Secondary structure and disorder prediction

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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

Y

K

I

T

A

T

I

E

K

E

G

G

T

P

T

N

W

T

R

Y

S

K

S

K

L

T

K

S

E

C

E

K

M

L

S

G

K

K

E

A

G

V

S

R

E

Q

K

V

K

L

I

N

F

N

C

E

K

L

Q

Secondary structure

SS confidence

Disorder

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?

Disorder confidence

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Sequence

S

S

R

I

A

L

Y

S

N

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 1ocs chain A Region: 2 - 39 Aligned: 38 Modelled: 38 Confidence: 27.2% Identity: 13% Fold: PX domain Superfamily: PX domain Family: PX domain Phyre2 PDB 1ocu chain A Region: 2 - 39 Aligned: 38 Modelled: 38 Confidence: 20.9% Identity: 13% PDB header:sorting protein Chain: A: PDB Molecule:sorting nexin; PDBTitle: crystal structure of the yeast px-domain protein grd19p2 (sorting nexin 3) complexed to3 phosphatidylinosytol-3-phospahte. Phyre2 PDB 1go3 chain E Region: 2 - 18 Aligned: 17 Modelled: 17 Confidence: 18.8% Identity: 24% PDB header:transferase Chain: E: PDB Molecule:dna-directed rna polymerase subunit e; PDBTitle: structure of an archeal homolog of the eukaryotic rna2 polymerase ii rpb4/rpb7 complex Phyre2 PDB 1lc0 chain A domain 2 Region: 3 - 19 Aligned: 17 Modelled: 17 Confidence: 12.8% Identity: 24% Fold: FwdE/GAPDH domain-like Superfamily: Glyceraldehyde-3-phosphate dehydrogenase-like, C-terminal domain Family: Biliverdin reductase Phyre2 PDB 3iq2 chain B Region: 2 - 37 Aligned: 36 Modelled: 36 Confidence: 12.7% Identity: 17% PDB header:protein transport Chain: B: PDB Molecule:sorting nexin-7; PDBTitle: human sorting nexin 7, phox homology (px) domain Phyre2 PDB 2bze chain A domain 1 Region: 22 - 45 Aligned: 24 Modelled: 24 Confidence: 12.3% Identity: 29% Fold: SH3-like barrel Superfamily: Plus3-like Family: Plus3 Phyre2 PDB 2jv4 chain A Region: 13 - 25 Aligned: 13 Modelled: 13 Confidence: 10.0% Identity: 54% PDB header:isomerase Chain: A: PDB Molecule:peptidyl-prolyl cis/trans isomerase; PDBTitle: structure characterisation of pina ww domain and comparison2 with other group iv ww domains, pin1 and ess1 Phyre2 PDB 2pmz chain E Region: 3 - 18 Aligned: 16 Modelled: 16 Confidence: 9.8% Identity: 19% PDB header:translation, transferase Chain: E: PDB Molecule:dna-directed rna polymerase subunit e; PDBTitle: archaeal rna polymerase from sulfolobus solfataricus Phyre2 PDB 3m1m chain A Region: 7 - 65 Aligned: 59 Modelled: 59 Confidence: 9.3% Identity: 17% PDB header:replication Chain: A: PDB Molecule:orf904; PDBTitle: crystal structure of the primase-polymerase from sulfolobus islandicus Phyre2 PDB 2v2g chain C Region: 14 - 39 Aligned: 26 Modelled: 26 Confidence: 8.7% Identity: 15% PDB header:oxidoreductase Chain: C: PDB Molecule:peroxiredoxin 6; PDBTitle: crystal structure of the c45s mutant of the peroxiredoxin 62 of arenicola marina. monoclinic form Phyre2 PDB 2p06 chain A Region: 10 - 22 Aligned: 13 Modelled: 13 Confidence: 8.4% Identity: 38% PDB header:structural genomics, unknown function Chain: A: PDB Molecule:hypothetical protein af_0060; PDBTitle: crystal structure of a predicted coding region af_0060 from2 archaeoglobus fulgidus dsm 4304 Phyre2 PDB 2p06 chain A domain 1 Region: 10 - 22 Aligned: 13 Modelled: 13 Confidence: 8.4% Identity: 38% Fold: all-alpha NTP pyrophosphatases Superfamily: all-alpha NTP pyrophosphatases Family: AF0060-like Phyre2 PDB 1mli chain A Region: 2 - 15 Aligned: 14 Modelled: 14 Confidence: 7.7% Identity: 7% Fold: Ferredoxin-like Superfamily: Dimeric alpha+beta barrel Family: Muconalactone isomerase, MLI Phyre2 PDB 2anx chain B Region: 10 - 35 Aligned: 22 Modelled: 26 Confidence: 7.6% Identity: 18% PDB header:hydrolase Chain: B: PDB Molecule:lysozyme; PDBTitle: crystal structure of bacteriophage p22 lysozyme mutant l87m Phyre2 PDB 1sa3 chain A Region: 13 - 25 Aligned: 13 Modelled: 13 Confidence: 7.2% Identity: 62% Fold: Restriction endonuclease-like Superfamily: Restriction endonuclease-like Family: Restriction endonuclease MspI Phyre2 1 d1ocsa_ 2 c1ocuA_ 3 c1go3E_ 4 d1lc0a2 5 c3iq2B_ 6 d2bzea1 7 c2jv4A_ 8 c2pmzE_ 9 c3m1mA_ 10 c2v2gC_ 11 c2p06A_ 12 d2p06a1 13 d1mlia_ 14 c2anxB_ 15 d1sa3a_

Detailed template information

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

1 d1ocsa_ 27.2 13 Fold:PX domain Superfamily:PX domain Family:PX domain 2 c1ocuA_ 20.9 13 PDB header:sorting protein Chain: A: PDB Molecule:sorting nexin; PDBTitle: crystal structure of the yeast px-domain protein grd19p2 (sorting nexin 3) complexed to3 phosphatidylinosytol-3-phospahte. 3 c1go3E_ 18.8 24 PDB header:transferase Chain: E: PDB Molecule:dna-directed rna polymerase subunit e; PDBTitle: structure of an archeal homolog of the eukaryotic rna2 polymerase ii rpb4/rpb7 complex 4 d1lc0a2 12.8 24 Fold:FwdE/GAPDH domain-like Superfamily:Glyceraldehyde-3-phosphate dehydrogenase-like, C-terminal domain Family:Biliverdin reductase 5 c3iq2B_ 12.7 17 PDB header:protein transport Chain: B: PDB Molecule:sorting nexin-7; PDBTitle: human sorting nexin 7, phox homology (px) domain 6 d2bzea1 12.3 29 Fold:SH3-like barrel Superfamily:Plus3-like Family:Plus3 7 c2jv4A_ 10.0 54 PDB header:isomerase Chain: A: PDB Molecule:peptidyl-prolyl cis/trans isomerase; PDBTitle: structure characterisation of pina ww domain and comparison2 with other group iv ww domains, pin1 and ess1 8 c2pmzE_ 9.8 19 PDB header:translation, transferase Chain: E: PDB Molecule:dna-directed rna polymerase subunit e; PDBTitle: archaeal rna polymerase from sulfolobus solfataricus 9 c3m1mA_ 9.3 17 PDB header:replication Chain: A: PDB Molecule:orf904; PDBTitle: crystal structure of the primase-polymerase from sulfolobus islandicus 10 c2v2gC_ 8.7 15 PDB header:oxidoreductase Chain: C: PDB Molecule:peroxiredoxin 6; PDBTitle: crystal structure of the c45s mutant of the peroxiredoxin 62 of arenicola marina. monoclinic form 11 c2p06A_ 8.4 38 PDB header:structural genomics, unknown function Chain: A: PDB Molecule:hypothetical protein af_0060; PDBTitle: crystal structure of a predicted coding region af_0060 from2 archaeoglobus fulgidus dsm 4304 12 d2p06a1 8.4 38 Fold:all-alpha NTP pyrophosphatases Superfamily:all-alpha NTP pyrophosphatases Family:AF0060-like 13 d1mlia_ 7.7 7 Fold:Ferredoxin-like Superfamily:Dimeric alpha+beta barrel Family:Muconalactone isomerase, MLI 14 c2anxB_ 7.6 18 PDB header:hydrolase Chain: B: PDB Molecule:lysozyme; PDBTitle: crystal structure of bacteriophage p22 lysozyme mutant l87m 15 d1sa3a_ 7.2 62 Fold:Restriction endonuclease-like Superfamily:Restriction endonuclease-like Family:Restriction endonuclease MspI

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