Secondary structure and disorder prediction

1

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10

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20

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30

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40

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50

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60

Sequence

M

Q

K

E

Q

L

S

A

L

M

D

G

E

T

L

D

S

E

L

L

N

E

L

A

H

N

P

E

M

Q

K

T

W

E

S

Y

H

L

I

R

D

S

M

R

G

D

T

P

E

V

L

H

F

D

I

S

S

R

V

M

Secondary structure

SS confidence

Disorder

?

?

?

?

?

?

?

?

?

?

?

?

?

?

?

?

Disorder confidence

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70

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80

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90

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100

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110

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120

Sequence

A

A

I

E

E

E

P

V

R

Q

P

A

T

L

I

P

E

A

Q

P

A

P

H

Q

W

Q

K

M

P

F

W

Q

K

V

R

P

W

A

A

Q

L

T

Q

M

G

V

A

A

C

V

S

L

A

V

I

V

G

V

Q

H

Secondary structure

SS confidence

Disorder

?

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?

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?

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?

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?

?

?

?

Disorder confidence

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130

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140

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150

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160

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170

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180

Sequence

Y

N

G

Q

S

E

T

S

Q

Q

P

E

T

P

V

F

N

T

L

P

M

M

G

K

A

S

P

V

S

L

G

V

P

S

E

A

T

A

N

N

G

Q

Q

Q

Q

V

Q

E

Q

R

R

R

I

N

A

M

L

Q

D

Y

Secondary structure

SS confidence

Disorder

?

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?

?

Disorder confidence

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190

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200

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.

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210

.

.

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.

.

.

Sequence

E

L

Q

R

R

L

H

S

E

Q

L

Q

F

E

Q

A

Q

T

Q

Q

A

A

V

Q

V

P

G

I

Q

T

L

G

T

Q

S

Q

Secondary structure

SS confidence

Disorder

?

?

?

?

?

?

?

?

?

?

?

?

?

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?

?

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?

?

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 1or7 chain C Region: 1 - 66 Aligned: 66 Modelled: 66 Confidence: 100.0% Identity: 100% PDB header:transcription Chain: C: PDB Molecule:sigma-e factor negative regulatory protein; PDBTitle: crystal structure of escherichia coli sigmae with the cytoplasmic2 domain of its anti-sigma rsea Phyre2 PDB 1or7 chain C Region: 1 - 66 Aligned: 66 Modelled: 66 Confidence: 100.0% Identity: 100% Fold: N-terminal, cytoplasmic domain of anti-sigmaE factor RseA Superfamily: N-terminal, cytoplasmic domain of anti-sigmaE factor RseA Family: N-terminal, cytoplasmic domain of anti-sigmaE factor RseA Phyre2 PDB 3m4w chain H Region: 134 - 188 Aligned: 31 Modelled: 31 Confidence: 97.3% Identity: 100% PDB header:signaling protein/signaling protein Chain: H: PDB Molecule:sigma-e factor negative regulatory protein; PDBTitle: structural basis for the negative regulation of bacterial stress2 response by rseb Phyre2 PDB 2z2s chain D Region: 2 - 67 Aligned: 66 Modelled: 65 Confidence: 95.0% Identity: 15% PDB header:transcription Chain: D: PDB Molecule:anti-sigma factor chrr, transcriptional activator chrr; PDBTitle: crystal structure of rhodobacter sphaeroides sige in complex with the2 anti-sigma chrr Phyre2 PDB 3hug chain J Region: 3 - 45 Aligned: 43 Modelled: 43 Confidence: 94.8% Identity: 16% PDB header:transcription/membrane protein Chain: J: PDB Molecule:probable conserved membrane protein; PDBTitle: crystal structure of mycobacterium tuberculosis anti-sigma factor rsla2 in complex with -35 promoter binding domain of sigl Phyre2 PDB 1t98 chain A domain 1 Region: 10 - 25 Aligned: 16 Modelled: 16 Confidence: 25.5% Identity: 38% Fold: DNA/RNA-binding 3-helical bundle Superfamily: "Winged helix" DNA-binding domain Family: MukF N-terminal domain-like Phyre2 PDB 1u04 chain A domain 1 Region: 23 - 40 Aligned: 18 Modelled: 18 Confidence: 19.8% Identity: 50% Fold: SH3-like barrel Superfamily: PAZ domain Family: PAZ domain Phyre2 PDB 1m98 chain A domain 1 Region: 18 - 67 Aligned: 50 Modelled: 50 Confidence: 9.9% Identity: 10% Fold: Orange carotenoid protein, N-terminal domain Superfamily: Orange carotenoid protein, N-terminal domain Family: Orange carotenoid protein, N-terminal domain Phyre2 PDB 1jhg chain A Region: 8 - 49 Aligned: 42 Modelled: 42 Confidence: 7.3% Identity: 19% Fold: DNA/RNA-binding 3-helical bundle Superfamily: TrpR-like Family: Trp repressor, TrpR Phyre2 PDB 1trr chain A Region: 10 - 67 Aligned: 58 Modelled: 58 Confidence: 7.1% Identity: 16% Fold: DNA/RNA-binding 3-helical bundle Superfamily: TrpR-like Family: Trp repressor, TrpR Phyre2 PDB 1yfn chain G Region: 77 - 91 Aligned: 15 Modelled: 15 Confidence: 6.5% Identity: 100% PDB header:protein binding Chain: G: PDB Molecule:sigma-e factor negative regulatory protein; PDBTitle: versatile modes of peptide recognition by the aaa+ adaptor2 protein sspb- the crystal structure of a sspb-rsea complex Phyre2 PDB 1g2y chain C Region: 1 - 23 Aligned: 23 Modelled: 23 Confidence: 6.3% Identity: 30% PDB header:transcription Chain: C: PDB Molecule:hepatocyte nuclear factor 1-alpha; PDBTitle: hnf-1alpha dimerization domain, with selenomethionine2 substitued at leu 12 Phyre2 PDB 1g2y chain D Region: 1 - 23 Aligned: 23 Modelled: 23 Confidence: 6.0% Identity: 30% PDB header:transcription Chain: D: PDB Molecule:hepatocyte nuclear factor 1-alpha; PDBTitle: hnf-1alpha dimerization domain, with selenomethionine2 substitued at leu 12 Phyre2 PDB 1g2y chain B Region: 1 - 23 Aligned: 23 Modelled: 23 Confidence: 6.0% Identity: 30% PDB header:transcription Chain: B: PDB Molecule:hepatocyte nuclear factor 1-alpha; PDBTitle: hnf-1alpha dimerization domain, with selenomethionine2 substitued at leu 12 Phyre2 PDB 1g2y chain A Region: 1 - 23 Aligned: 23 Modelled: 23 Confidence: 5.9% Identity: 30% Fold: Dimerisation interlock Superfamily: Dimerization cofactor of HNF-1 alpha Family: Dimerization cofactor of HNF-1 alpha Phyre2 PDB 1g2y chain A Region: 1 - 23 Aligned: 23 Modelled: 23 Confidence: 5.9% Identity: 30% PDB header:transcription Chain: A: PDB Molecule:hepatocyte nuclear factor 1-alpha; PDBTitle: hnf-1alpha dimerization domain, with selenomethionine2 substitued at leu 12 Phyre2 PDB 7cei chain B Region: 39 - 70 Aligned: 30 Modelled: 32 Confidence: 5.7% Identity: 27% PDB header:immune system Chain: B: PDB Molecule:protein (colicin e7 immunity protein); PDBTitle: the endonuclease domain of colicin e7 in complex with its inhibitor2 im7 protein Phyre2 1 c1or7C_ 2 d1or7c_ 3 c3m4wH_ 4 c2z2sD_ 5 c3hugJ_ 6 d1t98a1 7 d1u04a1 8 d1m98a1 9 d1jhga_ 10 d1trra_ 11 c1yfnG_ 12 c1g2yC_ 13 c1g2yD_ 14 c1g2yB_ 15 d1g2ya_ 16 c1g2yA_ 17 c7ceiB_

Detailed template information

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

1 c1or7C_ 100.0 100 PDB header:transcription Chain: C: PDB Molecule:sigma-e factor negative regulatory protein; PDBTitle: crystal structure of escherichia coli sigmae with the cytoplasmic2 domain of its anti-sigma rsea 2 d1or7c_ 100.0 100 Fold:N-terminal, cytoplasmic domain of anti-sigmaE factor RseA Superfamily:N-terminal, cytoplasmic domain of anti-sigmaE factor RseA Family:N-terminal, cytoplasmic domain of anti-sigmaE factor RseA 3 c3m4wH_ 97.3 100 PDB header:signaling protein/signaling protein Chain: H: PDB Molecule:sigma-e factor negative regulatory protein; PDBTitle: structural basis for the negative regulation of bacterial stress2 response by rseb 4 c2z2sD_ 95.0 15 PDB header:transcription Chain: D: PDB Molecule:anti-sigma factor chrr, transcriptional activator chrr; PDBTitle: crystal structure of rhodobacter sphaeroides sige in complex with the2 anti-sigma chrr 5 c3hugJ_ 94.8 16 PDB header:transcription/membrane protein Chain: J: PDB Molecule:probable conserved membrane protein; PDBTitle: crystal structure of mycobacterium tuberculosis anti-sigma factor rsla2 in complex with -35 promoter binding domain of sigl 6 d1t98a1 25.5 38 Fold:DNA/RNA-binding 3-helical bundle Superfamily:"Winged helix" DNA-binding domain Family:MukF N-terminal domain-like 7 d1u04a1 19.8 50 Fold:SH3-like barrel Superfamily:PAZ domain Family:PAZ domain 8 d1m98a1 9.9 10 Fold:Orange carotenoid protein, N-terminal domain Superfamily:Orange carotenoid protein, N-terminal domain Family:Orange carotenoid protein, N-terminal domain 9 d1jhga_ 7.3 19 Fold:DNA/RNA-binding 3-helical bundle Superfamily:TrpR-like Family:Trp repressor, TrpR 10 d1trra_ 7.1 16 Fold:DNA/RNA-binding 3-helical bundle Superfamily:TrpR-like Family:Trp repressor, TrpR 11 c1yfnG_ 6.5 100 PDB header:protein binding Chain: G: PDB Molecule:sigma-e factor negative regulatory protein; PDBTitle: versatile modes of peptide recognition by the aaa+ adaptor2 protein sspb- the crystal structure of a sspb-rsea complex 12 c1g2yC_ 6.3 30 PDB header:transcription Chain: C: PDB Molecule:hepatocyte nuclear factor 1-alpha; PDBTitle: hnf-1alpha dimerization domain, with selenomethionine2 substitued at leu 12 13 c1g2yD_ 6.0 30 PDB header:transcription Chain: D: PDB Molecule:hepatocyte nuclear factor 1-alpha; PDBTitle: hnf-1alpha dimerization domain, with selenomethionine2 substitued at leu 12 14 c1g2yB_ 6.0 30 PDB header:transcription Chain: B: PDB Molecule:hepatocyte nuclear factor 1-alpha; PDBTitle: hnf-1alpha dimerization domain, with selenomethionine2 substitued at leu 12 15 d1g2ya_ 5.9 30 Fold:Dimerisation interlock Superfamily:Dimerization cofactor of HNF-1 alpha Family:Dimerization cofactor of HNF-1 alpha 16 c1g2yA_ 5.9 30 PDB header:transcription Chain: A: PDB Molecule:hepatocyte nuclear factor 1-alpha; PDBTitle: hnf-1alpha dimerization domain, with selenomethionine2 substitued at leu 12 17 c7ceiB_ 5.7 27 PDB header:immune system Chain: B: PDB Molecule:protein (colicin e7 immunity protein); PDBTitle: the endonuclease domain of colicin e7 in complex with its inhibitor2 im7 protein

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

Transmembrane helix prediction

Transmembrane helices have been predicted in your sequence to adopt the topology shown below

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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