Secondary structure and disorder prediction

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Sequence		M	F	A	G	L	P	S	L	T	H	E	Q	Q	Q	K	A	V	E	R	I	Q	E	L	M	A	Q	G	M	S	S	G	Q	A	I	A	L	V	A	E	E	L	R	A	N	H	S	G	E	R	I	V	A	R	F	E	D	E	D	E
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 1wi9 chain A Region: 13 - 31 Aligned: 19 Modelled: 19 Confidence: 68.9% Identity: 42% Fold: DNA/RNA-binding 3-helical bundle Superfamily: "Winged helix" DNA-binding domain Family: PCI domain (PINT motif) Phyre2 PDB 1svd chain M domain 1 Region: 2 - 27 Aligned: 23 Modelled: 23 Confidence: 32.2% Identity: 30% Fold: RuBisCO, small subunit Superfamily: RuBisCO, small subunit Family: RuBisCO, small subunit Phyre2 PDB 1iwg chain A domain 4 Region: 25 - 39 Aligned: 15 Modelled: 15 Confidence: 28.9% Identity: 40% Fold: Ferredoxin-like Superfamily: Multidrug efflux transporter AcrB pore domain; PN1, PN2, PC1 and PC2 subdomains Family: Multidrug efflux transporter AcrB pore domain; PN1, PN2, PC1 and PC2 subdomains Phyre2 PDB 1rbl chain I Region: 2 - 27 Aligned: 23 Modelled: 23 Confidence: 28.8% Identity: 30% Fold: RuBisCO, small subunit Superfamily: RuBisCO, small subunit Family: RuBisCO, small subunit Phyre2 PDB 3m20 chain A Region: 5 - 26 Aligned: 22 Modelled: 22 Confidence: 26.0% Identity: 27% PDB header:isomerase Chain: A: PDB Molecule:4-oxalocrotonate tautomerase, putative; PDBTitle: crystal structure of dmpi from archaeoglobus fulgidus determined to2 2.37 angstroms resolution Phyre2 PDB 1uzh chain C domain 1 Region: 2 - 27 Aligned: 23 Modelled: 23 Confidence: 22.5% Identity: 30% Fold: RuBisCO, small subunit Superfamily: RuBisCO, small subunit Family: RuBisCO, small subunit Phyre2 PDB 2jnh chain A Region: 19 - 35 Aligned: 17 Modelled: 17 Confidence: 22.4% Identity: 24% PDB header:ligase Chain: A: PDB Molecule:e3 ubiquitin-protein ligase cbl-b; PDBTitle: solution structure of the uba domain from cbl-b Phyre2 PDB 1ir1 chain S Region: 2 - 27 Aligned: 23 Modelled: 26 Confidence: 21.3% Identity: 22% Fold: RuBisCO, small subunit Superfamily: RuBisCO, small subunit Family: RuBisCO, small subunit Phyre2 PDB 1bco chain A domain 1 Region: 43 - 58 Aligned: 16 Modelled: 16 Confidence: 20.5% Identity: 25% Fold: mu transposase, C-terminal domain Superfamily: mu transposase, C-terminal domain Family: mu transposase, C-terminal domain Phyre2 PDB 3itf chain A Region: 1 - 26 Aligned: 21 Modelled: 20 Confidence: 19.9% Identity: 38% PDB header:signaling protein Chain: A: PDB Molecule:periplasmic adaptor protein cpxp; PDBTitle: structural basis for the inhibitory function of the cpxp adaptor2 protein Phyre2 PDB 2kjw chain A Region: 1 - 27 Aligned: 27 Modelled: 27 Confidence: 18.0% Identity: 22% PDB header:ribosomal protein Chain: A: PDB Molecule:30s ribosomal protein s6; PDBTitle: solution structure and backbone dynamics of the permutant2 p54-55 Phyre2 PDB 2r9i chain A Region: 15 - 35 Aligned: 21 Modelled: 21 Confidence: 16.9% Identity: 33% PDB header:structural genomics, unknown function Chain: A: PDB Molecule:putative phage capsid protein; PDBTitle: crystal structure of putative phage capsid protein domain from2 corynebacterium diphtheriae Phyre2 PDB 2d9s chain A Region: 19 - 35 Aligned: 17 Modelled: 17 Confidence: 16.1% Identity: 35% PDB header:ligase Chain: A: PDB Molecule:cbl e3 ubiquitin protein ligase; PDBTitle: solution structure of rsgi ruh-049, a uba domain from mouse2 cdna Phyre2 PDB 2g3q chain A domain 1 Region: 18 - 35 Aligned: 18 Modelled: 18 Confidence: 15.8% Identity: 22% Fold: RuvA C-terminal domain-like Superfamily: UBA-like Family: UBA domain Phyre2 PDB 2rd0 chain A Region: 3 - 48 Aligned: 43 Modelled: 46 Confidence: 15.3% Identity: 21% PDB header:transferase/oncoprotein Chain: A: PDB Molecule:phosphatidylinositol-4,5-bisphosphate 3-kinase catalytic PDBTitle: structure of a human p110alpha/p85alpha complex Phyre2 PDB 3gyu chain A Region: 4 - 22 Aligned: 19 Modelled: 19 Confidence: 14.7% Identity: 21% PDB header:transcription Chain: A: PDB Molecule:nuclear hormone receptor of the steroid/thyroid PDBTitle: nuclear receptor daf-12 from parasitic nematode2 strongyloides stercoralis in complex with its physiological3 ligand dafachronic acid delta 7 Phyre2 PDB 2do6 chain A Region: 19 - 35 Aligned: 17 Modelled: 17 Confidence: 14.3% Identity: 24% PDB header:ligase Chain: A: PDB Molecule:e3 ubiquitin-protein ligase cbl-b; PDBTitle: solution structure of rsgi ruh-065, a uba domain from human2 cdna Phyre2 PDB 1fse chain A Region: 6 - 32 Aligned: 22 Modelled: 27 Confidence: 13.9% Identity: 27% Fold: DNA/RNA-binding 3-helical bundle Superfamily: C-terminal effector domain of the bipartite response regulators Family: GerE-like (LuxR/UhpA family of transcriptional regulators) Phyre2 PDB 3g0t chain A Region: 5 - 27 Aligned: 23 Modelled: 23 Confidence: 11.7% Identity: 30% PDB header:transferase Chain: A: PDB Molecule:putative aminotransferase; PDBTitle: crystal structure of putative aspartate aminotransferase (np_905498.1)2 from porphyromonas gingivalis w83 at 1.75 a resolution Phyre2 PDB 1gyx chain A Region: 8 - 26 Aligned: 19 Modelled: 19 Confidence: 11.4% Identity: 16% Fold: Tautomerase/MIF Superfamily: Tautomerase/MIF Family: 4-oxalocrotonate tautomerase-like Phyre2 1 d1wi9a_ 2 d1svdm1 3 d1iwga4 4 d1rbli_ 5 c3m20A_ 6 d1uzhc1 7 c2jnhA_ 8 d1ir1s_ 9 d1bcoa1 10 c3itfA_ 11 c2kjwA_ 12 c2r9iA_ 13 c2d9sA_ 14 d2g3qa1 15 c2rd0A_ 16 c3gyuA_ 17 c2do6A_ 18 d1fsea_ 19 c3g0tA_ 20 d1gyxa_ 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42

Detailed template information

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

1 d1wi9a_ 68.9 42 Fold:DNA/RNA-binding 3-helical bundle Superfamily:"Winged helix" DNA-binding domain Family:PCI domain (PINT motif) 2 d1svdm1 32.2 30 Fold:RuBisCO, small subunit Superfamily:RuBisCO, small subunit Family:RuBisCO, small subunit 3 d1iwga4 28.9 40 Fold:Ferredoxin-like Superfamily:Multidrug efflux transporter AcrB pore domain; PN1, PN2, PC1 and PC2 subdomains Family:Multidrug efflux transporter AcrB pore domain; PN1, PN2, PC1 and PC2 subdomains 4 d1rbli_ 28.8 30 Fold:RuBisCO, small subunit Superfamily:RuBisCO, small subunit Family:RuBisCO, small subunit 5 c3m20A_ 26.0 27 PDB header:isomerase Chain: A: PDB Molecule:4-oxalocrotonate tautomerase, putative; PDBTitle: crystal structure of dmpi from archaeoglobus fulgidus determined to2 2.37 angstroms resolution 6 d1uzhc1 22.5 30 Fold:RuBisCO, small subunit Superfamily:RuBisCO, small subunit Family:RuBisCO, small subunit 7 c2jnhA_ 22.4 24 PDB header:ligase Chain: A: PDB Molecule:e3 ubiquitin-protein ligase cbl-b; PDBTitle: solution structure of the uba domain from cbl-b 8 d1ir1s_ 21.3 22 Fold:RuBisCO, small subunit Superfamily:RuBisCO, small subunit Family:RuBisCO, small subunit 9 d1bcoa1 20.5 25 Fold:mu transposase, C-terminal domain Superfamily:mu transposase, C-terminal domain Family:mu transposase, C-terminal domain 10 c3itfA_ 19.9 38 PDB header:signaling protein Chain: A: PDB Molecule:periplasmic adaptor protein cpxp; PDBTitle: structural basis for the inhibitory function of the cpxp adaptor2 protein 11 c2kjwA_ 18.0 22 PDB header:ribosomal protein Chain: A: PDB Molecule:30s ribosomal protein s6; PDBTitle: solution structure and backbone dynamics of the permutant2 p54-55 12 c2r9iA_ 16.9 33 PDB header:structural genomics, unknown function Chain: A: PDB Molecule:putative phage capsid protein; PDBTitle: crystal structure of putative phage capsid protein domain from2 corynebacterium diphtheriae 13 c2d9sA_ 16.1 35 PDB header:ligase Chain: A: PDB Molecule:cbl e3 ubiquitin protein ligase; PDBTitle: solution structure of rsgi ruh-049, a uba domain from mouse2 cdna 14 d2g3qa1 15.8 22 Fold:RuvA C-terminal domain-like Superfamily:UBA-like Family:UBA domain 15 c2rd0A_ 15.3 21 PDB header:transferase/oncoprotein Chain: A: PDB Molecule:phosphatidylinositol-4,5-bisphosphate 3-kinase catalytic PDBTitle: structure of a human p110alpha/p85alpha complex 16 c3gyuA_ 14.7 21 PDB header:transcription Chain: A: PDB Molecule:nuclear hormone receptor of the steroid/thyroid PDBTitle: nuclear receptor daf-12 from parasitic nematode2 strongyloides stercoralis in complex with its physiological3 ligand dafachronic acid delta 7 17 c2do6A_ 14.3 24 PDB header:ligase Chain: A: PDB Molecule:e3 ubiquitin-protein ligase cbl-b; PDBTitle: solution structure of rsgi ruh-065, a uba domain from human2 cdna 18 d1fsea_ 13.9 27 Fold:DNA/RNA-binding 3-helical bundle Superfamily:C-terminal effector domain of the bipartite response regulators Family:GerE-like (LuxR/UhpA family of transcriptional regulators) 19 c3g0tA_ 11.7 30 PDB header:transferase Chain: A: PDB Molecule:putative aminotransferase; PDBTitle: crystal structure of putative aspartate aminotransferase (np_905498.1)2 from porphyromonas gingivalis w83 at 1.75 a resolution 20 d1gyxa_ 11.4 16 Fold:Tautomerase/MIF Superfamily:Tautomerase/MIF Family:4-oxalocrotonate tautomerase-like 21 d1g4us1 not modelled 11.2 17 Fold:Four-helical up-and-down bundle Superfamily:Bacterial GAP domain Family:Bacterial GAP domain 22 d1lq1a_ not modelled 11.2 41 Fold:DNA/RNA-binding 3-helical bundle Superfamily:C-terminal effector domain of the bipartite response regulators Family:Spo0A 23 d1cuka1 not modelled 11.1 27 Fold:RuvA C-terminal domain-like Superfamily:DNA helicase RuvA subunit, C-terminal domain Family:DNA helicase RuvA subunit, C-terminal domain 24 d1fc3a_ not modelled 10.4 39 Fold:DNA/RNA-binding 3-helical bundle Superfamily:C-terminal effector domain of the bipartite response regulators Family:Spo0A 25 d1pgya_ not modelled 10.4 40 Fold:RuvA C-terminal domain-like Superfamily:UBA-like Family:UBA domain 26 d1he1a_ not modelled 10.1 11 Fold:Four-helical up-and-down bundle Superfamily:Bacterial GAP domain Family:Bacterial GAP domain 27 d1oqya2 not modelled 9.3 33 Fold:RuvA C-terminal domain-like Superfamily:UBA-like Family:UBA domain 28 d1ifya_ not modelled 8.9 22 Fold:RuvA C-terminal domain-like Superfamily:UBA-like Family:UBA domain 29 d1hy5a_ not modelled 8.4 22 Fold:Four-helical up-and-down bundle Superfamily:Bacterial GAP domain Family:Bacterial GAP domain 30 d1nzja_ not modelled 8.1 32 Fold:Adenine nucleotide alpha hydrolase-like Superfamily:Nucleotidylyl transferase Family:Class I aminoacyl-tRNA synthetases (RS), catalytic domain 31 d1g1xb_ not modelled 8.0 19 Fold:S15/NS1 RNA-binding domain Superfamily:S15/NS1 RNA-binding domain Family:Ribosomal protein S15 32 c1yueA_ not modelled 7.5 32 PDB header:viral protein Chain: A: PDB Molecule:head vertex protein gp24; PDBTitle: bacteriophage t4 capsid vertex protein gp24 33 d1bwvs_ not modelled 7.3 42 Fold:RuBisCO, small subunit Superfamily:RuBisCO, small subunit Family:RuBisCO, small subunit 34 d3c2wa1 not modelled 7.0 20 Fold:Profilin-like Superfamily:GAF domain-like Family:GAF domain 35 d1oqya1 not modelled 6.5 22 Fold:RuvA C-terminal domain-like Superfamily:UBA-like Family:UBA domain 36 d1a04a1 not modelled 5.8 29 Fold:DNA/RNA-binding 3-helical bundle Superfamily:C-terminal effector domain of the bipartite response regulators Family:GerE-like (LuxR/UhpA family of transcriptional regulators) 37 d1bxni_ not modelled 5.7 47 Fold:RuBisCO, small subunit Superfamily:RuBisCO, small subunit Family:RuBisCO, small subunit 38 d2ctma1 not modelled 5.5 19 Fold:Eukaryotic type KH-domain (KH-domain type I) Superfamily:Eukaryotic type KH-domain (KH-domain type I) Family:Eukaryotic type KH-domain (KH-domain type I) 39 c1zljE_ not modelled 5.5 24 PDB header:transcription Chain: E: PDB Molecule:dormancy survival regulator; PDBTitle: crystal structure of the mycobacterium tuberculosis hypoxic2 response regulator dosr c-terminal domain 40 c2c4mA_ not modelled 5.2 26 PDB header:transferase Chain: A: PDB Molecule:glycogen phosphorylase; PDBTitle: starch phosphorylase: structural studies explain oxyanion-2 dependent kinetic stability and regulatory control. 41 c3cnfB_ not modelled 5.1 31 PDB header:virus Chain: B: PDB Molecule:vp1; PDBTitle: 3.88 angstrom structure of cytoplasmic polyhedrosis virus2 by cryo-electron microscopy 42 c1n93X_ not modelled 5.1 39 PDB header:viral protein Chain: X: PDB Molecule:p40 nucleoprotein; PDBTitle: crystal structure of the borna disease virus nucleoprotein

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