Secondary structure and disorder prediction

		1	.	.	.	.	.	.	.	.	10	.	.	.	.	.	.	.	.	.	20	.	.	.	.	.	.	.	.	.	30	.	.	.	.	.	.	.	.	.	40	.	.	.	.	.	.	.	.	.	50	.	.	.	.	.	.	.	.	.	60
Sequence		M	C	C	V	Y	R	M	N	R	P	A	S	G	L	T	V	V	F	C	G	K	L	S	G	K	P	G	P	K	S	A	A	W	R	M	P	W	Q	K	S	G	A	D	D	G	G	E	N	P	R	F	F	S	A	G	P	R	T	E	H
Secondary structure
SS confidence
Disorder		?	?	?			?	?																								?								?	?	?	?	?	?	?	?	?							?		?	?	?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	70	.	.	.	.	.	.	.	.	.	80	.	.	.	.	.	.	.	.	.	90	.	.	.	.	.	.	.	.	.	100	.	.	.	.	.	.	.	.	.	110	.	.	.	.	.	.	.	.	.	120
Sequence		K	G	S	R	R	R	L	R	F	T	R	P	C	A	W	P	C	G	F	S	V	M	W	P	P	C	R	V	R	A	V	P	C	L	H	L	S	R	A	G	G	D	A	R	V	R	F	A	A	A	V	T	R	S	L	L	P	V	C	R
Secondary structure
SS confidence
Disorder		?	?	?																																				?
Disorder confidence
		.	.	.	.	.	.	.	.	.	130	.	.	.	.	.	.	.	.	.	140	.	.	.	.	.	.	.	.	.	150	.	.	.	.	.	.	.	.	.	160	.	.	.	.	.	.	.	.	.	170	.	.	.	.
Sequence		D	F	P	V	V	H	P	L	R	F	R	G	L	T	L	Q	L	P	S	A	V	C	V	R	L	R	L	P	L	R	P	V	H	P	R	L	I	A	R	L	L	W	R	H	G	T	A	R	C	R	G	I	C	E
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 1edy chain A Region: 1 - 24 Aligned: 24 Modelled: 24 Confidence: 28.0% Identity: 29% Fold: Common fold of diphtheria toxin/transcription factors/cytochrome f Superfamily: Alpha-macroglobulin receptor domain Family: Alpha-macroglobulin receptor domain Phyre2 PDB 1bv8 chain A Region: 1 - 24 Aligned: 24 Modelled: 24 Confidence: 27.4% Identity: 29% Fold: Common fold of diphtheria toxin/transcription factors/cytochrome f Superfamily: Alpha-macroglobulin receptor domain Family: Alpha-macroglobulin receptor domain Phyre2 PDB 1ayo chain A Region: 1 - 24 Aligned: 24 Modelled: 24 Confidence: 24.1% Identity: 33% Fold: Common fold of diphtheria toxin/transcription factors/cytochrome f Superfamily: Alpha-macroglobulin receptor domain Family: Alpha-macroglobulin receptor domain Phyre2 PDB 1qhd chain A domain 2 Region: 118 - 142 Aligned: 25 Modelled: 24 Confidence: 19.6% Identity: 48% Fold: Viral protein domain Superfamily: Viral protein domain Family: Top domain of virus capsid protein Phyre2 PDB 1qgc chain 1 Region: 30 - 58 Aligned: 29 Modelled: 29 Confidence: 19.2% Identity: 28% PDB header:virus/immune system Chain: 1: PDB Molecule:protein (virus capsid protein); PDB Fragment:residues 133-156 PDBTitle: structure of the complex of an fab fragment of a neutralizing antibody2 with foot and mouth disease virus Phyre2 PDB 2knn chain A Region: 76 - 98 Aligned: 22 Modelled: 23 Confidence: 12.7% Identity: 45% PDB header:plant protein Chain: A: PDB Molecule:cycloviolacin-o2; PDBTitle: solution structure of the cyclotide cycloviolacin o2 with2 glu6 methylated (cyo2me) Phyre2 PDB 2wzr chain 1 Region: 32 - 73 Aligned: 36 Modelled: 41 Confidence: 12.6% Identity: 39% PDB header:virus Chain: 1: PDB Molecule:polyprotein; PDBTitle: the structure of foot and mouth disease virus serotype sat1 Phyre2 PDB 1dt9 chain A domain 3 Region: 10 - 27 Aligned: 17 Modelled: 18 Confidence: 10.9% Identity: 47% Fold: N-terminal domain of eukaryotic peptide chain release factor subunit 1, ERF1 Superfamily: N-terminal domain of eukaryotic peptide chain release factor subunit 1, ERF1 Family: N-terminal domain of eukaryotic peptide chain release factor subunit 1, ERF1 Phyre2 PDB 2jr7 chain A Region: 69 - 78 Aligned: 8 Modelled: 10 Confidence: 10.2% Identity: 63% PDB header:metal binding protein Chain: A: PDB Molecule:dph3 homolog; PDBTitle: solution structure of human desr1 Phyre2 PDB 2jra chain B Region: 59 - 71 Aligned: 13 Modelled: 13 Confidence: 7.9% Identity: 46% PDB header:structural genomics, unknown function Chain: B: PDB Molecule:protein rpa2121; PDBTitle: a novel domain-swapped solution nmr structure of protein rpa2121 from2 rhodopseudomonas palustris. northeast structural genomics target rpt6 Phyre2 PDB 2kcg chain A Region: 76 - 93 Aligned: 18 Modelled: 18 Confidence: 6.8% Identity: 50% PDB header:plant protein Chain: A: PDB Molecule:cycloviolacin-o2; PDBTitle: solution structure of cycloviolacin o2 Phyre2 PDB 2fug chain 7 domain 1 Region: 4 - 27 Aligned: 24 Modelled: 24 Confidence: 6.7% Identity: 38% Fold: N domain of copper amine oxidase-like Superfamily: Frataxin/Nqo15-like Family: Nqo15-like Phyre2 1 d1edya_ 2 d1bv8a_ 3 d1ayoa_ 4 d1qhda2 5 c1qgc1_ 6 c2knnA_ 7 c2wzr1_ 8 d1dt9a3 9 c2jr7A_ 10 c2jraB_ 11 c2kcgA_ 12 d2fug71

Detailed template information

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

1 d1edya_ 28.0 29 Fold:Common fold of diphtheria toxin/transcription factors/cytochrome f Superfamily:Alpha-macroglobulin receptor domain Family:Alpha-macroglobulin receptor domain 2 d1bv8a_ 27.4 29 Fold:Common fold of diphtheria toxin/transcription factors/cytochrome f Superfamily:Alpha-macroglobulin receptor domain Family:Alpha-macroglobulin receptor domain 3 d1ayoa_ 24.1 33 Fold:Common fold of diphtheria toxin/transcription factors/cytochrome f Superfamily:Alpha-macroglobulin receptor domain Family:Alpha-macroglobulin receptor domain 4 d1qhda2 19.6 48 Fold:Viral protein domain Superfamily:Viral protein domain Family:Top domain of virus capsid protein 5 c1qgc1_ 19.2 28 PDB header:virus/immune system Chain: 1: PDB Molecule:protein (virus capsid protein); PDB Fragment:residues 133-156 PDBTitle: structure of the complex of an fab fragment of a neutralizing antibody2 with foot and mouth disease virus 6 c2knnA_ 12.7 45 PDB header:plant protein Chain: A: PDB Molecule:cycloviolacin-o2; PDBTitle: solution structure of the cyclotide cycloviolacin o2 with2 glu6 methylated (cyo2me) 7 c2wzr1_ 12.6 39 PDB header:virus Chain: 1: PDB Molecule:polyprotein; PDBTitle: the structure of foot and mouth disease virus serotype sat1 8 d1dt9a3 10.9 47 Fold:N-terminal domain of eukaryotic peptide chain release factor subunit 1, ERF1 Superfamily:N-terminal domain of eukaryotic peptide chain release factor subunit 1, ERF1 Family:N-terminal domain of eukaryotic peptide chain release factor subunit 1, ERF1 9 c2jr7A_ 10.2 63 PDB header:metal binding protein Chain: A: PDB Molecule:dph3 homolog; PDBTitle: solution structure of human desr1 10 c2jraB_ 7.9 46 PDB header:structural genomics, unknown function Chain: B: PDB Molecule:protein rpa2121; PDBTitle: a novel domain-swapped solution nmr structure of protein rpa2121 from2 rhodopseudomonas palustris. northeast structural genomics target rpt6 11 c2kcgA_ 6.8 50 PDB header:plant protein Chain: A: PDB Molecule:cycloviolacin-o2; PDBTitle: solution structure of cycloviolacin o2 12 d2fug71 6.7 38 Fold:N domain of copper amine oxidase-like Superfamily:Frataxin/Nqo15-like Family:Nqo15-like

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