Secondary structure and disorder prediction

		1	.	.	.	.	.	.	.	.	10	.	.	.	.	.	.	.	.	.	20	.	.	.	.	.	.	.	.	.	30	.	.	.	.	.	.	.	.	.	40	.	.	.	.	.	.	.	.	.	50	.	.	.	.	.	.	.	.	.	60
Sequence		M	N	L	Q	H	H	F	L	I	A	M	P	A	L	Q	D	P	I	F	R	R	S	V	V	Y	I	C	E	H	N	T	N	G	A	M	G	I	I	V	N	K	P	L	E	N	L	K	I	E	G	I	L	E	K	L	K	I	T	P	E
Secondary structure
SS confidence
Disorder		?	?	?	?	?									?		?	?																													?	?											?
Disorder confidence
		.	.	.	.	.	.	.	.	.	70	.	.	.	.	.	.	.	.	.	80	.	.	.	.	.	.	.	.	.	90	.	.	.	.	.	.	.	.	.	100	.	.	.	.	.	.	.	.	.	110	.	.	.	.	.	.	.	.	.	120
Sequence		P	R	D	E	S	I	R	L	D	K	P	V	M	L	G	G	P	L	A	E	D	R	G	F	I	L	H	T	P	P	S	N	F	A	S	S	I	R	I	S	D	N	T	V	M	T	T	S	R	D	V	L	E	T	L	G	T	D	K	Q
Secondary structure
SS confidence
Disorder		?	?	?	?	?	?	?																										?																								?	?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	130	.	.	.	.	.	.	.	.	.	140	.	.	.	.	.	.	.	.	.	150	.	.	.	.	.	.	.	.	.	160	.	.	.	.	.	.	.	.	.	170	.	.	.	.	.	.	.	.	.	180
Sequence		P	S	D	V	L	V	A	L	G	Y	A	S	W	E	K	G	Q	L	E	Q	E	I	L	D	N	A	W	L	T	A	P	A	D	L	N	I	L	F	K	T	P	I	A	D	R	W	R	E	A	A	K	L	I	G	V	D	I	L	T	M
Secondary structure
SS confidence
Disorder																																																													?
Disorder confidence
		.	.	.	.	.	.	.
Sequence		P	G	V	A	G	H	A
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 2gzo chain A domain 1 Region: 2 - 187 Aligned: 185 Modelled: 186 Confidence: 100.0% Identity: 45% Fold: VC0467-like Superfamily: VC0467-like Family: VC0467-like Phyre2 PDB 2do8 chain A domain 1 Region: 2 - 187 Aligned: 182 Modelled: 186 Confidence: 100.0% Identity: 41% Fold: VC0467-like Superfamily: VC0467-like Family: VC0467-like Phyre2 PDB 2aj2 chain A Region: 2 - 179 Aligned: 177 Modelled: 178 Confidence: 100.0% Identity: 45% PDB header:unknown function Chain: A: PDB Molecule:hypothetical upf0301 protein vc0467; PDBTitle: x-ray crystal structure of protein vc0467 from vibrio2 cholerae. northeast structural genomics consortium target3 vcr8. Phyre2 PDB 2haf chain A domain 1 Region: 1 - 177 Aligned: 176 Modelled: 177 Confidence: 100.0% Identity: 47% Fold: VC0467-like Superfamily: VC0467-like Family: VC0467-like Phyre2 PDB 2ew0 chain A domain 1 Region: 3 - 182 Aligned: 174 Modelled: 180 Confidence: 100.0% Identity: 40% Fold: VC0467-like Superfamily: VC0467-like Family: VC0467-like Phyre2 PDB 2gs5 chain A domain 1 Region: 2 - 182 Aligned: 172 Modelled: 172 Confidence: 100.0% Identity: 19% Fold: VC0467-like Superfamily: VC0467-like Family: VC0467-like Phyre2 PDB 1vpq chain A Region: 125 - 134 Aligned: 10 Modelled: 10 Confidence: 15.5% Identity: 20% Fold: TIM beta/alpha-barrel Superfamily: TM1631-like Family: TM1631-like Phyre2 PDB 1jl3 chain A Region: 20 - 30 Aligned: 11 Modelled: 11 Confidence: 11.4% Identity: 18% Fold: Phosphotyrosine protein phosphatases I-like Superfamily: Phosphotyrosine protein phosphatases I Family: Low-molecular-weight phosphotyrosine protein phosphatases Phyre2 PDB 2ovr chain A domain 1 Region: 110 - 147 Aligned: 38 Modelled: 38 Confidence: 9.3% Identity: 13% Fold: Skp1 dimerisation domain-like Superfamily: Skp1 dimerisation domain-like Family: Skp1 dimerisation domain-like Phyre2 PDB 1sy6 chain A domain 1 Region: 13 - 27 Aligned: 15 Modelled: 15 Confidence: 8.2% Identity: 27% Fold: Immunoglobulin-like beta-sandwich Superfamily: Immunoglobulin Family: I set domains Phyre2 PDB 1vm6 chain A domain 3 Region: 107 - 140 Aligned: 34 Modelled: 34 Confidence: 8.1% Identity: 15% Fold: NAD(P)-binding Rossmann-fold domains Superfamily: NAD(P)-binding Rossmann-fold domains Family: Glyceraldehyde-3-phosphate dehydrogenase-like, N-terminal domain Phyre2 PDB 2eap chain A Region: 132 - 144 Aligned: 13 Modelled: 13 Confidence: 7.7% Identity: 15% PDB header:signaling protein Chain: A: PDB Molecule:lymphocyte cytosolic protein 2; PDBTitle: solution structure of the n-terminal sam-domain of human2 lymphocyte cytosolic protein 2 Phyre2 PDB 2dgd chain D Region: 126 - 176 Aligned: 43 Modelled: 51 Confidence: 7.2% Identity: 16% PDB header:lyase Chain: D: PDB Molecule:223aa long hypothetical arylmalonate decarboxylase; PDBTitle: crystal structure of st0656, a function unknown protein from2 sulfolobus tokodaii Phyre2 PDB 2ovq chain A Region: 111 - 147 Aligned: 37 Modelled: 37 Confidence: 6.7% Identity: 14% PDB header:transcription/cell cycle Chain: A: PDB Molecule:s-phase kinase-associated protein 1a; PDBTitle: structure of the skp1-fbw7-cyclinedegc complex Phyre2 PDB 1byy chain A Region: 155 - 174 Aligned: 20 Modelled: 20 Confidence: 6.1% Identity: 25% PDB header:membrane protein Chain: A: PDB Molecule:protein (sodium channel alpha-subunit); PDBTitle: sodium channel iia inactivation gate Phyre2 PDB 1j6o chain A Region: 103 - 183 Aligned: 77 Modelled: 81 Confidence: 6.0% Identity: 10% Fold: TIM beta/alpha-barrel Superfamily: Metallo-dependent hydrolases Family: TatD Mg-dependent DNase-like Phyre2 PDB 1jf8 chain A Region: 20 - 30 Aligned: 11 Modelled: 11 Confidence: 5.9% Identity: 18% Fold: Phosphotyrosine protein phosphatases I-like Superfamily: Phosphotyrosine protein phosphatases I Family: Low-molecular-weight phosphotyrosine protein phosphatases Phyre2 PDB 1p9e chain A Region: 145 - 180 Aligned: 36 Modelled: 36 Confidence: 5.8% Identity: 19% Fold: Metallo-hydrolase/oxidoreductase Superfamily: Metallo-hydrolase/oxidoreductase Family: Methyl parathion hydrolase Phyre2 PDB 1p9e chain A Region: 145 - 180 Aligned: 36 Modelled: 36 Confidence: 5.8% Identity: 19% PDB header:hydrolase Chain: A: PDB Molecule:methyl parathion hydrolase; PDBTitle: crystal structure analysis of methyl parathion hydrolase from2 pseudomonas sp wbc-3 Phyre2 PDB 1jbj chain A domain 1 Region: 15 - 27 Aligned: 13 Modelled: 13 Confidence: 5.6% Identity: 23% Fold: Immunoglobulin-like beta-sandwich Superfamily: Immunoglobulin Family: I set domains Phyre2 1 d2gzoa1 2 d2do8a1 3 c2aj2A_ 4 d2hafa1 5 d2ew0a1 6 d2gs5a1 7 d1vpqa_ 8 d1jl3a_ 9 d2ovra1 10 d1sy6a1 11 d1vm6a3 12 c2eapA_ 13 c2dgdD_ 14 c2ovqA_ 15 c1byyA_ 16 d1j6oa_ 17 d1jf8a_ 18 d1p9ea_ 19 c1p9eA_ 20 d1jbja1 21 22 23 24 25

Detailed template information

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

1 d2gzoa1 100.0 45 Fold:VC0467-like Superfamily:VC0467-like Family:VC0467-like 2 d2do8a1 100.0 41 Fold:VC0467-like Superfamily:VC0467-like Family:VC0467-like 3 c2aj2A_ 100.0 45 PDB header:unknown function Chain: A: PDB Molecule:hypothetical upf0301 protein vc0467; PDBTitle: x-ray crystal structure of protein vc0467 from vibrio2 cholerae. northeast structural genomics consortium target3 vcr8. 4 d2hafa1 100.0 47 Fold:VC0467-like Superfamily:VC0467-like Family:VC0467-like 5 d2ew0a1 100.0 40 Fold:VC0467-like Superfamily:VC0467-like Family:VC0467-like 6 d2gs5a1 100.0 19 Fold:VC0467-like Superfamily:VC0467-like Family:VC0467-like 7 d1vpqa_ 15.5 20 Fold:TIM beta/alpha-barrel Superfamily:TM1631-like Family:TM1631-like 8 d1jl3a_ 11.4 18 Fold:Phosphotyrosine protein phosphatases I-like Superfamily:Phosphotyrosine protein phosphatases I Family:Low-molecular-weight phosphotyrosine protein phosphatases 9 d2ovra1 9.3 13 Fold:Skp1 dimerisation domain-like Superfamily:Skp1 dimerisation domain-like Family:Skp1 dimerisation domain-like 10 d1sy6a1 8.2 27 Fold:Immunoglobulin-like beta-sandwich Superfamily:Immunoglobulin Family:I set domains 11 d1vm6a3 8.1 15 Fold:NAD(P)-binding Rossmann-fold domains Superfamily:NAD(P)-binding Rossmann-fold domains Family:Glyceraldehyde-3-phosphate dehydrogenase-like, N-terminal domain 12 c2eapA_ 7.7 15 PDB header:signaling protein Chain: A: PDB Molecule:lymphocyte cytosolic protein 2; PDBTitle: solution structure of the n-terminal sam-domain of human2 lymphocyte cytosolic protein 2 13 c2dgdD_ 7.2 16 PDB header:lyase Chain: D: PDB Molecule:223aa long hypothetical arylmalonate decarboxylase; PDBTitle: crystal structure of st0656, a function unknown protein from2 sulfolobus tokodaii 14 c2ovqA_ 6.7 14 PDB header:transcription/cell cycle Chain: A: PDB Molecule:s-phase kinase-associated protein 1a; PDBTitle: structure of the skp1-fbw7-cyclinedegc complex 15 c1byyA_ 6.1 25 PDB header:membrane protein Chain: A: PDB Molecule:protein (sodium channel alpha-subunit); PDBTitle: sodium channel iia inactivation gate 16 d1j6oa_ 6.0 10 Fold:TIM beta/alpha-barrel Superfamily:Metallo-dependent hydrolases Family:TatD Mg-dependent DNase-like 17 d1jf8a_ 5.9 18 Fold:Phosphotyrosine protein phosphatases I-like Superfamily:Phosphotyrosine protein phosphatases I Family:Low-molecular-weight phosphotyrosine protein phosphatases 18 d1p9ea_ 5.8 19 Fold:Metallo-hydrolase/oxidoreductase Superfamily:Metallo-hydrolase/oxidoreductase Family:Methyl parathion hydrolase 19 c1p9eA_ 5.8 19 PDB header:hydrolase Chain: A: PDB Molecule:methyl parathion hydrolase; PDBTitle: crystal structure analysis of methyl parathion hydrolase from2 pseudomonas sp wbc-3 20 d1jbja1 5.6 23 Fold:Immunoglobulin-like beta-sandwich Superfamily:Immunoglobulin Family:I set domains 21 c2y75F_ not modelled 5.6 14 PDB header:transcription Chain: F: PDB Molecule:hth-type transcriptional regulator cymr; PDBTitle: the structure of cymr (yrzc) the global cysteine regulator2 of b. subtilis 22 d1yl7a1 not modelled 5.4 15 Fold:NAD(P)-binding Rossmann-fold domains Superfamily:NAD(P)-binding Rossmann-fold domains Family:Glyceraldehyde-3-phosphate dehydrogenase-like, N-terminal domain 23 c3lwfD_ not modelled 5.3 24 PDB header:transcription regulator Chain: D: PDB Molecule:putative transcriptional regulator; PDBTitle: crystal structure of putative transcriptional regulator (np_470886.1)2 from listeria innocua at 2.06 a resolution 24 d1miua1 not modelled 5.3 24 Fold:BRCA2 helical domain Superfamily:BRCA2 helical domain Family:BRCA2 helical domain 25 c2p1nD_ not modelled 5.3 14 PDB header:signaling protein Chain: D: PDB Molecule:skp1-like protein 1a; PDBTitle: mechanism of auxin perception by the tir1 ubiqutin ligase

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