Secondary structure and disorder prediction

		1	.	.	.	.	.	.	.	.	10	.	.	.	.	.	.	.	.	.	20	.	.	.	.	.	.	.	.	.	30	.	.	.	.	.	.	.	.	.	40	.	.	.	.	.	.	.	.	.	50	.	.	.	.	.	.	.	.	.	60
Sequence		M	H	M	V	T	Y	P	C	L	T	S	R	R	F	Q	L	A	L	I	H	R	R	V	V	D	K	R	T	S	M	H	S	R	T	A	S	E	S	T	G	A	R	I	H	R	P	W	C	A	R	H	Q	V	R	P	A	W	R	C	Q
Secondary structure
SS confidence
Disorder		?	?	?		?	?	?																		?	?	?	?	?	?	?	?	?	?	?	?	?	?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	70	.	.	.	.	.	.	.	.	.	80	.	.	.	.	.	.	.	.	.
Sequence		Y	D	K	L	H	R	V	P	F	R	S	P	E	L	R	L	D	S	G	P	G	Y	T	T	G	S	Y	R	Y
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 1nvp chain C Region: 59 - 67 Aligned: 9 Modelled: 9 Confidence: 43.2% Identity: 78% PDB header:transcription/dna Chain: C: PDB Molecule:transcription initiation factor iia beta chain; PDBTitle: human tfiia/tbp/dna complex Phyre2 PDB 1nvp chain C Region: 59 - 67 Aligned: 9 Modelled: 9 Confidence: 43.2% Identity: 78% Fold: Transcription factor IIA (TFIIA), beta-barrel domain Superfamily: Transcription factor IIA (TFIIA), beta-barrel domain Family: Transcription factor IIA (TFIIA), beta-barrel domain Phyre2 PDB 1nh2 chain C Region: 59 - 67 Aligned: 9 Modelled: 9 Confidence: 42.0% Identity: 56% Fold: Transcription factor IIA (TFIIA), beta-barrel domain Superfamily: Transcription factor IIA (TFIIA), beta-barrel domain Family: Transcription factor IIA (TFIIA), beta-barrel domain Phyre2 PDB 1nh2 chain C Region: 59 - 67 Aligned: 9 Modelled: 9 Confidence: 42.0% Identity: 56% PDB header:transcription/dna Chain: C: PDB Molecule:transcription initiation factor iia large chain; PDBTitle: crystal structure of a yeast tfiia/tbp/dna complex Phyre2 PDB 1ytf chain C Region: 59 - 67 Aligned: 9 Modelled: 9 Confidence: 40.1% Identity: 56% Fold: Transcription factor IIA (TFIIA), beta-barrel domain Superfamily: Transcription factor IIA (TFIIA), beta-barrel domain Family: Transcription factor IIA (TFIIA), beta-barrel domain Phyre2 PDB 3eat chain X Region: 23 - 77 Aligned: 41 Modelled: 55 Confidence: 34.2% Identity: 27% PDB header:oxidoreductase Chain: X: PDB Molecule:pyoverdine biosynthesis protein pvcb; PDBTitle: crystal structure of the pvcb (pa2255) protein from2 pseudomonas aeruginosa Phyre2 PDB 1rm1 chain C Region: 59 - 67 Aligned: 9 Modelled: 9 Confidence: 28.7% Identity: 56% PDB header:transcription/dna Chain: C: PDB Molecule:transcription initiation factor iia large chain; PDBTitle: structure of a yeast tfiia/tbp/tata-box dna complex Phyre2 PDB 2vy4 chain A domain 1 Region: 59 - 73 Aligned: 15 Modelled: 15 Confidence: 24.1% Identity: 40% Fold: beta-beta-alpha zinc fingers Superfamily: beta-beta-alpha zinc fingers Family: CHHC finger Phyre2 PDB 3pvj chain B Region: 23 - 49 Aligned: 27 Modelled: 27 Confidence: 9.0% Identity: 22% PDB header:oxidoreductase Chain: B: PDB Molecule:alpha-ketoglutarate-dependent taurine dioxygenase; PDBTitle: crystal structure of the fe(ii)/alpha-ketoglutarate dependent taurine2 dioxygenase from pseudomonas putida kt2440 Phyre2 PDB 3c96 chain A domain 2 Region: 2 - 8 Aligned: 7 Modelled: 7 Confidence: 8.0% Identity: 43% Fold: FAD-linked reductases, C-terminal domain Superfamily: FAD-linked reductases, C-terminal domain Family: PHBH-like Phyre2 PDB 1x3h chain A domain 2 Region: 45 - 51 Aligned: 7 Modelled: 7 Confidence: 7.9% Identity: 57% Fold: Glucocorticoid receptor-like (DNA-binding domain) Superfamily: Glucocorticoid receptor-like (DNA-binding domain) Family: LIM domain Phyre2 PDB 1m06 chain F Region: 60 - 85 Aligned: 20 Modelled: 26 Confidence: 7.0% Identity: 55% Fold: Nucleoplasmin-like/VP (viral coat and capsid proteins) Superfamily: ssDNA viruses Family: Microviridae-like VP Phyre2 1 c1nvpC_ 2 d1nvpc_ 3 d1nh2c_ 4 c1nh2C_ 5 d1ytfc_ 6 c3eatX_ 7 c1rm1C_ 8 d2vy4a1 9 c3pvjB_ 10 d3c96a2 11 d1x3ha2 12 d1m06f_

Detailed template information

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

1 c1nvpC_ 43.2 78 PDB header:transcription/dna Chain: C: PDB Molecule:transcription initiation factor iia beta chain; PDBTitle: human tfiia/tbp/dna complex 2 d1nvpc_ 43.2 78 Fold:Transcription factor IIA (TFIIA), beta-barrel domain Superfamily:Transcription factor IIA (TFIIA), beta-barrel domain Family:Transcription factor IIA (TFIIA), beta-barrel domain 3 d1nh2c_ 42.0 56 Fold:Transcription factor IIA (TFIIA), beta-barrel domain Superfamily:Transcription factor IIA (TFIIA), beta-barrel domain Family:Transcription factor IIA (TFIIA), beta-barrel domain 4 c1nh2C_ 42.0 56 PDB header:transcription/dna Chain: C: PDB Molecule:transcription initiation factor iia large chain; PDBTitle: crystal structure of a yeast tfiia/tbp/dna complex 5 d1ytfc_ 40.1 56 Fold:Transcription factor IIA (TFIIA), beta-barrel domain Superfamily:Transcription factor IIA (TFIIA), beta-barrel domain Family:Transcription factor IIA (TFIIA), beta-barrel domain 6 c3eatX_ 34.2 27 PDB header:oxidoreductase Chain: X: PDB Molecule:pyoverdine biosynthesis protein pvcb; PDBTitle: crystal structure of the pvcb (pa2255) protein from2 pseudomonas aeruginosa 7 c1rm1C_ 28.7 56 PDB header:transcription/dna Chain: C: PDB Molecule:transcription initiation factor iia large chain; PDBTitle: structure of a yeast tfiia/tbp/tata-box dna complex 8 d2vy4a1 24.1 40 Fold:beta-beta-alpha zinc fingers Superfamily:beta-beta-alpha zinc fingers Family:CHHC finger 9 c3pvjB_ 9.0 22 PDB header:oxidoreductase Chain: B: PDB Molecule:alpha-ketoglutarate-dependent taurine dioxygenase; PDBTitle: crystal structure of the fe(ii)/alpha-ketoglutarate dependent taurine2 dioxygenase from pseudomonas putida kt2440 10 d3c96a2 8.0 43 Fold:FAD-linked reductases, C-terminal domain Superfamily:FAD-linked reductases, C-terminal domain Family:PHBH-like 11 d1x3ha2 7.9 57 Fold:Glucocorticoid receptor-like (DNA-binding domain) Superfamily:Glucocorticoid receptor-like (DNA-binding domain) Family:LIM domain 12 d1m06f_ 7.0 55 Fold:Nucleoplasmin-like/VP (viral coat and capsid proteins) Superfamily:ssDNA viruses Family:Microviridae-like VP

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