Secondary structure and disorder prediction

		1	.	.	.	.	.	.	.	.	10	.	.	.	.	.	.	.	.	.	20	.	.	.	.	.	.	.	.	.	30	.	.	.	.	.	.	.	.	.	40	.	.	.	.	.	.	.	.	.	50	.	.	.	.	.	.	.	.	.	60
Sequence		M	S	M	Q	D	P	I	A	D	M	L	T	R	I	R	N	G	Q	A	A	N	K	A	A	V	T	M	P	S	S	K	L	K	V	A	I	A	N	V	L	K	E	E	G	F	I	E	D	F	K	V	E	G	D	T	K	P	E	L	E
Secondary structure
SS confidence
Disorder		?	?	?	?	?																																									?						?		?
Disorder confidence
		.	.	.	.	.	.	.	.	.	70	.	.	.	.	.	.	.	.	.	80	.	.	.	.	.	.	.	.	.	90	.	.	.	.	.	.	.	.	.	100	.	.	.	.	.	.	.	.	.	110	.	.	.	.	.	.	.	.	.	120
Sequence		L	T	L	K	Y	F	Q	G	K	A	V	V	E	S	I	Q	R	V	S	R	P	G	L	R	I	Y	K	R	K	D	E	L	P	K	V	M	A	G	L	G	I	A	V	V	S	T	S	K	G	V	M	T	D	R	A	A	R	Q	A	G
Secondary structure
SS confidence
Disorder														?	?				?					?																																				?
Disorder confidence
		.	.	.	.	.	.	.	.	.	130
Sequence		L	G	G	E	I	I	C	Y	V	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 1sei chain A Region: 3 - 129 Aligned: 127 Modelled: 127 Confidence: 100.0% Identity: 51% Fold: Ribosomal protein S8 Superfamily: Ribosomal protein S8 Family: Ribosomal protein S8 Phyre2 PDB 2gy9 chain H domain 1 Region: 4 - 129 Aligned: 126 Modelled: 126 Confidence: 100.0% Identity: 100% Fold: Ribosomal protein S8 Superfamily: Ribosomal protein S8 Family: Ribosomal protein S8 Phyre2 PDB 3rf2 chain A Region: 4 - 129 Aligned: 126 Modelled: 126 Confidence: 100.0% Identity: 50% PDB header:ribosomal protein Chain: A: PDB Molecule:30s ribosomal protein s8; PDBTitle: crystal structure of 30s ribosomal protein s8 from aquifex aeolicus Phyre2 PDB 1i94 chain H Region: 3 - 129 Aligned: 127 Modelled: 127 Confidence: 100.0% Identity: 49% Fold: Ribosomal protein S8 Superfamily: Ribosomal protein S8 Family: Ribosomal protein S8 Phyre2 PDB 1i6u chain A Region: 2 - 129 Aligned: 125 Modelled: 128 Confidence: 100.0% Identity: 28% Fold: Ribosomal protein S8 Superfamily: Ribosomal protein S8 Family: Ribosomal protein S8 Phyre2 PDB 1an7 chain A Region: 4 - 129 Aligned: 126 Modelled: 126 Confidence: 100.0% Identity: 49% Fold: Ribosomal protein S8 Superfamily: Ribosomal protein S8 Family: Ribosomal protein S8 Phyre2 PDB 3bbn chain H Region: 1 - 129 Aligned: 128 Modelled: 129 Confidence: 100.0% Identity: 45% PDB header:ribosome Chain: H: PDB Molecule:ribosomal protein s8; PDBTitle: homology model for the spinach chloroplast 30s subunit2 fitted to 9.4a cryo-em map of the 70s chlororibosome. Phyre2 PDB 1s1h chain H Region: 4 - 129 Aligned: 123 Modelled: 126 Confidence: 100.0% Identity: 25% PDB header:ribosome Chain: H: PDB Molecule:40s ribosomal protein s22; PDBTitle: structure of the ribosomal 80s-eef2-sordarin complex from2 yeast obtained by docking atomic models for rna and protein3 components into a 11.7 a cryo-em map. this file, 1s1h,4 contains 40s subunit. the 60s ribosomal subunit is in file5 1s1i. Phyre2 PDB 2xzn chain H Region: 2 - 129 Aligned: 125 Modelled: 128 Confidence: 100.0% Identity: 22% PDB header:ribosome Chain: H: PDB Molecule:ribosomal protein s8 containing protein; 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 2 Phyre2 PDB 2zqe chain A Region: 1 - 64 Aligned: 64 Modelled: 64 Confidence: 25.2% Identity: 13% PDB header:dna binding protein Chain: A: PDB Molecule:muts2 protein; PDBTitle: crystal structure of the smr domain of thermus thermophilus muts2 Phyre2 PDB 2k19 chain A Region: 5 - 46 Aligned: 42 Modelled: 42 Confidence: 17.0% Identity: 14% PDB header:antimicrobial protein Chain: A: PDB Molecule:putative piscicolin 126 immunity protein; PDBTitle: nmr solution structure of pisi Phyre2 PDB 2hgc chain A Region: 37 - 54 Aligned: 18 Modelled: 18 Confidence: 16.5% Identity: 39% PDB header:structural genomics, unknown function Chain: A: PDB Molecule:yjcq protein; PDBTitle: solution nmr structure of the yjcq protein from bacillus2 subtilis. northeast structural genomics target sr346. Phyre2 PDB 2hgc chain A domain 1 Region: 37 - 54 Aligned: 18 Modelled: 18 Confidence: 16.5% Identity: 39% Fold: DNA/RNA-binding 3-helical bundle Superfamily: "Winged helix" DNA-binding domain Family: YjcQ-like Phyre2 PDB 2zrr chain A Region: 4 - 46 Aligned: 43 Modelled: 43 Confidence: 15.3% Identity: 16% PDB header:antimicrobial protein Chain: A: PDB Molecule:mundticin ks immunity protein; PDBTitle: crystal structure of an immunity protein that contributes2 to the self-protection of bacteriocin-producing3 enterococcus mundtii 15-1a Phyre2 PDB 2dk5 chain A domain 1 Region: 63 - 87 Aligned: 25 Modelled: 25 Confidence: 10.7% Identity: 20% Fold: DNA/RNA-binding 3-helical bundle Superfamily: "Winged helix" DNA-binding domain Family: RPO3F domain-like Phyre2 PDB 1a6s chain A Region: 28 - 48 Aligned: 21 Modelled: 21 Confidence: 10.5% Identity: 33% Fold: Retroviral matrix proteins Superfamily: Retroviral matrix proteins Family: GAG polyprotein M-domain Phyre2 PDB 1khi chain A domain 2 Region: 1 - 27 Aligned: 26 Modelled: 27 Confidence: 10.3% Identity: 12% Fold: OB-fold Superfamily: Nucleic acid-binding proteins Family: Cold shock DNA-binding domain-like Phyre2 PDB 2vkc chain A Region: 30 - 64 Aligned: 31 Modelled: 35 Confidence: 7.8% Identity: 26% PDB header:hydrolase Chain: A: PDB Molecule:nedd4-binding protein 2; PDBTitle: solution structure of the b3bp smr domain Phyre2 PDB 3ff4 chain A Region: 30 - 126 Aligned: 72 Modelled: 76 Confidence: 7.6% Identity: 21% PDB header:structural genomics, unknown function Chain: A: PDB Molecule:uncharacterized protein; PDBTitle: crystal structure of uncharacterized protein chu_1412 Phyre2 PDB 2qlv chain F Region: 3 - 60 Aligned: 57 Modelled: 58 Confidence: 7.4% Identity: 14% PDB header:transferase/protein binding Chain: F: PDB Molecule:nuclear protein snf4; PDBTitle: crystal structure of the heterotrimer core of the s.2 cerevisiae ampk homolog snf1 Phyre2 1 d1seia_ 2 d2gy9h1 3 c3rf2A_ 4 d1i94h_ 5 d1i6ua_ 6 d1an7a_ 7 c3bbnH_ 8 c1s1hH_ 9 c2xznH_ 10 c2zqeA_ 11 c2k19A_ 12 c2hgcA_ 13 d2hgca1 14 c2zrrA_ 15 d2dk5a1 16 d1a6sa_ 17 d1khia2 18 c2vkcA_ 19 c3ff4A_ 20 c2qlvF_ 21 22 23

Detailed template information

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

1 d1seia_ 100.0 51 Fold:Ribosomal protein S8 Superfamily:Ribosomal protein S8 Family:Ribosomal protein S8 2 d2gy9h1 100.0 100 Fold:Ribosomal protein S8 Superfamily:Ribosomal protein S8 Family:Ribosomal protein S8 3 c3rf2A_ 100.0 50 PDB header:ribosomal protein Chain: A: PDB Molecule:30s ribosomal protein s8; PDBTitle: crystal structure of 30s ribosomal protein s8 from aquifex aeolicus 4 d1i94h_ 100.0 49 Fold:Ribosomal protein S8 Superfamily:Ribosomal protein S8 Family:Ribosomal protein S8 5 d1i6ua_ 100.0 28 Fold:Ribosomal protein S8 Superfamily:Ribosomal protein S8 Family:Ribosomal protein S8 6 d1an7a_ 100.0 49 Fold:Ribosomal protein S8 Superfamily:Ribosomal protein S8 Family:Ribosomal protein S8 7 c3bbnH_ 100.0 45 PDB header:ribosome Chain: H: PDB Molecule:ribosomal protein s8; PDBTitle: homology model for the spinach chloroplast 30s subunit2 fitted to 9.4a cryo-em map of the 70s chlororibosome. 8 c1s1hH_ 100.0 25 PDB header:ribosome Chain: H: PDB Molecule:40s ribosomal protein s22; PDBTitle: structure of the ribosomal 80s-eef2-sordarin complex from2 yeast obtained by docking atomic models for rna and protein3 components into a 11.7 a cryo-em map. this file, 1s1h,4 contains 40s subunit. the 60s ribosomal subunit is in file5 1s1i. 9 c2xznH_ 100.0 22 PDB header:ribosome Chain: H: PDB Molecule:ribosomal protein s8 containing protein; 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 2 10 c2zqeA_ 25.2 13 PDB header:dna binding protein Chain: A: PDB Molecule:muts2 protein; PDBTitle: crystal structure of the smr domain of thermus thermophilus muts2 11 c2k19A_ 17.0 14 PDB header:antimicrobial protein Chain: A: PDB Molecule:putative piscicolin 126 immunity protein; PDBTitle: nmr solution structure of pisi 12 c2hgcA_ 16.5 39 PDB header:structural genomics, unknown function Chain: A: PDB Molecule:yjcq protein; PDBTitle: solution nmr structure of the yjcq protein from bacillus2 subtilis. northeast structural genomics target sr346. 13 d2hgca1 16.5 39 Fold:DNA/RNA-binding 3-helical bundle Superfamily:"Winged helix" DNA-binding domain Family:YjcQ-like 14 c2zrrA_ 15.3 16 PDB header:antimicrobial protein Chain: A: PDB Molecule:mundticin ks immunity protein; PDBTitle: crystal structure of an immunity protein that contributes2 to the self-protection of bacteriocin-producing3 enterococcus mundtii 15-1a 15 d2dk5a1 10.7 20 Fold:DNA/RNA-binding 3-helical bundle Superfamily:"Winged helix" DNA-binding domain Family:RPO3F domain-like 16 d1a6sa_ 10.5 33 Fold:Retroviral matrix proteins Superfamily:Retroviral matrix proteins Family:GAG polyprotein M-domain 17 d1khia2 10.3 12 Fold:OB-fold Superfamily:Nucleic acid-binding proteins Family:Cold shock DNA-binding domain-like 18 c2vkcA_ 7.8 26 PDB header:hydrolase Chain: A: PDB Molecule:nedd4-binding protein 2; PDBTitle: solution structure of the b3bp smr domain 19 c3ff4A_ 7.6 21 PDB header:structural genomics, unknown function Chain: A: PDB Molecule:uncharacterized protein; PDBTitle: crystal structure of uncharacterized protein chu_1412 20 c2qlvF_ 7.4 14 PDB header:transferase/protein binding Chain: F: PDB Molecule:nuclear protein snf4; PDBTitle: crystal structure of the heterotrimer core of the s.2 cerevisiae ampk homolog snf1 21 d2d9ia1 not modelled 5.7 26 Fold:IF3-like Superfamily:SMR domain-like Family:Smr domain 22 c3mioA_ not modelled 5.4 15 PDB header:lyase Chain: A: PDB Molecule:3,4-dihydroxy-2-butanone 4-phosphate synthase; PDBTitle: crystal structure of 3,4-dihydroxy-2-butanone 4-phosphate synthase2 domain from mycobacterium tuberculosis at ph 6.00 23 c2e1nA_ not modelled 5.3 11 PDB header:circadian clock protein Chain: A: PDB Molecule:pex; PDBTitle: crystal structure of the cyanobacterium circadian clock modifier pex

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