Secondary structure and disorder prediction

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Sequence		M	T	P	A	F	A	S	W	N	E	F	F	A	M	G	G	Y	A	F	F	V	W	L	A	V	V	M	T	V	I	P	L	V	V	L	V	V	H	S	V	M	Q	H	R	A	I	L	R	G	V	A	Q	Q	R	A	R	E	A	R	L
Secondary structure
SS confidence
Disorder		?	?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.
Sequence		R	A	A	Q	Q	Q	E	A	A
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 1e8o chain A Region: 3 - 13 Aligned: 11 Modelled: 11 Confidence: 36.4% Identity: 36% Fold: Signal recognition particle alu RNA binding heterodimer, SRP9/14 Superfamily: Signal recognition particle alu RNA binding heterodimer, SRP9/14 Family: Signal recognition particle alu RNA binding heterodimer, SRP9/14 Phyre2 PDB 2knc chain B Region: 13 - 64 Aligned: 52 Modelled: 52 Confidence: 18.0% Identity: 19% PDB header:cell adhesion Chain: B: PDB Molecule:integrin beta-3; PDBTitle: platelet integrin alfaiib-beta3 transmembrane-cytoplasmic2 heterocomplex Phyre2 PDB 1q88 chain B Region: 4 - 15 Aligned: 12 Modelled: 12 Confidence: 15.2% Identity: 33% PDB header:dna binding protein Chain: B: PDB Molecule:39 kda initiator binding protein; PDBTitle: crystal structure of the c-domain of the t.vaginalis inr2 binding protein, ibp39 (monoclinic form) Phyre2 PDB 1q88 chain A Region: 4 - 14 Aligned: 11 Modelled: 11 Confidence: 13.1% Identity: 36% Fold: 39 kda initiator binding protein, IBP39, C-terminal domains Superfamily: 39 kda initiator binding protein, IBP39, C-terminal domains Family: 39 kda initiator binding protein, IBP39, C-terminal domains Phyre2 PDB 2fv2 chain A Region: 18 - 32 Aligned: 15 Modelled: 15 Confidence: 12.2% Identity: 20% PDB header:transcription Chain: A: PDB Molecule:rcd1 required for cell differentiation1 homolog; PDBTitle: crystal structure analysis of human rcd-1 conserved region Phyre2 PDB 1nek chain D Region: 13 - 40 Aligned: 28 Modelled: 28 Confidence: 12.1% Identity: 25% Fold: Heme-binding four-helical bundle Superfamily: Fumarate reductase respiratory complex transmembrane subunits Family: Succinate dehydrogenase/Fumarate reductase transmembrane subunits (SdhC/FrdC and SdhD/FrdD) Phyre2 PDB 3hlz chain A Region: 22 - 35 Aligned: 14 Modelled: 14 Confidence: 10.1% Identity: 36% PDB header:structural genomics, unknown function Chain: A: PDB Molecule:uncharacterized protein bt_1490; PDBTitle: crystal structure of bt_1490 (np_810393.1) from bacteroides2 thetaiotaomicron vpi-5482 at 1.50 a resolution Phyre2 PDB 1914 chain A domain 1 Region: 5 - 13 Aligned: 9 Modelled: 9 Confidence: 9.3% Identity: 44% Fold: Signal recognition particle alu RNA binding heterodimer, SRP9/14 Superfamily: Signal recognition particle alu RNA binding heterodimer, SRP9/14 Family: Signal recognition particle alu RNA binding heterodimer, SRP9/14 Phyre2 PDB 1s5r chain A Region: 10 - 26 Aligned: 17 Modelled: 17 Confidence: 8.5% Identity: 24% PDB header:transcription Chain: A: PDB Molecule:high mobility group box transcription factor 1; PDBTitle: solution structure of hbp1 sid-msin3a pah2 complex Phyre2 PDB 1914 chain A Region: 5 - 13 Aligned: 9 Modelled: 9 Confidence: 8.1% Identity: 44% PDB header:alu domain Chain: A: PDB Molecule:signal recognition particle 9/14 fusion protein; PDBTitle: signal recognition particle alu rna binding heterodimer, srp9/14 Phyre2 PDB 3m4r chain A Region: 14 - 42 Aligned: 29 Modelled: 29 Confidence: 8.0% Identity: 3% PDB header:structural genomics, unknown function Chain: A: PDB Molecule:uncharacterized protein; PDBTitle: structure of the n-terminal class ii aldolase domain of a conserved2 protein from thermoplasma acidophilum Phyre2 PDB 3s8m chain A Region: 3 - 23 Aligned: 21 Modelled: 21 Confidence: 7.6% Identity: 19% PDB header:oxidoreductase Chain: A: PDB Molecule:enoyl-acp reductase; PDBTitle: the crystal structure of fabv Phyre2 PDB 2cq8 chain A Region: 10 - 17 Aligned: 8 Modelled: 8 Confidence: 6.4% Identity: 38% PDB header:oxidoreductase Chain: A: PDB Molecule:10-formyltetrahydrofolate dehydrogenase; PDBTitle: solution structure of rsgi ruh-033, a pp-binding domain of2 10-fthfdh from human cdna Phyre2 PDB 2je6 chain I domain 2 Region: 14 - 21 Aligned: 8 Modelled: 8 Confidence: 5.9% Identity: 0% Fold: Barrel-sandwich hybrid Superfamily: Ribosomal L27 protein-like Family: ECR1 N-terminal domain-like Phyre2 PDB 2fk5 chain B Region: 14 - 52 Aligned: 39 Modelled: 39 Confidence: 5.7% Identity: 13% PDB header:lyase Chain: B: PDB Molecule:fuculose-1-phosphate aldolase; PDBTitle: crystal structure of l-fuculose-1-phosphate aldolase from thermus2 thermophilus hb8 Phyre2 PDB 1sgg chain A Region: 3 - 21 Aligned: 19 Modelled: 19 Confidence: 5.6% Identity: 11% Fold: SAM domain-like Superfamily: SAM/Pointed domain Family: SAM (sterile alpha motif) domain Phyre2 1 d1e8oa_ 2 c2kncB_ 3 c1q88B_ 4 d1q88a_ 5 c2fv2A_ 6 d1nekd_ 7 c3hlzA_ 8 d1914a1 9 c1s5rA_ 10 c1914A_ 11 c3m4rA_ 12 c3s8mA_ 13 c2cq8A_ 14 d2je6i2 15 c2fk5B_ 16 d1sgga_

Detailed template information

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

1 d1e8oa_ 36.4 36 Fold:Signal recognition particle alu RNA binding heterodimer, SRP9/14 Superfamily:Signal recognition particle alu RNA binding heterodimer, SRP9/14 Family:Signal recognition particle alu RNA binding heterodimer, SRP9/14 2 c2kncB_ 18.0 19 PDB header:cell adhesion Chain: B: PDB Molecule:integrin beta-3; PDBTitle: platelet integrin alfaiib-beta3 transmembrane-cytoplasmic2 heterocomplex 3 c1q88B_ 15.2 33 PDB header:dna binding protein Chain: B: PDB Molecule:39 kda initiator binding protein; PDBTitle: crystal structure of the c-domain of the t.vaginalis inr2 binding protein, ibp39 (monoclinic form) 4 d1q88a_ 13.1 36 Fold:39 kda initiator binding protein, IBP39, C-terminal domains Superfamily:39 kda initiator binding protein, IBP39, C-terminal domains Family:39 kda initiator binding protein, IBP39, C-terminal domains 5 c2fv2A_ 12.2 20 PDB header:transcription Chain: A: PDB Molecule:rcd1 required for cell differentiation1 homolog; PDBTitle: crystal structure analysis of human rcd-1 conserved region 6 d1nekd_ 12.1 25 Fold:Heme-binding four-helical bundle Superfamily:Fumarate reductase respiratory complex transmembrane subunits Family:Succinate dehydrogenase/Fumarate reductase transmembrane subunits (SdhC/FrdC and SdhD/FrdD) 7 c3hlzA_ 10.1 36 PDB header:structural genomics, unknown function Chain: A: PDB Molecule:uncharacterized protein bt_1490; PDBTitle: crystal structure of bt_1490 (np_810393.1) from bacteroides2 thetaiotaomicron vpi-5482 at 1.50 a resolution 8 d1914a1 9.3 44 Fold:Signal recognition particle alu RNA binding heterodimer, SRP9/14 Superfamily:Signal recognition particle alu RNA binding heterodimer, SRP9/14 Family:Signal recognition particle alu RNA binding heterodimer, SRP9/14 9 c1s5rA_ 8.5 24 PDB header:transcription Chain: A: PDB Molecule:high mobility group box transcription factor 1; PDBTitle: solution structure of hbp1 sid-msin3a pah2 complex 10 c1914A_ 8.1 44 PDB header:alu domain Chain: A: PDB Molecule:signal recognition particle 9/14 fusion protein; PDBTitle: signal recognition particle alu rna binding heterodimer, srp9/14 11 c3m4rA_ 8.0 3 PDB header:structural genomics, unknown function Chain: A: PDB Molecule:uncharacterized protein; PDBTitle: structure of the n-terminal class ii aldolase domain of a conserved2 protein from thermoplasma acidophilum 12 c3s8mA_ 7.6 19 PDB header:oxidoreductase Chain: A: PDB Molecule:enoyl-acp reductase; PDBTitle: the crystal structure of fabv 13 c2cq8A_ 6.4 38 PDB header:oxidoreductase Chain: A: PDB Molecule:10-formyltetrahydrofolate dehydrogenase; PDBTitle: solution structure of rsgi ruh-033, a pp-binding domain of2 10-fthfdh from human cdna 14 d2je6i2 5.9 0 Fold:Barrel-sandwich hybrid Superfamily:Ribosomal L27 protein-like Family:ECR1 N-terminal domain-like 15 c2fk5B_ 5.7 13 PDB header:lyase Chain: B: PDB Molecule:fuculose-1-phosphate aldolase; PDBTitle: crystal structure of l-fuculose-1-phosphate aldolase from thermus2 thermophilus hb8 16 d1sgga_ 5.6 11 Fold:SAM domain-like Superfamily:SAM/Pointed domain Family:SAM (sterile alpha motif) 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