Secondary structure and disorder prediction

		1	.	.	.	.	.	.	.	.	10	.	.	.	.	.	.	.	.	.	20	.	.	.	.	.	.	.	.	.	30	.	.	.	.	.	.	.	.	.	40	.	.	.	.	.	.	.	.	.	50	.	.	.	.	.	.	.	.	.	60
Sequence		M	L	R	F	L	N	Q	C	S	Q	G	R	G	A	W	L	L	M	A	F	T	A	L	A	L	E	L	T	A	L	W	F	Q	H	V	M	L	L	K	P	C	V	L	C	I	Y	E	R	C	A	L	F	G	V	L	G	A	A	L	I
Secondary structure
SS confidence
Disorder		?	?					?
Disorder confidence
		.	.	.	.	.	.	.	.	.	70	.	.	.	.	.	.	.	.	.	80	.	.	.	.	.	.	.	.	.	90	.	.	.	.	.	.	.	.	.	100	.	.	.	.	.	.	.	.	.	110	.	.	.	.	.	.	.	.	.	120
Sequence		G	A	I	A	P	K	T	P	L	R	Y	V	A	M	V	I	W	L	Y	S	A	F	R	G	V	Q	L	T	Y	E	H	T	M	L	Q	L	Y	P	S	P	F	A	T	C	D	F	M	V	R	F	P	E	W	L	P	L	D	K	W	V
Secondary structure
SS confidence
Disorder
Disorder confidence
		.	.	.	.	.	.	.	.	.	130	.	.	.	.	.	.	.	.	.	140	.	.	.	.	.	.	.	.	.	150	.	.	.	.	.	.	.	.	.	160	.	.	.	.	.	.	.	.	.	170	.	.	.	.	.	.
Sequence		P	Q	V	F	V	A	S	G	D	C	A	E	R	Q	W	D	F	L	G	L	E	M	P	Q	W	L	L	G	I	F	I	A	Y	L	I	V	A	V	L	V	V	I	S	Q	P	F	K	A	K	K	R	D	L	F	G	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 2hi7 chain B domain 1 Region: 15 - 162 Aligned: 133 Modelled: 133 Confidence: 100.0% Identity: 94% Fold: Bromodomain-like Superfamily: DsbB-like Family: DsbB-like Phyre2 PDB 3e9j chain C Region: 15 - 162 Aligned: 133 Modelled: 133 Confidence: 100.0% Identity: 94% PDB header:oxidoreductase Chain: C: PDB Molecule:thiol/disulfide oxidoreductase dsbb; PDBTitle: structure of the charge-transfer intermediate of the2 transmembrane redox catalyst dsbb Phyre2 PDB 3kp9 chain A Region: 9 - 103 Aligned: 91 Modelled: 95 Confidence: 80.2% Identity: 13% PDB header:blood coagulation,oxidoreductase Chain: A: PDB Molecule:vkorc1/thioredoxin domain protein; PDBTitle: structure of a bacterial homolog of vitamin k epoxide reductase Phyre2 PDB 2g84 chain A domain 1 Region: 38 - 44 Aligned: 7 Modelled: 7 Confidence: 47.7% Identity: 57% Fold: Cytidine deaminase-like Superfamily: Cytidine deaminase-like Family: Deoxycytidylate deaminase-like Phyre2 PDB 3ocq chain A Region: 38 - 44 Aligned: 7 Modelled: 7 Confidence: 46.9% Identity: 71% PDB header:hydrolase Chain: A: PDB Molecule:putative cytosine/adenosine deaminase; PDBTitle: crystal structure of trna-specific adenosine deaminase from salmonella2 enterica Phyre2 PDB 1wkq chain A Region: 38 - 44 Aligned: 7 Modelled: 7 Confidence: 45.3% Identity: 43% Fold: Cytidine deaminase-like Superfamily: Cytidine deaminase-like Family: Deoxycytidylate deaminase-like Phyre2 PDB 2b3j chain A domain 1 Region: 38 - 44 Aligned: 7 Modelled: 7 Confidence: 45.0% Identity: 71% Fold: Cytidine deaminase-like Superfamily: Cytidine deaminase-like Family: Deoxycytidylate deaminase-like Phyre2 PDB 1z3a chain A domain 1 Region: 38 - 44 Aligned: 7 Modelled: 7 Confidence: 44.4% Identity: 71% Fold: Cytidine deaminase-like Superfamily: Cytidine deaminase-like Family: Deoxycytidylate deaminase-like Phyre2 PDB 1wwr chain A domain 1 Region: 38 - 44 Aligned: 7 Modelled: 7 Confidence: 41.9% Identity: 57% Fold: Cytidine deaminase-like Superfamily: Cytidine deaminase-like Family: Deoxycytidylate deaminase-like Phyre2 PDB 2nx8 chain A Region: 38 - 44 Aligned: 7 Modelled: 7 Confidence: 40.7% Identity: 57% PDB header:hydrolase Chain: A: PDB Molecule:trna-specific adenosine deaminase; PDBTitle: the crystal structure of the trna-specific adenosine deaminase from2 streptococcus pyogenes Phyre2 PDB 3dh1 chain D Region: 38 - 44 Aligned: 7 Modelled: 7 Confidence: 39.4% Identity: 43% PDB header:hydrolase Chain: D: PDB Molecule:trna-specific adenosine deaminase 2; PDBTitle: crystal structure of human trna-specific adenosine-34 deaminase2 subunit adat2 Phyre2 PDB 1p6o chain A Region: 38 - 44 Aligned: 7 Modelled: 7 Confidence: 38.6% Identity: 57% Fold: Cytidine deaminase-like Superfamily: Cytidine deaminase-like Family: Deoxycytidylate deaminase-like Phyre2 PDB 2a8n chain A domain 1 Region: 38 - 44 Aligned: 7 Modelled: 7 Confidence: 36.9% Identity: 57% Fold: Cytidine deaminase-like Superfamily: Cytidine deaminase-like Family: Deoxycytidylate deaminase-like Phyre2 PDB 2l0l chain A Region: 42 - 67 Aligned: 26 Modelled: 26 Confidence: 35.5% Identity: 85% PDB header:membrane protein Chain: A: PDB Molecule:oxidoreductase that catalyzes reoxidation of dsba protein PDBTitle: dsbb2 peptide structure in 70% tfe Phyre2 PDB 2hxv chain A domain 2 Region: 38 - 44 Aligned: 7 Modelled: 7 Confidence: 29.9% Identity: 14% Fold: Cytidine deaminase-like Superfamily: Cytidine deaminase-like Family: Deoxycytidylate deaminase-like Phyre2 PDB 2l0m chain A Region: 42 - 67 Aligned: 26 Modelled: 26 Confidence: 28.5% Identity: 85% PDB header:membrane protein Chain: A: PDB Molecule:oxidoreductase that catalyzes reoxidation of dsba protein PDBTitle: dsbb2 peptide structure in 100% tfe Phyre2 PDB 2o7p chain A Region: 38 - 44 Aligned: 7 Modelled: 7 Confidence: 28.0% Identity: 57% PDB header:hydrolase, oxidoreductase Chain: A: PDB Molecule:riboflavin biosynthesis protein ribd; PDBTitle: the crystal structure of ribd from escherichia coli in complex with2 the oxidised nadp+ cofactor in the active site of the reductase3 domain Phyre2 PDB 1vq2 chain A Region: 38 - 44 Aligned: 7 Modelled: 7 Confidence: 25.5% Identity: 57% Fold: Cytidine deaminase-like Superfamily: Cytidine deaminase-like Family: Deoxycytidylate deaminase-like Phyre2 PDB 2hvw chain C Region: 38 - 44 Aligned: 7 Modelled: 7 Confidence: 22.8% Identity: 43% PDB header:hydrolase Chain: C: PDB Molecule:deoxycytidylate deaminase; PDBTitle: crystal structure of dcmp deaminase from streptococcus2 mutans Phyre2 PDB 1m56 chain D Region: 136 - 160 Aligned: 25 Modelled: 25 Confidence: 22.5% Identity: 32% Fold: Single transmembrane helix Superfamily: Bacterial aa3 type cytochrome c oxidase subunit IV Family: Bacterial aa3 type cytochrome c oxidase subunit IV Phyre2 1 d2hi7b1 2 c3e9jC_ 3 c3kp9A_ 4 d2g84a1 5 c3ocqA_ 6 d1wkqa_ 7 d2b3ja1 8 d1z3aa1 9 d1wwra1 10 c2nx8A_ 11 c3dh1D_ 12 d1p6oa_ 13 d2a8na1 14 c2l0lA_ 15 d2hxva2 16 c2l0mA_ 17 c2o7pA_ 18 d1vq2a_ 19 c2hvwC_ 20 d1m56d_ 21 22 23 24 25 26 27 28 29 30 31 32 33

Detailed template information

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

1 d2hi7b1 100.0 94 Fold:Bromodomain-like Superfamily:DsbB-like Family:DsbB-like 2 c3e9jC_ 100.0 94 PDB header:oxidoreductase Chain: C: PDB Molecule:thiol/disulfide oxidoreductase dsbb; PDBTitle: structure of the charge-transfer intermediate of the2 transmembrane redox catalyst dsbb 3 c3kp9A_ 80.2 13 PDB header:blood coagulation,oxidoreductase Chain: A: PDB Molecule:vkorc1/thioredoxin domain protein; PDBTitle: structure of a bacterial homolog of vitamin k epoxide reductase 4 d2g84a1 47.7 57 Fold:Cytidine deaminase-like Superfamily:Cytidine deaminase-like Family:Deoxycytidylate deaminase-like 5 c3ocqA_ 46.9 71 PDB header:hydrolase Chain: A: PDB Molecule:putative cytosine/adenosine deaminase; PDBTitle: crystal structure of trna-specific adenosine deaminase from salmonella2 enterica 6 d1wkqa_ 45.3 43 Fold:Cytidine deaminase-like Superfamily:Cytidine deaminase-like Family:Deoxycytidylate deaminase-like 7 d2b3ja1 45.0 71 Fold:Cytidine deaminase-like Superfamily:Cytidine deaminase-like Family:Deoxycytidylate deaminase-like 8 d1z3aa1 44.4 71 Fold:Cytidine deaminase-like Superfamily:Cytidine deaminase-like Family:Deoxycytidylate deaminase-like 9 d1wwra1 41.9 57 Fold:Cytidine deaminase-like Superfamily:Cytidine deaminase-like Family:Deoxycytidylate deaminase-like 10 c2nx8A_ 40.7 57 PDB header:hydrolase Chain: A: PDB Molecule:trna-specific adenosine deaminase; PDBTitle: the crystal structure of the trna-specific adenosine deaminase from2 streptococcus pyogenes 11 c3dh1D_ 39.4 43 PDB header:hydrolase Chain: D: PDB Molecule:trna-specific adenosine deaminase 2; PDBTitle: crystal structure of human trna-specific adenosine-34 deaminase2 subunit adat2 12 d1p6oa_ 38.6 57 Fold:Cytidine deaminase-like Superfamily:Cytidine deaminase-like Family:Deoxycytidylate deaminase-like 13 d2a8na1 36.9 57 Fold:Cytidine deaminase-like Superfamily:Cytidine deaminase-like Family:Deoxycytidylate deaminase-like 14 c2l0lA_ 35.5 85 PDB header:membrane protein Chain: A: PDB Molecule:oxidoreductase that catalyzes reoxidation of dsba protein PDBTitle: dsbb2 peptide structure in 70% tfe 15 d2hxva2 29.9 14 Fold:Cytidine deaminase-like Superfamily:Cytidine deaminase-like Family:Deoxycytidylate deaminase-like 16 c2l0mA_ 28.5 85 PDB header:membrane protein Chain: A: PDB Molecule:oxidoreductase that catalyzes reoxidation of dsba protein PDBTitle: dsbb2 peptide structure in 100% tfe 17 c2o7pA_ 28.0 57 PDB header:hydrolase, oxidoreductase Chain: A: PDB Molecule:riboflavin biosynthesis protein ribd; PDBTitle: the crystal structure of ribd from escherichia coli in complex with2 the oxidised nadp+ cofactor in the active site of the reductase3 domain 18 d1vq2a_ 25.5 57 Fold:Cytidine deaminase-like Superfamily:Cytidine deaminase-like Family:Deoxycytidylate deaminase-like 19 c2hvwC_ 22.8 43 PDB header:hydrolase Chain: C: PDB Molecule:deoxycytidylate deaminase; PDBTitle: crystal structure of dcmp deaminase from streptococcus2 mutans 20 d1m56d_ 22.5 32 Fold:Single transmembrane helix Superfamily:Bacterial aa3 type cytochrome c oxidase subunit IV Family:Bacterial aa3 type cytochrome c oxidase subunit IV 21 c2w4lC_ not modelled 19.6 57 PDB header:hydrolase Chain: C: PDB Molecule:deoxycytidylate deaminase; PDBTitle: human dcmp deaminase 22 d2drpa2 not modelled 16.5 50 Fold:beta-beta-alpha zinc fingers Superfamily:beta-beta-alpha zinc fingers Family:Classic zinc finger, C2H2 23 d2a1ka1 not modelled 12.3 13 Fold:OB-fold Superfamily:Nucleic acid-binding proteins Family:Phage ssDNA-binding proteins 24 c3pcqX_ not modelled 10.3 25 PDB header:photosynthesis Chain: X: PDB Molecule:photosystem i 4.8k protein; PDBTitle: femtosecond x-ray protein nanocrystallography 25 d2eppa1 not modelled 9.6 50 Fold:beta-beta-alpha zinc fingers Superfamily:beta-beta-alpha zinc fingers Family:Classic zinc finger, C2H2 26 c1jb0X_ not modelled 8.5 25 PDB header:photosynthesis Chain: X: PDB Molecule:photosystem i subunit psax; PDBTitle: crystal structure of photosystem i: a photosynthetic reaction center2 and core antenna system from cyanobacteria 27 d1jb0x_ not modelled 8.5 25 Fold:Single transmembrane helix Superfamily:Subunit PsaX of photosystem I reaction centre Family:Subunit PsaX of photosystem I reaction centre 28 d1qled_ not modelled 7.5 29 Fold:Single transmembrane helix Superfamily:Bacterial aa3 type cytochrome c oxidase subunit IV Family:Bacterial aa3 type cytochrome c oxidase subunit IV 29 d2akla2 not modelled 7.3 57 Fold:Rubredoxin-like Superfamily:Zinc beta-ribbon Family:PhnA zinc-binding domain 30 c2aklA_ not modelled 7.2 57 PDB header:structural genomics, unknown function Chain: A: PDB Molecule:phna-like protein pa0128; PDBTitle: solution structure for phn-a like protein pa0128 from2 pseudomonas aeruginosa 31 c2riqA_ not modelled 6.5 36 PDB header:transferase Chain: A: PDB Molecule:poly [adp-ribose] polymerase 1; PDBTitle: crystal structure of the third zinc-binding domain of human parp-1 32 c2jvnA_ not modelled 6.1 40 PDB header:transferase Chain: A: PDB Molecule:poly [adp-ribose] polymerase 1; PDBTitle: domain c of human parp-1 33 d1eyfa_ not modelled 5.6 38 Fold:Ada DNA repair protein, N-terminal domain (N-Ada 10) Superfamily:Ada DNA repair protein, N-terminal domain (N-Ada 10) Family:Ada DNA repair protein, N-terminal domain (N-Ada 10)

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