Secondary structure and disorder prediction

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Sequence		M	K	T	L	L	P	N	V	N	T	S	E	G	C	F	E	I	G	V	T	I	S	N	P	V	F	T	E	D	A	I	N	K	R	K	Q	E	R	E	L	L	N	K	I	C	I	V	S	M	L	A	R	L	R	L	M	P	K	G	C
Secondary structure
SS confidence
Disorder		?	?	?	?	?	?	?			?																																																		?
Disorder confidence
		.	.
Sequence		A	Q
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 1xdp chain A domain 3 Region: 7 - 32 Aligned: 26 Modelled: 26 Confidence: 27.5% Identity: 12% Fold: Phospholipase D/nuclease Superfamily: Phospholipase D/nuclease Family: Polyphosphate kinase C-terminal domain Phyre2 PDB 2p62 chain A domain 1 Region: 26 - 53 Aligned: 28 Modelled: 28 Confidence: 22.9% Identity: 18% Fold: PH0156-like Superfamily: PH0156-like Family: PH0156-like Phyre2 PDB 2k6l chain A Region: 26 - 38 Aligned: 13 Modelled: 13 Confidence: 16.6% Identity: 46% PDB header:unknown function Chain: A: PDB Molecule:putative uncharacterized protein; PDBTitle: the solution structure of xacb0070 from xanthonomas2 axonopodis pv citri reveals this new protein is a member of3 the rhh family of transcriptional repressors Phyre2 PDB 1oxj chain A Region: 16 - 54 Aligned: 39 Modelled: 39 Confidence: 15.5% Identity: 28% PDB header:rna binding protein Chain: A: PDB Molecule:rna-binding protein smaug; PDBTitle: crystal structure of the smaug rna binding domain Phyre2 PDB 2o8r chain A domain 3 Region: 7 - 32 Aligned: 26 Modelled: 26 Confidence: 10.4% Identity: 15% Fold: Phospholipase D/nuclease Superfamily: Phospholipase D/nuclease Family: Polyphosphate kinase C-terminal domain Phyre2 PDB 1fav chain C Region: 28 - 41 Aligned: 14 Modelled: 14 Confidence: 6.7% Identity: 43% PDB header:viral protein Chain: C: PDB Molecule:protein (transmembrane glycoprotein); PDBTitle: the structure of an hiv-1 specific cell entry inhibitor in complex2 with the hiv-1 gp41 trimeric core Phyre2 PDB 1ef1 chain A domain 3 Region: 15 - 45 Aligned: 30 Modelled: 31 Confidence: 5.4% Identity: 20% Fold: beta-Grasp (ubiquitin-like) Superfamily: Ubiquitin-like Family: First domain of FERM Phyre2 PDB 1ny7 chain 2 domain 2 Region: 6 - 20 Aligned: 15 Modelled: 15 Confidence: 5.4% Identity: 33% Fold: Nucleoplasmin-like/VP (viral coat and capsid proteins) Superfamily: Positive stranded ssRNA viruses Family: Comoviridae-like VP Phyre2 PDB 1h4r chain A domain 3 Region: 15 - 45 Aligned: 30 Modelled: 31 Confidence: 5.1% Identity: 13% Fold: beta-Grasp (ubiquitin-like) Superfamily: Ubiquitin-like Family: First domain of FERM Phyre2 1 d1xdpa3 2 d2p62a1 3 c2k6lA_ 4 c1oxjA_ 5 d2o8ra3 6 c1favC_ 7 d1ef1a3 8 d1ny722 9 d1h4ra3

Detailed template information

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

1 d1xdpa3 27.5 12 Fold:Phospholipase D/nuclease Superfamily:Phospholipase D/nuclease Family:Polyphosphate kinase C-terminal domain 2 d2p62a1 22.9 18 Fold:PH0156-like Superfamily:PH0156-like Family:PH0156-like 3 c2k6lA_ 16.6 46 PDB header:unknown function Chain: A: PDB Molecule:putative uncharacterized protein; PDBTitle: the solution structure of xacb0070 from xanthonomas2 axonopodis pv citri reveals this new protein is a member of3 the rhh family of transcriptional repressors 4 c1oxjA_ 15.5 28 PDB header:rna binding protein Chain: A: PDB Molecule:rna-binding protein smaug; PDBTitle: crystal structure of the smaug rna binding domain 5 d2o8ra3 10.4 15 Fold:Phospholipase D/nuclease Superfamily:Phospholipase D/nuclease Family:Polyphosphate kinase C-terminal domain 6 c1favC_ 6.7 43 PDB header:viral protein Chain: C: PDB Molecule:protein (transmembrane glycoprotein); PDBTitle: the structure of an hiv-1 specific cell entry inhibitor in complex2 with the hiv-1 gp41 trimeric core 7 d1ef1a3 5.4 20 Fold:beta-Grasp (ubiquitin-like) Superfamily:Ubiquitin-like Family:First domain of FERM 8 d1ny722 5.4 33 Fold:Nucleoplasmin-like/VP (viral coat and capsid proteins) Superfamily:Positive stranded ssRNA viruses Family:Comoviridae-like VP 9 d1h4ra3 5.1 13 Fold:beta-Grasp (ubiquitin-like) Superfamily:Ubiquitin-like Family:First domain of FERM

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