Secondary structure and disorder prediction

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Sequence		M	H	T	P	I	G	V	K	P	V	A	G	S	K	E	W	R	E	A	W	Q	K	R	A	F	A	H	I	S	N	G	Y	K	Y	I	Y	I	A	I	D	S	P	E	I	F	L	L	V	C	S	L	I	R	I
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 1v29 chain B Region: 4 - 26 Aligned: 23 Modelled: 23 Confidence: 24.8% Identity: 13% Fold: SH3-like barrel Superfamily: Electron transport accessory proteins Family: Nitrile hydratase beta chain Phyre2 PDB 1xg8 chain A Region: 14 - 42 Aligned: 27 Modelled: 29 Confidence: 22.7% Identity: 30% Fold: Thioredoxin fold Superfamily: Thioredoxin-like Family: YuzD-like Phyre2 PDB 2pof chain A domain 1 Region: 16 - 42 Aligned: 27 Modelled: 27 Confidence: 22.0% Identity: 33% Fold: HIT-like Superfamily: HIT-like Family: CDH-like Phyre2 PDB 1ugp chain B Region: 7 - 26 Aligned: 20 Modelled: 20 Confidence: 20.0% Identity: 35% Fold: SH3-like barrel Superfamily: Electron transport accessory proteins Family: Nitrile hydratase beta chain Phyre2 PDB 3dlr chain A Region: 29 - 40 Aligned: 12 Modelled: 12 Confidence: 18.5% Identity: 42% PDB header:transferase Chain: A: PDB Molecule:integrase; PDBTitle: crystal structure of the catalytic core domain from pfv2 integrase Phyre2 PDB 2x5c chain B Region: 30 - 37 Aligned: 8 Modelled: 8 Confidence: 13.5% Identity: 75% PDB header:viral protein Chain: B: PDB Molecule:hypothetical protein orf131; PDBTitle: crystal structure of hypothetical protein orf131 from2 pyrobaculum spherical virus Phyre2 PDB 2qrd chain A domain 1 Region: 29 - 52 Aligned: 22 Modelled: 24 Confidence: 12.2% Identity: 50% Fold: TBP-like Superfamily: KA1-like Family: Ssp2 C-terminal domain-like Phyre2 PDB 3qz9 chain D Region: 7 - 26 Aligned: 20 Modelled: 20 Confidence: 12.1% Identity: 20% PDB header:lyase Chain: D: PDB Molecule:co-type nitrile hydratase beta subunit; PDBTitle: crystal structure of co-type nitrile hydratase beta-y215f from2 pseudomonas putida. Phyre2 PDB 3l2t chain B Region: 29 - 40 Aligned: 12 Modelled: 12 Confidence: 9.5% Identity: 42% PDB header:recombination/dna Chain: B: PDB Molecule:integrase; PDBTitle: crystal structure of the prototype foamy virus (pfv) intasome in2 complex with magnesium and mk0518 (raltegravir) Phyre2 PDB 1c0m chain A domain 2 Region: 28 - 40 Aligned: 13 Modelled: 13 Confidence: 8.8% Identity: 8% Fold: Ribonuclease H-like motif Superfamily: Ribonuclease H-like Family: Retroviral integrase, catalytic domain Phyre2 PDB 2ipq chain X domain 1 Region: 21 - 50 Aligned: 26 Modelled: 30 Confidence: 7.7% Identity: 27% Fold: DNA/RNA-binding 3-helical bundle Superfamily: "Winged helix" DNA-binding domain Family: STY4665 C-terminal domain-like Phyre2 PDB 2de0 chain X Region: 15 - 45 Aligned: 31 Modelled: 31 Confidence: 7.6% Identity: 19% PDB header:transferase Chain: X: PDB Molecule:alpha-(1,6)-fucosyltransferase; PDBTitle: crystal structure of human alpha 1,6-fucosyltransferase, fut8 Phyre2 PDB 1u5t chain A domain 1 Region: 1 - 25 Aligned: 25 Modelled: 25 Confidence: 6.9% Identity: 20% Fold: DNA/RNA-binding 3-helical bundle Superfamily: "Winged helix" DNA-binding domain Family: Vacuolar sorting protein domain Phyre2 PDB 2x5f chain B Region: 9 - 32 Aligned: 24 Modelled: 24 Confidence: 6.6% Identity: 25% PDB header:transferase Chain: B: PDB Molecule:aspartate_tyrosine_phenylalanine pyridoxal-5' PDBTitle: crystal structure of the methicillin-resistant2 staphylococcus aureus sar2028, an3 aspartate_tyrosine_phenylalanine pyridoxal-5'-phosphate4 dependent aminotransferase Phyre2 PDB 1cxq chain A Region: 29 - 40 Aligned: 12 Modelled: 12 Confidence: 6.4% Identity: 8% Fold: Ribonuclease H-like motif Superfamily: Ribonuclease H-like Family: Retroviral integrase, catalytic domain Phyre2 PDB 2b9s chain A Region: 27 - 41 Aligned: 15 Modelled: 15 Confidence: 6.3% Identity: 27% PDB header:isomerase/dna Chain: A: PDB Molecule:topoisomerase i-like protein; PDBTitle: crystal structure of heterodimeric l. donovani2 topoisomerase i-vanadate-dna complex Phyre2 PDB 3f1f chain 4 Region: 42 - 50 Aligned: 9 Modelled: 9 Confidence: 5.8% Identity: 67% PDB header:ribosome Chain: 4: PDB Molecule:50s ribosomal protein l31; PDBTitle: crystal structure of a translation termination complex2 formed with release factor rf2. this file contains the 50s3 subunit of one 70s ribosome. the entire crystal structure4 contains two 70s ribosomes as described in remark 400. Phyre2 PDB 2wh4 chain 4 Region: 42 - 50 Aligned: 9 Modelled: 9 Confidence: 5.3% Identity: 67% PDB header:ribosome Chain: 4: PDB Molecule:50s ribosomal protein l31; PDBTitle: insights into translational termination from the structure2 of rf2 bound to the ribosome Phyre2 1 d1v29b_ 2 d1xg8a_ 3 d2pofa1 4 d1ugpb_ 5 c3dlrA_ 6 c2x5cB_ 7 d2qrda1 8 c3qz9D_ 9 c3l2tB_ 10 d1c0ma2 11 d2ipqx1 12 c2de0X_ 13 d1u5ta1 14 c2x5fB_ 15 d1cxqa_ 16 c2b9sA_ 17 c3f1f4_ 18 c2wh44_

Detailed template information

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

1 d1v29b_ 24.8 13 Fold:SH3-like barrel Superfamily:Electron transport accessory proteins Family:Nitrile hydratase beta chain 2 d1xg8a_ 22.7 30 Fold:Thioredoxin fold Superfamily:Thioredoxin-like Family:YuzD-like 3 d2pofa1 22.0 33 Fold:HIT-like Superfamily:HIT-like Family:CDH-like 4 d1ugpb_ 20.0 35 Fold:SH3-like barrel Superfamily:Electron transport accessory proteins Family:Nitrile hydratase beta chain 5 c3dlrA_ 18.5 42 PDB header:transferase Chain: A: PDB Molecule:integrase; PDBTitle: crystal structure of the catalytic core domain from pfv2 integrase 6 c2x5cB_ 13.5 75 PDB header:viral protein Chain: B: PDB Molecule:hypothetical protein orf131; PDBTitle: crystal structure of hypothetical protein orf131 from2 pyrobaculum spherical virus 7 d2qrda1 12.2 50 Fold:TBP-like Superfamily:KA1-like Family:Ssp2 C-terminal domain-like 8 c3qz9D_ 12.1 20 PDB header:lyase Chain: D: PDB Molecule:co-type nitrile hydratase beta subunit; PDBTitle: crystal structure of co-type nitrile hydratase beta-y215f from2 pseudomonas putida. 9 c3l2tB_ 9.5 42 PDB header:recombination/dna Chain: B: PDB Molecule:integrase; PDBTitle: crystal structure of the prototype foamy virus (pfv) intasome in2 complex with magnesium and mk0518 (raltegravir) 10 d1c0ma2 8.8 8 Fold:Ribonuclease H-like motif Superfamily:Ribonuclease H-like Family:Retroviral integrase, catalytic domain 11 d2ipqx1 7.7 27 Fold:DNA/RNA-binding 3-helical bundle Superfamily:"Winged helix" DNA-binding domain Family:STY4665 C-terminal domain-like 12 c2de0X_ 7.6 19 PDB header:transferase Chain: X: PDB Molecule:alpha-(1,6)-fucosyltransferase; PDBTitle: crystal structure of human alpha 1,6-fucosyltransferase, fut8 13 d1u5ta1 6.9 20 Fold:DNA/RNA-binding 3-helical bundle Superfamily:"Winged helix" DNA-binding domain Family:Vacuolar sorting protein domain 14 c2x5fB_ 6.6 25 PDB header:transferase Chain: B: PDB Molecule:aspartate_tyrosine_phenylalanine pyridoxal-5' PDBTitle: crystal structure of the methicillin-resistant2 staphylococcus aureus sar2028, an3 aspartate_tyrosine_phenylalanine pyridoxal-5'-phosphate4 dependent aminotransferase 15 d1cxqa_ 6.4 8 Fold:Ribonuclease H-like motif Superfamily:Ribonuclease H-like Family:Retroviral integrase, catalytic domain 16 c2b9sA_ 6.3 27 PDB header:isomerase/dna Chain: A: PDB Molecule:topoisomerase i-like protein; PDBTitle: crystal structure of heterodimeric l. donovani2 topoisomerase i-vanadate-dna complex 17 c3f1f4_ 5.8 67 PDB header:ribosome Chain: 4: PDB Molecule:50s ribosomal protein l31; PDBTitle: crystal structure of a translation termination complex2 formed with release factor rf2. this file contains the 50s3 subunit of one 70s ribosome. the entire crystal structure4 contains two 70s ribosomes as described in remark 400. 18 c2wh44_ 5.3 67 PDB header:ribosome Chain: 4: PDB Molecule:50s ribosomal protein l31; PDBTitle: insights into translational termination from the structure2 of rf2 bound to the ribosome

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