Secondary structure and disorder prediction

		1	.	.	.	.	.	.	.	.	10	.	.	.	.	.	.	.	.	.	20	.	.	.	.	.	.	.	.	.	30	.	.	.	.	.	.	.	.	.	40	.	.	.	.	.	.	.	.	.	50	.	.	.	.	.	.	.	.	.	60
Sequence		M	I	L	D	R	H	I	T	S	R	G	Y	V	C	M	R	P	A	T	I	A	P	L	T	P	Y	D	K	W	D	G	E	K	W	V	T	D	T	E	A	Q	H	S	V	A	V	D	A	A	E	A	Q	R	Q	S	L	I	D	T	A
Secondary structure
SS confidence
Disorder		?	?	?	?	?	?	?								?				?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	70	.	.	.	.	.	.	.	.	.	80	.	.	.	.	.	.	.	.	.	90	.	.	.	.	.	.	.	.	.	100	.	.	.	.	.	.	.	.	.	110	.	.	.	.
Sequence		M	A	S	I	S	L	I	Q	L	K	L	Q	A	G	R	K	L	M	Q	A	E	T	S	R	L	N	T	V	L	D	Y	I	D	A	V	T	A	T	D	T	S	T	A	P	D	V	I	W	P	E	L	P	E	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 2kz6 chain A Region: 39 - 112 Aligned: 64 Modelled: 74 Confidence: 97.6% Identity: 16% PDB header:structural genomics, unknown function Chain: A: PDB Molecule:uncharacterized protein; PDBTitle: solution structure of protein cv0426 from chromobacterium violaceum,2 northeast structural genomics consortium (nesg) target cvt2 Phyre2 PDB 2kt9 chain A Region: 21 - 69 Aligned: 49 Modelled: 49 Confidence: 53.5% Identity: 24% PDB header:ribosomal protein Chain: A: PDB Molecule:probable 30s ribosomal protein psrp-3; PDBTitle: solution nmr structure of probable 30s ribosomal protein2 psrp-3 (ycf65-like protein) from synechocystis sp. (strain3 pcc 6803), northeast structural genomics consortium target4 target sgr46 Phyre2 PDB 3o0r chain C Region: 77 - 105 Aligned: 26 Modelled: 29 Confidence: 37.3% Identity: 23% PDB header:immune system/oxidoreductase Chain: C: PDB Molecule:nitric oxide reductase subunit c; PDBTitle: crystal structure of nitric oxide reductase from pseudomonas2 aeruginosa in complex with antibody fragment Phyre2 PDB 2oa5 chain A domain 1 Region: 38 - 95 Aligned: 54 Modelled: 58 Confidence: 13.0% Identity: 19% Fold: BLRF2-like Superfamily: BLRF2-like Family: BLRF2-like Phyre2 PDB 1ew4 chain A Region: 21 - 35 Aligned: 15 Modelled: 15 Confidence: 11.9% Identity: 20% Fold: N domain of copper amine oxidase-like Superfamily: Frataxin/Nqo15-like Family: Frataxin-like Phyre2 PDB 2z8n chain B Region: 19 - 29 Aligned: 11 Modelled: 11 Confidence: 10.9% Identity: 36% PDB header:lyase Chain: B: PDB Molecule:27.5 kda virulence protein; PDBTitle: structural basis for the catalytic mechanism of phosphothreonine lyase Phyre2 PDB 3ok8 chain A Region: 29 - 97 Aligned: 69 Modelled: 69 Confidence: 9.0% Identity: 4% PDB header:protein binding Chain: A: PDB Molecule:brain-specific angiogenesis inhibitor 1-associated protein PDBTitle: i-bar of pinkbar Phyre2 PDB 1b35 chain D Region: 8 - 21 Aligned: 14 Modelled: 14 Confidence: 7.9% Identity: 21% PDB header:virus Chain: D: PDB Molecule:protein (cricket paralysis virus, vp4); PDBTitle: cricket paralysis virus (crpv) Phyre2 PDB 2f2a chain C domain 1 Region: 70 - 102 Aligned: 33 Modelled: 33 Confidence: 7.6% Identity: 24% Fold: Non-globular all-alpha subunits of globular proteins Superfamily: Glu-tRNAGln amidotransferase C subunit Family: Glu-tRNAGln amidotransferase C subunit Phyre2 PDB 2vzb chain A Region: 2 - 103 Aligned: 99 Modelled: 102 Confidence: 7.6% Identity: 10% PDB header:metal transport Chain: A: PDB Molecule:putative bacterioferritin-related protein; PDBTitle: a dodecameric thioferritin in the bacterial domain, characterization2 of the bacterioferritin-related protein from bacteroides fragilis Phyre2 PDB 2dii chain A domain 1 Region: 51 - 81 Aligned: 30 Modelled: 31 Confidence: 7.2% Identity: 7% Fold: BSD domain-like Superfamily: BSD domain-like Family: BSD domain Phyre2 PDB 1nwd chain C Region: 78 - 91 Aligned: 14 Modelled: 14 Confidence: 7.2% Identity: 0% PDB header:binding protein/hydrolase Chain: C: PDB Molecule:glutamate decarboxylase; PDBTitle: solution structure of ca2+/calmodulin bound to the c-2 terminal domain of petunia glutamate decarboxylase Phyre2 PDB 1nwd chain B Region: 78 - 91 Aligned: 14 Modelled: 14 Confidence: 7.2% Identity: 0% PDB header:binding protein/hydrolase Chain: B: PDB Molecule:glutamate decarboxylase; PDBTitle: solution structure of ca2+/calmodulin bound to the c-2 terminal domain of petunia glutamate decarboxylase Phyre2 PDB 2axp chain A domain 1 Region: 2 - 41 Aligned: 39 Modelled: 40 Confidence: 7.1% Identity: 28% Fold: P-loop containing nucleoside triphosphate hydrolases Superfamily: P-loop containing nucleoside triphosphate hydrolases Family: Nucleotide and nucleoside kinases Phyre2 PDB 2dii chain A Region: 51 - 81 Aligned: 30 Modelled: 31 Confidence: 6.8% Identity: 7% PDB header:transcription Chain: A: PDB Molecule:tfiih basal transcription factor complex p62 PDBTitle: solution structure of the bsd domain of human tfiih basal2 transcription factor complex p62 subunit Phyre2 PDB 2paj chain A domain 1 Region: 27 - 60 Aligned: 34 Modelled: 34 Confidence: 6.8% Identity: 12% Fold: Composite domain of metallo-dependent hydrolases Superfamily: Composite domain of metallo-dependent hydrolases Family: SAH/MTA deaminase-like Phyre2 PDB 3lvy chain B Region: 65 - 112 Aligned: 46 Modelled: 48 Confidence: 5.9% Identity: 4% PDB header:lyase Chain: B: PDB Molecule:carboxymuconolactone decarboxylase family; PDBTitle: crystal structure of carboxymuconolactone decarboxylase2 family protein smu.961 from streptococcus mutans Phyre2 PDB 2d5k chain C Region: 3 - 82 Aligned: 79 Modelled: 80 Confidence: 5.5% Identity: 10% PDB header:metal binding protein Chain: C: PDB Molecule:dps family protein; PDBTitle: crystal structure of dps from staphylococcus aureus Phyre2 PDB 1bgv chain A domain 2 Region: 78 - 101 Aligned: 24 Modelled: 24 Confidence: 5.3% Identity: 13% Fold: Aminoacid dehydrogenase-like, N-terminal domain Superfamily: Aminoacid dehydrogenase-like, N-terminal domain Family: Aminoacid dehydrogenases Phyre2 1 c2kz6A_ 2 c2kt9A_ 3 c3o0rC_ 4 d2oa5a1 5 d1ew4a_ 6 c2z8nB_ 7 c3ok8A_ 8 c1b35D_ 9 d2f2ac1 10 c2vzbA_ 11 d2diia1 12 c1nwdC_ 13 c1nwdB_ 14 d2axpa1 15 c2diiA_ 16 d2paja1 17 c3lvyB_ 18 c2d5kC_ 19 d1bgva2

Detailed template information

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

1 c2kz6A_ 97.6 16 PDB header:structural genomics, unknown function Chain: A: PDB Molecule:uncharacterized protein; PDBTitle: solution structure of protein cv0426 from chromobacterium violaceum,2 northeast structural genomics consortium (nesg) target cvt2 2 c2kt9A_ 53.5 24 PDB header:ribosomal protein Chain: A: PDB Molecule:probable 30s ribosomal protein psrp-3; PDBTitle: solution nmr structure of probable 30s ribosomal protein2 psrp-3 (ycf65-like protein) from synechocystis sp. (strain3 pcc 6803), northeast structural genomics consortium target4 target sgr46 3 c3o0rC_ 37.3 23 PDB header:immune system/oxidoreductase Chain: C: PDB Molecule:nitric oxide reductase subunit c; PDBTitle: crystal structure of nitric oxide reductase from pseudomonas2 aeruginosa in complex with antibody fragment 4 d2oa5a1 13.0 19 Fold:BLRF2-like Superfamily:BLRF2-like Family:BLRF2-like 5 d1ew4a_ 11.9 20 Fold:N domain of copper amine oxidase-like Superfamily:Frataxin/Nqo15-like Family:Frataxin-like 6 c2z8nB_ 10.9 36 PDB header:lyase Chain: B: PDB Molecule:27.5 kda virulence protein; PDBTitle: structural basis for the catalytic mechanism of phosphothreonine lyase 7 c3ok8A_ 9.0 4 PDB header:protein binding Chain: A: PDB Molecule:brain-specific angiogenesis inhibitor 1-associated protein PDBTitle: i-bar of pinkbar 8 c1b35D_ 7.9 21 PDB header:virus Chain: D: PDB Molecule:protein (cricket paralysis virus, vp4); PDBTitle: cricket paralysis virus (crpv) 9 d2f2ac1 7.6 24 Fold:Non-globular all-alpha subunits of globular proteins Superfamily:Glu-tRNAGln amidotransferase C subunit Family:Glu-tRNAGln amidotransferase C subunit 10 c2vzbA_ 7.6 10 PDB header:metal transport Chain: A: PDB Molecule:putative bacterioferritin-related protein; PDBTitle: a dodecameric thioferritin in the bacterial domain, characterization2 of the bacterioferritin-related protein from bacteroides fragilis 11 d2diia1 7.2 7 Fold:BSD domain-like Superfamily:BSD domain-like Family:BSD domain 12 c1nwdC_ 7.2 0 PDB header:binding protein/hydrolase Chain: C: PDB Molecule:glutamate decarboxylase; PDBTitle: solution structure of ca2+/calmodulin bound to the c-2 terminal domain of petunia glutamate decarboxylase 13 c1nwdB_ 7.2 0 PDB header:binding protein/hydrolase Chain: B: PDB Molecule:glutamate decarboxylase; PDBTitle: solution structure of ca2+/calmodulin bound to the c-2 terminal domain of petunia glutamate decarboxylase 14 d2axpa1 7.1 28 Fold:P-loop containing nucleoside triphosphate hydrolases Superfamily:P-loop containing nucleoside triphosphate hydrolases Family:Nucleotide and nucleoside kinases 15 c2diiA_ 6.8 7 PDB header:transcription Chain: A: PDB Molecule:tfiih basal transcription factor complex p62 PDBTitle: solution structure of the bsd domain of human tfiih basal2 transcription factor complex p62 subunit 16 d2paja1 6.8 12 Fold:Composite domain of metallo-dependent hydrolases Superfamily:Composite domain of metallo-dependent hydrolases Family:SAH/MTA deaminase-like 17 c3lvyB_ 5.9 4 PDB header:lyase Chain: B: PDB Molecule:carboxymuconolactone decarboxylase family; PDBTitle: crystal structure of carboxymuconolactone decarboxylase2 family protein smu.961 from streptococcus mutans 18 c2d5kC_ 5.5 10 PDB header:metal binding protein Chain: C: PDB Molecule:dps family protein; PDBTitle: crystal structure of dps from staphylococcus aureus 19 d1bgva2 5.3 13 Fold:Aminoacid dehydrogenase-like, N-terminal domain Superfamily:Aminoacid dehydrogenase-like, N-terminal domain Family:Aminoacid dehydrogenases

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