Secondary structure and disorder prediction

		1	.	.	.	.	.	.	.	.	10	.	.	.	.	.	.	.	.	.	20	.	.	.	.	.	.	.	.	.	30	.	.	.	.	.	.	.	.	.	40	.	.	.	.	.	.	.	.	.	50	.	.	.	.	.	.	.	.	.	60
Sequence		M	K	K	F	I	I	L	L	S	L	L	I	L	L	P	L	T	A	A	S	K	P	L	I	P	I	M	K	T	L	F	T	D	V	T	G	T	V	P	D	A	E	E	I	A	H	K	A	E	L	F	R	Q	Q	T	G	I	A	P	F
Secondary structure
SS confidence
Disorder		?	?	?	?		?									?			?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	70	.	.	.	.	.	.	.	.	.	80	.	.	.	.	.	.	.	.	.	90	.	.	.	.	.	.	.	.	.	100	.	.	.	.	.	.	.	.	.	110	.	.	.	.	.	.	.	.	.	120
Sequence		I	V	V	L	P	D	I	N	N	E	A	S	L	R	Q	N	G	K	A	M	L	A	H	A	S	S	S	L	S	D	V	K	G	S	V	L	L	L	F	T	T	R	E	P	R	L	I	M	I	T	N	G	Q	V	E	S	G	L	D	D
Secondary structure
SS confidence
Disorder												?	?	?	?	?	?	?					?	?		?	?		?			?																							?	?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	130	.	.	.	.	.	.	.	.	.	140	.	.	.	.	.	.	.	.	.	150	.	.	.	.	.	.	.	.	.	160	.	.	.	.	.	.	.	.	.	170	.	.	.	.	.	.	.	.	.	180
Sequence		K	H	L	G	L	L	I	E	N	H	T	L	A	Y	L	N	A	D	L	W	Y	Q	G	I	N	N	A	L	A	V	L	Q	A	Q	I	L	K	Q	S	T	P	P	L	T	Y	Y	P	H	P	G	Q	Q	H	E	N	A	P	P	G	S
Secondary structure
SS confidence
Disorder																																						?	?												?	?	?	?	?	?	?	?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	190	.	.	.	.	.	.	.	.	.	200	.	.	.	.	.	.	.	.	.	210	.	.	.	.	.	.	.	.	.	220	.	.	.	.	.	.	.	.	.	230	.	.	.	.	.	.	.	.	.	240
Sequence		T	N	T	L	G	F	I	A	W	A	A	T	F	I	L	F	S	R	I	F	Y	Y	T	T	R	F	I	Y	A	L	K	F	A	V	A	M	T	I	A	N	M	G	Y	Q	A	L	C	L	Y	I	D	N	S	F	A	I	T	R	I	S
Secondary structure
SS confidence
Disorder
Disorder confidence
		.	.	.	.	.	.	.	.	.	250	.	.	.	.	.	.	.	.	.	260	.	.
Sequence		P	L	W	A	G	L	I	G	V	C	T	F	I	A	A	L	L	L	T	S	K	R
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 3ptj chain A Region: 41 - 162 Aligned: 122 Modelled: 122 Confidence: 98.1% Identity: 8% PDB header:hydrolase Chain: A: PDB Molecule:upf0603 protein at1g54780, chloroplastic; PDBTitle: structural and functional analysis of arabidopsis thaliana thylakoid2 lumen protein attlp18.3 Phyre2 PDB 2kw7 chain A Region: 32 - 155 Aligned: 123 Modelled: 124 Confidence: 97.9% Identity: 20% PDB header:structural genomics, unknown function Chain: A: PDB Molecule:conserved domain protein; PDBTitle: solution nmr structure of the n-terminal domain of protein pg_03612 from p.gingivalis, northeast structural genomics consortium target3 pgr37a Phyre2 PDB 2kpt chain A Region: 40 - 161 Aligned: 111 Modelled: 119 Confidence: 62.0% Identity: 16% PDB header:structural genomics, unknown function Chain: A: PDB Molecule:putative secreted protein; PDBTitle: solution nmr structure of the n-terminal domain of cg24962 protein from corynebacterium glutamicum. northeast3 structural genomics consortium target cgr26a Phyre2 PDB 2y69 chain S Region: 36 - 60 Aligned: 25 Modelled: 25 Confidence: 22.8% Identity: 32% PDB header:electron transport Chain: S: PDB Molecule:cytochrome c oxidase subunit 5b; PDBTitle: bovine heart cytochrome c oxidase re-refined with molecular2 oxygen Phyre2 PDB 1q90 chain N Region: 187 - 197 Aligned: 11 Modelled: 11 Confidence: 18.4% Identity: 64% Fold: Single transmembrane helix Superfamily: PetN subunit of the cytochrome b6f complex Family: PetN subunit of the cytochrome b6f complex Phyre2 PDB 1v54 chain F Region: 35 - 60 Aligned: 26 Modelled: 26 Confidence: 15.8% Identity: 31% Fold: Rubredoxin-like Superfamily: Rubredoxin-like Family: Cytochrome c oxidase Subunit F Phyre2 PDB 1ppr chain M domain 2 Region: 36 - 55 Aligned: 20 Modelled: 20 Confidence: 13.2% Identity: 25% Fold: Peridinin-chlorophyll protein Superfamily: Peridinin-chlorophyll protein Family: Peridinin-chlorophyll protein Phyre2 PDB 3ism chain C Region: 160 - 170 Aligned: 11 Modelled: 11 Confidence: 12.3% Identity: 64% PDB header:hydrolase inhibitor/hydrolase Chain: C: PDB Molecule:cg4930; PDBTitle: crystal structure of the endog/endogi complex: mechanism of endog2 inhibition Phyre2 PDB 3mpo chain D Region: 27 - 62 Aligned: 32 Modelled: 36 Confidence: 11.7% Identity: 22% PDB header:hydrolase Chain: D: PDB Molecule:predicted hydrolase of the had superfamily; PDBTitle: the crystal structure of a hydrolase from lactobacillus brevis Phyre2 PDB 1wr8 chain A Region: 27 - 62 Aligned: 35 Modelled: 36 Confidence: 10.3% Identity: 23% Fold: HAD-like Superfamily: HAD-like Family: Predicted hydrolases Cof Phyre2 PDB 3svi chain A Region: 35 - 44 Aligned: 10 Modelled: 10 Confidence: 8.4% Identity: 60% PDB header:signaling protein Chain: A: PDB Molecule:type iii effector hopab2; PDBTitle: structure of the pto-binding domain of hoppmal generated by limited2 thermolysin digestion Phyre2 PDB 2axt chain M domain 1 Region: 182 - 200 Aligned: 18 Modelled: 19 Confidence: 8.3% Identity: 50% Fold: Single transmembrane helix Superfamily: Photosystem II reaction center protein M, PsbM Family: PsbM-like Phyre2 PDB 1dwn chain A Region: 71 - 77 Aligned: 7 Modelled: 7 Confidence: 6.7% Identity: 100% Fold: RNA bacteriophage capsid protein Superfamily: RNA bacteriophage capsid protein Family: RNA bacteriophage capsid protein Phyre2 PDB 2wnm chain A Region: 229 - 241 Aligned: 13 Modelled: 13 Confidence: 6.4% Identity: 38% PDB header:hydrolase Chain: A: PDB Molecule:gene 2; PDBTitle: solution structure of gp2 Phyre2 PDB 2apj chain A domain 1 Region: 139 - 147 Aligned: 9 Modelled: 9 Confidence: 6.2% Identity: 56% Fold: Flavodoxin-like Superfamily: SGNH hydrolase Family: Putative acetylxylan esterase-like Phyre2 PDB 1zmb chain A domain 1 Region: 139 - 147 Aligned: 9 Modelled: 9 Confidence: 6.2% Identity: 44% Fold: Flavodoxin-like Superfamily: SGNH hydrolase Family: Putative acetylxylan esterase-like Phyre2 PDB 1gkp chain A domain 1 Region: 107 - 139 Aligned: 33 Modelled: 33 Confidence: 5.8% Identity: 18% Fold: Composite domain of metallo-dependent hydrolases Superfamily: Composite domain of metallo-dependent hydrolases Family: Hydantoinase (dihydropyrimidinase) Phyre2 PDB 2r5v chain A Region: 111 - 177 Aligned: 53 Modelled: 53 Confidence: 5.6% Identity: 23% PDB header:oxidoreductase Chain: A: PDB Molecule:pcza361.1; PDBTitle: hydroxymandelate synthase crystal structure Phyre2 PDB 1f20 chain A Region: 55 - 104 Aligned: 36 Modelled: 50 Confidence: 5.3% Identity: 33% PDB header:oxidoreductase Chain: A: PDB Molecule:nitric-oxide synthase; PDBTitle: crystal structure of rat neuronal nitric-oxide synthase fad/nadp+2 domain at 1.9a resolution. Phyre2 PDB 2kne chain B Region: 139 - 155 Aligned: 13 Modelled: 17 Confidence: 5.3% Identity: 54% PDB header:metal transport Chain: B: PDB Molecule:atpase, ca++ transporting, plasma membrane 4; PDBTitle: calmodulin wraps around its binding domain in the plasma2 membrane ca2+ pump anchored by a novel 18-1 motif Phyre2 1 c3ptjA_ 2 c2kw7A_ 3 c2kptA_ 4 c2y69S_ 5 d1q90n_ 6 d1v54f_ 7 d1pprm2 8 c3ismC_ 9 c3mpoD_ 10 d1wr8a_ 11 c3sviA_ 12 d2axtm1 13 d1dwna_ 14 c2wnmA_ 15 d2apja1 16 d1zmba1 17 d1gkpa1 18 c2r5vA_ 19 c1f20A_ 20 c2kneB_

Detailed template information

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

1 c3ptjA_ 98.1 8 PDB header:hydrolase Chain: A: PDB Molecule:upf0603 protein at1g54780, chloroplastic; PDBTitle: structural and functional analysis of arabidopsis thaliana thylakoid2 lumen protein attlp18.3 2 c2kw7A_ 97.9 20 PDB header:structural genomics, unknown function Chain: A: PDB Molecule:conserved domain protein; PDBTitle: solution nmr structure of the n-terminal domain of protein pg_03612 from p.gingivalis, northeast structural genomics consortium target3 pgr37a 3 c2kptA_ 62.0 16 PDB header:structural genomics, unknown function Chain: A: PDB Molecule:putative secreted protein; PDBTitle: solution nmr structure of the n-terminal domain of cg24962 protein from corynebacterium glutamicum. northeast3 structural genomics consortium target cgr26a 4 c2y69S_ 22.8 32 PDB header:electron transport Chain: S: PDB Molecule:cytochrome c oxidase subunit 5b; PDBTitle: bovine heart cytochrome c oxidase re-refined with molecular2 oxygen 5 d1q90n_ 18.4 64 Fold:Single transmembrane helix Superfamily:PetN subunit of the cytochrome b6f complex Family:PetN subunit of the cytochrome b6f complex 6 d1v54f_ 15.8 31 Fold:Rubredoxin-like Superfamily:Rubredoxin-like Family:Cytochrome c oxidase Subunit F 7 d1pprm2 13.2 25 Fold:Peridinin-chlorophyll protein Superfamily:Peridinin-chlorophyll protein Family:Peridinin-chlorophyll protein 8 c3ismC_ 12.3 64 PDB header:hydrolase inhibitor/hydrolase Chain: C: PDB Molecule:cg4930; PDBTitle: crystal structure of the endog/endogi complex: mechanism of endog2 inhibition 9 c3mpoD_ 11.7 22 PDB header:hydrolase Chain: D: PDB Molecule:predicted hydrolase of the had superfamily; PDBTitle: the crystal structure of a hydrolase from lactobacillus brevis 10 d1wr8a_ 10.3 23 Fold:HAD-like Superfamily:HAD-like Family:Predicted hydrolases Cof 11 c3sviA_ 8.4 60 PDB header:signaling protein Chain: A: PDB Molecule:type iii effector hopab2; PDBTitle: structure of the pto-binding domain of hoppmal generated by limited2 thermolysin digestion 12 d2axtm1 8.3 50 Fold:Single transmembrane helix Superfamily:Photosystem II reaction center protein M, PsbM Family:PsbM-like 13 d1dwna_ 6.7 100 Fold:RNA bacteriophage capsid protein Superfamily:RNA bacteriophage capsid protein Family:RNA bacteriophage capsid protein 14 c2wnmA_ 6.4 38 PDB header:hydrolase Chain: A: PDB Molecule:gene 2; PDBTitle: solution structure of gp2 15 d2apja1 6.2 56 Fold:Flavodoxin-like Superfamily:SGNH hydrolase Family:Putative acetylxylan esterase-like 16 d1zmba1 6.2 44 Fold:Flavodoxin-like Superfamily:SGNH hydrolase Family:Putative acetylxylan esterase-like 17 d1gkpa1 5.8 18 Fold:Composite domain of metallo-dependent hydrolases Superfamily:Composite domain of metallo-dependent hydrolases Family:Hydantoinase (dihydropyrimidinase) 18 c2r5vA_ 5.6 23 PDB header:oxidoreductase Chain: A: PDB Molecule:pcza361.1; PDBTitle: hydroxymandelate synthase crystal structure 19 c1f20A_ 5.3 33 PDB header:oxidoreductase Chain: A: PDB Molecule:nitric-oxide synthase; PDBTitle: crystal structure of rat neuronal nitric-oxide synthase fad/nadp+2 domain at 1.9a resolution. 20 c2kneB_ 5.3 54 PDB header:metal transport Chain: B: PDB Molecule:atpase, ca++ transporting, plasma membrane 4; PDBTitle: calmodulin wraps around its binding domain in the plasma2 membrane ca2+ pump anchored by a novel 18-1 motif

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