Secondary structure and disorder prediction

		1	.	.	.	.	.	.	.	.	10	.	.	.	.	.	.	.	.	.	20	.	.	.	.	.	.	.	.	.	30	.	.	.	.	.	.	.	.	.	40	.	.	.	.	.	.	.	.	.	50	.	.	.	.	.	.	.	.	.	60
Sequence		M	E	F	A	F	Y	I	C	G	L	I	A	I	L	A	T	L	R	V	I	T	H	T	N	P	V	H	A	L	L	Y	L	I	I	S	L	L	A	I	S	G	V	F	F	S	L	G	A	Y	F	A	G	A	L	E	I	I	V	Y	A
Secondary structure
SS confidence
Disorder		?
Disorder confidence
		.	.	.	.	.	.	.	.	.	70	.	.	.	.	.	.	.	.	.	80	.	.	.	.	.	.	.	.	.	90	.	.	.	.	.	.	.	.	.	100	.	.	.	.	.	.	.	.	.	110	.	.	.	.	.	.	.	.	.	120
Sequence		G	A	I	M	V	L	F	V	F	V	V	M	M	L	N	L	G	G	S	E	I	E	Q	E	R	Q	W	L	K	P	Q	V	W	I	G	P	A	I	L	S	A	I	M	L	V	V	I	V	Y	A	I	L	G	V	N	D	Q	G	I	D
Secondary structure
SS confidence
Disorder														?			?	?	?	?	?	?	?	?	?	?	?	?	?	?																					?	?	?	?	?	?	?	?	?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	130	.	.	.	.	.	.	.	.	.	140	.	.	.	.	.	.	.	.	.	150	.	.	.	.	.	.	.	.	.	160	.	.	.	.	.	.	.	.	.	170	.	.	.	.	.	.	.	.	.	180
Sequence		G	T	P	I	S	A	K	A	V	G	I	T	L	F	G	P	Y	V	L	A	V	E	L	A	S	M	L	L	L	A	G	L	V	V	A	F	H	V	G	R	E	E	R	A	G	E	V	L	S	N	R	K	D	D	S	A	K	R	K	T
Secondary structure
SS confidence
Disorder		?	?	?																																						?	?	?	?	?	?	?	?	?	?									?	?
Disorder confidence
		.	.	.	.
Sequence		E	E	H	A
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 3rko chain F Region: 1 - 168 Aligned: 168 Modelled: 168 Confidence: 100.0% Identity: 100% PDB header:oxidoreductase Chain: F: PDB Molecule:nadh-quinone oxidoreductase subunit j; PDBTitle: crystal structure of the membrane domain of respiratory complex i from2 e. coli at 3.0 angstrom resolution Phyre2 PDB 2fd5 chain A domain 2 Region: 145 - 178 Aligned: 33 Modelled: 34 Confidence: 67.9% Identity: 21% Fold: Tetracyclin repressor-like, C-terminal domain Superfamily: Tetracyclin repressor-like, C-terminal domain Family: Tetracyclin repressor-like, C-terminal domain Phyre2 PDB 3kp9 chain A Region: 4 - 138 Aligned: 130 Modelled: 135 Confidence: 20.4% Identity: 15% PDB header:blood coagulation,oxidoreductase Chain: A: PDB Molecule:vkorc1/thioredoxin domain protein; PDBTitle: structure of a bacterial homolog of vitamin k epoxide reductase Phyre2 PDB 2a93 chain B Region: 162 - 180 Aligned: 19 Modelled: 19 Confidence: 13.1% Identity: 16% PDB header:leucine zippers Chain: B: PDB Molecule:c-myc-max heterodimeric leucine zipper; PDBTitle: nmr solution structure of the c-myc-max heterodimeric2 leucine zipper, 40 structures Phyre2 PDB 2qts chain A Region: 23 - 60 Aligned: 36 Modelled: 38 Confidence: 12.4% Identity: 28% PDB header:membrane protein Chain: A: PDB Molecule:acid-sensing ion channel; PDBTitle: structure of an acid-sensing ion channel 1 at 1.9 a resolution and low2 ph Phyre2 PDB 3b5o chain A Region: 115 - 151 Aligned: 37 Modelled: 37 Confidence: 9.0% Identity: 16% PDB header:oxidoreductase Chain: A: PDB Molecule:cadd-like protein of unknown function; PDBTitle: crystal structure of a cadd-like protein of unknown function2 (npun_f6505) from nostoc punctiforme pcc 73102 at 1.35 a resolution Phyre2 PDB 1h2s chain B Region: 56 - 67 Aligned: 12 Modelled: 12 Confidence: 8.9% Identity: 42% Fold: Transmembrane helix hairpin Superfamily: Htr2 transmembrane domain-like Family: Htr2 transmembrane domain-like Phyre2 PDB 1h2s chain B Region: 56 - 67 Aligned: 12 Modelled: 12 Confidence: 8.9% Identity: 42% PDB header:membrane protein Chain: B: PDB Molecule:sensory rhodopsin ii transducer; PDBTitle: molecular basis of transmenbrane signalling by sensory2 rhodopsin ii-transducer complex Phyre2 PDB 1u2m chain A Region: 161 - 184 Aligned: 24 Modelled: 24 Confidence: 6.9% Identity: 21% Fold: OmpH-like Superfamily: OmpH-like Family: OmpH-like Phyre2 PDB 2hep chain A Region: 158 - 181 Aligned: 24 Modelled: 24 Confidence: 5.9% Identity: 21% PDB header:structural genomics, unknown function Chain: A: PDB Molecule:upf0291 protein ynzc; PDBTitle: solution nmr structure of the upf0291 protein ynzc from2 bacillus subtilis. northeast structural genomics target3 sr384. Phyre2 PDB 2hep chain A domain 1 Region: 158 - 181 Aligned: 24 Modelled: 24 Confidence: 5.9% Identity: 21% Fold: Long alpha-hairpin Superfamily: YnzC-like Family: YznC-like Phyre2 PDB 2f95 chain B Region: 58 - 67 Aligned: 10 Modelled: 10 Confidence: 5.4% Identity: 50% PDB header:membrane protein Chain: B: PDB Molecule:sensory rhodopsin ii transducer; PDBTitle: m intermediate structure of sensory rhodopsin ii/transducer complex in2 combination with the ground state structure Phyre2 PDB 3rko chain K Region: 2 - 90 Aligned: 89 Modelled: 89 Confidence: 5.4% Identity: 13% PDB header:oxidoreductase Chain: K: PDB Molecule:nadh-quinone oxidoreductase subunit k; PDBTitle: crystal structure of the membrane domain of respiratory complex i from2 e. coli at 3.0 angstrom resolution Phyre2 1 c3rkoF_ 2 d2fd5a2 3 c3kp9A_ 4 c2a93B_ 5 c2qtsA_ 6 c3b5oA_ 7 d1h2sb_ 8 c1h2sB_ 9 d1u2ma_ 10 c2hepA_ 11 d2hepa1 12 c2f95B_ 13 c3rkoK_

Detailed template information

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

1 c3rkoF_ 100.0 100 PDB header:oxidoreductase Chain: F: PDB Molecule:nadh-quinone oxidoreductase subunit j; PDBTitle: crystal structure of the membrane domain of respiratory complex i from2 e. coli at 3.0 angstrom resolution 2 d2fd5a2 67.9 21 Fold:Tetracyclin repressor-like, C-terminal domain Superfamily:Tetracyclin repressor-like, C-terminal domain Family:Tetracyclin repressor-like, C-terminal domain 3 c3kp9A_ 20.4 15 PDB header:blood coagulation,oxidoreductase Chain: A: PDB Molecule:vkorc1/thioredoxin domain protein; PDBTitle: structure of a bacterial homolog of vitamin k epoxide reductase 4 c2a93B_ 13.1 16 PDB header:leucine zippers Chain: B: PDB Molecule:c-myc-max heterodimeric leucine zipper; PDBTitle: nmr solution structure of the c-myc-max heterodimeric2 leucine zipper, 40 structures 5 c2qtsA_ 12.4 28 PDB header:membrane protein Chain: A: PDB Molecule:acid-sensing ion channel; PDBTitle: structure of an acid-sensing ion channel 1 at 1.9 a resolution and low2 ph 6 c3b5oA_ 9.0 16 PDB header:oxidoreductase Chain: A: PDB Molecule:cadd-like protein of unknown function; PDBTitle: crystal structure of a cadd-like protein of unknown function2 (npun_f6505) from nostoc punctiforme pcc 73102 at 1.35 a resolution 7 d1h2sb_ 8.9 42 Fold:Transmembrane helix hairpin Superfamily:Htr2 transmembrane domain-like Family:Htr2 transmembrane domain-like 8 c1h2sB_ 8.9 42 PDB header:membrane protein Chain: B: PDB Molecule:sensory rhodopsin ii transducer; PDBTitle: molecular basis of transmenbrane signalling by sensory2 rhodopsin ii-transducer complex 9 d1u2ma_ 6.9 21 Fold:OmpH-like Superfamily:OmpH-like Family:OmpH-like 10 c2hepA_ 5.9 21 PDB header:structural genomics, unknown function Chain: A: PDB Molecule:upf0291 protein ynzc; PDBTitle: solution nmr structure of the upf0291 protein ynzc from2 bacillus subtilis. northeast structural genomics target3 sr384. 11 d2hepa1 5.9 21 Fold:Long alpha-hairpin Superfamily:YnzC-like Family:YznC-like 12 c2f95B_ 5.4 50 PDB header:membrane protein Chain: B: PDB Molecule:sensory rhodopsin ii transducer; PDBTitle: m intermediate structure of sensory rhodopsin ii/transducer complex in2 combination with the ground state structure 13 c3rkoK_ 5.4 13 PDB header:oxidoreductase Chain: K: PDB Molecule:nadh-quinone oxidoreductase subunit k; PDBTitle: crystal structure of the membrane domain of respiratory complex i from2 e. coli at 3.0 angstrom resolution

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