Phyre Home Retrieve Phyre Job Id
Emaill.a.kelley@imperial.ac.uk
DescriptionP06722
DateThu Jan 5 10:59:25 GMT 2012
Unique Job ID30e79a90584c63f7

Summary 

Top model
Image coloured by rainbow N → C terminus
Model (left) based on template d1azoa_
Top template information
Fold:Restriction endonuclease-like
Superfamily:Restriction endonuclease-like
Family:DNA mismatch repair protein MutH from
Confidence and coverage
Confidence:100.0% Coverage: 93%
214 residues ( 93% of your sequence) have been modelled with 100.0% confidence by the single highest scoring template.
3D viewing
Interactive 3D view in Jmol

Sequence analysis 

Secondary structure and disorder prediction 

   1........10.........20.........30.........40.........50.........60
Sequence  MSQPRPLLSPPETEEQLLAQAQQLSGYTLGELAALVGLVTPENLKRDKGWIGVLLEIWLG
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Disorder  ???????

























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   .........70.........80.........90.........100.........110.........120
Sequence  ASAGSKPEQDFAALGVELKTIPVDSLGRPLETTFVCVAPLTGNSGVTWETSHVRHKLKRV
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??????































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   .........130.........140.........150.........160.........170.........180
Sequence  LWIPVEGERSIPLAQRRVGSPLLWSPNEEEDRQLREDWEELMDMIVLGQVERITARHGEY
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?????????


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   .........190.........200.........210.........220.........
Sequence  LQIRPKAANAKALTEAIGARGERILTLPRGFYLKKNFTSALLARHFLIQ
Secondary structure 





























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Disorder 



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????
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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

RankAligned region

PDB 1azo chain A

3D model

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

3D model

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

3D model

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

3D model

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

3D model

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

3D model

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

3D model

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

3D model

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

3D model

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

3D model

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

3D model

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

3D model

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

3D model

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

3D model

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

3D model

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

3D model

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

3D model

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

3D model

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

3D model

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

3D model

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 Coverage3D Model Confidence
% i.d. Template Information
1d1azoa_



100.0 99 Fold:Restriction endonuclease-like
Superfamily:Restriction endonuclease-like
Family:DNA mismatch repair protein MutH from
2c2aorB_



100.0 60 PDB header:hydrolase/dna
Chain: B: PDB Molecule:dna mismatch repair protein muth;
PDBTitle: crystal structure of muth-hemimethylated dna complex
3c2reuA_



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
4c2odiA_



97.9 22 PDB header:hydrolase/dna
Chain: A: PDB Molecule:r.bcni;
PDBTitle: restriction endonuclease bcni-cognate dna substrate complex
5c2oa9B_



94.3 32 PDB header:hydrolase
Chain: B: PDB Molecule:r.mvai;
PDBTitle: restriction endonuclease mvai in the absence of dna
6d1ku3a_



35.7 21 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:Sigma3 and sigma4 domains of RNA polymerase sigma factors
Family:Sigma4 domain
7c6paxA_



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
8d1pdnc_



24.8 24 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:Homeodomain-like
Family:Paired domain
9c1q0wA_



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
10d1ttya_



22.6 19 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:Sigma3 and sigma4 domains of RNA polymerase sigma factors
Family:Sigma4 domain
11d1ku7a_



22.3 21 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:Sigma3 and sigma4 domains of RNA polymerase sigma factors
Family:Sigma4 domain
12d2p7vb1



21.6 19 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:Sigma3 and sigma4 domains of RNA polymerase sigma factors
Family:Sigma4 domain
13c3gcgB_



15.2 17 PDB header:signaling protein/transcription
Chain: B: PDB Molecule:l0028 (mitochondria associated protein);
PDBTitle: crystal structure of map and cdc42 complex
14d1k78a1



13.8 26 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:Homeodomain-like
Family:Paired domain
15c3abdY_



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
16c1rp3G_



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
17d1rp3a2



11.7 11 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:Sigma3 and sigma4 domains of RNA polymerase sigma factors
Family:Sigma4 domain
18d1or7a1



11.4 20 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:Sigma3 and sigma4 domains of RNA polymerase sigma factors
Family:Sigma4 domain
19d1pqwa_



10.7 10 Fold:NAD(P)-binding Rossmann-fold domains
Superfamily:NAD(P)-binding Rossmann-fold domains
Family:Alcohol dehydrogenase-like, C-terminal domain
20d1gu7a2



10.7 3 Fold:NAD(P)-binding Rossmann-fold domains
Superfamily:NAD(P)-binding Rossmann-fold domains
Family:Alcohol dehydrogenase-like, C-terminal domain
21d2jn6a1



not modelled 10.6 20 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:Homeodomain-like
Family:Cgl2762-like
22d1ngra_



not modelled 10.3 26 Fold:DEATH domain
Superfamily:DEATH domain
Family:DEATH domain, DD
23c2l4aA_



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
24d2hfha_



not modelled 9.0 19 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:"Winged helix" DNA-binding domain
Family:Forkhead DNA-binding domain
25d1bkba2



not modelled 8.7 24 Fold:OB-fold
Superfamily:Nucleic acid-binding proteins
Family:Cold shock DNA-binding domain-like
26c3mzyA_



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
27c2pbxB_



not modelled 7.9 24 PDB header:transcription
Chain: B: PDB Molecule:hemagglutinin/protease regulatory protein;
PDBTitle: vibrio cholerae hapr
28c2g7lA_



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
29c2fjrB_



not modelled 7.6 12 PDB header:transcription regulator
Chain: B: PDB Molecule:repressor protein ci;
PDBTitle: crystal structure of bacteriophage 186
30c2e5zA_



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
31c2k27A_



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
32d1iz6a2



not modelled 6.3 19 Fold:OB-fold
Superfamily:Nucleic acid-binding proteins
Family:Cold shock DNA-binding domain-like
33c2iv1J_



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
34d1d5va_



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



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