Secondary structure and disorder prediction

		1	.	.	.	.	.	.	.	.	10	.	.	.	.	.	.	.	.	.	20	.	.	.	.	.	.	.	.	.	30	.	.	.	.	.	.	.	.	.	40	.	.	.	.	.	.	.	.	.	50	.	.	.	.	.	.	.	.	.	60
Sequence		M	R	F	S	T	Q	M	M	Y	Q	Q	N	M	R	G	I	T	N	S	Q	A	E	W	M	K	Y	G	E	Q	M	S	T	G	K	R	V	V	N	P	S	D	D	P	I	A	A	S	Q	A	V	V	L	S	Q	A	Q	A	Q	N	S
Secondary structure
SS confidence
Disorder		?	?	?	?																											?	?	?	?	?	?		?
Disorder confidence
		.	.	.	.	.	.	.	.	.	70	.	.	.	.	.	.	.	.	.	80	.	.	.	.	.	.	.	.	.	90	.	.	.	.	.	.	.	.	.	100	.	.	.	.	.	.	.	.	.	110	.	.	.	.	.	.	.	.	.	120
Sequence		Q	Y	T	L	A	R	T	F	A	T	Q	K	V	S	L	E	E	S	V	L	S	Q	V	T	T	A	I	Q	N	A	Q	E	K	I	V	Y	A	S	N	G	T	L	S	D	D	D	R	A	S	L	A	T	D	I	Q	G	L	R	D	Q
Secondary structure
SS confidence
Disorder																																					?	?		?	?	?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	130	.	.	.	.	.	.	.	.	.	140	.	.	.	.	.	.	.	.	.	150	.	.	.	.	.	.	.	.	.	160	.	.	.	.	.	.	.	.	.	170	.	.	.	.	.	.	.	.	.	180
Sequence		L	L	N	L	A	N	T	T	D	G	N	G	R	Y	I	F	A	G	Y	K	T	E	T	A	P	F	S	E	E	K	G	K	Y	V	G	G	A	E	S	I	K	Q	Q	V	D	A	S	R	S	M	V	I	G	H	T	G	D	K	I	F
Secondary structure
SS confidence
Disorder						?	?	?	?	?	?		?									?	?	?				?	?					?	?												?	?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	190	.	.	.	.	.	.	.	.	.	200	.	.	.	.	.	.	.	.	.	210	.	.	.	.	.	.	.	.	.	220	.	.	.	.	.	.	.	.	.	230	.	.	.	.	.	.	.	.	.	240
Sequence		D	S	I	T	S	N	A	V	A	E	P	D	G	S	A	S	E	T	N	L	F	A	M	L	D	S	A	I	A	A	L	K	T	P	V	A	D	S	E	A	D	K	E	T	A	A	A	A	L	D	K	T	N	R	G	L	K	N	S	L
Secondary structure
SS confidence
Disorder							?	?			?	?	?		?	?	?	?				?											?	?	?	?	?	?	?	?	?	?	?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	250	.	.	.	.	.	.	.	.	.	260	.	.	.	.	.	.	.	.	.	270	.	.	.	.	.	.	.	.	.	280	.	.	.	.	.	.	.	.	.	290	.	.	.	.	.	.	.	.	.	300
Sequence		N	N	V	L	T	V	R	A	E	L	G	T	Q	L	N	E	L	E	S	L	D	S	L	G	S	D	R	A	L	G	Q	T	Q	Q	M	S	D	L	V	D	V	D	W	N	A	T	I	S	S	Y	I	M	Q	Q	T	A	L	Q	A	S
Secondary structure
SS confidence
Disorder																								?		?
Disorder confidence
		.	.	.	.	.	.	.	.	.	310	.	.	.	.	.	.	.
Sequence		Y	K	A	F	T	D	M	Q	G	L	S	L	F	Q	L	S	K
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 1ucu chain A Region: 1 - 317 Aligned: 317 Modelled: 317 Confidence: 100.0% Identity: 21% Fold: Phase 1 flagellin Superfamily: Phase 1 flagellin Family: Phase 1 flagellin Phyre2 PDB 3k8v chain B Region: 44 - 300 Aligned: 257 Modelled: 257 Confidence: 100.0% Identity: 19% PDB header:structural protein Chain: B: PDB Molecule:flagellin homolog; PDBTitle: crysatl structure of a bacterial cell-surface flagellin n20c20 Phyre2 PDB 2d4x chain A Region: 50 - 262 Aligned: 213 Modelled: 213 Confidence: 100.0% Identity: 81% PDB header:structural protein Chain: A: PDB Molecule:flagellar hook-associated protein 3; PDBTitle: crystal structure of a 26k fragment of hap3 (flgl) Phyre2 PDB 3k8w chain A Region: 42 - 275 Aligned: 234 Modelled: 234 Confidence: 100.0% Identity: 19% PDB header:structural protein Chain: A: PDB Molecule:flagellin homolog; PDBTitle: crysatl structure of a bacterial cell-surface flagellin n20c45 Phyre2 PDB 3pwx chain B Region: 42 - 278 Aligned: 194 Modelled: 201 Confidence: 100.0% Identity: 24% PDB header:structural protein Chain: B: PDB Molecule:putative flagellar hook-associated protein; PDBTitle: structure of putative flagellar hook-associated protein from vibrio2 parahaemolyticus Phyre2 PDB 2zbi chain B Region: 61 - 264 Aligned: 204 Modelled: 204 Confidence: 100.0% Identity: 22% PDB header:structural protein Chain: B: PDB Molecule:flagellin homolog; PDBTitle: crysatl structure of a bacterial cell-surface flagellin Phyre2 PDB 1io1 chain A Region: 56 - 275 Aligned: 220 Modelled: 220 Confidence: 100.0% Identity: 22% Fold: Phase 1 flagellin Superfamily: Phase 1 flagellin Family: Phase 1 flagellin Phyre2 PDB 1ory chain B Region: 280 - 317 Aligned: 38 Modelled: 37 Confidence: 94.1% Identity: 18% PDB header:chaperone Chain: B: PDB Molecule:flagellin; PDBTitle: flagellar export chaperone in complex with its cognate binding partner Phyre2 PDB 3a69 chain A Region: 280 - 310 Aligned: 31 Modelled: 31 Confidence: 45.8% Identity: 10% 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 2kyy chain A Region: 115 - 137 Aligned: 23 Modelled: 23 Confidence: 9.3% Identity: 13% PDB header:hydrolase Chain: A: PDB Molecule:possible atp-dependent dna helicase recg-related protein; PDBTitle: solution nmr structure of the n-terminal domain of putative atp-2 dependent dna helicase recg-related protein from nitrosomonas3 europaea, northeast structural genomics consortium target ner70a Phyre2 PDB 2ieq chain C Region: 229 - 310 Aligned: 76 Modelled: 82 Confidence: 8.5% Identity: 12% PDB header:viral protein Chain: C: PDB Molecule:spike glycoprotein; PDBTitle: core structure of s2 from the human coronavirus nl63 spike2 glycoprotein Phyre2 PDB 3pzd chain B Region: 37 - 67 Aligned: 31 Modelled: 31 Confidence: 8.3% Identity: 19% PDB header:motor protein/apoptosis Chain: B: PDB Molecule:netrin receptor dcc; PDBTitle: structure of the myosin x myth4-ferm/dcc complex Phyre2 PDB 2do9 chain A Region: 281 - 316 Aligned: 36 Modelled: 36 Confidence: 7.0% Identity: 19% PDB header:signaling protein Chain: A: PDB Molecule:nacht-, lrr- and pyd-containing protein 10; PDBTitle: solution structure of the pyrin/paad-dapin domain in mouse2 nalp10 (nacht, leucine rich repeat and pyd containing 10) Phyre2 PDB 1ffv chain A domain 2 Region: 309 - 317 Aligned: 9 Modelled: 9 Confidence: 7.0% Identity: 11% Fold: beta-Grasp (ubiquitin-like) Superfamily: 2Fe-2S ferredoxin-like Family: 2Fe-2S ferredoxin domains from multidomain proteins Phyre2 PDB 3lmm chain A Region: 112 - 146 Aligned: 34 Modelled: 35 Confidence: 6.7% Identity: 24% PDB header:structural genomics, unknown function Chain: A: PDB Molecule:uncharacterized protein; PDBTitle: crystal structure of the dip2311 protein from2 corynebacterium diphtheriae, northeast structural genomics3 consortium target cdr35 Phyre2 PDB 3a1y chain F Region: 271 - 289 Aligned: 19 Modelled: 19 Confidence: 6.4% Identity: 16% PDB header:ribosomal protein Chain: F: PDB Molecule:50s ribosomal protein p1 (l12p); PDBTitle: the structure of protein complex Phyre2 PDB 2w6j chain G Region: 243 - 290 Aligned: 48 Modelled: 48 Confidence: 6.2% Identity: 6% PDB header:hydrolase Chain: G: PDB Molecule:atp synthase subunit gamma, mitochondrial; PDBTitle: low resolution structures of bovine mitochondrial f1-atpase2 during controlled dehydration: hydration state 5. Phyre2 PDB 3fks chain Y Region: 243 - 290 Aligned: 48 Modelled: 48 Confidence: 6.2% Identity: 8% PDB header:hydrolase Chain: Y: PDB Molecule:atp synthase subunit gamma, mitochondrial; PDBTitle: yeast f1 atpase in the absence of bound nucleotides Phyre2 1 d1ucua_ 2 c3k8vB_ 3 c2d4xA_ 4 c3k8wA_ 5 c3pwxB_ 6 c2zbiB_ 7 d1io1a_ 8 c1oryB_ 9 c3a69A_ 10 c2kyyA_ 11 c2ieqC_ 12 c3pzdB_ 13 c2do9A_ 14 d1ffva2 15 c3lmmA_ 16 c3a1yF_ 17 c2w6jG_ 18 c3fksY_

Detailed template information

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

1 d1ucua_ 100.0 21 Fold:Phase 1 flagellin Superfamily:Phase 1 flagellin Family:Phase 1 flagellin 2 c3k8vB_ 100.0 19 PDB header:structural protein Chain: B: PDB Molecule:flagellin homolog; PDBTitle: crysatl structure of a bacterial cell-surface flagellin n20c20 3 c2d4xA_ 100.0 81 PDB header:structural protein Chain: A: PDB Molecule:flagellar hook-associated protein 3; PDBTitle: crystal structure of a 26k fragment of hap3 (flgl) 4 c3k8wA_ 100.0 19 PDB header:structural protein Chain: A: PDB Molecule:flagellin homolog; PDBTitle: crysatl structure of a bacterial cell-surface flagellin n20c45 5 c3pwxB_ 100.0 24 PDB header:structural protein Chain: B: PDB Molecule:putative flagellar hook-associated protein; PDBTitle: structure of putative flagellar hook-associated protein from vibrio2 parahaemolyticus 6 c2zbiB_ 100.0 22 PDB header:structural protein Chain: B: PDB Molecule:flagellin homolog; PDBTitle: crysatl structure of a bacterial cell-surface flagellin 7 d1io1a_ 100.0 22 Fold:Phase 1 flagellin Superfamily:Phase 1 flagellin Family:Phase 1 flagellin 8 c1oryB_ 94.1 18 PDB header:chaperone Chain: B: PDB Molecule:flagellin; PDBTitle: flagellar export chaperone in complex with its cognate binding partner 9 c3a69A_ 45.8 10 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 10 c2kyyA_ 9.3 13 PDB header:hydrolase Chain: A: PDB Molecule:possible atp-dependent dna helicase recg-related protein; PDBTitle: solution nmr structure of the n-terminal domain of putative atp-2 dependent dna helicase recg-related protein from nitrosomonas3 europaea, northeast structural genomics consortium target ner70a 11 c2ieqC_ 8.5 12 PDB header:viral protein Chain: C: PDB Molecule:spike glycoprotein; PDBTitle: core structure of s2 from the human coronavirus nl63 spike2 glycoprotein 12 c3pzdB_ 8.3 19 PDB header:motor protein/apoptosis Chain: B: PDB Molecule:netrin receptor dcc; PDBTitle: structure of the myosin x myth4-ferm/dcc complex 13 c2do9A_ 7.0 19 PDB header:signaling protein Chain: A: PDB Molecule:nacht-, lrr- and pyd-containing protein 10; PDBTitle: solution structure of the pyrin/paad-dapin domain in mouse2 nalp10 (nacht, leucine rich repeat and pyd containing 10) 14 d1ffva2 7.0 11 Fold:beta-Grasp (ubiquitin-like) Superfamily:2Fe-2S ferredoxin-like Family:2Fe-2S ferredoxin domains from multidomain proteins 15 c3lmmA_ 6.7 24 PDB header:structural genomics, unknown function Chain: A: PDB Molecule:uncharacterized protein; PDBTitle: crystal structure of the dip2311 protein from2 corynebacterium diphtheriae, northeast structural genomics3 consortium target cdr35 16 c3a1yF_ 6.4 16 PDB header:ribosomal protein Chain: F: PDB Molecule:50s ribosomal protein p1 (l12p); PDBTitle: the structure of protein complex 17 c2w6jG_ 6.2 6 PDB header:hydrolase Chain: G: PDB Molecule:atp synthase subunit gamma, mitochondrial; PDBTitle: low resolution structures of bovine mitochondrial f1-atpase2 during controlled dehydration: hydration state 5. 18 c3fksY_ 6.2 8 PDB header:hydrolase Chain: Y: PDB Molecule:atp synthase subunit gamma, mitochondrial; PDBTitle: yeast f1 atpase in the absence of bound nucleotides

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