Secondary structure and disorder prediction

		1	.	.	.	.	.	.	.	.	10	.	.	.	.	.	.	.	.	.	20	.	.	.	.	.	.	.	.	.	30	.	.	.	.	.	.	.	.	.	40	.	.	.	.	.	.	.	.	.	50	.	.	.	.	.	.	.	.	.	60
Sequence		M	E	T	V	A	Y	A	D	F	A	R	L	E	M	R	V	G	K	I	V	E	V	K	R	H	E	N	A	D	K	L	Y	I	V	Q	V	D	V	G	Q	K	T	L	Q	T	V	T	S	L	V	P	Y	Y	S	E	E	E	L	M	G
Secondary structure
SS confidence
Disorder		?	?	?	?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	70	.	.	.	.	.	.	.	.	.	80	.	.	.	.	.	.	.	.	.	90	.	.	.	.	.	.	.	.	.	100	.	.	.	.	.	.	.	.	.	110
Sequence		K	T	V	V	V	L	C	N	L	Q	K	A	K	M	R	G	E	T	S	E	C	M	L	L	C	A	E	T	D	D	G	S	E	S	V	L	L	T	P	E	R	M	M	P	A	G	V	R	V	V
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 1pxf chain A Region: 1 - 110 Aligned: 110 Modelled: 110 Confidence: 100.0% Identity: 100% Fold: OB-fold Superfamily: Nucleic acid-binding proteins Family: Myf domain Phyre2 PDB 2cwp chain A Region: 1 - 109 Aligned: 108 Modelled: 109 Confidence: 100.0% Identity: 32% PDB header:ligase Chain: A: PDB Molecule:metrs related protein; PDBTitle: crystal structure of metrs related protein from pyrococcus horikoshii Phyre2 PDB 1pyb chain A Region: 2 - 109 Aligned: 106 Modelled: 108 Confidence: 100.0% Identity: 28% Fold: OB-fold Superfamily: Nucleic acid-binding proteins Family: Myf domain Phyre2 PDB 1gd7 chain A Region: 3 - 109 Aligned: 106 Modelled: 107 Confidence: 100.0% Identity: 33% Fold: OB-fold Superfamily: Nucleic acid-binding proteins Family: Myf domain Phyre2 PDB 2q2i chain A Region: 3 - 109 Aligned: 106 Modelled: 107 Confidence: 100.0% Identity: 30% PDB header:chaperone Chain: A: PDB Molecule:secretion chaperone; PDBTitle: crystal structure of the protein secretion chaperone csaa from2 agrobacterium tumefaciens. Phyre2 PDB 1fl0 chain A Region: 8 - 110 Aligned: 101 Modelled: 103 Confidence: 100.0% Identity: 37% Fold: OB-fold Superfamily: Nucleic acid-binding proteins Family: Myf domain Phyre2 PDB 1mkh chain A Region: 3 - 109 Aligned: 104 Modelled: 104 Confidence: 100.0% Identity: 49% Fold: OB-fold Superfamily: Nucleic acid-binding proteins Family: Myf domain Phyre2 PDB 1ntg chain A Region: 9 - 109 Aligned: 101 Modelled: 101 Confidence: 100.0% Identity: 43% Fold: OB-fold Superfamily: Nucleic acid-binding proteins Family: Myf domain Phyre2 PDB 2nzo chain D Region: 2 - 109 Aligned: 107 Modelled: 108 Confidence: 100.0% Identity: 27% PDB header:chaperone Chain: D: PDB Molecule:protein csaa; PDBTitle: crystal structure of a secretion chaperone csaa from bacillus subtilis2 in the space group p 32 2 1 Phyre2 PDB 3bu2 chain B Region: 3 - 110 Aligned: 108 Modelled: 108 Confidence: 99.9% Identity: 19% PDB header:rna binding protein Chain: B: PDB Molecule:putative trna-binding protein; PDBTitle: crystal structure of a trna-binding protein from2 staphylococcus saprophyticus subsp. saprophyticus.3 northeast structural genomics consortium target syr77 Phyre2 PDB 3pco chain D Region: 13 - 109 Aligned: 97 Modelled: 97 Confidence: 99.9% Identity: 29% PDB header:ligase Chain: D: PDB Molecule:phenylalanyl-trna synthetase, beta chain; PDBTitle: crystal structure of e. coli phenylalanine-trna synthetase complexed2 with phenylalanine and amp Phyre2 PDB 2e8g chain B Region: 7 - 107 Aligned: 95 Modelled: 101 Confidence: 99.9% Identity: 21% PDB header:rna binding protein Chain: B: PDB Molecule:hypothetical protein ph0536; PDBTitle: the structure of protein from p. horikoshii at 1.7 angstrom2 resolution Phyre2 PDB 1jjc chain B domain 3 Region: 13 - 109 Aligned: 95 Modelled: 97 Confidence: 99.9% Identity: 18% Fold: OB-fold Superfamily: Nucleic acid-binding proteins Family: Myf domain Phyre2 PDB 2akw chain B Region: 13 - 109 Aligned: 95 Modelled: 96 Confidence: 99.9% Identity: 17% PDB header:ligase Chain: B: PDB Molecule:phenylalanyl-trna synthetase beta chain; PDBTitle: crystal structure of t.thermophilus phenylalanyl-trna synthetase2 complexed with p-cl-phenylalanine Phyre2 PDB 2rhs chain B Region: 13 - 109 Aligned: 86 Modelled: 97 Confidence: 99.7% Identity: 28% PDB header:ligase Chain: B: PDB Molecule:phenylalanyl-trna synthetase beta chain; PDBTitle: phers from staphylococcus haemolyticus- rational protein2 engineering and inhibitor studies Phyre2 PDB 3l4g chain L Region: 70 - 110 Aligned: 41 Modelled: 41 Confidence: 89.2% Identity: 7% PDB header:ligase Chain: L: PDB Molecule:phenylalanyl-trna synthetase beta chain; PDBTitle: crystal structure of homo sapiens cytoplasmic phenylalanyl-trna2 synthetase Phyre2 PDB 1jjc chain B domain 1 Region: 18 - 31 Aligned: 14 Modelled: 14 Confidence: 15.2% Identity: 21% Fold: Putative DNA-binding domain Superfamily: Putative DNA-binding domain Family: Domains B1 and B5 of PheRS-beta, PheT Phyre2 PDB 1vjn chain A Region: 5 - 37 Aligned: 33 Modelled: 33 Confidence: 10.6% Identity: 21% Fold: Metallo-hydrolase/oxidoreductase Superfamily: Metallo-hydrolase/oxidoreductase Family: Hypothetical protein TM0207 Phyre2 PDB 2fhd chain A Region: 2 - 33 Aligned: 32 Modelled: 32 Confidence: 8.3% Identity: 19% PDB header:cell cycle Chain: A: PDB Molecule:dna repair protein rhp9/crb2; PDBTitle: crystal structure of crb2 tandem tudor domains Phyre2 PDB 1qmg chain A domain 2 Region: 27 - 66 Aligned: 40 Modelled: 40 Confidence: 6.8% Identity: 13% Fold: NAD(P)-binding Rossmann-fold domains Superfamily: NAD(P)-binding Rossmann-fold domains Family: 6-phosphogluconate dehydrogenase-like, N-terminal domain Phyre2 1 d1pxfa_ 2 c2cwpA_ 3 d1pyba_ 4 d1gd7a_ 5 c2q2iA_ 6 d1fl0a_ 7 d1mkha_ 8 d1ntga_ 9 c2nzoD_ 10 c3bu2B_ 11 c3pcoD_ 12 c2e8gB_ 13 d1jjcb3 14 c2akwB_ 15 c2rhsB_ 16 c3l4gL_ 17 d1jjcb1 18 d1vjna_ 19 c2fhdA_ 20 d1qmga2 21 22 23 24 25

Detailed template information

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

1 d1pxfa_ 100.0 100 Fold:OB-fold Superfamily:Nucleic acid-binding proteins Family:Myf domain 2 c2cwpA_ 100.0 32 PDB header:ligase Chain: A: PDB Molecule:metrs related protein; PDBTitle: crystal structure of metrs related protein from pyrococcus horikoshii 3 d1pyba_ 100.0 28 Fold:OB-fold Superfamily:Nucleic acid-binding proteins Family:Myf domain 4 d1gd7a_ 100.0 33 Fold:OB-fold Superfamily:Nucleic acid-binding proteins Family:Myf domain 5 c2q2iA_ 100.0 30 PDB header:chaperone Chain: A: PDB Molecule:secretion chaperone; PDBTitle: crystal structure of the protein secretion chaperone csaa from2 agrobacterium tumefaciens. 6 d1fl0a_ 100.0 37 Fold:OB-fold Superfamily:Nucleic acid-binding proteins Family:Myf domain 7 d1mkha_ 100.0 49 Fold:OB-fold Superfamily:Nucleic acid-binding proteins Family:Myf domain 8 d1ntga_ 100.0 43 Fold:OB-fold Superfamily:Nucleic acid-binding proteins Family:Myf domain 9 c2nzoD_ 100.0 27 PDB header:chaperone Chain: D: PDB Molecule:protein csaa; PDBTitle: crystal structure of a secretion chaperone csaa from bacillus subtilis2 in the space group p 32 2 1 10 c3bu2B_ 99.9 19 PDB header:rna binding protein Chain: B: PDB Molecule:putative trna-binding protein; PDBTitle: crystal structure of a trna-binding protein from2 staphylococcus saprophyticus subsp. saprophyticus.3 northeast structural genomics consortium target syr77 11 c3pcoD_ 99.9 29 PDB header:ligase Chain: D: PDB Molecule:phenylalanyl-trna synthetase, beta chain; PDBTitle: crystal structure of e. coli phenylalanine-trna synthetase complexed2 with phenylalanine and amp 12 c2e8gB_ 99.9 21 PDB header:rna binding protein Chain: B: PDB Molecule:hypothetical protein ph0536; PDBTitle: the structure of protein from p. horikoshii at 1.7 angstrom2 resolution 13 d1jjcb3 99.9 18 Fold:OB-fold Superfamily:Nucleic acid-binding proteins Family:Myf domain 14 c2akwB_ 99.9 17 PDB header:ligase Chain: B: PDB Molecule:phenylalanyl-trna synthetase beta chain; PDBTitle: crystal structure of t.thermophilus phenylalanyl-trna synthetase2 complexed with p-cl-phenylalanine 15 c2rhsB_ 99.7 28 PDB header:ligase Chain: B: PDB Molecule:phenylalanyl-trna synthetase beta chain; PDBTitle: phers from staphylococcus haemolyticus- rational protein2 engineering and inhibitor studies 16 c3l4gL_ 89.2 7 PDB header:ligase Chain: L: PDB Molecule:phenylalanyl-trna synthetase beta chain; PDBTitle: crystal structure of homo sapiens cytoplasmic phenylalanyl-trna2 synthetase 17 d1jjcb1 15.2 21 Fold:Putative DNA-binding domain Superfamily:Putative DNA-binding domain Family:Domains B1 and B5 of PheRS-beta, PheT 18 d1vjna_ 10.6 21 Fold:Metallo-hydrolase/oxidoreductase Superfamily:Metallo-hydrolase/oxidoreductase Family:Hypothetical protein TM0207 19 c2fhdA_ 8.3 19 PDB header:cell cycle Chain: A: PDB Molecule:dna repair protein rhp9/crb2; PDBTitle: crystal structure of crb2 tandem tudor domains 20 d1qmga2 6.8 13 Fold:NAD(P)-binding Rossmann-fold domains Superfamily:NAD(P)-binding Rossmann-fold domains Family:6-phosphogluconate dehydrogenase-like, N-terminal domain 21 d2gyci1 not modelled 6.6 16 Fold:Ribosomal protein L14 Superfamily:Ribosomal protein L14 Family:Ribosomal protein L14 22 c3iz6D_ not modelled 6.3 26 PDB header:ribosome Chain: D: PDB Molecule:40s ribosomal protein s4 (s4e); PDBTitle: localization of the small subunit ribosomal proteins into a 5.5 a2 cryo-em map of triticum aestivum translating 80s ribosome 23 c2xzmW_ not modelled 6.1 23 PDB header:ribosome Chain: W: PDB Molecule:40s ribosomal protein s4; PDBTitle: crystal structure of the eukaryotic 40s ribosomal2 subunit in complex with initiation factor 1. this file3 contains the 40s subunit and initiation factor for4 molecule 1 24 d1rbla2 not modelled 5.8 14 Fold:Ferredoxin-like Superfamily:RuBisCO, large subunit, small (N-terminal) domain Family:Ribulose 1,5-bisphosphate carboxylase-oxygenase 25 c3si5X_ not modelled 5.6 20 PDB header:cell cycle Chain: X: PDB Molecule:protein casc5; PDBTitle: kinetochore-bubr1 kinase complex

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