Secondary structure and disorder prediction

		1	.	.	.	.	.	.	.	.	10	.	.	.	.	.	.	.	.	.	20	.	.	.	.	.	.	.	.	.	30	.	.	.	.	.	.	.	.	.	40	.	.	.	.	.	.	.	.	.	50	.	.	.	.	.	.	.	.	.	60
Sequence		M	T	P	W	F	L	Y	L	I	R	T	A	D	N	K	L	Y	T	G	I	T	T	D	V	E	R	R	Y	Q	Q	H	Q	S	G	K	G	A	K	A	L	R	G	K	G	E	L	T	L	V	F	S	A	P	V	G	D	R	S	L	A
Secondary structure
SS confidence
Disorder		?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	70	.	.	.	.	.	.	.	.	.	80	.	.	.	.	.	.	.	.	.	90	.	.	.	.	.	.	.	.	.	100
Sequence		L	R	A	E	Y	R	V	K	Q	L	T	K	R	Q	K	E	R	L	V	A	E	G	A	G	F	A	E	L	L	S	S	L	Q	T	P	E	I	K	S	D
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 1zg2 chain A Region: 3 - 95 Aligned: 93 Modelled: 93 Confidence: 100.0% Identity: 42% PDB header:structural genomics, unknown function Chain: A: PDB Molecule:hypothetical upf0213 protein bh0048; PDBTitle: solution nmr structure of the upf0213 protein bh0048 from2 bacillus halodurans. northeast structural genomics target3 bhr2. Phyre2 PDB 1ywl chain A Region: 2 - 81 Aligned: 80 Modelled: 80 Confidence: 100.0% Identity: 34% PDB header:structural genomics, unknown function Chain: A: PDB Molecule:hypothetical upf0213 protein ef2693; PDBTitle: solution nmr structure of the protein ef2693 from e.2 faecalis: northeast structural genomics consortium target3 efr36 Phyre2 PDB 1yd6 chain A Region: 6 - 67 Aligned: 62 Modelled: 62 Confidence: 98.3% Identity: 16% PDB header:dna binding protein Chain: A: PDB Molecule:uvrc; PDBTitle: crystal structure of the giy-yig n-terminal endonuclease2 domain of uvrc from bacillus caldotenax Phyre2 PDB 1yd2 chain A Region: 6 - 67 Aligned: 62 Modelled: 62 Confidence: 97.8% Identity: 15% PDB header:dna binding protein Chain: A: PDB Molecule:uvrabc system protein c; PDBTitle: crystal structure of the giy-yig n-terminal endonuclease domain of2 uvrc from thermotoga maritima: point mutant y19f bound to the3 catalytic divalent cation Phyre2 PDB 1mk0 chain A Region: 1 - 67 Aligned: 66 Modelled: 67 Confidence: 97.5% Identity: 21% Fold: GIY-YIG endonuclease Superfamily: GIY-YIG endonuclease Family: GIY-YIG endonuclease Phyre2 PDB 2wsh chain C Region: 6 - 67 Aligned: 62 Modelled: 62 Confidence: 89.9% Identity: 6% PDB header:hydrolase Chain: C: PDB Molecule:endonuclease ii; PDBTitle: structure of bacteriophage t4 endoii e118a mutant Phyre2 PDB 3h8t chain A Region: 6 - 17 Aligned: 12 Modelled: 12 Confidence: 22.0% Identity: 25% PDB header:heme-binding protein Chain: A: PDB Molecule:hmuy; PDBTitle: structure of porphyromonas gingivalis heme-binding protein hmuy in2 complex with heme Phyre2 PDB 1f0c chain B Region: 5 - 19 Aligned: 15 Modelled: 15 Confidence: 21.0% Identity: 53% PDB header:viral protein Chain: B: PDB Molecule:ice inhibitor; PDBTitle: structure of the viral serpin crma Phyre2 PDB 1a6q chain A domain 1 Region: 59 - 99 Aligned: 41 Modelled: 41 Confidence: 17.2% Identity: 15% Fold: Another 3-helical bundle Superfamily: Protein serine/threonine phosphatase 2C, C-terminal domain Family: Protein serine/threonine phosphatase 2C, C-terminal domain Phyre2 PDB 2yrv chain A Region: 7 - 18 Aligned: 12 Modelled: 12 Confidence: 11.0% Identity: 42% PDB header:transcription Chain: A: PDB Molecule:at-rich interactive domain-containing protein 4a; PDBTitle: solution structure of the rbb1nt domain of human2 rb(retinoblastoma)-binding protein 1 Phyre2 PDB 1ylx chain A domain 1 Region: 6 - 23 Aligned: 18 Modelled: 18 Confidence: 10.4% Identity: 22% Fold: N domain of copper amine oxidase-like Superfamily: GK1464-like Family: GK1464-like Phyre2 PDB 2xk0 chain A Region: 8 - 19 Aligned: 12 Modelled: 12 Confidence: 9.4% Identity: 33% PDB header:transcription Chain: A: PDB Molecule:polycomb protein pcl; PDBTitle: solution structure of the tudor domain from drosophila2 polycomblike (pcl) Phyre2 PDB 2z3g chain A domain 1 Region: 8 - 20 Aligned: 13 Modelled: 13 Confidence: 9.4% Identity: 23% Fold: Cytidine deaminase-like Superfamily: Cytidine deaminase-like Family: Cytidine deaminase Phyre2 PDB 3oj6 chain C Region: 8 - 20 Aligned: 13 Modelled: 13 Confidence: 9.3% Identity: 15% PDB header:hydrolase Chain: C: PDB Molecule:blasticidin-s deaminase; PDBTitle: crystal structure of blasticidin s deaminase from coccidioides immitis Phyre2 PDB 1lkt chain A Region: 10 - 19 Aligned: 10 Modelled: 10 Confidence: 8.9% Identity: 40% Fold: Head-binding domain of phage P22 tailspike protein Superfamily: Head-binding domain of phage P22 tailspike protein Family: Head-binding domain of phage P22 tailspike protein Phyre2 PDB 3orc chain A Region: 6 - 27 Aligned: 22 Modelled: 22 Confidence: 8.5% Identity: 27% Fold: lambda repressor-like DNA-binding domains Superfamily: lambda repressor-like DNA-binding domains Family: Phage repressors Phyre2 PDB 2fr5 chain A domain 1 Region: 8 - 20 Aligned: 13 Modelled: 13 Confidence: 8.3% Identity: 23% Fold: Cytidine deaminase-like Superfamily: Cytidine deaminase-like Family: Cytidine deaminase Phyre2 PDB 3b8f chain B Region: 9 - 20 Aligned: 12 Modelled: 12 Confidence: 8.3% Identity: 42% PDB header:hydrolase Chain: B: PDB Molecule:putative blasticidin s deaminase; PDBTitle: crystal structure of the cytidine deaminase from bacillus anthracis Phyre2 PDB 2eqj chain A Region: 8 - 19 Aligned: 12 Modelled: 12 Confidence: 7.8% Identity: 42% PDB header:transcription Chain: A: PDB Molecule:metal-response element-binding transcription PDBTitle: solution structure of the tudor domain of metal-response2 element-binding transcription factor 2 Phyre2 PDB 1mq0 chain A Region: 8 - 20 Aligned: 13 Modelled: 13 Confidence: 7.8% Identity: 15% Fold: Cytidine deaminase-like Superfamily: Cytidine deaminase-like Family: Cytidine deaminase Phyre2 1 c1zg2A_ 2 c1ywlA_ 3 c1yd6A_ 4 c1yd2A_ 5 d1mk0a_ 6 c2wshC_ 7 c3h8tA_ 8 c1f0cB_ 9 d1a6qa1 10 c2yrvA_ 11 d1ylxa1 12 c2xk0A_ 13 d2z3ga1 14 c3oj6C_ 15 d1lkta_ 16 d3orca_ 17 d2fr5a1 18 c3b8fB_ 19 c2eqjA_ 20 d1mq0a_ 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35

Detailed template information

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

1 c1zg2A_ 100.0 42 PDB header:structural genomics, unknown function Chain: A: PDB Molecule:hypothetical upf0213 protein bh0048; PDBTitle: solution nmr structure of the upf0213 protein bh0048 from2 bacillus halodurans. northeast structural genomics target3 bhr2. 2 c1ywlA_ 100.0 34 PDB header:structural genomics, unknown function Chain: A: PDB Molecule:hypothetical upf0213 protein ef2693; PDBTitle: solution nmr structure of the protein ef2693 from e.2 faecalis: northeast structural genomics consortium target3 efr36 3 c1yd6A_ 98.3 16 PDB header:dna binding protein Chain: A: PDB Molecule:uvrc; PDBTitle: crystal structure of the giy-yig n-terminal endonuclease2 domain of uvrc from bacillus caldotenax 4 c1yd2A_ 97.8 15 PDB header:dna binding protein Chain: A: PDB Molecule:uvrabc system protein c; PDBTitle: crystal structure of the giy-yig n-terminal endonuclease domain of2 uvrc from thermotoga maritima: point mutant y19f bound to the3 catalytic divalent cation 5 d1mk0a_ 97.5 21 Fold:GIY-YIG endonuclease Superfamily:GIY-YIG endonuclease Family:GIY-YIG endonuclease 6 c2wshC_ 89.9 6 PDB header:hydrolase Chain: C: PDB Molecule:endonuclease ii; PDBTitle: structure of bacteriophage t4 endoii e118a mutant 7 c3h8tA_ 22.0 25 PDB header:heme-binding protein Chain: A: PDB Molecule:hmuy; PDBTitle: structure of porphyromonas gingivalis heme-binding protein hmuy in2 complex with heme 8 c1f0cB_ 21.0 53 PDB header:viral protein Chain: B: PDB Molecule:ice inhibitor; PDBTitle: structure of the viral serpin crma 9 d1a6qa1 17.2 15 Fold:Another 3-helical bundle Superfamily:Protein serine/threonine phosphatase 2C, C-terminal domain Family:Protein serine/threonine phosphatase 2C, C-terminal domain 10 c2yrvA_ 11.0 42 PDB header:transcription Chain: A: PDB Molecule:at-rich interactive domain-containing protein 4a; PDBTitle: solution structure of the rbb1nt domain of human2 rb(retinoblastoma)-binding protein 1 11 d1ylxa1 10.4 22 Fold:N domain of copper amine oxidase-like Superfamily:GK1464-like Family:GK1464-like 12 c2xk0A_ 9.4 33 PDB header:transcription Chain: A: PDB Molecule:polycomb protein pcl; PDBTitle: solution structure of the tudor domain from drosophila2 polycomblike (pcl) 13 d2z3ga1 9.4 23 Fold:Cytidine deaminase-like Superfamily:Cytidine deaminase-like Family:Cytidine deaminase 14 c3oj6C_ 9.3 15 PDB header:hydrolase Chain: C: PDB Molecule:blasticidin-s deaminase; PDBTitle: crystal structure of blasticidin s deaminase from coccidioides immitis 15 d1lkta_ 8.9 40 Fold:Head-binding domain of phage P22 tailspike protein Superfamily:Head-binding domain of phage P22 tailspike protein Family:Head-binding domain of phage P22 tailspike protein 16 d3orca_ 8.5 27 Fold:lambda repressor-like DNA-binding domains Superfamily:lambda repressor-like DNA-binding domains Family:Phage repressors 17 d2fr5a1 8.3 23 Fold:Cytidine deaminase-like Superfamily:Cytidine deaminase-like Family:Cytidine deaminase 18 c3b8fB_ 8.3 42 PDB header:hydrolase Chain: B: PDB Molecule:putative blasticidin s deaminase; PDBTitle: crystal structure of the cytidine deaminase from bacillus anthracis 19 c2eqjA_ 7.8 42 PDB header:transcription Chain: A: PDB Molecule:metal-response element-binding transcription PDBTitle: solution structure of the tudor domain of metal-response2 element-binding transcription factor 2 20 d1mq0a_ 7.8 15 Fold:Cytidine deaminase-like Superfamily:Cytidine deaminase-like Family:Cytidine deaminase 21 d2d30a1 not modelled 7.8 38 Fold:Cytidine deaminase-like Superfamily:Cytidine deaminase-like Family:Cytidine deaminase 22 c3r2nC_ not modelled 7.7 31 PDB header:hydrolase Chain: C: PDB Molecule:cytidine deaminase; PDBTitle: crystal structure of cytidine deaminase from mycobacterium leprae 23 c3ijfX_ not modelled 7.6 23 PDB header:hydrolase Chain: X: PDB Molecule:cytidine deaminase; PDBTitle: crystal structure of cytidine deaminase from mycobacterium2 tuberculosis 24 c2diiA_ not modelled 7.1 20 PDB header:transcription Chain: A: PDB Molecule:tfiih basal transcription factor complex p62 PDBTitle: solution structure of the bsd domain of human tfiih basal2 transcription factor complex p62 subunit 25 d1d0na5 not modelled 7.1 11 Fold:Gelsolin-like Superfamily:Actin depolymerizing proteins Family:Gelsolin-like 26 d1yu0a1 not modelled 6.7 23 Fold:Pseudo beta-prism Superfamily:Bacteriophage trimeric proteins domain Family:Mtd domain-like 27 d1uwza_ not modelled 6.5 38 Fold:Cytidine deaminase-like Superfamily:Cytidine deaminase-like Family:Cytidine deaminase 28 d2bj7a1 not modelled 6.5 40 Fold:Ribbon-helix-helix Superfamily:Ribbon-helix-helix Family:CopG-like 29 c2dybA_ not modelled 6.5 28 PDB header:oxidoreductase Chain: A: PDB Molecule:neutrophil cytosol factor 4; PDBTitle: the crystal structure of human p40(phox) 30 d2diia1 not modelled 6.4 20 Fold:BSD domain-like Superfamily:BSD domain-like Family:BSD domain 31 d2hzab1 not modelled 6.3 40 Fold:Ribbon-helix-helix Superfamily:Ribbon-helix-helix Family:CopG-like 32 c2e5pA_ not modelled 6.3 50 PDB header:transcription Chain: A: PDB Molecule:phd finger protein 1; PDBTitle: solution structure of the tudor domain of phd finger2 protein 1 (phf1 protein) 33 c3dmoD_ not modelled 6.0 31 PDB header:hydrolase Chain: D: PDB Molecule:cytidine deaminase; PDBTitle: 1.6 a crystal structure of cytidine deaminase from2 burkholderia pseudomallei 34 c2vkyB_ not modelled 5.6 40 PDB header:viral protein Chain: B: PDB Molecule:tail protein, piigcn4; PDBTitle: headbinding domain of phage p22 tailspike c-terminally2 fused to isoleucine zipper piigcn4 (chimera i) 35 d1svya_ not modelled 5.5 7 Fold:Gelsolin-like Superfamily:Actin depolymerizing proteins Family:Gelsolin-like

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