Secondary structure and disorder prediction

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Sequence		M	D	H	S	L	N	S	L	N	N	F	D	F	L	A	R	S	F	A	R	M	H	A	E	G	R	P	V	D	I	L	A	V	T	G	N	M	D	E	E	H	R	T	W	F	C	A	R	Y	A	W	Y	C	Q	Q	M	M	Q	A	R
Secondary structure
SS confidence
Disorder		?	?	?	?	?																	?	?											?	?	?																							?	?
Disorder confidence
		.	.	.	.	.	.
Sequence		E	L	E	L	E	H
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 1rrz chain A Region: 1 - 66 Aligned: 66 Modelled: 66 Confidence: 100.0% Identity: 100% Fold: Spectrin repeat-like Superfamily: Glycogen synthesis protein GlgS Family: Glycogen synthesis protein GlgS Phyre2 PDB 1rrz chain A Region: 1 - 66 Aligned: 66 Modelled: 66 Confidence: 100.0% Identity: 100% PDB header:structural genomics,biosynthetic protein Chain: A: PDB Molecule:glycogen synthesis protein glgs; PDBTitle: solution structure of glgs protein from e. coli Phyre2 PDB 1se7 chain A Region: 10 - 58 Aligned: 49 Modelled: 49 Confidence: 96.1% Identity: 31% Fold: DNA polymerase III theta subunit-like Superfamily: DNA polymerase III theta subunit-like Family: DNA polymerase III theta subunit-like Phyre2 PDB 2ae9 chain A domain 1 Region: 10 - 65 Aligned: 56 Modelled: 56 Confidence: 96.0% Identity: 27% Fold: DNA polymerase III theta subunit-like Superfamily: DNA polymerase III theta subunit-like Family: DNA polymerase III theta subunit-like Phyre2 PDB 2ido chain B domain 1 Region: 10 - 58 Aligned: 49 Modelled: 49 Confidence: 95.7% Identity: 31% Fold: DNA polymerase III theta subunit-like Superfamily: DNA polymerase III theta subunit-like Family: DNA polymerase III theta subunit-like Phyre2 PDB 2azp chain A Region: 21 - 58 Aligned: 38 Modelled: 38 Confidence: 21.3% Identity: 18% PDB header:structural genomics, unknown function Chain: A: PDB Molecule:hypothetical protein pa1268; PDBTitle: crystal structure of pa1268 solved by sulfur sad Phyre2 PDB 1em8 chain A Region: 38 - 58 Aligned: 21 Modelled: 21 Confidence: 17.8% Identity: 14% Fold: DNA polymerase III chi subunit Superfamily: DNA polymerase III chi subunit Family: DNA polymerase III chi subunit Phyre2 PDB 2qjx chain A Region: 8 - 53 Aligned: 45 Modelled: 46 Confidence: 16.2% Identity: 20% PDB header:protein binding Chain: A: PDB Molecule:protein bim1; PDBTitle: structural basis of microtubule plus end tracking by2 xmap215, clip-170 and eb1 Phyre2 PDB 1w62 chain B Region: 21 - 58 Aligned: 38 Modelled: 38 Confidence: 14.1% Identity: 24% PDB header:racemase Chain: B: PDB Molecule:b-cell mitogen; PDBTitle: proline racemase in complex with one molecule of pyrrole-2-2 carboxylic acid (hemi form) Phyre2 PDB 1hf0 chain A Region: 28 - 48 Aligned: 21 Modelled: 21 Confidence: 13.2% Identity: 38% PDB header:transcription factor Chain: A: PDB Molecule:octamer-binding transcription factor 1; PDBTitle: crystal structure of the dna-binding domain of oct-1 bound2 to dna as a dimer Phyre2 PDB 1v5k chain A Region: 8 - 50 Aligned: 42 Modelled: 43 Confidence: 9.8% Identity: 29% Fold: CH domain-like Superfamily: Calponin-homology domain, CH-domain Family: Calponin-homology domain, CH-domain Phyre2 PDB 3d1n chain K Region: 31 - 48 Aligned: 18 Modelled: 17 Confidence: 9.5% Identity: 44% PDB header:transcription regulator/dna Chain: K: PDB Molecule:pou domain, class 6, transcription factor 1; PDBTitle: structure of human brn-5 transcription factor in complex2 with corticotrophin-releasing hormone gene promoter Phyre2 PDB 1skv chain A Region: 28 - 59 Aligned: 27 Modelled: 32 Confidence: 9.2% Identity: 30% Fold: ROP-like Superfamily: Hypothetical protein D-63 Family: Hypothetical protein D-63 Phyre2 PDB 1b9u chain A Region: 44 - 51 Aligned: 8 Modelled: 8 Confidence: 9.1% Identity: 50% PDB header:hydrolase Chain: A: PDB Molecule:protein (atp synthase); PDBTitle: membrane domain of the subunit b of the e.coli atp synthase Phyre2 PDB 1y7u chain A domain 1 Region: 17 - 62 Aligned: 46 Modelled: 46 Confidence: 8.6% Identity: 17% Fold: Thioesterase/thiol ester dehydrase-isomerase Superfamily: Thioesterase/thiol ester dehydrase-isomerase Family: 4HBT-like Phyre2 PDB 2diu chain A Region: 2 - 24 Aligned: 23 Modelled: 23 Confidence: 8.4% Identity: 26% PDB header:rna binding protein Chain: A: PDB Molecule:kiaa0430 protein; PDBTitle: solution structure of the rrm domain of kiaa0430 protein Phyre2 PDB 1s6l chain A domain 1 Region: 16 - 31 Aligned: 16 Modelled: 16 Confidence: 8.0% Identity: 38% Fold: DNA/RNA-binding 3-helical bundle Superfamily: "Winged helix" DNA-binding domain Family: MerB N-terminal domain-like Phyre2 PDB 2gm2 chain A Region: 15 - 41 Aligned: 27 Modelled: 27 Confidence: 7.7% Identity: 30% PDB header:structural genomics, unknown function Chain: A: PDB Molecule:conserved hypothetical protein; PDBTitle: nmr structure of xanthomonas campestris xcc1710: northeast2 structural genomics consortium target xcr35 Phyre2 PDB 1au7 chain A domain 1 Region: 28 - 48 Aligned: 21 Modelled: 21 Confidence: 7.6% Identity: 38% Fold: DNA/RNA-binding 3-helical bundle Superfamily: Homeodomain-like Family: Homeodomain Phyre2 PDB 2qjz chain A domain 1 Region: 8 - 53 Aligned: 45 Modelled: 46 Confidence: 6.9% Identity: 24% Fold: CH domain-like Superfamily: Calponin-homology domain, CH-domain Family: Calponin-homology domain, CH-domain Phyre2 1 d1rrza_ 2 c1rrzA_ 3 d1se7a_ 4 d2ae9a1 5 d2idob1 6 c2azpA_ 7 d1em8a_ 8 c2qjxA_ 9 c1w62B_ 10 c1hf0A_ 11 d1v5ka_ 12 c3d1nK_ 13 d1skva_ 14 c1b9uA_ 15 d1y7ua1 16 c2diuA_ 17 d1s6la1 18 c2gm2A_ 19 d1au7a1 20 d2qjza1 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36

Detailed template information

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

1 d1rrza_ 100.0 100 Fold:Spectrin repeat-like Superfamily:Glycogen synthesis protein GlgS Family:Glycogen synthesis protein GlgS 2 c1rrzA_ 100.0 100 PDB header:structural genomics,biosynthetic protein Chain: A: PDB Molecule:glycogen synthesis protein glgs; PDBTitle: solution structure of glgs protein from e. coli 3 d1se7a_ 96.1 31 Fold:DNA polymerase III theta subunit-like Superfamily:DNA polymerase III theta subunit-like Family:DNA polymerase III theta subunit-like 4 d2ae9a1 96.0 27 Fold:DNA polymerase III theta subunit-like Superfamily:DNA polymerase III theta subunit-like Family:DNA polymerase III theta subunit-like 5 d2idob1 95.7 31 Fold:DNA polymerase III theta subunit-like Superfamily:DNA polymerase III theta subunit-like Family:DNA polymerase III theta subunit-like 6 c2azpA_ 21.3 18 PDB header:structural genomics, unknown function Chain: A: PDB Molecule:hypothetical protein pa1268; PDBTitle: crystal structure of pa1268 solved by sulfur sad 7 d1em8a_ 17.8 14 Fold:DNA polymerase III chi subunit Superfamily:DNA polymerase III chi subunit Family:DNA polymerase III chi subunit 8 c2qjxA_ 16.2 20 PDB header:protein binding Chain: A: PDB Molecule:protein bim1; PDBTitle: structural basis of microtubule plus end tracking by2 xmap215, clip-170 and eb1 9 c1w62B_ 14.1 24 PDB header:racemase Chain: B: PDB Molecule:b-cell mitogen; PDBTitle: proline racemase in complex with one molecule of pyrrole-2-2 carboxylic acid (hemi form) 10 c1hf0A_ 13.2 38 PDB header:transcription factor Chain: A: PDB Molecule:octamer-binding transcription factor 1; PDBTitle: crystal structure of the dna-binding domain of oct-1 bound2 to dna as a dimer 11 d1v5ka_ 9.8 29 Fold:CH domain-like Superfamily:Calponin-homology domain, CH-domain Family:Calponin-homology domain, CH-domain 12 c3d1nK_ 9.5 44 PDB header:transcription regulator/dna Chain: K: PDB Molecule:pou domain, class 6, transcription factor 1; PDBTitle: structure of human brn-5 transcription factor in complex2 with corticotrophin-releasing hormone gene promoter 13 d1skva_ 9.2 30 Fold:ROP-like Superfamily:Hypothetical protein D-63 Family:Hypothetical protein D-63 14 c1b9uA_ 9.1 50 PDB header:hydrolase Chain: A: PDB Molecule:protein (atp synthase); PDBTitle: membrane domain of the subunit b of the e.coli atp synthase 15 d1y7ua1 8.6 17 Fold:Thioesterase/thiol ester dehydrase-isomerase Superfamily:Thioesterase/thiol ester dehydrase-isomerase Family:4HBT-like 16 c2diuA_ 8.4 26 PDB header:rna binding protein Chain: A: PDB Molecule:kiaa0430 protein; PDBTitle: solution structure of the rrm domain of kiaa0430 protein 17 d1s6la1 8.0 38 Fold:DNA/RNA-binding 3-helical bundle Superfamily:"Winged helix" DNA-binding domain Family:MerB N-terminal domain-like 18 c2gm2A_ 7.7 30 PDB header:structural genomics, unknown function Chain: A: PDB Molecule:conserved hypothetical protein; PDBTitle: nmr structure of xanthomonas campestris xcc1710: northeast2 structural genomics consortium target xcr35 19 d1au7a1 7.6 38 Fold:DNA/RNA-binding 3-helical bundle Superfamily:Homeodomain-like Family:Homeodomain 20 d2qjza1 6.9 24 Fold:CH domain-like Superfamily:Calponin-homology domain, CH-domain Family:Calponin-homology domain, CH-domain 21 d1bama_ not modelled 6.9 33 Fold:Restriction endonuclease-like Superfamily:Restriction endonuclease-like Family:Restriction endonuclease BamHI 22 d3d1ma1 not modelled 6.8 70 Fold:Hedgehog/DD-peptidase Superfamily:Hedgehog/DD-peptidase Family:Hedgehog (development protein), N-terminal signaling domain 23 c3swfA_ not modelled 6.6 44 PDB header:transport protein Chain: A: PDB Molecule:cgmp-gated cation channel alpha-1; PDBTitle: cnga1 621-690 containing clz domain 24 c2hl7A_ not modelled 6.6 40 PDB header:oxidoreductase Chain: A: PDB Molecule:cytochrome c-type biogenesis protein ccmh; PDBTitle: crystal structure of the periplasmic domain of ccmh from pseudomonas2 aeruginosa 25 c3m1nB_ not modelled 6.6 70 PDB header:signaling protein Chain: B: PDB Molecule:sonic hedgehog protein; PDBTitle: crystal structure of human sonic hedgehog n-terminal domain 26 c1geaA_ not modelled 6.5 42 PDB header:neuropeptide Chain: A: PDB Molecule:pituitary adenylate cyclase activating PDBTitle: receptor-bound conformation of pacap21 27 d1b79a_ not modelled 6.3 24 Fold:N-terminal domain of DnaB helicase Superfamily:N-terminal domain of DnaB helicase Family:N-terminal domain of DnaB helicase 28 d2pp6a1 not modelled 6.1 32 Fold:Phage tail proteins Superfamily:Phage tail proteins Family:gpFII-like 29 c3byaB_ not modelled 6.1 71 PDB header:metal binding protein Chain: B: PDB Molecule:glutamate [nmda] receptor subunit zeta-1 peptide; PDBTitle: structure of a calmodulin complex 30 d1b8ia_ not modelled 6.0 19 Fold:DNA/RNA-binding 3-helical bundle Superfamily:Homeodomain-like Family:Homeodomain 31 d1ejxb_ not modelled 6.0 39 Fold:beta-clip Superfamily:Urease, beta-subunit Family:Urease, beta-subunit 32 c2jtxA_ not modelled 5.9 19 PDB header:transcription Chain: A: PDB Molecule:transcription initiation factor iie subunit PDBTitle: nmr structure of the tfiie-alpha carboxyl terminus 33 c2yqeA_ not modelled 5.5 15 PDB header:dna binding protein Chain: A: PDB Molecule:jumonji/arid domain-containing protein 1d; PDBTitle: solution structure of the arid domain of jarid1d protein 34 c2rnqA_ not modelled 5.5 19 PDB header:transcription Chain: A: PDB Molecule:transcription initiation factor iie subunit PDBTitle: solution structure of the c-terminal acidic domain of tfiie2 alpha 35 c2hqwB_ not modelled 5.4 71 PDB header:metal binding protein Chain: B: PDB Molecule:glutamate nmda receptor subunit zeta 1; PDBTitle: crystal structure of ca2+/calmodulin bound to nmda receptor nr1c12 peptide 36 c2kw0A_ not modelled 5.3 33 PDB header:oxidoreductase Chain: A: PDB Molecule:ccmh protein; PDBTitle: solution structure of n-terminal domain of ccmh from escherichia.coli

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