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

K

Q

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S

F

F

I

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L

L

G

T

L

L

L

Y

G

C

A

G

T

S

T

E

F

E

C

N

A

T

T

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D

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C

M

T

M

E

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A

N

E

K

A

K

K

L

E

R

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S

E

A

K

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V

A

A

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

L

P

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L

A

E

G

N

F

R

T

M

P

V

Q

T

V

T

A

T

T

P

S

G

S

R

P

A

V

T

A

H

P

E

Q

K

L

L

A

P

R

P

L

F

T

A

A

R

E

V

K

T

V

V

P

V

S

S

V

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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170

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Sequence

T

P

V

T

P

P

R

P

L

R

T

G

E

Q

T

A

A

L

W

I

A

P

Y

I

D

N

Q

D

V

Y

H

Q

P

S

S

V

F

F

V

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W

G

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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 1jb0 chain A Region: 25 - 36 Aligned: 12 Modelled: 12 Confidence: 23.6% Identity: 33% Fold: Photosystem I subunits PsaA/PsaB Superfamily: Photosystem I subunits PsaA/PsaB Family: Photosystem I subunits PsaA/PsaB Phyre2 PDB 1jb0 chain B Region: 25 - 36 Aligned: 12 Modelled: 12 Confidence: 21.2% Identity: 33% Fold: Photosystem I subunits PsaA/PsaB Superfamily: Photosystem I subunits PsaA/PsaB Family: Photosystem I subunits PsaA/PsaB Phyre2 PDB 2l61 chain A Region: 17 - 38 Aligned: 17 Modelled: 22 Confidence: 19.6% Identity: 35% PDB header:metal binding protein Chain: A: PDB Molecule:ec protein i/ii; PDBTitle: protein and metal cluster structure of the wheat metallothionein2 domain g-ec-1. the second part of the puzzle. Phyre2 PDB 3d0f chain A Region: 139 - 170 Aligned: 32 Modelled: 32 Confidence: 16.7% Identity: 6% PDB header:transferase Chain: A: PDB Molecule:penicillin-binding 1 transmembrane protein mrca; PDBTitle: structure of the big_1156.2 domain of putative penicillin-binding2 protein mrca from nitrosomonas europaea atcc 19718 Phyre2 PDB 2vsa chain A Region: 134 - 148 Aligned: 15 Modelled: 15 Confidence: 14.3% Identity: 27% PDB header:toxin Chain: A: PDB Molecule:mosquitocidal toxin; PDBTitle: structure and mode of action of a mosquitocidal holotoxin Phyre2 PDB 3e9v chain A domain 1 Region: 133 - 144 Aligned: 12 Modelled: 12 Confidence: 12.8% Identity: 33% Fold: BTG domain-like Superfamily: BTG domain-like Family: BTG domain-like Phyre2 PDB 2z15 chain A domain 1 Region: 133 - 144 Aligned: 12 Modelled: 12 Confidence: 11.8% Identity: 33% Fold: BTG domain-like Superfamily: BTG domain-like Family: BTG domain-like Phyre2 PDB 2ktr chain A Region: 143 - 151 Aligned: 9 Modelled: 9 Confidence: 9.2% Identity: 11% PDB header:signaling protein, transport protein Chain: A: PDB Molecule:sequestosome-1; PDBTitle: nmr structure of p62 pb1 dimer determined based on pcs Phyre2 PDB 1q90 chain C Region: 137 - 147 Aligned: 11 Modelled: 11 Confidence: 9.0% Identity: 0% Fold: ISP domain Superfamily: ISP domain Family: Rieske iron-sulfur protein (ISP) Phyre2 PDB 2jvy chain A Region: 23 - 30 Aligned: 8 Modelled: 8 Confidence: 8.7% Identity: 38% PDB header:metal binding protein Chain: A: PDB Molecule:nf-kappa-b essential modulator; PDBTitle: solution structure of the eda-id-related c417f mutant of2 human nemo zinc finger Phyre2 PDB 2aap chain A Region: 18 - 30 Aligned: 13 Modelled: 13 Confidence: 8.4% Identity: 38% PDB header:toxin Chain: A: PDB Molecule:jingzhaotoxin-vii; PDBTitle: solution structure of jingzhaotoxin-vii Phyre2 PDB 1e1h chain C Region: 137 - 157 Aligned: 21 Modelled: 21 Confidence: 8.2% Identity: 19% PDB header:hydrolase Chain: C: PDB Molecule:botulinum neurotoxin type a light chain; PDBTitle: crystal structure of recombinant botulinum neurotoxin type2 a light chain, self-inhibiting zn endopeptidase. Phyre2 PDB 1wmh chain A Region: 130 - 142 Aligned: 13 Modelled: 13 Confidence: 8.0% Identity: 8% Fold: beta-Grasp (ubiquitin-like) Superfamily: CAD & PB1 domains Family: PB1 domain Phyre2 PDB 3k3q chain B Region: 137 - 157 Aligned: 21 Modelled: 21 Confidence: 7.8% Identity: 19% PDB header:immune system Chain: B: PDB Molecule:botulinum neurotoxin type a; PDBTitle: crystal structure of a llama antibody complexed with the c.2 botulinum neurotoxin serotype a catalytic domain Phyre2 PDB 1ymz chain A Region: 144 - 170 Aligned: 24 Modelled: 27 Confidence: 7.6% Identity: 17% PDB header:unknown function Chain: A: PDB Molecule:cc45; PDBTitle: cc45, an artificial ww domain designed using statistical2 coupling analysis Phyre2 PDB 2iyj chain A Region: 143 - 157 Aligned: 15 Modelled: 15 Confidence: 7.6% Identity: 13% PDB header:isomerase Chain: A: PDB Molecule:thiol disulfide interchange protein dsbc; PDBTitle: crystal structure of the n-terminal dimer domain of e.coli2 dsbc Phyre2 PDB 3ic3 chain C Region: 134 - 141 Aligned: 8 Modelled: 8 Confidence: 7.2% Identity: 0% PDB header:oxidoreductase Chain: C: PDB Molecule:putative pyruvate dehydrogenase; PDBTitle: structure of a putative pyruvate dehydrogenase from the photosynthetic2 bacterium rhodopseudomonas palustrus cga009 Phyre2 PDB 1e0m chain A Region: 144 - 170 Aligned: 24 Modelled: 27 Confidence: 7.1% Identity: 21% PDB header:de novo protein Chain: A: PDB Molecule:wwprototype; PDBTitle: prototype ww domain Phyre2 PDB 1rfs chain A Region: 137 - 147 Aligned: 11 Modelled: 11 Confidence: 7.0% Identity: 9% Fold: ISP domain Superfamily: ISP domain Family: Rieske iron-sulfur protein (ISP) Phyre2 PDB 1cew chain I Region: 136 - 146 Aligned: 11 Modelled: 11 Confidence: 7.0% Identity: 9% Fold: Cystatin-like Superfamily: Cystatin/monellin Family: Cystatins Phyre2 1 d1jb0a_ 2 d1jb0b_ 3 c2l61A_ 4 c3d0fA_ 5 c2vsaA_ 6 d3e9va1 7 d2z15a1 8 c2ktrA_ 9 d1q90c_ 10 c2jvyA_ 11 c2aapA_ 12 c1e1hC_ 13 d1wmha_ 14 c3k3qB_ 15 c1ymzA_ 16 c2iyjA_ 17 c3ic3C_ 18 c1e0mA_ 19 d1rfsa_ 20 d1cewi_ 21 22 23 24 25 26 27 28 29 30 31 32 33

Detailed template information

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

1 d1jb0a_ 23.6 33 Fold:Photosystem I subunits PsaA/PsaB Superfamily:Photosystem I subunits PsaA/PsaB Family:Photosystem I subunits PsaA/PsaB 2 d1jb0b_ 21.2 33 Fold:Photosystem I subunits PsaA/PsaB Superfamily:Photosystem I subunits PsaA/PsaB Family:Photosystem I subunits PsaA/PsaB 3 c2l61A_ 19.6 35 PDB header:metal binding protein Chain: A: PDB Molecule:ec protein i/ii; PDBTitle: protein and metal cluster structure of the wheat metallothionein2 domain g-ec-1. the second part of the puzzle. 4 c3d0fA_ 16.7 6 PDB header:transferase Chain: A: PDB Molecule:penicillin-binding 1 transmembrane protein mrca; PDBTitle: structure of the big_1156.2 domain of putative penicillin-binding2 protein mrca from nitrosomonas europaea atcc 19718 5 c2vsaA_ 14.3 27 PDB header:toxin Chain: A: PDB Molecule:mosquitocidal toxin; PDBTitle: structure and mode of action of a mosquitocidal holotoxin 6 d3e9va1 12.8 33 Fold:BTG domain-like Superfamily:BTG domain-like Family:BTG domain-like 7 d2z15a1 11.8 33 Fold:BTG domain-like Superfamily:BTG domain-like Family:BTG domain-like 8 c2ktrA_ 9.2 11 PDB header:signaling protein, transport protein Chain: A: PDB Molecule:sequestosome-1; PDBTitle: nmr structure of p62 pb1 dimer determined based on pcs 9 d1q90c_ 9.0 0 Fold:ISP domain Superfamily:ISP domain Family:Rieske iron-sulfur protein (ISP) 10 c2jvyA_ 8.7 38 PDB header:metal binding protein Chain: A: PDB Molecule:nf-kappa-b essential modulator; PDBTitle: solution structure of the eda-id-related c417f mutant of2 human nemo zinc finger 11 c2aapA_ 8.4 38 PDB header:toxin Chain: A: PDB Molecule:jingzhaotoxin-vii; PDBTitle: solution structure of jingzhaotoxin-vii 12 c1e1hC_ 8.2 19 PDB header:hydrolase Chain: C: PDB Molecule:botulinum neurotoxin type a light chain; PDBTitle: crystal structure of recombinant botulinum neurotoxin type2 a light chain, self-inhibiting zn endopeptidase. 13 d1wmha_ 8.0 8 Fold:beta-Grasp (ubiquitin-like) Superfamily:CAD & PB1 domains Family:PB1 domain 14 c3k3qB_ 7.8 19 PDB header:immune system Chain: B: PDB Molecule:botulinum neurotoxin type a; PDBTitle: crystal structure of a llama antibody complexed with the c.2 botulinum neurotoxin serotype a catalytic domain 15 c1ymzA_ 7.6 17 PDB header:unknown function Chain: A: PDB Molecule:cc45; PDBTitle: cc45, an artificial ww domain designed using statistical2 coupling analysis 16 c2iyjA_ 7.6 13 PDB header:isomerase Chain: A: PDB Molecule:thiol disulfide interchange protein dsbc; PDBTitle: crystal structure of the n-terminal dimer domain of e.coli2 dsbc 17 c3ic3C_ 7.2 0 PDB header:oxidoreductase Chain: C: PDB Molecule:putative pyruvate dehydrogenase; PDBTitle: structure of a putative pyruvate dehydrogenase from the photosynthetic2 bacterium rhodopseudomonas palustrus cga009 18 c1e0mA_ 7.1 21 PDB header:de novo protein Chain: A: PDB Molecule:wwprototype; PDBTitle: prototype ww domain 19 d1rfsa_ 7.0 9 Fold:ISP domain Superfamily:ISP domain Family:Rieske iron-sulfur protein (ISP) 20 d1cewi_ 7.0 9 Fold:Cystatin-like Superfamily:Cystatin/monellin Family:Cystatins 21 c2j4mA_ not modelled 7.0 24 PDB header:protein binding Chain: A: PDB Molecule:endoglucanase 45a; PDBTitle: double dockerin from piromyces equi cel45a 22 c2wwaJ_ not modelled 6.8 33 PDB header:ribosome Chain: J: PDB Molecule:60s ribosomal protein l19; PDBTitle: cryo-em structure of idle yeast ssh1 complex bound to the2 yeast 80s ribosome 23 d1p90a_ not modelled 6.6 26 Fold:Ribonuclease H-like motif Superfamily:Nitrogenase accessory factor-like Family:Nitrogenase accessory factor 24 d1hc1a3 not modelled 6.6 14 Fold:Immunoglobulin-like beta-sandwich Superfamily:E set domains Family:Arthropod hemocyanin, C-terminal domain 25 d2jmfa1 not modelled 6.4 13 Fold:WW domain-like Superfamily:WW domain Family:WW domain 26 d1plqa2 not modelled 6.3 15 Fold:DNA clamp Superfamily:DNA clamp Family:DNA polymerase processivity factor 27 d2rm0w1 not modelled 6.0 21 Fold:WW domain-like Superfamily:WW domain Family:WW domain 28 c2kykA_ not modelled 5.8 20 PDB header:ligase Chain: A: PDB Molecule:e3 ubiquitin-protein ligase itchy homolog; PDBTitle: the sandwich region between two lmp2a py motif regulates the2 interaction between aip4ww2domain and py motif 29 d1mzga_ not modelled 5.7 16 Fold:SufE/NifU Superfamily:SufE/NifU Family:SufE-like 30 d1t3ba2 not modelled 5.6 13 Fold:Cystatin-like Superfamily:DsbC/DsbG N-terminal domain-like Family:DsbC/DsbG N-terminal domain-like 31 c2djyA_ not modelled 5.2 13 PDB header:ligase/signaling protein Chain: A: PDB Molecule:smad ubiquitination regulatory factor 2; PDBTitle: solution structure of smurf2 ww3 domain-smad7 py peptide2 complex 32 d1pqsa_ not modelled 5.1 20 Fold:beta-Grasp (ubiquitin-like) Superfamily:CAD & PB1 domains Family:PB1 domain 33 d1r46a2 not modelled 5.0 14 Fold:TIM beta/alpha-barrel Superfamily:(Trans)glycosidases Family:Amylase, catalytic 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