Secondary structure and disorder prediction

		1	.	.	.	.	.	.	.	.	10	.	.	.	.	.	.	.	.	.	20	.	.	.	.	.	.	.	.	.	30	.	.	.	.	.	.	.	.	.	40	.	.	.	.	.	.	.	.	.	50	.	.	.	.	.
Sequence		M	K	R	Q	K	R	D	R	L	E	R	A	H	Q	R	G	Y	Q	A	G	I	A	G	R	S	K	E	M	C	P	Y	Q	T	L	N	Q	R	S	Q	W	L	G	G	W	R	E	A	M	A	D	R	V	V	M	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 2jrm chain A Region: 1 - 52 Aligned: 52 Modelled: 52 Confidence: 100.0% Identity: 63% PDB header:structural genomics, unknown function Chain: A: PDB Molecule:ribosome modulation factor; PDBTitle: solution nmr structure of ribosome modulation factor vp1593 from2 vibrio parahaemolyticus. northeast structural genomics target vpr55 Phyre2 PDB 2rus chain B Region: 11 - 49 Aligned: 39 Modelled: 39 Confidence: 13.0% Identity: 21% PDB header:lyase(carbon-carbon) Chain: B: PDB Molecule:rubisco (ribulose-1,5-bisphosphate PDBTitle: crystal structure of the ternary complex of ribulose-1,5-2 bisphosphate carboxylase, mg(ii), and activator co2 at 2.3-3 angstroms resolution Phyre2 PDB 9rub chain B Region: 11 - 49 Aligned: 39 Modelled: 39 Confidence: 13.0% Identity: 23% PDB header:lyase(carbon-carbon) Chain: B: PDB Molecule:ribulose-1,5-bisphosphate carboxylase; PDBTitle: crystal structure of activated ribulose-1,5-bisphosphate2 carboxylase complexed with its substrate, ribulose-1,5-3 bisphosphate Phyre2 PDB 3bux chain B domain 3 Region: 32 - 47 Aligned: 16 Modelled: 16 Confidence: 9.9% Identity: 19% Fold: SH2-like Superfamily: SH2 domain Family: SH2 domain Phyre2 PDB 2caz chain B Region: 7 - 17 Aligned: 11 Modelled: 11 Confidence: 8.6% Identity: 27% PDB header:protein transport Chain: B: PDB Molecule:vacuolar protein sorting-associated protein PDBTitle: escrt-i core Phyre2 PDB 2caz chain B domain 1 Region: 7 - 17 Aligned: 11 Modelled: 11 Confidence: 8.6% Identity: 27% Fold: Long alpha-hairpin Superfamily: Endosomal sorting complex assembly domain Family: VPS28 N-terminal domain Phyre2 PDB 5rub chain A domain 1 Region: 11 - 49 Aligned: 39 Modelled: 39 Confidence: 8.6% Identity: 23% Fold: TIM beta/alpha-barrel Superfamily: RuBisCo, C-terminal domain Family: RuBisCo, large subunit, C-terminal domain Phyre2 PDB 2wyb chain A Region: 7 - 22 Aligned: 16 Modelled: 16 Confidence: 7.7% Identity: 31% PDB header:hydrolase Chain: A: PDB Molecule:acyl-homoserine lactone acylase pvdq subunit PDBTitle: the quorum quenching n-acyl homoserine lactone acylase pvdq2 with a covalently bound dodecanoic acid Phyre2 PDB 2f6m chain B domain 1 Region: 7 - 17 Aligned: 11 Modelled: 11 Confidence: 7.7% Identity: 27% Fold: Long alpha-hairpin Superfamily: Endosomal sorting complex assembly domain Family: VPS28 N-terminal domain Phyre2 PDB 1k0m chain A domain 2 Region: 18 - 43 Aligned: 26 Modelled: 26 Confidence: 7.6% Identity: 31% Fold: Thioredoxin fold Superfamily: Thioredoxin-like Family: Glutathione S-transferase (GST), N-terminal domain Phyre2 PDB 1t1j chain A Region: 29 - 36 Aligned: 8 Modelled: 8 Confidence: 7.0% Identity: 38% Fold: Flavodoxin-like Superfamily: N-(deoxy)ribosyltransferase-like Family: Hypothetical protein PA1492 Phyre2 PDB 3bit chain A Region: 21 - 46 Aligned: 26 Modelled: 26 Confidence: 6.6% Identity: 27% PDB header:transcription Chain: A: PDB Molecule:fact complex subunit spt16; PDBTitle: crystal structure of yeast spt16 n-terminal domain Phyre2 PDB 2ae3 chain A Region: 7 - 22 Aligned: 16 Modelled: 16 Confidence: 5.9% Identity: 31% PDB header:hydrolase Chain: A: PDB Molecule:glutaryl 7-aminocephalosporanic acid acylase; PDBTitle: glutaryl 7-aminocephalosporanic acid acylase: mutational study of2 activation mechanism Phyre2 1 c2jrmA_ 2 c2rusB_ 3 c9rubB_ 4 d3buxb3 5 c2cazB_ 6 d2cazb1 7 d5ruba1 8 c2wybA_ 9 d2f6mb1 10 d1k0ma2 11 d1t1ja_ 12 c3bitA_ 13 c2ae3A_

Detailed template information

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

1 c2jrmA_ 100.0 63 PDB header:structural genomics, unknown function Chain: A: PDB Molecule:ribosome modulation factor; PDBTitle: solution nmr structure of ribosome modulation factor vp1593 from2 vibrio parahaemolyticus. northeast structural genomics target vpr55 2 c2rusB_ 13.0 21 PDB header:lyase(carbon-carbon) Chain: B: PDB Molecule:rubisco (ribulose-1,5-bisphosphate PDBTitle: crystal structure of the ternary complex of ribulose-1,5-2 bisphosphate carboxylase, mg(ii), and activator co2 at 2.3-3 angstroms resolution 3 c9rubB_ 13.0 23 PDB header:lyase(carbon-carbon) Chain: B: PDB Molecule:ribulose-1,5-bisphosphate carboxylase; PDBTitle: crystal structure of activated ribulose-1,5-bisphosphate2 carboxylase complexed with its substrate, ribulose-1,5-3 bisphosphate 4 d3buxb3 9.9 19 Fold:SH2-like Superfamily:SH2 domain Family:SH2 domain 5 c2cazB_ 8.6 27 PDB header:protein transport Chain: B: PDB Molecule:vacuolar protein sorting-associated protein PDBTitle: escrt-i core 6 d2cazb1 8.6 27 Fold:Long alpha-hairpin Superfamily:Endosomal sorting complex assembly domain Family:VPS28 N-terminal domain 7 d5ruba1 8.6 23 Fold:TIM beta/alpha-barrel Superfamily:RuBisCo, C-terminal domain Family:RuBisCo, large subunit, C-terminal domain 8 c2wybA_ 7.7 31 PDB header:hydrolase Chain: A: PDB Molecule:acyl-homoserine lactone acylase pvdq subunit PDBTitle: the quorum quenching n-acyl homoserine lactone acylase pvdq2 with a covalently bound dodecanoic acid 9 d2f6mb1 7.7 27 Fold:Long alpha-hairpin Superfamily:Endosomal sorting complex assembly domain Family:VPS28 N-terminal domain 10 d1k0ma2 7.6 31 Fold:Thioredoxin fold Superfamily:Thioredoxin-like Family:Glutathione S-transferase (GST), N-terminal domain 11 d1t1ja_ 7.0 38 Fold:Flavodoxin-like Superfamily:N-(deoxy)ribosyltransferase-like Family:Hypothetical protein PA1492 12 c3bitA_ 6.6 27 PDB header:transcription Chain: A: PDB Molecule:fact complex subunit spt16; PDBTitle: crystal structure of yeast spt16 n-terminal domain 13 c2ae3A_ 5.9 31 PDB header:hydrolase Chain: A: PDB Molecule:glutaryl 7-aminocephalosporanic acid acylase; PDBTitle: glutaryl 7-aminocephalosporanic acid acylase: mutational study of2 activation mechanism

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