Secondary structure and disorder prediction

		1	.	.	.	.	.	.	.	.	10	.	.	.	.	.	.	.	.	.	20	.	.	.	.	.	.	.	.	.	30	.	.	.	.	.	.	.	.	.	40	.	.	.	.	.	.	.	.	.	50	.	.	.	.	.	.	.	.	.	60
Sequence		M	R	E	Q	I	K	Q	D	I	D	L	I	E	I	L	F	Y	L	K	K	K	I	R	V	I	L	F	I	M	A	I	C	M	A	M	V	L	L	F	L	Y	I	N	K	D	N	I	K	V	I	Y	S	L	K	I	N	Q	T	T	P
Secondary structure
SS confidence
Disorder		?	?	?				?																																																		?			?
Disorder confidence
		.	.	.	.	.	.	.	.	.	70	.	.	.	.	.	.	.	.	.	80	.	.	.	.	.	.	.	.	.	90	.	.	.	.	.	.	.	.	.	100	.	.	.	.	.	.	.	.	.	110	.	.	.	.	.	.	.	.	.	120
Sequence		G	I	L	V	S	C	D	S	N	N	N	F	A	C	Q	T	T	M	T	E	D	V	I	Q	R	I	T	T	F	F	H	T	S	P	D	V	K	N	R	E	I	R	L	E	W	S	G	D	K	R	A	L	P	T	A	E	E	E	I	S
Secondary structure
SS confidence
Disorder																																							?
Disorder confidence
		.	.	.	.	.	.	.	.	.	130	.	.	.	.	.	.	.	.	.	140	.	.	.	.	.	.	.	.	.	150	.	.	.	.	.	.	.	.	.	160	.	.	.	.	.	.	.	.	.	170	.	.	.	.	.	.	.	.	.	180
Sequence		R	V	Q	A	S	I	I	K	W	Y	A	S	E	Y	H	N	G	R	Q	V	L	D	E	I	Q	T	P	S	A	I	N	S	E	L	Y	T	K	M	I	Y	L	T	R	N	W	S	L	Y	P	N	G	D	G	C	V	T	I	S	S	P
Secondary structure
SS confidence
Disorder																											?	?	?		?													?		?		?
Disorder confidence
		.	.	.	.	.	.	.	.	.	190	.	.	.	.	.	.	.	.	.	200	.	.	.	.	.	.	.	.	.	210	.	.	.	.	.	.	.	.	.	220	.	.
Sequence		E	I	K	N	K	Y	P	A	A	I	C	L	A	L	G	F	F	L	S	I	V	I	S	V	M	F	C	L	V	K	K	M	V	D	E	Y	Q	Q	N	S	G	Q
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 1jb0 chain I Region: 17 - 45 Aligned: 29 Modelled: 29 Confidence: 40.2% Identity: 28% Fold: Single transmembrane helix Superfamily: Subunit VIII of photosystem I reaction centre, PsaI Family: Subunit VIII of photosystem I reaction centre, PsaI Phyre2 PDB 3lw5 chain I Region: 29 - 44 Aligned: 16 Modelled: 16 Confidence: 37.0% Identity: 38% PDB header:photosynthesis Chain: I: PDB Molecule:photosystem i reaction center subunit viii; PDBTitle: improved model of plant photosystem i Phyre2 PDB 2wse chain I Region: 29 - 44 Aligned: 16 Modelled: 16 Confidence: 37.0% Identity: 38% PDB header:photosynthesis Chain: I: PDB Molecule:photosystem i reaction center subunit viii; PDBTitle: improved model of plant photosystem i Phyre2 PDB 2o01 chain I Region: 29 - 44 Aligned: 16 Modelled: 16 Confidence: 30.9% Identity: 38% PDB header:photosynthesis Chain: I: PDB Molecule:photosystem i reaction center subunit viii; PDBTitle: the structure of a plant photosystem i supercomplex at 3.42 angstrom resolution Phyre2 PDB 2nlv chain A domain 1 Region: 77 - 110 Aligned: 34 Modelled: 34 Confidence: 23.4% Identity: 18% Fold: XisI-like Superfamily: XisI-like Family: XisI-like Phyre2 PDB 1n8i chain A Region: 117 - 144 Aligned: 28 Modelled: 28 Confidence: 21.4% Identity: 36% Fold: TIM beta/alpha-barrel Superfamily: Malate synthase G Family: Malate synthase G Phyre2 PDB 3d7q chain B Region: 77 - 110 Aligned: 34 Modelled: 34 Confidence: 19.2% Identity: 24% PDB header:unknown function Chain: B: PDB Molecule:xisi protein-like; PDBTitle: crystal structure of a xisi-like protein (npun_ar114) from nostoc2 punctiforme pcc 73102 at 2.30 a resolution Phyre2 PDB 2czv chain C domain 1 Region: 85 - 134 Aligned: 48 Modelled: 50 Confidence: 17.1% Identity: 21% Fold: Ferredoxin-like Superfamily: Rnp2-like Family: Rpp14/Pop5-like Phyre2 PDB 2hxj chain A domain 1 Region: 75 - 181 Aligned: 87 Modelled: 105 Confidence: 11.5% Identity: 16% Fold: FinO-like Superfamily: FinO-like Family: FinO-like Phyre2 PDB 1cf1 chain A domain 2 Region: 47 - 75 Aligned: 27 Modelled: 29 Confidence: 10.8% Identity: 33% Fold: Immunoglobulin-like beta-sandwich Superfamily: E set domains Family: Arrestin/Vps26-like Phyre2 PDB 2axt chain H domain 1 Region: 28 - 42 Aligned: 15 Modelled: 15 Confidence: 10.4% Identity: 47% Fold: Single transmembrane helix Superfamily: Photosystem II 10 kDa phosphoprotein PsbH Family: PsbH-like Phyre2 PDB 2pgg chain A domain 1 Region: 127 - 174 Aligned: 46 Modelled: 48 Confidence: 10.3% Identity: 22% Fold: DNA/RNA polymerases Superfamily: DNA/RNA polymerases Family: RNA-dependent RNA-polymerase Phyre2 PDB 1wi9 chain A Region: 79 - 107 Aligned: 29 Modelled: 29 Confidence: 10.2% Identity: 38% Fold: DNA/RNA-binding 3-helical bundle Superfamily: "Winged helix" DNA-binding domain Family: PCI domain (PINT motif) Phyre2 PDB 2v52 chain M Region: 17 - 24 Aligned: 8 Modelled: 8 Confidence: 10.0% Identity: 75% PDB header:structural protein/contractile protein Chain: M: PDB Molecule:mkl/myocardin-like protein 1; PDBTitle: structure of mal-rpel2 complexed to g-actin Phyre2 PDB 3ady chain A Region: 87 - 108 Aligned: 21 Modelled: 22 Confidence: 9.9% Identity: 19% PDB header:proton transport Chain: A: PDB Molecule:dotd; PDBTitle: crystal structure of dotd from legionella Phyre2 PDB 2adz chain A domain 1 Region: 157 - 181 Aligned: 25 Modelled: 25 Confidence: 9.6% Identity: 20% Fold: PH domain-like barrel Superfamily: PH domain-like Family: Pleckstrin-homology domain (PH domain) Phyre2 PDB 2ozb chain B domain 1 Region: 110 - 195 Aligned: 71 Modelled: 86 Confidence: 9.2% Identity: 11% Fold: Nop domain Superfamily: Nop domain Family: Nop domain Phyre2 PDB 1li4 chain A domain 2 Region: 103 - 202 Aligned: 89 Modelled: 100 Confidence: 8.7% Identity: 15% Fold: Flavodoxin-like Superfamily: Formate/glycerate dehydrogenase catalytic domain-like Family: S-adenosylhomocystein hydrolase Phyre2 PDB 2efv chain A domain 1 Region: 138 - 198 Aligned: 57 Modelled: 61 Confidence: 7.1% Identity: 14% Fold: Ribbon-helix-helix Superfamily: Ribbon-helix-helix Family: MJ0366-like Phyre2 PDB 1ew4 chain A Region: 108 - 148 Aligned: 40 Modelled: 41 Confidence: 6.4% Identity: 18% Fold: N domain of copper amine oxidase-like Superfamily: Frataxin/Nqo15-like Family: Frataxin-like Phyre2 1 d1jb0i_ 2 c3lw5I_ 3 c2wseI_ 4 c2o01I_ 5 d2nlva1 6 d1n8ia_ 7 c3d7qB_ 8 d2czvc1 9 d2hxja1 10 d1cf1a2 11 d2axth1 12 d2pgga1 13 d1wi9a_ 14 c2v52M_ 15 c3adyA_ 16 d2adza1 17 d2ozbb1 18 d1li4a2 19 d2efva1 20 d1ew4a_ 21 22 23 24 25 26 27 28 29 30

Detailed template information

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

1 d1jb0i_ 40.2 28 Fold:Single transmembrane helix Superfamily:Subunit VIII of photosystem I reaction centre, PsaI Family:Subunit VIII of photosystem I reaction centre, PsaI 2 c3lw5I_ 37.0 38 PDB header:photosynthesis Chain: I: PDB Molecule:photosystem i reaction center subunit viii; PDBTitle: improved model of plant photosystem i 3 c2wseI_ 37.0 38 PDB header:photosynthesis Chain: I: PDB Molecule:photosystem i reaction center subunit viii; PDBTitle: improved model of plant photosystem i 4 c2o01I_ 30.9 38 PDB header:photosynthesis Chain: I: PDB Molecule:photosystem i reaction center subunit viii; PDBTitle: the structure of a plant photosystem i supercomplex at 3.42 angstrom resolution 5 d2nlva1 23.4 18 Fold:XisI-like Superfamily:XisI-like Family:XisI-like 6 d1n8ia_ 21.4 36 Fold:TIM beta/alpha-barrel Superfamily:Malate synthase G Family:Malate synthase G 7 c3d7qB_ 19.2 24 PDB header:unknown function Chain: B: PDB Molecule:xisi protein-like; PDBTitle: crystal structure of a xisi-like protein (npun_ar114) from nostoc2 punctiforme pcc 73102 at 2.30 a resolution 8 d2czvc1 17.1 21 Fold:Ferredoxin-like Superfamily:Rnp2-like Family:Rpp14/Pop5-like 9 d2hxja1 11.5 16 Fold:FinO-like Superfamily:FinO-like Family:FinO-like 10 d1cf1a2 10.8 33 Fold:Immunoglobulin-like beta-sandwich Superfamily:E set domains Family:Arrestin/Vps26-like 11 d2axth1 10.4 47 Fold:Single transmembrane helix Superfamily:Photosystem II 10 kDa phosphoprotein PsbH Family:PsbH-like 12 d2pgga1 10.3 22 Fold:DNA/RNA polymerases Superfamily:DNA/RNA polymerases Family:RNA-dependent RNA-polymerase 13 d1wi9a_ 10.2 38 Fold:DNA/RNA-binding 3-helical bundle Superfamily:"Winged helix" DNA-binding domain Family:PCI domain (PINT motif) 14 c2v52M_ 10.0 75 PDB header:structural protein/contractile protein Chain: M: PDB Molecule:mkl/myocardin-like protein 1; PDBTitle: structure of mal-rpel2 complexed to g-actin 15 c3adyA_ 9.9 19 PDB header:proton transport Chain: A: PDB Molecule:dotd; PDBTitle: crystal structure of dotd from legionella 16 d2adza1 9.6 20 Fold:PH domain-like barrel Superfamily:PH domain-like Family:Pleckstrin-homology domain (PH domain) 17 d2ozbb1 9.2 11 Fold:Nop domain Superfamily:Nop domain Family:Nop domain 18 d1li4a2 8.7 15 Fold:Flavodoxin-like Superfamily:Formate/glycerate dehydrogenase catalytic domain-like Family:S-adenosylhomocystein hydrolase 19 d2efva1 7.1 14 Fold:Ribbon-helix-helix Superfamily:Ribbon-helix-helix Family:MJ0366-like 20 d1ew4a_ 6.4 18 Fold:N domain of copper amine oxidase-like Superfamily:Frataxin/Nqo15-like Family:Frataxin-like 21 c2p7vA_ not modelled 6.3 15 PDB header:transcription Chain: A: PDB Molecule:regulator of sigma d; PDBTitle: crystal structure of the escherichia coli regulator of sigma 70, rsd,2 in complex with sigma 70 domain 4 22 c2xi1A_ not modelled 6.3 33 PDB header:viral protein Chain: A: PDB Molecule:nef; PDBTitle: crystal structure of the hiv-1 nef sequenced from a patient's sample 23 d1uuja_ not modelled 6.0 30 Fold:Lissencephaly-1 protein (Lis-1, PAF-AH alpha) N-terminal domain Superfamily:Lissencephaly-1 protein (Lis-1, PAF-AH alpha) N-terminal domain Family:Lissencephaly-1 protein (Lis-1, PAF-AH alpha) N-terminal domain 24 d2qw6a1 not modelled 6.0 50 Fold:post-AAA+ oligomerization domain-like Superfamily:post-AAA+ oligomerization domain-like Family:MgsA/YrvN C-terminal domain-like 25 c2qw6A_ not modelled 6.0 50 PDB header:hydrolase Chain: A: PDB Molecule:aaa atpase, central region; PDBTitle: crystal structure of the c-terminal domain of an aaa atpase from2 enterococcus faecium do 26 c2kw3C_ not modelled 5.9 23 PDB header:dna binding protein Chain: C: PDB Molecule:regulatory factor x-associated protein; PDBTitle: heterotrimeric interaction between rfx5 and rfxap 27 c2r70A_ not modelled 5.8 22 PDB header:transferase Chain: A: PDB Molecule:infectious bursal virus vp1 polymerase; PDBTitle: crystal structure of infectious bursal disease virus vp12 polymerase, cocrystallized with an oligopeptide mimicking3 the vp3 c-terminus. 28 c3ik5A_ not modelled 5.6 25 PDB header:viral protein/signaling protein Chain: A: PDB Molecule:protein nef; PDBTitle: sivmac239 nef in complex with tcr zeta itam 1 polypeptide2 (a63-r80) 29 d1ayra2 not modelled 5.5 33 Fold:Immunoglobulin-like beta-sandwich Superfamily:E set domains Family:Arrestin/Vps26-like 30 d1efnb_ not modelled 5.4 25 Fold:Regulatory factor Nef Superfamily:Regulatory factor Nef Family:Regulatory factor Nef

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