Secondary structure and disorder prediction

		1	.	.	.	.	.	.	.	.	10	.	.	.	.	.	.	.	.	.	20	.	.	.	.	.	.	.	.	.	30	.	.	.	.	.	.	.	.	.	40	.	.	.	.	.	.	.	.	.	50	.	.	.	.	.	.	.	.	.	60
Sequence		M	A	F	S	Q	A	V	S	G	L	N	A	A	A	T	N	L	D	V	I	G	N	N	I	A	N	S	A	T	Y	G	F	K	S	G	T	A	S	F	A	D	M	F	A	G	S	K	V	G	L	G	V	K	V	A	G	I	T	Q	D
Secondary structure
SS confidence
Disorder		?	?															?	?															?	?	?				?			?	?	?	?	?	?	?	?	?	?	?			?				?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	70	.	.	.	.	.	.	.	.	.	80	.	.	.	.	.	.	.	.	.	90	.	.	.	.	.	.	.	.	.	100	.	.	.	.	.	.	.	.	.	110	.	.	.	.	.	.	.	.	.	120
Sequence		F	T	D	G	T	T	T	N	T	G	R	G	L	D	V	A	I	S	Q	N	G	F	F	R	L	V	D	S	N	G	S	V	F	Y	S	R	N	G	Q	F	K	L	D	E	N	R	N	L	V	N	M	Q	G	L	Q	L	T	G	Y	P
Secondary structure
SS confidence
Disorder					?			?
Disorder confidence
		.	.	.	.	.	.	.	.	.	130	.	.	.	.	.	.	.	.	.	140	.	.	.	.	.	.	.	.	.	150	.	.	.	.	.	.	.	.	.	160	.	.	.	.	.	.	.	.	.	170	.	.	.	.	.	.	.	.	.	180
Sequence		A	T	G	T	P	P	T	I	Q	Q	G	A	N	P	T	N	I	S	I	P	N	T	L	M	A	A	K	T	T	T	T	A	S	M	Q	I	N	L	N	S	S	D	P	L	P	T	V	T	P	F	S	A	S	N	A	D	S	Y	N	K
Secondary structure
SS confidence
Disorder				?	?	?	?	?	?	?	?	?	?	?	?	?	?	?	?	?	?	?	?	?	?	?	?	?	?	?	?	?	?	?	?	?	?	?	?	?	?	?	?	?	?	?	?	?	?	?	?	?	?	?	?	?	?	?	?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	190	.	.	.	.	.	.	.	.	.	200	.	.	.	.	.	.	.	.	.	210	.	.	.	.	.	.	.	.	.	220	.	.	.	.	.	.	.	.	.	230	.	.	.	.	.	.	.	.	.	240
Sequence		K	G	S	V	T	V	F	D	S	Q	G	N	A	H	D	M	S	V	Y	F	V	K	T	G	D	N	N	W	Q	V	Y	T	Q	D	S	S	D	P	N	S	I	A	K	T	A	T	T	L	E	F	N	A	N	G	T	L	V	D	G	A
Secondary structure
SS confidence
Disorder		?				?	?		?	?																										?		?	?	?	?	?																?	?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	250	.	.	.	.	.	.	.	.	.	260	.	.	.	.	.	.	.	.	.	270	.	.	.	.	.	.	.	.	.	280	.	.	.	.	.	.	.	.	.	290	.	.	.	.	.	.	.	.	.	300
Sequence		M	A	N	N	I	A	T	G	A	I	N	G	A	E	P	A	T	F	S	L	S	F	L	N	S	M	Q	Q	N	T	G	A	N	N	I	V	A	T	T	Q	N	G	Y	K	P	G	D	L	V	S	Y	Q	I	N	D	D	G	T	V	V
Secondary structure
SS confidence
Disorder		?	?	?	?	?	?	?	?	?	?	?	?			?	?				?	?			?		?									?			?		?
Disorder confidence
		.	.	.	.	.	.	.	.	.	310	.	.	.	.	.	.	.	.	.	320	.	.	.	.	.	.	.	.	.	330	.	.	.	.	.	.	.	.	.	340	.	.	.	.	.	.	.	.	.	350	.	.	.	.	.	.	.	.	.	360
Sequence		G	N	Y	S	N	E	Q	T	Q	L	L	G	Q	I	V	L	A	N	F	A	N	N	E	G	L	A	S	E	G	D	N	V	W	S	A	T	Q	S	S	G	V	A	L	L	G	T	A	G	T	G	N	F	G	T	L	T	N	G	A	L
Secondary structure
SS confidence
Disorder																											?	?	?	?	?	?	?			?					?	?				?	?	?				?						?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	370	.	.	.	.	.	.	.	.	.	380	.	.	.	.	.	.	.	.	.	390	.	.	.	.	.	.	.	.	.	400	.	.
Sequence		E	A	S	N	V	D	L	S	K	E	L	V	N	M	I	V	A	Q	R	N	Y	Q	S	N	A	Q	T	I	K	T	Q	D	Q	I	L	N	T	L	V	N	L	R
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: 2 - 402 Aligned: 346 Modelled: 353 Confidence: 100.0% Identity: 85% 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 1wlg chain A Region: 73 - 363 Aligned: 290 Modelled: 291 Confidence: 99.9% Identity: 84% Fold: Flagellar hook protein flgE Superfamily: Flagellar hook protein flgE Family: Flagellar hook protein flgE Phyre2 PDB 2d4y chain A Region: 96 - 196 Aligned: 95 Modelled: 101 Confidence: 97.0% Identity: 11% PDB header:structural protein Chain: A: PDB Molecule:flagellar hook-associated protein 1; PDBTitle: crystal structure of a 49k fragment of hap1 (flgk) Phyre2 PDB 1ucu chain A Region: 365 - 401 Aligned: 37 Modelled: 37 Confidence: 92.7% Identity: 24% Fold: Phase 1 flagellin Superfamily: Phase 1 flagellin Family: Phase 1 flagellin Phyre2 PDB 3k8v chain B Region: 365 - 384 Aligned: 20 Modelled: 20 Confidence: 53.8% Identity: 30% PDB header:structural protein Chain: B: PDB Molecule:flagellin homolog; PDBTitle: crysatl structure of a bacterial cell-surface flagellin n20c20 Phyre2 PDB 1ory chain B Region: 365 - 401 Aligned: 37 Modelled: 37 Confidence: 29.7% Identity: 22% PDB header:chaperone Chain: B: PDB Molecule:flagellin; PDBTitle: flagellar export chaperone in complex with its cognate binding partner Phyre2 PDB 1lvo chain A Region: 23 - 37 Aligned: 15 Modelled: 15 Confidence: 13.3% Identity: 27% Fold: Trypsin-like serine proteases Superfamily: Trypsin-like serine proteases Family: Viral cysteine protease of trypsin fold Phyre2 PDB 2q6f chain B Region: 23 - 37 Aligned: 15 Modelled: 15 Confidence: 12.9% Identity: 33% 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 1nrj chain A Region: 24 - 32 Aligned: 9 Modelled: 9 Confidence: 12.6% Identity: 56% Fold: Profilin-like Superfamily: SNARE-like Family: SRP alpha N-terminal domain-like Phyre2 PDB 1p9s chain A Region: 23 - 37 Aligned: 15 Modelled: 15 Confidence: 11.4% Identity: 20% Fold: Trypsin-like serine proteases Superfamily: Trypsin-like serine proteases Family: Viral cysteine protease of trypsin fold Phyre2 PDB 3d23 chain A Region: 23 - 37 Aligned: 15 Modelled: 15 Confidence: 9.9% Identity: 20% PDB header:hydrolase Chain: A: PDB Molecule:3c-like proteinase; PDBTitle: main protease of hcov-hku1 Phyre2 PDB 2duc chain A domain 1 Region: 23 - 37 Aligned: 15 Modelled: 15 Confidence: 9.4% Identity: 20% Fold: Trypsin-like serine proteases Superfamily: Trypsin-like serine proteases Family: Viral cysteine protease of trypsin fold Phyre2 PDB 2npt chain A domain 1 Region: 365 - 377 Aligned: 13 Modelled: 13 Confidence: 8.9% Identity: 23% Fold: beta-Grasp (ubiquitin-like) Superfamily: CAD & PB1 domains Family: PB1 domain Phyre2 PDB 2gom chain A domain 1 Region: 371 - 382 Aligned: 12 Modelled: 12 Confidence: 6.6% Identity: 17% Fold: Spectrin repeat-like Superfamily: Efb C-domain-like Family: Efb C-domain-like Phyre2 PDB 1q8h chain A Region: 369 - 381 Aligned: 13 Modelled: 13 Confidence: 6.4% Identity: 38% PDB header:metal binding protein Chain: A: PDB Molecule:osteocalcin; PDBTitle: crystal structure of porcine osteocalcin Phyre2 PDB 1q8h chain A Region: 369 - 381 Aligned: 13 Modelled: 13 Confidence: 6.4% Identity: 38% Fold: GLA-domain Superfamily: GLA-domain Family: GLA-domain Phyre2 PDB 3j0g chain O Region: 26 - 32 Aligned: 7 Modelled: 7 Confidence: 6.3% Identity: 29% PDB header:virus Chain: O: PDB Molecule:e3 protein; PDBTitle: homology model of e3 protein of venezuelan equine encephalitis virus2 tc-83 strain fitted with a cryo-em map Phyre2 PDB 1q3m chain A Region: 369 - 381 Aligned: 13 Modelled: 13 Confidence: 6.2% Identity: 38% Fold: GLA-domain Superfamily: GLA-domain Family: GLA-domain Phyre2 PDB 3ikm chain D Region: 1 - 17 Aligned: 17 Modelled: 17 Confidence: 6.1% Identity: 35% PDB header:transferase Chain: D: PDB Molecule:dna polymerase subunit gamma-1; PDBTitle: crystal structure of human mitochondrial dna polymerase2 holoenzyme Phyre2 PDB 2dld chain A domain 2 Region: 22 - 34 Aligned: 13 Modelled: 13 Confidence: 6.0% Identity: 0% Fold: Flavodoxin-like Superfamily: Formate/glycerate dehydrogenase catalytic domain-like Family: Formate/glycerate dehydrogenases, substrate-binding domain Phyre2 1 c3a69A_ 2 d1wlga_ 3 c2d4yA_ 4 d1ucua_ 5 c3k8vB_ 6 c1oryB_ 7 d1lvoa_ 8 c2q6fB_ 9 d1nrja_ 10 d1p9sa_ 11 c3d23A_ 12 d2duca1 13 d2npta1 14 d2goma1 15 c1q8hA_ 16 d1q8ha_ 17 c3j0gO_ 18 d1q3ma_ 19 c3ikmD_ 20 d2dlda2 21 22

Detailed template information

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

1 c3a69A_ 100.0 85 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 d1wlga_ 99.9 84 Fold:Flagellar hook protein flgE Superfamily:Flagellar hook protein flgE Family:Flagellar hook protein flgE 3 c2d4yA_ 97.0 11 PDB header:structural protein Chain: A: PDB Molecule:flagellar hook-associated protein 1; PDBTitle: crystal structure of a 49k fragment of hap1 (flgk) 4 d1ucua_ 92.7 24 Fold:Phase 1 flagellin Superfamily:Phase 1 flagellin Family:Phase 1 flagellin 5 c3k8vB_ 53.8 30 PDB header:structural protein Chain: B: PDB Molecule:flagellin homolog; PDBTitle: crysatl structure of a bacterial cell-surface flagellin n20c20 6 c1oryB_ 29.7 22 PDB header:chaperone Chain: B: PDB Molecule:flagellin; PDBTitle: flagellar export chaperone in complex with its cognate binding partner 7 d1lvoa_ 13.3 27 Fold:Trypsin-like serine proteases Superfamily:Trypsin-like serine proteases Family:Viral cysteine protease of trypsin fold 8 c2q6fB_ 12.9 33 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 9 d1nrja_ 12.6 56 Fold:Profilin-like Superfamily:SNARE-like Family:SRP alpha N-terminal domain-like 10 d1p9sa_ 11.4 20 Fold:Trypsin-like serine proteases Superfamily:Trypsin-like serine proteases Family:Viral cysteine protease of trypsin fold 11 c3d23A_ 9.9 20 PDB header:hydrolase Chain: A: PDB Molecule:3c-like proteinase; PDBTitle: main protease of hcov-hku1 12 d2duca1 9.4 20 Fold:Trypsin-like serine proteases Superfamily:Trypsin-like serine proteases Family:Viral cysteine protease of trypsin fold 13 d2npta1 8.9 23 Fold:beta-Grasp (ubiquitin-like) Superfamily:CAD & PB1 domains Family:PB1 domain 14 d2goma1 6.6 17 Fold:Spectrin repeat-like Superfamily:Efb C-domain-like Family:Efb C-domain-like 15 c1q8hA_ 6.4 38 PDB header:metal binding protein Chain: A: PDB Molecule:osteocalcin; PDBTitle: crystal structure of porcine osteocalcin 16 d1q8ha_ 6.4 38 Fold:GLA-domain Superfamily:GLA-domain Family:GLA-domain 17 c3j0gO_ 6.3 29 PDB header:virus Chain: O: PDB Molecule:e3 protein; PDBTitle: homology model of e3 protein of venezuelan equine encephalitis virus2 tc-83 strain fitted with a cryo-em map 18 d1q3ma_ 6.2 38 Fold:GLA-domain Superfamily:GLA-domain Family:GLA-domain 19 c3ikmD_ 6.1 35 PDB header:transferase Chain: D: PDB Molecule:dna polymerase subunit gamma-1; PDBTitle: crystal structure of human mitochondrial dna polymerase2 holoenzyme 20 d2dlda2 6.0 0 Fold:Flavodoxin-like Superfamily:Formate/glycerate dehydrogenase catalytic domain-like Family:Formate/glycerate dehydrogenases, substrate-binding domain 21 d2g3qa1 not modelled 5.9 27 Fold:RuvA C-terminal domain-like Superfamily:UBA-like Family:UBA domain 22 c3m9hB_ not modelled 5.8 26 PDB header:chaperone Chain: B: PDB Molecule:proteasome-associated atpase; PDBTitle: crystal structure of the amino terminal coiled coil domain of the2 mycobacterium tuberculosis proteasomal atpase mpa

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