Secondary structure and disorder prediction

		1	.	.	.	.	.	.	.	.	10	.	.	.	.	.	.	.	.	.	20	.	.	.	.	.	.	.	.	.	30	.	.	.	.	.	.	.	.	.	40	.	.	.	.	.	.	.	.	.	50	.	.	.	.	.	.	.	.	.	60
Sequence		M	S	E	K	V	V	F	S	Q	L	S	R	K	F	I	D	E	N	D	A	T	P	A	E	A	Q	Q	V	V	Y	Y	S	L	A	I	G	H	H	L	G	V	I	D	C	L	E	A	A	L	T	C	P	W	D	E	Y	L	A	W	I
Secondary structure
SS confidence
Disorder		?	?	?	?													?	?	?	?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	70	.	.	.	.	.	.	.	.	.	80	.	.	.	.	.	.	.	.	.	90	.	.	.	.	.	.	.	.	.	100	.	.	.	.	.	.	.	.	.	110	.	.	.	.	.	.	.	.	.	120
Sequence		A	T	L	E	A	G	S	E	A	R	R	K	M	E	G	V	P	K	Y	G	E	I	V	I	D	I	N	H	V	P	M	L	A	N	A	F	D	K	A	R	A	A	Q	T	S	Q	Q	Q	E	W	S	T	M	L	L	S	M	L	H	D
Secondary structure
SS confidence
Disorder						?	?																																?	?	?	?	?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	130	.	.	.	.	.	.
Sequence		I	H	Q	E	N	A	I	Y	L	M	V	R	R	L	R	D
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 1a6c chain A domain 1 Region: 36 - 62 Aligned: 27 Modelled: 27 Confidence: 70.4% Identity: 30% Fold: Nucleoplasmin-like/VP (viral coat and capsid proteins) Superfamily: Positive stranded ssRNA viruses Family: Comoviridae-like VP Phyre2 PDB 1wii chain A Region: 49 - 66 Aligned: 18 Modelled: 18 Confidence: 26.8% Identity: 44% Fold: Rubredoxin-like Superfamily: Zinc beta-ribbon Family: Putative zinc binding domain Phyre2 PDB 3e11 chain A domain 1 Region: 1 - 41 Aligned: 38 Modelled: 41 Confidence: 19.3% Identity: 24% Fold: Zincin-like Superfamily: Metalloproteases ("zincins"), catalytic domain Family: TTHA0227-like Phyre2 PDB 1a6c chain A Region: 36 - 62 Aligned: 27 Modelled: 27 Confidence: 16.2% Identity: 30% PDB header:virus Chain: A: PDB Molecule:tobacco ringspot virus capsid protein; PDBTitle: structure of tobacco ringspot virus Phyre2 PDB 2gk9 chain D Region: 24 - 45 Aligned: 22 Modelled: 22 Confidence: 16.1% Identity: 41% PDB header:transferase Chain: D: PDB Molecule:phosphatidylinositol-4-phosphate 5-kinase, type PDBTitle: human phosphatidylinositol-4-phosphate 5-kinase, type ii,2 gamma Phyre2 PDB 2y7u chain M Region: 36 - 62 Aligned: 27 Modelled: 27 Confidence: 13.8% Identity: 19% PDB header:virus Chain: M: PDB Molecule:coat protein; PDBTitle: x-ray structure of the grapevine fanleaf virus Phyre2 PDB 2q9l chain A Region: 16 - 41 Aligned: 26 Modelled: 26 Confidence: 13.8% Identity: 27% PDB header:hydrolase Chain: A: PDB Molecule:hypothetical protein; PDBTitle: crystal structure of imazg from vibrio dat 722: ctag-imazg (p43212) Phyre2 PDB 3dl8 chain D Region: 28 - 43 Aligned: 16 Modelled: 16 Confidence: 12.6% Identity: 50% PDB header:protein transport Chain: D: PDB Molecule:sece; PDBTitle: structure of the complex of aquifex aeolicus secyeg and2 bacillus subtilis seca Phyre2 PDB 1dxq chain A Region: 31 - 40 Aligned: 10 Modelled: 10 Confidence: 10.6% Identity: 60% Fold: Flavodoxin-like Superfamily: Flavoproteins Family: Quinone reductase Phyre2 PDB 3obc chain B Region: 16 - 50 Aligned: 34 Modelled: 35 Confidence: 9.7% Identity: 21% PDB header:hydrolase Chain: B: PDB Molecule:pyrophosphatase; PDBTitle: crystal structure of a pyrophosphatase (af1178) from archaeoglobus2 fulgidus at 1.80 a resolution Phyre2 PDB 2khs chain B Region: 52 - 81 Aligned: 26 Modelled: 30 Confidence: 9.6% Identity: 27% PDB header:hydrolase Chain: B: PDB Molecule:nuclease; PDBTitle: solution structure of snase121:snase(111-143) complex Phyre2 PDB 2oie chain A domain 1 Region: 16 - 41 Aligned: 26 Modelled: 26 Confidence: 8.6% Identity: 27% Fold: all-alpha NTP pyrophosphatases Superfamily: all-alpha NTP pyrophosphatases Family: MazG-like Phyre2 PDB 2ejq chain A domain 1 Region: 1 - 39 Aligned: 37 Modelled: 39 Confidence: 8.4% Identity: 19% Fold: Zincin-like Superfamily: Metalloproteases ("zincins"), catalytic domain Family: TTHA0227-like Phyre2 PDB 1ebf chain A domain 1 Region: 30 - 62 Aligned: 33 Modelled: 33 Confidence: 8.4% Identity: 9% Fold: NAD(P)-binding Rossmann-fold domains Superfamily: NAD(P)-binding Rossmann-fold domains Family: Glyceraldehyde-3-phosphate dehydrogenase-like, N-terminal domain Phyre2 PDB 2gta chain D domain 1 Region: 16 - 41 Aligned: 26 Modelled: 26 Confidence: 8.3% Identity: 12% Fold: all-alpha NTP pyrophosphatases Superfamily: all-alpha NTP pyrophosphatases Family: MazG-like Phyre2 PDB 2gta chain A domain 1 Region: 16 - 41 Aligned: 26 Modelled: 26 Confidence: 8.1% Identity: 12% Fold: all-alpha NTP pyrophosphatases Superfamily: all-alpha NTP pyrophosphatases Family: MazG-like Phyre2 PDB 1vmg chain A Region: 16 - 41 Aligned: 26 Modelled: 26 Confidence: 7.5% Identity: 19% Fold: all-alpha NTP pyrophosphatases Superfamily: all-alpha NTP pyrophosphatases Family: MazG-like Phyre2 PDB 1cmc chain A Region: 16 - 29 Aligned: 14 Modelled: 14 Confidence: 7.3% Identity: 21% Fold: Ribbon-helix-helix Superfamily: Ribbon-helix-helix Family: Met repressor, MetJ (MetR) Phyre2 PDB 1qgp chain A Region: 79 - 114 Aligned: 36 Modelled: 36 Confidence: 7.1% Identity: 11% Fold: DNA/RNA-binding 3-helical bundle Superfamily: "Winged helix" DNA-binding domain Family: Z-DNA binding domain Phyre2 PDB 2q4p chain A Region: 16 - 50 Aligned: 34 Modelled: 35 Confidence: 7.1% Identity: 24% PDB header:structural genomics, unknown function Chain: A: PDB Molecule:protein rs21-c6; PDBTitle: ensemble refinement of the crystal structure of protein from mus2 musculus mm.29898 Phyre2 1 d1a6ca1 2 d1wiia_ 3 d3e11a1 4 c1a6cA_ 5 c2gk9D_ 6 c2y7uM_ 7 c2q9lA_ 8 c3dl8D_ 9 d1dxqa_ 10 c3obcB_ 11 c2khsB_ 12 d2oiea1 13 d2ejqa1 14 d1ebfa1 15 d2gtad1 16 d2gtaa1 17 d1vmga_ 18 d1cmca_ 19 d1qgpa_ 20 c2q4pA_ 21 22 23 24 25 26 27 28 29 30

Detailed template information

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

1 d1a6ca1 70.4 30 Fold:Nucleoplasmin-like/VP (viral coat and capsid proteins) Superfamily:Positive stranded ssRNA viruses Family:Comoviridae-like VP 2 d1wiia_ 26.8 44 Fold:Rubredoxin-like Superfamily:Zinc beta-ribbon Family:Putative zinc binding domain 3 d3e11a1 19.3 24 Fold:Zincin-like Superfamily:Metalloproteases ("zincins"), catalytic domain Family:TTHA0227-like 4 c1a6cA_ 16.2 30 PDB header:virus Chain: A: PDB Molecule:tobacco ringspot virus capsid protein; PDBTitle: structure of tobacco ringspot virus 5 c2gk9D_ 16.1 41 PDB header:transferase Chain: D: PDB Molecule:phosphatidylinositol-4-phosphate 5-kinase, type PDBTitle: human phosphatidylinositol-4-phosphate 5-kinase, type ii,2 gamma 6 c2y7uM_ 13.8 19 PDB header:virus Chain: M: PDB Molecule:coat protein; PDBTitle: x-ray structure of the grapevine fanleaf virus 7 c2q9lA_ 13.8 27 PDB header:hydrolase Chain: A: PDB Molecule:hypothetical protein; PDBTitle: crystal structure of imazg from vibrio dat 722: ctag-imazg (p43212) 8 c3dl8D_ 12.6 50 PDB header:protein transport Chain: D: PDB Molecule:sece; PDBTitle: structure of the complex of aquifex aeolicus secyeg and2 bacillus subtilis seca 9 d1dxqa_ 10.6 60 Fold:Flavodoxin-like Superfamily:Flavoproteins Family:Quinone reductase 10 c3obcB_ 9.7 21 PDB header:hydrolase Chain: B: PDB Molecule:pyrophosphatase; PDBTitle: crystal structure of a pyrophosphatase (af1178) from archaeoglobus2 fulgidus at 1.80 a resolution 11 c2khsB_ 9.6 27 PDB header:hydrolase Chain: B: PDB Molecule:nuclease; PDBTitle: solution structure of snase121:snase(111-143) complex 12 d2oiea1 8.6 27 Fold:all-alpha NTP pyrophosphatases Superfamily:all-alpha NTP pyrophosphatases Family:MazG-like 13 d2ejqa1 8.4 19 Fold:Zincin-like Superfamily:Metalloproteases ("zincins"), catalytic domain Family:TTHA0227-like 14 d1ebfa1 8.4 9 Fold:NAD(P)-binding Rossmann-fold domains Superfamily:NAD(P)-binding Rossmann-fold domains Family:Glyceraldehyde-3-phosphate dehydrogenase-like, N-terminal domain 15 d2gtad1 8.3 12 Fold:all-alpha NTP pyrophosphatases Superfamily:all-alpha NTP pyrophosphatases Family:MazG-like 16 d2gtaa1 8.1 12 Fold:all-alpha NTP pyrophosphatases Superfamily:all-alpha NTP pyrophosphatases Family:MazG-like 17 d1vmga_ 7.5 19 Fold:all-alpha NTP pyrophosphatases Superfamily:all-alpha NTP pyrophosphatases Family:MazG-like 18 d1cmca_ 7.3 21 Fold:Ribbon-helix-helix Superfamily:Ribbon-helix-helix Family:Met repressor, MetJ (MetR) 19 d1qgpa_ 7.1 11 Fold:DNA/RNA-binding 3-helical bundle Superfamily:"Winged helix" DNA-binding domain Family:Z-DNA binding domain 20 c2q4pA_ 7.1 24 PDB header:structural genomics, unknown function Chain: A: PDB Molecule:protein rs21-c6; PDBTitle: ensemble refinement of the crystal structure of protein from mus2 musculus mm.29898 21 d2a3qa1 not modelled 7.1 24 Fold:all-alpha NTP pyrophosphatases Superfamily:all-alpha NTP pyrophosphatases Family:MazG-like 22 c2p7vA_ not modelled 6.9 24 PDB header:transcription Chain: A: PDB Molecule:regulator of sigma d; PDBTitle: crystal structure of the escherichia coli regulator of sigma 70, rsd,2 in complex with sigma 70 domain 4 23 c3lj4i_ not modelled 6.9 20 PDB header:viral protein Chain: I: PDB Molecule:portal protein; PDBTitle: bacteriophage p22 portal protein bound to middle tail factor gp4. this2 file contain the first biological assembly 24 d1xq5a_ not modelled 6.8 7 Fold:Globin-like Superfamily:Globin-like Family:Globins 25 c2dzjA_ not modelled 6.0 33 PDB header:sugar binding protein Chain: A: PDB Molecule:synaptic glycoprotein sc2; PDBTitle: 2dzj/solution structure of the n-terminal ubiquitin-like2 domain in human synaptic glycoprotein sc2 26 d2yzca2 not modelled 6.0 15 Fold:T-fold Superfamily:Tetrahydrobiopterin biosynthesis enzymes-like Family:Urate oxidase (uricase) 27 c3efyB_ not modelled 6.0 15 PDB header:cell cycle Chain: B: PDB Molecule:cif (cell cycle inhibiting factor); PDBTitle: structure of the cyclomodulin cif from pathogenic2 escherichia coli 28 d1pcfa_ not modelled 5.9 13 Fold:ssDNA-binding transcriptional regulator domain Superfamily:ssDNA-binding transcriptional regulator domain Family:Transcriptional coactivator PC4 C-terminal domain 29 d1jl6a_ not modelled 5.6 13 Fold:Globin-like Superfamily:Globin-like Family:Globins 30 c1otpA_ not modelled 5.2 24 PDB header:phosphorylase Chain: A: PDB Molecule:thymidine phosphorylase; PDBTitle: structural and theoretical studies suggest domain movement produces an2 active conformation of thymidine phosphorylase

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