Secondary structure and disorder prediction

		1	.	.	.	.	.	.	.	.	10	.	.	.	.	.	.	.	.	.	20	.	.	.	.	.	.	.	.	.	30	.	.	.	.	.	.	.	.	.	40	.	.	.	.	.	.	.	.	.	50	.	.	.	.	.	.	.	.	.	60
Sequence		M	T	E	E	C	G	E	I	V	F	W	T	L	R	K	K	F	V	A	S	S	D	E	M	P	E	H	S	S	Q	V	M	Y	Y	S	L	A	I	G	H	H	V	G	V	I	D	C	L	N	V	A	F	R	C	P	L	T	E	Y	E
Secondary structure
SS confidence
Disorder		?	?	?	?	?	?														?	?	?	?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	70	.	.	.	.	.	.	.	.	.	80	.	.	.	.	.	.	.	.	.	90	.	.	.	.	.	.	.	.	.	100	.	.	.	.	.	.	.	.	.	110	.	.	.	.	.	.	.	.	.	120
Sequence		D	W	L	A	L	V	E	E	E	Q	A	R	R	K	M	L	G	V	M	T	F	G	E	I	V	I	D	A	S	H	T	A	L	L	T	R	A	F	A	P	L	A	D	D	A	T	S	V	W	Q	A	R	S	I	Q	F	I	H	L	L
Secondary structure
SS confidence
Disorder								?																																	?	?	?	?	?	?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	130	.	.	.	.	.	.	.
Sequence		D	E	I	V	Q	E	P	A	I	Y	L	M	A	R	K	I	A
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: 39 - 65 Aligned: 27 Modelled: 27 Confidence: 69.0% Identity: 22% Fold: Nucleoplasmin-like/VP (viral coat and capsid proteins) Superfamily: Positive stranded ssRNA viruses Family: Comoviridae-like VP Phyre2 PDB 1wii chain A Region: 52 - 69 Aligned: 18 Modelled: 18 Confidence: 20.5% Identity: 28% Fold: Rubredoxin-like Superfamily: Zinc beta-ribbon Family: Putative zinc binding domain Phyre2 PDB 2p7v chain A Region: 44 - 76 Aligned: 33 Modelled: 33 Confidence: 17.5% Identity: 18% 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 Phyre2 PDB 2gk9 chain D Region: 27 - 48 Aligned: 22 Modelled: 22 Confidence: 16.1% Identity: 45% 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 1a6c chain A Region: 39 - 65 Aligned: 27 Modelled: 27 Confidence: 16.0% Identity: 22% PDB header:virus Chain: A: PDB Molecule:tobacco ringspot virus capsid protein; PDBTitle: structure of tobacco ringspot virus Phyre2 PDB 2q9l chain A Region: 19 - 44 Aligned: 26 Modelled: 26 Confidence: 16.0% 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: 31 - 46 Aligned: 16 Modelled: 16 Confidence: 14.0% Identity: 44% PDB header:protein transport Chain: D: PDB Molecule:sece; PDBTitle: structure of the complex of aquifex aeolicus secyeg and2 bacillus subtilis seca Phyre2 PDB 2y7u chain M Region: 39 - 65 Aligned: 27 Modelled: 27 Confidence: 13.5% Identity: 15% PDB header:virus Chain: M: PDB Molecule:coat protein; PDBTitle: x-ray structure of the grapevine fanleaf virus Phyre2 PDB 1dxq chain A Region: 34 - 43 Aligned: 10 Modelled: 10 Confidence: 11.3% Identity: 50% Fold: Flavodoxin-like Superfamily: Flavoproteins Family: Quinone reductase Phyre2 PDB 3aq0 chain G Region: 15 - 81 Aligned: 63 Modelled: 67 Confidence: 11.3% Identity: 11% PDB header:transferase Chain: G: PDB Molecule:geranyl diphosphate synthase; PDBTitle: ligand-bound form of arabidopsis medium/long-chain length prenyl2 pyrophosphate synthase (surface polar residue mutant) Phyre2 PDB 1cmc chain A Region: 19 - 32 Aligned: 14 Modelled: 14 Confidence: 11.2% Identity: 43% Fold: Ribbon-helix-helix Superfamily: Ribbon-helix-helix Family: Met repressor, MetJ (MetR) Phyre2 PDB 2id6 chain A domain 2 Region: 41 - 73 Aligned: 33 Modelled: 33 Confidence: 11.2% Identity: 18% Fold: Tetracyclin repressor-like, C-terminal domain Superfamily: Tetracyclin repressor-like, C-terminal domain Family: Tetracyclin repressor-like, C-terminal domain Phyre2 PDB 3obc chain B Region: 19 - 53 Aligned: 34 Modelled: 35 Confidence: 10.2% 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 2gta chain A domain 1 Region: 19 - 44 Aligned: 26 Modelled: 26 Confidence: 9.8% Identity: 8% Fold: all-alpha NTP pyrophosphatases Superfamily: all-alpha NTP pyrophosphatases Family: MazG-like Phyre2 PDB 2oie chain A domain 1 Region: 19 - 44 Aligned: 26 Modelled: 26 Confidence: 9.6% Identity: 23% Fold: all-alpha NTP pyrophosphatases Superfamily: all-alpha NTP pyrophosphatases Family: MazG-like Phyre2 PDB 3a9f chain A Region: 5 - 34 Aligned: 30 Modelled: 30 Confidence: 9.5% Identity: 10% PDB header:electron transport Chain: A: PDB Molecule:cytochrome c; PDBTitle: crystal structure of the c-terminal domain of cytochrome cz2 from chlorobium tepidum Phyre2 PDB 2gta chain D domain 1 Region: 19 - 44 Aligned: 26 Modelled: 26 Confidence: 9.4% Identity: 8% Fold: all-alpha NTP pyrophosphatases Superfamily: all-alpha NTP pyrophosphatases Family: MazG-like Phyre2 PDB 2f3i chain A Region: 118 - 137 Aligned: 20 Modelled: 20 Confidence: 9.2% Identity: 25% PDB header:transferase Chain: A: PDB Molecule:dna-directed rna polymerases i, ii, and iii 17.1 PDBTitle: solution structure of a subunit of rna polymerase ii Phyre2 PDB 1np3 chain A domain 1 Region: 81 - 132 Aligned: 52 Modelled: 52 Confidence: 8.7% Identity: 21% Fold: 6-phosphogluconate dehydrogenase C-terminal domain-like Superfamily: 6-phosphogluconate dehydrogenase C-terminal domain-like Family: Acetohydroxy acid isomeroreductase (ketol-acid reductoisomerase, KARI) Phyre2 PDB 1vmg chain A Region: 19 - 44 Aligned: 26 Modelled: 26 Confidence: 8.5% Identity: 19% Fold: all-alpha NTP pyrophosphatases Superfamily: all-alpha NTP pyrophosphatases Family: MazG-like Phyre2 1 d1a6ca1 2 d1wiia_ 3 c2p7vA_ 4 c2gk9D_ 5 c1a6cA_ 6 c2q9lA_ 7 c3dl8D_ 8 c2y7uM_ 9 d1dxqa_ 10 c3aq0G_ 11 d1cmca_ 12 d2id6a2 13 c3obcB_ 14 d2gtaa1 15 d2oiea1 16 c3a9fA_ 17 d2gtad1 18 c2f3iA_ 19 d1np3a1 20 d1vmga_ 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47

Detailed template information

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

1 d1a6ca1 69.0 22 Fold:Nucleoplasmin-like/VP (viral coat and capsid proteins) Superfamily:Positive stranded ssRNA viruses Family:Comoviridae-like VP 2 d1wiia_ 20.5 28 Fold:Rubredoxin-like Superfamily:Zinc beta-ribbon Family:Putative zinc binding domain 3 c2p7vA_ 17.5 18 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 4 c2gk9D_ 16.1 45 PDB header:transferase Chain: D: PDB Molecule:phosphatidylinositol-4-phosphate 5-kinase, type PDBTitle: human phosphatidylinositol-4-phosphate 5-kinase, type ii,2 gamma 5 c1a6cA_ 16.0 22 PDB header:virus Chain: A: PDB Molecule:tobacco ringspot virus capsid protein; PDBTitle: structure of tobacco ringspot virus 6 c2q9lA_ 16.0 27 PDB header:hydrolase Chain: A: PDB Molecule:hypothetical protein; PDBTitle: crystal structure of imazg from vibrio dat 722: ctag-imazg (p43212) 7 c3dl8D_ 14.0 44 PDB header:protein transport Chain: D: PDB Molecule:sece; PDBTitle: structure of the complex of aquifex aeolicus secyeg and2 bacillus subtilis seca 8 c2y7uM_ 13.5 15 PDB header:virus Chain: M: PDB Molecule:coat protein; PDBTitle: x-ray structure of the grapevine fanleaf virus 9 d1dxqa_ 11.3 50 Fold:Flavodoxin-like Superfamily:Flavoproteins Family:Quinone reductase 10 c3aq0G_ 11.3 11 PDB header:transferase Chain: G: PDB Molecule:geranyl diphosphate synthase; PDBTitle: ligand-bound form of arabidopsis medium/long-chain length prenyl2 pyrophosphate synthase (surface polar residue mutant) 11 d1cmca_ 11.2 43 Fold:Ribbon-helix-helix Superfamily:Ribbon-helix-helix Family:Met repressor, MetJ (MetR) 12 d2id6a2 11.2 18 Fold:Tetracyclin repressor-like, C-terminal domain Superfamily:Tetracyclin repressor-like, C-terminal domain Family:Tetracyclin repressor-like, C-terminal domain 13 c3obcB_ 10.2 21 PDB header:hydrolase Chain: B: PDB Molecule:pyrophosphatase; PDBTitle: crystal structure of a pyrophosphatase (af1178) from archaeoglobus2 fulgidus at 1.80 a resolution 14 d2gtaa1 9.8 8 Fold:all-alpha NTP pyrophosphatases Superfamily:all-alpha NTP pyrophosphatases Family:MazG-like 15 d2oiea1 9.6 23 Fold:all-alpha NTP pyrophosphatases Superfamily:all-alpha NTP pyrophosphatases Family:MazG-like 16 c3a9fA_ 9.5 10 PDB header:electron transport Chain: A: PDB Molecule:cytochrome c; PDBTitle: crystal structure of the c-terminal domain of cytochrome cz2 from chlorobium tepidum 17 d2gtad1 9.4 8 Fold:all-alpha NTP pyrophosphatases Superfamily:all-alpha NTP pyrophosphatases Family:MazG-like 18 c2f3iA_ 9.2 25 PDB header:transferase Chain: A: PDB Molecule:dna-directed rna polymerases i, ii, and iii 17.1 PDBTitle: solution structure of a subunit of rna polymerase ii 19 d1np3a1 8.7 21 Fold:6-phosphogluconate dehydrogenase C-terminal domain-like Superfamily:6-phosphogluconate dehydrogenase C-terminal domain-like Family:Acetohydroxy acid isomeroreductase (ketol-acid reductoisomerase, KARI) 20 d1vmga_ 8.5 19 Fold:all-alpha NTP pyrophosphatases Superfamily:all-alpha NTP pyrophosphatases Family:MazG-like 21 d1ebfa1 not modelled 8.2 12 Fold:NAD(P)-binding Rossmann-fold domains Superfamily:NAD(P)-binding Rossmann-fold domains Family:Glyceraldehyde-3-phosphate dehydrogenase-like, N-terminal domain 22 c2khsB_ not modelled 7.9 27 PDB header:hydrolase Chain: B: PDB Molecule:nuclease; PDBTitle: solution structure of snase121:snase(111-143) complex 23 c2l5fA_ not modelled 7.6 10 PDB header:protein binding Chain: A: PDB Molecule:pre-mrna-processing factor 40 homolog a; PDBTitle: solution structure of the tandem ww domains from hypa/fbp11 24 c2q4pA_ not modelled 7.2 18 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 25 d2a3qa1 not modelled 7.2 18 Fold:all-alpha NTP pyrophosphatases Superfamily:all-alpha NTP pyrophosphatases Family:MazG-like 26 c3lj4i_ not modelled 7.0 10 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 27 c3iz5W_ not modelled 6.1 39 PDB header:ribosome Chain: W: PDB Molecule:60s ribosomal protein l22 (l22e); PDBTitle: localization of the large subunit ribosomal proteins into a 5.5 a2 cryo-em map of triticum aestivum translating 80s ribosome 28 c3p7jA_ not modelled 6.0 16 PDB header:transcription Chain: A: PDB Molecule:heterochromatin protein 1; PDBTitle: drosophila hp1a chromo shadow domain 29 d1pn2a1 not modelled 6.0 33 Fold:Thioesterase/thiol ester dehydrase-isomerase Superfamily:Thioesterase/thiol ester dehydrase-isomerase Family:MaoC-like 30 d1d8ca_ not modelled 6.0 19 Fold:TIM beta/alpha-barrel Superfamily:Malate synthase G Family:Malate synthase G 31 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 32 d2rm0w1 not modelled 5.8 20 Fold:WW domain-like Superfamily:WW domain Family:WW domain 33 d1unda_ not modelled 5.8 6 Fold:VHP, Villin headpiece domain Superfamily:VHP, Villin headpiece domain Family:VHP, Villin headpiece domain 34 d2hanb1 not modelled 5.8 25 Fold:Glucocorticoid receptor-like (DNA-binding domain) Superfamily:Glucocorticoid receptor-like (DNA-binding domain) Family:Nuclear receptor 35 c3oyrA_ not modelled 5.7 15 PDB header:transferase Chain: A: PDB Molecule:trans-isoprenyl diphosphate synthase; PDBTitle: crystal structure of polyprenyl synthase from caulobacter crescentus2 cb15 complexed with calcium and isoprenyl diphosphate 36 d1gpca_ not modelled 5.6 24 Fold:OB-fold Superfamily:Nucleic acid-binding proteins Family:Phage ssDNA-binding proteins 37 c2dzjA_ not modelled 5.5 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 38 d1qzpa_ not modelled 5.4 12 Fold:VHP, Villin headpiece domain Superfamily:VHP, Villin headpiece domain Family:VHP, Villin headpiece domain 39 c3efyB_ not modelled 5.4 19 PDB header:cell cycle Chain: B: PDB Molecule:cif (cell cycle inhibiting factor); PDBTitle: structure of the cyclomodulin cif from pathogenic2 escherichia coli 40 c3gp2B_ not modelled 5.4 71 PDB header:metal binding protein/transferase Chain: B: PDB Molecule:calcium/calmodulin-dependent protein kinase type PDBTitle: calmodulin bound to peptide from calmodulin kinase ii2 (camkii) 41 c1cm4B_ not modelled 5.4 71 PDB header:complex (calcium-binding/transferase) Chain: B: PDB Molecule:calmodulin-dependent protein kinase ii-alpha; PDBTitle: motions of calmodulin-four-conformer refinement 42 c1cdmB_ not modelled 5.4 71 PDB header:calcium-binding protein Chain: B: PDB Molecule:calmodulin; PDBTitle: modulation of calmodulin plasticity in molecular2 recognition on the basis of x-ray structures 43 c1cm1B_ not modelled 5.4 71 PDB header:complex (calcium-binding/transferase) Chain: B: PDB Molecule:calmodulin-dependent protein kinase ii-alpha; PDBTitle: motions of calmodulin-single-conformer refinement 44 d2fmma1 not modelled 5.2 23 Fold:SH3-like barrel Superfamily:Chromo domain-like Family:Chromo domain 45 d1thta_ not modelled 5.1 55 Fold:alpha/beta-Hydrolases Superfamily:alpha/beta-Hydrolases Family:Thioesterases 46 d2o3bb1 not modelled 5.1 40 Fold:Nuclease A inhibitor (NuiA) Superfamily:Nuclease A inhibitor (NuiA) Family:Nuclease A inhibitor (NuiA) 47 c3cbbA_ not modelled 5.0 31 PDB header:transcription/dna Chain: A: PDB Molecule:hepatocyte nuclear factor 4-alpha, dna binding PDBTitle: crystal structure of hepatocyte nuclear factor 4alpha in2 complex with dna: diabetes gene product

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