Secondary structure and disorder prediction

		1	.	.	.	.	.	.	.	.	10	.	.	.	.	.	.	.	.	.	20	.	.	.	.	.	.	.	.	.	30	.	.	.	.	.	.	.	.	.	40	.	.	.	.	.	.	.	.	.	50	.	.	.	.	.	.	.	.	.	60
Sequence		M	L	D	K	L	D	A	A	L	R	F	Q	Q	E	A	L	N	L	R	A	Q	R	Q	E	V	L	A	A	N	I	A	N	A	D	T	P	G	Y	Q	A	R	D	I	D	F	A	S	E	L	K	K	V	M	Q	R	G	R	D	A	T
Secondary structure
SS confidence
Disorder		?	?	?	?																																								?										?	?	?	?	?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	70	.	.	.	.	.	.	.	.	.	80	.	.	.	.	.	.	.	.	.	90	.	.	.	.	.	.	.	.	.	100	.	.	.	.	.	.	.	.	.	110	.	.	.	.	.	.	.	.	.	120
Sequence		S	V	V	A	L	T	M	T	S	T	Q	H	I	P	A	Q	A	L	T	P	P	T	A	E	L	Q	Y	R	I	P	D	Q	P	S	L	D	G	N	T	V	D	M	D	R	E	R	T	Q	F	A	D	N	S	L	Q	Y	Q	M	S	L
Secondary structure
SS confidence
Disorder		?	?	?	?	?	?	?	?	?	?	?	?	?	?	?	?	?	?	?	?	?	?	?	?	?	?	?	?	?	?	?	?	?	?	?	?		?
Disorder confidence
		.	.	.	.	.	.	.	.	.	130	.	.	.	.	.	.	.	.
Sequence		S	A	L	S	G	Q	I	K	G	M	M	N	V	L	Q	S	G	N
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 3a69 chain A Region: 97 - 136 Aligned: 40 Modelled: 40 Confidence: 98.7% Identity: 13% PDB header:motor protein Chain: A: PDB Molecule:flagellar hook protein flge; PDBTitle: atomic model of the bacterial flagellar hook based on2 docking an x-ray derived structure and terminal two alpha-3 helices into an 7.1 angstrom resolution cryoem map Phyre2 PDB 1ucu chain A Region: 99 - 136 Aligned: 38 Modelled: 38 Confidence: 90.4% Identity: 21% Fold: Phase 1 flagellin Superfamily: Phase 1 flagellin Family: Phase 1 flagellin Phyre2 PDB 1ory chain B Region: 99 - 136 Aligned: 38 Modelled: 38 Confidence: 88.2% Identity: 26% PDB header:chaperone Chain: B: PDB Molecule:flagellin; PDBTitle: flagellar export chaperone in complex with its cognate binding partner Phyre2 PDB 3k8v chain B Region: 99 - 119 Aligned: 21 Modelled: 21 Confidence: 44.7% Identity: 14% PDB header:structural protein Chain: B: PDB Molecule:flagellin homolog; PDBTitle: crysatl structure of a bacterial cell-surface flagellin n20c20 Phyre2 PDB 1r6f chain A Region: 102 - 136 Aligned: 35 Modelled: 35 Confidence: 39.3% Identity: 23% Fold: Virulence-associated V antigen Superfamily: Virulence-associated V antigen Family: Virulence-associated V antigen Phyre2 PDB 1lvo chain A Region: 29 - 39 Aligned: 11 Modelled: 11 Confidence: 21.7% Identity: 36% Fold: Trypsin-like serine proteases Superfamily: Trypsin-like serine proteases Family: Viral cysteine protease of trypsin fold Phyre2 PDB 2q6f chain B Region: 29 - 39 Aligned: 11 Modelled: 11 Confidence: 19.5% Identity: 55% PDB header:hydrolase Chain: B: PDB Molecule:infectious bronchitis virus (ibv) main protease; PDBTitle: crystal structure of infectious bronchitis virus (ibv) main2 protease in complex with a michael acceptor inhibitor n3 Phyre2 PDB 3d23 chain A Region: 29 - 39 Aligned: 11 Modelled: 11 Confidence: 16.0% Identity: 36% PDB header:hydrolase Chain: A: PDB Molecule:3c-like proteinase; PDBTitle: main protease of hcov-hku1 Phyre2 PDB 1p9s chain A Region: 29 - 39 Aligned: 11 Modelled: 10 Confidence: 15.0% Identity: 27% Fold: Trypsin-like serine proteases Superfamily: Trypsin-like serine proteases Family: Viral cysteine protease of trypsin fold Phyre2 PDB 2duc chain A domain 1 Region: 29 - 39 Aligned: 11 Modelled: 11 Confidence: 14.4% Identity: 36% Fold: Trypsin-like serine proteases Superfamily: Trypsin-like serine proteases Family: Viral cysteine protease of trypsin fold Phyre2 PDB 1nrj chain A Region: 30 - 38 Aligned: 9 Modelled: 9 Confidence: 8.0% Identity: 56% Fold: Profilin-like Superfamily: SNARE-like Family: SRP alpha N-terminal domain-like Phyre2 1 c3a69A_ 2 d1ucua_ 3 c1oryB_ 4 c3k8vB_ 5 d1r6fa_ 6 d1lvoa_ 7 c2q6fB_ 8 c3d23A_ 9 d1p9sa_ 10 d2duca1 11 d1nrja_

Detailed template information

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

1 c3a69A_ 98.7 13 PDB header:motor protein Chain: A: PDB Molecule:flagellar hook protein flge; PDBTitle: atomic model of the bacterial flagellar hook based on2 docking an x-ray derived structure and terminal two alpha-3 helices into an 7.1 angstrom resolution cryoem map 2 d1ucua_ 90.4 21 Fold:Phase 1 flagellin Superfamily:Phase 1 flagellin Family:Phase 1 flagellin 3 c1oryB_ 88.2 26 PDB header:chaperone Chain: B: PDB Molecule:flagellin; PDBTitle: flagellar export chaperone in complex with its cognate binding partner 4 c3k8vB_ 44.7 14 PDB header:structural protein Chain: B: PDB Molecule:flagellin homolog; PDBTitle: crysatl structure of a bacterial cell-surface flagellin n20c20 5 d1r6fa_ 39.3 23 Fold:Virulence-associated V antigen Superfamily:Virulence-associated V antigen Family:Virulence-associated V antigen 6 d1lvoa_ 21.7 36 Fold:Trypsin-like serine proteases Superfamily:Trypsin-like serine proteases Family:Viral cysteine protease of trypsin fold 7 c2q6fB_ 19.5 55 PDB header:hydrolase Chain: B: PDB Molecule:infectious bronchitis virus (ibv) main protease; PDBTitle: crystal structure of infectious bronchitis virus (ibv) main2 protease in complex with a michael acceptor inhibitor n3 8 c3d23A_ 16.0 36 PDB header:hydrolase Chain: A: PDB Molecule:3c-like proteinase; PDBTitle: main protease of hcov-hku1 9 d1p9sa_ 15.0 27 Fold:Trypsin-like serine proteases Superfamily:Trypsin-like serine proteases Family:Viral cysteine protease of trypsin fold 10 d2duca1 14.4 36 Fold:Trypsin-like serine proteases Superfamily:Trypsin-like serine proteases Family:Viral cysteine protease of trypsin fold 11 d1nrja_ 8.0 56 Fold:Profilin-like Superfamily:SNARE-like Family:SRP alpha N-terminal domain-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