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	G	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	L	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	D	R	V	E	E	K	R	D	A	M	Q	S	L	L	L	P	P	P	A	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	S	H	T	R	A	V	R	G	I	D	G	D	V	K	L	N	R	A	L	W	V	M	A	E	A	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: 35.2% 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 3kzt chain B Region: 100 - 128 Aligned: 29 Modelled: 29 Confidence: 25.0% 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 1xl7 chain A domain 2 Region: 78 - 169 Aligned: 89 Modelled: 89 Confidence: 24.8% Identity: 17% Fold: CoA-dependent acyltransferases Superfamily: CoA-dependent acyltransferases Family: Choline/Carnitine O-acyltransferase Phyre2 PDB 1w6g chain A domain 2 Region: 18 - 48 Aligned: 30 Modelled: 31 Confidence: 16.0% Identity: 17% Fold: Cystatin-like Superfamily: Amine oxidase N-terminal region Family: Amine oxidase N-terminal region Phyre2 PDB 3hp7 chain A Region: 52 - 96 Aligned: 43 Modelled: 45 Confidence: 12.9% Identity: 9% PDB header:structural genomics, unknown function Chain: A: PDB Molecule:hemolysin, putative; PDBTitle: putative hemolysin from streptococcus thermophilus. Phyre2 PDB 2qi2 chain A domain 1 Region: 212 - 227 Aligned: 16 Modelled: 16 Confidence: 12.1% Identity: 25% Fold: Sm-like fold Superfamily: Dom34/Pelota N-terminal domain-like Family: Dom34/Pelota N-terminal domain-like Phyre2 PDB 3lg8 chain B Region: 121 - 128 Aligned: 8 Modelled: 8 Confidence: 10.9% 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 3lyd chain A Region: 211 - 228 Aligned: 18 Modelled: 18 Confidence: 10.4% 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 1xl8 chain B Region: 78 - 120 Aligned: 43 Modelled: 42 Confidence: 9.6% Identity: 26% PDB header:transferase Chain: B: PDB Molecule:peroxisomal carnitine o-octanoyltransferase; PDBTitle: crystal structure of mouse carnitine octanoyltransferase in2 complex with octanoylcarnitine Phyre2 PDB 2vgn chain A domain 1 Region: 212 - 226 Aligned: 15 Modelled: 15 Confidence: 9.6% Identity: 33% Fold: Sm-like fold Superfamily: Dom34/Pelota N-terminal domain-like Family: Dom34/Pelota N-terminal domain-like Phyre2 PDB 1whz chain A Region: 45 - 70 Aligned: 26 Modelled: 26 Confidence: 9.0% Identity: 19% Fold: dsRBD-like Superfamily: YcfA/nrd intein domain Family: YcfA-like Phyre2 PDB 2qi2 chain A Region: 212 - 225 Aligned: 14 Modelled: 14 Confidence: 8.7% 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 1em8 chain B Region: 231 - 262 Aligned: 32 Modelled: 32 Confidence: 8.6% Identity: 19% Fold: DNA polymerase III psi subunit Superfamily: DNA polymerase III psi subunit Family: DNA polymerase III psi subunit Phyre2 PDB 1e2v chain B Region: 121 - 126 Aligned: 6 Modelled: 6 Confidence: 8.3% Identity: 67% PDB header:electron transport proteins Chain: B: PDB Molecule:cytochrome f; PDBTitle: n153q mutant of cytochrome f from chlamydomonas reinhardtii Phyre2 PDB 1vf5 chain C domain 1 Region: 121 - 126 Aligned: 6 Modelled: 6 Confidence: 8.1% Identity: 67% Fold: Common fold of diphtheria toxin/transcription factors/cytochrome f Superfamily: Cytochrome f, large domain Family: Cytochrome f, large domain Phyre2 PDB 1ci3 chain M domain 1 Region: 121 - 126 Aligned: 6 Modelled: 6 Confidence: 8.0% Identity: 67% Fold: Common fold of diphtheria toxin/transcription factors/cytochrome f Superfamily: Cytochrome f, large domain Family: Cytochrome f, large domain Phyre2 PDB 1e2w chain A domain 1 Region: 121 - 126 Aligned: 6 Modelled: 6 Confidence: 7.9% Identity: 67% Fold: Common fold of diphtheria toxin/transcription factors/cytochrome f Superfamily: Cytochrome f, large domain Family: Cytochrome f, large domain Phyre2 PDB 3oby chain B Region: 212 - 225 Aligned: 14 Modelled: 14 Confidence: 7.8% 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 1q6x chain A Region: 78 - 165 Aligned: 86 Modelled: 88 Confidence: 7.7% Identity: 19% PDB header:transferase Chain: A: PDB Molecule:choline o-acetyltransferase; PDBTitle: crystal structure of rat choline acetyltransferase Phyre2 PDB 3agj chain D Region: 212 - 225 Aligned: 14 Modelled: 14 Confidence: 7.7% Identity: 21% PDB header:translation/hydrolase Chain: D: PDB Molecule:protein pelota homolog; PDBTitle: crystal structure of archaeal pelota and gtp-bound ef1 alpha complex Phyre2 1 c2f9jP_ 2 c3kztB_ 3 d1xl7a2 4 d1w6ga2 5 c3hp7A_ 6 d2qi2a1 7 c3lg8B_ 8 c3lydA_ 9 c1xl8B_ 10 d2vgna1 11 d1whza_ 12 c2qi2A_ 13 d1em8b_ 14 c1e2vB_ 15 d1vf5c1 16 d1ci3m1 17 d1e2wa1 18 c3obyB_ 19 c1q6xA_ 20 c3agjD_ 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

Detailed template information

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

1 c2f9jP_ 35.2 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 c3kztB_ 25.0 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 3 d1xl7a2 24.8 17 Fold:CoA-dependent acyltransferases Superfamily:CoA-dependent acyltransferases Family:Choline/Carnitine O-acyltransferase 4 d1w6ga2 16.0 17 Fold:Cystatin-like Superfamily:Amine oxidase N-terminal region Family:Amine oxidase N-terminal region 5 c3hp7A_ 12.9 9 PDB header:structural genomics, unknown function Chain: A: PDB Molecule:hemolysin, putative; PDBTitle: putative hemolysin from streptococcus thermophilus. 6 d2qi2a1 12.1 25 Fold:Sm-like fold Superfamily:Dom34/Pelota N-terminal domain-like Family:Dom34/Pelota N-terminal domain-like 7 c3lg8B_ 10.9 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 8 c3lydA_ 10.4 28 PDB header:structural genomics, unknown function Chain: A: PDB Molecule:uncharacterized protein; PDBTitle: crystal structure of putative uncharacterized protein from jonesia2 denitrificans 9 c1xl8B_ 9.6 26 PDB header:transferase Chain: B: PDB Molecule:peroxisomal carnitine o-octanoyltransferase; PDBTitle: crystal structure of mouse carnitine octanoyltransferase in2 complex with octanoylcarnitine 10 d2vgna1 9.6 33 Fold:Sm-like fold Superfamily:Dom34/Pelota N-terminal domain-like Family:Dom34/Pelota N-terminal domain-like 11 d1whza_ 9.0 19 Fold:dsRBD-like Superfamily:YcfA/nrd intein domain Family:YcfA-like 12 c2qi2A_ 8.7 21 PDB header:cell cycle Chain: A: PDB Molecule:cell division protein pelota related protein; PDBTitle: crystal structure of the thermoplasma acidophilum pelota2 protein 13 d1em8b_ 8.6 19 Fold:DNA polymerase III psi subunit Superfamily:DNA polymerase III psi subunit Family:DNA polymerase III psi subunit 14 c1e2vB_ 8.3 67 PDB header:electron transport proteins Chain: B: PDB Molecule:cytochrome f; PDBTitle: n153q mutant of cytochrome f from chlamydomonas reinhardtii 15 d1vf5c1 8.1 67 Fold:Common fold of diphtheria toxin/transcription factors/cytochrome f Superfamily:Cytochrome f, large domain Family:Cytochrome f, large domain 16 d1ci3m1 8.0 67 Fold:Common fold of diphtheria toxin/transcription factors/cytochrome f Superfamily:Cytochrome f, large domain Family:Cytochrome f, large domain 17 d1e2wa1 7.9 67 Fold:Common fold of diphtheria toxin/transcription factors/cytochrome f Superfamily:Cytochrome f, large domain Family:Cytochrome f, large domain 18 c3obyB_ 7.8 29 PDB header:hydrolase Chain: B: PDB Molecule:protein pelota homolog; PDBTitle: crystal structure of archaeoglobus fulgidus pelota reveals inter-2 domain structural plasticity 19 c1q6xA_ 7.7 19 PDB header:transferase Chain: A: PDB Molecule:choline o-acetyltransferase; PDBTitle: crystal structure of rat choline acetyltransferase 20 c3agjD_ 7.7 21 PDB header:translation/hydrolase Chain: D: PDB Molecule:protein pelota homolog; PDBTitle: crystal structure of archaeal pelota and gtp-bound ef1 alpha complex 21 c3agjB_ not modelled 7.7 21 PDB header:translation/hydrolase Chain: B: PDB Molecule:protein pelota homolog; PDBTitle: crystal structure of archaeal pelota and gtp-bound ef1 alpha complex 22 d1hcza1 not modelled 7.5 67 Fold:Common fold of diphtheria toxin/transcription factors/cytochrome f Superfamily:Cytochrome f, large domain Family:Cytochrome f, large domain 23 c3m9vA_ not modelled 7.0 23 PDB header:oxidoreductase Chain: A: PDB Molecule:fad-dependent oxidoreductase; PDBTitle: x-ray structure of a kijd3 in complex with dtdp 24 d1t1ua2 not modelled 7.0 17 Fold:CoA-dependent acyltransferases Superfamily:CoA-dependent acyltransferases Family:Choline/Carnitine O-acyltransferase 25 d1vbka2 not modelled 6.8 16 Fold:THUMP domain Superfamily:THUMP domain-like Family:THUMP domain 26 c3obwA_ not modelled 6.7 21 PDB header:hydrolase Chain: A: PDB Molecule:protein pelota homolog; PDBTitle: crystal structure of two archaeal pelotas reveal inter-domain2 structural plasticity 27 d1y1pa1 not modelled 6.4 8 Fold:NAD(P)-binding Rossmann-fold domains Superfamily:NAD(P)-binding Rossmann-fold domains Family:Tyrosine-dependent oxidoreductases 28 d1gsoa2 not modelled 6.3 17 Fold:PreATP-grasp domain Superfamily:PreATP-grasp domain Family:BC N-terminal domain-like 29 c2h4tB_ not modelled 6.2 20 PDB header:transferase Chain: B: PDB Molecule:carnitine o-palmitoyltransferase ii, PDBTitle: crystal structure of rat carnitine palmitoyltransferase ii 30 c2e75C_ not modelled 6.1 67 PDB header:photosynthesis Chain: C: PDB Molecule:apocytochrome f; PDBTitle: crystal structure of the cytochrome b6f complex with 2-nonyl-4-2 hydroxyquinoline n-oxide (nqno) from m.laminosus 31 c3b54A_ not modelled 6.0 14 PDB header:transferase Chain: A: PDB Molecule:nucleoside diphosphate kinase; PDBTitle: saccharomyces cerevisiae nucleoside diphosphate kinase 32 c1q90A_ not modelled 5.8 67 PDB header:photosynthesis Chain: A: PDB Molecule:apocytochrome f; PDBTitle: structure of the cytochrome b6f (plastohydroquinone : plastocyanin2 oxidoreductase) from chlamydomonas reinhardtii 33 c3fa4D_ not modelled 5.7 22 PDB header:lyase Chain: D: PDB Molecule:2,3-dimethylmalate lyase; PDBTitle: crystal structure of 2,3-dimethylmalate lyase, a pep mutase/isocitrate2 lyase superfamily member, triclinic crystal form 34 d1tu2b1 not modelled 5.6 67 Fold:Common fold of diphtheria toxin/transcription factors/cytochrome f Superfamily:Cytochrome f, large domain Family:Cytochrome f, large domain 35 c2jxmB_ not modelled 5.5 50 PDB header:electron transport Chain: B: PDB Molecule:cytochrome f; PDBTitle: ensemble of twenty structures of the prochlorothrix2 hollandica plastocyanin- cytochrome f complex 36 d1ndba2 not modelled 5.5 16 Fold:CoA-dependent acyltransferases Superfamily:CoA-dependent acyltransferases Family:Choline/Carnitine O-acyltransferase 37 c1ctmA_ not modelled 5.4 67 PDB header:electron transport(cytochrome) Chain: A: PDB Molecule:cytochrome f; PDBTitle: crystal structure of chloroplast cytochrome f reveals a2 novel cytochrome fold and unexpected heme ligation 38 d1ukua_ not modelled 5.4 35 Fold:Ferredoxin-like Superfamily:GlnB-like Family:Divalent ion tolerance proteins CutA (CutA1) 39 c3jywW_ not modelled 5.3 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 40 c2vu5A_ not modelled 5.3 22 PDB header:transferase Chain: A: PDB Molecule:nucleoside diphosphate kinase; PDBTitle: crystal structure of pndk from bacillus anthracis 41 d1xqia1 not modelled 5.2 3 Fold:Ferredoxin-like Superfamily:Nucleoside diphosphate kinase, NDK Family:Nucleoside diphosphate kinase, NDK 42 d1zs6a1 not modelled 5.2 17 Fold:Ferredoxin-like Superfamily:Nucleoside diphosphate kinase, NDK Family:Nucleoside diphosphate kinase, NDK 43 d1kx5b_ not modelled 5.1 19 Fold:Histone-fold Superfamily:Histone-fold Family:Nucleosome core histones 44 c2fipA_ not modelled 5.1 30 PDB header:transcription Chain: A: PDB Molecule:late genes activator; PDBTitle: phage phi29 transcription regulator p4 45 d1vhfa_ not modelled 5.0 24 Fold:Ferredoxin-like Superfamily:GlnB-like Family:Divalent ion tolerance proteins CutA (CutA1)

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