Secondary structure and disorder prediction

		1	.	.	.	.	.	.	.	.	10	.	.	.	.	.	.	.	.	.	20	.	.	.	.	.	.	.	.	.	30	.	.	.	.	.	.	.	.	.	40	.	.	.	.	.	.	.	.	.	50	.	.	.	.	.	.	.	.	.	60
Sequence		I	N	N	W	N	L	L	P	L	I	C	L	L	S	G	C	H	F	Y	R	E	R	F	A	E	R	G	F	F	Y	K	V	P	D	V	L	R	D	Y	L	S	A	I	P	L	E	I	N	E	K	A	R	Y	K	P	G	I	A	N	Y
Secondary structure
SS confidence
Disorder		?	?	?																											?	?										?	?	?	?	?	?	?	?	?	?	?	?	?	?	?	?	?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	70	.	.	.	.	.	.	.	.	.	80	.	.	.	.	.	.	.	.	.	90	.	.	.	.	.	.	.	.	.	100	.	.	.	.	.	.	.	.	.	110	.	.	.	.	.	.	.	.	.	120
Sequence		H	N	I	I	T	C	G	F	S	T	L	L	P	Y	I	R	Q	Q	P	L	A	M	Q	Q	R	F	N	L	L	F	P	D	F	V	D	H	I	Q	S	P	L	P	L	A	S	T	L	L	E	R	I	T	F	Y	A	K	K	N	R	D
Secondary structure
SS confidence
Disorder																		?	?	?																		?	?	?	?	?	?	?	?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	130	.	.
Sequence		E	L	D	K	I	S	C	K	W	C	C	D
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 1pp7 chain U Region: 108 - 132 Aligned: 25 Modelled: 25 Confidence: 54.5% Identity: 24% Fold: DNA/RNA-binding 3-helical bundle Superfamily: "Winged helix" DNA-binding domain Family: 39 kda initiator binding protein, IBP39, N-terminal domain Phyre2 PDB 2ga1 chain A domain 1 Region: 108 - 124 Aligned: 17 Modelled: 17 Confidence: 20.8% Identity: 24% Fold: DNA/RNA-binding 3-helical bundle Superfamily: Homeodomain-like Family: Alr1493-like Phyre2 PDB 3s81 chain A Region: 86 - 121 Aligned: 36 Modelled: 36 Confidence: 12.8% Identity: 8% PDB header:isomerase Chain: A: PDB Molecule:putative aspartate racemase; PDBTitle: crystal structure of putative aspartate racemase from salmonella2 typhimurium Phyre2 PDB 2i4c chain A Region: 113 - 132 Aligned: 20 Modelled: 20 Confidence: 10.5% Identity: 25% PDB header:transport protein Chain: A: PDB Molecule:bicarbonate transporter; PDBTitle: crystal structure of bicarbonate transport protein cmpa from2 synechocystis sp. pcc 6803 in complex with bicarbonate and calcium Phyre2 PDB 2fhw chain A Region: 127 - 131 Aligned: 5 Modelled: 5 Confidence: 6.9% Identity: 80% PDB header:signaling protein Chain: A: PDB Molecule:relaxin 3 (prorelaxin h3) (insulin-like peptide PDBTitle: solution structure of human relaxin-3 Phyre2 PDB 2g29 chain A Region: 113 - 132 Aligned: 20 Modelled: 20 Confidence: 6.7% Identity: 15% PDB header:transport protein Chain: A: PDB Molecule:nitrate transport protein nrta; PDBTitle: crystal structure of the periplasmic nitrate-binding2 protein nrta from synechocystis pcc 6803 Phyre2 PDB 1sxj chain A domain 1 Region: 3 - 13 Aligned: 11 Modelled: 11 Confidence: 6.2% Identity: 55% Fold: post-AAA+ oligomerization domain-like Superfamily: post-AAA+ oligomerization domain-like Family: DNA polymerase III clamp loader subunits, C-terminal domain Phyre2 PDB 2h7a chain A domain 1 Region: 20 - 34 Aligned: 15 Modelled: 15 Confidence: 5.9% Identity: 20% Fold: YcgL-like Superfamily: YcgL-like Family: YcgL-like Phyre2 PDB 1xkp chain C domain 1 Region: 106 - 122 Aligned: 17 Modelled: 17 Confidence: 5.8% Identity: 24% Fold: Secretion chaperone-like Superfamily: Type III secretory system chaperone-like Family: Type III secretory system chaperone Phyre2 PDB 1itw chain A Region: 113 - 126 Aligned: 14 Modelled: 14 Confidence: 5.8% Identity: 29% Fold: Isocitrate/Isopropylmalate dehydrogenase-like Superfamily: Isocitrate/Isopropylmalate dehydrogenase-like Family: Monomeric isocitrate dehydrogenase Phyre2 PDB 2b0t chain A Region: 113 - 126 Aligned: 14 Modelled: 14 Confidence: 5.3% Identity: 21% PDB header:oxidoreductase Chain: A: PDB Molecule:nadp isocitrate dehydrogenase; PDBTitle: structure of monomeric nadp isocitrate dehydrogenase Phyre2 1 d1pp7u_ 2 d2ga1a1 3 c3s81A_ 4 c2i4cA_ 5 c2fhwA_ 6 c2g29A_ 7 d1sxja1 8 d2h7aa1 9 d1xkpc1 10 d1itwa_ 11 c2b0tA_

Detailed template information

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

1 d1pp7u_ 54.5 24 Fold:DNA/RNA-binding 3-helical bundle Superfamily:"Winged helix" DNA-binding domain Family:39 kda initiator binding protein, IBP39, N-terminal domain 2 d2ga1a1 20.8 24 Fold:DNA/RNA-binding 3-helical bundle Superfamily:Homeodomain-like Family:Alr1493-like 3 c3s81A_ 12.8 8 PDB header:isomerase Chain: A: PDB Molecule:putative aspartate racemase; PDBTitle: crystal structure of putative aspartate racemase from salmonella2 typhimurium 4 c2i4cA_ 10.5 25 PDB header:transport protein Chain: A: PDB Molecule:bicarbonate transporter; PDBTitle: crystal structure of bicarbonate transport protein cmpa from2 synechocystis sp. pcc 6803 in complex with bicarbonate and calcium 5 c2fhwA_ 6.9 80 PDB header:signaling protein Chain: A: PDB Molecule:relaxin 3 (prorelaxin h3) (insulin-like peptide PDBTitle: solution structure of human relaxin-3 6 c2g29A_ 6.7 15 PDB header:transport protein Chain: A: PDB Molecule:nitrate transport protein nrta; PDBTitle: crystal structure of the periplasmic nitrate-binding2 protein nrta from synechocystis pcc 6803 7 d1sxja1 6.2 55 Fold:post-AAA+ oligomerization domain-like Superfamily:post-AAA+ oligomerization domain-like Family:DNA polymerase III clamp loader subunits, C-terminal domain 8 d2h7aa1 5.9 20 Fold:YcgL-like Superfamily:YcgL-like Family:YcgL-like 9 d1xkpc1 5.8 24 Fold:Secretion chaperone-like Superfamily:Type III secretory system chaperone-like Family:Type III secretory system chaperone 10 d1itwa_ 5.8 29 Fold:Isocitrate/Isopropylmalate dehydrogenase-like Superfamily:Isocitrate/Isopropylmalate dehydrogenase-like Family:Monomeric isocitrate dehydrogenase 11 c2b0tA_ 5.3 21 PDB header:oxidoreductase Chain: A: PDB Molecule:nadp isocitrate dehydrogenase; PDBTitle: structure of monomeric nadp isocitrate dehydrogenase

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