Secondary structure and disorder prediction

		1	.	.	.	.	.	.	.	.	10	.	.	.	.	.	.	.	.	.	20	.	.	.	.	.	.	.	.	.	30	.	.	.	.	.	.	.	.	.	40	.	.	.	.	.	.	.	.	.	50	.	.	.	.	.	.	.	.	.	60
Sequence		M	S	H	Y	H	E	Q	F	L	K	Q	N	P	L	A	V	L	G	V	L	R	D	L	H	K	A	A	I	P	L	R	L	S	W	N	G	G	Q	L	I	S	K	L	L	A	I	T	P	D	K	L	V	L	D	F	G	S	Q	A	E
Secondary structure
SS confidence
Disorder		?	?	?	?	?	?		?	?	?																																																		?
Disorder confidence
		.	.	.	.	.	.	.	.	.	70	.	.	.	.	.	.	.	.	.	80	.	.	.	.	.	.	.	.	.	90	.	.	.	.	.	.	.	.	.	100	.	.	.	.	.	.	.	.	.	110	.	.	.	.	.	.	.	.	.	120
Sequence		D	N	I	A	V	L	K	A	Q	H	I	T	I	T	A	E	T	Q	G	A	K	V	E	F	T	V	E	Q	L	Q	Q	S	E	Y	L	Q	L	P	A	F	I	T	V	P	P	P	T	L	W	F	V	Q	R	R	R	Y	F	R	I	S
Secondary structure
SS confidence
Disorder		?
Disorder confidence
		.	.	.	.	.	.	.	.	.	130	.	.	.	.	.	.	.	.	.	140	.	.	.	.	.	.	.	.	.	150	.	.	.	.	.	.	.	.	.	160	.	.	.	.	.	.	.	.	.	170	.	.	.	.	.	.	.	.	.	180
Sequence		A	P	L	H	P	P	Y	F	C	Q	T	K	L	A	D	N	S	T	L	R	F	R	L	Y	D	L	S	L	G	G	M	G	A	L	L	E	T	A	K	P	A	E	L	Q	E	G	M	R	F	A	Q	I	E	V	N	M	G	Q	W	G
Secondary structure
SS confidence
Disorder																																								?	?	?	?	?																?
Disorder confidence
		.	.	.	.	.	.	.	.	.	190	.	.	.	.	.	.	.	.	.	200	.	.	.	.	.	.	.	.	.	210	.	.	.	.	.	.	.	.	.	220	.	.	.	.	.	.	.	.	.	230	.	.	.	.	.	.	.	.	.	240
Sequence		V	F	H	F	D	A	Q	L	I	S	I	S	E	R	K	V	I	D	G	K	N	E	T	I	T	T	P	R	L	S	F	R	F	L	N	V	S	P	T	V	E	R	Q	L	Q	R	I	I	F	S	L	E	R	E	A	R	E	K	A	D
Secondary structure
SS confidence
Disorder																?	?	?	?	?		?															?	?
Disorder confidence
		.	.	.	.
Sequence		K	V	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 2gjg chain A Region: 8 - 240 Aligned: 225 Modelled: 233 Confidence: 100.0% Identity: 21% PDB header:motor protein Chain: A: PDB Molecule:hypothetical protein pp4397; PDBTitle: crystal structure of a pilz-containing protein (pp4397) from2 pseudomonas putida kt2440 at 2.25 a resolution Phyre2 PDB 3kyg chain B Region: 22 - 227 Aligned: 191 Modelled: 206 Confidence: 99.9% Identity: 16% PDB header:unknown function Chain: B: PDB Molecule:putative uncharacterized protein vca0042; PDBTitle: crystal structure of vca0042 (l135r) complexed with c-di-gmp Phyre2 PDB 2rde chain B Region: 22 - 227 Aligned: 191 Modelled: 206 Confidence: 99.9% Identity: 15% PDB header:structural genomics, unknown function Chain: B: PDB Molecule:uncharacterized protein vca0042; PDBTitle: crystal structure of vca0042 complexed with c-di-gmp Phyre2 PDB 1ywu chain A domain 1 Region: 113 - 228 Aligned: 95 Modelled: 116 Confidence: 99.1% Identity: 20% Fold: Split barrel-like Superfamily: PilZ domain-like Family: PilZ domain Phyre2 PDB 1ywu chain A Region: 113 - 228 Aligned: 95 Modelled: 116 Confidence: 99.1% Identity: 20% PDB header:structural genomics, unknown function Chain: A: PDB Molecule:hypothetical protein pa4608; PDBTitle: solution nmr structure of pseudomonas aeruginosa protein pa4608.2 northeast structural genomics target pat7 Phyre2 PDB 3ph1 chain C Region: 136 - 237 Aligned: 88 Modelled: 102 Confidence: 98.8% Identity: 17% PDB header:unknown function Chain: C: PDB Molecule:putative uncharacterized protein; PDBTitle: the crystal structure of a pathogenic protein from the xanthomonas2 campestris reveals a new tetrameric pilz domain self-assembled via a3 unusual helical bundle Phyre2 PDB 2rde chain A domain 1 Region: 117 - 227 Aligned: 97 Modelled: 111 Confidence: 98.7% Identity: 12% Fold: Split barrel-like Superfamily: PilZ domain-like Family: PilZ domain Phyre2 PDB 3cnr chain A Region: 139 - 228 Aligned: 74 Modelled: 90 Confidence: 98.2% Identity: 8% PDB header:unknown function Chain: A: PDB Molecule:type iv fimbriae assembly protein; PDBTitle: crystal structure of pilz (xac1133) from xanthomonas2 axonopodis pv citri Phyre2 PDB 2rde chain A domain 2 Region: 22 - 115 Aligned: 93 Modelled: 94 Confidence: 97.4% Identity: 20% Fold: Split barrel-like Superfamily: PilZ domain-like Family: PilZ domain-associated domain Phyre2 PDB 2l1t chain A Region: 26 - 117 Aligned: 89 Modelled: 92 Confidence: 88.4% Identity: 12% PDB header:structural genomics, unknown function Chain: A: PDB Molecule:uncharacterized protein; PDBTitle: solution structure of the n-terminal domain of np_954075.1 Phyre2 PDB 2ix0 chain A domain 3 Region: 134 - 185 Aligned: 46 Modelled: 52 Confidence: 81.2% Identity: 13% Fold: OB-fold Superfamily: Nucleic acid-binding proteins Family: Cold shock DNA-binding domain-like Phyre2 PDB 1x9l chain A Region: 144 - 189 Aligned: 44 Modelled: 46 Confidence: 33.1% Identity: 18% Fold: Common fold of diphtheria toxin/transcription factors/cytochrome f Superfamily: DR1885-like metal-binding protein Family: DR1885-like metal-binding protein Phyre2 PDB 2k6z chain A Region: 144 - 189 Aligned: 44 Modelled: 46 Confidence: 20.5% Identity: 18% PDB header:metal transport Chain: A: PDB Molecule:putative uncharacterized protein ttha1943; PDBTitle: solution structures of copper loaded form pcua (trans2 conformation of the peptide bond involving the nitrogen of3 p14) Phyre2 PDB 1kwg chain A domain 1 Region: 102 - 154 Aligned: 51 Modelled: 53 Confidence: 16.1% Identity: 8% Fold: Glycosyl hydrolase domain Superfamily: Glycosyl hydrolase domain Family: alpha-Amylases, C-terminal beta-sheet domain Phyre2 PDB 3fwa chain A Region: 11 - 56 Aligned: 46 Modelled: 46 Confidence: 14.4% Identity: 13% PDB header:flavoprotein Chain: A: PDB Molecule:reticuline oxidase; PDBTitle: structure of berberine bridge enzyme, c166a variant in complex with2 (s)-reticuline Phyre2 PDB 3cw4 chain A Region: 126 - 162 Aligned: 37 Modelled: 37 Confidence: 13.9% Identity: 14% PDB header:transferase Chain: A: PDB Molecule:polymerase basic protein 2; PDBTitle: large c-terminal domain of influenza a virus rna-dependent polymerase2 pb2 Phyre2 PDB 3d2h chain A Region: 11 - 56 Aligned: 46 Modelled: 46 Confidence: 13.6% Identity: 13% PDB header:oxidoreductase Chain: A: PDB Molecule:berberine bridge-forming enzyme; PDBTitle: structure of berberine bridge enzyme from eschscholzia californica,2 monoclinic crystal form Phyre2 PDB 2fts chain A domain 1 Region: 98 - 175 Aligned: 78 Modelled: 78 Confidence: 12.3% Identity: 14% Fold: beta-clip Superfamily: MoeA C-terminal domain-like Family: MoeA C-terminal domain-like Phyre2 PDB 1gtr chain A domain 1 Region: 105 - 126 Aligned: 22 Modelled: 22 Confidence: 11.0% Identity: 14% Fold: Ribosomal protein L25-like Superfamily: Ribosomal protein L25-like Family: Gln-tRNA synthetase (GlnRS), C-terminal (anticodon-binding) domain Phyre2 PDB 1zr6 chain A Region: 11 - 56 Aligned: 46 Modelled: 46 Confidence: 9.9% Identity: 11% PDB header:oxidoreductase Chain: A: PDB Molecule:glucooligosaccharide oxidase; PDBTitle: the crystal structure of an acremonium strictum glucooligosaccharide2 oxidase reveals a novel flavinylation Phyre2 1 c2gjgA_ 2 c3kygB_ 3 c2rdeB_ 4 d1ywua1 5 c1ywuA_ 6 c3ph1C_ 7 d2rdea1 8 c3cnrA_ 9 d2rdea2 10 c2l1tA_ 11 d2ix0a3 12 d1x9la_ 13 c2k6zA_ 14 d1kwga1 15 c3fwaA_ 16 c3cw4A_ 17 c3d2hA_ 18 d2ftsa1 19 d1gtra1 20 c1zr6A_ 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37

Detailed template information

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

1 c2gjgA_ 100.0 21 PDB header:motor protein Chain: A: PDB Molecule:hypothetical protein pp4397; PDBTitle: crystal structure of a pilz-containing protein (pp4397) from2 pseudomonas putida kt2440 at 2.25 a resolution 2 c3kygB_ 99.9 16 PDB header:unknown function Chain: B: PDB Molecule:putative uncharacterized protein vca0042; PDBTitle: crystal structure of vca0042 (l135r) complexed with c-di-gmp 3 c2rdeB_ 99.9 15 PDB header:structural genomics, unknown function Chain: B: PDB Molecule:uncharacterized protein vca0042; PDBTitle: crystal structure of vca0042 complexed with c-di-gmp 4 d1ywua1 99.1 20 Fold:Split barrel-like Superfamily:PilZ domain-like Family:PilZ domain 5 c1ywuA_ 99.1 20 PDB header:structural genomics, unknown function Chain: A: PDB Molecule:hypothetical protein pa4608; PDBTitle: solution nmr structure of pseudomonas aeruginosa protein pa4608.2 northeast structural genomics target pat7 6 c3ph1C_ 98.8 17 PDB header:unknown function Chain: C: PDB Molecule:putative uncharacterized protein; PDBTitle: the crystal structure of a pathogenic protein from the xanthomonas2 campestris reveals a new tetrameric pilz domain self-assembled via a3 unusual helical bundle 7 d2rdea1 98.7 12 Fold:Split barrel-like Superfamily:PilZ domain-like Family:PilZ domain 8 c3cnrA_ 98.2 8 PDB header:unknown function Chain: A: PDB Molecule:type iv fimbriae assembly protein; PDBTitle: crystal structure of pilz (xac1133) from xanthomonas2 axonopodis pv citri 9 d2rdea2 97.4 20 Fold:Split barrel-like Superfamily:PilZ domain-like Family:PilZ domain-associated domain 10 c2l1tA_ 88.4 12 PDB header:structural genomics, unknown function Chain: A: PDB Molecule:uncharacterized protein; PDBTitle: solution structure of the n-terminal domain of np_954075.1 11 d2ix0a3 81.2 13 Fold:OB-fold Superfamily:Nucleic acid-binding proteins Family:Cold shock DNA-binding domain-like 12 d1x9la_ 33.1 18 Fold:Common fold of diphtheria toxin/transcription factors/cytochrome f Superfamily:DR1885-like metal-binding protein Family:DR1885-like metal-binding protein 13 c2k6zA_ 20.5 18 PDB header:metal transport Chain: A: PDB Molecule:putative uncharacterized protein ttha1943; PDBTitle: solution structures of copper loaded form pcua (trans2 conformation of the peptide bond involving the nitrogen of3 p14) 14 d1kwga1 16.1 8 Fold:Glycosyl hydrolase domain Superfamily:Glycosyl hydrolase domain Family:alpha-Amylases, C-terminal beta-sheet domain 15 c3fwaA_ 14.4 13 PDB header:flavoprotein Chain: A: PDB Molecule:reticuline oxidase; PDBTitle: structure of berberine bridge enzyme, c166a variant in complex with2 (s)-reticuline 16 c3cw4A_ 13.9 14 PDB header:transferase Chain: A: PDB Molecule:polymerase basic protein 2; PDBTitle: large c-terminal domain of influenza a virus rna-dependent polymerase2 pb2 17 c3d2hA_ 13.6 13 PDB header:oxidoreductase Chain: A: PDB Molecule:berberine bridge-forming enzyme; PDBTitle: structure of berberine bridge enzyme from eschscholzia californica,2 monoclinic crystal form 18 d2ftsa1 12.3 14 Fold:beta-clip Superfamily:MoeA C-terminal domain-like Family:MoeA C-terminal domain-like 19 d1gtra1 11.0 14 Fold:Ribosomal protein L25-like Superfamily:Ribosomal protein L25-like Family:Gln-tRNA synthetase (GlnRS), C-terminal (anticodon-binding) domain 20 c1zr6A_ 9.9 11 PDB header:oxidoreductase Chain: A: PDB Molecule:glucooligosaccharide oxidase; PDBTitle: the crystal structure of an acremonium strictum glucooligosaccharide2 oxidase reveals a novel flavinylation 21 c2oxgD_ not modelled 9.6 24 PDB header:transport protein Chain: D: PDB Molecule:soxy protein; PDBTitle: the soxyz complex of paracoccus pantotrophus 22 c2k8iA_ not modelled 7.5 20 PDB header:isomerase Chain: A: PDB Molecule:peptidyl-prolyl cis-trans isomerase; PDBTitle: solution structure of e.coli slyd 23 c2kfwA_ not modelled 7.3 20 PDB header:isomerase Chain: A: PDB Molecule:fkbp-type peptidyl-prolyl cis-trans isomerase PDBTitle: solution structure of full-length slyd from e.coli 24 c2vs1A_ not modelled 7.3 16 PDB header:transferase Chain: A: PDB Molecule:uncharacterized rna methyltransferase pyrab10780; PDBTitle: the crystal structure of pyrococcus abyssi trna (uracil-54,2 c5)-methyltransferase in complex with s-adenosyl-l-3 homocysteine 25 d2d9ra1 not modelled 6.8 10 Fold:Double-split beta-barrel Superfamily:AF2212/PG0164-like Family:PG0164-like 26 d2fg9a1 not modelled 6.6 11 Fold:Split barrel-like Superfamily:FMN-binding split barrel Family:PNP-oxidase like 27 d2z1ea2 not modelled 6.6 22 Fold:PurM C-terminal domain-like Superfamily:PurM C-terminal domain-like Family:PurM C-terminal domain-like 28 c2ipiD_ not modelled 6.2 11 PDB header:oxidoreductase Chain: D: PDB Molecule:aclacinomycin oxidoreductase (aknox); PDBTitle: crystal structure of aclacinomycin oxidoreductase 29 d1vk3a3 not modelled 6.1 44 Fold:PurM C-terminal domain-like Superfamily:PurM C-terminal domain-like Family:PurM C-terminal domain-like 30 d1kq1a_ not modelled 6.1 13 Fold:Sm-like fold Superfamily:Sm-like ribonucleoproteins Family:Pleiotropic translational regulator Hfq 31 c3uc0B_ not modelled 6.0 19 PDB header:viral protein/immune system Chain: B: PDB Molecule:envelope protein; PDBTitle: crystal structure of domain i of the envelope glycoprotein ectodomain2 from dengue virus serotype 4 in complex with the fab fragment of the3 chimpanzee monoclonal antibody 5h2 32 d1ib8a1 not modelled 5.9 3 Fold:Sm-like fold Superfamily:YhbC-like, C-terminal domain Family:YhbC-like, C-terminal domain 33 d1hl9a1 not modelled 5.9 11 Fold:Glycosyl hydrolase domain Superfamily:Glycosyl hydrolase domain Family:Putative alpha-L-fucosidase C-terminal domain 34 c1kq1W_ not modelled 5.7 13 PDB header:translation Chain: W: PDB Molecule:host factor for q beta; PDBTitle: 1.55 a crystal structure of the pleiotropic translational2 regulator, hfq 35 d1hk9a_ not modelled 5.5 19 Fold:Sm-like fold Superfamily:Sm-like ribonucleoproteins Family:Pleiotropic translational regulator Hfq 36 c3qhsD_ not modelled 5.4 19 PDB header:rna binding protein Chain: D: PDB Molecule:protein hfq; PDBTitle: crystal structure of full-length hfq from escherichia coli 37 d1t3ta6 not modelled 5.3 33 Fold:PurM C-terminal domain-like Superfamily:PurM C-terminal domain-like Family:PurM C-terminal domain-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