Secondary structure and disorder prediction

		1	.	.	.	.	.	.	.	.	10	.	.	.	.	.	.	.	.	.	20	.	.	.	.	.	.	.	.	.	30	.	.	.	.	.	.	.	.	.	40	.	.	.	.	.	.	.	.	.	50	.	.	.	.	.	.	.	.	.	60
Sequence		M	Q	M	L	D	R	L	E	S	E	I	L	A	D	R	V	S	E	E	S	R	R	W	L	A	S	C	G	L	T	V	E	Q	M	K	N	Q	M	D	P	V	Y	T	P	A	R	K	I	H	L	Y	H	C	D	H	R	G	L	P	L
Secondary structure
SS confidence
Disorder		?	?	?	?	?	?	?																													?		?	?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	70	.	.	.	.	.	.	.	.	.	80	.	.	.	.	.	.	.	.	.	90	.	.	.	.	.	.	.	.	.	100	.	.	.	.	.	.	.	.	.	110	.	.	.	.	.	.	.	.	.	120
Sequence		A	L	I	S	T	E	G	A	T	A	W	C	A	E	Y	D	E	W	G	N	L	L	S	D	E	N	P	H	H	L	Q	Q	L	I	R	L	P	G	Q	Q	Y	D	E	E	S	G	L	Y	Y	N	R	H	R	Y	Y	D	P	L	L	G
Secondary structure
SS confidence
Disorder																									?	?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	130	.	.	.	.	.	.	.	.	.	140	.	.	.	.	.	.	.	.	.	150	.	.	.	.	.	.	.	.	.	160	.	.	.	.	.	.	.	.	.	170	.	.	.	.	.	.	.	.	.	180
Sequence		R	Y	I	T	Q	D	P	I	G	L	K	G	G	W	N	F	Y	Q	Y	P	L	N	P	V	I	N	V	D	P	Q	G	L	V	D	I	N	L	Y	P	E	S	D	L	I	H	S	V	A	D	E	I	N	I	P	G	V	F	T	I	G
Secondary structure
SS confidence
Disorder																																									?													?	?	?	?	?	?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	190	.	.	.	.	.	.	.	.	.	200	.	.	.	.	.	.	.	.	.	210	.	.	.	.	.	.	.	.	.	220	.	.	.	.	.	.	.	.	.	230	.	.	.
Sequence		G	H	G	T	P	T	S	I	E	S	A	T	R	S	I	M	T	A	K	D	L	A	Y	L	I	K	F	D	G	N	Y	K	D	G	M	T	V	W	L	F	S	C	N	T	G	K	G	Q	N	S	F	A	S
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 1j5q chain B Region: 94 - 212 Aligned: 105 Modelled: 119 Confidence: 15.8% Identity: 19% PDB header:viral protein Chain: B: PDB Molecule:major capsid protein; PDBTitle: the structure and evolution of the major capsid protein of a large,2 lipid-containing, dna virus. Phyre2 PDB 1f1s chain A domain 3 Region: 64 - 120 Aligned: 51 Modelled: 57 Confidence: 13.6% Identity: 20% Fold: Hyaluronate lyase-like, C-terminal domain Superfamily: Hyaluronate lyase-like, C-terminal domain Family: Hyaluronate lyase-like, C-terminal domain Phyre2 PDB 1n7o chain A domain 2 Region: 58 - 124 Aligned: 61 Modelled: 67 Confidence: 11.9% Identity: 20% Fold: Hyaluronate lyase-like, C-terminal domain Superfamily: Hyaluronate lyase-like, C-terminal domain Family: Hyaluronate lyase-like, C-terminal domain Phyre2 PDB 2x12 chain A Region: 54 - 105 Aligned: 48 Modelled: 52 Confidence: 10.4% Identity: 29% PDB header:cell adhesion Chain: A: PDB Molecule:fimbriae-associated protein fap1; PDBTitle: ph-induced modulation of streptococcus parasanguinis2 adhesion by fap1 fimbriae Phyre2 PDB 1bco chain A domain 1 Region: 106 - 123 Aligned: 18 Modelled: 18 Confidence: 8.2% Identity: 22% Fold: mu transposase, C-terminal domain Superfamily: mu transposase, C-terminal domain Family: mu transposase, C-terminal domain Phyre2 PDB 2sh1 chain A Region: 215 - 225 Aligned: 11 Modelled: 11 Confidence: 7.3% Identity: 64% Fold: Defensin-like Superfamily: Defensin-like Family: Defensin Phyre2 PDB 1x3z chain A domain 1 Region: 114 - 147 Aligned: 34 Modelled: 34 Confidence: 7.1% Identity: 15% Fold: Cysteine proteinases Superfamily: Cysteine proteinases Family: Transglutaminase core Phyre2 PDB 1ulv chain A domain 3 Region: 125 - 158 Aligned: 31 Modelled: 34 Confidence: 6.7% Identity: 35% Fold: Immunoglobulin-like beta-sandwich Superfamily: CBD9-like Family: Glucodextranase, domain C Phyre2 PDB 2f4m chain A domain 1 Region: 114 - 156 Aligned: 43 Modelled: 43 Confidence: 6.0% Identity: 16% Fold: Cysteine proteinases Superfamily: Cysteine proteinases Family: Transglutaminase core Phyre2 PDB 2izp chain A domain 1 Region: 2 - 14 Aligned: 13 Modelled: 13 Confidence: 5.9% Identity: 46% Fold: IpaD-like Superfamily: IpaD-like Family: IpaD-like Phyre2 PDB 2izp chain B Region: 2 - 14 Aligned: 13 Modelled: 13 Confidence: 5.8% Identity: 46% PDB header:toxin Chain: B: PDB Molecule:putative membrane antigen; PDBTitle: bipd - an invasion prtein associated with the type-iii2 secretion system of burkholderia pseudomallei. Phyre2 PDB 3m1h chain B Region: 96 - 128 Aligned: 33 Modelled: 33 Confidence: 5.4% Identity: 15% PDB header:cell invasion Chain: B: PDB Molecule:lysine specific cysteine protease; PDBTitle: crystal structure analysis of the k3 cleaved adhesin domain of lys-2 gingipain (kgp) from porphyromonas gingivalis w83 Phyre2 PDB 1nvp chain D domain 2 Region: 128 - 147 Aligned: 20 Modelled: 20 Confidence: 5.2% Identity: 25% Fold: Transcription factor IIA (TFIIA), beta-barrel domain Superfamily: Transcription factor IIA (TFIIA), beta-barrel domain Family: Transcription factor IIA (TFIIA), beta-barrel domain Phyre2 1 c1j5qB_ 2 d1f1sa3 3 d1n7oa2 4 c2x12A_ 5 d1bcoa1 6 d2sh1a_ 7 d1x3za1 8 d1ulva3 9 d2f4ma1 10 d2izpa1 11 c2izpB_ 12 c3m1hB_ 13 d1nvpd2

Detailed template information

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

1 c1j5qB_ 15.8 19 PDB header:viral protein Chain: B: PDB Molecule:major capsid protein; PDBTitle: the structure and evolution of the major capsid protein of a large,2 lipid-containing, dna virus. 2 d1f1sa3 13.6 20 Fold:Hyaluronate lyase-like, C-terminal domain Superfamily:Hyaluronate lyase-like, C-terminal domain Family:Hyaluronate lyase-like, C-terminal domain 3 d1n7oa2 11.9 20 Fold:Hyaluronate lyase-like, C-terminal domain Superfamily:Hyaluronate lyase-like, C-terminal domain Family:Hyaluronate lyase-like, C-terminal domain 4 c2x12A_ 10.4 29 PDB header:cell adhesion Chain: A: PDB Molecule:fimbriae-associated protein fap1; PDBTitle: ph-induced modulation of streptococcus parasanguinis2 adhesion by fap1 fimbriae 5 d1bcoa1 8.2 22 Fold:mu transposase, C-terminal domain Superfamily:mu transposase, C-terminal domain Family:mu transposase, C-terminal domain 6 d2sh1a_ 7.3 64 Fold:Defensin-like Superfamily:Defensin-like Family:Defensin 7 d1x3za1 7.1 15 Fold:Cysteine proteinases Superfamily:Cysteine proteinases Family:Transglutaminase core 8 d1ulva3 6.7 35 Fold:Immunoglobulin-like beta-sandwich Superfamily:CBD9-like Family:Glucodextranase, domain C 9 d2f4ma1 6.0 16 Fold:Cysteine proteinases Superfamily:Cysteine proteinases Family:Transglutaminase core 10 d2izpa1 5.9 46 Fold:IpaD-like Superfamily:IpaD-like Family:IpaD-like 11 c2izpB_ 5.8 46 PDB header:toxin Chain: B: PDB Molecule:putative membrane antigen; PDBTitle: bipd - an invasion prtein associated with the type-iii2 secretion system of burkholderia pseudomallei. 12 c3m1hB_ 5.4 15 PDB header:cell invasion Chain: B: PDB Molecule:lysine specific cysteine protease; PDBTitle: crystal structure analysis of the k3 cleaved adhesin domain of lys-2 gingipain (kgp) from porphyromonas gingivalis w83 13 d1nvpd2 5.2 25 Fold:Transcription factor IIA (TFIIA), beta-barrel domain Superfamily:Transcription factor IIA (TFIIA), beta-barrel domain Family:Transcription factor IIA (TFIIA), beta-barrel domain

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