Secondary structure and disorder prediction

		1	.	.	.	.	.	.	.	.	10	.	.	.	.	.	.	.	.	.	20	.	.	.	.	.	.	.	.	.	30	.	.	.	.	.	.	.	.	.	40	.	.	.	.	.	.	.	.	.	50	.	.	.	.	.	.	.	.	.	60
Sequence		M	K	I	S	R	L	G	E	A	P	D	Y	R	F	S	L	A	N	E	R	T	F	L	A	W	I	R	T	A	L	G	F	L	A	A	G	V	G	L	D	Q	L	A	P	D	F	A	T	P	V	I	R	E	L	L	A	L	L	L	C
Secondary structure
SS confidence
Disorder		?	?	?	?	?	?	?	?	?		?																																	?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	70	.	.	.	.	.	.	.	.	.	80	.	.	.	.	.	.	.	.	.	90	.	.	.	.	.	.	.	.	.	100	.	.	.	.	.	.	.	.	.	110	.	.	.	.	.
Sequence		L	F	S	G	G	L	A	M	Y	G	Y	L	R	W	L	R	N	E	K	A	M	R	L	K	E	D	L	P	Y	T	N	S	L	L	I	I	S	L	I	L	M	V	V	A	V	I	V	M	G	L	V	L	Y	A	G
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 1om2 chain A Region: 4 - 36 Aligned: 33 Modelled: 33 Confidence: 32.8% Identity: 30% Fold: Open three-helical up-and-down bundle Superfamily: Mitochondrial import receptor subunit Tom20 Family: Mitochondrial import receptor subunit Tom20 Phyre2 PDB 1n1c chain A Region: 1 - 26 Aligned: 24 Modelled: 26 Confidence: 18.8% Identity: 17% Fold: TorD-like Superfamily: TorD-like Family: TorD-like Phyre2 PDB 2d68 chain A Region: 4 - 19 Aligned: 15 Modelled: 16 Confidence: 14.1% Identity: 20% PDB header:cell cycle Chain: A: PDB Molecule:fop; PDBTitle: structure of the n-terminal domain of fop (fgfr1op) protein Phyre2 PDB 2lc2 chain A Region: 1 - 23 Aligned: 18 Modelled: 23 Confidence: 12.4% Identity: 33% PDB header:protein binding Chain: A: PDB Molecule:avr3a4; PDBTitle: solution structure of the rxlr effector p. capsici avr3a4 Phyre2 PDB 3g43 chain F Region: 21 - 32 Aligned: 12 Modelled: 12 Confidence: 11.8% Identity: 50% PDB header:metal binding protein Chain: F: PDB Molecule:voltage-dependent l-type calcium channel subunit PDBTitle: crystal structure of the calmodulin-bound cav1.2 c-terminal2 regulatory domain dimer Phyre2 PDB 1p4e chain A domain 1 Region: 17 - 28 Aligned: 12 Modelled: 12 Confidence: 10.9% Identity: 50% Fold: SAM domain-like Superfamily: lambda integrase-like, N-terminal domain Family: lambda integrase-like, N-terminal domain Phyre2 PDB 2l0g chain A Region: 8 - 29 Aligned: 22 Modelled: 22 Confidence: 10.6% Identity: 36% PDB header:protein binding Chain: A: PDB Molecule:dna polymerase iota; PDBTitle: solution nmr structure of ubiquitin-binding motif (ubm2) of human2 polymerase iota Phyre2 PDB 3b4q chain A Region: 6 - 18 Aligned: 13 Modelled: 13 Confidence: 10.6% Identity: 46% PDB header:structural genomics, unknown function Chain: A: PDB Molecule:uncharacterized protein; PDBTitle: crystal structure of a conserved protein domain (unknown2 function) from corynebacterium diphtheriae Phyre2 PDB 2khu chain A Region: 8 - 29 Aligned: 22 Modelled: 22 Confidence: 10.0% Identity: 36% PDB header:transferase/protein binding Chain: A: PDB Molecule:immunoglobulin g-binding protein g, dna PDBTitle: solution structure of the ubiquitin-binding motif of human2 polymerase iota Phyre2 PDB 2ipq chain X domain 1 Region: 22 - 31 Aligned: 10 Modelled: 10 Confidence: 10.0% Identity: 40% Fold: DNA/RNA-binding 3-helical bundle Superfamily: "Winged helix" DNA-binding domain Family: STY4665 C-terminal domain-like Phyre2 PDB 2axt chain C Region: 26 - 114 Aligned: 89 Modelled: 89 Confidence: 9.4% Identity: 21% PDB header:electron transport Chain: C: PDB Molecule:photosystem ii cp43 protein; PDBTitle: crystal structure of photosystem ii from thermosynechococcus elongatus Phyre2 PDB 2axt chain C domain 1 Region: 26 - 114 Aligned: 89 Modelled: 89 Confidence: 9.4% Identity: 21% Fold: Photosystem II antenna protein-like Superfamily: Photosystem II antenna protein-like Family: Photosystem II antenna protein-like Phyre2 PDB 3mk7 chain F Region: 57 - 114 Aligned: 58 Modelled: 58 Confidence: 9.2% Identity: 16% PDB header:oxidoreductase Chain: F: PDB Molecule:cytochrome c oxidase, cbb3-type, subunit p; PDBTitle: the structure of cbb3 cytochrome oxidase Phyre2 PDB 3pro chain C domain 1 Region: 8 - 21 Aligned: 14 Modelled: 14 Confidence: 8.4% Identity: 14% Fold: Alpha-lytic protease prodomain-like Superfamily: Alpha-lytic protease prodomain Family: Alpha-lytic protease prodomain Phyre2 PDB 2v1s chain D Region: 10 - 36 Aligned: 27 Modelled: 27 Confidence: 7.7% Identity: 30% PDB header:oxidoreductase Chain: D: PDB Molecule:mitochondrial import receptor subunit tom20 homolog; PDBTitle: crystal structure of rat tom20-aldh presequence complex Phyre2 PDB 1h2s chain B Region: 56 - 111 Aligned: 56 Modelled: 56 Confidence: 7.6% Identity: 14% 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 1h2s chain B Region: 56 - 111 Aligned: 56 Modelled: 56 Confidence: 7.6% Identity: 14% Fold: Transmembrane helix hairpin Superfamily: Htr2 transmembrane domain-like Family: Htr2 transmembrane domain-like Phyre2 PDB 1fft chain G Region: 50 - 113 Aligned: 64 Modelled: 64 Confidence: 7.6% Identity: 9% PDB header:oxidoreductase Chain: G: PDB Molecule:ubiquinol oxidase; PDBTitle: the structure of ubiquinol oxidase from escherichia coli Phyre2 PDB 2ret chain E Region: 19 - 26 Aligned: 8 Modelled: 1 Confidence: 6.8% Identity: 25% PDB header:protein transport Chain: E: PDB Molecule:pseudopilin epsi; PDBTitle: the crystal structure of a binary complex of two pseudopilins: epsi2 and epsj from the type 2 secretion system of vibrio vulnificus Phyre2 PDB 2qm2 chain B Region: 4 - 25 Aligned: 21 Modelled: 19 Confidence: 6.7% Identity: 19% PDB header:structural genomics, unknown function Chain: B: PDB Molecule:putative hopj type iii effector protein; PDBTitle: putative hopj type iii effector protein from vibrio parahaemolyticus Phyre2 1 d1om2a_ 2 d1n1ca_ 3 c2d68A_ 4 c2lc2A_ 5 c3g43F_ 6 d1p4ea1 7 c2l0gA_ 8 c3b4qA_ 9 c2khuA_ 10 d2ipqx1 11 c2axtc_ 12 d2axtc1 13 c3mk7F_ 14 d3proc1 15 c2v1sD_ 16 c1h2sB_ 17 d1h2sb_ 18 c1fftG_ 19 c2retE_ 20 c2qm2B_ 21 22 23 24 25 26 27

Detailed template information

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

1 d1om2a_ 32.8 30 Fold:Open three-helical up-and-down bundle Superfamily:Mitochondrial import receptor subunit Tom20 Family:Mitochondrial import receptor subunit Tom20 2 d1n1ca_ 18.8 17 Fold:TorD-like Superfamily:TorD-like Family:TorD-like 3 c2d68A_ 14.1 20 PDB header:cell cycle Chain: A: PDB Molecule:fop; PDBTitle: structure of the n-terminal domain of fop (fgfr1op) protein 4 c2lc2A_ 12.4 33 PDB header:protein binding Chain: A: PDB Molecule:avr3a4; PDBTitle: solution structure of the rxlr effector p. capsici avr3a4 5 c3g43F_ 11.8 50 PDB header:metal binding protein Chain: F: PDB Molecule:voltage-dependent l-type calcium channel subunit PDBTitle: crystal structure of the calmodulin-bound cav1.2 c-terminal2 regulatory domain dimer 6 d1p4ea1 10.9 50 Fold:SAM domain-like Superfamily:lambda integrase-like, N-terminal domain Family:lambda integrase-like, N-terminal domain 7 c2l0gA_ 10.6 36 PDB header:protein binding Chain: A: PDB Molecule:dna polymerase iota; PDBTitle: solution nmr structure of ubiquitin-binding motif (ubm2) of human2 polymerase iota 8 c3b4qA_ 10.6 46 PDB header:structural genomics, unknown function Chain: A: PDB Molecule:uncharacterized protein; PDBTitle: crystal structure of a conserved protein domain (unknown2 function) from corynebacterium diphtheriae 9 c2khuA_ 10.0 36 PDB header:transferase/protein binding Chain: A: PDB Molecule:immunoglobulin g-binding protein g, dna PDBTitle: solution structure of the ubiquitin-binding motif of human2 polymerase iota 10 d2ipqx1 10.0 40 Fold:DNA/RNA-binding 3-helical bundle Superfamily:"Winged helix" DNA-binding domain Family:STY4665 C-terminal domain-like 11 c2axtc_ 9.4 21 PDB header:electron transport Chain: C: PDB Molecule:photosystem ii cp43 protein; PDBTitle: crystal structure of photosystem ii from thermosynechococcus elongatus 12 d2axtc1 9.4 21 Fold:Photosystem II antenna protein-like Superfamily:Photosystem II antenna protein-like Family:Photosystem II antenna protein-like 13 c3mk7F_ 9.2 16 PDB header:oxidoreductase Chain: F: PDB Molecule:cytochrome c oxidase, cbb3-type, subunit p; PDBTitle: the structure of cbb3 cytochrome oxidase 14 d3proc1 8.4 14 Fold:Alpha-lytic protease prodomain-like Superfamily:Alpha-lytic protease prodomain Family:Alpha-lytic protease prodomain 15 c2v1sD_ 7.7 30 PDB header:oxidoreductase Chain: D: PDB Molecule:mitochondrial import receptor subunit tom20 homolog; PDBTitle: crystal structure of rat tom20-aldh presequence complex 16 c1h2sB_ 7.6 14 PDB header:membrane protein Chain: B: PDB Molecule:sensory rhodopsin ii transducer; PDBTitle: molecular basis of transmenbrane signalling by sensory2 rhodopsin ii-transducer complex 17 d1h2sb_ 7.6 14 Fold:Transmembrane helix hairpin Superfamily:Htr2 transmembrane domain-like Family:Htr2 transmembrane domain-like 18 c1fftG_ 7.6 9 PDB header:oxidoreductase Chain: G: PDB Molecule:ubiquinol oxidase; PDBTitle: the structure of ubiquinol oxidase from escherichia coli 19 c2retE_ 6.8 25 PDB header:protein transport Chain: E: PDB Molecule:pseudopilin epsi; PDBTitle: the crystal structure of a binary complex of two pseudopilins: epsi2 and epsj from the type 2 secretion system of vibrio vulnificus 20 c2qm2B_ 6.7 19 PDB header:structural genomics, unknown function Chain: B: PDB Molecule:putative hopj type iii effector protein; PDBTitle: putative hopj type iii effector protein from vibrio parahaemolyticus 21 d2reta1 not modelled 6.3 25 Fold:Pili subunits Superfamily:Pili subunits Family:GSPII I/J protein-like 22 d1c99a_ not modelled 6.3 21 Fold:Transmembrane helix hairpin Superfamily:F1F0 ATP synthase subunit C Family:F1F0 ATP synthase subunit C 23 d3b2ua2 not modelled 5.8 40 Fold:Knottins (small inhibitors, toxins, lectins) Superfamily:Growth factor receptor domain Family:Growth factor receptor domain 24 d1dxxa1 not modelled 5.7 23 Fold:CH domain-like Superfamily:Calponin-homology domain, CH-domain Family:Calponin-homology domain, CH-domain 25 d2fj6a1 not modelled 5.3 25 Fold:SAM domain-like Superfamily:YozE-like Family:YozE-like 26 c3m7kA_ not modelled 5.2 100 PDB header:hydrolase/dna Chain: A: PDB Molecule:restriction endonuclease paci; PDBTitle: crystal structure of paci-dna enzyme product complex 27 d1bhda_ not modelled 5.2 29 Fold:CH domain-like Superfamily:Calponin-homology domain, CH-domain Family:Calponin-homology domain, CH-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