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

A

A

P

Q

R

E

E

T

E

W

R

V

Q

S

K

R

G

L

M

P

A

Y

R

G

E

A

G

Q

Q

V

N

I

K

I

M

E

Y

S

E

R

N

V

R

Q

L

A

S

N

E

Q

E

E

Y

I

P

R

K

I

Secondary structure

SS confidence

Disorder

?

?

?

?

?

?

?

?

?

?

?

?

?

?

?

?

?

?

?

?

?

?

?

Disorder confidence

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70

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Sequence

N

V

G

V

I

N

T

P

T

L

I

R

S

D

Y

Secondary structure

SS confidence

Disorder

?

?

?

?

?

?

?

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 2iub chain A domain 1 Region: 17 - 65 Aligned: 49 Modelled: 49 Confidence: 35.7% Identity: 27% Fold: CorA soluble domain-like Superfamily: CorA soluble domain-like Family: CorA soluble domain-like Phyre2 PDB 2bbj chain B Region: 17 - 65 Aligned: 49 Modelled: 49 Confidence: 22.0% Identity: 27% PDB header:metal transport/membrane protein Chain: B: PDB Molecule:divalent cation transport-related protein; PDBTitle: crystal structure of the cora mg2+ transporter Phyre2 PDB 1dml chain A domain 1 Region: 14 - 39 Aligned: 24 Modelled: 26 Confidence: 11.5% Identity: 33% Fold: DNA clamp Superfamily: DNA clamp Family: DNA polymerase processivity factor Phyre2 PDB 3fo8 chain D Region: 19 - 37 Aligned: 19 Modelled: 19 Confidence: 7.5% Identity: 37% PDB header:viral protein Chain: D: PDB Molecule:tail sheath protein gp18; PDBTitle: crystal structure of the bacteriophage t4 tail sheath2 protein, protease resistant fragment gp18pr Phyre2 PDB 3nkg chain A Region: 56 - 71 Aligned: 16 Modelled: 16 Confidence: 7.1% Identity: 50% PDB header:structural genomics, unknown function Chain: A: PDB Molecule:uncharacterized protein geba250068378; PDBTitle: crystal structure of geba250068378 from sulfurospirillum deleyianum Phyre2 PDB 3ghp chain A Region: 28 - 35 Aligned: 8 Modelled: 8 Confidence: 6.9% Identity: 75% PDB header:structural protein Chain: A: PDB Molecule:cellulosomal scaffoldin adaptor protein b; PDBTitle: structure of the second type ii cohesin module from the2 adaptor scaa scaffoldin of acetivibrio cellulolyticus3 (including long c-terminal linker) Phyre2 PDB 1t4z chain A Region: 63 - 72 Aligned: 10 Modelled: 10 Confidence: 6.7% Identity: 30% Fold: Thioredoxin fold Superfamily: Thioredoxin-like Family: KaiB-like Phyre2 PDB 2bm3 chain A domain 1 Region: 28 - 35 Aligned: 8 Modelled: 8 Confidence: 6.5% Identity: 75% Fold: Common fold of diphtheria toxin/transcription factors/cytochrome f Superfamily: Carbohydrate-binding domain Family: Cellulose-binding domain family III Phyre2 PDB 1zv9 chain A domain 1 Region: 28 - 35 Aligned: 8 Modelled: 6 Confidence: 6.5% Identity: 50% Fold: Common fold of diphtheria toxin/transcription factors/cytochrome f Superfamily: Carbohydrate-binding domain Family: Cellulose-binding domain family III Phyre2 PDB 1tyj chain A domain 1 Region: 28 - 35 Aligned: 8 Modelled: 8 Confidence: 6.2% Identity: 63% Fold: Common fold of diphtheria toxin/transcription factors/cytochrome f Superfamily: Carbohydrate-binding domain Family: Cellulose-binding domain family III Phyre2 PDB 2b59 chain A Region: 28 - 35 Aligned: 8 Modelled: 8 Confidence: 6.1% Identity: 75% PDB header:hydrolase/structural protein Chain: A: PDB Molecule:cog1196: chromosome segregation atpases; PDBTitle: the type ii cohesin dockerin complex Phyre2 PDB 3fnk chain A Region: 28 - 35 Aligned: 8 Modelled: 8 Confidence: 5.9% Identity: 75% PDB header:structural protein Chain: A: PDB Molecule:cellulosomal scaffoldin adaptor protein b; PDBTitle: crystal structure of the second type ii cohesin module from2 the cellulosomal adaptor scaa scaffoldin of acetivibrio3 cellulolyticus Phyre2 PDB 3izb chain T Region: 53 - 59 Aligned: 7 Modelled: 7 Confidence: 5.9% Identity: 71% PDB header:ribosome Chain: T: PDB Molecule:40s ribosomal protein rps21 (s21e); PDBTitle: localization of the small subunit ribosomal proteins into a 6.1 a2 cryo-em map of saccharomyces cerevisiae translating 80s ribosome Phyre2 PDB 1dml chain G Region: 14 - 39 Aligned: 24 Modelled: 26 Confidence: 5.4% Identity: 33% PDB header:dna binding protein/transferase Chain: G: PDB Molecule:dna polymerase processivity factor; PDBTitle: crystal structure of herpes simplex ul42 bound to the c-2 terminus of hsv pol Phyre2 PDB 3fcg chain B Region: 16 - 37 Aligned: 22 Modelled: 22 Confidence: 5.4% Identity: 23% PDB header:membrane protein, protein transport Chain: B: PDB Molecule:f1 capsule-anchoring protein; PDBTitle: crystal structure analysis of the middle domain of the2 caf1a usher Phyre2 1 d2iuba1 2 c2bbjB_ 3 d1dmla1 4 c3fo8D_ 5 c3nkgA_ 6 c3ghpA_ 7 d1t4za_ 8 d2bm3a1 9 d1zv9a1 10 d1tyja1 11 c2b59A_ 12 c3fnkA_ 13 c3izbT_ 14 c1dmlG_ 15 c3fcgB_

Detailed template information

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

1 d2iuba1 35.7 27 Fold:CorA soluble domain-like Superfamily:CorA soluble domain-like Family:CorA soluble domain-like 2 c2bbjB_ 22.0 27 PDB header:metal transport/membrane protein Chain: B: PDB Molecule:divalent cation transport-related protein; PDBTitle: crystal structure of the cora mg2+ transporter 3 d1dmla1 11.5 33 Fold:DNA clamp Superfamily:DNA clamp Family:DNA polymerase processivity factor 4 c3fo8D_ 7.5 37 PDB header:viral protein Chain: D: PDB Molecule:tail sheath protein gp18; PDBTitle: crystal structure of the bacteriophage t4 tail sheath2 protein, protease resistant fragment gp18pr 5 c3nkgA_ 7.1 50 PDB header:structural genomics, unknown function Chain: A: PDB Molecule:uncharacterized protein geba250068378; PDBTitle: crystal structure of geba250068378 from sulfurospirillum deleyianum 6 c3ghpA_ 6.9 75 PDB header:structural protein Chain: A: PDB Molecule:cellulosomal scaffoldin adaptor protein b; PDBTitle: structure of the second type ii cohesin module from the2 adaptor scaa scaffoldin of acetivibrio cellulolyticus3 (including long c-terminal linker) 7 d1t4za_ 6.7 30 Fold:Thioredoxin fold Superfamily:Thioredoxin-like Family:KaiB-like 8 d2bm3a1 6.5 75 Fold:Common fold of diphtheria toxin/transcription factors/cytochrome f Superfamily:Carbohydrate-binding domain Family:Cellulose-binding domain family III 9 d1zv9a1 6.5 50 Fold:Common fold of diphtheria toxin/transcription factors/cytochrome f Superfamily:Carbohydrate-binding domain Family:Cellulose-binding domain family III 10 d1tyja1 6.2 63 Fold:Common fold of diphtheria toxin/transcription factors/cytochrome f Superfamily:Carbohydrate-binding domain Family:Cellulose-binding domain family III 11 c2b59A_ 6.1 75 PDB header:hydrolase/structural protein Chain: A: PDB Molecule:cog1196: chromosome segregation atpases; PDBTitle: the type ii cohesin dockerin complex 12 c3fnkA_ 5.9 75 PDB header:structural protein Chain: A: PDB Molecule:cellulosomal scaffoldin adaptor protein b; PDBTitle: crystal structure of the second type ii cohesin module from2 the cellulosomal adaptor scaa scaffoldin of acetivibrio3 cellulolyticus 13 c3izbT_ 5.9 71 PDB header:ribosome Chain: T: PDB Molecule:40s ribosomal protein rps21 (s21e); PDBTitle: localization of the small subunit ribosomal proteins into a 6.1 a2 cryo-em map of saccharomyces cerevisiae translating 80s ribosome 14 c1dmlG_ 5.4 33 PDB header:dna binding protein/transferase Chain: G: PDB Molecule:dna polymerase processivity factor; PDBTitle: crystal structure of herpes simplex ul42 bound to the c-2 terminus of hsv pol 15 c3fcgB_ 5.4 23 PDB header:membrane protein, protein transport Chain: B: PDB Molecule:f1 capsule-anchoring protein; PDBTitle: crystal structure analysis of the middle domain of the2 caf1a usher

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