Secondary structure and disorder prediction

		1	.	.	.	.	.	.	.	.	10	.	.	.	.	.	.	.	.	.	20	.	.	.	.	.	.	.	.	.	30	.	.	.	.	.	.	.	.	.	40	.	.	.	.	.	.	.	.	.	50	.	.	.	.	.	.	.	.	.	60
Sequence		M	T	R	L	A	S	R	F	G	A	A	N	L	I	R	R	D	R	P	L	T	R	E	E	L	F	R	V	V	P	S	V	F	S	E	D	K	H	E	S	R	S	E	R	Y	T	Y	I	P	T	I	S	L	L	D	S	L	Q	R	E
Secondary structure
SS confidence
Disorder		?	?	?							?	?	?	?	?	?	?	?	?	?	?															?	?	?	?	?	?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	70	.	.	.	.	.	.	.	.	.	80	.	.	.	.	.	.	.	.	.	90	.	.	.	.	.	.	.	.	.	100	.	.	.	.	.	.	.	.	.	110	.	.	.	.	.	.	.	.	.	120
Sequence		G	F	Q	P	F	F	A	C	Q	T	R	V	R	D	P	R	R	R	E	H	T	K	H	M	L	R	L	R	R	E	G	Q	I	T	G	K	Q	V	P	E	I	I	L	L	N	S	H	D	G	T	S	S	Y	Q	M	L	P	G	M	F
Secondary structure
SS confidence
Disorder									?		?	?	?	?	?	?	?	?											?	?	?		?	?																						?		?
Disorder confidence
		.	.	.	.	.	.	.	.	.	130	.	.	.	.	.	.	.	.	.	140	.	.	.	.	.	.	.	.	.	150	.	.	.	.	.	.	.	.	.	160	.	.	.	.	.	.	.	.	.	170	.	.	.	.	.	.	.	.	.	180
Sequence		R	A	V	C	Q	N	G	L	V	C	G	E	S	F	G	E	V	R	V	P	H	K	G	D	V	V	S	Q	V	I	E	G	A	Y	E	V	L	G	I	F	E	R	V	E	E	K	R	D	A	M	Q	S	L	L	L	P	P	P	V	Q
Secondary structure
SS confidence
Disorder										?		?	?	?	?	?																																				?		?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	190	.	.	.	.	.	.	.	.	.	200	.	.	.	.	.	.	.	.	.	210	.	.	.	.	.	.	.	.	.	220	.	.	.	.	.	.	.	.	.	230	.	.	.	.	.	.	.	.	.	240
Sequence		Q	A	L	A	K	A	A	L	T	Y	R	F	G	E	D	H	Q	P	V	T	E	S	Q	I	L	S	P	R	R	W	Q	D	E	S	N	D	L	W	T	T	Y	Q	R	I	Q	E	N	L	I	K	G	G	L	S	G	R	N	A	K	G
Secondary structure
SS confidence
Disorder																																?				?																			?	?	?	?	?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	250	.	.	.	.	.	.	.	.	.	260	.	.	.	.	.	.	.	.	.	270	.	.	.
Sequence		G	R	T	H	T	R	A	V	R	G	I	D	G	D	V	K	L	N	R	A	L	W	V	M	A	E	T	L	L	T	Q	L	Q
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 2f9j chain P Region: 15 - 30 Aligned: 16 Modelled: 16 Confidence: 32.7% Identity: 50% PDB header:rna binding protein Chain: P: PDB Molecule:splicing factor 3b subunit 1; PDBTitle: 3.0 angstrom resolution structure of a y22m mutant of the spliceosomal2 protein p14 bound to a region of sf3b155 Phyre2 PDB 3agj chain D Region: 212 - 255 Aligned: 34 Modelled: 44 Confidence: 21.7% Identity: 18% PDB header:translation/hydrolase Chain: D: PDB Molecule:protein pelota homolog; PDBTitle: crystal structure of archaeal pelota and gtp-bound ef1 alpha complex Phyre2 PDB 3agj chain B Region: 212 - 255 Aligned: 34 Modelled: 44 Confidence: 21.7% Identity: 18% PDB header:translation/hydrolase Chain: B: PDB Molecule:protein pelota homolog; PDBTitle: crystal structure of archaeal pelota and gtp-bound ef1 alpha complex Phyre2 PDB 2qi2 chain A domain 1 Region: 212 - 227 Aligned: 16 Modelled: 16 Confidence: 16.5% Identity: 25% Fold: Sm-like fold Superfamily: Dom34/Pelota N-terminal domain-like Family: Dom34/Pelota N-terminal domain-like Phyre2 PDB 3lyd chain A Region: 211 - 228 Aligned: 18 Modelled: 18 Confidence: 14.3% Identity: 28% PDB header:structural genomics, unknown function Chain: A: PDB Molecule:uncharacterized protein; PDBTitle: crystal structure of putative uncharacterized protein from jonesia2 denitrificans Phyre2 PDB 2vgn chain A domain 1 Region: 212 - 227 Aligned: 16 Modelled: 16 Confidence: 13.4% Identity: 31% Fold: Sm-like fold Superfamily: Dom34/Pelota N-terminal domain-like Family: Dom34/Pelota N-terminal domain-like Phyre2 PDB 2qi2 chain A Region: 212 - 225 Aligned: 14 Modelled: 14 Confidence: 12.6% Identity: 21% PDB header:cell cycle Chain: A: PDB Molecule:cell division protein pelota related protein; PDBTitle: crystal structure of the thermoplasma acidophilum pelota2 protein Phyre2 PDB 3oby chain B Region: 212 - 225 Aligned: 14 Modelled: 14 Confidence: 11.2% Identity: 29% PDB header:hydrolase Chain: B: PDB Molecule:protein pelota homolog; PDBTitle: crystal structure of archaeoglobus fulgidus pelota reveals inter-2 domain structural plasticity Phyre2 PDB 1w6g chain A domain 2 Region: 18 - 48 Aligned: 30 Modelled: 31 Confidence: 10.5% Identity: 17% Fold: Cystatin-like Superfamily: Amine oxidase N-terminal region Family: Amine oxidase N-terminal region Phyre2 PDB 3obw chain A Region: 212 - 225 Aligned: 14 Modelled: 14 Confidence: 9.9% Identity: 21% PDB header:hydrolase Chain: A: PDB Molecule:protein pelota homolog; PDBTitle: crystal structure of two archaeal pelotas reveal inter-domain2 structural plasticity Phyre2 PDB 2zkr chain X Region: 254 - 262 Aligned: 9 Modelled: 9 Confidence: 9.3% Identity: 56% PDB header:ribosomal protein/rna Chain: X: PDB Molecule:rna helices; PDBTitle: structure of a mammalian ribosomal 60s subunit within an2 80s complex obtained by docking homology models of the rna3 and proteins into an 8.7 a cryo-em map Phyre2 PDB 1xl7 chain A domain 2 Region: 78 - 166 Aligned: 86 Modelled: 86 Confidence: 9.3% Identity: 15% Fold: CoA-dependent acyltransferases Superfamily: CoA-dependent acyltransferases Family: Choline/Carnitine O-acyltransferase Phyre2 PDB 3jyw chain W Region: 254 - 262 Aligned: 9 Modelled: 9 Confidence: 9.0% Identity: 44% PDB header:ribosome Chain: W: PDB Molecule:60s ribosomal protein l31(a); PDBTitle: structure of the 60s proteins for eukaryotic ribosome based on cryo-em2 map of thermomyces lanuginosus ribosome at 8.9a resolution Phyre2 PDB 3kzt chain B Region: 100 - 128 Aligned: 29 Modelled: 29 Confidence: 8.9% Identity: 17% PDB header:structural genomics, unknown function Chain: B: PDB Molecule:uncharacterized protein; PDBTitle: crystal structure of protein of unknown function (np_812423.1) from2 bacteroides thetaiotaomicron vpi-5482 at 2.10 a resolution Phyre2 PDB 3lg8 chain B Region: 121 - 128 Aligned: 8 Modelled: 8 Confidence: 8.7% Identity: 25% PDB header:hydrolase Chain: B: PDB Molecule:a-type atp synthase subunit e; PDBTitle: crystal structure of the c-terminal part of subunit e (e101-206) from2 methanocaldococcus jannaschii of a1ao atp synthase Phyre2 PDB 4a1e chain W Region: 254 - 262 Aligned: 9 Modelled: 9 Confidence: 8.5% Identity: 44% PDB header:ribosome Chain: W: PDB Molecule:60s ribosomal protein l31; PDBTitle: t.thermophila 60s ribosomal subunit in complex with2 initiation factor 6. this file contains 5s rrna, 5.8s rrna3 and proteins of molecule 1 Phyre2 PDB 2j37 chain 6 Region: 254 - 262 Aligned: 9 Modelled: 9 Confidence: 8.4% Identity: 67% PDB header:ribosome Chain: 6: PDB Molecule:ribosomal protein l31; PDBTitle: model of mammalian srp bound to 80s rncs Phyre2 PDB 1q7e chain A Region: 12 - 32 Aligned: 21 Modelled: 21 Confidence: 8.1% Identity: 24% Fold: CoA-transferase family III (CaiB/BaiF) Superfamily: CoA-transferase family III (CaiB/BaiF) Family: CoA-transferase family III (CaiB/BaiF) Phyre2 PDB 2fip chain A Region: 121 - 130 Aligned: 10 Modelled: 10 Confidence: 7.8% Identity: 30% PDB header:transcription Chain: A: PDB Molecule:late genes activator; PDBTitle: phage phi29 transcription regulator p4 Phyre2 PDB 1vqo chain X domain 1 Region: 254 - 262 Aligned: 9 Modelled: 9 Confidence: 7.8% Identity: 44% Fold: Ribosomal protein L31e Superfamily: Ribosomal protein L31e Family: Ribosomal protein L31e Phyre2 1 c2f9jP_ 2 c3agjD_ 3 c3agjB_ 4 d2qi2a1 5 c3lydA_ 6 d2vgna1 7 c2qi2A_ 8 c3obyB_ 9 d1w6ga2 10 c3obwA_ 11 c2zkrx_ 12 d1xl7a2 13 c3jywW_ 14 c3kztB_ 15 c3lg8B_ 16 c4a1eW_ 17 c2j376_ 18 d1q7ea_ 19 c2fipA_ 20 d1vqox1 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

Detailed template information

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

1 c2f9jP_ 32.7 50 PDB header:rna binding protein Chain: P: PDB Molecule:splicing factor 3b subunit 1; PDBTitle: 3.0 angstrom resolution structure of a y22m mutant of the spliceosomal2 protein p14 bound to a region of sf3b155 2 c3agjD_ 21.7 18 PDB header:translation/hydrolase Chain: D: PDB Molecule:protein pelota homolog; PDBTitle: crystal structure of archaeal pelota and gtp-bound ef1 alpha complex 3 c3agjB_ 21.7 18 PDB header:translation/hydrolase Chain: B: PDB Molecule:protein pelota homolog; PDBTitle: crystal structure of archaeal pelota and gtp-bound ef1 alpha complex 4 d2qi2a1 16.5 25 Fold:Sm-like fold Superfamily:Dom34/Pelota N-terminal domain-like Family:Dom34/Pelota N-terminal domain-like 5 c3lydA_ 14.3 28 PDB header:structural genomics, unknown function Chain: A: PDB Molecule:uncharacterized protein; PDBTitle: crystal structure of putative uncharacterized protein from jonesia2 denitrificans 6 d2vgna1 13.4 31 Fold:Sm-like fold Superfamily:Dom34/Pelota N-terminal domain-like Family:Dom34/Pelota N-terminal domain-like 7 c2qi2A_ 12.6 21 PDB header:cell cycle Chain: A: PDB Molecule:cell division protein pelota related protein; PDBTitle: crystal structure of the thermoplasma acidophilum pelota2 protein 8 c3obyB_ 11.2 29 PDB header:hydrolase Chain: B: PDB Molecule:protein pelota homolog; PDBTitle: crystal structure of archaeoglobus fulgidus pelota reveals inter-2 domain structural plasticity 9 d1w6ga2 10.5 17 Fold:Cystatin-like Superfamily:Amine oxidase N-terminal region Family:Amine oxidase N-terminal region 10 c3obwA_ 9.9 21 PDB header:hydrolase Chain: A: PDB Molecule:protein pelota homolog; PDBTitle: crystal structure of two archaeal pelotas reveal inter-domain2 structural plasticity 11 c2zkrx_ 9.3 56 PDB header:ribosomal protein/rna Chain: X: PDB Molecule:rna helices; PDBTitle: structure of a mammalian ribosomal 60s subunit within an2 80s complex obtained by docking homology models of the rna3 and proteins into an 8.7 a cryo-em map 12 d1xl7a2 9.3 15 Fold:CoA-dependent acyltransferases Superfamily:CoA-dependent acyltransferases Family:Choline/Carnitine O-acyltransferase 13 c3jywW_ 9.0 44 PDB header:ribosome Chain: W: PDB Molecule:60s ribosomal protein l31(a); PDBTitle: structure of the 60s proteins for eukaryotic ribosome based on cryo-em2 map of thermomyces lanuginosus ribosome at 8.9a resolution 14 c3kztB_ 8.9 17 PDB header:structural genomics, unknown function Chain: B: PDB Molecule:uncharacterized protein; PDBTitle: crystal structure of protein of unknown function (np_812423.1) from2 bacteroides thetaiotaomicron vpi-5482 at 2.10 a resolution 15 c3lg8B_ 8.7 25 PDB header:hydrolase Chain: B: PDB Molecule:a-type atp synthase subunit e; PDBTitle: crystal structure of the c-terminal part of subunit e (e101-206) from2 methanocaldococcus jannaschii of a1ao atp synthase 16 c4a1eW_ 8.5 44 PDB header:ribosome Chain: W: PDB Molecule:60s ribosomal protein l31; PDBTitle: t.thermophila 60s ribosomal subunit in complex with2 initiation factor 6. this file contains 5s rrna, 5.8s rrna3 and proteins of molecule 1 17 c2j376_ 8.4 67 PDB header:ribosome Chain: 6: PDB Molecule:ribosomal protein l31; PDBTitle: model of mammalian srp bound to 80s rncs 18 d1q7ea_ 8.1 24 Fold:CoA-transferase family III (CaiB/BaiF) Superfamily:CoA-transferase family III (CaiB/BaiF) Family:CoA-transferase family III (CaiB/BaiF) 19 c2fipA_ 7.8 30 PDB header:transcription Chain: A: PDB Molecule:late genes activator; PDBTitle: phage phi29 transcription regulator p4 20 d1vqox1 7.8 44 Fold:Ribosomal protein L31e Superfamily:Ribosomal protein L31e Family:Ribosomal protein L31e 21 d1u5tb1 not modelled 7.7 33 Fold:DNA/RNA-binding 3-helical bundle Superfamily:"Winged helix" DNA-binding domain Family:Vacuolar sorting protein domain 22 d1xhmb1 not modelled 7.6 14 Fold:Non-globular all-alpha subunits of globular proteins Superfamily:Transducin (heterotrimeric G protein), gamma chain Family:Transducin (heterotrimeric G protein), gamma chain 23 c3mcaB_ not modelled 7.5 38 PDB header:translation regulation/hydrolase Chain: B: PDB Molecule:protein dom34; PDBTitle: structure of the dom34-hbs1 complex and implications for its role in2 no-go decay 24 c1xhmB_ not modelled 7.5 14 PDB header:signaling protein Chain: B: PDB Molecule:guanine nucleotide-binding protein g(i)/g(s) PDBTitle: the crystal structure of a biologically active peptide2 (sigk) bound to a g protein beta:gamma heterodimer 25 c3hogA_ not modelled 7.5 16 PDB header:oxidoreductase Chain: A: PDB Molecule:superoxide dismutase [cu-zn], chloroplastic; PDBTitle: metal-free tomato chloroplast superoxide dismutase 26 c3hxxA_ not modelled 7.4 21 PDB header:ligase Chain: A: PDB Molecule:alanyl-trna synthetase; PDBTitle: crystal structure of catalytic fragment of e. coli alars in complex2 with amppcp 27 c1yfsB_ not modelled 7.3 17 PDB header:ligase Chain: B: PDB Molecule:alanyl-trna synthetase; PDBTitle: the crystal structure of alanyl-trna synthetase in complex2 with l-alanine 28 d1riqa2 not modelled 7.2 21 Fold:Class II aaRS and biotin synthetases Superfamily:Class II aaRS and biotin synthetases Family:Class II aminoacyl-tRNA synthetase (aaRS)-like, catalytic domain 29 c2cv8A_ not modelled 6.8 20 PDB header:hydrolase Chain: A: PDB Molecule:trna-splicing endonuclease; PDBTitle: crystal structure of trna-intron endonuclease from2 sulfolobus tokodaii 30 c3m9vA_ not modelled 6.5 21 PDB header:oxidoreductase Chain: A: PDB Molecule:fad-dependent oxidoreductase; PDBTitle: x-ray structure of a kijd3 in complex with dtdp 31 d1whza_ not modelled 6.4 21 Fold:dsRBD-like Superfamily:YcfA/nrd intein domain Family:YcfA-like 32 c1wqeA_ not modelled 6.3 46 PDB header:toxin Chain: A: PDB Molecule:omtx3; PDBTitle: an unusual fold for potassium channel blockers: nmr2 structure of three toxins from the scorpion opisthacanthus3 madagascariensis 33 c3nbmA_ not modelled 6.1 10 PDB header:transferase Chain: A: PDB Molecule:pts system, lactose-specific iibc components; PDBTitle: the lactose-specific iib component domain structure of the2 phosphoenolpyruvate:carbohydrate phosphotransferase system (pts) from3 streptococcus pneumoniae. 34 c1e2vB_ not modelled 6.0 67 PDB header:electron transport proteins Chain: B: PDB Molecule:cytochrome f; PDBTitle: n153q mutant of cytochrome f from chlamydomonas reinhardtii 35 d1ukua_ not modelled 5.9 35 Fold:Ferredoxin-like Superfamily:GlnB-like Family:Divalent ion tolerance proteins CutA (CutA1) 36 d1vf5c1 not modelled 5.9 67 Fold:Common fold of diphtheria toxin/transcription factors/cytochrome f Superfamily:Cytochrome f, large domain Family:Cytochrome f, large domain 37 c1s1iW_ not modelled 5.8 44 PDB header:ribosome Chain: W: PDB Molecule:60s ribosomal protein l31; PDBTitle: structure of the ribosomal 80s-eef2-sordarin complex from2 yeast obtained by docking atomic models for rna and protein3 components into a 11.7 a cryo-em map. this file, 1s1i,4 contains 60s subunit. the 40s ribosomal subunit is in file5 1s1h. 38 d1ci3m1 not modelled 5.8 67 Fold:Common fold of diphtheria toxin/transcription factors/cytochrome f Superfamily:Cytochrome f, large domain Family:Cytochrome f, large domain 39 d1e2wa1 not modelled 5.8 67 Fold:Common fold of diphtheria toxin/transcription factors/cytochrome f Superfamily:Cytochrome f, large domain Family:Cytochrome f, large domain 40 d1gg2g_ not modelled 5.8 16 Fold:Non-globular all-alpha subunits of globular proteins Superfamily:Transducin (heterotrimeric G protein), gamma chain Family:Transducin (heterotrimeric G protein), gamma chain 41 c3phfX_ not modelled 5.7 15 PDB header:viral protein Chain: X: PDB Molecule:envelope glycoprotein l; PDBTitle: crystal structure of the epstein-barr virus gh and gl complex 42 d1vhfa_ not modelled 5.6 24 Fold:Ferredoxin-like Superfamily:GlnB-like Family:Divalent ion tolerance proteins CutA (CutA1) 43 d1hcza1 not modelled 5.5 67 Fold:Common fold of diphtheria toxin/transcription factors/cytochrome f Superfamily:Cytochrome f, large domain Family:Cytochrome f, large domain 44 d2zfha1 not modelled 5.4 35 Fold:Ferredoxin-like Superfamily:GlnB-like Family:Divalent ion tolerance proteins CutA (CutA1) 45 c1xk8A_ not modelled 5.4 35 PDB header:structural genomics, unknown function Chain: A: PDB Molecule:divalent cation tolerant protein cuta; PDBTitle: divalent cation tolerant protein cuta from homo sapiens2 o60888 46 d1y1pa1 not modelled 5.4 8 Fold:NAD(P)-binding Rossmann-fold domains Superfamily:NAD(P)-binding Rossmann-fold domains Family:Tyrosine-dependent oxidoreductases 47 d1vkra_ not modelled 5.4 22 Fold:Phosphotyrosine protein phosphatases I-like Superfamily:PTS system IIB component-like Family:PTS system, Lactose/Cellobiose specific IIB subunit 48 c1vkrA_ not modelled 5.4 22 PDB header:transferase Chain: A: PDB Molecule:mannitol-specific pts system enzyme iiabc components; PDBTitle: structure of iib domain of the mannitol-specific permease enzyme ii 49 c2ezvA_ not modelled 5.3 18 PDB header:hydrolase/dna Chain: A: PDB Molecule:type ii restriction enzyme sfii; PDBTitle: crystal structure of tetrameric restriction endonuclease2 sfii bound to cognate dna. 50 d1kx5b_ not modelled 5.2 19 Fold:Histone-fold Superfamily:Histone-fold Family:Nucleosome core histones

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

---

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