Secondary structure and disorder prediction

		1	.	.	.	.	.	.	.	.	10	.	.	.	.	.	.	.	.	.	20	.	.	.	.	.	.	.	.	.	30	.	.
Sequence		M	T	A	L	L	R	V	I	S	L	V	V	I	S	V	V	V	I	I	I	P	P	C	G	A	A	L	G	R	G	K	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 3mra chain A Region: 7 - 18 Aligned: 12 Modelled: 12 Confidence: 25.8% Identity: 67% PDB header:membrane protein Chain: A: PDB Molecule:nicotinic acetylcholine receptor; PDBTitle: m3 transmembrane segment of alpha-subunit of nicotinic2 acetylcholine receptor from torpedo californica, nmr, 153 structures Phyre2 PDB 3b8f chain B Region: 19 - 25 Aligned: 7 Modelled: 7 Confidence: 14.1% Identity: 43% PDB header:hydrolase Chain: B: PDB Molecule:putative blasticidin s deaminase; PDBTitle: crystal structure of the cytidine deaminase from bacillus anthracis Phyre2 PDB 3oj6 chain C Region: 19 - 25 Aligned: 7 Modelled: 7 Confidence: 9.0% Identity: 57% PDB header:hydrolase Chain: C: PDB Molecule:blasticidin-s deaminase; PDBTitle: crystal structure of blasticidin s deaminase from coccidioides immitis Phyre2 PDB 1r5t chain A Region: 20 - 25 Aligned: 6 Modelled: 6 Confidence: 6.2% Identity: 50% Fold: Cytidine deaminase-like Superfamily: Cytidine deaminase-like Family: Cytidine deaminase Phyre2 PDB 1mtx chain A Region: 20 - 29 Aligned: 10 Modelled: 10 Confidence: 5.6% Identity: 50% Fold: Knottins (small inhibitors, toxins, lectins) Superfamily: Scorpion toxin-like Family: Short-chain scorpion toxins Phyre2 PDB 1q90 chain M Region: 4 - 11 Aligned: 8 Modelled: 8 Confidence: 5.3% Identity: 88% Fold: Single transmembrane helix Superfamily: PetM subunit of the cytochrome b6f complex Family: PetM subunit of the cytochrome b6f complex Phyre2 PDB 2z3g chain A domain 1 Region: 19 - 25 Aligned: 7 Modelled: 7 Confidence: 5.2% Identity: 57% Fold: Cytidine deaminase-like Superfamily: Cytidine deaminase-like Family: Cytidine deaminase Phyre2 1 c3mraA_ 2 c3b8fB_ 3 c3oj6C_ 4 d1r5ta_ 5 d1mtxa_ 6 d1q90m_ 7 d2z3ga1

Detailed template information

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

1 c3mraA_ 25.8 67 PDB header:membrane protein Chain: A: PDB Molecule:nicotinic acetylcholine receptor; PDBTitle: m3 transmembrane segment of alpha-subunit of nicotinic2 acetylcholine receptor from torpedo californica, nmr, 153 structures 2 c3b8fB_ 14.1 43 PDB header:hydrolase Chain: B: PDB Molecule:putative blasticidin s deaminase; PDBTitle: crystal structure of the cytidine deaminase from bacillus anthracis 3 c3oj6C_ 9.0 57 PDB header:hydrolase Chain: C: PDB Molecule:blasticidin-s deaminase; PDBTitle: crystal structure of blasticidin s deaminase from coccidioides immitis 4 d1r5ta_ 6.2 50 Fold:Cytidine deaminase-like Superfamily:Cytidine deaminase-like Family:Cytidine deaminase 5 d1mtxa_ 5.6 50 Fold:Knottins (small inhibitors, toxins, lectins) Superfamily:Scorpion toxin-like Family:Short-chain scorpion toxins 6 d1q90m_ 5.3 88 Fold:Single transmembrane helix Superfamily:PetM subunit of the cytochrome b6f complex Family:PetM subunit of the cytochrome b6f complex 7 d2z3ga1 5.2 57 Fold:Cytidine deaminase-like Superfamily:Cytidine deaminase-like Family:Cytidine deaminase

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