Secondary structure and disorder prediction

		1	.	.	.	.	.	.	.	.	10	.	.	.	.	.	.	.	.	.	20	.	.	.	.	.	.	.	.	.	30	.	.	.	.	.	.	.	.	.	40	.	.	.	.	.	.	.	.	.	50	.	.	.	.	.	.	.	.	.	60
Sequence		M	S	N	V	Y	W	P	L	Y	E	V	F	V	R	G	K	Q	G	L	S	H	R	H	V	G	S	L	H	A	A	D	E	R	M	A	L	E	N	A	R	D	A	Y	T	R	R	S	E	G	C	S	I	W	V	V	K	A	S	E	I
Secondary structure
SS confidence
Disorder		?	?	?	?	?	?										?	?				?
Disorder confidence
		.	.	.	.	.	.	.	.	.	70	.	.	.	.	.	.	.	.	.	80	.	.	.	.	.	.	.	.	.	90	.	.	.	.	.
Sequence		V	A	S	Q	P	E	E	R	G	E	F	F	D	P	A	E	S	K	V	Y	R	H	P	T	F	Y	T	I	P	D	G	I	E	H	M
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 3egr chain B Region: 4 - 65 Aligned: 62 Modelled: 62 Confidence: 100.0% Identity: 65% PDB header:oxidoreductase Chain: B: PDB Molecule:phenylacetate-coa oxygenase subunit paab; PDBTitle: crystal structure of a phenylacetate-coa oxygenase subunit paab2 (reut_a2307) from ralstonia eutropha jmp134 at 2.65 a resolution Phyre2 PDB 1na6 chain A domain 1 Region: 49 - 59 Aligned: 11 Modelled: 11 Confidence: 14.2% Identity: 27% Fold: DNA-binding pseudobarrel domain Superfamily: DNA-binding pseudobarrel domain Family: Type II restriction endonuclease effector domain Phyre2 PDB 2fgc chain A domain 2 Region: 22 - 52 Aligned: 29 Modelled: 31 Confidence: 12.5% Identity: 21% Fold: Ferredoxin-like Superfamily: ACT-like Family: IlvH-like Phyre2 PDB 2f1f chain A domain 1 Region: 22 - 52 Aligned: 29 Modelled: 31 Confidence: 10.2% Identity: 28% Fold: Ferredoxin-like Superfamily: ACT-like Family: IlvH-like Phyre2 PDB 2j6a chain A Region: 83 - 95 Aligned: 13 Modelled: 13 Confidence: 9.7% Identity: 31% PDB header:transferase Chain: A: PDB Molecule:protein trm112; PDBTitle: crystal structure of s. cerevisiae ynr046w, a zinc finger2 protein from the erf1 methyltransferase complex. Phyre2 PDB 2pc6 chain A domain 2 Region: 21 - 52 Aligned: 30 Modelled: 31 Confidence: 9.5% Identity: 33% Fold: Ferredoxin-like Superfamily: ACT-like Family: IlvH-like Phyre2 PDB 1a0i chain A domain 1 Region: 68 - 85 Aligned: 18 Modelled: 18 Confidence: 7.9% Identity: 22% Fold: OB-fold Superfamily: Nucleic acid-binding proteins Family: DNA ligase/mRNA capping enzyme postcatalytic domain Phyre2 PDB 2f1f chain A Region: 22 - 52 Aligned: 29 Modelled: 31 Confidence: 6.8% Identity: 28% PDB header:transferase Chain: A: PDB Molecule:acetolactate synthase isozyme iii small subunit; PDBTitle: crystal structure of the regulatory subunit of2 acetohydroxyacid synthase isozyme iii from e. coli Phyre2 PDB 1wv8 chain A domain 1 Region: 44 - 60 Aligned: 16 Modelled: 17 Confidence: 6.5% Identity: 19% Fold: TTHA1013/TTHA0281-like Superfamily: TTHA1013/TTHA0281-like Family: TTHA1013-like Phyre2 PDB 2pc6 chain C Region: 22 - 52 Aligned: 29 Modelled: 31 Confidence: 6.2% Identity: 34% PDB header:lyase Chain: C: PDB Molecule:probable acetolactate synthase isozyme iii (small subunit); PDBTitle: crystal structure of putative acetolactate synthase- small subunit2 from nitrosomonas europaea Phyre2 PDB 2gu3 chain A domain 1 Region: 7 - 18 Aligned: 12 Modelled: 12 Confidence: 6.0% Identity: 42% Fold: Cystatin-like Superfamily: Cystatin/monellin Family: PepSY-like Phyre2 1 c3egrB_ 2 d1na6a1 3 d2fgca2 4 d2f1fa1 5 c2j6aA_ 6 d2pc6a2 7 d1a0ia1 8 c2f1fA_ 9 d1wv8a1 10 c2pc6C_ 11 d2gu3a1

Detailed template information

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

1 c3egrB_ 100.0 65 PDB header:oxidoreductase Chain: B: PDB Molecule:phenylacetate-coa oxygenase subunit paab; PDBTitle: crystal structure of a phenylacetate-coa oxygenase subunit paab2 (reut_a2307) from ralstonia eutropha jmp134 at 2.65 a resolution 2 d1na6a1 14.2 27 Fold:DNA-binding pseudobarrel domain Superfamily:DNA-binding pseudobarrel domain Family:Type II restriction endonuclease effector domain 3 d2fgca2 12.5 21 Fold:Ferredoxin-like Superfamily:ACT-like Family:IlvH-like 4 d2f1fa1 10.2 28 Fold:Ferredoxin-like Superfamily:ACT-like Family:IlvH-like 5 c2j6aA_ 9.7 31 PDB header:transferase Chain: A: PDB Molecule:protein trm112; PDBTitle: crystal structure of s. cerevisiae ynr046w, a zinc finger2 protein from the erf1 methyltransferase complex. 6 d2pc6a2 9.5 33 Fold:Ferredoxin-like Superfamily:ACT-like Family:IlvH-like 7 d1a0ia1 7.9 22 Fold:OB-fold Superfamily:Nucleic acid-binding proteins Family:DNA ligase/mRNA capping enzyme postcatalytic domain 8 c2f1fA_ 6.8 28 PDB header:transferase Chain: A: PDB Molecule:acetolactate synthase isozyme iii small subunit; PDBTitle: crystal structure of the regulatory subunit of2 acetohydroxyacid synthase isozyme iii from e. coli 9 d1wv8a1 6.5 19 Fold:TTHA1013/TTHA0281-like Superfamily:TTHA1013/TTHA0281-like Family:TTHA1013-like 10 c2pc6C_ 6.2 34 PDB header:lyase Chain: C: PDB Molecule:probable acetolactate synthase isozyme iii (small subunit); PDBTitle: crystal structure of putative acetolactate synthase- small subunit2 from nitrosomonas europaea 11 d2gu3a1 6.0 42 Fold:Cystatin-like Superfamily:Cystatin/monellin Family:PepSY-like

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