Secondary structure and disorder prediction

		1	.	.	.	.	.	.	.	.	10	.	.	.	.	.	.	.	.	.	20	.	.	.	.	.	.	.	.	.	30	.	.	.	.	.	.	.	.	.	40	.	.	.	.	.	.	.	.	.	50	.	.	.	.	.	.	.	.	.	60
Sequence		M	A	T	P	A	T	V	S	I	E	P	T	L	A	A	I	R	A	R	W	C	I	N	S	S	K	T	T	Q	S	F	N	D	P	A	S	M	E	E	V	V	E	Y	L	K	G	T	Y	S	A	L	R	K	S	V	A	C	A	K	L
Secondary structure
SS confidence
Disorder		?	?	?	?	?	?	?		?																	?	?	?	?	?	?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	70	.	.	.	.	.	.	.	.	.	80	.	.	.	.	.	.	.	.	.	90	.	.	.	.	.	.	.	.	.	100	.	.	.	.	.	.	.	.	.	110	.	.	.	.	.	.	.	.	.	120
Sequence		K	I	L	H	L	K	Q	R	M	Q	N	A	T	N	F	L	A	R	L	M	S	C	K	N	Q	A	S	R	S	H	H	S	T	A	K	S	A	K	S	A	L	S	S	D	S	G	D	G	S	D	P	D	P	E	P	E	T	F	P	S
Secondary structure
SS confidence
Disorder																							?	?	?	?	?	?	?	?	?	?	?	?							?	?	?	?	?	?	?	?	?	?	?	?	?	?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	130	.	.	.	.	.	.	.	.	.	140	.	.	.	.	.	.
Sequence		A	F	I	T	T	P	T	N	S	I	M	L	K	A	F	F	A	N	I	S	I	T	E	V	A	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 1deb chain A Region: 47 - 81 Aligned: 35 Modelled: 35 Confidence: 48.0% Identity: 29% PDB header:structural protein Chain: A: PDB Molecule:adenomatous polyposis coli protein; PDBTitle: crystal structure of the n-terminal coiled coil domain from2 apc Phyre2 PDB 1v2z chain A Region: 133 - 144 Aligned: 12 Modelled: 12 Confidence: 29.2% Identity: 67% Fold: KaiA/RbsU domain Superfamily: KaiA/RbsU domain Family: Circadian clock protein KaiA, C-terminal domain Phyre2 PDB 1sv1 chain A Region: 133 - 144 Aligned: 12 Modelled: 12 Confidence: 27.8% Identity: 67% Fold: KaiA/RbsU domain Superfamily: KaiA/RbsU domain Family: Circadian clock protein KaiA, C-terminal domain Phyre2 PDB 1r8j chain A domain 1 Region: 133 - 144 Aligned: 12 Modelled: 12 Confidence: 27.7% Identity: 50% Fold: KaiA/RbsU domain Superfamily: KaiA/RbsU domain Family: Circadian clock protein KaiA, C-terminal domain Phyre2 PDB 1r5q chain A Region: 133 - 144 Aligned: 12 Modelled: 12 Confidence: 26.4% Identity: 42% Fold: KaiA/RbsU domain Superfamily: KaiA/RbsU domain Family: Circadian clock protein KaiA, C-terminal domain Phyre2 PDB 1r8j chain B Region: 133 - 144 Aligned: 12 Modelled: 12 Confidence: 18.9% Identity: 50% PDB header:circadian clock protein Chain: B: PDB Molecule:kaia; PDBTitle: crystal structure of circadian clock protein kaia from2 synechococcus elongatus Phyre2 PDB 2kao chain A Region: 19 - 24 Aligned: 6 Modelled: 6 Confidence: 18.9% Identity: 67% PDB header:oxidoreductase Chain: A: PDB Molecule:methionine-r-sulfoxide reductase b1; PDBTitle: structure of reduced mouse methionine sulfoxide reductase b12 (sec95cys mutant) Phyre2 PDB 2fe9 chain A Region: 23 - 46 Aligned: 24 Modelled: 24 Confidence: 17.6% Identity: 33% PDB header:rna binding protein Chain: A: PDB Molecule:protein vts1; PDBTitle: solution structure of the vts1 sam domain in the presence2 of rna Phyre2 PDB 3zqo chain K Region: 35 - 44 Aligned: 10 Modelled: 10 Confidence: 16.7% Identity: 40% PDB header:dna-binding protein Chain: K: PDB Molecule:terminase small subunit; PDBTitle: crystal structure of the small terminase oligomerization2 core domain from a spp1-like bacteriophage (crystal form 3) Phyre2 PDB 3lup chain A Region: 32 - 83 Aligned: 52 Modelled: 52 Confidence: 13.5% Identity: 15% PDB header:structure genomics, unknown function Chain: A: PDB Molecule:degv family protein; PDBTitle: crystal structure of fatty acid binding degv family protein sag13422 from streptococcus agalactiae Phyre2 PDB 3hcj chain B Region: 19 - 24 Aligned: 6 Modelled: 6 Confidence: 11.8% Identity: 67% PDB header:oxidoreductase Chain: B: PDB Molecule:peptide methionine sulfoxide reductase; PDBTitle: structure of msrb from xanthomonas campestris (oxidized2 form) Phyre2 PDB 3iym chain A Region: 105 - 124 Aligned: 20 Modelled: 20 Confidence: 11.6% Identity: 45% PDB header:virus Chain: A: PDB Molecule:capsid protein; PDBTitle: backbone trace of the capsid protein dimer of a fungal partitivirus2 from electron cryomicroscopy and homology modeling Phyre2 PDB 2kon chain A Region: 50 - 62 Aligned: 13 Modelled: 13 Confidence: 11.5% Identity: 62% PDB header:structural genomics, unknown function Chain: A: PDB Molecule:uncharacterized protein; PDBTitle: nmr solution structure of cv_2116 from chromobacterium2 violaceum. northeast structural genomics consortium target3 cvt4(1-82) Phyre2 PDB 1xm0 chain A domain 1 Region: 19 - 24 Aligned: 6 Modelled: 6 Confidence: 10.6% Identity: 83% Fold: Mss4-like Superfamily: Mss4-like Family: SelR domain Phyre2 PDB 3e0m chain B Region: 19 - 24 Aligned: 6 Modelled: 6 Confidence: 9.2% Identity: 83% PDB header:oxidoreductase Chain: B: PDB Molecule:peptide methionine sulfoxide reductase msra/msrb PDBTitle: crystal structure of fusion protein of msra and msrb Phyre2 PDB 1jun chain B Region: 35 - 71 Aligned: 37 Modelled: 37 Confidence: 8.9% Identity: 32% PDB header:transcription regulation Chain: B: PDB Molecule:c-jun homodimer; PDBTitle: nmr study of c-jun homodimer Phyre2 PDB 3q4f chain G Region: 29 - 74 Aligned: 42 Modelled: 46 Confidence: 8.7% Identity: 17% PDB header:dna binding protein/protein binding Chain: G: PDB Molecule:dna repair protein xrcc4; PDBTitle: crystal structure of xrcc4/xlf-cernunnos complex Phyre2 PDB 3mud chain A Region: 29 - 84 Aligned: 56 Modelled: 56 Confidence: 7.2% Identity: 23% PDB header:contractile protein Chain: A: PDB Molecule:dna repair protein xrcc4, tropomyosin alpha-1 chain; PDBTitle: structure of the tropomyosin overlap complex from chicken smooth2 muscle Phyre2 PDB 1iic chain A domain 1 Region: 3 - 48 Aligned: 40 Modelled: 46 Confidence: 6.8% Identity: 25% Fold: Acyl-CoA N-acyltransferases (Nat) Superfamily: Acyl-CoA N-acyltransferases (Nat) Family: N-myristoyl transferase, NMT Phyre2 PDB 1u2u chain B Region: 50 - 70 Aligned: 21 Modelled: 21 Confidence: 5.9% Identity: 43% PDB header:transcription Chain: B: PDB Molecule:general control protein gcn4; PDBTitle: nmr solution structure of a designed heterodimeric leucine2 zipper Phyre2 1 c1debA_ 2 d1v2za_ 3 d1sv1a_ 4 d1r8ja1 5 d1r5qa_ 6 c1r8jB_ 7 c2kaoA_ 8 c2fe9A_ 9 c3zqoK_ 10 c3lupA_ 11 c3hcjB_ 12 c3iymA_ 13 c2konA_ 14 d1xm0a1 15 c3e0mB_ 16 c1junB_ 17 c3q4fG_ 18 c3mudA_ 19 d1iica1 20 c1u2uB_ 21 22 23 24

Detailed template information

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

1 c1debA_ 48.0 29 PDB header:structural protein Chain: A: PDB Molecule:adenomatous polyposis coli protein; PDBTitle: crystal structure of the n-terminal coiled coil domain from2 apc 2 d1v2za_ 29.2 67 Fold:KaiA/RbsU domain Superfamily:KaiA/RbsU domain Family:Circadian clock protein KaiA, C-terminal domain 3 d1sv1a_ 27.8 67 Fold:KaiA/RbsU domain Superfamily:KaiA/RbsU domain Family:Circadian clock protein KaiA, C-terminal domain 4 d1r8ja1 27.7 50 Fold:KaiA/RbsU domain Superfamily:KaiA/RbsU domain Family:Circadian clock protein KaiA, C-terminal domain 5 d1r5qa_ 26.4 42 Fold:KaiA/RbsU domain Superfamily:KaiA/RbsU domain Family:Circadian clock protein KaiA, C-terminal domain 6 c1r8jB_ 18.9 50 PDB header:circadian clock protein Chain: B: PDB Molecule:kaia; PDBTitle: crystal structure of circadian clock protein kaia from2 synechococcus elongatus 7 c2kaoA_ 18.9 67 PDB header:oxidoreductase Chain: A: PDB Molecule:methionine-r-sulfoxide reductase b1; PDBTitle: structure of reduced mouse methionine sulfoxide reductase b12 (sec95cys mutant) 8 c2fe9A_ 17.6 33 PDB header:rna binding protein Chain: A: PDB Molecule:protein vts1; PDBTitle: solution structure of the vts1 sam domain in the presence2 of rna 9 c3zqoK_ 16.7 40 PDB header:dna-binding protein Chain: K: PDB Molecule:terminase small subunit; PDBTitle: crystal structure of the small terminase oligomerization2 core domain from a spp1-like bacteriophage (crystal form 3) 10 c3lupA_ 13.5 15 PDB header:structure genomics, unknown function Chain: A: PDB Molecule:degv family protein; PDBTitle: crystal structure of fatty acid binding degv family protein sag13422 from streptococcus agalactiae 11 c3hcjB_ 11.8 67 PDB header:oxidoreductase Chain: B: PDB Molecule:peptide methionine sulfoxide reductase; PDBTitle: structure of msrb from xanthomonas campestris (oxidized2 form) 12 c3iymA_ 11.6 45 PDB header:virus Chain: A: PDB Molecule:capsid protein; PDBTitle: backbone trace of the capsid protein dimer of a fungal partitivirus2 from electron cryomicroscopy and homology modeling 13 c2konA_ 11.5 62 PDB header:structural genomics, unknown function Chain: A: PDB Molecule:uncharacterized protein; PDBTitle: nmr solution structure of cv_2116 from chromobacterium2 violaceum. northeast structural genomics consortium target3 cvt4(1-82) 14 d1xm0a1 10.6 83 Fold:Mss4-like Superfamily:Mss4-like Family:SelR domain 15 c3e0mB_ 9.2 83 PDB header:oxidoreductase Chain: B: PDB Molecule:peptide methionine sulfoxide reductase msra/msrb PDBTitle: crystal structure of fusion protein of msra and msrb 16 c1junB_ 8.9 32 PDB header:transcription regulation Chain: B: PDB Molecule:c-jun homodimer; PDBTitle: nmr study of c-jun homodimer 17 c3q4fG_ 8.7 17 PDB header:dna binding protein/protein binding Chain: G: PDB Molecule:dna repair protein xrcc4; PDBTitle: crystal structure of xrcc4/xlf-cernunnos complex 18 c3mudA_ 7.2 23 PDB header:contractile protein Chain: A: PDB Molecule:dna repair protein xrcc4, tropomyosin alpha-1 chain; PDBTitle: structure of the tropomyosin overlap complex from chicken smooth2 muscle 19 d1iica1 6.8 25 Fold:Acyl-CoA N-acyltransferases (Nat) Superfamily:Acyl-CoA N-acyltransferases (Nat) Family:N-myristoyl transferase, NMT 20 c1u2uB_ 5.9 43 PDB header:transcription Chain: B: PDB Molecule:general control protein gcn4; PDBTitle: nmr solution structure of a designed heterodimeric leucine2 zipper 21 c3fovA_ not modelled 5.4 41 PDB header:structural genomics, unknown function Chain: A: PDB Molecule:upf0102 protein rpa0323; PDBTitle: crystal structure of protein rpa0323 of unknown function from2 rhodopseudomonas palustris 22 d1hwxa2 not modelled 5.3 13 Fold:Aminoacid dehydrogenase-like, N-terminal domain Superfamily:Aminoacid dehydrogenase-like, N-terminal domain Family:Aminoacid dehydrogenases 23 c2d1lA_ not modelled 5.2 18 PDB header:protein binding Chain: A: PDB Molecule:metastasis suppressor protein 1; PDBTitle: structure of f-actin binding domain imd of mim (missing in metastasis) 24 c3fdjA_ not modelled 5.1 13 PDB header:structural genomics, unknown function Chain: A: PDB Molecule:degv family protein; PDBTitle: the structure of a degv family protein from eubacterium eligens.

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

Transmembrane helix prediction

Transmembrane helices have been predicted in your sequence to adopt the topology shown below

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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