Secondary structure and disorder prediction

		1	.	.	.	.	.	.	.	.	10	.	.	.	.	.	.	.	.	.	20	.	.	.	.	.	.	.	.	.	30	.	.	.	.	.	.	.	.	.	40	.	.	.	.	.	.	.	.	.	50	.	.	.	.	.	.	.	.	.	60
Sequence		M	Q	T	Q	V	L	F	E	H	P	L	N	E	K	M	R	T	W	L	R	I	E	F	L	I	Q	Q	L	T	V	N	L	P	I	V	D	H	A	G	A	L	H	F	F	R	N	V	S	E	L	L	D	V	F	E	R	G	E	V	R
Secondary structure
SS confidence
Disorder		?	?	?	?																											?	?	?	?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	70	.	.	.	.	.	.	.	.	.	80	.	.	.	.	.	.	.	.	.	90	.	.	.	.	.	.	.	.	.	100	.	.	.	.	.	.	.	.	.	110	.	.	.	.	.	.	.	.	.	120
Sequence		T	E	L	L	K	E	L	D	R	Q	Q	R	K	L	Q	T	W	I	G	V	P	G	V	D	Q	S	R	I	E	A	L	I	Q	Q	L	K	A	A	G	S	V	L	I	S	A	P	R	I	G	Q	F	L	R	E	D	R	L	I	A	L
Secondary structure
SS confidence
Disorder																				?	?	?	?	?																				?	?	?	?	?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	130	.	.	.	.	.	.	.	.	.	140	.	.	.	.	.	.	.	.	.	150	.	.	.	.	.	.	.	.	.	160	.	.	.	.	.	.	.	.	.	170	.	.	.	.	.	.	.	.	.	180
Sequence		V	R	Q	R	L	S	I	P	G	G	C	C	S	F	D	L	P	T	L	H	I	W	L	H	L	P	Q	A	Q	R	D	S	Q	V	E	T	W	I	A	S	L	N	P	L	T	Q	A	L	T	M	V	L	D	L	I	R	Q	S	A	P
Secondary structure
SS confidence
Disorder					?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	190	.	.	.	.	.	.	.	.	.	200	.	.	.	.	.	.	.	.	.	210	.	.	.	.	.	.	.	.	.	220	.	.	.	.	.	.	.	.	.	230	.	.	.	.	.	.	.	.	.	240
Sequence		F	R	K	Q	T	S	L	N	G	F	Y	Q	D	N	G	G	D	A	D	L	L	R	L	N	L	S	L	D	S	Q	L	Y	P	Q	I	S	G	H	K	S	R	F	A	I	R	F	M	P	L	D	T	E	N	G	Q	V	P	E	R	L
Secondary structure
SS confidence
Disorder							?	?							?														?	?																					?	?	?	?	?	?	?	?	?
Disorder confidence
		.	.	.	.	.	.	.
Sequence		D	F	E	L	A	C	C
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 2oez chain A domain 1 Region: 2 - 247 Aligned: 241 Modelled: 246 Confidence: 100.0% Identity: 39% Fold: YacF-like Superfamily: YacF-like Family: YacF-like Phyre2 PDB 1eg3 chain A domain 2 Region: 68 - 167 Aligned: 91 Modelled: 100 Confidence: 51.4% Identity: 19% Fold: EF Hand-like Superfamily: EF-hand Family: EF-hand modules in multidomain proteins Phyre2 PDB 1wmi chain B domain 1 Region: 62 - 99 Aligned: 38 Modelled: 38 Confidence: 35.2% Identity: 29% Fold: Non-globular all-alpha subunits of globular proteins Superfamily: RelB-like Family: RelB-like Phyre2 PDB 2f5t chain X domain 2 Region: 58 - 69 Aligned: 12 Modelled: 12 Confidence: 24.3% Identity: 42% Fold: Phospholipase D/nuclease Superfamily: Phospholipase D/nuclease Family: TrmB middle domain-like Phyre2 PDB 3lay chain F Region: 61 - 104 Aligned: 44 Modelled: 44 Confidence: 23.1% Identity: 16% PDB header:metal binding protein Chain: F: PDB Molecule:zinc resistance-associated protein; PDBTitle: alpha-helical barrel formed by the decamer of the zinc resistance-2 associated protein (stm4172) from salmonella enterica subsp. enterica3 serovar typhimurium str. lt2 Phyre2 PDB 2r5i chain L Region: 206 - 222 Aligned: 17 Modelled: 17 Confidence: 22.6% Identity: 24% PDB header:viral protein Chain: L: PDB Molecule:l1 protein; PDBTitle: pentamer structure of major capsid protein l1 of human2 papilloma virus type 18 Phyre2 PDB 3iyj chain E Region: 205 - 222 Aligned: 18 Modelled: 18 Confidence: 21.4% Identity: 22% PDB header:virus Chain: E: PDB Molecule:major capsid protein l1; PDBTitle: bovine papillomavirus type 1 outer capsid Phyre2 PDB 2r5k chain E Region: 206 - 222 Aligned: 17 Modelled: 17 Confidence: 20.9% Identity: 24% PDB header:viral protein Chain: E: PDB Molecule:major capsid protein l1; PDBTitle: pentamer structure of major capsid protein l1 of human2 papilloma virus type 11 Phyre2 PDB 1dzl chain A Region: 200 - 222 Aligned: 23 Modelled: 23 Confidence: 20.4% Identity: 30% PDB header:virus Chain: A: PDB Molecule:late major capsid protein l1; PDBTitle: l1 protein of human papillomavirus 16 Phyre2 PDB 1dzl chain A Region: 200 - 222 Aligned: 23 Modelled: 23 Confidence: 20.4% Identity: 30% Fold: Nucleoplasmin-like/VP (viral coat and capsid proteins) Superfamily: Group I dsDNA viruses Family: Papovaviridae-like VP Phyre2 PDB 2f5t chain X Region: 58 - 69 Aligned: 12 Modelled: 12 Confidence: 20.0% Identity: 42% PDB header:transcription Chain: X: PDB Molecule:archaeal transcriptional regulator trmb; PDBTitle: crystal structure of the sugar binding domain of the archaeal2 transcriptional regulator trmb Phyre2 PDB 1x79 chain A Region: 47 - 103 Aligned: 54 Modelled: 57 Confidence: 16.1% Identity: 19% Fold: Spectrin repeat-like Superfamily: GAT-like domain Family: GAT domain Phyre2 PDB 1hf9 chain B Region: 63 - 84 Aligned: 22 Modelled: 22 Confidence: 13.0% Identity: 23% PDB header:atpase inhibitor Chain: B: PDB Molecule:atpase inhibitor (mitochondrial); PDBTitle: c-terminal coiled-coil domain from bovine if1 Phyre2 PDB 1w8x chain N Region: 202 - 225 Aligned: 24 Modelled: 24 Confidence: 12.2% Identity: 17% PDB header:virus Chain: N: PDB Molecule:protein p31; PDBTitle: structural analysis of prd1 Phyre2 PDB 1j8y chain F domain 1 Region: 68 - 99 Aligned: 32 Modelled: 32 Confidence: 12.2% Identity: 13% Fold: Four-helical up-and-down bundle Superfamily: Domain of the SRP/SRP receptor G-proteins Family: Domain of the SRP/SRP receptor G-proteins Phyre2 PDB 2it9 chain A domain 1 Region: 199 - 234 Aligned: 35 Modelled: 36 Confidence: 12.1% Identity: 14% Fold: ssDNA-binding transcriptional regulator domain Superfamily: ssDNA-binding transcriptional regulator domain Family: PMN2A0962/syc2379c-like Phyre2 PDB 1p3q chain Q Region: 61 - 92 Aligned: 32 Modelled: 32 Confidence: 11.4% Identity: 28% Fold: RuvA C-terminal domain-like Superfamily: UBA-like Family: CUE domain Phyre2 PDB 1wr6 chain A domain 1 Region: 44 - 103 Aligned: 60 Modelled: 60 Confidence: 11.3% Identity: 22% Fold: Spectrin repeat-like Superfamily: GAT-like domain Family: GAT domain Phyre2 PDB 3m8j chain A Region: 115 - 143 Aligned: 24 Modelled: 29 Confidence: 10.7% Identity: 21% PDB header:transcription Chain: A: PDB Molecule:focb protein; PDBTitle: crystal structure of e.coli focb at 1.4 a resolution Phyre2 PDB 3ktd chain C Region: 60 - 134 Aligned: 75 Modelled: 75 Confidence: 10.4% Identity: 15% PDB header:oxidoreductase Chain: C: PDB Molecule:prephenate dehydrogenase; PDBTitle: crystal structure of a putative prephenate dehydrogenase (cgl0226)2 from corynebacterium glutamicum atcc 13032 at 2.60 a resolution Phyre2 1 d2oeza1 2 d1eg3a2 3 d1wmib1 4 d2f5tx2 5 c3layF_ 6 c2r5iL_ 7 c3iyjE_ 8 c2r5kE_ 9 c1dzlA_ 10 d1dzla_ 11 c2f5tX_ 12 d1x79a_ 13 c1hf9B_ 14 c1w8xN_ 15 d1j8yf1 16 d2it9a1 17 d1p3qq_ 18 d1wr6a1 19 c3m8jA_ 20 c3ktdC_ 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 48 49 50 51 52 53 54 55 56 57 58

Detailed template information

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

1 d2oeza1 100.0 39 Fold:YacF-like Superfamily:YacF-like Family:YacF-like 2 d1eg3a2 51.4 19 Fold:EF Hand-like Superfamily:EF-hand Family:EF-hand modules in multidomain proteins 3 d1wmib1 35.2 29 Fold:Non-globular all-alpha subunits of globular proteins Superfamily:RelB-like Family:RelB-like 4 d2f5tx2 24.3 42 Fold:Phospholipase D/nuclease Superfamily:Phospholipase D/nuclease Family:TrmB middle domain-like 5 c3layF_ 23.1 16 PDB header:metal binding protein Chain: F: PDB Molecule:zinc resistance-associated protein; PDBTitle: alpha-helical barrel formed by the decamer of the zinc resistance-2 associated protein (stm4172) from salmonella enterica subsp. enterica3 serovar typhimurium str. lt2 6 c2r5iL_ 22.6 24 PDB header:viral protein Chain: L: PDB Molecule:l1 protein; PDBTitle: pentamer structure of major capsid protein l1 of human2 papilloma virus type 18 7 c3iyjE_ 21.4 22 PDB header:virus Chain: E: PDB Molecule:major capsid protein l1; PDBTitle: bovine papillomavirus type 1 outer capsid 8 c2r5kE_ 20.9 24 PDB header:viral protein Chain: E: PDB Molecule:major capsid protein l1; PDBTitle: pentamer structure of major capsid protein l1 of human2 papilloma virus type 11 9 c1dzlA_ 20.4 30 PDB header:virus Chain: A: PDB Molecule:late major capsid protein l1; PDBTitle: l1 protein of human papillomavirus 16 10 d1dzla_ 20.4 30 Fold:Nucleoplasmin-like/VP (viral coat and capsid proteins) Superfamily:Group I dsDNA viruses Family:Papovaviridae-like VP 11 c2f5tX_ 20.0 42 PDB header:transcription Chain: X: PDB Molecule:archaeal transcriptional regulator trmb; PDBTitle: crystal structure of the sugar binding domain of the archaeal2 transcriptional regulator trmb 12 d1x79a_ 16.1 19 Fold:Spectrin repeat-like Superfamily:GAT-like domain Family:GAT domain 13 c1hf9B_ 13.0 23 PDB header:atpase inhibitor Chain: B: PDB Molecule:atpase inhibitor (mitochondrial); PDBTitle: c-terminal coiled-coil domain from bovine if1 14 c1w8xN_ 12.2 17 PDB header:virus Chain: N: PDB Molecule:protein p31; PDBTitle: structural analysis of prd1 15 d1j8yf1 12.2 13 Fold:Four-helical up-and-down bundle Superfamily:Domain of the SRP/SRP receptor G-proteins Family:Domain of the SRP/SRP receptor G-proteins 16 d2it9a1 12.1 14 Fold:ssDNA-binding transcriptional regulator domain Superfamily:ssDNA-binding transcriptional regulator domain Family:PMN2A0962/syc2379c-like 17 d1p3qq_ 11.4 28 Fold:RuvA C-terminal domain-like Superfamily:UBA-like Family:CUE domain 18 d1wr6a1 11.3 22 Fold:Spectrin repeat-like Superfamily:GAT-like domain Family:GAT domain 19 c3m8jA_ 10.7 21 PDB header:transcription Chain: A: PDB Molecule:focb protein; PDBTitle: crystal structure of e.coli focb at 1.4 a resolution 20 c3ktdC_ 10.4 15 PDB header:oxidoreductase Chain: C: PDB Molecule:prephenate dehydrogenase; PDBTitle: crystal structure of a putative prephenate dehydrogenase (cgl0226)2 from corynebacterium glutamicum atcc 13032 at 2.60 a resolution 21 c1yisA_ not modelled 10.1 13 PDB header:lyase Chain: A: PDB Molecule:adenylosuccinate lyase; PDBTitle: structural genomics of caenorhabditis elegans: adenylosuccinate lyase 22 c1o7dD_ not modelled 10.0 26 PDB header:hydrolase Chain: D: PDB Molecule:lysosomal alpha-mannosidase; PDBTitle: the structure of the bovine lysosomal a-mannosidase2 suggests a novel mechanism for low ph activation 23 c3bqsB_ not modelled 7.7 24 PDB header:structural genomics, unknown function Chain: B: PDB Molecule:uncharacterized protein; PDBTitle: crystal structure of an uncharacterized protein from2 listeria monocytogenes, trigonal form 24 d1qzxa1 not modelled 7.6 9 Fold:Four-helical up-and-down bundle Superfamily:Domain of the SRP/SRP receptor G-proteins Family:Domain of the SRP/SRP receptor G-proteins 25 c2zxjB_ not modelled 7.4 18 PDB header:transcription Chain: B: PDB Molecule:transcriptional regulatory protein walr; PDBTitle: crystal structure of yycf dna-binding domain from staphylococcus2 aureus 26 c2gqcA_ not modelled 7.4 14 PDB header:hydrolase Chain: A: PDB Molecule:rhomboid intramembrane protease; PDBTitle: solution structure of the n-terminal domain of rhomboid intramembrane2 protease from p. aeruginosa 27 d1p30a1 not modelled 7.4 33 Fold:Nucleoplasmin-like/VP (viral coat and capsid proteins) Superfamily:Group II dsDNA viruses VP Family:Adenovirus hexon 28 c2w9pC_ not modelled 7.3 4 PDB header:hydrolase inhibitor Chain: C: PDB Molecule:multicystatin; PDBTitle: crystal structure of potato multicystatin 29 c3cjlA_ not modelled 7.2 13 PDB header:unknown function Chain: A: PDB Molecule:domain of unknown function; PDBTitle: crystal structure of a protein of unknown function (eca1910) from2 pectobacterium atrosepticum scri1043 at 2.20 a resolution 30 d1txna_ not modelled 7.1 26 Fold:Coproporphyrinogen III oxidase Superfamily:Coproporphyrinogen III oxidase Family:Coproporphyrinogen III oxidase 31 c2inyA_ not modelled 7.1 26 PDB header:viral protein Chain: A: PDB Molecule:hexon protein; PDBTitle: nanoporous crystals of chicken embryo lethal orphan (celo) adenovirus2 major coat protein, hexon 32 c2pjwH_ not modelled 7.0 16 PDB header:endocytosis/exocytosis Chain: H: PDB Molecule:uncharacterized protein yhl002w; PDBTitle: the vps27/hse1 complex is a gat domain-based scaffold for2 ubiquitin-dependent sorting 33 d2fug51 not modelled 7.0 11 Fold:Nqo5-like Superfamily:Nqo5-like Family:Nqo5-like 34 c2js5B_ not modelled 6.8 17 PDB header:structural genomics, unknown function Chain: B: PDB Molecule:uncharacterized protein; PDBTitle: nmr structure of protein q60c73_metca. northeast structural2 genomics consortium target mcr1 35 c1ot0A_ not modelled 6.7 21 PDB header:antibiotic Chain: A: PDB Molecule:50s ribosomal protein l1; PDBTitle: structure of antimicrobial peptide, hp (2-20) and its2 analogues derived from helicobacter pylori, as determined3 by 1h nmr spectroscopy 36 c1p0jA_ not modelled 6.7 21 PDB header:ribosome Chain: A: PDB Molecule:19-mer peptide from 50s ribosomal protein l1; PDBTitle: hp (2-20) substitution asp to trp modification in sds-d252 micelles 37 c1p0gA_ not modelled 6.6 21 PDB header:ribosome Chain: A: PDB Molecule:19-mer peptide from 50s ribosomal protein l1; PDBTitle: structure of antimicrobial peptide, hp (2-20) and its2 analogues derived from helicobacter pylori, as determined3 by 1h nmr spectroscopy 38 c2yy0D_ not modelled 6.5 11 PDB header:transcription Chain: D: PDB Molecule:c-myc-binding protein; PDBTitle: crystal structure of ms0802, c-myc-1 binding protein domain2 from homo sapiens 39 c3epuB_ not modelled 6.4 36 PDB header:chaperone Chain: B: PDB Molecule:stm2138 virulence chaperone; PDBTitle: crystal structure of stm2138, a novel virulence chaperone in2 salmonella 40 d1wgwa_ not modelled 6.4 9 Fold:Four-helical up-and-down bundle Superfamily:Domain of the SRP/SRP receptor G-proteins Family:Domain of the SRP/SRP receptor G-proteins 41 c2e21A_ not modelled 6.3 20 PDB header:ligase Chain: A: PDB Molecule:trna(ile)-lysidine synthase; PDBTitle: crystal structure of tils in a complex with amppnp from aquifex2 aeolicus. 42 d1p2za1 not modelled 6.3 33 Fold:Nucleoplasmin-like/VP (viral coat and capsid proteins) Superfamily:Group II dsDNA viruses VP Family:Adenovirus hexon 43 c2qbxB_ not modelled 6.3 43 PDB header:signaling protein Chain: B: PDB Molecule:ephrin type-b receptor 2; PDBTitle: ephb2/snew antagonistic peptide complex 44 d1shwb_ not modelled 6.3 48 Fold:Galactose-binding domain-like Superfamily:Galactose-binding domain-like Family:Ephrin receptor ligand binding domain 45 c3iqtA_ not modelled 6.2 19 PDB header:transferase Chain: A: PDB Molecule:signal transduction histidine-protein kinase bara; PDBTitle: structure of the hpt domain of sensor protein bara from escherichia2 coli cft073. 46 d2bm8a1 not modelled 6.0 15 Fold:S-adenosyl-L-methionine-dependent methyltransferases Superfamily:S-adenosyl-L-methionine-dependent methyltransferases Family:CmcI-like 47 d1rwsa_ not modelled 6.0 38 Fold:beta-Grasp (ubiquitin-like) Superfamily:MoaD/ThiS Family:ThiS 48 d2bbaa1 not modelled 5.9 52 Fold:Galactose-binding domain-like Superfamily:Galactose-binding domain-like Family:Ephrin receptor ligand binding domain 49 d1p65a_ not modelled 5.7 30 Fold:Nucleocapsid protein dimerization domain Superfamily:Nucleocapsid protein dimerization domain Family:Arterivirus nucleocapsid protein 50 c1p65A_ not modelled 5.7 30 PDB header:viral protein Chain: A: PDB Molecule:nucleocapsid protein; PDBTitle: crystal structure of the nucleocapsid protein of porcine reproductive2 and respiratory syndrome virus (prrsv) 51 c2qmlA_ not modelled 5.5 20 PDB header:unknown function Chain: A: PDB Molecule:bh2621 protein; PDBTitle: crystal structure of an uncharacterized protein (bh2621) from bacillus2 halodurans at 1.55 a resolution 52 c2pqrD_ not modelled 5.5 41 PDB header:apoptosis Chain: D: PDB Molecule:wd repeat protein ykr036c; PDBTitle: crystal structure of yeast fis1 complexed with a fragment of yeast2 caf4 53 c1p5lA_ not modelled 5.5 30 PDB header:ribosome Chain: A: PDB Molecule:19-mer peptide from 50s ribosomal protein l1; PDBTitle: hp (2-20) substitution phe5 to ser modification in sds-d252 micelles 54 c3ic8D_ not modelled 5.4 37 PDB header:structural genomics, unknown function Chain: D: PDB Molecule:uncharacterized gst-like proteinprotein; PDBTitle: the crystal structure of a gst-like protein from pseudomonas syringae2 to 2.4a 55 c1p0oA_ not modelled 5.3 23 PDB header:ribosome Chain: A: PDB Molecule:19-mer peptide from 50s ribosomal protein l1; PDBTitle: hp (2-20) substitution of trp for gln and asp at position2 17 and 19 modification in sds-d25 micelles 56 c3c8xA_ not modelled 5.2 38 PDB header:transferase Chain: A: PDB Molecule:ephrin type-a receptor 2; PDBTitle: crystal structure of the ligand binding domain of human ephrin a22 (epha2) receptor protein kinase 57 c1p0lA_ not modelled 5.2 23 PDB header:ribosome Chain: A: PDB Molecule:19-mer peptide from 50s ribosomal protein l1; PDBTitle: hp (2-20) substitution gln to trp modification in sds-d252 micelles 58 d1ls1a1 not modelled 5.1 16 Fold:Four-helical up-and-down bundle Superfamily:Domain of the SRP/SRP receptor G-proteins Family:Domain of the SRP/SRP receptor G-proteins

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