Secondary structure and disorder prediction

		1	.	.	.	.	.	.	.	.	10	.	.	.	.	.	.	.	.	.	20	.	.	.	.	.	.	.	.	.	30	.	.	.	.	.	.	.	.	.	40	.	.	.	.	.	.	.	.	.	50	.	.	.	.	.	.	.	.	.	60
Sequence		M	Q	F	K	V	Y	T	Y	K	R	E	S	R	Y	R	L	F	V	D	V	Q	S	D	I	I	D	T	P	G	R	R	M	V	I	P	L	A	S	A	R	L	L	S	D	K	V	S	R	E	L	Y	P	V	V	H	I	G	D	E	S
Secondary structure
SS confidence
Disorder		?	?	?																																		?	?				?	?	?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	70	.	.	.	.	.	.	.	.	.	80	.	.	.	.	.	.	.	.	.	90	.	.	.	.	.	.	.	.	.	100	.
Sequence		W	R	M	M	T	T	D	M	A	S	V	P	V	S	V	I	G	E	E	V	A	D	L	S	H	R	E	N	D	I	K	N	A	I	N	L	M	F	W	G	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 3vub chain A Region: 1 - 101 Aligned: 101 Modelled: 101 Confidence: 100.0% Identity: 100% Fold: SH3-like barrel Superfamily: Cell growth inhibitor/plasmid maintenance toxic component Family: CcdB Phyre2 PDB 3jrz chain A Region: 2 - 101 Aligned: 95 Modelled: 100 Confidence: 100.0% Identity: 42% PDB header:toxin Chain: A: PDB Molecule:ccdb; PDBTitle: ccdbvfi-formii-ph5.6 Phyre2 PDB 1ub4 chain A Region: 2 - 98 Aligned: 90 Modelled: 96 Confidence: 95.5% Identity: 13% Fold: SH3-like barrel Superfamily: Cell growth inhibitor/plasmid maintenance toxic component Family: Kid/PemK Phyre2 PDB 1m1f chain A Region: 3 - 99 Aligned: 92 Modelled: 97 Confidence: 90.4% Identity: 8% Fold: SH3-like barrel Superfamily: Cell growth inhibitor/plasmid maintenance toxic component Family: Kid/PemK Phyre2 PDB 1ne8 chain A Region: 3 - 98 Aligned: 91 Modelled: 96 Confidence: 89.9% Identity: 11% Fold: SH3-like barrel Superfamily: Cell growth inhibitor/plasmid maintenance toxic component Family: Kid/PemK Phyre2 PDB 1ify chain A Region: 83 - 101 Aligned: 19 Modelled: 19 Confidence: 29.8% Identity: 26% Fold: RuvA C-terminal domain-like Superfamily: UBA-like Family: UBA domain Phyre2 PDB 3l9v chain E Region: 51 - 100 Aligned: 39 Modelled: 50 Confidence: 28.9% Identity: 8% PDB header:oxidoreductase Chain: E: PDB Molecule:putative thiol-disulfide isomerase or thioredoxin; PDBTitle: crystal structure of salmonella enterica serovar typhimurium srga Phyre2 PDB 1fvk chain A Region: 51 - 99 Aligned: 38 Modelled: 49 Confidence: 24.4% Identity: 8% Fold: Thioredoxin fold Superfamily: Thioredoxin-like Family: DsbA-like Phyre2 PDB 1mof chain A Region: 74 - 98 Aligned: 25 Modelled: 25 Confidence: 17.8% Identity: 20% PDB header:viral protein Chain: A: PDB Molecule:moloney murine leukemia virus p15; PDBTitle: coat protein Phyre2 PDB 1y4m chain C Region: 74 - 98 Aligned: 25 Modelled: 25 Confidence: 17.1% Identity: 8% PDB header:membrane protein Chain: C: PDB Molecule:herv-frd_6p24.1 provirus ancestral env polyprotein; PDBTitle: crystal structure of human endogenous retrovirus herv-frd envelope2 protein (syncitin-2) Phyre2 PDB 2bwb chain A domain 1 Region: 83 - 100 Aligned: 18 Modelled: 18 Confidence: 16.5% Identity: 17% Fold: RuvA C-terminal domain-like Superfamily: UBA-like Family: UBA domain Phyre2 PDB 2ebo chain B Region: 73 - 98 Aligned: 26 Modelled: 26 Confidence: 16.0% Identity: 12% PDB header:envelope glycoprotein Chain: B: PDB Molecule:ebola virus envelope glycoprotein; PDBTitle: core structure of gp2 from ebola virus Phyre2 PDB 1wr1 chain B Region: 83 - 100 Aligned: 18 Modelled: 18 Confidence: 15.8% Identity: 17% PDB header:signaling protein Chain: B: PDB Molecule:ubiquitin-like protein dsk2; PDBTitle: the complex sturcture of dsk2p uba with ubiquitin Phyre2 PDB 1exb chain E Region: 53 - 89 Aligned: 37 Modelled: 37 Confidence: 13.5% Identity: 14% Fold: POZ domain Superfamily: POZ domain Family: Tetramerization domain of potassium channels Phyre2 PDB 2cwb chain A Region: 83 - 100 Aligned: 18 Modelled: 18 Confidence: 11.1% Identity: 39% PDB header:protein binding Chain: A: PDB Molecule:chimera of immunoglobulin g binding protein g PDBTitle: solution structure of the ubiquitin-associated domain of2 human bmsc-ubp and its complex with ubiquitin Phyre2 PDB 2wta chain A Region: 7 - 27 Aligned: 21 Modelled: 21 Confidence: 10.2% Identity: 19% PDB header:hydrolase Chain: A: PDB Molecule:nicotinamidase; PDBTitle: acinetobacter baumanii nicotinamidase pyrazinamidease Phyre2 PDB 2jy5 chain A Region: 83 - 100 Aligned: 18 Modelled: 18 Confidence: 9.7% Identity: 28% PDB header:signaling protein Chain: A: PDB Molecule:ubiquilin-1; PDBTitle: nmr structure of ubiquilin 1 uba domain Phyre2 PDB 3h93 chain A Region: 51 - 99 Aligned: 32 Modelled: 33 Confidence: 9.2% Identity: 9% PDB header:transcription regulator Chain: A: PDB Molecule:thiol:disulfide interchange protein dsba; PDBTitle: crystal structure of pseudomonas aeruginosa dsba Phyre2 PDB 2v8q chain A domain 1 Region: 1 - 22 Aligned: 19 Modelled: 22 Confidence: 8.7% Identity: 21% Fold: TBP-like Superfamily: KA1-like Family: Ssp2 C-terminal domain-like Phyre2 PDB 1q1v chain A Region: 81 - 100 Aligned: 20 Modelled: 20 Confidence: 8.6% Identity: 25% Fold: Another 3-helical bundle Superfamily: DEK C-terminal domain Family: DEK C-terminal domain Phyre2 1 d3vuba_ 2 c3jrzA_ 3 d1ub4a_ 4 d1m1fa_ 5 d1ne8a_ 6 d1ifya_ 7 c3l9vE_ 8 d1fvka_ 9 c1mofA_ 10 c1y4mC_ 11 d2bwba1 12 c2eboB_ 13 c1wr1B_ 14 d1exbe_ 15 c2cwbA_ 16 c2wtaA_ 17 c2jy5A_ 18 c3h93A_ 19 d2v8qa1 20 d1q1va_ 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44

Detailed template information

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

1 d3vuba_ 100.0 100 Fold:SH3-like barrel Superfamily:Cell growth inhibitor/plasmid maintenance toxic component Family:CcdB 2 c3jrzA_ 100.0 42 PDB header:toxin Chain: A: PDB Molecule:ccdb; PDBTitle: ccdbvfi-formii-ph5.6 3 d1ub4a_ 95.5 13 Fold:SH3-like barrel Superfamily:Cell growth inhibitor/plasmid maintenance toxic component Family:Kid/PemK 4 d1m1fa_ 90.4 8 Fold:SH3-like barrel Superfamily:Cell growth inhibitor/plasmid maintenance toxic component Family:Kid/PemK 5 d1ne8a_ 89.9 11 Fold:SH3-like barrel Superfamily:Cell growth inhibitor/plasmid maintenance toxic component Family:Kid/PemK 6 d1ifya_ 29.8 26 Fold:RuvA C-terminal domain-like Superfamily:UBA-like Family:UBA domain 7 c3l9vE_ 28.9 8 PDB header:oxidoreductase Chain: E: PDB Molecule:putative thiol-disulfide isomerase or thioredoxin; PDBTitle: crystal structure of salmonella enterica serovar typhimurium srga 8 d1fvka_ 24.4 8 Fold:Thioredoxin fold Superfamily:Thioredoxin-like Family:DsbA-like 9 c1mofA_ 17.8 20 PDB header:viral protein Chain: A: PDB Molecule:moloney murine leukemia virus p15; PDBTitle: coat protein 10 c1y4mC_ 17.1 8 PDB header:membrane protein Chain: C: PDB Molecule:herv-frd_6p24.1 provirus ancestral env polyprotein; PDBTitle: crystal structure of human endogenous retrovirus herv-frd envelope2 protein (syncitin-2) 11 d2bwba1 16.5 17 Fold:RuvA C-terminal domain-like Superfamily:UBA-like Family:UBA domain 12 c2eboB_ 16.0 12 PDB header:envelope glycoprotein Chain: B: PDB Molecule:ebola virus envelope glycoprotein; PDBTitle: core structure of gp2 from ebola virus 13 c1wr1B_ 15.8 17 PDB header:signaling protein Chain: B: PDB Molecule:ubiquitin-like protein dsk2; PDBTitle: the complex sturcture of dsk2p uba with ubiquitin 14 d1exbe_ 13.5 14 Fold:POZ domain Superfamily:POZ domain Family:Tetramerization domain of potassium channels 15 c2cwbA_ 11.1 39 PDB header:protein binding Chain: A: PDB Molecule:chimera of immunoglobulin g binding protein g PDBTitle: solution structure of the ubiquitin-associated domain of2 human bmsc-ubp and its complex with ubiquitin 16 c2wtaA_ 10.2 19 PDB header:hydrolase Chain: A: PDB Molecule:nicotinamidase; PDBTitle: acinetobacter baumanii nicotinamidase pyrazinamidease 17 c2jy5A_ 9.7 28 PDB header:signaling protein Chain: A: PDB Molecule:ubiquilin-1; PDBTitle: nmr structure of ubiquilin 1 uba domain 18 c3h93A_ 9.2 9 PDB header:transcription regulator Chain: A: PDB Molecule:thiol:disulfide interchange protein dsba; PDBTitle: crystal structure of pseudomonas aeruginosa dsba 19 d2v8qa1 8.7 21 Fold:TBP-like Superfamily:KA1-like Family:Ssp2 C-terminal domain-like 20 d1q1va_ 8.6 25 Fold:Another 3-helical bundle Superfamily:DEK C-terminal domain Family:DEK C-terminal domain 21 d3kvta_ not modelled 8.4 7 Fold:POZ domain Superfamily:POZ domain Family:Tetramerization domain of potassium channels 22 c1eboE_ not modelled 8.3 9 PDB header:viral protein Chain: E: PDB Molecule:ebola virus envelope protein chimera consisting PDBTitle: crystal structure of the ebola virus membrane-fusion2 subunit, gp2, from the envelope glycoprotein ectodomain 23 c3lqyA_ not modelled 7.7 24 PDB header:hydrolase Chain: A: PDB Molecule:putative isochorismatase hydrolase; PDBTitle: crystal structure of putative isochorismatase hydrolase from2 oleispira antarctica 24 d1nf9a_ not modelled 7.4 21 Fold:Isochorismatase-like hydrolases Superfamily:Isochorismatase-like hydrolases Family:Isochorismatase-like hydrolases 25 c3mcwA_ not modelled 7.1 18 PDB header:hydrolase Chain: A: PDB Molecule:putative hydrolase; PDBTitle: crystal structure of an a putative hydrolase of the isochorismatase2 family (cv_1320) from chromobacterium violaceum atcc 12472 at 1.06 a3 resolution 26 c2a67C_ not modelled 7.0 29 PDB header:structural genomics, unknown function Chain: C: PDB Molecule:isochorismatase family protein; PDBTitle: crystal structure of isochorismatase family protein 27 d1t1da_ not modelled 6.7 12 Fold:POZ domain Superfamily:POZ domain Family:Tetramerization domain of potassium channels 28 d1nn7a_ not modelled 6.7 12 Fold:POZ domain Superfamily:POZ domain Family:Tetramerization domain of potassium channels 29 c1hynQ_ not modelled 6.5 8 PDB header:membrane protein Chain: Q: PDB Molecule:band 3 anion transport protein; PDBTitle: crystal structure of the cytoplasmic domain of human2 erythrocyte band-3 protein 30 d1nbaa_ not modelled 6.3 6 Fold:Isochorismatase-like hydrolases Superfamily:Isochorismatase-like hydrolases Family:Isochorismatase-like hydrolases 31 c3feuA_ not modelled 6.2 13 PDB header:oxidoreductase Chain: A: PDB Molecule:putative lipoprotein; PDBTitle: crystal structure of dsba-like thioredoxin domain vf_a0457 from vibrio2 fischeri 32 d1dsxa_ not modelled 6.1 19 Fold:POZ domain Superfamily:POZ domain Family:Tetramerization domain of potassium channels 33 d1hynp_ not modelled 6.1 8 Fold:Phoshotransferase/anion transport protein Superfamily:Phoshotransferase/anion transport protein Family:Anion transport protein, cytoplasmic domain 34 d1b7yb4 not modelled 6.1 10 Fold:Ferredoxin-like Superfamily:Anticodon-binding domain of PheRS Family:Anticodon-binding domain of PheRS 35 d2qrda1 not modelled 5.8 20 Fold:TBP-like Superfamily:KA1-like Family:Ssp2 C-terminal domain-like 36 c1dpuA_ not modelled 5.7 14 PDB header:dna binding protein Chain: A: PDB Molecule:replication protein a (rpa32) c-terminal domain; PDBTitle: solution structure of the c-terminal domain of human rpa322 complexed with ung2(73-88) 37 d1dpua_ not modelled 5.7 14 Fold:DNA/RNA-binding 3-helical bundle Superfamily:"Winged helix" DNA-binding domain Family:C-terminal domain of RPA32 38 d1s1ga_ not modelled 5.7 15 Fold:POZ domain Superfamily:POZ domain Family:Tetramerization domain of potassium channels 39 c3oqpB_ not modelled 5.6 21 PDB header:hydrolase Chain: B: PDB Molecule:putative isochorismatase; PDBTitle: crystal structure of a putative isochorismatase (bxe_a0706) from2 burkholderia xenovorans lb400 at 1.22 a resolution 40 c2wsfH_ not modelled 5.4 32 PDB header:photosynthesis Chain: H: PDB Molecule:photosystem i reaction center subunit vi, PDBTitle: improved model of plant photosystem i 41 c3lw5H_ not modelled 5.4 28 PDB header:photosynthesis Chain: H: PDB Molecule:putative uncharacterized protein; PDBTitle: improved model of plant photosystem i 42 d1jjcb4 not modelled 5.4 10 Fold:Ferredoxin-like Superfamily:Anticodon-binding domain of PheRS Family:Anticodon-binding domain of PheRS 43 c2h0rD_ not modelled 5.3 42 PDB header:hydrolase Chain: D: PDB Molecule:nicotinamidase; PDBTitle: structure of the yeast nicotinamidase pnc1p 44 d1ev7a_ not modelled 5.2 13 Fold:Restriction endonuclease-like Superfamily:Restriction endonuclease-like Family:Restriction endonuclease NaeI

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

---

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