Secondary structure and disorder prediction

		1	.	.	.	.	.	.	.	.	10	.	.	.	.	.	.	.	.	.	20	.	.	.	.	.	.	.	.	.	30	.	.	.	.	.	.	.	.	.	40	.	.	.	.	.	.	.	.	.	50	.	.	.	.	.	.	.	.	.	60
Sequence		M	N	I	N	R	D	K	I	V	Q	L	V	D	T	D	T	I	E	N	L	T	S	A	L	S	Q	R	L	I	A	D	Q	L	R	L	T	T	A	E	S	C	T	G	G	K	L	A	S	A	L	C	A	A	E	D	T	P	K	F	Y
Secondary structure
SS confidence
Disorder		?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	70	.	.	.	.	.	.	.	.	.	80	.	.	.	.	.	.	.	.	.	90	.	.	.	.	.	.	.	.	.	100	.	.	.	.	.	.	.	.	.	110	.	.	.	.	.	.	.	.	.	120
Sequence		G	A	G	F	V	T	F	T	D	Q	A	K	M	K	I	L	S	V	S	Q	Q	S	L	E	R	Y	S	A	V	S	E	K	V	A	A	E	M	A	T	G	A	I	E	R	A	D	A	D	V	S	I	A	I	T	G	Y	G	G	P	E
Secondary structure
SS confidence
Disorder																																																												?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	130	.	.	.	.	.	.	.	.	.	140	.	.	.	.	.	.	.	.	.	150	.	.	.	.	.	.	.	.	.	160	.	.	.	.	.	.	.	.	.	170	.	.
Sequence		G	G	E	D	G	T	P	A	G	T	V	W	F	A	W	H	I	K	G	Q	N	Y	T	A	V	M	H	F	A	G	D	C	E	T	V	L	A	L	A	V	R	F	A	L	A	Q	L	L	Q	L	L	L
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: 10 - 171 Aligned: 162 Modelled: 162 Confidence: 100.0% Identity: 33% Fold: Anticodon-binding domain-like Superfamily: CinA-like Family: CinA-like Phyre2 PDB 1pzn chain A domain 1 Region: 50 - 106 Aligned: 57 Modelled: 57 Confidence: 55.5% Identity: 14% 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: 50 - 106 Aligned: 57 Modelled: 57 Confidence: 46.0% Identity: 26% Fold: SAM domain-like Superfamily: Rad51 N-terminal domain-like Family: DNA repair protein Rad51, N-terminal domain Phyre2 PDB 3b33 chain A Region: 45 - 83 Aligned: 39 Modelled: 39 Confidence: 37.2% Identity: 10% 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: 46 - 134 Aligned: 66 Modelled: 89 Confidence: 36.1% Identity: 14% 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: 63 - 83 Aligned: 21 Modelled: 21 Confidence: 17.8% Identity: 5% Fold: Profilin-like Superfamily: PYP-like sensor domain (PAS domain) Family: PYP-like Phyre2 PDB 1kft chain A Region: 47 - 103 Aligned: 56 Modelled: 57 Confidence: 17.4% Identity: 11% Fold: SAM domain-like Superfamily: RuvA domain 2-like Family: Excinuclease UvrC C-terminal domain Phyre2 PDB 1kft chain A Region: 47 - 103 Aligned: 56 Modelled: 57 Confidence: 17.4% 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 1v9y chain A Region: 44 - 83 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: 44 - 83 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: 45 - 83 Aligned: 39 Modelled: 39 Confidence: 16.1% Identity: 18% 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 1saz chain A domain 1 Region: 54 - 133 Aligned: 75 Modelled: 74 Confidence: 15.1% Identity: 13% Fold: Ribonuclease H-like motif Superfamily: Actin-like ATPase domain Family: Acetokinase-like Phyre2 PDB 2o8k chain A Region: 4 - 36 Aligned: 33 Modelled: 33 Confidence: 13.8% Identity: 9% PDB header:transcription/dna Chain: A: PDB Molecule:rna polymerase sigma factor rpon; PDBTitle: nmr structure of the sigma-54 rpon domain bound to the-242 promoter element Phyre2 PDB 3h3y chain F Region: 110 - 140 Aligned: 23 Modelled: 31 Confidence: 12.4% Identity: 22% PDB header:viral protein Chain: F: PDB Molecule:baseplate structural protein gp6; PDBTitle: fitting of the gp6 crystal structure into 3d cryo-em2 reconstruction of bacteriophage t4 star-shaped baseplate Phyre2 PDB 1j3m chain A Region: 19 - 105 Aligned: 87 Modelled: 87 Confidence: 12.2% Identity: 15% Fold: TBP-like Superfamily: TT1751-like Family: TT1751-like Phyre2 PDB 1nwz chain A Region: 63 - 83 Aligned: 21 Modelled: 21 Confidence: 11.6% Identity: 14% Fold: Profilin-like Superfamily: PYP-like sensor domain (PAS domain) Family: PYP-like Phyre2 PDB 2phn chain A domain 1 Region: 92 - 139 Aligned: 41 Modelled: 48 Confidence: 11.0% Identity: 29% Fold: CofE-like Superfamily: CofE-like Family: CofE-like Phyre2 PDB 1a4i chain A domain 1 Region: 24 - 133 Aligned: 54 Modelled: 55 Confidence: 10.6% Identity: 31% 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: 63 - 83 Aligned: 21 Modelled: 21 Confidence: 10.4% Identity: 10% 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: 83 - 114 Aligned: 30 Modelled: 32 Confidence: 10.4% Identity: 33% 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 d1kfta_ 8 c1kftA_ 9 d1v9ya_ 10 c1v9yA_ 11 c3mfxA_ 12 d1saza1 13 c2o8kA_ 14 c3h3yF_ 15 d1j3ma_ 16 d1nwza_ 17 d2phna1 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 45 46 47 48

Detailed template information

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

1 d2a9sa1 100.0 33 Fold:Anticodon-binding domain-like Superfamily:CinA-like Family:CinA-like 2 d1pzna1 55.5 14 Fold:SAM domain-like Superfamily:Rad51 N-terminal domain-like Family:DNA repair protein Rad51, N-terminal domain 3 d2i1qa1 46.0 26 Fold:SAM domain-like Superfamily:Rad51 N-terminal domain-like Family:DNA repair protein Rad51, N-terminal domain 4 c3b33A_ 37.2 10 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_ 36.1 14 PDB header:hydrolase Chain: B: PDB Molecule:poly-gamma-glutamate hydrolase; PDBTitle: structure of bacteriophage poly-gamma-glutamate hydrolase 6 d1mzua_ 17.8 5 Fold:Profilin-like Superfamily:PYP-like sensor domain (PAS domain) Family:PYP-like 7 d1kfta_ 17.4 11 Fold:SAM domain-like Superfamily:RuvA domain 2-like Family:Excinuclease UvrC C-terminal domain 8 c1kftA_ 17.4 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 9 d1v9ya_ 17.0 18 Fold:Profilin-like Superfamily:PYP-like sensor domain (PAS domain) Family:Heme-binding PAS domain 10 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) 11 c3mfxA_ 16.1 18 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 12 d1saza1 15.1 13 Fold:Ribonuclease H-like motif Superfamily:Actin-like ATPase domain Family:Acetokinase-like 13 c2o8kA_ 13.8 9 PDB header:transcription/dna Chain: A: PDB Molecule:rna polymerase sigma factor rpon; PDBTitle: nmr structure of the sigma-54 rpon domain bound to the-242 promoter element 14 c3h3yF_ 12.4 22 PDB header:viral protein Chain: F: PDB Molecule:baseplate structural protein gp6; PDBTitle: fitting of the gp6 crystal structure into 3d cryo-em2 reconstruction of bacteriophage t4 star-shaped baseplate 15 d1j3ma_ 12.2 15 Fold:TBP-like Superfamily:TT1751-like Family:TT1751-like 16 d1nwza_ 11.6 14 Fold:Profilin-like Superfamily:PYP-like sensor domain (PAS domain) Family:PYP-like 17 d2phna1 11.0 29 Fold:CofE-like Superfamily:CofE-like Family:CofE-like 18 d1a4ia1 10.6 31 Fold:NAD(P)-binding Rossmann-fold domains Superfamily:NAD(P)-binding Rossmann-fold domains Family:Aminoacid dehydrogenase-like, C-terminal domain 19 c3a0vA_ 10.4 10 PDB header:transferase Chain: A: PDB Molecule:sensor protein; PDBTitle: pas domain of histidine kinase thka (tm1359) (semet,2 f486m/f489m) 20 c2w1tB_ 10.4 33 PDB header:transcription Chain: B: PDB Molecule:stage v sporulation protein t; PDBTitle: crystal structure of b. subtilis spovt 21 d2bgwa1 not modelled 9.8 10 Fold:SAM domain-like Superfamily:RuvA domain 2-like Family:Hef domain-like 22 c3mqoB_ not modelled 9.7 11 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 c3ju7B_ not modelled 9.6 7 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 24 c3giuA_ not modelled 8.9 31 PDB header:hydrolase Chain: A: PDB Molecule:pyrrolidone-carboxylate peptidase; PDBTitle: 1.25 angstrom crystal structure of pyrrolidone-carboxylate peptidase2 (pcp) from staphylococcus aureus 25 d1xjca_ not modelled 8.8 12 Fold:P-loop containing nucleoside triphosphate hydrolases Superfamily:P-loop containing nucleoside triphosphate hydrolases Family:Nitrogenase iron protein-like 26 c2v1bA_ not modelled 8.8 15 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)) 27 c1zpdA_ not modelled 8.4 17 PDB header:alcohol fermentation Chain: A: PDB Molecule:pyruvate decarboxylase; PDBTitle: pyruvate decarboxylase from zymomonas mobilis 28 c1wu8B_ not modelled 8.2 38 PDB header:structural genomics, unknown function Chain: B: PDB Molecule:hypothetical protein ph0463; PDBTitle: crystal structure of project ph0463 from pyrococcus horikoshii ot3 29 c3p7nB_ not modelled 8.1 13 PDB header:dna binding protein Chain: B: PDB Molecule:sensor histidine kinase; PDBTitle: crystal structure of light activated transcription factor el222 from2 erythrobacter litoralis 30 c3fg8B_ not modelled 7.9 10 PDB header:structural genomics, unknown function Chain: B: PDB Molecule:uncharacterized protein rha05790; PDBTitle: crystal structure of pas domain of rha05790 31 d1otda_ not modelled 7.8 14 Fold:Profilin-like Superfamily:PYP-like sensor domain (PAS domain) Family:PYP-like 32 c2zbvC_ not modelled 7.5 31 PDB header:structural genomics, unknown function Chain: C: PDB Molecule:uncharacterized conserved protein; PDBTitle: crystal structure of uncharacterized conserved protein from thermotoga2 maritima 33 d1rqpa2 not modelled 7.5 31 Fold:Bacterial fluorinating enzyme, N-terminal domain Superfamily:Bacterial fluorinating enzyme, N-terminal domain Family:Bacterial fluorinating enzyme, N-terminal domain 34 d1iu8a_ not modelled 7.2 50 Fold:Phosphorylase/hydrolase-like Superfamily:Pyrrolidone carboxyl peptidase (pyroglutamate aminopeptidase) Family:Pyrrolidone carboxyl peptidase (pyroglutamate aminopeptidase) 35 c3lacA_ not modelled 7.0 44 PDB header:hydrolase Chain: A: PDB Molecule:pyrrolidone-carboxylate peptidase; PDBTitle: crystal structure of bacillus anthracis pyrrolidone-carboxylate2 peptidase, pcp 36 c3gdwA_ not modelled 6.7 15 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 37 c2ebjB_ not modelled 6.7 38 PDB header:hydrolase Chain: B: PDB Molecule:pyrrolidone carboxyl peptidase; PDBTitle: crystal structure of pyrrolidone carboxyl peptidase from thermus2 thermophilus 38 c2v3wC_ not modelled 6.1 16 PDB header:lyase Chain: C: PDB Molecule:benzoylformate decarboxylase; PDBTitle: crystal structure of the benzoylformate decarboxylase2 variant l461a from pseudomonas putida 39 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 40 d1s2da_ not modelled 5.8 11 Fold:Flavodoxin-like Superfamily:N-(deoxy)ribosyltransferase-like Family:N-deoxyribosyltransferase 41 d1iofa_ not modelled 5.7 44 Fold:Phosphorylase/hydrolase-like Superfamily:Pyrrolidone carboxyl peptidase (pyroglutamate aminopeptidase) Family:Pyrrolidone carboxyl peptidase (pyroglutamate aminopeptidase) 42 c2cw5B_ not modelled 5.6 18 PDB header:structural genomics, unknown function Chain: B: PDB Molecule:bacterial fluorinating enzyme homolog; PDBTitle: crystal structure of a conserved hypothetical protein from2 thermus thermophilus hb8 43 c2q6oB_ not modelled 5.5 38 PDB header:biosynthetic protein Chain: B: PDB Molecule:hypothetical protein; PDBTitle: sall-y70t with sam and cl 44 c2e62A_ not modelled 5.3 12 PDB header:rna binding protein Chain: A: PDB Molecule:protein at5g25060; PDBTitle: solution structure of the cwf21 domain in protein aak25922 45 d1auga_ not modelled 5.3 44 Fold:Phosphorylase/hydrolase-like Superfamily:Pyrrolidone carboxyl peptidase (pyroglutamate aminopeptidase) Family:Pyrrolidone carboxyl peptidase (pyroglutamate aminopeptidase) 46 c1rqrA_ not modelled 5.2 31 PDB header:transferase Chain: A: PDB Molecule:5'-fluoro-5'-deoxyadenosine synthase; PDBTitle: crystal structure and mechanism of a bacterial fluorinating enzyme,2 product complex 47 c2obxH_ not modelled 5.2 11 PDB header:transferase Chain: H: PDB Molecule:6,7-dimethyl-8-ribityllumazine synthase 1; PDBTitle: lumazine synthase ribh2 from mesorhizobium loti (gene mll7281, swiss-2 prot entry q986n2) complexed with inhibitor 5-nitro-6-(d-3 ribitylamino)-2,4(1h,3h) pyrimidinedione 48 c1hvwA_ not modelled 5.0 100 PDB header:toxin Chain: A: PDB Molecule:omega-atracotoxin-hv1a; PDBTitle: hairpinless mutant of omega-atracotoxin-hv1a

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