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

M

K

T

V

K

H

L

L

C

C

A

I

A

A

S

A

L

I

S

T

G

V

H

A

A

S

W

K

D

A

L

S

S

A

A

S

E

L

G

N

Q

N

S

T

T

Q

E

G

G

W

S

L

A

S

L

T

N

L

L

Secondary structure

SS confidence

Disorder

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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

S

S

G

N

Q

A

L

S

A

D

N

M

N

N

A

A

G

I

L

Q

Y

C

A

K

Q

K

L

A

S

V

T

D

A

E

N

I

K

N

Q

V

L

E

K

L

G

L

N

S

E

E

Q

K

E

D

T

N

Y

L

D

G

Secondary structure

SS confidence

Disorder

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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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Sequence

I

Q

G

L

L

K

T

K

D

G

Q

Q

L

N

L

D

N

I

G

T

T

P

L

A

E

K

V

K

T

K

A

C

D

L

V

L

K

Q

G

L

N

F

I

S

Secondary structure

SS confidence

Disorder

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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 1xhm chain B domain 1 Region: 75 - 85 Aligned: 11 Modelled: 11 Confidence: 30.5% Identity: 36% Fold: Non-globular all-alpha subunits of globular proteins Superfamily: Transducin (heterotrimeric G protein), gamma chain Family: Transducin (heterotrimeric G protein), gamma chain Phyre2 PDB 1xhm chain B Region: 75 - 85 Aligned: 11 Modelled: 11 Confidence: 30.4% Identity: 36% PDB header:signaling protein Chain: B: PDB Molecule:guanine nucleotide-binding protein g(i)/g(s) PDBTitle: the crystal structure of a biologically active peptide2 (sigk) bound to a g protein beta:gamma heterodimer Phyre2 PDB 2kel chain B Region: 81 - 103 Aligned: 23 Modelled: 23 Confidence: 26.5% Identity: 35% PDB header:transcription repressor Chain: B: PDB Molecule:uncharacterized protein 56b; PDBTitle: structure of the transcription regulator svtr from the2 hyperthermophilic archaeal virus sirv1 Phyre2 PDB 1elk chain A Region: 78 - 85 Aligned: 8 Modelled: 8 Confidence: 11.0% Identity: 38% Fold: alpha-alpha superhelix Superfamily: ENTH/VHS domain Family: VHS domain Phyre2 PDB 1xb4 chain A domain 1 Region: 78 - 87 Aligned: 10 Modelled: 10 Confidence: 10.6% Identity: 50% Fold: DNA/RNA-binding 3-helical bundle Superfamily: "Winged helix" DNA-binding domain Family: Vacuolar sorting protein domain Phyre2 PDB 1g8m chain A domain 2 Region: 85 - 107 Aligned: 23 Modelled: 23 Confidence: 8.9% Identity: 17% Fold: Cytidine deaminase-like Superfamily: Cytidine deaminase-like Family: AICAR transformylase domain of bifunctional purine biosynthesis enzyme ATIC Phyre2 PDB 2ahm chain A domain 1 Region: 80 - 104 Aligned: 25 Modelled: 25 Confidence: 8.4% Identity: 12% Fold: immunoglobulin/albumin-binding domain-like Superfamily: Coronavirus NSP7-like Family: Coronavirus NSP7-like Phyre2 PDB 2zme chain D Region: 78 - 86 Aligned: 9 Modelled: 9 Confidence: 7.7% Identity: 33% PDB header:protein transport Chain: D: PDB Molecule:vacuolar protein-sorting-associated protein 25; PDBTitle: integrated structural and functional model of the human escrt-ii2 complex Phyre2 PDB 1ysy chain A domain 1 Region: 80 - 104 Aligned: 25 Modelled: 25 Confidence: 7.4% Identity: 12% Fold: immunoglobulin/albumin-binding domain-like Superfamily: Coronavirus NSP7-like Family: Coronavirus NSP7-like Phyre2 PDB 1ldm chain A domain 2 Region: 92 - 159 Aligned: 60 Modelled: 68 Confidence: 7.3% Identity: 22% Fold: LDH C-terminal domain-like Superfamily: LDH C-terminal domain-like Family: Lactate & malate dehydrogenases, C-terminal domain Phyre2 PDB 3rru chain A Region: 78 - 85 Aligned: 8 Modelled: 8 Confidence: 6.7% Identity: 13% PDB header:signaling protein Chain: A: PDB Molecule:tom1l1 protein; PDBTitle: x-ray crystal structure of the vhs domain of human tom1-like protein,2 northeast structural genomics consortium target hr3050e Phyre2 PDB 1pkx chain A domain 2 Region: 85 - 107 Aligned: 23 Modelled: 23 Confidence: 6.6% Identity: 22% Fold: Cytidine deaminase-like Superfamily: Cytidine deaminase-like Family: AICAR transformylase domain of bifunctional purine biosynthesis enzyme ATIC Phyre2 PDB 3cuq chain D Region: 78 - 86 Aligned: 9 Modelled: 9 Confidence: 6.4% Identity: 33% PDB header:protein transport Chain: D: PDB Molecule:vacuolar protein-sorting-associated protein 25; PDBTitle: integrated structural and functional model of the human escrt-ii2 complex Phyre2 PDB 1mwp chain A Region: 77 - 84 Aligned: 8 Modelled: 8 Confidence: 6.4% Identity: 75% Fold: SRCR-like Superfamily: A heparin-binding domain Family: A heparin-binding domain Phyre2 PDB 3c2q chain A Region: 77 - 87 Aligned: 11 Modelled: 11 Confidence: 5.9% Identity: 36% PDB header:structural genomics, unknown function Chain: A: PDB Molecule:uncharacterized conserved protein; PDBTitle: crystal structure of conserved putative lor/sdh protein2 from methanococcus maripaludis s2 Phyre2 PDB 1omw chain G Region: 75 - 85 Aligned: 11 Modelled: 11 Confidence: 5.9% Identity: 36% Fold: Non-globular all-alpha subunits of globular proteins Superfamily: Transducin (heterotrimeric G protein), gamma chain Family: Transducin (heterotrimeric G protein), gamma chain Phyre2 PDB 1mhq chain A Region: 78 - 85 Aligned: 8 Modelled: 8 Confidence: 5.7% Identity: 25% Fold: alpha-alpha superhelix Superfamily: ENTH/VHS domain Family: VHS domain Phyre2 PDB 1ceu chain A Region: 75 - 85 Aligned: 11 Modelled: 11 Confidence: 5.5% Identity: 9% PDB header:viral protein Chain: A: PDB Molecule:protein (hiv-1 regulatory protein n-terminal PDBTitle: nmr structure of the (1-51) n-terminal domain of the hiv-12 regulatory protein Phyre2 1 d1xhmb1 2 c1xhmB_ 3 c2kelB_ 4 d1elka_ 5 d1xb4a1 6 d1g8ma2 7 d2ahma1 8 c2zmeD_ 9 d1ysya1 10 d1ldma2 11 c3rruA_ 12 d1pkxa2 13 c3cuqD_ 14 d1mwpa_ 15 c3c2qA_ 16 d1omwg_ 17 d1mhqa_ 18 c1ceuA_

Detailed template information

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

1 d1xhmb1 30.5 36 Fold:Non-globular all-alpha subunits of globular proteins Superfamily:Transducin (heterotrimeric G protein), gamma chain Family:Transducin (heterotrimeric G protein), gamma chain 2 c1xhmB_ 30.4 36 PDB header:signaling protein Chain: B: PDB Molecule:guanine nucleotide-binding protein g(i)/g(s) PDBTitle: the crystal structure of a biologically active peptide2 (sigk) bound to a g protein beta:gamma heterodimer 3 c2kelB_ 26.5 35 PDB header:transcription repressor Chain: B: PDB Molecule:uncharacterized protein 56b; PDBTitle: structure of the transcription regulator svtr from the2 hyperthermophilic archaeal virus sirv1 4 d1elka_ 11.0 38 Fold:alpha-alpha superhelix Superfamily:ENTH/VHS domain Family:VHS domain 5 d1xb4a1 10.6 50 Fold:DNA/RNA-binding 3-helical bundle Superfamily:"Winged helix" DNA-binding domain Family:Vacuolar sorting protein domain 6 d1g8ma2 8.9 17 Fold:Cytidine deaminase-like Superfamily:Cytidine deaminase-like Family:AICAR transformylase domain of bifunctional purine biosynthesis enzyme ATIC 7 d2ahma1 8.4 12 Fold:immunoglobulin/albumin-binding domain-like Superfamily:Coronavirus NSP7-like Family:Coronavirus NSP7-like 8 c2zmeD_ 7.7 33 PDB header:protein transport Chain: D: PDB Molecule:vacuolar protein-sorting-associated protein 25; PDBTitle: integrated structural and functional model of the human escrt-ii2 complex 9 d1ysya1 7.4 12 Fold:immunoglobulin/albumin-binding domain-like Superfamily:Coronavirus NSP7-like Family:Coronavirus NSP7-like 10 d1ldma2 7.3 22 Fold:LDH C-terminal domain-like Superfamily:LDH C-terminal domain-like Family:Lactate & malate dehydrogenases, C-terminal domain 11 c3rruA_ 6.7 13 PDB header:signaling protein Chain: A: PDB Molecule:tom1l1 protein; PDBTitle: x-ray crystal structure of the vhs domain of human tom1-like protein,2 northeast structural genomics consortium target hr3050e 12 d1pkxa2 6.6 22 Fold:Cytidine deaminase-like Superfamily:Cytidine deaminase-like Family:AICAR transformylase domain of bifunctional purine biosynthesis enzyme ATIC 13 c3cuqD_ 6.4 33 PDB header:protein transport Chain: D: PDB Molecule:vacuolar protein-sorting-associated protein 25; PDBTitle: integrated structural and functional model of the human escrt-ii2 complex 14 d1mwpa_ 6.4 75 Fold:SRCR-like Superfamily:A heparin-binding domain Family:A heparin-binding domain 15 c3c2qA_ 5.9 36 PDB header:structural genomics, unknown function Chain: A: PDB Molecule:uncharacterized conserved protein; PDBTitle: crystal structure of conserved putative lor/sdh protein2 from methanococcus maripaludis s2 16 d1omwg_ 5.9 36 Fold:Non-globular all-alpha subunits of globular proteins Superfamily:Transducin (heterotrimeric G protein), gamma chain Family:Transducin (heterotrimeric G protein), gamma chain 17 d1mhqa_ 5.7 25 Fold:alpha-alpha superhelix Superfamily:ENTH/VHS domain Family:VHS domain 18 c1ceuA_ 5.5 9 PDB header:viral protein Chain: A: PDB Molecule:protein (hiv-1 regulatory protein n-terminal PDBTitle: nmr structure of the (1-51) n-terminal domain of the hiv-12 regulatory 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

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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