Secondary structure and disorder prediction

		1	.	.	.	.	.	.	.	.	10	.	.	.	.	.	.	.	.	.	20	.	.	.	.	.	.	.	.	.	30	.	.	.	.	.	.	.	.	.	40	.	.	.	.	.	.	.	.	.	50	.	.	.	.	.	.	.	.	.	60
Sequence		M	T	W	N	P	L	A	L	A	T	A	L	Q	T	V	P	E	Q	N	I	D	V	T	N	S	E	N	A	L	I	I	K	M	N	D	Y	G	D	L	Q	I	N	I	L	F	T	S	R	Q	M	I	I	E	T	F	I	C	P	V	S
Secondary structure
SS confidence
Disorder		?	?	?	?										?	?	?	?	?		?	?		?
Disorder confidence
		.	.	.	.	.	.	.	.	.	70	.	.	.	.	.	.	.	.	.	80	.	.	.	.	.	.	.	.	.	90	.	.	.	.	.	.	.	.	.	100	.	.	.	.	.	.	.	.	.	110	.	.	.	.	.	.	.	.	.	120
Sequence		S	I	S	N	P	D	E	F	N	T	F	L	L	R	N	Q	K	M	M	P	L	S	S	V	G	I	S	S	V	Q	Q	E	E	Y	Y	I	V	F	G	A	L	S	L	K	S	S	L	E	D	I	L	L	E	I	T	S	L	V	D	N
Secondary structure
SS confidence
Disorder			?														?										?	?																?			?
Disorder confidence
		.	.	.	.	.	.	.	.	.	130	.	.	.
Sequence		A	L	D	L	A	E	I	T	E	E	Y	S	H
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 1jyo chain A Region: 6 - 133 Aligned: 126 Modelled: 128 Confidence: 86.1% Identity: 15% Fold: Secretion chaperone-like Superfamily: Type III secretory system chaperone-like Family: Type III secretory system chaperone Phyre2 PDB 2plg chain A domain 1 Region: 36 - 130 Aligned: 91 Modelled: 95 Confidence: 54.5% Identity: 16% Fold: Secretion chaperone-like Superfamily: Type III secretory system chaperone-like Family: Tll0839-like Phyre2 PDB 2fm8 chain A domain 1 Region: 8 - 104 Aligned: 97 Modelled: 97 Confidence: 53.3% Identity: 10% Fold: Secretion chaperone-like Superfamily: Type III secretory system chaperone-like Family: Type III secretory system chaperone Phyre2 PDB 2l6l chain A Region: 85 - 118 Aligned: 33 Modelled: 34 Confidence: 34.7% Identity: 12% PDB header:chaperone Chain: A: PDB Molecule:dnaj homolog subfamily c member 24; PDBTitle: solution structure of human j-protein co-chaperone, dph4 Phyre2 PDB 1hdj chain A Region: 91 - 118 Aligned: 27 Modelled: 28 Confidence: 30.8% Identity: 26% Fold: Long alpha-hairpin Superfamily: Chaperone J-domain Family: Chaperone J-domain Phyre2 PDB 2ijo chain A Region: 17 - 41 Aligned: 25 Modelled: 25 Confidence: 25.3% Identity: 24% PDB header:hydrolase/hydrolase inhibitor Chain: A: PDB Molecule:polyprotein; PDBTitle: crystal structure of the west nile virus ns2b-ns3 protease2 complexed with bovine pancreatic trypsin inhibitor Phyre2 PDB 3e90 chain C Region: 17 - 41 Aligned: 25 Modelled: 25 Confidence: 24.8% Identity: 24% PDB header:hydrolase Chain: C: PDB Molecule:ns2b cofactor; PDBTitle: west nile vi rus ns2b-ns3protease in complexed with2 inhibitor naph-kkr-h Phyre2 PDB 2ga5 chain A domain 1 Region: 4 - 54 Aligned: 51 Modelled: 51 Confidence: 24.8% Identity: 20% Fold: N domain of copper amine oxidase-like Superfamily: Frataxin/Nqo15-like Family: Frataxin-like Phyre2 PDB 2ieq chain C Region: 98 - 124 Aligned: 25 Modelled: 27 Confidence: 22.1% Identity: 28% PDB header:viral protein Chain: C: PDB Molecule:spike glycoprotein; PDBTitle: core structure of s2 from the human coronavirus nl63 spike2 glycoprotein Phyre2 PDB 1ry9 chain A Region: 8 - 104 Aligned: 93 Modelled: 97 Confidence: 20.8% Identity: 16% Fold: Secretion chaperone-like Superfamily: Type III secretory system chaperone-like Family: Type III secretory system chaperone Phyre2 PDB 1ew4 chain A Region: 4 - 54 Aligned: 51 Modelled: 51 Confidence: 20.1% Identity: 20% Fold: N domain of copper amine oxidase-like Superfamily: Frataxin/Nqo15-like Family: Frataxin-like Phyre2 PDB 2v75 chain A Region: 101 - 119 Aligned: 19 Modelled: 19 Confidence: 19.8% Identity: 26% PDB header:nuclear protein Chain: A: PDB Molecule:nuclear polyadenylated rna-binding protein nab2; PDBTitle: n-terminal domain of nab2 Phyre2 PDB 2fql chain A domain 1 Region: 4 - 54 Aligned: 51 Modelled: 51 Confidence: 18.2% Identity: 20% Fold: N domain of copper amine oxidase-like Superfamily: Frataxin/Nqo15-like Family: Frataxin-like Phyre2 PDB 1et9 chain A domain 1 Region: 84 - 106 Aligned: 23 Modelled: 23 Confidence: 16.6% Identity: 35% Fold: OB-fold Superfamily: Bacterial enterotoxins Family: Superantigen toxins, N-terminal domain Phyre2 PDB 1wjz chain A Region: 82 - 118 Aligned: 36 Modelled: 37 Confidence: 15.3% Identity: 14% Fold: Long alpha-hairpin Superfamily: Chaperone J-domain Family: Chaperone J-domain Phyre2 PDB 3uc0 chain B Region: 13 - 41 Aligned: 29 Modelled: 29 Confidence: 12.2% Identity: 21% 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 Phyre2 PDB 1iwg chain A domain 6 Region: 36 - 85 Aligned: 50 Modelled: 50 Confidence: 11.7% Identity: 16% Fold: Multidrug efflux transporter AcrB TolC docking domain; DN and DC subdomains Superfamily: Multidrug efflux transporter AcrB TolC docking domain; DN and DC subdomains Family: Multidrug efflux transporter AcrB TolC docking domain; DN and DC subdomains Phyre2 PDB 1ekg chain A Region: 4 - 54 Aligned: 51 Modelled: 51 Confidence: 11.1% Identity: 22% Fold: N domain of copper amine oxidase-like Superfamily: Frataxin/Nqo15-like Family: Frataxin-like Phyre2 PDB 3kop chain B Region: 40 - 101 Aligned: 55 Modelled: 62 Confidence: 10.7% Identity: 22% PDB header:structural genomics, unknown function Chain: B: PDB Molecule:uncharacterized protein; PDBTitle: crystal structure of protein with a cyclophilin-like fold2 (yp_831253.1) from arthrobacter sp. fb24 at 1.90 a resolution Phyre2 PDB 2hqn chain A Region: 56 - 94 Aligned: 39 Modelled: 39 Confidence: 9.5% Identity: 18% PDB header:signaling protein Chain: A: PDB Molecule:putative transcriptional regulator; PDBTitle: structure of a atypical orphan response regulator protein revealed a2 new phosphorylation-independent regulatory mechanism Phyre2 1 d1jyoa_ 2 d2plga1 3 d2fm8a1 4 c2l6lA_ 5 d1hdja_ 6 c2ijoA_ 7 c3e90C_ 8 d2ga5a1 9 c2ieqC_ 10 d1ry9a_ 11 d1ew4a_ 12 c2v75A_ 13 d2fqla1 14 d1et9a1 15 d1wjza_ 16 c3uc0B_ 17 d1iwga6 18 d1ekga_ 19 c3kopB_ 20 c2hqnA_ 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

Detailed template information

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

1 d1jyoa_ 86.1 15 Fold:Secretion chaperone-like Superfamily:Type III secretory system chaperone-like Family:Type III secretory system chaperone 2 d2plga1 54.5 16 Fold:Secretion chaperone-like Superfamily:Type III secretory system chaperone-like Family:Tll0839-like 3 d2fm8a1 53.3 10 Fold:Secretion chaperone-like Superfamily:Type III secretory system chaperone-like Family:Type III secretory system chaperone 4 c2l6lA_ 34.7 12 PDB header:chaperone Chain: A: PDB Molecule:dnaj homolog subfamily c member 24; PDBTitle: solution structure of human j-protein co-chaperone, dph4 5 d1hdja_ 30.8 26 Fold:Long alpha-hairpin Superfamily:Chaperone J-domain Family:Chaperone J-domain 6 c2ijoA_ 25.3 24 PDB header:hydrolase/hydrolase inhibitor Chain: A: PDB Molecule:polyprotein; PDBTitle: crystal structure of the west nile virus ns2b-ns3 protease2 complexed with bovine pancreatic trypsin inhibitor 7 c3e90C_ 24.8 24 PDB header:hydrolase Chain: C: PDB Molecule:ns2b cofactor; PDBTitle: west nile vi rus ns2b-ns3protease in complexed with2 inhibitor naph-kkr-h 8 d2ga5a1 24.8 20 Fold:N domain of copper amine oxidase-like Superfamily:Frataxin/Nqo15-like Family:Frataxin-like 9 c2ieqC_ 22.1 28 PDB header:viral protein Chain: C: PDB Molecule:spike glycoprotein; PDBTitle: core structure of s2 from the human coronavirus nl63 spike2 glycoprotein 10 d1ry9a_ 20.8 16 Fold:Secretion chaperone-like Superfamily:Type III secretory system chaperone-like Family:Type III secretory system chaperone 11 d1ew4a_ 20.1 20 Fold:N domain of copper amine oxidase-like Superfamily:Frataxin/Nqo15-like Family:Frataxin-like 12 c2v75A_ 19.8 26 PDB header:nuclear protein Chain: A: PDB Molecule:nuclear polyadenylated rna-binding protein nab2; PDBTitle: n-terminal domain of nab2 13 d2fqla1 18.2 20 Fold:N domain of copper amine oxidase-like Superfamily:Frataxin/Nqo15-like Family:Frataxin-like 14 d1et9a1 16.6 35 Fold:OB-fold Superfamily:Bacterial enterotoxins Family:Superantigen toxins, N-terminal domain 15 d1wjza_ 15.3 14 Fold:Long alpha-hairpin Superfamily:Chaperone J-domain Family:Chaperone J-domain 16 c3uc0B_ 12.2 21 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 17 d1iwga6 11.7 16 Fold:Multidrug efflux transporter AcrB TolC docking domain; DN and DC subdomains Superfamily:Multidrug efflux transporter AcrB TolC docking domain; DN and DC subdomains Family:Multidrug efflux transporter AcrB TolC docking domain; DN and DC subdomains 18 d1ekga_ 11.1 22 Fold:N domain of copper amine oxidase-like Superfamily:Frataxin/Nqo15-like Family:Frataxin-like 19 c3kopB_ 10.7 22 PDB header:structural genomics, unknown function Chain: B: PDB Molecule:uncharacterized protein; PDBTitle: crystal structure of protein with a cyclophilin-like fold2 (yp_831253.1) from arthrobacter sp. fb24 at 1.90 a resolution 20 c2hqnA_ 9.5 18 PDB header:signaling protein Chain: A: PDB Molecule:putative transcriptional regulator; PDBTitle: structure of a atypical orphan response regulator protein revealed a2 new phosphorylation-independent regulatory mechanism 21 c3muwU_ not modelled 8.8 5 PDB header:virus Chain: U: PDB Molecule:structural polyprotein; PDBTitle: pseudo-atomic structure of the e2-e1 protein shell in sindbis virus 22 c2ochA_ not modelled 8.4 18 PDB header:chaperone Chain: A: PDB Molecule:hypothetical protein dnj-12; PDBTitle: j-domain of dnj-12 from caenorhabditis elegans 23 c3iwcD_ not modelled 8.3 14 PDB header:lyase Chain: D: PDB Molecule:s-adenosylmethionine decarboxylase; PDBTitle: t. maritima adometdc complex with s-adenosylmethionine2 methyl ester 24 c2iiiA_ not modelled 8.3 7 PDB header:lyase Chain: A: PDB Molecule:s-adenosylmethionine decarboxylase proenzyme; PDBTitle: crystal structure of the adenosylmethionine decarboxylase (aq_254)2 from aquifex aeolicus vf5 25 d1vlya2 not modelled 8.2 6 Fold:Folate-binding domain Superfamily:Folate-binding domain Family:Aminomethyltransferase folate-binding domain 26 c2bezC_ not modelled 7.9 43 PDB header:viral protein Chain: C: PDB Molecule:e2 glycoprotein; PDBTitle: structure of a proteolitically resistant core from the2 severe acute respiratory syndrome coronavirus s2 fusion3 protein 27 c2o37A_ not modelled 7.6 13 PDB header:chaperone Chain: A: PDB Molecule:protein sis1; PDBTitle: j-domain of sis1 protein, hsp40 co-chaperone from2 saccharomyces cerevisiae. 28 c2ys8A_ not modelled 7.5 11 PDB header:protein binding Chain: A: PDB Molecule:rab-related gtp-binding protein rabj; PDBTitle: solution structure of the dnaj-like domain from human ras-2 associated protein rap1 29 d1vr7a1 not modelled 7.4 14 Fold:S-adenosylmethionine decarboxylase Superfamily:S-adenosylmethionine decarboxylase Family:Bacterial S-adenosylmethionine decarboxylase 30 c2dn9A_ not modelled 7.3 21 PDB header:apoptosis, chaperone Chain: A: PDB Molecule:dnaj homolog subfamily a member 3; PDBTitle: solution structure of j-domain from the dnaj homolog, human2 tid1 protein 31 c3r84O_ not modelled 7.3 30 PDB header:transcription Chain: O: PDB Molecule:mediator of rna polymerase ii transcription subunit 11; PDBTitle: structure of the mediator head subcomplex med11/22 32 c1vr7A_ not modelled 7.3 14 PDB header:lyase Chain: A: PDB Molecule:s-adenosylmethionine decarboxylase proenzyme; PDBTitle: crystal structure of s-adenosylmethionine decarboxylase proenzyme2 (tm0655) from thermotoga maritima at 1.2 a resolution 33 c3lkxB_ not modelled 7.0 38 PDB header:chaperone Chain: B: PDB Molecule:nascent polypeptide-associated complex subunit alpha; PDBTitle: human nac dimerization domain 34 c1wyyB_ not modelled 6.8 43 PDB header:viral protein Chain: B: PDB Molecule:e2 glycoprotein; PDBTitle: post-fusion hairpin conformation of the sars coronavirus spike2 glycoprotein 35 c2lgwA_ not modelled 6.7 19 PDB header:chaperone Chain: A: PDB Molecule:dnaj homolog subfamily b member 2; PDBTitle: solution structure of the j domain of hsj1a 36 c2jzyA_ not modelled 6.6 13 PDB header:transcription Chain: A: PDB Molecule:transcriptional regulatory protein pcor; PDBTitle: solution structure of c-terminal effector domain of2 putative two-component-system response regulator involved3 in copper resistance from klebsiella pneumoniae 37 d2gu3a2 not modelled 6.5 50 Fold:Cystatin-like Superfamily:Cystatin/monellin Family:PepSY-like 38 d1wf9a1 not modelled 6.2 16 Fold:beta-Grasp (ubiquitin-like) Superfamily:Ubiquitin-like Family:Ubiquitin-related 39 d1yu0a1 not modelled 6.0 38 Fold:Pseudo beta-prism Superfamily:Bacteriophage trimeric proteins domain Family:Mtd domain-like 40 c2ctqA_ not modelled 6.0 36 PDB header:chaperone Chain: A: PDB Molecule:dnaj homolog subfamily c member 12; PDBTitle: solution structure of j-domain from human dnaj subfamily c2 menber 12 41 c2ctrA_ not modelled 5.9 21 PDB header:chaperone Chain: A: PDB Molecule:dnaj homolog subfamily b member 9; PDBTitle: solution structure of j-domain from human dnaj subfamily b2 menber 9 42 d1aiea_ not modelled 5.8 21 Fold:p53 tetramerization domain Superfamily:p53 tetramerization domain Family:p53 tetramerization domain 43 d3saka_ not modelled 5.8 18 Fold:p53 tetramerization domain Superfamily:p53 tetramerization domain Family:p53 tetramerization domain 44 d1iqoa_ not modelled 5.8 24 Fold:Hypothetical protein MTH1880 Superfamily:Hypothetical protein MTH1880 Family:Hypothetical protein MTH1880 45 d1s6la1 not modelled 5.8 18 Fold:DNA/RNA-binding 3-helical bundle Superfamily:"Winged helix" DNA-binding domain Family:MerB N-terminal domain-like 46 c1zldA_ not modelled 5.6 33 PDB header:toxin Chain: A: PDB Molecule:ptr necrosis toxin; PDBTitle: crystal structure of a rgd-containing host-selective toxin:2 pyrenophora tritici-repentis ptr toxa 47 c2j10B_ not modelled 5.5 21 PDB header:transcription Chain: B: PDB Molecule:cellular tumor antigen p53; PDBTitle: p53 tetramerization domain mutant t329f q331k 48 c2j10D_ not modelled 5.5 21 PDB header:transcription Chain: D: PDB Molecule:cellular tumor antigen p53; PDBTitle: p53 tetramerization domain mutant t329f q331k 49 c2j10A_ not modelled 5.5 21 PDB header:transcription Chain: A: PDB Molecule:cellular tumor antigen p53; PDBTitle: p53 tetramerization domain mutant t329f q331k 50 d2i3oa1 not modelled 5.3 10 Fold:Ntn hydrolase-like Superfamily:N-terminal nucleophile aminohydrolases (Ntn hydrolases) Family:Gamma-glutamyltranspeptidase-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