Secondary structure and disorder prediction

		1	.	.	.	.	.	.	.	.	10	.	.	.	.	.	.	.	.	.	20	.	.	.	.	.	.	.	.	.	30	.	.	.	.	.	.	.	.	.	40	.	.	.	.	.	.	.	.	.	50	.	.	.	.	.	.	.	.	.	60
Sequence		M	K	R	Y	L	R	W	I	V	A	A	E	F	L	F	A	A	G	N	L	H	A	V	E	V	E	V	P	G	L	L	T	D	H	T	V	S	S	I	G	H	D	F	Y	R	A	F	S	D	K	W	E	S	D	Y	T	G	N	L	T
Secondary structure
SS confidence
Disorder		?	?													?							?	?																															?		?		?
Disorder confidence
		.	.	.	.	.	.	.	.	.	70	.	.	.	.	.	.	.	.	.	80	.	.	.	.	.	.	.	.	.	90	.	.	.	.	.	.	.	.	.	100	.	.	.	.	.	.	.	.	.	110	.	.	.	.	.	.	.	.	.	120
Sequence		I	N	E	R	P	S	A	R	W	G	S	W	I	T	I	T	V	N	Q	D	V	I	F	Q	T	F	L	F	P	L	K	R	D	F	E	K	T	V	V	F	A	L	I	Q	T	E	E	A	L	N	R	R	Q	I	N	Q	A	L	L	S
Secondary structure
SS confidence
Disorder						?	?	?	?		?																				?	?	?																										?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.
Sequence		T	G	D	L	A	H	D	E	F
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 1qmh chain A domain 1 Region: 37 - 109 Aligned: 73 Modelled: 73 Confidence: 78.0% Identity: 3% Fold: Thioredoxin fold Superfamily: RNA 3'-terminal phosphate cyclase, RPTC, insert domain Family: RNA 3'-terminal phosphate cyclase, RPTC, insert domain Phyre2 PDB 3fcg chain B Region: 66 - 90 Aligned: 25 Modelled: 25 Confidence: 54.2% Identity: 8% PDB header:membrane protein, protein transport Chain: B: PDB Molecule:f1 capsule-anchoring protein; PDBTitle: crystal structure analysis of the middle domain of the2 caf1a usher Phyre2 PDB 1ixc chain A domain 1 Region: 19 - 49 Aligned: 31 Modelled: 29 Confidence: 17.3% Identity: 19% Fold: DNA/RNA-binding 3-helical bundle Superfamily: "Winged helix" DNA-binding domain Family: LysR-like transcriptional regulators Phyre2 PDB 3ohn chain A Region: 64 - 90 Aligned: 27 Modelled: 27 Confidence: 17.0% Identity: 26% PDB header:membrane protein Chain: A: PDB Molecule:outer membrane usher protein fimd; PDBTitle: crystal structure of the fimd translocation domain Phyre2 PDB 2vqi chain A Region: 64 - 90 Aligned: 27 Modelled: 27 Confidence: 16.7% Identity: 7% PDB header:transport Chain: A: PDB Molecule:outer membrane usher protein papc; PDBTitle: structure of the p pilus usher (papc) translocation pore Phyre2 PDB 2lf0 chain A Region: 27 - 42 Aligned: 16 Modelled: 16 Confidence: 15.2% Identity: 31% PDB header:structural genomics, unknown function Chain: A: PDB Molecule:uncharacterized protein yibl; PDBTitle: solution structure of sf3636, a two-domain unknown function protein2 from shigella flexneri 2a, determined by joint refinement of nmr,3 residual dipolar couplings and small-angle x-ray scatting, nesg4 target sfr339/ocsp target sf3636 Phyre2 PDB 3rfz chain B Region: 64 - 90 Aligned: 27 Modelled: 27 Confidence: 13.3% Identity: 26% PDB header:cell adhesion/transport/chaperone Chain: B: PDB Molecule:outer membrane usher protein, type 1 fimbrial synthesis; PDBTitle: crystal structure of the fimd usher bound to its cognate fimc:fimh2 substrate Phyre2 PDB 2npb chain A Region: 44 - 113 Aligned: 70 Modelled: 70 Confidence: 12.7% Identity: 19% PDB header:oxidoreductase Chain: A: PDB Molecule:selenoprotein w; PDBTitle: nmr solution structure of mouse selw Phyre2 PDB 1vyt chain E Region: 1 - 12 Aligned: 12 Modelled: 12 Confidence: 10.8% Identity: 58% PDB header:transport protein Chain: E: PDB Molecule:voltage-dependent l-type calcium channel PDBTitle: beta3 subunit complexed with aid Phyre2 PDB 2eny chain A Region: 58 - 70 Aligned: 13 Modelled: 13 Confidence: 10.3% Identity: 31% PDB header:contractile protein Chain: A: PDB Molecule:obscurin; PDBTitle: solution structure of the ig-like domain (2735-2825) of2 human obscurin Phyre2 PDB 1bw8 chain A Region: 51 - 88 Aligned: 38 Modelled: 38 Confidence: 8.5% Identity: 26% PDB header:peptide binding protein Chain: A: PDB Molecule:protein (mu2 adaptin subunit); PDBTitle: mu2 adaptin subunit (ap50) of ap2 adaptor (second domain),2 complexed with egfr internalization peptide fyralm Phyre2 PDB 2pr9 chain A domain 1 Region: 51 - 88 Aligned: 38 Modelled: 38 Confidence: 7.4% Identity: 26% Fold: Common fold of diphtheria toxin/transcription factors/cytochrome f Superfamily: Second domain of Mu2 adaptin subunit (ap50) of ap2 adaptor Family: Second domain of Mu2 adaptin subunit (ap50) of ap2 adaptor Phyre2 PDB 1vyt chain F Region: 1 - 14 Aligned: 14 Modelled: 12 Confidence: 7.3% Identity: 50% PDB header:transport protein Chain: F: PDB Molecule:voltage-dependent l-type calcium channel PDBTitle: beta3 subunit complexed with aid Phyre2 PDB 2wtg chain A Region: 32 - 51 Aligned: 20 Modelled: 20 Confidence: 6.4% Identity: 30% PDB header:oxygen transport Chain: A: PDB Molecule:globin-like protein; PDBTitle: high resolution 3d structure of c.elegans globin-like2 protein glb-1 Phyre2 PDB 3q13 chain A Region: 64 - 99 Aligned: 36 Modelled: 36 Confidence: 6.1% Identity: 8% PDB header:cell adhesion Chain: A: PDB Molecule:spondin-1; PDBTitle: the structure of the ca2+-binding, glycosylated f-spondin domain of f-2 spondin, a c2-domain variant from extracellular matrix Phyre2 PDB 1zh5 chain A domain 1 Region: 11 - 24 Aligned: 14 Modelled: 14 Confidence: 5.8% Identity: 29% Fold: DNA/RNA-binding 3-helical bundle Superfamily: "Winged helix" DNA-binding domain Family: La domain Phyre2 PDB 1wu9 chain A domain 1 Region: 41 - 45 Aligned: 5 Modelled: 5 Confidence: 5.8% Identity: 60% Fold: EB1 dimerisation domain-like Superfamily: EB1 dimerisation domain-like Family: EB1 dimerisation domain-like Phyre2 PDB 3gr1 chain A Region: 27 - 62 Aligned: 35 Modelled: 36 Confidence: 5.3% Identity: 17% PDB header:membrane protein Chain: A: PDB Molecule:protein prgh; PDBTitle: periplamic domain of the t3ss inner membrane protein prgh2 from s.typhimurium (fragment 170-392) Phyre2 PDB 2dag chain A Region: 95 - 128 Aligned: 34 Modelled: 34 Confidence: 5.1% Identity: 12% PDB header:hydrolase Chain: A: PDB Molecule:ubiquitin carboxyl-terminal hydrolase 5; PDBTitle: solution structure of the first uba domain in the human2 ubiquitin specific protease 5 (isopeptidase 5) Phyre2 PDB 1nw1 chain A Region: 20 - 108 Aligned: 89 Modelled: 89 Confidence: 5.1% Identity: 9% PDB header:transferase Chain: A: PDB Molecule:choline kinase (49.2 kd); PDBTitle: crystal structure of choline kinase Phyre2 1 d1qmha1 2 c3fcgB_ 3 d1ixca1 4 c3ohnA_ 5 c2vqiA_ 6 c2lf0A_ 7 c3rfzB_ 8 c2npbA_ 9 c1vytE_ 10 c2enyA_ 11 c1bw8A_ 12 d2pr9a1 13 c1vytF_ 14 c2wtgA_ 15 c3q13A_ 16 d1zh5a1 17 d1wu9a1 18 c3gr1A_ 19 c2dagA_ 20 c1nw1A_ 21

Detailed template information

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

1 d1qmha1 78.0 3 Fold:Thioredoxin fold Superfamily:RNA 3'-terminal phosphate cyclase, RPTC, insert domain Family:RNA 3'-terminal phosphate cyclase, RPTC, insert domain 2 c3fcgB_ 54.2 8 PDB header:membrane protein, protein transport Chain: B: PDB Molecule:f1 capsule-anchoring protein; PDBTitle: crystal structure analysis of the middle domain of the2 caf1a usher 3 d1ixca1 17.3 19 Fold:DNA/RNA-binding 3-helical bundle Superfamily:"Winged helix" DNA-binding domain Family:LysR-like transcriptional regulators 4 c3ohnA_ 17.0 26 PDB header:membrane protein Chain: A: PDB Molecule:outer membrane usher protein fimd; PDBTitle: crystal structure of the fimd translocation domain 5 c2vqiA_ 16.7 7 PDB header:transport Chain: A: PDB Molecule:outer membrane usher protein papc; PDBTitle: structure of the p pilus usher (papc) translocation pore 6 c2lf0A_ 15.2 31 PDB header:structural genomics, unknown function Chain: A: PDB Molecule:uncharacterized protein yibl; PDBTitle: solution structure of sf3636, a two-domain unknown function protein2 from shigella flexneri 2a, determined by joint refinement of nmr,3 residual dipolar couplings and small-angle x-ray scatting, nesg4 target sfr339/ocsp target sf3636 7 c3rfzB_ 13.3 26 PDB header:cell adhesion/transport/chaperone Chain: B: PDB Molecule:outer membrane usher protein, type 1 fimbrial synthesis; PDBTitle: crystal structure of the fimd usher bound to its cognate fimc:fimh2 substrate 8 c2npbA_ 12.7 19 PDB header:oxidoreductase Chain: A: PDB Molecule:selenoprotein w; PDBTitle: nmr solution structure of mouse selw 9 c1vytE_ 10.8 58 PDB header:transport protein Chain: E: PDB Molecule:voltage-dependent l-type calcium channel PDBTitle: beta3 subunit complexed with aid 10 c2enyA_ 10.3 31 PDB header:contractile protein Chain: A: PDB Molecule:obscurin; PDBTitle: solution structure of the ig-like domain (2735-2825) of2 human obscurin 11 c1bw8A_ 8.5 26 PDB header:peptide binding protein Chain: A: PDB Molecule:protein (mu2 adaptin subunit); PDBTitle: mu2 adaptin subunit (ap50) of ap2 adaptor (second domain),2 complexed with egfr internalization peptide fyralm 12 d2pr9a1 7.4 26 Fold:Common fold of diphtheria toxin/transcription factors/cytochrome f Superfamily:Second domain of Mu2 adaptin subunit (ap50) of ap2 adaptor Family:Second domain of Mu2 adaptin subunit (ap50) of ap2 adaptor 13 c1vytF_ 7.3 50 PDB header:transport protein Chain: F: PDB Molecule:voltage-dependent l-type calcium channel PDBTitle: beta3 subunit complexed with aid 14 c2wtgA_ 6.4 30 PDB header:oxygen transport Chain: A: PDB Molecule:globin-like protein; PDBTitle: high resolution 3d structure of c.elegans globin-like2 protein glb-1 15 c3q13A_ 6.1 8 PDB header:cell adhesion Chain: A: PDB Molecule:spondin-1; PDBTitle: the structure of the ca2+-binding, glycosylated f-spondin domain of f-2 spondin, a c2-domain variant from extracellular matrix 16 d1zh5a1 5.8 29 Fold:DNA/RNA-binding 3-helical bundle Superfamily:"Winged helix" DNA-binding domain Family:La domain 17 d1wu9a1 5.8 60 Fold:EB1 dimerisation domain-like Superfamily:EB1 dimerisation domain-like Family:EB1 dimerisation domain-like 18 c3gr1A_ 5.3 17 PDB header:membrane protein Chain: A: PDB Molecule:protein prgh; PDBTitle: periplamic domain of the t3ss inner membrane protein prgh2 from s.typhimurium (fragment 170-392) 19 c2dagA_ 5.1 12 PDB header:hydrolase Chain: A: PDB Molecule:ubiquitin carboxyl-terminal hydrolase 5; PDBTitle: solution structure of the first uba domain in the human2 ubiquitin specific protease 5 (isopeptidase 5) 20 c1nw1A_ 5.1 9 PDB header:transferase Chain: A: PDB Molecule:choline kinase (49.2 kd); PDBTitle: crystal structure of choline kinase 21 d1nw1a_ not modelled 5.1 9 Fold:Protein kinase-like (PK-like) Superfamily:Protein kinase-like (PK-like) Family:Choline kinase

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