Secondary structure and disorder prediction

		1	.	.	.	.	.	.	.	.	10	.	.	.	.	.	.	.	.	.	20	.	.	.	.	.	.	.	.	.	30	.	.	.	.	.	.	.	.	.	40	.	.	.	.	.	.	.	.	.	50	.	.	.	.	.	.	.	.	.	60
Sequence		M	S	Q	P	R	P	L	L	S	P	P	E	T	E	E	Q	L	L	A	Q	A	Q	Q	L	S	G	Y	T	L	G	E	L	A	A	L	V	G	L	V	T	P	E	N	L	K	R	D	K	G	W	I	G	V	L	L	E	I	W	L	G
Secondary structure
SS confidence
Disorder		?	?	?	?	?	?	?																											?	?	?		?	?	?	?	?	?	?	?	?	?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	70	.	.	.	.	.	.	.	.	.	80	.	.	.	.	.	.	.	.	.	90	.	.	.	.	.	.	.	.	.	100	.	.	.	.	.	.	.	.	.	110	.	.	.	.	.	.	.	.	.	120
Sequence		A	S	A	G	S	K	P	E	Q	D	F	A	A	L	G	V	E	L	K	T	I	P	V	D	S	L	G	R	P	L	E	T	T	F	V	C	V	A	P	L	T	G	N	S	G	V	T	W	E	T	S	H	V	R	H	K	L	K	R	V
Secondary structure
SS confidence
Disorder																								?	?	?	?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	130	.	.	.	.	.	.	.	.	.	140	.	.	.	.	.	.	.	.	.	150	.	.	.	.	.	.	.	.	.	160	.	.	.	.	.	.	.	.	.	170	.	.	.	.	.	.	.	.	.	180
Sequence		L	W	I	P	V	E	G	E	R	S	I	P	L	A	Q	R	R	V	G	S	P	L	L	W	S	P	N	E	E	E	D	R	Q	L	R	E	D	W	E	E	L	M	D	M	I	V	L	G	Q	V	E	R	I	T	A	R	H	G	E	Y
Secondary structure
SS confidence
Disorder																																																		?	?	?	?	?	?	?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	190	.	.	.	.	.	.	.	.	.	200	.	.	.	.	.	.	.	.	.	210	.	.	.	.	.	.	.	.	.	220	.	.	.	.	.	.	.	.	.
Sequence		L	Q	I	R	P	K	A	A	N	A	K	A	L	T	E	A	I	G	A	R	G	E	R	I	L	T	L	P	R	G	F	Y	L	K	K	N	F	T	S	A	L	L	A	R	H	F	L	I	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 1azo chain A Region: 4 - 229 Aligned: 214 Modelled: 226 Confidence: 100.0% Identity: 99% Fold: Restriction endonuclease-like Superfamily: Restriction endonuclease-like Family: DNA mismatch repair protein MutH from Phyre2 PDB 2aor chain B Region: 11 - 225 Aligned: 215 Modelled: 215 Confidence: 100.0% Identity: 60% PDB header:hydrolase/dna Chain: B: PDB Molecule:dna mismatch repair protein muth; PDBTitle: crystal structure of muth-hemimethylated dna complex Phyre2 PDB 2reu chain A Region: 14 - 225 Aligned: 192 Modelled: 212 Confidence: 100.0% Identity: 15% PDB header:hydrolase Chain: A: PDB Molecule:type ii restriction enzyme sau3ai; PDBTitle: crystal structure of the c-terminal of sau3ai fragment Phyre2 PDB 2odi chain A Region: 13 - 89 Aligned: 67 Modelled: 77 Confidence: 97.9% Identity: 22% PDB header:hydrolase/dna Chain: A: PDB Molecule:r.bcni; PDBTitle: restriction endonuclease bcni-cognate dna substrate complex Phyre2 PDB 2oa9 chain B Region: 51 - 80 Aligned: 28 Modelled: 30 Confidence: 94.3% Identity: 32% PDB header:hydrolase Chain: B: PDB Molecule:r.mvai; PDBTitle: restriction endonuclease mvai in the absence of dna Phyre2 PDB 1ku3 chain A Region: 10 - 59 Aligned: 42 Modelled: 42 Confidence: 35.7% Identity: 21% Fold: DNA/RNA-binding 3-helical bundle Superfamily: Sigma3 and sigma4 domains of RNA polymerase sigma factors Family: Sigma4 domain Phyre2 PDB 6pax chain A Region: 5 - 58 Aligned: 42 Modelled: 54 Confidence: 28.9% Identity: 29% PDB header:gene regulation/dna Chain: A: PDB Molecule:homeobox protein pax-6; PDBTitle: crystal structure of the human pax-6 paired domain-dna2 complex reveals a general model for pax protein-dna3 interactions Phyre2 PDB 1pdn chain C Region: 5 - 58 Aligned: 42 Modelled: 46 Confidence: 24.8% Identity: 24% Fold: DNA/RNA-binding 3-helical bundle Superfamily: Homeodomain-like Family: Paired domain Phyre2 PDB 1q0w chain A Region: 11 - 24 Aligned: 14 Modelled: 14 Confidence: 23.6% Identity: 50% PDB header:transport protein Chain: A: PDB Molecule:vacuolar protein sorting-associated protein PDBTitle: solution structure of vps27 amino-terminal uim-ubiquitin2 complex Phyre2 PDB 1tty chain A Region: 10 - 59 Aligned: 42 Modelled: 50 Confidence: 22.6% Identity: 19% Fold: DNA/RNA-binding 3-helical bundle Superfamily: Sigma3 and sigma4 domains of RNA polymerase sigma factors Family: Sigma4 domain Phyre2 PDB 1ku7 chain A Region: 10 - 59 Aligned: 42 Modelled: 42 Confidence: 22.3% Identity: 21% Fold: DNA/RNA-binding 3-helical bundle Superfamily: Sigma3 and sigma4 domains of RNA polymerase sigma factors Family: Sigma4 domain Phyre2 PDB 2p7v chain B domain 1 Region: 10 - 59 Aligned: 42 Modelled: 42 Confidence: 21.6% Identity: 19% Fold: DNA/RNA-binding 3-helical bundle Superfamily: Sigma3 and sigma4 domains of RNA polymerase sigma factors Family: Sigma4 domain Phyre2 PDB 3gcg chain B Region: 15 - 69 Aligned: 52 Modelled: 55 Confidence: 15.2% Identity: 17% PDB header:signaling protein/transcription Chain: B: PDB Molecule:l0028 (mitochondria associated protein); PDBTitle: crystal structure of map and cdc42 complex Phyre2 PDB 1k78 chain A domain 1 Region: 5 - 58 Aligned: 42 Modelled: 46 Confidence: 13.8% Identity: 26% Fold: DNA/RNA-binding 3-helical bundle Superfamily: Homeodomain-like Family: Paired domain Phyre2 PDB 3abd chain Y Region: 5 - 17 Aligned: 13 Modelled: 13 Confidence: 12.1% Identity: 54% PDB header:cell cycle/replication Chain: Y: PDB Molecule:dna polymerase zeta catalytic subunit; PDBTitle: structure of human rev7 in complex with a human rev3 fragment in a2 monoclinic crystal Phyre2 PDB 1rp3 chain G Region: 10 - 59 Aligned: 40 Modelled: 42 Confidence: 11.9% Identity: 15% PDB header:transcription Chain: G: PDB Molecule:rna polymerase sigma factor sigma-28 (flia); PDBTitle: cocrystal structure of the flagellar sigma/anti-sigma2 complex, sigma-28/flgm Phyre2 PDB 1rp3 chain A domain 2 Region: 10 - 39 Aligned: 28 Modelled: 30 Confidence: 11.7% Identity: 11% Fold: DNA/RNA-binding 3-helical bundle Superfamily: Sigma3 and sigma4 domains of RNA polymerase sigma factors Family: Sigma4 domain Phyre2 PDB 1or7 chain A domain 1 Region: 10 - 41 Aligned: 30 Modelled: 32 Confidence: 11.4% Identity: 20% Fold: DNA/RNA-binding 3-helical bundle Superfamily: Sigma3 and sigma4 domains of RNA polymerase sigma factors Family: Sigma4 domain Phyre2 PDB 1pqw chain A Region: 133 - 171 Aligned: 39 Modelled: 39 Confidence: 10.7% Identity: 10% Fold: NAD(P)-binding Rossmann-fold domains Superfamily: NAD(P)-binding Rossmann-fold domains Family: Alcohol dehydrogenase-like, C-terminal domain Phyre2 PDB 1gu7 chain A domain 2 Region: 133 - 169 Aligned: 37 Modelled: 37 Confidence: 10.7% Identity: 3% Fold: NAD(P)-binding Rossmann-fold domains Superfamily: NAD(P)-binding Rossmann-fold domains Family: Alcohol dehydrogenase-like, C-terminal domain Phyre2 1 d1azoa_ 2 c2aorB_ 3 c2reuA_ 4 c2odiA_ 5 c2oa9B_ 6 d1ku3a_ 7 c6paxA_ 8 d1pdnc_ 9 c1q0wA_ 10 d1ttya_ 11 d1ku7a_ 12 d2p7vb1 13 c3gcgB_ 14 d1k78a1 15 c3abdY_ 16 c1rp3G_ 17 d1rp3a2 18 d1or7a1 19 d1pqwa_ 20 d1gu7a2 21 22 23 24 25 26 27 28 29 30 31 32 33 34

Detailed template information

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

1 d1azoa_ 100.0 99 Fold:Restriction endonuclease-like Superfamily:Restriction endonuclease-like Family:DNA mismatch repair protein MutH from 2 c2aorB_ 100.0 60 PDB header:hydrolase/dna Chain: B: PDB Molecule:dna mismatch repair protein muth; PDBTitle: crystal structure of muth-hemimethylated dna complex 3 c2reuA_ 100.0 15 PDB header:hydrolase Chain: A: PDB Molecule:type ii restriction enzyme sau3ai; PDBTitle: crystal structure of the c-terminal of sau3ai fragment 4 c2odiA_ 97.9 22 PDB header:hydrolase/dna Chain: A: PDB Molecule:r.bcni; PDBTitle: restriction endonuclease bcni-cognate dna substrate complex 5 c2oa9B_ 94.3 32 PDB header:hydrolase Chain: B: PDB Molecule:r.mvai; PDBTitle: restriction endonuclease mvai in the absence of dna 6 d1ku3a_ 35.7 21 Fold:DNA/RNA-binding 3-helical bundle Superfamily:Sigma3 and sigma4 domains of RNA polymerase sigma factors Family:Sigma4 domain 7 c6paxA_ 28.9 29 PDB header:gene regulation/dna Chain: A: PDB Molecule:homeobox protein pax-6; PDBTitle: crystal structure of the human pax-6 paired domain-dna2 complex reveals a general model for pax protein-dna3 interactions 8 d1pdnc_ 24.8 24 Fold:DNA/RNA-binding 3-helical bundle Superfamily:Homeodomain-like Family:Paired domain 9 c1q0wA_ 23.6 50 PDB header:transport protein Chain: A: PDB Molecule:vacuolar protein sorting-associated protein PDBTitle: solution structure of vps27 amino-terminal uim-ubiquitin2 complex 10 d1ttya_ 22.6 19 Fold:DNA/RNA-binding 3-helical bundle Superfamily:Sigma3 and sigma4 domains of RNA polymerase sigma factors Family:Sigma4 domain 11 d1ku7a_ 22.3 21 Fold:DNA/RNA-binding 3-helical bundle Superfamily:Sigma3 and sigma4 domains of RNA polymerase sigma factors Family:Sigma4 domain 12 d2p7vb1 21.6 19 Fold:DNA/RNA-binding 3-helical bundle Superfamily:Sigma3 and sigma4 domains of RNA polymerase sigma factors Family:Sigma4 domain 13 c3gcgB_ 15.2 17 PDB header:signaling protein/transcription Chain: B: PDB Molecule:l0028 (mitochondria associated protein); PDBTitle: crystal structure of map and cdc42 complex 14 d1k78a1 13.8 26 Fold:DNA/RNA-binding 3-helical bundle Superfamily:Homeodomain-like Family:Paired domain 15 c3abdY_ 12.1 54 PDB header:cell cycle/replication Chain: Y: PDB Molecule:dna polymerase zeta catalytic subunit; PDBTitle: structure of human rev7 in complex with a human rev3 fragment in a2 monoclinic crystal 16 c1rp3G_ 11.9 15 PDB header:transcription Chain: G: PDB Molecule:rna polymerase sigma factor sigma-28 (flia); PDBTitle: cocrystal structure of the flagellar sigma/anti-sigma2 complex, sigma-28/flgm 17 d1rp3a2 11.7 11 Fold:DNA/RNA-binding 3-helical bundle Superfamily:Sigma3 and sigma4 domains of RNA polymerase sigma factors Family:Sigma4 domain 18 d1or7a1 11.4 20 Fold:DNA/RNA-binding 3-helical bundle Superfamily:Sigma3 and sigma4 domains of RNA polymerase sigma factors Family:Sigma4 domain 19 d1pqwa_ 10.7 10 Fold:NAD(P)-binding Rossmann-fold domains Superfamily:NAD(P)-binding Rossmann-fold domains Family:Alcohol dehydrogenase-like, C-terminal domain 20 d1gu7a2 10.7 3 Fold:NAD(P)-binding Rossmann-fold domains Superfamily:NAD(P)-binding Rossmann-fold domains Family:Alcohol dehydrogenase-like, C-terminal domain 21 d2jn6a1 not modelled 10.6 20 Fold:DNA/RNA-binding 3-helical bundle Superfamily:Homeodomain-like Family:Cgl2762-like 22 d1ngra_ not modelled 10.3 26 Fold:DEATH domain Superfamily:DEATH domain Family:DEATH domain, DD 23 c2l4aA_ not modelled 9.1 26 PDB header:dna binding protein Chain: A: PDB Molecule:leucine responsive regulatory protein; PDBTitle: nmr structure of the dna-binding domain of e.coli lrp 24 d2hfha_ not modelled 9.0 19 Fold:DNA/RNA-binding 3-helical bundle Superfamily:"Winged helix" DNA-binding domain Family:Forkhead DNA-binding domain 25 d1bkba2 not modelled 8.7 24 Fold:OB-fold Superfamily:Nucleic acid-binding proteins Family:Cold shock DNA-binding domain-like 26 c3mzyA_ not modelled 8.3 21 PDB header:rna binding protein Chain: A: PDB Molecule:rna polymerase sigma-h factor; PDBTitle: the crystal structure of the rna polymerase sigma-h factor from2 fusobacterium nucleatum to 2.5a 27 c2pbxB_ not modelled 7.9 24 PDB header:transcription Chain: B: PDB Molecule:hemagglutinin/protease regulatory protein; PDBTitle: vibrio cholerae hapr 28 c2g7lA_ not modelled 7.9 26 PDB header:transcription Chain: A: PDB Molecule:tetr-family transcriptional regulator; PDBTitle: crystal structure of putative transcription regulator sco7704 from2 streptomyces coelicor 29 c2fjrB_ not modelled 7.6 12 PDB header:transcription regulator Chain: B: PDB Molecule:repressor protein ci; PDBTitle: crystal structure of bacteriophage 186 30 c2e5zA_ not modelled 7.2 8 PDB header:rna binding protein Chain: A: PDB Molecule:splicing factor, arginine/serine-rich 8; PDBTitle: solution structure of the surp2 domain in splicing factor,2 arginine/serine-rich 8 31 c2k27A_ not modelled 6.7 28 PDB header:transcription regulator Chain: A: PDB Molecule:paired box protein pax-8; PDBTitle: solution structure of human pax8 paired box domain 32 d1iz6a2 not modelled 6.3 19 Fold:OB-fold Superfamily:Nucleic acid-binding proteins Family:Cold shock DNA-binding domain-like 33 c2iv1J_ not modelled 6.0 15 PDB header:lyase Chain: J: PDB Molecule:cyanate hydratase; PDBTitle: site directed mutagenesis of key residues involved in the2 catalytic mechanism of cyanase 34 d1d5va_ not modelled 5.8 23 Fold:DNA/RNA-binding 3-helical bundle Superfamily:"Winged helix" DNA-binding domain Family:Forkhead DNA-binding 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