Secondary structure and disorder prediction

		1	.	.	.	.	.	.	.	.	10	.	.	.	.	.	.	.	.	.	20	.	.	.	.	.	.	.	.	.	30	.	.	.	.	.	.	.	.	.	40	.	.	.	.	.	.	.	.	.	50	.	.	.	.	.	.	.	.	.	60
Sequence		M	T	D	Y	A	I	S	K	K	S	K	R	S	L	W	I	P	I	L	V	F	I	T	L	A	A	C	A	S	A	G	Y	S	Y	W	H	S	H	Q	V	A	A	D	D	K	A	Q	Q	R	V	V	P	S	P	V	F	Y	A	L	D
Secondary structure
SS confidence
Disorder		?	?	?	?	?	?	?	?	?	?	?																											?	?	?	?	?	?	?	?	?	?	?	?	?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	70	.	.	.	.	.	.	.	.	.	80	.	.	.	.	.	.	.	.	.	90	.	.	.	.	.	.	.	.	.	100	.	.	.	.	.	.	.	.	.	110	.	.	.	.	.	.	.	.	.	120
Sequence		T	F	T	V	N	L	G	D	A	D	R	V	L	Y	I	G	I	T	L	R	L	K	D	E	A	T	R	S	R	L	S	E	Y	L	P	E	V	R	S	R	L	L	L	L	F	S	R	Q	D	A	A	V	L	A	T	E	E	G	K	K
Secondary structure
SS confidence
Disorder																																	?																?	?				?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	130	.	.	.	.	.	.	.	.	.	140	.	.	.	.	.	.	.	.	.	150	.	.	.	.
Sequence		N	L	I	A	E	I	K	T	T	L	S	T	P	L	V	A	G	Q	P	K	Q	D	V	T	D	V	L	Y	T	A	F	I	L	R
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 2rrl chain A Region: 58 - 101 Aligned: 42 Modelled: 44 Confidence: 60.7% Identity: 21% PDB header:protein transport Chain: A: PDB Molecule:flagellar hook-length control protein; PDBTitle: solution structure of the c-terminal domain of the flik Phyre2 PDB 2rpb chain A Region: 57 - 151 Aligned: 91 Modelled: 95 Confidence: 42.9% Identity: 11% PDB header:membrane protein Chain: A: PDB Molecule:hypothetical membrane protein; PDBTitle: the solution structure of membrane protein Phyre2 PDB 3bk6 chain C Region: 57 - 151 Aligned: 91 Modelled: 95 Confidence: 42.7% Identity: 10% PDB header:membrane protein Chain: C: PDB Molecule:ph stomatin; PDBTitle: crystal structure of a core domain of stomatin from2 pyrococcus horikoshii Phyre2 PDB 3gxq chain B Region: 95 - 126 Aligned: 31 Modelled: 32 Confidence: 33.3% Identity: 13% PDB header:dna binding protein/dna Chain: B: PDB Molecule:putative regulator of transfer genes arta; PDBTitle: structure of arta and dna complex Phyre2 PDB 3u5g chain B Region: 62 - 150 Aligned: 81 Modelled: 88 Confidence: 19.7% Identity: 19% PDB header:ribosome Chain: B: PDB Molecule:40s ribosomal protein s1-a; PDBTitle: the structure of the eukaryotic ribosome at 3.0 a resolution Phyre2 PDB 1win chain A Region: 41 - 151 Aligned: 107 Modelled: 111 Confidence: 13.2% Identity: 7% Fold: EF-Ts domain-like Superfamily: Band 7/SPFH domain Family: Band 7/SPFH domain Phyre2 PDB 2xzm chain 4 Region: 62 - 150 Aligned: 81 Modelled: 89 Confidence: 11.0% Identity: 9% PDB header:ribosome Chain: 4: PDB Molecule:40s ribosomal protein s3a; PDBTitle: crystal structure of the eukaryotic 40s ribosomal2 subunit in complex with initiation factor 1. this file3 contains the 40s subunit and initiation factor for4 molecule 1 Phyre2 PDB 2od5 chain A domain 1 Region: 93 - 147 Aligned: 44 Modelled: 55 Confidence: 7.5% Identity: 20% Fold: DNA/RNA-binding 3-helical bundle Superfamily: "Winged helix" DNA-binding domain Family: Marine metagenome family WH1 Phyre2 PDB 2od5 chain A Region: 93 - 147 Aligned: 44 Modelled: 55 Confidence: 7.5% Identity: 20% PDB header:dna binding protein Chain: A: PDB Molecule:hypothetical protein; PDBTitle: crystal structure of a putative nucleic acid binding protein2 (jcvi_pep_1096688149193) from uncultured marine organism at 1.79 a3 resolution Phyre2 PDB 3dyd chain B Region: 95 - 150 Aligned: 52 Modelled: 52 Confidence: 7.1% Identity: 21% PDB header:transferase Chain: B: PDB Molecule:tyrosine aminotransferase; PDBTitle: human tyrosine aminotransferase Phyre2 PDB 2dyj chain A domain 1 Region: 64 - 101 Aligned: 38 Modelled: 38 Confidence: 6.1% Identity: 21% Fold: Alpha-lytic protease prodomain-like Superfamily: Ribosome-binding factor A, RbfA Family: Ribosome-binding factor A, RbfA Phyre2 PDB 3pdx chain A Region: 95 - 150 Aligned: 52 Modelled: 52 Confidence: 5.5% Identity: 19% PDB header:transferase Chain: A: PDB Molecule:tyrosine aminotransferase; PDBTitle: crystal structural of mouse tyrosine aminotransferase Phyre2 1 c2rrlA_ 2 c2rpbA_ 3 c3bk6C_ 4 c3gxqB_ 5 c3u5gB_ 6 d1wina_ 7 c2xzm4_ 8 d2od5a1 9 c2od5A_ 10 c3dydB_ 11 d2dyja1 12 c3pdxA_

Detailed template information

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

1 c2rrlA_ 60.7 21 PDB header:protein transport Chain: A: PDB Molecule:flagellar hook-length control protein; PDBTitle: solution structure of the c-terminal domain of the flik 2 c2rpbA_ 42.9 11 PDB header:membrane protein Chain: A: PDB Molecule:hypothetical membrane protein; PDBTitle: the solution structure of membrane protein 3 c3bk6C_ 42.7 10 PDB header:membrane protein Chain: C: PDB Molecule:ph stomatin; PDBTitle: crystal structure of a core domain of stomatin from2 pyrococcus horikoshii 4 c3gxqB_ 33.3 13 PDB header:dna binding protein/dna Chain: B: PDB Molecule:putative regulator of transfer genes arta; PDBTitle: structure of arta and dna complex 5 c3u5gB_ 19.7 19 PDB header:ribosome Chain: B: PDB Molecule:40s ribosomal protein s1-a; PDBTitle: the structure of the eukaryotic ribosome at 3.0 a resolution 6 d1wina_ 13.2 7 Fold:EF-Ts domain-like Superfamily:Band 7/SPFH domain Family:Band 7/SPFH domain 7 c2xzm4_ 11.0 9 PDB header:ribosome Chain: 4: PDB Molecule:40s ribosomal protein s3a; PDBTitle: crystal structure of the eukaryotic 40s ribosomal2 subunit in complex with initiation factor 1. this file3 contains the 40s subunit and initiation factor for4 molecule 1 8 d2od5a1 7.5 20 Fold:DNA/RNA-binding 3-helical bundle Superfamily:"Winged helix" DNA-binding domain Family:Marine metagenome family WH1 9 c2od5A_ 7.5 20 PDB header:dna binding protein Chain: A: PDB Molecule:hypothetical protein; PDBTitle: crystal structure of a putative nucleic acid binding protein2 (jcvi_pep_1096688149193) from uncultured marine organism at 1.79 a3 resolution 10 c3dydB_ 7.1 21 PDB header:transferase Chain: B: PDB Molecule:tyrosine aminotransferase; PDBTitle: human tyrosine aminotransferase 11 d2dyja1 6.1 21 Fold:Alpha-lytic protease prodomain-like Superfamily:Ribosome-binding factor A, RbfA Family:Ribosome-binding factor A, RbfA 12 c3pdxA_ 5.5 19 PDB header:transferase Chain: A: PDB Molecule:tyrosine aminotransferase; PDBTitle: crystal structural of mouse tyrosine aminotransferase

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