Secondary structure and disorder prediction

		1	.	.	.	.	.	.	.	.	10	.	.	.	.	.	.	.	.	.	20	.	.	.	.	.	.	.	.	.	30	.	.	.	.	.	.	.	.	.	40	.	.	.	.	.	.	.	.	.	50	.	.	.	.	.	.	.	.	.	60
Sequence		M	G	R	I	S	S	G	G	M	M	F	K	A	I	T	T	V	A	A	L	V	I	A	T	S	A	M	A	Q	D	D	L	T	I	S	S	L	A	K	G	E	T	T	K	A	A	F	N	Q	M	V	Q	G	H	K	L	P	A	W	V
Secondary structure
SS confidence
Disorder		?	?	?	?	?	?	?	?	?	?													?	?	?	?	?	?	?	?	?	?	?					?	?	?	?	?										?	?	?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	70	.	.	.	.	.	.	.	.	.	80	.	.	.	.	.	.	.	.	.	90	.	.	.	.	.	.	.	.	.	100	.	.	.	.	.	.	.	.	.	110	.	.	.	.	.	.	.	.	.	120
Sequence		M	K	G	G	T	Y	T	P	A	Q	T	V	T	L	G	D	E	T	Y	Q	V	M	S	A	C	K	P	H	D	C	G	S	Q	R	I	A	V	M	W	S	E	K	S	N	Q	M	T	G	L	F	S	T	I	D	E	K	T	S	Q	E
Secondary structure
SS confidence
Disorder			?		?	?	?	?	?	?		?	?	?	?																																											?
Disorder confidence
		.	.	.	.	.	.	.	.	.	130	.	.	.	.	.	.	.	.	.	140	.	.	.	.	.	.	.	.	.	150	.	.	.	.	.	.	.
Sequence		K	L	T	W	L	N	V	N	D	A	L	S	I	D	G	K	T	V	L	F	A	A	L	T	G	S	L	E	N	H	P	D	G	F	N	F	K
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 1gpq chain A Region: 30 - 156 Aligned: 127 Modelled: 127 Confidence: 100.0% Identity: 100% Fold: Inhibitor of vertebrate lysozyme, Ivy Superfamily: Inhibitor of vertebrate lysozyme, Ivy Family: Inhibitor of vertebrate lysozyme, Ivy Phyre2 PDB 1uuz chain A Region: 31 - 152 Aligned: 115 Modelled: 122 Confidence: 100.0% Identity: 26% Fold: Inhibitor of vertebrate lysozyme, Ivy Superfamily: Inhibitor of vertebrate lysozyme, Ivy Family: Inhibitor of vertebrate lysozyme, Ivy Phyre2 PDB 1fpo chain A domain 1 Region: 122 - 157 Aligned: 36 Modelled: 36 Confidence: 49.9% Identity: 17% Fold: Long alpha-hairpin Superfamily: Chaperone J-domain Family: Chaperone J-domain Phyre2 PDB 2jkg chain A Region: 72 - 113 Aligned: 40 Modelled: 42 Confidence: 37.9% Identity: 23% PDB header:protein-binding Chain: A: PDB Molecule:profilin; PDBTitle: plasmodium falciparum profilin Phyre2 PDB 1k0h chain A Region: 67 - 97 Aligned: 30 Modelled: 31 Confidence: 28.2% Identity: 30% Fold: Phage tail proteins Superfamily: Phage tail proteins Family: gpFII-like Phyre2 PDB 1h3i chain A domain 2 Region: 88 - 126 Aligned: 39 Modelled: 39 Confidence: 18.1% Identity: 5% Fold: beta-clip Superfamily: SET domain Family: Histone lysine methyltransferases Phyre2 PDB 3ebq chain A Region: 41 - 62 Aligned: 22 Modelled: 22 Confidence: 14.6% Identity: 23% PDB header:hydrolase Chain: A: PDB Molecule:molecule: pppde1 (permuted papain fold PDBTitle: crystal structure of human pppde1 Phyre2 PDB 2xgl chain B Region: 54 - 81 Aligned: 28 Modelled: 28 Confidence: 13.5% Identity: 25% PDB header:antibiotic Chain: B: PDB Molecule:colicin-m immunity protein; PDBTitle: the x-ray structure of the escherichia coli colicin m immunity2 protein demonstrates the presence of a disulphide bridge, which is3 functionally essential Phyre2 PDB 1xg8 chain A Region: 116 - 156 Aligned: 27 Modelled: 27 Confidence: 12.8% Identity: 22% Fold: Thioredoxin fold Superfamily: Thioredoxin-like Family: YuzD-like Phyre2 PDB 2ww9 chain O Region: 48 - 61 Aligned: 14 Modelled: 14 Confidence: 12.0% Identity: 29% PDB header:ribosome Chain: O: PDB Molecule:60s ribosomal protein l39; PDBTitle: cryo-em structure of the active yeast ssh1 complex bound to the2 yeast 80s ribosome Phyre2 PDB 3c5t chain B Region: 58 - 67 Aligned: 10 Modelled: 10 Confidence: 11.3% Identity: 30% PDB header:signaling protein/signaling protein Chain: B: PDB Molecule:exendin-4; PDBTitle: crystal structure of the ligand-bound glucagon-like peptide-1 receptor2 extracellular domain Phyre2 PDB 1ixt chain A Region: 83 - 95 Aligned: 13 Modelled: 13 Confidence: 10.3% Identity: 46% Fold: Knottins (small inhibitors, toxins, lectins) Superfamily: omega toxin-like Family: Conotoxin Phyre2 PDB 1ixt chain A Region: 83 - 95 Aligned: 13 Modelled: 13 Confidence: 10.3% Identity: 46% PDB header:toxin Chain: A: PDB Molecule:spasmodic protein tx9a-like protein; PDBTitle: structure of a novel p-superfamily spasmodic conotoxin2 reveals an inhibitory cystine knot motif Phyre2 PDB 2l23 chain A Region: 90 - 109 Aligned: 20 Modelled: 20 Confidence: 10.3% Identity: 25% PDB header:transcription Chain: A: PDB Molecule:mediator of rna polymerase ii transcription subunit 25; PDBTitle: nmr structure of the acid (activator interacting domain) of the human2 mediator med25 protein Phyre2 PDB 2zkr chain 3 Region: 48 - 61 Aligned: 14 Modelled: 14 Confidence: 9.5% Identity: 21% PDB header:ribosomal protein/rna Chain: 3: PDB Molecule:60s ribosomal protein l39e; PDBTitle: structure of a mammalian ribosomal 60s subunit within an2 80s complex obtained by docking homology models of the rna3 and proteins into an 8.7 a cryo-em map Phyre2 PDB 1vqo chain 2 domain 1 Region: 52 - 61 Aligned: 10 Modelled: 10 Confidence: 9.4% Identity: 60% Fold: Non-globular all-alpha subunits of globular proteins Superfamily: Ribosomal protein L39e Family: Ribosomal protein L39e Phyre2 PDB 4a1b chain B Region: 48 - 61 Aligned: 14 Modelled: 14 Confidence: 9.4% Identity: 29% PDB header:ribosome Chain: B: PDB Molecule:rpl39; PDBTitle: t.thermophila 60s ribosomal subunit in complex with2 initiation factor 6. this file contains 26s rrna and3 proteins of molecule 3. Phyre2 PDB 3if4 chain C Region: 123 - 146 Aligned: 16 Modelled: 24 Confidence: 9.1% Identity: 44% PDB header:structural genomics, unknown function Chain: C: PDB Molecule:integron cassette protein hfx_cass5; PDBTitle: structure from the mobile metagenome of north west arm2 sewage outfall: integron cassette protein hfx_cass5 Phyre2 PDB 2jof chain A Region: 59 - 67 Aligned: 9 Modelled: 9 Confidence: 8.9% Identity: 33% PDB header:de novo protein Chain: A: PDB Molecule:trp-cage; PDBTitle: the trp-cage: optimizing the stability of a globular2 miniprotein Phyre2 PDB 1t27 chain A Region: 53 - 86 Aligned: 31 Modelled: 34 Confidence: 8.3% Identity: 16% Fold: TBP-like Superfamily: Bet v1-like Family: Phoshatidylinositol transfer protein, PITP Phyre2 1 d1gpqa_ 2 d1uuza_ 3 d1fpoa1 4 c2jkgA_ 5 d1k0ha_ 6 d1h3ia2 7 c3ebqA_ 8 c2xglB_ 9 d1xg8a_ 10 c2ww9O_ 11 c3c5tB_ 12 d1ixta_ 13 c1ixtA_ 14 c2l23A_ 15 c2zkr3_ 16 d1vqo21 17 c4a1bB_ 18 c3if4C_ 19 c2jofA_ 20 d1t27a_ 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

Detailed template information

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

1 d1gpqa_ 100.0 100 Fold:Inhibitor of vertebrate lysozyme, Ivy Superfamily:Inhibitor of vertebrate lysozyme, Ivy Family:Inhibitor of vertebrate lysozyme, Ivy 2 d1uuza_ 100.0 26 Fold:Inhibitor of vertebrate lysozyme, Ivy Superfamily:Inhibitor of vertebrate lysozyme, Ivy Family:Inhibitor of vertebrate lysozyme, Ivy 3 d1fpoa1 49.9 17 Fold:Long alpha-hairpin Superfamily:Chaperone J-domain Family:Chaperone J-domain 4 c2jkgA_ 37.9 23 PDB header:protein-binding Chain: A: PDB Molecule:profilin; PDBTitle: plasmodium falciparum profilin 5 d1k0ha_ 28.2 30 Fold:Phage tail proteins Superfamily:Phage tail proteins Family:gpFII-like 6 d1h3ia2 18.1 5 Fold:beta-clip Superfamily:SET domain Family:Histone lysine methyltransferases 7 c3ebqA_ 14.6 23 PDB header:hydrolase Chain: A: PDB Molecule:molecule: pppde1 (permuted papain fold PDBTitle: crystal structure of human pppde1 8 c2xglB_ 13.5 25 PDB header:antibiotic Chain: B: PDB Molecule:colicin-m immunity protein; PDBTitle: the x-ray structure of the escherichia coli colicin m immunity2 protein demonstrates the presence of a disulphide bridge, which is3 functionally essential 9 d1xg8a_ 12.8 22 Fold:Thioredoxin fold Superfamily:Thioredoxin-like Family:YuzD-like 10 c2ww9O_ 12.0 29 PDB header:ribosome Chain: O: PDB Molecule:60s ribosomal protein l39; PDBTitle: cryo-em structure of the active yeast ssh1 complex bound to the2 yeast 80s ribosome 11 c3c5tB_ 11.3 30 PDB header:signaling protein/signaling protein Chain: B: PDB Molecule:exendin-4; PDBTitle: crystal structure of the ligand-bound glucagon-like peptide-1 receptor2 extracellular domain 12 d1ixta_ 10.3 46 Fold:Knottins (small inhibitors, toxins, lectins) Superfamily:omega toxin-like Family:Conotoxin 13 c1ixtA_ 10.3 46 PDB header:toxin Chain: A: PDB Molecule:spasmodic protein tx9a-like protein; PDBTitle: structure of a novel p-superfamily spasmodic conotoxin2 reveals an inhibitory cystine knot motif 14 c2l23A_ 10.3 25 PDB header:transcription Chain: A: PDB Molecule:mediator of rna polymerase ii transcription subunit 25; PDBTitle: nmr structure of the acid (activator interacting domain) of the human2 mediator med25 protein 15 c2zkr3_ 9.5 21 PDB header:ribosomal protein/rna Chain: 3: PDB Molecule:60s ribosomal protein l39e; PDBTitle: structure of a mammalian ribosomal 60s subunit within an2 80s complex obtained by docking homology models of the rna3 and proteins into an 8.7 a cryo-em map 16 d1vqo21 9.4 60 Fold:Non-globular all-alpha subunits of globular proteins Superfamily:Ribosomal protein L39e Family:Ribosomal protein L39e 17 c4a1bB_ 9.4 29 PDB header:ribosome Chain: B: PDB Molecule:rpl39; PDBTitle: t.thermophila 60s ribosomal subunit in complex with2 initiation factor 6. this file contains 26s rrna and3 proteins of molecule 3. 18 c3if4C_ 9.1 44 PDB header:structural genomics, unknown function Chain: C: PDB Molecule:integron cassette protein hfx_cass5; PDBTitle: structure from the mobile metagenome of north west arm2 sewage outfall: integron cassette protein hfx_cass5 19 c2jofA_ 8.9 33 PDB header:de novo protein Chain: A: PDB Molecule:trp-cage; PDBTitle: the trp-cage: optimizing the stability of a globular2 miniprotein 20 d1t27a_ 8.3 16 Fold:TBP-like Superfamily:Bet v1-like Family:Phoshatidylinositol transfer protein, PITP 21 d1bqka_ not modelled 8.3 26 Fold:Cupredoxin-like Superfamily:Cupredoxins Family:Plastocyanin/azurin-like 22 c1rijA_ not modelled 8.1 33 PDB header:de novo protein Chain: A: PDB Molecule:e6apn1 peptide; PDBTitle: e6-bind trp-cage (e6apn1) 23 d1s7ea2 not modelled 8.0 18 Fold:lambda repressor-like DNA-binding domains Superfamily:lambda repressor-like DNA-binding domains Family:CUT domain 24 c2guzO_ not modelled 7.3 30 PDB header:chaperone, protein transport Chain: O: PDB Molecule:mitochondrial import inner membrane translocase PDBTitle: structure of the tim14-tim16 complex of the mitochondrial2 protein import motor 25 c2d9tA_ not modelled 7.2 6 PDB header:structural genomics, unknown function Chain: A: PDB Molecule:tudor domain-containing protein 3; PDBTitle: solution structure of the tudor domain of tudor domain2 containing protein 3 from mouse 26 c2yy8B_ not modelled 7.0 30 PDB header:transferase Chain: B: PDB Molecule:upf0106 protein ph0461; PDBTitle: crystal structure of archaeal trna-methylase for position2 56 (atrm56) from pyrococcus horikoshii, complexed with s-3 adenosyl-l-methionine 27 c1l2yA_ not modelled 6.6 33 PDB header:de novo protein Chain: A: PDB Molecule:tc5b; PDBTitle: nmr structure of trp-cage miniprotein construct tc5b 28 d8ruca1 not modelled 6.6 18 Fold:TIM beta/alpha-barrel Superfamily:RuBisCo, C-terminal domain Family:RuBisCo, large subunit, C-terminal domain 29 d1fm4a_ not modelled 6.5 27 Fold:TBP-like Superfamily:Bet v1-like Family:Pathogenesis-related protein 10 (PR10)-like 30 c3b4qA_ not modelled 6.4 23 PDB header:structural genomics, unknown function Chain: A: PDB Molecule:uncharacterized protein; PDBTitle: crystal structure of a conserved protein domain (unknown2 function) from corynebacterium diphtheriae 31 d1ugja_ not modelled 6.4 15 Fold:PRC-barrel domain Superfamily:PRC-barrel domain Family:RIKEN cDNA 2310057j16 protein (KIAA1543) 32 c2v36A_ not modelled 6.3 15 PDB header:transferase Chain: A: PDB Molecule:gamma-glutamyltranspeptidase large chain; PDBTitle: crystal structure of gamma-glutamyl transferase from2 bacillus subtilis 33 d2a8ea1 not modelled 6.1 14 Fold:YktB/PF0168-like Superfamily:YktB/PF0168-like Family:YktB-like 34 d2ah2a2 not modelled 6.1 18 Fold:6-bladed beta-propeller Superfamily:Sialidases Family:Sialidases (neuraminidases) 35 c3a4cA_ not modelled 5.9 26 PDB header:cell cycle, replication Chain: A: PDB Molecule:dna replication factor cdt1; PDBTitle: crystal structure of cdt1 c terminal domain 36 d1ykwa1 not modelled 5.9 19 Fold:TIM beta/alpha-barrel Superfamily:RuBisCo, C-terminal domain Family:RuBisCo, large subunit, C-terminal domain 37 c2hw2A_ not modelled 5.9 33 PDB header:transferase Chain: A: PDB Molecule:rifampin adp-ribosyl transferase; PDBTitle: crystal structure of rifampin adp-ribosyl transferase in2 complex with rifampin 38 d1ooya2 not modelled 5.9 8 Fold:NagB/RpiA/CoA transferase-like Superfamily:NagB/RpiA/CoA transferase-like Family:CoA transferase alpha subunit-like 39 d1qmra_ not modelled 5.8 27 Fold:TBP-like Superfamily:Bet v1-like Family:Pathogenesis-related protein 10 (PR10)-like 40 d1fafa_ not modelled 5.7 32 Fold:Long alpha-hairpin Superfamily:Chaperone J-domain Family:Chaperone J-domain 41 d1e09a_ not modelled 5.4 32 Fold:TBP-like Superfamily:Bet v1-like Family:Pathogenesis-related protein 10 (PR10)-like 42 c3f9xA_ not modelled 5.3 20 PDB header:transferase Chain: A: PDB Molecule:histone-lysine n-methyltransferase setd8; PDBTitle: structural insights into lysine multiple methylation by set2 domain methyltransferases, set8-y334f / h4-lys20me2 /3 adohcy 43 c1zc1A_ not modelled 5.3 19 PDB header:protein turnover Chain: A: PDB Molecule:ubiquitin fusion degradation protein 1; PDBTitle: ufd1 exhibits the aaa-atpase fold with two distinct2 ubiquitin interaction sites 44 d3d85d2 not modelled 5.1 17 Fold:Immunoglobulin-like beta-sandwich Superfamily:Fibronectin type III Family:Fibronectin type III 45 d1gh6a_ not modelled 5.1 25 Fold:Long alpha-hairpin Superfamily:Chaperone J-domain Family:Chaperone J-domain

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