Secondary structure and disorder prediction

		1	.	.	.	.	.	.	.	.	10	.	.	.	.	.	.	.	.	.	20	.	.	.	.	.	.	.	.	.	30	.	.	.	.	.	.	.	.	.	40	.	.	.	.	.	.	.	.	.	50	.	.	.	.	.	.	.	.	.	60
Sequence		M	V	D	Q	A	Q	D	T	L	R	P	N	N	R	L	S	D	M	Q	A	T	M	E	Q	T	Q	A	F	E	N	R	V	L	E	R	L	N	A	G	K	T	V	R	S	F	L	I	T	A	V	E	L	L	T	E	A	V	N	L	L
Secondary structure
SS confidence
Disorder		?	?	?	?	?		?			?	?	?					?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	70	.	.	.	.	.	.	.	.	.	80	.	.	.	.	.	.	.	.	.	90	.	.	.	.	.	.	.	.	.	100	.	.	.	.	.	.	.	.	.	110	.	.	.	.	.	.	.	.	.	120
Sequence		V	L	Q	V	F	R	K	D	D	Y	A	V	K	Y	A	V	E	P	L	L	D	G	D	G	P	L	G	D	L	S	V	R	L	K	L	I	Y	G	L	G	V	I	N	R	Q	E	Y	E	D	A	E	L	L	M	A	L	R	E	E	L
Secondary structure
SS confidence
Disorder																						?				?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	130	.	.	.	.	.	.	.	.	.	140	.	.	.	.	.	.	.	.	.	150	.	.	.	.	.	.	.	.	.	160	.	.	.	.	.	.	.	.	.	170	.	.	.	.	.	.	.	.	.	180
Sequence		N	H	D	G	N	E	Y	A	F	T	D	D	E	I	L	G	P	F	G	E	L	H	C	V	A	A	L	P	P	P	P	Q	F	E	P	A	D	S	S	L	Y	A	M	Q	I	Q	R	Y	Q	Q	A	V	R	S	T	M	V	L	S	L
Secondary structure
SS confidence
Disorder					?	?		?	?															?		?	?	?	?	?	?	?	?	?	?	?	?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	190	.	.	.	.	.
Sequence		T	E	L	I	S	K	I	S	L	K	K	A	F	Q	K
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 3brj chain A domain 1 Region: 29 - 189 Aligned: 161 Modelled: 161 Confidence: 100.0% Identity: 40% Fold: MtlR-like Superfamily: MtlR-like Family: MtlR-like Phyre2 PDB 3c8g chain A domain 1 Region: 29 - 188 Aligned: 153 Modelled: 160 Confidence: 100.0% Identity: 27% Fold: MtlR-like Superfamily: MtlR-like Family: MtlR-like Phyre2 PDB 1wwp chain A Region: 58 - 122 Aligned: 65 Modelled: 65 Confidence: 59.0% Identity: 12% PDB header:structural genomics, unknown function Chain: A: PDB Molecule:hypothetical protein ttha0636; PDBTitle: crystal structure of ttk003001694 from thermus thermophilus2 hb8 Phyre2 PDB 1wty chain A Region: 57 - 122 Aligned: 64 Modelled: 66 Confidence: 39.7% Identity: 13% Fold: Four-helical up-and-down bundle Superfamily: Nucleotidyltransferase substrate binding subunit/domain Family: Family 1 bi-partite nucleotidyltransferase subunit Phyre2 PDB 1ylm chain A Region: 19 - 140 Aligned: 112 Modelled: 122 Confidence: 21.8% Identity: 15% PDB header:structural genomics, unknown function Chain: A: PDB Molecule:hypothetical protein bsu32300; PDBTitle: structure of cytosolic protein of unknown function yute2 from bacillus subtilis Phyre2 PDB 2nn4 chain A domain 1 Region: 93 - 115 Aligned: 23 Modelled: 23 Confidence: 20.1% Identity: 22% Fold: YqgQ-like Superfamily: YqgQ-like Family: YqgQ-like Phyre2 PDB 2fex chain A domain 1 Region: 78 - 114 Aligned: 36 Modelled: 37 Confidence: 14.9% Identity: 11% Fold: Flavodoxin-like Superfamily: Class I glutamine amidotransferase-like Family: DJ-1/PfpI Phyre2 PDB 1twf chain C domain 2 Region: 95 - 103 Aligned: 9 Modelled: 9 Confidence: 10.7% Identity: 33% Fold: Insert subdomain of RNA polymerase alpha subunit Superfamily: Insert subdomain of RNA polymerase alpha subunit Family: Insert subdomain of RNA polymerase alpha subunit Phyre2 PDB 1vkf chain A Region: 65 - 102 Aligned: 36 Modelled: 38 Confidence: 10.1% Identity: 11% Fold: TIM beta/alpha-barrel Superfamily: GlpP-like Family: GlpP-like Phyre2 PDB 1gxs chain C Region: 82 - 110 Aligned: 29 Modelled: 29 Confidence: 10.0% Identity: 14% PDB header:lyase Chain: C: PDB Molecule:p-(s)-hydroxymandelonitrile lyase chain a; PDBTitle: crystal structure of hydroxynitrile lyase from sorghum2 bicolor in complex with inhibitor benzoic acid: a novel3 cyanogenic enzyme Phyre2 PDB 1bcr chain A Region: 84 - 111 Aligned: 28 Modelled: 28 Confidence: 9.7% Identity: 11% PDB header:hydrolase/hydrolase inhibitor Chain: A: PDB Molecule:serine carboxypeptidase ii; PDBTitle: complex of the wheat serine carboxypeptidase, cpdw-ii, with the2 microbial peptide aldehyde inhibitor, antipain, and arginine at room3 temperature Phyre2 PDB 1qki chain A domain 1 Region: 40 - 83 Aligned: 42 Modelled: 44 Confidence: 7.9% Identity: 17% 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 2gsc chain A domain 1 Region: 84 - 110 Aligned: 27 Modelled: 27 Confidence: 7.3% Identity: 19% Fold: Bromodomain-like Superfamily: IVS-encoded protein-like Family: IVS-encoded protein-like Phyre2 PDB 1a9x chain A domain 1 Region: 93 - 139 Aligned: 47 Modelled: 47 Confidence: 7.2% Identity: 23% Fold: Carbamoyl phosphate synthetase, large subunit connection domain Superfamily: Carbamoyl phosphate synthetase, large subunit connection domain Family: Carbamoyl phosphate synthetase, large subunit connection domain Phyre2 PDB 2ztt chain A Region: 60 - 123 Aligned: 62 Modelled: 64 Confidence: 7.1% Identity: 16% PDB header:transferase Chain: A: PDB Molecule:rna-directed rna polymerase catalytic subunit; PDBTitle: crystal structure of rna polymerase pb1-pb2 subunits from2 influenza a virus Phyre2 PDB 2ful chain E Region: 34 - 107 Aligned: 74 Modelled: 74 Confidence: 6.5% Identity: 19% PDB header:translation Chain: E: PDB Molecule:eukaryotic translation initiation factor 5; PDBTitle: crystal structure of the c-terminal domain of s. cerevisiae eif5 Phyre2 PDB 2a45 chain J Region: 96 - 120 Aligned: 25 Modelled: 25 Confidence: 6.4% Identity: 16% PDB header:hydrolase/hydrolase inhibitor Chain: J: PDB Molecule:fibrinogen alpha chain; PDBTitle: crystal structure of the complex between thrombin and the central "e"2 region of fibrin Phyre2 PDB 2rld chain A domain 1 Region: 84 - 110 Aligned: 27 Modelled: 27 Confidence: 6.0% Identity: 22% Fold: Bromodomain-like Superfamily: IVS-encoded protein-like Family: IVS-encoded protein-like Phyre2 PDB 2bcw chain C Region: 20 - 41 Aligned: 22 Modelled: 22 Confidence: 5.6% Identity: 9% PDB header:ribosome Chain: C: PDB Molecule:elongation factor g; PDBTitle: coordinates of the n-terminal domain of ribosomal protein2 l11,c-terminal domain of ribosomal protein l7/l12 and a3 portion of the g' domain of elongation factor g, as fitted4 into cryo-em map of an escherichia coli 70s*ef-5 g*gdp*fusidic acid complex Phyre2 PDB 2wpy chain A Region: 51 - 71 Aligned: 21 Modelled: 21 Confidence: 5.4% Identity: 19% PDB header:transcription Chain: A: PDB Molecule:general control protein gcn4; PDBTitle: gcn4 leucine zipper mutant with one vxxnxxx motif2 coordinating chloride Phyre2 1 d3brja1 2 d3c8ga1 3 c1wwpA_ 4 d1wtya_ 5 c1ylmA_ 6 d2nn4a1 7 d2fexa1 8 d1twfc2 9 d1vkfa_ 10 c1gxsC_ 11 c1bcrA_ 12 d1qkia1 13 d2gsca1 14 d1a9xa1 15 c2zttA_ 16 c2fulE_ 17 c2a45J_ 18 d2rlda1 19 c2bcwC_ 20 c2wpyA_ 21

Detailed template information

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

1 d3brja1 100.0 40 Fold:MtlR-like Superfamily:MtlR-like Family:MtlR-like 2 d3c8ga1 100.0 27 Fold:MtlR-like Superfamily:MtlR-like Family:MtlR-like 3 c1wwpA_ 59.0 12 PDB header:structural genomics, unknown function Chain: A: PDB Molecule:hypothetical protein ttha0636; PDBTitle: crystal structure of ttk003001694 from thermus thermophilus2 hb8 4 d1wtya_ 39.7 13 Fold:Four-helical up-and-down bundle Superfamily:Nucleotidyltransferase substrate binding subunit/domain Family:Family 1 bi-partite nucleotidyltransferase subunit 5 c1ylmA_ 21.8 15 PDB header:structural genomics, unknown function Chain: A: PDB Molecule:hypothetical protein bsu32300; PDBTitle: structure of cytosolic protein of unknown function yute2 from bacillus subtilis 6 d2nn4a1 20.1 22 Fold:YqgQ-like Superfamily:YqgQ-like Family:YqgQ-like 7 d2fexa1 14.9 11 Fold:Flavodoxin-like Superfamily:Class I glutamine amidotransferase-like Family:DJ-1/PfpI 8 d1twfc2 10.7 33 Fold:Insert subdomain of RNA polymerase alpha subunit Superfamily:Insert subdomain of RNA polymerase alpha subunit Family:Insert subdomain of RNA polymerase alpha subunit 9 d1vkfa_ 10.1 11 Fold:TIM beta/alpha-barrel Superfamily:GlpP-like Family:GlpP-like 10 c1gxsC_ 10.0 14 PDB header:lyase Chain: C: PDB Molecule:p-(s)-hydroxymandelonitrile lyase chain a; PDBTitle: crystal structure of hydroxynitrile lyase from sorghum2 bicolor in complex with inhibitor benzoic acid: a novel3 cyanogenic enzyme 11 c1bcrA_ 9.7 11 PDB header:hydrolase/hydrolase inhibitor Chain: A: PDB Molecule:serine carboxypeptidase ii; PDBTitle: complex of the wheat serine carboxypeptidase, cpdw-ii, with the2 microbial peptide aldehyde inhibitor, antipain, and arginine at room3 temperature 12 d1qkia1 7.9 17 Fold:NAD(P)-binding Rossmann-fold domains Superfamily:NAD(P)-binding Rossmann-fold domains Family:Glyceraldehyde-3-phosphate dehydrogenase-like, N-terminal domain 13 d2gsca1 7.3 19 Fold:Bromodomain-like Superfamily:IVS-encoded protein-like Family:IVS-encoded protein-like 14 d1a9xa1 7.2 23 Fold:Carbamoyl phosphate synthetase, large subunit connection domain Superfamily:Carbamoyl phosphate synthetase, large subunit connection domain Family:Carbamoyl phosphate synthetase, large subunit connection domain 15 c2zttA_ 7.1 16 PDB header:transferase Chain: A: PDB Molecule:rna-directed rna polymerase catalytic subunit; PDBTitle: crystal structure of rna polymerase pb1-pb2 subunits from2 influenza a virus 16 c2fulE_ 6.5 19 PDB header:translation Chain: E: PDB Molecule:eukaryotic translation initiation factor 5; PDBTitle: crystal structure of the c-terminal domain of s. cerevisiae eif5 17 c2a45J_ 6.4 16 PDB header:hydrolase/hydrolase inhibitor Chain: J: PDB Molecule:fibrinogen alpha chain; PDBTitle: crystal structure of the complex between thrombin and the central "e"2 region of fibrin 18 d2rlda1 6.0 22 Fold:Bromodomain-like Superfamily:IVS-encoded protein-like Family:IVS-encoded protein-like 19 c2bcwC_ 5.6 9 PDB header:ribosome Chain: C: PDB Molecule:elongation factor g; PDBTitle: coordinates of the n-terminal domain of ribosomal protein2 l11,c-terminal domain of ribosomal protein l7/l12 and a3 portion of the g' domain of elongation factor g, as fitted4 into cryo-em map of an escherichia coli 70s*ef-5 g*gdp*fusidic acid complex 20 c2wpyA_ 5.4 19 PDB header:transcription Chain: A: PDB Molecule:general control protein gcn4; PDBTitle: gcn4 leucine zipper mutant with one vxxnxxx motif2 coordinating chloride 21 c2ll0A_ not modelled 5.1 23 PDB header:structural genomics, unknown function Chain: A: PDB Molecule:uncharacterized protein; PDBTitle: nmr structure of the putative atpase regulatory protein yp_916642.12 from paracoccus denitrificans

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