Secondary structure and disorder prediction

		1	.	.	.	.	.	.	.	.	10	.	.	.	.	.	.	.	.	.	20	.	.	.	.	.	.	.	.	.	30	.	.	.	.	.	.	.	.	.	40	.	.	.	.	.	.	.	.	.	50	.	.	.	.	.	.	.	.	.	60
Sequence		M	S	Q	P	L	N	A	D	Q	E	L	V	S	D	V	V	A	C	Q	L	V	I	K	Q	I	L	D	V	L	D	V	I	A	P	V	E	V	R	E	K	M	S	S	Q	L	K	N	I	D	F	T	N	H	P	A	A	A	D	P	V
Secondary structure
SS confidence
Disorder		?	?	?	?	?	?	?																																																			?
Disorder confidence
		.	.	.	.	.	.	.	.	.	70	.	.	.	.	.	.	.	.	.	80	.	.	.
Sequence		T	M	R	A	I	Q	K	A	I	A	L	I	E	L	K	F	T	P	Q	G	E	S	H
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 1wih chain A Region: 58 - 83 Aligned: 26 Modelled: 26 Confidence: 10.4% Identity: 27% Fold: RRF/tRNA synthetase additional domain-like Superfamily: Ribosome recycling factor, RRF Family: Ribosome recycling factor, RRF Phyre2 PDB 1xco chain A Region: 36 - 69 Aligned: 31 Modelled: 34 Confidence: 9.9% Identity: 29% Fold: Isocitrate/Isopropylmalate dehydrogenase-like Superfamily: Isocitrate/Isopropylmalate dehydrogenase-like Family: Phosphotransacetylase Phyre2 PDB 1r5j chain A Region: 36 - 69 Aligned: 31 Modelled: 34 Confidence: 9.8% Identity: 29% Fold: Isocitrate/Isopropylmalate dehydrogenase-like Superfamily: Isocitrate/Isopropylmalate dehydrogenase-like Family: Phosphotransacetylase Phyre2 PDB 3ke2 chain A Region: 63 - 83 Aligned: 21 Modelled: 21 Confidence: 9.3% Identity: 52% PDB header:unknown function Chain: A: PDB Molecule:uncharacterized protein yp_928783.1; PDBTitle: crystal structure of a duf2131 family protein (sama_2911) from2 shewanella amazonensis sb2b at 2.50 a resolution Phyre2 PDB 2k9i chain B Region: 12 - 30 Aligned: 17 Modelled: 19 Confidence: 8.9% Identity: 65% PDB header:dna binding protein Chain: B: PDB Molecule:plasmid prn1, complete sequence; PDBTitle: nmr structure of plasmid copy control protein orf56 from2 sulfolobus islandicus Phyre2 PDB 3ogi chain C Region: 9 - 32 Aligned: 24 Modelled: 24 Confidence: 8.0% Identity: 50% PDB header:structural genomics, unknown function Chain: C: PDB Molecule:putative esat-6-like protein 6; PDBTitle: crystal structure of the mycobacterium tuberculosis h37rv esxop2 complex (rv2346c-rv2347c) Phyre2 PDB 1wqg chain A domain 1 Region: 58 - 83 Aligned: 26 Modelled: 26 Confidence: 7.9% Identity: 27% Fold: RRF/tRNA synthetase additional domain-like Superfamily: Ribosome recycling factor, RRF Family: Ribosome recycling factor, RRF Phyre2 PDB 1jqn chain A Region: 32 - 70 Aligned: 39 Modelled: 39 Confidence: 7.7% Identity: 13% Fold: TIM beta/alpha-barrel Superfamily: Phosphoenolpyruvate/pyruvate domain Family: Phosphoenolpyruvate carboxylase Phyre2 PDB 2hzs chain L Region: 74 - 83 Aligned: 10 Modelled: 10 Confidence: 7.1% Identity: 70% PDB header:transcription Chain: L: PDB Molecule:rna polymerase ii mediator complex subunit 8; PDBTitle: structure of the mediator head submodule med8c/18/20 Phyre2 PDB 2hzs chain J Region: 74 - 83 Aligned: 10 Modelled: 10 Confidence: 7.1% Identity: 70% PDB header:transcription Chain: J: PDB Molecule:rna polymerase ii mediator complex subunit 8; PDBTitle: structure of the mediator head submodule med8c/18/20 Phyre2 PDB 1yl7 chain A domain 1 Region: 48 - 72 Aligned: 24 Modelled: 25 Confidence: 6.9% Identity: 33% 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 1jqo chain A Region: 32 - 70 Aligned: 39 Modelled: 39 Confidence: 6.9% Identity: 26% PDB header:lyase Chain: A: PDB Molecule:phosphoenolpyruvate carboxylase; PDBTitle: crystal structure of c4-form phosphoenolpyruvate carboxylase from2 maize Phyre2 PDB 1jqo chain A Region: 32 - 70 Aligned: 39 Modelled: 39 Confidence: 6.9% Identity: 26% Fold: TIM beta/alpha-barrel Superfamily: Phosphoenolpyruvate/pyruvate domain Family: Phosphoenolpyruvate carboxylase Phyre2 1 d1wiha_ 2 d1xcoa_ 3 d1r5ja_ 4 c3ke2A_ 5 c2k9iB_ 6 c3ogiC_ 7 d1wqga1 8 d1jqna_ 9 c2hzsL_ 10 c2hzsJ_ 11 d1yl7a1 12 c1jqoA_ 13 d1jqoa_

Detailed template information

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

1 d1wiha_ 10.4 27 Fold:RRF/tRNA synthetase additional domain-like Superfamily:Ribosome recycling factor, RRF Family:Ribosome recycling factor, RRF 2 d1xcoa_ 9.9 29 Fold:Isocitrate/Isopropylmalate dehydrogenase-like Superfamily:Isocitrate/Isopropylmalate dehydrogenase-like Family:Phosphotransacetylase 3 d1r5ja_ 9.8 29 Fold:Isocitrate/Isopropylmalate dehydrogenase-like Superfamily:Isocitrate/Isopropylmalate dehydrogenase-like Family:Phosphotransacetylase 4 c3ke2A_ 9.3 52 PDB header:unknown function Chain: A: PDB Molecule:uncharacterized protein yp_928783.1; PDBTitle: crystal structure of a duf2131 family protein (sama_2911) from2 shewanella amazonensis sb2b at 2.50 a resolution 5 c2k9iB_ 8.9 65 PDB header:dna binding protein Chain: B: PDB Molecule:plasmid prn1, complete sequence; PDBTitle: nmr structure of plasmid copy control protein orf56 from2 sulfolobus islandicus 6 c3ogiC_ 8.0 50 PDB header:structural genomics, unknown function Chain: C: PDB Molecule:putative esat-6-like protein 6; PDBTitle: crystal structure of the mycobacterium tuberculosis h37rv esxop2 complex (rv2346c-rv2347c) 7 d1wqga1 7.9 27 Fold:RRF/tRNA synthetase additional domain-like Superfamily:Ribosome recycling factor, RRF Family:Ribosome recycling factor, RRF 8 d1jqna_ 7.7 13 Fold:TIM beta/alpha-barrel Superfamily:Phosphoenolpyruvate/pyruvate domain Family:Phosphoenolpyruvate carboxylase 9 c2hzsL_ 7.1 70 PDB header:transcription Chain: L: PDB Molecule:rna polymerase ii mediator complex subunit 8; PDBTitle: structure of the mediator head submodule med8c/18/20 10 c2hzsJ_ 7.1 70 PDB header:transcription Chain: J: PDB Molecule:rna polymerase ii mediator complex subunit 8; PDBTitle: structure of the mediator head submodule med8c/18/20 11 d1yl7a1 6.9 33 Fold:NAD(P)-binding Rossmann-fold domains Superfamily:NAD(P)-binding Rossmann-fold domains Family:Glyceraldehyde-3-phosphate dehydrogenase-like, N-terminal domain 12 c1jqoA_ 6.9 26 PDB header:lyase Chain: A: PDB Molecule:phosphoenolpyruvate carboxylase; PDBTitle: crystal structure of c4-form phosphoenolpyruvate carboxylase from2 maize 13 d1jqoa_ 6.9 26 Fold:TIM beta/alpha-barrel Superfamily:Phosphoenolpyruvate/pyruvate domain Family:Phosphoenolpyruvate carboxylase

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