Secondary structure and disorder prediction

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Sequence		M	S	L	S	T	E	A	T	A	K	I	V	S	E	F	G	R	D	A	N	D	T	G	S	T	E	V	Q	V	A	L	L	T	A	Q	I	N	H	L	Q	G	H	F	A	E	H	K	K	D	H	H	S	R	R	G	L	L	R	M	V
Secondary structure
SS confidence
Disorder		?	?	?	?															?	?	?	?																									?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	70	.	.	.	.	.	.	.	.	.	80	.	.	.	.	.	.	.	.	.
Sequence		S	Q	R	R	K	L	L	D	Y	L	K	R	K	D	V	A	R	Y	T	Q	L	I	E	R	L	G	L	R	R
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 1vs5 chain O domain 1 Region: 2 - 89 Aligned: 88 Modelled: 88 Confidence: 100.0% Identity: 99% Fold: S15/NS1 RNA-binding domain Superfamily: S15/NS1 RNA-binding domain Family: Ribosomal protein S15 Phyre2 PDB 1g1x chain B Region: 2 - 88 Aligned: 87 Modelled: 87 Confidence: 100.0% Identity: 59% Fold: S15/NS1 RNA-binding domain Superfamily: S15/NS1 RNA-binding domain Family: Ribosomal protein S15 Phyre2 PDB 1a32 chain A Region: 3 - 87 Aligned: 85 Modelled: 85 Confidence: 100.0% Identity: 59% Fold: S15/NS1 RNA-binding domain Superfamily: S15/NS1 RNA-binding domain Family: Ribosomal protein S15 Phyre2 PDB 3ulw chain A Region: 3 - 87 Aligned: 85 Modelled: 85 Confidence: 100.0% Identity: 54% PDB header:ribosomal protein Chain: A: PDB Molecule:30s ribosomal protein s15; PDBTitle: 30s ribosomal protein s15 from campylobacter jejuni Phyre2 PDB 1kuq chain A Region: 5 - 87 Aligned: 83 Modelled: 83 Confidence: 100.0% Identity: 61% Fold: S15/NS1 RNA-binding domain Superfamily: S15/NS1 RNA-binding domain Family: Ribosomal protein S15 Phyre2 PDB 3bbn chain O Region: 7 - 89 Aligned: 83 Modelled: 83 Confidence: 100.0% Identity: 35% PDB header:ribosome Chain: O: PDB Molecule:ribosomal protein s15; PDBTitle: homology model for the spinach chloroplast 30s subunit2 fitted to 9.4a cryo-em map of the 70s chlororibosome. Phyre2 PDB 2xzm chain O Region: 12 - 74 Aligned: 63 Modelled: 63 Confidence: 99.4% Identity: 16% PDB header:ribosome Chain: O: PDB Molecule:rps13e; 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 Phyre2 PDB 3izb chain O Region: 12 - 87 Aligned: 76 Modelled: 76 Confidence: 99.4% Identity: 11% PDB header:ribosome Chain: O: PDB Molecule:40s ribosomal protein rps13 (s15p); PDBTitle: localization of the small subunit ribosomal proteins into a 6.1 a2 cryo-em map of saccharomyces cerevisiae translating 80s ribosome Phyre2 PDB 1ysh chain E Region: 2 - 74 Aligned: 69 Modelled: 73 Confidence: 98.3% Identity: 20% PDB header:structural protein/rna Chain: E: PDB Molecule:40s ribosomal protein s13; PDBTitle: localization and dynamic behavior of ribosomal protein l30e Phyre2 PDB 1s1h chain O Region: 12 - 69 Aligned: 58 Modelled: 58 Confidence: 96.6% Identity: 14% PDB header:ribosome Chain: O: PDB Molecule:40s ribosomal protein s13; 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 1y0u chain A Region: 63 - 87 Aligned: 23 Modelled: 25 Confidence: 32.2% Identity: 30% Fold: DNA/RNA-binding 3-helical bundle Superfamily: "Winged helix" DNA-binding domain Family: ArsR-like transcriptional regulators Phyre2 PDB 2y50 chain A Region: 64 - 86 Aligned: 23 Modelled: 23 Confidence: 25.8% Identity: 26% PDB header:hydrolase Chain: A: PDB Molecule:collagenase; PDBTitle: crystal structure of collagenase g from clostridium2 histolyticum at 2.80 angstrom resolution Phyre2 PDB 2ke4 chain A Region: 9 - 46 Aligned: 38 Modelled: 38 Confidence: 18.8% Identity: 21% PDB header:membrane protein Chain: A: PDB Molecule:cdc42-interacting protein 4; PDBTitle: the nmr structure of the tc10 and cdc42 interacting domain2 of cip4 Phyre2 PDB 2zvn chain F Region: 27 - 71 Aligned: 45 Modelled: 45 Confidence: 17.0% Identity: 16% PDB header:signaling protein/transcription Chain: F: PDB Molecule:nf-kappa-b essential modulator; PDBTitle: nemo cozi domain incomplex with diubiquitin in p2121212 space group Phyre2 PDB 3f1i chain H Region: 28 - 86 Aligned: 59 Modelled: 59 Confidence: 12.4% Identity: 17% PDB header:protein binding Chain: H: PDB Molecule:hepatocyte growth factor-regulated tyrosine kinase PDBTitle: human escrt-0 core complex Phyre2 PDB 2vog chain B Region: 25 - 30 Aligned: 6 Modelled: 6 Confidence: 8.7% Identity: 67% PDB header:apoptosis Chain: B: PDB Molecule:bcl-2-modifying factor; PDBTitle: structure of mouse a1 bound to the bmf bh3-domain Phyre2 PDB 2v4h chain A Region: 28 - 71 Aligned: 44 Modelled: 44 Confidence: 8.1% Identity: 16% PDB header:transcription Chain: A: PDB Molecule:nf-kappa-b essential modulator; PDBTitle: nemo cc2-lz domain - 1d5 darpin complex Phyre2 PDB 1sxj chain D domain 1 Region: 1 - 39 Aligned: 39 Modelled: 39 Confidence: 7.1% Identity: 18% Fold: post-AAA+ oligomerization domain-like Superfamily: post-AAA+ oligomerization domain-like Family: DNA polymerase III clamp loader subunits, C-terminal domain Phyre2 PDB 2f5x chain C Region: 72 - 89 Aligned: 18 Modelled: 18 Confidence: 6.7% Identity: 17% PDB header:transport protein Chain: C: PDB Molecule:bugd; PDBTitle: structure of periplasmic binding protein bugd Phyre2 PDB 3nqw chain B Region: 5 - 87 Aligned: 77 Modelled: 83 Confidence: 6.7% Identity: 12% PDB header:hydrolase Chain: B: PDB Molecule:cg11900; PDBTitle: a metazoan ortholog of spot hydrolyzes ppgpp and plays a role in2 starvation responses Phyre2 1 d1vs5o1 2 d1g1xb_ 3 d1a32a_ 4 c3ulwA_ 5 d1kuqa_ 6 c3bbnO_ 7 c2xzmO_ 8 c3izbO_ 9 c1yshE_ 10 c1s1hO_ 11 d1y0ua_ 12 c2y50A_ 13 c2ke4A_ 14 c2zvnF_ 15 c3f1iH_ 16 c2vogB_ 17 c2v4hA_ 18 d1sxjd1 19 c2f5xC_ 20 c3nqwB_ 21 22 23 24 25 26

Detailed template information

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

1 d1vs5o1 100.0 99 Fold:S15/NS1 RNA-binding domain Superfamily:S15/NS1 RNA-binding domain Family:Ribosomal protein S15 2 d1g1xb_ 100.0 59 Fold:S15/NS1 RNA-binding domain Superfamily:S15/NS1 RNA-binding domain Family:Ribosomal protein S15 3 d1a32a_ 100.0 59 Fold:S15/NS1 RNA-binding domain Superfamily:S15/NS1 RNA-binding domain Family:Ribosomal protein S15 4 c3ulwA_ 100.0 54 PDB header:ribosomal protein Chain: A: PDB Molecule:30s ribosomal protein s15; PDBTitle: 30s ribosomal protein s15 from campylobacter jejuni 5 d1kuqa_ 100.0 61 Fold:S15/NS1 RNA-binding domain Superfamily:S15/NS1 RNA-binding domain Family:Ribosomal protein S15 6 c3bbnO_ 100.0 35 PDB header:ribosome Chain: O: PDB Molecule:ribosomal protein s15; PDBTitle: homology model for the spinach chloroplast 30s subunit2 fitted to 9.4a cryo-em map of the 70s chlororibosome. 7 c2xzmO_ 99.4 16 PDB header:ribosome Chain: O: PDB Molecule:rps13e; 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 8 c3izbO_ 99.4 11 PDB header:ribosome Chain: O: PDB Molecule:40s ribosomal protein rps13 (s15p); PDBTitle: localization of the small subunit ribosomal proteins into a 6.1 a2 cryo-em map of saccharomyces cerevisiae translating 80s ribosome 9 c1yshE_ 98.3 20 PDB header:structural protein/rna Chain: E: PDB Molecule:40s ribosomal protein s13; PDBTitle: localization and dynamic behavior of ribosomal protein l30e 10 c1s1hO_ 96.6 14 PDB header:ribosome Chain: O: PDB Molecule:40s ribosomal protein s13; 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. 11 d1y0ua_ 32.2 30 Fold:DNA/RNA-binding 3-helical bundle Superfamily:"Winged helix" DNA-binding domain Family:ArsR-like transcriptional regulators 12 c2y50A_ 25.8 26 PDB header:hydrolase Chain: A: PDB Molecule:collagenase; PDBTitle: crystal structure of collagenase g from clostridium2 histolyticum at 2.80 angstrom resolution 13 c2ke4A_ 18.8 21 PDB header:membrane protein Chain: A: PDB Molecule:cdc42-interacting protein 4; PDBTitle: the nmr structure of the tc10 and cdc42 interacting domain2 of cip4 14 c2zvnF_ 17.0 16 PDB header:signaling protein/transcription Chain: F: PDB Molecule:nf-kappa-b essential modulator; PDBTitle: nemo cozi domain incomplex with diubiquitin in p2121212 space group 15 c3f1iH_ 12.4 17 PDB header:protein binding Chain: H: PDB Molecule:hepatocyte growth factor-regulated tyrosine kinase PDBTitle: human escrt-0 core complex 16 c2vogB_ 8.7 67 PDB header:apoptosis Chain: B: PDB Molecule:bcl-2-modifying factor; PDBTitle: structure of mouse a1 bound to the bmf bh3-domain 17 c2v4hA_ 8.1 16 PDB header:transcription Chain: A: PDB Molecule:nf-kappa-b essential modulator; PDBTitle: nemo cc2-lz domain - 1d5 darpin complex 18 d1sxjd1 7.1 18 Fold:post-AAA+ oligomerization domain-like Superfamily:post-AAA+ oligomerization domain-like Family:DNA polymerase III clamp loader subunits, C-terminal domain 19 c2f5xC_ 6.7 17 PDB header:transport protein Chain: C: PDB Molecule:bugd; PDBTitle: structure of periplasmic binding protein bugd 20 c3nqwB_ 6.7 12 PDB header:hydrolase Chain: B: PDB Molecule:cg11900; PDBTitle: a metazoan ortholog of spot hydrolyzes ppgpp and plays a role in2 starvation responses 21 c2pnvA_ not modelled 5.5 18 PDB header:membrane protein Chain: A: PDB Molecule:small conductance calcium-activated potassium PDBTitle: crystal structure of the leucine zipper domain of small-2 conductance ca2+-activated k+ (skca) channel from rattus3 norvegicus 22 c3cuoB_ not modelled 5.5 24 PDB header:transcription regulator Chain: B: PDB Molecule:uncharacterized hth-type transcriptional regulator ygav; PDBTitle: crystal structure of the predicted dna-binding transcriptional2 regulator from e. coli 23 c1m7lA_ not modelled 5.5 43 PDB header:sugar binding protein Chain: A: PDB Molecule:pulmonary surfactant-associated protein d; PDBTitle: solution structure of the coiled-coil trimerization domain2 from lung surfactant protein d 24 d3crda_ not modelled 5.3 20 Fold:DEATH domain Superfamily:DEATH domain Family:Caspase recruitment domain, CARD 25 d1biaa1 not modelled 5.3 30 Fold:DNA/RNA-binding 3-helical bundle Superfamily:"Winged helix" DNA-binding domain Family:Biotin repressor-like 26 c2bmmA_ not modelled 5.2 6 PDB header:oxygen storage/transport Chain: A: PDB Molecule:thermostable hemoglobin from thermobifida fusca; PDBTitle: x-ray structure of a novel thermostable hemoglobin from the2 actinobacterium thermobifida fusca

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