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

T

K

M

S

R

Y

A

L

I

T

A

L

A

M

F

L

A

G

C

V

G

Q

R

E

P

A

P

V

E

E

V

K

P

A

P

E

Q

P

A

E

P

Q

Q

P

V

P

T

V

P

S

V

P

T

I

P

Q

Q

P

G

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

P

I

E

H

E

D

Q

T

A

P

P

A

P

H

I

R

H

Y

D

W

N

G

A

M

Q

P

M

V

S

K

M

L

G

A

D

G

V

T

A

G

S

V

L

L

V

D

S

V

N

N

R

T

N

G

S

L

N

A

A

E

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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180

Sequence

A

T

E

T

L

R

N

A

L

A

N

N

G

K

F

T

L

V

S

A

Q

Q

L

S

M

A

K

Q

Q

L

G

L

S

P

Q

D

S

L

G

T

R

S

K

A

I

G

I

A

R

N

V

G

A

H

Y

V

L

Y

S

S

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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210

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Sequence

A

S

G

N

V

N

A

P

T

L

Q

M

Q

L

M

L

V

Q

T

G

E

I

I

W

S

G

K

G

A

V

S

Q

Q

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 3ly8 chain A Region: 110 - 211 Aligned: 84 Modelled: 85 Confidence: 99.5% Identity: 8% PDB header:signaling protein Chain: A: PDB Molecule:transcriptional activator cadc; PDBTitle: crystal structure of mutant d471e of the periplasmic domain of cadc Phyre2 PDB 2hqs chain A domain 2 Region: 100 - 213 Aligned: 99 Modelled: 114 Confidence: 99.2% Identity: 16% Fold: Anticodon-binding domain-like Superfamily: TolB, N-terminal domain Family: TolB, N-terminal domain Phyre2 PDB 2w8b chain B Region: 103 - 213 Aligned: 100 Modelled: 111 Confidence: 87.8% Identity: 19% PDB header:protein transport/membrane protein Chain: B: PDB Molecule:protein tolb; PDBTitle: crystal structure of processed tolb in complex with pal Phyre2 PDB 2ijr chain A domain 1 Region: 6 - 37 Aligned: 32 Modelled: 32 Confidence: 85.2% Identity: 38% Fold: Api92-like Superfamily: Api92-like Family: Api92-like Phyre2 PDB 2ifs chain A Region: 192 - 207 Aligned: 16 Modelled: 16 Confidence: 35.2% Identity: 13% PDB header:signaling protein Chain: A: PDB Molecule:wiskott-aldrich syndrome protien ineracting PDBTitle: structure of the n-wasp evh1 domain in complex with an2 extended wip peptide Phyre2 PDB 2iqi chain A domain 1 Region: 118 - 211 Aligned: 63 Modelled: 63 Confidence: 24.2% Identity: 19% Fold: Anticodon-binding domain-like Superfamily: XCC0632-like Family: XCC0632-like Phyre2 PDB 1mke chain A domain 1 Region: 190 - 207 Aligned: 18 Modelled: 18 Confidence: 17.1% Identity: 11% Fold: PH domain-like barrel Superfamily: PH domain-like Family: Enabled/VASP homology 1 domain (EVH1 domain) Phyre2 PDB 1flg chain A Region: 191 - 205 Aligned: 15 Modelled: 15 Confidence: 13.0% Identity: 13% Fold: 8-bladed beta-propeller Superfamily: Quinoprotein alcohol dehydrogenase-like Family: Quinoprotein alcohol dehydrogenase-like Phyre2 PDB 3gr1 chain A Region: 96 - 194 Aligned: 91 Modelled: 99 Confidence: 11.8% Identity: 19% PDB header:membrane protein Chain: A: PDB Molecule:protein prgh; PDBTitle: periplamic domain of the t3ss inner membrane protein prgh2 from s.typhimurium (fragment 170-392) Phyre2 PDB 2ivz chain D Region: 98 - 213 Aligned: 101 Modelled: 116 Confidence: 9.3% Identity: 18% PDB header:protein transport/hydrolase Chain: D: PDB Molecule:protein tolb; PDBTitle: structure of tolb in complex with a peptide of the colicin2 e9 t-domain Phyre2 PDB 2be1 chain A Region: 191 - 205 Aligned: 15 Modelled: 15 Confidence: 8.0% Identity: 33% PDB header:transcription Chain: A: PDB Molecule:serine/threonine-protein kinase/endoribonuclease ire1; PDBTitle: structure of the compact lumenal domain of yeast ire1 Phyre2 PDB 1kv9 chain A domain 2 Region: 191 - 205 Aligned: 15 Modelled: 15 Confidence: 8.0% Identity: 33% Fold: 8-bladed beta-propeller Superfamily: Quinoprotein alcohol dehydrogenase-like Family: Quinoprotein alcohol dehydrogenase-like Phyre2 PDB 3tek chain A Region: 123 - 209 Aligned: 66 Modelled: 75 Confidence: 7.6% Identity: 18% PDB header:dna binding protein Chain: A: PDB Molecule:thermodbp-single stranded dna binding protein; PDBTitle: thermodbp: a non-canonical single-stranded dna binding protein with a2 novel structure and mechanism Phyre2 PDB 2ad6 chain A domain 1 Region: 191 - 205 Aligned: 15 Modelled: 15 Confidence: 7.1% Identity: 13% Fold: 8-bladed beta-propeller Superfamily: Quinoprotein alcohol dehydrogenase-like Family: Quinoprotein alcohol dehydrogenase-like Phyre2 PDB 3d33 chain B Region: 190 - 206 Aligned: 17 Modelled: 16 Confidence: 7.1% Identity: 6% PDB header:unknown function Chain: B: PDB Molecule:domain of unknown function with an immunoglobulin-like PDBTitle: crystal structure of a duf3244 family protein with an immunoglobulin-2 like beta-sandwich fold (bvu_0276) from bacteroides vulgatus atcc3 8482 at 1.70 a resolution Phyre2 PDB 1kv9 chain A Region: 191 - 205 Aligned: 15 Modelled: 15 Confidence: 7.0% Identity: 33% PDB header:oxidoreductase Chain: A: PDB Molecule:type ii quinohemoprotein alcohol dehydrogenase; PDBTitle: structure at 1.9 a resolution of a quinohemoprotein alcohol2 dehydrogenase from pseudomonas putida hk5 Phyre2 PDB 1bml chain C domain 1 Region: 105 - 182 Aligned: 75 Modelled: 78 Confidence: 6.4% Identity: 9% Fold: beta-Grasp (ubiquitin-like) Superfamily: Staphylokinase/streptokinase Family: Staphylokinase/streptokinase Phyre2 PDB 3o47 chain A Region: 84 - 139 Aligned: 55 Modelled: 56 Confidence: 6.0% Identity: 18% PDB header:hydrolase, hydrolase activator Chain: A: PDB Molecule:adp-ribosylation factor gtpase-activating protein 1, adp- PDBTitle: crystal structure of arfgap1-arf1 fusion protein Phyre2 PDB 1w6s chain A Region: 191 - 205 Aligned: 15 Modelled: 15 Confidence: 5.9% Identity: 20% Fold: 8-bladed beta-propeller Superfamily: Quinoprotein alcohol dehydrogenase-like Family: Quinoprotein alcohol dehydrogenase-like Phyre2 PDB 3sd2 chain A Region: 190 - 206 Aligned: 17 Modelled: 17 Confidence: 5.4% Identity: 29% PDB header:unknown function Chain: A: PDB Molecule:putative member of duf3244 protein family; PDBTitle: crystal structure of a putative member of duf3244 protein family2 (bt_3571) from bacteroides thetaiotaomicron vpi-5482 at 1.40 a3 resolution Phyre2 1 c3ly8A_ 2 d2hqsa2 3 c2w8bB_ 4 d2ijra1 5 c2ifsA_ 6 d2iqia1 7 d1mkea1 8 d1flga_ 9 c3gr1A_ 10 c2ivzD_ 11 c2be1A_ 12 d1kv9a2 13 c3tekA_ 14 d2ad6a1 15 c3d33B_ 16 c1kv9A_ 17 d1bmlc1 18 c3o47A_ 19 d1w6sa_ 20 c3sd2A_ 21

Detailed template information

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

1 c3ly8A_ 99.5 8 PDB header:signaling protein Chain: A: PDB Molecule:transcriptional activator cadc; PDBTitle: crystal structure of mutant d471e of the periplasmic domain of cadc 2 d2hqsa2 99.2 16 Fold:Anticodon-binding domain-like Superfamily:TolB, N-terminal domain Family:TolB, N-terminal domain 3 c2w8bB_ 87.8 19 PDB header:protein transport/membrane protein Chain: B: PDB Molecule:protein tolb; PDBTitle: crystal structure of processed tolb in complex with pal 4 d2ijra1 85.2 38 Fold:Api92-like Superfamily:Api92-like Family:Api92-like 5 c2ifsA_ 35.2 13 PDB header:signaling protein Chain: A: PDB Molecule:wiskott-aldrich syndrome protien ineracting PDBTitle: structure of the n-wasp evh1 domain in complex with an2 extended wip peptide 6 d2iqia1 24.2 19 Fold:Anticodon-binding domain-like Superfamily:XCC0632-like Family:XCC0632-like 7 d1mkea1 17.1 11 Fold:PH domain-like barrel Superfamily:PH domain-like Family:Enabled/VASP homology 1 domain (EVH1 domain) 8 d1flga_ 13.0 13 Fold:8-bladed beta-propeller Superfamily:Quinoprotein alcohol dehydrogenase-like Family:Quinoprotein alcohol dehydrogenase-like 9 c3gr1A_ 11.8 19 PDB header:membrane protein Chain: A: PDB Molecule:protein prgh; PDBTitle: periplamic domain of the t3ss inner membrane protein prgh2 from s.typhimurium (fragment 170-392) 10 c2ivzD_ 9.3 18 PDB header:protein transport/hydrolase Chain: D: PDB Molecule:protein tolb; PDBTitle: structure of tolb in complex with a peptide of the colicin2 e9 t-domain 11 c2be1A_ 8.0 33 PDB header:transcription Chain: A: PDB Molecule:serine/threonine-protein kinase/endoribonuclease ire1; PDBTitle: structure of the compact lumenal domain of yeast ire1 12 d1kv9a2 8.0 33 Fold:8-bladed beta-propeller Superfamily:Quinoprotein alcohol dehydrogenase-like Family:Quinoprotein alcohol dehydrogenase-like 13 c3tekA_ 7.6 18 PDB header:dna binding protein Chain: A: PDB Molecule:thermodbp-single stranded dna binding protein; PDBTitle: thermodbp: a non-canonical single-stranded dna binding protein with a2 novel structure and mechanism 14 d2ad6a1 7.1 13 Fold:8-bladed beta-propeller Superfamily:Quinoprotein alcohol dehydrogenase-like Family:Quinoprotein alcohol dehydrogenase-like 15 c3d33B_ 7.1 6 PDB header:unknown function Chain: B: PDB Molecule:domain of unknown function with an immunoglobulin-like PDBTitle: crystal structure of a duf3244 family protein with an immunoglobulin-2 like beta-sandwich fold (bvu_0276) from bacteroides vulgatus atcc3 8482 at 1.70 a resolution 16 c1kv9A_ 7.0 33 PDB header:oxidoreductase Chain: A: PDB Molecule:type ii quinohemoprotein alcohol dehydrogenase; PDBTitle: structure at 1.9 a resolution of a quinohemoprotein alcohol2 dehydrogenase from pseudomonas putida hk5 17 d1bmlc1 6.4 9 Fold:beta-Grasp (ubiquitin-like) Superfamily:Staphylokinase/streptokinase Family:Staphylokinase/streptokinase 18 c3o47A_ 6.0 18 PDB header:hydrolase, hydrolase activator Chain: A: PDB Molecule:adp-ribosylation factor gtpase-activating protein 1, adp- PDBTitle: crystal structure of arfgap1-arf1 fusion protein 19 d1w6sa_ 5.9 20 Fold:8-bladed beta-propeller Superfamily:Quinoprotein alcohol dehydrogenase-like Family:Quinoprotein alcohol dehydrogenase-like 20 c3sd2A_ 5.4 29 PDB header:unknown function Chain: A: PDB Molecule:putative member of duf3244 protein family; PDBTitle: crystal structure of a putative member of duf3244 protein family2 (bt_3571) from bacteroides thetaiotaomicron vpi-5482 at 1.40 a3 resolution 21 d2a2pa1 not modelled 5.3 24 Fold:Thioredoxin fold Superfamily:Thioredoxin-like Family:Selenoprotein W-related

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