA_ not modelled 6.1 13 PDB header:structural genomics, unknown function Chain: A: PDB Molecule:hypothetical protein ypjq; PDBTitle: crystal structure of protein ypjq from bacillus subtilis, pfam duf64 42 d1tlqa_ not modelled 6.1 13 Fold:YutG-like Superfamily:YutG-like Family:YutG-like 43 d1k4ta3 not modelled 5.4 13 Fold:Eukaryotic DNA topoisomerase I, N-terminal DNA-binding fragment Superfamily:Eukaryotic DNA topoisomerase I, N-terminal DNA-binding fragment Family:Eukaryotic DNA topoisomerase I, N-terminal DNA-binding fragment 44 d1y9ia_ not modelled 5.3 13 Fold:YutG-like Superfamily:YutG-like Family:YutG-like 45 c3bbnD_ not modelled 5.3 13 PDB header:ribosome Chain: D: PDB Molecule:ribosomal protein s4; PDBTitle: homology model for the spinach chloroplast 30s subunit2 fitted to 9.4a cryo-em map of the 70s chlororibosome. 46 c1vs3B_ not modelled 5.2 40 PDB header:isomerase Chain: B: PDB Molecule:trna pseudouridine synthase a; PDBTitle: crystal structure of the trna pseudouridine synthase trua from thermus2 thermophilus hb8 47 c2x5pA_ not modelled 5.2 18 PDB header:protein binding Chain: A: PDB Molecule:fibronectin binding protein; PDBTitle: crystal structure of the streptococcus pyogenes fibronectin binding2 protein fbab-b

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