Secondary structure and disorder prediction

		1	.	.	.	.	.	.	.	.	10	.	.	.	.	.	.	.	.	.	20	.	.	.	.	.	.	.	.	.	30	.	.	.	.	.	.	.	.	.	40	.	.	.	.	.	.	.	.	.	50	.	.
Sequence		M	G	F	W	R	I	V	I	T	I	I	L	P	P	L	G	V	L	L	G	K	G	F	G	W	A	F	I	I	N	I	L	L	T	L	L	G	Y	I	P	G	L	I	H	A	F	W	V	Q	T	R	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 1qf8 chain A Region: 41 - 52 Aligned: 12 Modelled: 12 Confidence: 24.6% Identity: 50% Fold: Rubredoxin-like Superfamily: Casein kinase II beta subunit Family: Casein kinase II beta subunit Phyre2 PDB 1jwh chain C Region: 41 - 52 Aligned: 12 Modelled: 12 Confidence: 23.9% Identity: 50% Fold: Rubredoxin-like Superfamily: Casein kinase II beta subunit Family: Casein kinase II beta subunit Phyre2 PDB 2y69 chain W Region: 15 - 50 Aligned: 35 Modelled: 36 Confidence: 16.7% Identity: 20% PDB header:electron transport Chain: W: PDB Molecule:cytochrome c oxidase polypeptide 7a1; PDBTitle: bovine heart cytochrome c oxidase re-refined with molecular2 oxygen Phyre2 PDB 1v54 chain J Region: 15 - 50 Aligned: 35 Modelled: 36 Confidence: 14.0% Identity: 20% Fold: Single transmembrane helix Superfamily: Mitochondrial cytochrome c oxidase subunit VIIa Family: Mitochondrial cytochrome c oxidase subunit VIIa Phyre2 PDB 1rfy chain A Region: 29 - 40 Aligned: 12 Modelled: 12 Confidence: 12.6% Identity: 50% Fold: Long alpha-hairpin Superfamily: Transcriptional repressor TraM Family: Transcriptional repressor TraM Phyre2 PDB 2hjd chain A Region: 29 - 40 Aligned: 12 Modelled: 12 Confidence: 11.4% Identity: 58% PDB header:signaling protein Chain: A: PDB Molecule:quorum-sensing antiactivator; PDBTitle: crystal structure of a second quorum sensing antiactivator tram2 from2 a. tumefaciens strain a6 Phyre2 PDB 1upg chain B Region: 29 - 40 Aligned: 12 Modelled: 12 Confidence: 10.7% Identity: 50% Fold: Long alpha-hairpin Superfamily: Transcriptional repressor TraM Family: Transcriptional repressor TraM Phyre2 PDB 1lns chain A domain 1 Region: 15 - 42 Aligned: 28 Modelled: 28 Confidence: 10.4% Identity: 29% Fold: CH domain-like Superfamily: X-Prolyl dipeptidyl aminopeptidase PepX, N-terminal domain Family: X-Prolyl dipeptidyl aminopeptidase PepX, N-terminal domain Phyre2 PDB 2k1v chain B Region: 23 - 37 Aligned: 15 Modelled: 15 Confidence: 8.9% Identity: 33% PDB header:hormone Chain: B: PDB Molecule:relaxin-3; PDBTitle: r3/i5 relaxin chimera Phyre2 PDB 2iub chain A domain 2 Region: 1 - 14 Aligned: 14 Modelled: 14 Confidence: 5.2% Identity: 36% Fold: Transmembrane helix hairpin Superfamily: Magnesium transport protein CorA, transmembrane region Family: Magnesium transport protein CorA, transmembrane region Phyre2 1 d1qf8a_ 2 d1jwhc_ 3 c2y69W_ 4 d1v54j_ 5 d1rfya_ 6 c2hjdA_ 7 d1upgb_ 8 d1lnsa1 9 c2k1vB_ 10 d2iuba2

Detailed template information

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

1 d1qf8a_ 24.6 50 Fold:Rubredoxin-like Superfamily:Casein kinase II beta subunit Family:Casein kinase II beta subunit 2 d1jwhc_ 23.9 50 Fold:Rubredoxin-like Superfamily:Casein kinase II beta subunit Family:Casein kinase II beta subunit 3 c2y69W_ 16.7 20 PDB header:electron transport Chain: W: PDB Molecule:cytochrome c oxidase polypeptide 7a1; PDBTitle: bovine heart cytochrome c oxidase re-refined with molecular2 oxygen 4 d1v54j_ 14.0 20 Fold:Single transmembrane helix Superfamily:Mitochondrial cytochrome c oxidase subunit VIIa Family:Mitochondrial cytochrome c oxidase subunit VIIa 5 d1rfya_ 12.6 50 Fold:Long alpha-hairpin Superfamily:Transcriptional repressor TraM Family:Transcriptional repressor TraM 6 c2hjdA_ 11.4 58 PDB header:signaling protein Chain: A: PDB Molecule:quorum-sensing antiactivator; PDBTitle: crystal structure of a second quorum sensing antiactivator tram2 from2 a. tumefaciens strain a6 7 d1upgb_ 10.7 50 Fold:Long alpha-hairpin Superfamily:Transcriptional repressor TraM Family:Transcriptional repressor TraM 8 d1lnsa1 10.4 29 Fold:CH domain-like Superfamily:X-Prolyl dipeptidyl aminopeptidase PepX, N-terminal domain Family:X-Prolyl dipeptidyl aminopeptidase PepX, N-terminal domain 9 c2k1vB_ 8.9 33 PDB header:hormone Chain: B: PDB Molecule:relaxin-3; PDBTitle: r3/i5 relaxin chimera 10 d2iuba2 5.2 36 Fold:Transmembrane helix hairpin Superfamily:Magnesium transport protein CorA, transmembrane region Family:Magnesium transport protein CorA, transmembrane region

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