Secondary structure and disorder prediction

		1	.	.	.	.	.	.	.	.	10	.	.	.	.	.	.	.	.	.	20	.	.	.	.	.	.	.	.	.	30	.	.	.	.	.	.	.	.	.	40	.	.	.	.	.	.	.	.	.	50	.	.	.	.	.	.	.	.	.	60
Sequence		M	V	T	I	R	L	A	R	H	G	A	K	K	R	P	F	Y	Q	V	V	V	A	D	S	R	N	A	R	N	G	R	F	I	E	R	V	G	F	F	N	P	I	A	S	E	K	E	E	G	T	R	L	D	L	D	R	I	A	H	W
Secondary structure
SS confidence
Disorder		?	?			?	?	?	?																			?	?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	70	.	.	.	.	.	.	.	.	.	80	.	.
Sequence		V	G	Q	G	A	T	I	S	D	R	V	A	A	L	I	K	E	V	N	K	A	A
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 2gy9 chain P domain 1 Region: 1 - 78 Aligned: 78 Modelled: 78 Confidence: 100.0% Identity: 100% Fold: Ribosomal protein S16 Superfamily: Ribosomal protein S16 Family: Ribosomal protein S16 Phyre2 PDB 2uub chain P domain 1 Region: 1 - 79 Aligned: 78 Modelled: 79 Confidence: 100.0% Identity: 36% Fold: Ribosomal protein S16 Superfamily: Ribosomal protein S16 Family: Ribosomal protein S16 Phyre2 PDB 3bbn chain P Region: 1 - 79 Aligned: 75 Modelled: 79 Confidence: 100.0% Identity: 37% PDB header:ribosome Chain: P: PDB Molecule:ribosomal protein s16; PDBTitle: homology model for the spinach chloroplast 30s subunit2 fitted to 9.4a cryo-em map of the 70s chlororibosome. Phyre2 PDB 3bn0 chain A domain 1 Region: 2 - 79 Aligned: 69 Modelled: 78 Confidence: 100.0% Identity: 29% Fold: Ribosomal protein S16 Superfamily: Ribosomal protein S16 Family: Ribosomal protein S16 Phyre2 PDB 1vbv chain A domain 1 Region: 12 - 27 Aligned: 16 Modelled: 16 Confidence: 48.4% Identity: 31% Fold: SH3-like barrel Superfamily: YccV-like Family: YccV-like Phyre2 PDB 3f62 chain A Region: 20 - 37 Aligned: 18 Modelled: 18 Confidence: 25.7% Identity: 28% PDB header:cytokine Chain: A: PDB Molecule:interleukin 18 binding protein; PDBTitle: crystal structure of human il-18 in complex with ectromelia virus il-2 18 binding protein Phyre2 PDB 3g0k chain A Region: 1 - 46 Aligned: 44 Modelled: 46 Confidence: 18.6% Identity: 11% PDB header:ca-binding protein Chain: A: PDB Molecule:putative membrane protein; PDBTitle: crystal structure of a protein of unknown function with a cystatin-2 like fold (saro_2880) from novosphingobium aromaticivorans dsm at3 1.30 a resolution Phyre2 PDB 1vqo chain L domain 1 Region: 7 - 64 Aligned: 46 Modelled: 58 Confidence: 10.2% Identity: 28% Fold: Ribosomal proteins L15p and L18e Superfamily: Ribosomal proteins L15p and L18e Family: Ribosomal proteins L15p and L18e Phyre2 PDB 2heq chain A domain 1 Region: 7 - 36 Aligned: 19 Modelled: 30 Confidence: 10.0% Identity: 37% Fold: SH3-like barrel Superfamily: YorP-like Family: YorP-like Phyre2 PDB 3dkx chain A Region: 10 - 22 Aligned: 13 Modelled: 13 Confidence: 9.7% Identity: 23% PDB header:replication Chain: A: PDB Molecule:replication protein repb; PDBTitle: crystal structure of the replication initiator protein2 encoded on plasmid pmv158 (repb), trigonal form, to 2.7 ang3 resolution Phyre2 PDB 3cmc chain O domain 2 Region: 13 - 40 Aligned: 28 Modelled: 28 Confidence: 9.1% Identity: 14% Fold: FwdE/GAPDH domain-like Superfamily: Glyceraldehyde-3-phosphate dehydrogenase-like, C-terminal domain Family: GAPDH-like Phyre2 PDB 2dlx chain A domain 1 Region: 6 - 41 Aligned: 31 Modelled: 36 Confidence: 8.8% Identity: 10% Fold: Thioredoxin fold Superfamily: Thioredoxin-like Family: UAS domain Phyre2 PDB 2v3m chain F Region: 9 - 19 Aligned: 11 Modelled: 11 Confidence: 7.9% Identity: 36% PDB header:ribosomal protein Chain: F: PDB Molecule:naf1; PDBTitle: structure of the gar1 domain of naf1 Phyre2 PDB 3ngv chain A Region: 32 - 58 Aligned: 21 Modelled: 27 Confidence: 7.7% Identity: 24% PDB header:transport protein Chain: A: PDB Molecule:d7 protein; PDBTitle: crystal structure of anst-d7l1 Phyre2 PDB 2pkq chain O domain 2 Region: 13 - 40 Aligned: 28 Modelled: 28 Confidence: 7.4% Identity: 11% Fold: FwdE/GAPDH domain-like Superfamily: Glyceraldehyde-3-phosphate dehydrogenase-like, C-terminal domain Family: GAPDH-like Phyre2 PDB 1rm4 chain A domain 2 Region: 13 - 40 Aligned: 28 Modelled: 28 Confidence: 7.1% Identity: 0% Fold: FwdE/GAPDH domain-like Superfamily: Glyceraldehyde-3-phosphate dehydrogenase-like, C-terminal domain Family: GAPDH-like Phyre2 PDB 1swi chain C Region: 66 - 78 Aligned: 13 Modelled: 13 Confidence: 5.9% Identity: 23% PDB header:leucine zipper Chain: C: PDB Molecule:gcn4p1; PDBTitle: gcn4-leucine zipper core mutant as n16a complexed with2 benzene Phyre2 PDB 2w2r chain A Region: 13 - 20 Aligned: 8 Modelled: 8 Confidence: 5.2% Identity: 63% PDB header:viral protein Chain: A: PDB Molecule:matrix protein; PDBTitle: structure of the vesicular stomatitis virus matrix protein Phyre2 1 d2gy9p1 2 d2uubp1 3 c3bbnP_ 4 d3bn0a1 5 d1vbva1 6 c3f62A_ 7 c3g0kA_ 8 d1vqol1 9 d2heqa1 10 c3dkxA_ 11 d3cmco2 12 d2dlxa1 13 c2v3mF_ 14 c3ngvA_ 15 d2pkqo2 16 d1rm4a2 17 c1swiC_ 18 c2w2rA_

Detailed template information

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

1 d2gy9p1 100.0 100 Fold:Ribosomal protein S16 Superfamily:Ribosomal protein S16 Family:Ribosomal protein S16 2 d2uubp1 100.0 36 Fold:Ribosomal protein S16 Superfamily:Ribosomal protein S16 Family:Ribosomal protein S16 3 c3bbnP_ 100.0 37 PDB header:ribosome Chain: P: PDB Molecule:ribosomal protein s16; PDBTitle: homology model for the spinach chloroplast 30s subunit2 fitted to 9.4a cryo-em map of the 70s chlororibosome. 4 d3bn0a1 100.0 29 Fold:Ribosomal protein S16 Superfamily:Ribosomal protein S16 Family:Ribosomal protein S16 5 d1vbva1 48.4 31 Fold:SH3-like barrel Superfamily:YccV-like Family:YccV-like 6 c3f62A_ 25.7 28 PDB header:cytokine Chain: A: PDB Molecule:interleukin 18 binding protein; PDBTitle: crystal structure of human il-18 in complex with ectromelia virus il-2 18 binding protein 7 c3g0kA_ 18.6 11 PDB header:ca-binding protein Chain: A: PDB Molecule:putative membrane protein; PDBTitle: crystal structure of a protein of unknown function with a cystatin-2 like fold (saro_2880) from novosphingobium aromaticivorans dsm at3 1.30 a resolution 8 d1vqol1 10.2 28 Fold:Ribosomal proteins L15p and L18e Superfamily:Ribosomal proteins L15p and L18e Family:Ribosomal proteins L15p and L18e 9 d2heqa1 10.0 37 Fold:SH3-like barrel Superfamily:YorP-like Family:YorP-like 10 c3dkxA_ 9.7 23 PDB header:replication Chain: A: PDB Molecule:replication protein repb; PDBTitle: crystal structure of the replication initiator protein2 encoded on plasmid pmv158 (repb), trigonal form, to 2.7 ang3 resolution 11 d3cmco2 9.1 14 Fold:FwdE/GAPDH domain-like Superfamily:Glyceraldehyde-3-phosphate dehydrogenase-like, C-terminal domain Family:GAPDH-like 12 d2dlxa1 8.8 10 Fold:Thioredoxin fold Superfamily:Thioredoxin-like Family:UAS domain 13 c2v3mF_ 7.9 36 PDB header:ribosomal protein Chain: F: PDB Molecule:naf1; PDBTitle: structure of the gar1 domain of naf1 14 c3ngvA_ 7.7 24 PDB header:transport protein Chain: A: PDB Molecule:d7 protein; PDBTitle: crystal structure of anst-d7l1 15 d2pkqo2 7.4 11 Fold:FwdE/GAPDH domain-like Superfamily:Glyceraldehyde-3-phosphate dehydrogenase-like, C-terminal domain Family:GAPDH-like 16 d1rm4a2 7.1 0 Fold:FwdE/GAPDH domain-like Superfamily:Glyceraldehyde-3-phosphate dehydrogenase-like, C-terminal domain Family:GAPDH-like 17 c1swiC_ 5.9 23 PDB header:leucine zipper Chain: C: PDB Molecule:gcn4p1; PDBTitle: gcn4-leucine zipper core mutant as n16a complexed with2 benzene 18 c2w2rA_ 5.2 63 PDB header:viral protein Chain: A: PDB Molecule:matrix protein; PDBTitle: structure of the vesicular stomatitis virus matrix protein

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