Secondary structure and disorder prediction

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Sequence		M	G	L	K	W	T	D	S	R	E	I	G	E	A	L	Y	D	A	Y	P	D	L	D	P	K	T	V	R	F	T	D	M	H	Q	W	I	C	D	L	E	D	F	D	D	D	P	Q	A	S	N	E	K	I	L	E	A	I	L	L	V
Secondary structure
SS confidence
Disorder		?	?	?	?	?	?																																					?	?	?		?	?	?	?
Disorder confidence
		.	.	.	.	.	.
Sequence		W	L	D	E	A	E
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 1uj8 chain A domain 1 Region: 2 - 65 Aligned: 64 Modelled: 64 Confidence: 100.0% Identity: 100% Fold: Another 3-helical bundle Superfamily: IscX-like Family: IscX-like Phyre2 PDB 2kzv chain A Region: 5 - 43 Aligned: 39 Modelled: 39 Confidence: 82.1% Identity: 21% PDB header:structural genomics, unknown function Chain: A: PDB Molecule:uncharacterized protein; PDBTitle: solution nmr structure of cv_0373(175-257) protein from2 chromobacterium violaceum, northeast structural genomics consortium3 target cvr118a Phyre2 PDB 2kpm chain A Region: 5 - 42 Aligned: 38 Modelled: 38 Confidence: 39.7% Identity: 18% PDB header:structural genomics, unknown function Chain: A: PDB Molecule:uncharacterized protein; PDBTitle: solution nmr structure of uncharacterized protein from gene2 locus ne0665 of nitrosomonas europaea. northeast structural3 genomics target ner103a Phyre2 PDB 3gr1 chain A Region: 8 - 62 Aligned: 55 Modelled: 55 Confidence: 20.4% Identity: 16% PDB header:membrane protein Chain: A: PDB Molecule:protein prgh; PDBTitle: periplamic domain of the t3ss inner membrane protein prgh2 from s.typhimurium (fragment 170-392) Phyre2 PDB 1gwc chain A domain 2 Region: 7 - 24 Aligned: 18 Modelled: 18 Confidence: 15.6% Identity: 17% Fold: Thioredoxin fold Superfamily: Thioredoxin-like Family: Glutathione S-transferase (GST), N-terminal domain Phyre2 PDB 3ktb chain D Region: 20 - 60 Aligned: 41 Modelled: 41 Confidence: 12.7% Identity: 17% PDB header:transcription regulator Chain: D: PDB Molecule:arsenical resistance operon trans-acting repressor; PDBTitle: crystal structure of arsenical resistance operon trans-acting2 repressor from bacteroides vulgatus atcc 8482 Phyre2 PDB 3mg9 chain A Region: 5 - 57 Aligned: 53 Modelled: 53 Confidence: 9.3% Identity: 19% PDB header:transferase/antibiotic Chain: A: PDB Molecule:teg12; PDBTitle: teg 12 binary structure complexed with the teicoplanin aglycone Phyre2 PDB 1mzb chain A Region: 4 - 27 Aligned: 24 Modelled: 24 Confidence: 8.0% Identity: 25% Fold: DNA/RNA-binding 3-helical bundle Superfamily: "Winged helix" DNA-binding domain Family: FUR-like Phyre2 PDB 1n2a chain A domain 2 Region: 2 - 21 Aligned: 20 Modelled: 20 Confidence: 7.8% Identity: 35% Fold: Thioredoxin fold Superfamily: Thioredoxin-like Family: Glutathione S-transferase (GST), N-terminal domain Phyre2 PDB 1gnw chain A domain 2 Region: 7 - 24 Aligned: 18 Modelled: 18 Confidence: 7.8% Identity: 22% Fold: Thioredoxin fold Superfamily: Thioredoxin-like Family: Glutathione S-transferase (GST), N-terminal domain Phyre2 PDB 1e6b chain A domain 2 Region: 7 - 21 Aligned: 15 Modelled: 15 Confidence: 7.7% Identity: 40% Fold: Thioredoxin fold Superfamily: Thioredoxin-like Family: Glutathione S-transferase (GST), N-terminal domain Phyre2 PDB 1fw1 chain A domain 2 Region: 7 - 21 Aligned: 15 Modelled: 15 Confidence: 7.0% Identity: 33% Fold: Thioredoxin fold Superfamily: Thioredoxin-like Family: Glutathione S-transferase (GST), N-terminal domain Phyre2 PDB 2o03 chain A Region: 7 - 27 Aligned: 21 Modelled: 21 Confidence: 6.6% Identity: 19% PDB header:gene regulation Chain: A: PDB Molecule:probable zinc uptake regulation protein furb; PDBTitle: crystal structure of furb from m. tuberculosis- a zinc uptake2 regulator Phyre2 PDB 12as chain A Region: 12 - 26 Aligned: 15 Modelled: 15 Confidence: 6.3% Identity: 47% Fold: Class II aaRS and biotin synthetases Superfamily: Class II aaRS and biotin synthetases Family: Class II aminoacyl-tRNA synthetase (aaRS)-like, catalytic domain Phyre2 PDB 2xig chain A Region: 8 - 27 Aligned: 20 Modelled: 20 Confidence: 6.2% Identity: 15% PDB header:transcription Chain: A: PDB Molecule:ferric uptake regulation protein; PDBTitle: the structure of the helicobacter pylori ferric uptake2 regulator fur reveals three functional metal binding sites Phyre2 PDB 1dgs chain A domain 1 Region: 9 - 60 Aligned: 48 Modelled: 49 Confidence: 6.2% Identity: 17% Fold: SAM domain-like Superfamily: RuvA domain 2-like Family: NAD+-dependent DNA ligase, domain 3 Phyre2 PDB 1rqt chain A Region: 49 - 57 Aligned: 9 Modelled: 9 Confidence: 6.0% Identity: 33% Fold: Ribosomal protein L7/12, oligomerisation (N-terminal) domain Superfamily: Ribosomal protein L7/12, oligomerisation (N-terminal) domain Family: Ribosomal protein L7/12, oligomerisation (N-terminal) domain Phyre2 PDB 1rqt chain B Region: 49 - 57 Aligned: 9 Modelled: 9 Confidence: 6.0% Identity: 33% PDB header:ribosome Chain: B: PDB Molecule:50s ribosomal protein l7/l12; PDBTitle: nmr structure of dimeric n-terminal domain of ribosomal2 protein l7 from e.coli Phyre2 PDB 1rqt chain A Region: 49 - 57 Aligned: 9 Modelled: 9 Confidence: 6.0% Identity: 33% PDB header:ribosome Chain: A: PDB Molecule:50s ribosomal protein l7/l12; PDBTitle: nmr structure of dimeric n-terminal domain of ribosomal2 protein l7 from e.coli Phyre2 PDB 1oyj chain A domain 2 Region: 7 - 21 Aligned: 15 Modelled: 15 Confidence: 5.5% Identity: 40% Fold: Thioredoxin fold Superfamily: Thioredoxin-like Family: Glutathione S-transferase (GST), N-terminal domain Phyre2 1 d1uj8a1 2 c2kzvA_ 3 c2kpmA_ 4 c3gr1A_ 5 d1gwca2 6 c3ktbD_ 7 c3mg9A_ 8 d1mzba_ 9 d1n2aa2 10 d1gnwa2 11 d1e6ba2 12 d1fw1a2 13 c2o03A_ 14 d12asa_ 15 c2xigA_ 16 d1dgsa1 17 d1rqta_ 18 c1rqtB_ 19 c1rqtA_ 20 d1oyja2 21 22 23

Detailed template information

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

1 d1uj8a1 100.0 100 Fold:Another 3-helical bundle Superfamily:IscX-like Family:IscX-like 2 c2kzvA_ 82.1 21 PDB header:structural genomics, unknown function Chain: A: PDB Molecule:uncharacterized protein; PDBTitle: solution nmr structure of cv_0373(175-257) protein from2 chromobacterium violaceum, northeast structural genomics consortium3 target cvr118a 3 c2kpmA_ 39.7 18 PDB header:structural genomics, unknown function Chain: A: PDB Molecule:uncharacterized protein; PDBTitle: solution nmr structure of uncharacterized protein from gene2 locus ne0665 of nitrosomonas europaea. northeast structural3 genomics target ner103a 4 c3gr1A_ 20.4 16 PDB header:membrane protein Chain: A: PDB Molecule:protein prgh; PDBTitle: periplamic domain of the t3ss inner membrane protein prgh2 from s.typhimurium (fragment 170-392) 5 d1gwca2 15.6 17 Fold:Thioredoxin fold Superfamily:Thioredoxin-like Family:Glutathione S-transferase (GST), N-terminal domain 6 c3ktbD_ 12.7 17 PDB header:transcription regulator Chain: D: PDB Molecule:arsenical resistance operon trans-acting repressor; PDBTitle: crystal structure of arsenical resistance operon trans-acting2 repressor from bacteroides vulgatus atcc 8482 7 c3mg9A_ 9.3 19 PDB header:transferase/antibiotic Chain: A: PDB Molecule:teg12; PDBTitle: teg 12 binary structure complexed with the teicoplanin aglycone 8 d1mzba_ 8.0 25 Fold:DNA/RNA-binding 3-helical bundle Superfamily:"Winged helix" DNA-binding domain Family:FUR-like 9 d1n2aa2 7.8 35 Fold:Thioredoxin fold Superfamily:Thioredoxin-like Family:Glutathione S-transferase (GST), N-terminal domain 10 d1gnwa2 7.8 22 Fold:Thioredoxin fold Superfamily:Thioredoxin-like Family:Glutathione S-transferase (GST), N-terminal domain 11 d1e6ba2 7.7 40 Fold:Thioredoxin fold Superfamily:Thioredoxin-like Family:Glutathione S-transferase (GST), N-terminal domain 12 d1fw1a2 7.0 33 Fold:Thioredoxin fold Superfamily:Thioredoxin-like Family:Glutathione S-transferase (GST), N-terminal domain 13 c2o03A_ 6.6 19 PDB header:gene regulation Chain: A: PDB Molecule:probable zinc uptake regulation protein furb; PDBTitle: crystal structure of furb from m. tuberculosis- a zinc uptake2 regulator 14 d12asa_ 6.3 47 Fold:Class II aaRS and biotin synthetases Superfamily:Class II aaRS and biotin synthetases Family:Class II aminoacyl-tRNA synthetase (aaRS)-like, catalytic domain 15 c2xigA_ 6.2 15 PDB header:transcription Chain: A: PDB Molecule:ferric uptake regulation protein; PDBTitle: the structure of the helicobacter pylori ferric uptake2 regulator fur reveals three functional metal binding sites 16 d1dgsa1 6.2 17 Fold:SAM domain-like Superfamily:RuvA domain 2-like Family:NAD+-dependent DNA ligase, domain 3 17 d1rqta_ 6.0 33 Fold:Ribosomal protein L7/12, oligomerisation (N-terminal) domain Superfamily:Ribosomal protein L7/12, oligomerisation (N-terminal) domain Family:Ribosomal protein L7/12, oligomerisation (N-terminal) domain 18 c1rqtB_ 6.0 33 PDB header:ribosome Chain: B: PDB Molecule:50s ribosomal protein l7/l12; PDBTitle: nmr structure of dimeric n-terminal domain of ribosomal2 protein l7 from e.coli 19 c1rqtA_ 6.0 33 PDB header:ribosome Chain: A: PDB Molecule:50s ribosomal protein l7/l12; PDBTitle: nmr structure of dimeric n-terminal domain of ribosomal2 protein l7 from e.coli 20 d1oyja2 5.5 40 Fold:Thioredoxin fold Superfamily:Thioredoxin-like Family:Glutathione S-transferase (GST), N-terminal domain 21 d1qhma_ not modelled 5.3 22 Fold:PFL-like glycyl radical enzymes Superfamily:PFL-like glycyl radical enzymes Family:PFL-like 22 c2jg0A_ not modelled 5.3 12 PDB header:hydrolase Chain: A: PDB Molecule:periplasmic trehalase; PDBTitle: family 37 trehalase from escherichia coli in complex with 1-2 thiatrehazolin 23 d2jg0a1 not modelled 5.3 12 Fold:alpha/alpha toroid Superfamily:Six-hairpin glycosidases Family:Trehalase-like

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