Secondary structure and disorder prediction

		1	.	.	.	.	.	.	.	.	10	.	.	.	.	.	.	.	.	.	20	.	.	.	.	.	.	.	.	.	30	.	.	.	.	.	.	.	.	.	40	.	.	.	.	.	.	.	.	.	50	.	.	.	.	.	.	.	.	.	60
Sequence		M	K	C	K	R	L	N	E	V	I	E	L	L	Q	P	A	W	Q	K	E	P	D	L	N	L	L	Q	F	L	Q	K	L	A	K	E	S	G	F	D	G	E	L	A	D	L	T	D	D	I	L	I	Y	H	L	K	M	R	D	S	A
Secondary structure
SS confidence
Disorder		?	?	?																															?		?	?	?	?	?	?																		?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	70	.	.	.	.	.	.	.	.	.	80	.	.	.	.	.	.	.	.	.
Sequence		K	D	A	V	I	P	G	L	Q	K	D	Y	E	E	D	F	K	T	A	L	L	R	A	R	G	V	I	K	E
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 2ko6 chain A Region: 1 - 89 Aligned: 89 Modelled: 89 Confidence: 100.0% Identity: 99% PDB header:structural genomics, unknown function Chain: A: PDB Molecule:uncharacterized protein yihd; PDBTitle: solution structure of protein sf3929 from shigella flexneri2 2a. northeast structural genomics consortium target3 sfr81/ontario center for structural proteomics target4 sf3929 Phyre2 PDB 2ibg chain E domain 1 Region: 20 - 39 Aligned: 20 Modelled: 20 Confidence: 29.6% Identity: 40% Fold: Hedgehog/DD-peptidase Superfamily: Hedgehog/DD-peptidase Family: Hedgehog (development protein), N-terminal signaling domain Phyre2 PDB 1ufw chain A Region: 36 - 85 Aligned: 39 Modelled: 50 Confidence: 29.3% Identity: 31% Fold: Ferredoxin-like Superfamily: RNA-binding domain, RBD Family: Canonical RBD Phyre2 PDB 3m1n chain B Region: 20 - 39 Aligned: 20 Modelled: 20 Confidence: 25.7% Identity: 40% PDB header:signaling protein Chain: B: PDB Molecule:sonic hedgehog protein; PDBTitle: crystal structure of human sonic hedgehog n-terminal domain Phyre2 PDB 3d1m chain A domain 1 Region: 20 - 39 Aligned: 20 Modelled: 20 Confidence: 24.7% Identity: 40% Fold: Hedgehog/DD-peptidase Superfamily: Hedgehog/DD-peptidase Family: Hedgehog (development protein), N-terminal signaling domain Phyre2 PDB 1ias chain A Region: 7 - 37 Aligned: 31 Modelled: 31 Confidence: 15.6% Identity: 19% Fold: Protein kinase-like (PK-like) Superfamily: Protein kinase-like (PK-like) Family: Protein kinases, catalytic subunit Phyre2 PDB 1dpu chain A Region: 7 - 53 Aligned: 46 Modelled: 47 Confidence: 13.9% Identity: 22% PDB header:dna binding protein Chain: A: PDB Molecule:replication protein a (rpa32) c-terminal domain; PDBTitle: solution structure of the c-terminal domain of human rpa322 complexed with ung2(73-88) Phyre2 PDB 1dpu chain A Region: 7 - 53 Aligned: 46 Modelled: 47 Confidence: 13.9% Identity: 22% Fold: DNA/RNA-binding 3-helical bundle Superfamily: "Winged helix" DNA-binding domain Family: C-terminal domain of RPA32 Phyre2 PDB 2kxh chain B Region: 74 - 86 Aligned: 13 Modelled: 13 Confidence: 10.6% Identity: 54% PDB header:protein binding Chain: B: PDB Molecule:peptide of far upstream element-binding protein 1; PDBTitle: solution structure of the first two rrm domains of fir in the complex2 with fbp nbox peptide Phyre2 PDB 2cpg chain A Region: 24 - 40 Aligned: 17 Modelled: 17 Confidence: 10.1% Identity: 35% Fold: Ribbon-helix-helix Superfamily: Ribbon-helix-helix Family: CopG-like Phyre2 PDB 2ayx chain A domain 2 Region: 17 - 38 Aligned: 22 Modelled: 22 Confidence: 10.1% Identity: 32% Fold: Flavodoxin-like Superfamily: CheY-like Family: RcsC linker domain-like Phyre2 PDB 1ygm chain A Region: 26 - 48 Aligned: 23 Modelled: 23 Confidence: 9.1% Identity: 39% PDB header:membrane protein Chain: A: PDB Molecule:hypothetical protein bsu31320; PDBTitle: nmr structure of mistic Phyre2 PDB 2nox chain P Region: 4 - 39 Aligned: 36 Modelled: 36 Confidence: 8.6% Identity: 22% PDB header:oxidoreductase Chain: P: PDB Molecule:tryptophan 2,3-dioxygenase; PDBTitle: crystal structure of tryptophan 2,3-dioxygenase from ralstonia2 metallidurans Phyre2 PDB 1bl0 chain A domain 2 Region: 4 - 41 Aligned: 29 Modelled: 38 Confidence: 7.9% Identity: 31% Fold: DNA/RNA-binding 3-helical bundle Superfamily: Homeodomain-like Family: AraC type transcriptional activator Phyre2 PDB 3kzq chain E Region: 11 - 39 Aligned: 29 Modelled: 29 Confidence: 7.7% Identity: 17% PDB header:structural genomics, unknown function Chain: E: PDB Molecule:putative uncharacterized protein vp2116; PDBTitle: the crystal structure of the protein with unknown function from vibrio2 parahaemolyticus rimd 2210633 Phyre2 PDB 3db3 chain A Region: 48 - 65 Aligned: 18 Modelled: 18 Confidence: 7.5% Identity: 33% PDB header:ligase Chain: A: PDB Molecule:e3 ubiquitin-protein ligase uhrf1; PDBTitle: crystal structure of the tandem tudor domains of the e3 ubiquitin-2 protein ligase uhrf1 in complex with trimethylated histone h3-k93 peptide Phyre2 PDB 1r4w chain A Region: 9 - 44 Aligned: 36 Modelled: 36 Confidence: 7.3% Identity: 22% Fold: Thioredoxin fold Superfamily: Thioredoxin-like Family: DsbA-like Phyre2 PDB 1kz7 chain A domain 2 Region: 36 - 53 Aligned: 16 Modelled: 16 Confidence: 7.2% Identity: 44% Fold: PH domain-like barrel Superfamily: PH domain-like Family: Pleckstrin-homology domain (PH domain) Phyre2 PDB 1aop chain A domain 4 Region: 4 - 47 Aligned: 44 Modelled: 44 Confidence: 6.9% Identity: 18% Fold: Nitrite and sulphite reductase 4Fe-4S domain-like Superfamily: Nitrite and sulphite reductase 4Fe-4S domain-like Family: Nitrite and sulphite reductase 4Fe-4S domain-like Phyre2 PDB 2in3 chain A Region: 12 - 39 Aligned: 28 Modelled: 28 Confidence: 6.9% Identity: 25% PDB header:isomerase Chain: A: PDB Molecule:hypothetical protein; PDBTitle: crystal structure of a putative protein disulfide isomerase from2 nitrosomonas europaea Phyre2 1 c2ko6A_ 2 d2ibge1 3 d1ufwa_ 4 c3m1nB_ 5 d3d1ma1 6 d1iasa_ 7 c1dpuA_ 8 d1dpua_ 9 c2kxhB_ 10 d2cpga_ 11 d2ayxa2 12 c1ygmA_ 13 c2noxP_ 14 d1bl0a2 15 c3kzqE_ 16 c3db3A_ 17 d1r4wa_ 18 d1kz7a2 19 d1aopa4 20 c2in3A_ 21 22 23 24 25

Detailed template information

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

1 c2ko6A_ 100.0 99 PDB header:structural genomics, unknown function Chain: A: PDB Molecule:uncharacterized protein yihd; PDBTitle: solution structure of protein sf3929 from shigella flexneri2 2a. northeast structural genomics consortium target3 sfr81/ontario center for structural proteomics target4 sf3929 2 d2ibge1 29.6 40 Fold:Hedgehog/DD-peptidase Superfamily:Hedgehog/DD-peptidase Family:Hedgehog (development protein), N-terminal signaling domain 3 d1ufwa_ 29.3 31 Fold:Ferredoxin-like Superfamily:RNA-binding domain, RBD Family:Canonical RBD 4 c3m1nB_ 25.7 40 PDB header:signaling protein Chain: B: PDB Molecule:sonic hedgehog protein; PDBTitle: crystal structure of human sonic hedgehog n-terminal domain 5 d3d1ma1 24.7 40 Fold:Hedgehog/DD-peptidase Superfamily:Hedgehog/DD-peptidase Family:Hedgehog (development protein), N-terminal signaling domain 6 d1iasa_ 15.6 19 Fold:Protein kinase-like (PK-like) Superfamily:Protein kinase-like (PK-like) Family:Protein kinases, catalytic subunit 7 c1dpuA_ 13.9 22 PDB header:dna binding protein Chain: A: PDB Molecule:replication protein a (rpa32) c-terminal domain; PDBTitle: solution structure of the c-terminal domain of human rpa322 complexed with ung2(73-88) 8 d1dpua_ 13.9 22 Fold:DNA/RNA-binding 3-helical bundle Superfamily:"Winged helix" DNA-binding domain Family:C-terminal domain of RPA32 9 c2kxhB_ 10.6 54 PDB header:protein binding Chain: B: PDB Molecule:peptide of far upstream element-binding protein 1; PDBTitle: solution structure of the first two rrm domains of fir in the complex2 with fbp nbox peptide 10 d2cpga_ 10.1 35 Fold:Ribbon-helix-helix Superfamily:Ribbon-helix-helix Family:CopG-like 11 d2ayxa2 10.1 32 Fold:Flavodoxin-like Superfamily:CheY-like Family:RcsC linker domain-like 12 c1ygmA_ 9.1 39 PDB header:membrane protein Chain: A: PDB Molecule:hypothetical protein bsu31320; PDBTitle: nmr structure of mistic 13 c2noxP_ 8.6 22 PDB header:oxidoreductase Chain: P: PDB Molecule:tryptophan 2,3-dioxygenase; PDBTitle: crystal structure of tryptophan 2,3-dioxygenase from ralstonia2 metallidurans 14 d1bl0a2 7.9 31 Fold:DNA/RNA-binding 3-helical bundle Superfamily:Homeodomain-like Family:AraC type transcriptional activator 15 c3kzqE_ 7.7 17 PDB header:structural genomics, unknown function Chain: E: PDB Molecule:putative uncharacterized protein vp2116; PDBTitle: the crystal structure of the protein with unknown function from vibrio2 parahaemolyticus rimd 2210633 16 c3db3A_ 7.5 33 PDB header:ligase Chain: A: PDB Molecule:e3 ubiquitin-protein ligase uhrf1; PDBTitle: crystal structure of the tandem tudor domains of the e3 ubiquitin-2 protein ligase uhrf1 in complex with trimethylated histone h3-k93 peptide 17 d1r4wa_ 7.3 22 Fold:Thioredoxin fold Superfamily:Thioredoxin-like Family:DsbA-like 18 d1kz7a2 7.2 44 Fold:PH domain-like barrel Superfamily:PH domain-like Family:Pleckstrin-homology domain (PH domain) 19 d1aopa4 6.9 18 Fold:Nitrite and sulphite reductase 4Fe-4S domain-like Superfamily:Nitrite and sulphite reductase 4Fe-4S domain-like Family:Nitrite and sulphite reductase 4Fe-4S domain-like 20 c2in3A_ 6.9 25 PDB header:isomerase Chain: A: PDB Molecule:hypothetical protein; PDBTitle: crystal structure of a putative protein disulfide isomerase from2 nitrosomonas europaea 21 c1yzxB_ not modelled 6.3 25 PDB header:transferase Chain: B: PDB Molecule:glutathione s-transferase kappa 1; PDBTitle: crystal structure of human kappa class glutathione2 transferase 22 c2nw7C_ not modelled 5.3 24 PDB header:oxidoreductase Chain: C: PDB Molecule:tryptophan 2,3-dioxygenase; PDBTitle: crystal structure of tryptophan 2,3-dioxygenase (tdo) from2 xanthomonas campestris in complex with ferric heme.3 northeast structural genomics target xcr13 23 c2htfA_ not modelled 5.2 50 PDB header:transferase Chain: A: PDB Molecule:dna polymerase mu; PDBTitle: the solution structure of the brct domain from human2 polymerase reveals homology with the tdt brct domain 24 d2ivya1 not modelled 5.1 21 Fold:Ferredoxin-like Superfamily:TTP0101/SSO1404-like Family:TTP0101/SSO1404-like 25 d1d5ya2 not modelled 5.1 24 Fold:DNA/RNA-binding 3-helical bundle Superfamily:Homeodomain-like Family:AraC type transcriptional activator

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