Secondary structure and disorder prediction

		1	.	.	.	.	.	.	.	.	10	.	.	.	.	.	.	.	.	.	20	.	.	.	.	.	.	.	.	.	30	.	.	.	.	.	.	.	.	.	40	.	.	.	.	.	.	.	.	.	50	.	.	.	.	.	.	.	.	.	60
Sequence		M	E	R	G	P	H	P	R	A	A	I	Y	A	G	L	Q	E	D	R	A	S	R	R	S	G	Q	L	L	T	N	K	S	F	A	K	G	I	A	N	P	T	K	S	G	V	F	Q	T	K	T	R	Y	A	C	M	K	A	G	V	K
Secondary structure
SS confidence
Disorder		?	?	?	?	?	?	?													?	?	?	?	?	?		?	?	?													?															?	?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	70	.	.	.	.	.	.	.	.	.	80	.	.	.	.	.	.	.	.	.
Sequence		R	R	T	A	T	P	L	F	I	G	R	F	I	L	L	R	F	V	V	D	H	I	A	Q	H	R	E	Q	H
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 3lw5 chain K Region: 63 - 78 Aligned: 16 Modelled: 16 Confidence: 17.1% Identity: 44% PDB header:photosynthesis Chain: K: PDB Molecule:photosystem i reaction center subunit x psak; PDBTitle: improved model of plant photosystem i Phyre2 PDB 1e8g chain A domain 1 Region: 35 - 56 Aligned: 22 Modelled: 22 Confidence: 15.1% Identity: 36% Fold: Ferredoxin-like Superfamily: FAD-linked oxidases, C-terminal domain Family: Vanillyl-alcohol oxidase-like Phyre2 PDB 2hkv chain A domain 1 Region: 71 - 88 Aligned: 18 Modelled: 18 Confidence: 11.8% Identity: 28% Fold: DinB/YfiT-like putative metalloenzymes Superfamily: DinB/YfiT-like putative metalloenzymes Family: DinB-like Phyre2 PDB 2q66 chain A domain 2 Region: 8 - 41 Aligned: 34 Modelled: 34 Confidence: 11.5% Identity: 18% Fold: Nucleotidyltransferase Superfamily: Nucleotidyltransferase Family: Poly(A) polymerase, PAP, N-terminal domain Phyre2 PDB 3k13 chain A Region: 28 - 59 Aligned: 30 Modelled: 31 Confidence: 10.9% Identity: 20% PDB header:transferase Chain: A: PDB Molecule:5-methyltetrahydrofolate-homocysteine methyltransferase; PDBTitle: structure of the pterin-binding domain metr of 5-2 methyltetrahydrofolate-homocysteine methyltransferase from3 bacteroides thetaiotaomicron Phyre2 PDB 2cmp chain A Region: 8 - 38 Aligned: 31 Modelled: 31 Confidence: 8.1% Identity: 29% PDB header:terminase Chain: A: PDB Molecule:terminase small subunit; PDBTitle: crystal structure of the dna binding domain of g1p small2 terminase subunit from bacteriophage sf6 Phyre2 PDB 1ahu chain B Region: 35 - 56 Aligned: 22 Modelled: 22 Confidence: 6.9% Identity: 36% PDB header:flavoenzyme Chain: B: PDB Molecule:vanillyl-alcohol oxidase; PDBTitle: structure of the octameric flavoenzyme vanillyl-alcohol2 oxidase in complex with p-cresol Phyre2 PDB 3c66 chain B Region: 8 - 41 Aligned: 34 Modelled: 34 Confidence: 6.3% Identity: 18% PDB header:transferase Chain: B: PDB Molecule:poly(a) polymerase; PDBTitle: yeast poly(a) polymerase in complex with fip1 residues 80-105 Phyre2 PDB 2g9l chain A Region: 25 - 47 Aligned: 23 Modelled: 23 Confidence: 5.7% Identity: 43% PDB header:antibiotic Chain: A: PDB Molecule:gaegurin-4; PDBTitle: the high-resolution solution conformation of an2 antimicrobial peptide gaegurin 4 and its mode of membrane3 interaction Phyre2 PDB 2wsf chain G Region: 63 - 78 Aligned: 16 Modelled: 16 Confidence: 5.3% Identity: 44% PDB header:photosynthesis Chain: G: PDB Molecule:photosystem i reaction center subunit v, PDBTitle: improved model of plant photosystem i Phyre2 1 c3lw5K_ 2 d1e8ga1 3 d2hkva1 4 d2q66a2 5 c3k13A_ 6 c2cmpA_ 7 c1ahuB_ 8 c3c66B_ 9 c2g9lA_ 10 c2wsfG_

Detailed template information

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

1 c3lw5K_ 17.1 44 PDB header:photosynthesis Chain: K: PDB Molecule:photosystem i reaction center subunit x psak; PDBTitle: improved model of plant photosystem i 2 d1e8ga1 15.1 36 Fold:Ferredoxin-like Superfamily:FAD-linked oxidases, C-terminal domain Family:Vanillyl-alcohol oxidase-like 3 d2hkva1 11.8 28 Fold:DinB/YfiT-like putative metalloenzymes Superfamily:DinB/YfiT-like putative metalloenzymes Family:DinB-like 4 d2q66a2 11.5 18 Fold:Nucleotidyltransferase Superfamily:Nucleotidyltransferase Family:Poly(A) polymerase, PAP, N-terminal domain 5 c3k13A_ 10.9 20 PDB header:transferase Chain: A: PDB Molecule:5-methyltetrahydrofolate-homocysteine methyltransferase; PDBTitle: structure of the pterin-binding domain metr of 5-2 methyltetrahydrofolate-homocysteine methyltransferase from3 bacteroides thetaiotaomicron 6 c2cmpA_ 8.1 29 PDB header:terminase Chain: A: PDB Molecule:terminase small subunit; PDBTitle: crystal structure of the dna binding domain of g1p small2 terminase subunit from bacteriophage sf6 7 c1ahuB_ 6.9 36 PDB header:flavoenzyme Chain: B: PDB Molecule:vanillyl-alcohol oxidase; PDBTitle: structure of the octameric flavoenzyme vanillyl-alcohol2 oxidase in complex with p-cresol 8 c3c66B_ 6.3 18 PDB header:transferase Chain: B: PDB Molecule:poly(a) polymerase; PDBTitle: yeast poly(a) polymerase in complex with fip1 residues 80-105 9 c2g9lA_ 5.7 43 PDB header:antibiotic Chain: A: PDB Molecule:gaegurin-4; PDBTitle: the high-resolution solution conformation of an2 antimicrobial peptide gaegurin 4 and its mode of membrane3 interaction 10 c2wsfG_ 5.3 44 PDB header:photosynthesis Chain: G: PDB Molecule:photosystem i reaction center subunit v, PDBTitle: improved model of plant photosystem i

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