Secondary structure and disorder prediction

		1	.	.	.	.	.	.	.	.	10	.	.	.	.	.	.	.	.	.	20	.	.	.	.	.	.	.	.	.	30	.	.	.	.	.	.	.	.	.	40	.	.	.	.	.	.	.	.	.	50	.	.	.	.	.	.	.	.	.	60
Sequence		M	T	D	S	E	L	M	Q	L	S	E	Q	V	G	Q	A	L	K	A	R	G	A	T	V	T	T	A	E	S	C	T	G	G	W	V	A	K	V	I	T	D	I	A	G	S	S	A	W	F	E	R	G	F	V	T	Y	S	N	E	A
Secondary structure
SS confidence
Disorder		?	?	?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	70	.	.	.	.	.	.	.	.	.	80	.	.	.	.	.	.	.	.	.	90	.	.	.	.	.	.	.	.	.	100	.	.	.	.	.	.	.	.	.	110	.	.	.	.	.	.	.	.	.	120
Sequence		K	A	Q	M	I	G	V	R	E	E	T	L	A	Q	H	G	A	V	S	E	P	V	V	V	E	M	A	I	G	A	L	K	A	A	R	A	D	Y	A	V	S	I	S	G	I	A	G	P	D	G	G	S	E	E	K	P	V	G	T	V
Secondary structure
SS confidence
Disorder																																																	?	?		?	?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	130	.	.	.	.	.	.	.	.	.	140	.	.	.	.	.	.	.	.	.	150	.	.	.	.	.	.	.	.	.	160	.	.	.	.	.
Sequence		W	F	A	F	A	T	A	R	G	E	G	I	T	R	R	E	C	F	S	G	D	R	D	A	V	R	R	Q	A	T	A	Y	A	L	Q	T	L	W	Q	Q	F	L	Q	N	T
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 2a9s chain A domain 1 Region: 4 - 163 Aligned: 160 Modelled: 160 Confidence: 100.0% Identity: 43% Fold: Anticodon-binding domain-like Superfamily: CinA-like Family: CinA-like Phyre2 PDB 1pzn chain A domain 1 Region: 39 - 95 Aligned: 57 Modelled: 57 Confidence: 51.6% Identity: 18% Fold: SAM domain-like Superfamily: Rad51 N-terminal domain-like Family: DNA repair protein Rad51, N-terminal domain Phyre2 PDB 2i1q chain A domain 1 Region: 39 - 95 Aligned: 57 Modelled: 57 Confidence: 42.3% Identity: 18% Fold: SAM domain-like Superfamily: Rad51 N-terminal domain-like Family: DNA repair protein Rad51, N-terminal domain Phyre2 PDB 3b33 chain A Region: 34 - 72 Aligned: 39 Modelled: 39 Confidence: 38.6% Identity: 8% PDB header:transferase Chain: A: PDB Molecule:sensor protein; PDBTitle: crystal structure of the pas domain of nitrogen regulation protein2 nr(ii) from vibrio parahaemolyticus Phyre2 PDB 3a9l chain B Region: 35 - 123 Aligned: 66 Modelled: 89 Confidence: 36.5% Identity: 23% PDB header:hydrolase Chain: B: PDB Molecule:poly-gamma-glutamate hydrolase; PDBTitle: structure of bacteriophage poly-gamma-glutamate hydrolase Phyre2 PDB 1mzu chain A Region: 52 - 72 Aligned: 21 Modelled: 21 Confidence: 18.1% Identity: 19% Fold: Profilin-like Superfamily: PYP-like sensor domain (PAS domain) Family: PYP-like Phyre2 PDB 1xjc chain A Region: 7 - 27 Aligned: 21 Modelled: 21 Confidence: 17.0% Identity: 29% Fold: P-loop containing nucleoside triphosphate hydrolases Superfamily: P-loop containing nucleoside triphosphate hydrolases Family: Nitrogenase iron protein-like Phyre2 PDB 1v9y chain A Region: 33 - 72 Aligned: 40 Modelled: 40 Confidence: 17.0% Identity: 18% Fold: Profilin-like Superfamily: PYP-like sensor domain (PAS domain) Family: Heme-binding PAS domain Phyre2 PDB 1v9y chain A Region: 33 - 72 Aligned: 40 Modelled: 40 Confidence: 17.0% Identity: 18% PDB header:signaling protein Chain: A: PDB Molecule:heme pas sensor protein; PDBTitle: crystal structure of the heme pas sensor domain of ec dos (ferric2 form) Phyre2 PDB 3mfx chain A Region: 34 - 72 Aligned: 39 Modelled: 39 Confidence: 15.9% Identity: 15% PDB header:transcription Chain: A: PDB Molecule:sensory box/ggdef family protein; PDBTitle: crystal structure of the sensory box domain of the sensory-2 box/ggdef protein so_1695 from shewanella oneidensis,3 northeast structural genomics consortium target sor288b Phyre2 PDB 2bgw chain A domain 1 Region: 37 - 95 Aligned: 58 Modelled: 59 Confidence: 13.6% Identity: 5% Fold: SAM domain-like Superfamily: RuvA domain 2-like Family: Hef domain-like Phyre2 PDB 3ju7 chain B Region: 5 - 108 Aligned: 104 Modelled: 104 Confidence: 13.1% Identity: 11% PDB header:transferase Chain: B: PDB Molecule:putative plp-dependent aminotransferase; PDBTitle: crystal structure of putative plp-dependent aminotransferase2 (np_978343.1) from bacillus cereus atcc 10987 at 2.19 a resolution Phyre2 PDB 3pro chain C domain 1 Region: 60 - 99 Aligned: 38 Modelled: 40 Confidence: 11.8% Identity: 18% Fold: Alpha-lytic protease prodomain-like Superfamily: Alpha-lytic protease prodomain Family: Alpha-lytic protease prodomain Phyre2 PDB 1zpd chain A Region: 8 - 104 Aligned: 71 Modelled: 73 Confidence: 11.0% Identity: 17% PDB header:alcohol fermentation Chain: A: PDB Molecule:pyruvate decarboxylase; PDBTitle: pyruvate decarboxylase from zymomonas mobilis Phyre2 PDB 1nwz chain A Region: 52 - 72 Aligned: 21 Modelled: 21 Confidence: 10.7% Identity: 19% Fold: Profilin-like Superfamily: PYP-like sensor domain (PAS domain) Family: PYP-like Phyre2 PDB 1kft chain A Region: 36 - 92 Aligned: 56 Modelled: 57 Confidence: 10.6% Identity: 11% PDB header:dna binding protein Chain: A: PDB Molecule:excinuclease abc subunit c; PDBTitle: solution structure of the c-terminal domain of uvrc from e-2 coli Phyre2 PDB 1kft chain A Region: 36 - 92 Aligned: 56 Modelled: 57 Confidence: 10.6% Identity: 11% Fold: SAM domain-like Superfamily: RuvA domain 2-like Family: Excinuclease UvrC C-terminal domain Phyre2 PDB 1a4i chain A domain 1 Region: 13 - 127 Aligned: 59 Modelled: 60 Confidence: 10.3% Identity: 36% Fold: NAD(P)-binding Rossmann-fold domains Superfamily: NAD(P)-binding Rossmann-fold domains Family: Aminoacid dehydrogenase-like, C-terminal domain Phyre2 PDB 3a0v chain A Region: 52 - 72 Aligned: 21 Modelled: 21 Confidence: 10.2% Identity: 29% PDB header:transferase Chain: A: PDB Molecule:sensor protein; PDBTitle: pas domain of histidine kinase thka (tm1359) (semet,2 f486m/f489m) Phyre2 PDB 2w1t chain B Region: 72 - 103 Aligned: 30 Modelled: 32 Confidence: 9.7% Identity: 23% PDB header:transcription Chain: B: PDB Molecule:stage v sporulation protein t; PDBTitle: crystal structure of b. subtilis spovt Phyre2 1 d2a9sa1 2 d1pzna1 3 d2i1qa1 4 c3b33A_ 5 c3a9lB_ 6 d1mzua_ 7 d1xjca_ 8 d1v9ya_ 9 c1v9yA_ 10 c3mfxA_ 11 d2bgwa1 12 c3ju7B_ 13 d3proc1 14 c1zpdA_ 15 d1nwza_ 16 c1kftA_ 17 d1kfta_ 18 d1a4ia1 19 c3a0vA_ 20 c2w1tB_ 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44

Detailed template information

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

1 d2a9sa1 100.0 43 Fold:Anticodon-binding domain-like Superfamily:CinA-like Family:CinA-like 2 d1pzna1 51.6 18 Fold:SAM domain-like Superfamily:Rad51 N-terminal domain-like Family:DNA repair protein Rad51, N-terminal domain 3 d2i1qa1 42.3 18 Fold:SAM domain-like Superfamily:Rad51 N-terminal domain-like Family:DNA repair protein Rad51, N-terminal domain 4 c3b33A_ 38.6 8 PDB header:transferase Chain: A: PDB Molecule:sensor protein; PDBTitle: crystal structure of the pas domain of nitrogen regulation protein2 nr(ii) from vibrio parahaemolyticus 5 c3a9lB_ 36.5 23 PDB header:hydrolase Chain: B: PDB Molecule:poly-gamma-glutamate hydrolase; PDBTitle: structure of bacteriophage poly-gamma-glutamate hydrolase 6 d1mzua_ 18.1 19 Fold:Profilin-like Superfamily:PYP-like sensor domain (PAS domain) Family:PYP-like 7 d1xjca_ 17.0 29 Fold:P-loop containing nucleoside triphosphate hydrolases Superfamily:P-loop containing nucleoside triphosphate hydrolases Family:Nitrogenase iron protein-like 8 d1v9ya_ 17.0 18 Fold:Profilin-like Superfamily:PYP-like sensor domain (PAS domain) Family:Heme-binding PAS domain 9 c1v9yA_ 17.0 18 PDB header:signaling protein Chain: A: PDB Molecule:heme pas sensor protein; PDBTitle: crystal structure of the heme pas sensor domain of ec dos (ferric2 form) 10 c3mfxA_ 15.9 15 PDB header:transcription Chain: A: PDB Molecule:sensory box/ggdef family protein; PDBTitle: crystal structure of the sensory box domain of the sensory-2 box/ggdef protein so_1695 from shewanella oneidensis,3 northeast structural genomics consortium target sor288b 11 d2bgwa1 13.6 5 Fold:SAM domain-like Superfamily:RuvA domain 2-like Family:Hef domain-like 12 c3ju7B_ 13.1 11 PDB header:transferase Chain: B: PDB Molecule:putative plp-dependent aminotransferase; PDBTitle: crystal structure of putative plp-dependent aminotransferase2 (np_978343.1) from bacillus cereus atcc 10987 at 2.19 a resolution 13 d3proc1 11.8 18 Fold:Alpha-lytic protease prodomain-like Superfamily:Alpha-lytic protease prodomain Family:Alpha-lytic protease prodomain 14 c1zpdA_ 11.0 17 PDB header:alcohol fermentation Chain: A: PDB Molecule:pyruvate decarboxylase; PDBTitle: pyruvate decarboxylase from zymomonas mobilis 15 d1nwza_ 10.7 19 Fold:Profilin-like Superfamily:PYP-like sensor domain (PAS domain) Family:PYP-like 16 c1kftA_ 10.6 11 PDB header:dna binding protein Chain: A: PDB Molecule:excinuclease abc subunit c; PDBTitle: solution structure of the c-terminal domain of uvrc from e-2 coli 17 d1kfta_ 10.6 11 Fold:SAM domain-like Superfamily:RuvA domain 2-like Family:Excinuclease UvrC C-terminal domain 18 d1a4ia1 10.3 36 Fold:NAD(P)-binding Rossmann-fold domains Superfamily:NAD(P)-binding Rossmann-fold domains Family:Aminoacid dehydrogenase-like, C-terminal domain 19 c3a0vA_ 10.2 29 PDB header:transferase Chain: A: PDB Molecule:sensor protein; PDBTitle: pas domain of histidine kinase thka (tm1359) (semet,2 f486m/f489m) 20 c2w1tB_ 9.7 23 PDB header:transcription Chain: B: PDB Molecule:stage v sporulation protein t; PDBTitle: crystal structure of b. subtilis spovt 21 d1j3ma_ not modelled 9.6 9 Fold:TBP-like Superfamily:TT1751-like Family:TT1751-like 22 c3mqoB_ not modelled 9.6 8 PDB header:transcription regulator Chain: B: PDB Molecule:transcriptional regulator, luxr family; PDBTitle: the crystal structure of the pas domain in complex with isopropanol of2 a transcriptional regulator in the luxr family from burkholderia3 thailandensis to 1.7a 23 c3fg8B_ not modelled 9.5 14 PDB header:structural genomics, unknown function Chain: B: PDB Molecule:uncharacterized protein rha05790; PDBTitle: crystal structure of pas domain of rha05790 24 c2v3wC_ not modelled 8.6 22 PDB header:lyase Chain: C: PDB Molecule:benzoylformate decarboxylase; PDBTitle: crystal structure of the benzoylformate decarboxylase2 variant l461a from pseudomonas putida 25 c2v1bA_ not modelled 8.3 10 PDB header:transferase Chain: A: PDB Molecule:nph1-1; PDBTitle: n- and c-terminal helices of oat lov2 (404-546) are2 involved in light-induced signal transduction (room3 temperature (293k) light structure of lov2 (404-546)) 26 c3p7nB_ not modelled 8.0 26 PDB header:dna binding protein Chain: B: PDB Molecule:sensor histidine kinase; PDBTitle: crystal structure of light activated transcription factor el222 from2 erythrobacter litoralis 27 d1otda_ not modelled 7.2 17 Fold:Profilin-like Superfamily:PYP-like sensor domain (PAS domain) Family:PYP-like 28 c2xc7A_ not modelled 7.2 10 PDB header:rna binding protein Chain: A: PDB Molecule:phosphorylated adapter rna export protein; PDBTitle: solution structure of phax-rbd in complex with ssrna 29 d1s2da_ not modelled 6.5 14 Fold:Flavodoxin-like Superfamily:N-(deoxy)ribosyltransferase-like Family:N-deoxyribosyltransferase 30 d2a1jb1 not modelled 6.3 13 Fold:SAM domain-like Superfamily:RuvA domain 2-like Family:Hef domain-like 31 d1rqpa2 not modelled 6.2 31 Fold:Bacterial fluorinating enzyme, N-terminal domain Superfamily:Bacterial fluorinating enzyme, N-terminal domain Family:Bacterial fluorinating enzyme, N-terminal domain 32 c1wu8B_ not modelled 6.1 31 PDB header:structural genomics, unknown function Chain: B: PDB Molecule:hypothetical protein ph0463; PDBTitle: crystal structure of project ph0463 from pyrococcus horikoshii ot3 33 c3rtyA_ not modelled 6.0 19 PDB header:circadian clock protein Chain: A: PDB Molecule:period circadian protein; PDBTitle: structure of an enclosed dimer formed by the drosophila period protein 34 d2ge7a1 not modelled 6.0 23 Fold:Nucleocapsid protein dimerization domain Superfamily:Nucleocapsid protein dimerization domain Family:Coronavirus nucleocapsid protein 35 d2ca1a1 not modelled 5.9 23 Fold:Nucleocapsid protein dimerization domain Superfamily:Nucleocapsid protein dimerization domain Family:Coronavirus nucleocapsid protein 36 c2npbA_ not modelled 5.8 14 PDB header:oxidoreductase Chain: A: PDB Molecule:selenoprotein w; PDBTitle: nmr solution structure of mouse selw 37 d1ciia1 not modelled 5.8 30 Fold:Toxins' membrane translocation domains Superfamily:Colicin Family:Colicin 38 c2zbvC_ not modelled 5.8 23 PDB header:structural genomics, unknown function Chain: C: PDB Molecule:uncharacterized conserved protein; PDBTitle: crystal structure of uncharacterized conserved protein from thermotoga2 maritima 39 c2e62A_ not modelled 5.8 25 PDB header:rna binding protein Chain: A: PDB Molecule:protein at5g25060; PDBTitle: solution structure of the cwf21 domain in protein aak25922 40 c2guzO_ not modelled 5.7 16 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 41 c3gdwA_ not modelled 5.6 9 PDB header:structural genomics, unknown function Chain: A: PDB Molecule:sigma-54 interaction domain protein; PDBTitle: crystal structure of sigma-54 interaction domain protein from2 enterococcus faecalis 42 d1e5qa2 not modelled 5.2 23 Fold:FwdE/GAPDH domain-like Superfamily:Glyceraldehyde-3-phosphate dehydrogenase-like, C-terminal domain Family:Homoserine dehydrogenase-like 43 c1hvwA_ not modelled 5.2 100 PDB header:toxin Chain: A: PDB Molecule:omega-atracotoxin-hv1a; PDBTitle: hairpinless mutant of omega-atracotoxin-hv1a 44 d1hvwa_ not modelled 5.2 100 Fold:Knottins (small inhibitors, toxins, lectins) Superfamily:omega toxin-like Family:Spider toxins

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