Secondary structure and disorder prediction

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Sequence		M	A	R	Y	F	R	R	R	K	F	C	R	F	T	A	E	G	V	Q	E	I	D	Y	K	D	I	A	T	L	K	N	Y	I	T	E	S	G	K	I	V	P	S	R	I	T	G	T	R	A	K	Y	Q	R	Q	L	A	R	A	I	K
Secondary structure
SS confidence
Disorder		?	?	?	?	?	?	?																														?		?							?
Disorder confidence
		.	.	.	.	.	.	.	.	.	70	.	.	.	.	.
Sequence		R	A	R	Y	L	S	L	L	P	Y	T	D	R	H	Q
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 1i94 chain R Region: 3 - 74 Aligned: 71 Modelled: 72 Confidence: 100.0% Identity: 42% Fold: DNA/RNA-binding 3-helical bundle Superfamily: Ribosomal protein S18 Family: Ribosomal protein S18 Phyre2 PDB 2uub chain R domain 1 Region: 8 - 74 Aligned: 67 Modelled: 67 Confidence: 99.9% Identity: 43% Fold: DNA/RNA-binding 3-helical bundle Superfamily: Ribosomal protein S18 Family: Ribosomal protein S18 Phyre2 PDB 2qal chain R domain 1 Region: 20 - 74 Aligned: 55 Modelled: 55 Confidence: 99.9% Identity: 100% Fold: DNA/RNA-binding 3-helical bundle Superfamily: Ribosomal protein S18 Family: Ribosomal protein S18 Phyre2 PDB 3df1 chain R Region: 20 - 74 Aligned: 55 Modelled: 55 Confidence: 99.9% Identity: 100% PDB header:ribosome Chain: R: PDB Molecule:30s ribosomal protein s18; PDBTitle: crystal structure of the bacterial ribosome from escherichia2 coli in complex with hygromycin b. this file contains the3 30s subunit of the first 70s ribosome, with hygromycin b4 bound. the entire crystal structure contains two 70s5 ribosomes. Phyre2 PDB 3bbn chain R Region: 19 - 75 Aligned: 57 Modelled: 57 Confidence: 99.9% Identity: 39% PDB header:ribosome Chain: R: PDB Molecule:ribosomal protein s18; PDBTitle: homology model for the spinach chloroplast 30s subunit2 fitted to 9.4a cryo-em map of the 70s chlororibosome. Phyre2 PDB 1g1x chain C Region: 19 - 71 Aligned: 46 Modelled: 53 Confidence: 99.8% Identity: 52% Fold: DNA/RNA-binding 3-helical bundle Superfamily: Ribosomal protein S18 Family: Ribosomal protein S18 Phyre2 PDB 2pmz chain G Region: 13 - 48 Aligned: 35 Modelled: 36 Confidence: 17.6% Identity: 17% PDB header:translation, transferase Chain: G: PDB Molecule:dna-directed rna polymerase subunit a"; PDBTitle: archaeal rna polymerase from sulfolobus solfataricus Phyre2 PDB 2ect chain A Region: 1 - 22 Aligned: 22 Modelled: 22 Confidence: 17.2% Identity: 5% PDB header:metal binding protein Chain: A: PDB Molecule:ring finger protein 126; PDBTitle: solution structure of the zinc finger, c3hc4 type (ring2 finger) domain of ring finger protein 126 Phyre2 PDB 2d8t chain A Region: 3 - 25 Aligned: 22 Modelled: 23 Confidence: 15.2% Identity: 18% PDB header:metal binding protein Chain: A: PDB Molecule:ring finger protein 146; PDBTitle: solution structure of the ring domain of the human ring2 finger protein 146 Phyre2 PDB 2csy chain A Region: 3 - 31 Aligned: 29 Modelled: 29 Confidence: 15.0% Identity: 14% PDB header:structural genomics, unknown function Chain: A: PDB Molecule:zinc finger protein 183-like 1; PDBTitle: solution structure of the ring domain of the zinc finger2 protein 183-like 1 Phyre2 PDB 3h0g chain A Region: 13 - 47 Aligned: 34 Modelled: 35 Confidence: 13.4% Identity: 21% PDB header:transcription Chain: A: PDB Molecule:dna-directed rna polymerase ii subunit rpb1; PDBTitle: rna polymerase ii from schizosaccharomyces pombe Phyre2 PDB 1iym chain A Region: 3 - 18 Aligned: 16 Modelled: 16 Confidence: 13.4% Identity: 13% Fold: RING/U-box Superfamily: RING/U-box Family: RING finger domain, C3HC4 Phyre2 PDB 2aam chain A Region: 48 - 72 Aligned: 25 Modelled: 25 Confidence: 12.3% Identity: 12% PDB header:hydrolase Chain: A: PDB Molecule:hypothetical protein tm1410; PDBTitle: crystal structure of a putative glycosidase (tm1410) from thermotoga2 maritima at 2.20 a resolution Phyre2 PDB 2aam chain A domain 1 Region: 48 - 72 Aligned: 25 Modelled: 25 Confidence: 12.3% Identity: 12% Fold: TIM beta/alpha-barrel Superfamily: (Trans)glycosidases Family: TM1410-like Phyre2 PDB 2k6x chain A Region: 49 - 70 Aligned: 22 Modelled: 22 Confidence: 12.0% Identity: 14% PDB header:transcription Chain: A: PDB Molecule:rna polymerase sigma factor rpod; PDBTitle: autoregulation of a group 1 bacterial sigma factor involves2 the formation of a region 1.1- induced compacted structure Phyre2 PDB 1chc chain A Region: 3 - 23 Aligned: 21 Modelled: 21 Confidence: 11.5% Identity: 19% Fold: RING/U-box Superfamily: RING/U-box Family: RING finger domain, C3HC4 Phyre2 PDB 2ecn chain A Region: 3 - 22 Aligned: 20 Modelled: 20 Confidence: 10.7% Identity: 10% PDB header:metal binding protein Chain: A: PDB Molecule:ring finger protein 141; PDBTitle: solution structure of the ring domain of the human ring2 finger protein 141 Phyre2 PDB 1twf chain A Region: 13 - 47 Aligned: 34 Modelled: 35 Confidence: 10.2% Identity: 21% Fold: beta and beta-prime subunits of DNA dependent RNA-polymerase Superfamily: beta and beta-prime subunits of DNA dependent RNA-polymerase Family: RNA-polymerase beta-prime Phyre2 PDB 2ep4 chain A Region: 3 - 23 Aligned: 21 Modelled: 21 Confidence: 9.6% Identity: 19% PDB header:protein binding Chain: A: PDB Molecule:ring finger protein 24; PDBTitle: solution structure of ring finger from human ring finger2 protein 24 Phyre2 PDB 2c2l chain A domain 2 Region: 8 - 37 Aligned: 30 Modelled: 30 Confidence: 8.6% Identity: 20% Fold: RING/U-box Superfamily: RING/U-box Family: U-box Phyre2 1 d1i94r_ 2 d2uubr1 3 d2qalr1 4 c3df1R_ 5 c3bbnR_ 6 d1g1xc_ 7 c2pmzG_ 8 c2ectA_ 9 c2d8tA_ 10 c2csyA_ 11 c3h0gA_ 12 d1iyma_ 13 c2aamA_ 14 d2aama1 15 c2k6xA_ 16 d1chca_ 17 c2ecnA_ 18 d1twfa_ 19 c2ep4A_ 20 d2c2la2 21 22 23 24 25 26 27 28 29 30 31 32

Detailed template information

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

1 d1i94r_ 100.0 42 Fold:DNA/RNA-binding 3-helical bundle Superfamily:Ribosomal protein S18 Family:Ribosomal protein S18 2 d2uubr1 99.9 43 Fold:DNA/RNA-binding 3-helical bundle Superfamily:Ribosomal protein S18 Family:Ribosomal protein S18 3 d2qalr1 99.9 100 Fold:DNA/RNA-binding 3-helical bundle Superfamily:Ribosomal protein S18 Family:Ribosomal protein S18 4 c3df1R_ 99.9 100 PDB header:ribosome Chain: R: PDB Molecule:30s ribosomal protein s18; PDBTitle: crystal structure of the bacterial ribosome from escherichia2 coli in complex with hygromycin b. this file contains the3 30s subunit of the first 70s ribosome, with hygromycin b4 bound. the entire crystal structure contains two 70s5 ribosomes. 5 c3bbnR_ 99.9 39 PDB header:ribosome Chain: R: PDB Molecule:ribosomal protein s18; PDBTitle: homology model for the spinach chloroplast 30s subunit2 fitted to 9.4a cryo-em map of the 70s chlororibosome. 6 d1g1xc_ 99.8 52 Fold:DNA/RNA-binding 3-helical bundle Superfamily:Ribosomal protein S18 Family:Ribosomal protein S18 7 c2pmzG_ 17.6 17 PDB header:translation, transferase Chain: G: PDB Molecule:dna-directed rna polymerase subunit a"; PDBTitle: archaeal rna polymerase from sulfolobus solfataricus 8 c2ectA_ 17.2 5 PDB header:metal binding protein Chain: A: PDB Molecule:ring finger protein 126; PDBTitle: solution structure of the zinc finger, c3hc4 type (ring2 finger) domain of ring finger protein 126 9 c2d8tA_ 15.2 18 PDB header:metal binding protein Chain: A: PDB Molecule:ring finger protein 146; PDBTitle: solution structure of the ring domain of the human ring2 finger protein 146 10 c2csyA_ 15.0 14 PDB header:structural genomics, unknown function Chain: A: PDB Molecule:zinc finger protein 183-like 1; PDBTitle: solution structure of the ring domain of the zinc finger2 protein 183-like 1 11 c3h0gA_ 13.4 21 PDB header:transcription Chain: A: PDB Molecule:dna-directed rna polymerase ii subunit rpb1; PDBTitle: rna polymerase ii from schizosaccharomyces pombe 12 d1iyma_ 13.4 13 Fold:RING/U-box Superfamily:RING/U-box Family:RING finger domain, C3HC4 13 c2aamA_ 12.3 12 PDB header:hydrolase Chain: A: PDB Molecule:hypothetical protein tm1410; PDBTitle: crystal structure of a putative glycosidase (tm1410) from thermotoga2 maritima at 2.20 a resolution 14 d2aama1 12.3 12 Fold:TIM beta/alpha-barrel Superfamily:(Trans)glycosidases Family:TM1410-like 15 c2k6xA_ 12.0 14 PDB header:transcription Chain: A: PDB Molecule:rna polymerase sigma factor rpod; PDBTitle: autoregulation of a group 1 bacterial sigma factor involves2 the formation of a region 1.1- induced compacted structure 16 d1chca_ 11.5 19 Fold:RING/U-box Superfamily:RING/U-box Family:RING finger domain, C3HC4 17 c2ecnA_ 10.7 10 PDB header:metal binding protein Chain: A: PDB Molecule:ring finger protein 141; PDBTitle: solution structure of the ring domain of the human ring2 finger protein 141 18 d1twfa_ 10.2 21 Fold:beta and beta-prime subunits of DNA dependent RNA-polymerase Superfamily:beta and beta-prime subunits of DNA dependent RNA-polymerase Family:RNA-polymerase beta-prime 19 c2ep4A_ 9.6 19 PDB header:protein binding Chain: A: PDB Molecule:ring finger protein 24; PDBTitle: solution structure of ring finger from human ring finger2 protein 24 20 d2c2la2 8.6 20 Fold:RING/U-box Superfamily:RING/U-box Family:U-box 21 c1d2vD_ not modelled 7.3 26 PDB header:oxidoreductase Chain: D: PDB Molecule:myeloperoxidase; PDBTitle: crystal structure of bromide-bound human myeloperoxidase isoform c at2 ph 5.5 22 c2vjfB_ not modelled 6.9 16 PDB header:ligase Chain: B: PDB Molecule:mdm4 protein; PDBTitle: crystal structure of the mdm2-mdmx ring domain heterodimer 23 d1g25a_ not modelled 6.7 10 Fold:RING/U-box Superfamily:RING/U-box Family:RING finger domain, C3HC4 24 c2hdpB_ not modelled 6.5 26 PDB header:ligase Chain: B: PDB Molecule:ubiquitin-protein ligase e3 mdm2; PDBTitle: solution structure of hdm2 ring finger domain 25 c2eclA_ not modelled 6.1 6 PDB header:metal binding protein Chain: A: PDB Molecule:ring-box protein 2; PDBTitle: solution structure of the ring domain of the human ring-box2 protein 2 26 c2kreA_ not modelled 5.7 19 PDB header:protein binding Chain: A: PDB Molecule:ubiquitin conjugation factor e4 b; PDBTitle: solution structure of e4b/ufd2a u-box domain 27 d2nn6c2 not modelled 5.5 21 Fold:Ribonuclease PH domain 2-like Superfamily:Ribonuclease PH domain 2-like Family:Ribonuclease PH domain 2-like 28 c2xeuA_ not modelled 5.5 9 PDB header:transcription Chain: A: PDB Molecule:ring finger protein 4; PDBTitle: ring domain 29 d1z84a1 not modelled 5.5 13 Fold:HIT-like Superfamily:HIT-like Family:Hexose-1-phosphate uridylyltransferase 30 d1g4yb_ not modelled 5.4 35 Fold:Small-conductance potassium channel Superfamily:Small-conductance potassium channel Family:Small-conductance potassium channel 31 c3ktsA_ not modelled 5.4 40 PDB header:transcriptional regulator Chain: A: PDB Molecule:glycerol uptake operon antiterminator regulatory protein; PDBTitle: crystal structure of glycerol uptake operon antiterminator regulatory2 protein from listeria monocytogenes str. 4b f2365 32 c2kizA_ not modelled 5.3 10 PDB header:metal binding protein Chain: A: PDB Molecule:e3 ubiquitin-protein ligase arkadia; PDBTitle: solution structure of arkadia ring-h2 finger domain

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