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

G

E

I

S

I

T

K

L

L

V

V

A

A

L

V

V

L

L

F

G

T

K

K

L

R

T

L

G

G

D

L

G

A

A

I

K

G

F

K

K

A

M

N

D

D

D

A

A

A

K

K

G

A

D

V

D

L

Q

A

Secondary structure

SS confidence

Disorder

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Disorder confidence

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Sequence

E

K

L

S

H

K

E

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 2l16 chain A Region: 1 - 51 Aligned: 51 Modelled: 51 Confidence: 99.8% Identity: 25% PDB header:protein transport Chain: A: PDB Molecule:sec-independent protein translocase protein tatad; PDBTitle: solution structure of bacillus subtilits tatad protein in dpc micelles Phyre2 PDB 2cqq chain A domain 1 Region: 12 - 52 Aligned: 41 Modelled: 41 Confidence: 18.5% Identity: 12% Fold: DNA/RNA-binding 3-helical bundle Superfamily: Homeodomain-like Family: Myb/SANT domain Phyre2 PDB 2axt chain I domain 1 Region: 9 - 21 Aligned: 13 Modelled: 13 Confidence: 15.0% Identity: 23% Fold: Single transmembrane helix Superfamily: Photosystem II reaction center protein I, PsbI Family: PsbI-like Phyre2 PDB 2axt chain L domain 1 Region: 6 - 19 Aligned: 14 Modelled: 14 Confidence: 9.2% Identity: 29% Fold: Single transmembrane helix Superfamily: Photosystem II reaction center protein L, PsbL Family: PsbL-like Phyre2 PDB 3a0h chain L Region: 6 - 19 Aligned: 14 Modelled: 14 Confidence: 9.2% Identity: 29% PDB header:electron transport Chain: L: PDB Molecule:photosystem ii reaction center protein l; PDBTitle: crystal structure of i-substituted photosystem ii complex Phyre2 PDB 3bz1 chain L Region: 6 - 19 Aligned: 14 Modelled: 14 Confidence: 9.2% Identity: 29% PDB header:electron transport Chain: L: PDB Molecule:photosystem ii reaction center protein l; PDBTitle: crystal structure of cyanobacterial photosystem ii (part 12 of 2). this file contains first monomer of psii dimer Phyre2 PDB 3prq chain L Region: 6 - 19 Aligned: 14 Modelled: 14 Confidence: 9.2% Identity: 29% PDB header:photosynthesis Chain: L: PDB Molecule:photosystem ii reaction center protein l; PDBTitle: crystal structure of cyanobacterial photosystem ii in complex with2 terbutryn (part 1 of 2). this file contains first monomer of psii3 dimer Phyre2 PDB 2axt chain L Region: 6 - 19 Aligned: 14 Modelled: 14 Confidence: 9.2% Identity: 29% PDB header:electron transport Chain: L: PDB Molecule:photosystem ii reaction center l protein; PDBTitle: crystal structure of photosystem ii from thermosynechococcus elongatus Phyre2 PDB 3prr chain L Region: 6 - 19 Aligned: 14 Modelled: 14 Confidence: 9.2% Identity: 29% PDB header:photosynthesis Chain: L: PDB Molecule:photosystem ii reaction center protein l; PDBTitle: crystal structure of cyanobacterial photosystem ii in complex with2 terbutryn (part 2 of 2). this file contains second monomer of psii3 dimer Phyre2 PDB 3arc chain L Region: 6 - 19 Aligned: 14 Modelled: 14 Confidence: 9.2% Identity: 29% PDB header:electron transport, photosynthesis Chain: L: PDB Molecule:photosystem ii reaction center protein l; PDBTitle: crystal structure of oxygen-evolving photosystem ii at 1.9 angstrom2 resolution Phyre2 PDB 3bz2 chain L Region: 6 - 19 Aligned: 14 Modelled: 14 Confidence: 9.2% Identity: 29% PDB header:electron transport Chain: L: PDB Molecule:photosystem ii reaction center protein l; PDBTitle: crystal structure of cyanobacterial photosystem ii (part 22 of 2). this file contains second monomer of psii dimer Phyre2 PDB 3a0b chain L Region: 6 - 19 Aligned: 14 Modelled: 14 Confidence: 9.2% Identity: 29% PDB header:electron transport Chain: L: PDB Molecule:photosystem ii reaction center protein l; PDBTitle: crystal structure of br-substituted photosystem ii complex Phyre2 PDB 3kzi chain L Region: 6 - 19 Aligned: 14 Modelled: 14 Confidence: 9.2% Identity: 29% PDB header:electron transport Chain: L: PDB Molecule:photosystem ii reaction center protein l; PDBTitle: crystal structure of monomeric form of cyanobacterial photosystem ii Phyre2 PDB 1s5l chain L Region: 6 - 19 Aligned: 14 Modelled: 14 Confidence: 9.2% Identity: 29% PDB header:photosynthesis Chain: L: PDB Molecule:photosystem ii reaction center l protein; PDBTitle: architecture of the photosynthetic oxygen evolving center Phyre2 PDB 3a0b chain L Region: 6 - 19 Aligned: 14 Modelled: 14 Confidence: 9.2% Identity: 29% PDB header:electron transport Chain: L: PDB Molecule:photosystem ii reaction center protein l; PDBTitle: crystal structure of br-substituted photosystem ii complex Phyre2 PDB 1s5l chain L Region: 6 - 19 Aligned: 14 Modelled: 14 Confidence: 9.2% Identity: 29% PDB header:photosynthesis Chain: L: PDB Molecule:photosystem ii reaction center l protein; PDBTitle: architecture of the photosynthetic oxygen evolving center Phyre2 PDB 2axt chain L Region: 6 - 19 Aligned: 14 Modelled: 14 Confidence: 9.2% Identity: 29% PDB header:electron transport Chain: L: PDB Molecule:photosystem ii reaction center l protein; PDBTitle: crystal structure of photosystem ii from thermosynechococcus elongatus Phyre2 PDB 3a0h chain L Region: 6 - 19 Aligned: 14 Modelled: 14 Confidence: 9.2% Identity: 29% PDB header:electron transport Chain: L: PDB Molecule:photosystem ii reaction center protein l; PDBTitle: crystal structure of i-substituted photosystem ii complex Phyre2 PDB 2axt chain J domain 1 Region: 9 - 22 Aligned: 14 Modelled: 14 Confidence: 8.3% Identity: 14% Fold: Single transmembrane helix Superfamily: Photosystem II reaction center protein J, PsbJ Family: PsbJ-like Phyre2 PDB 3arc chain L Region: 6 - 19 Aligned: 14 Modelled: 14 Confidence: 8.1% Identity: 29% PDB header:electron transport, photosynthesis Chain: L: PDB Molecule:photosystem ii reaction center protein l; PDBTitle: crystal structure of oxygen-evolving photosystem ii at 1.9 angstrom2 resolution Phyre2 1 c2l16A_ 2 d2cqqa1 3 d2axti1 4 d2axtl1 5 c3a0hl_ 6 c3bz1L_ 7 c3prqL_ 8 c2axtl_ 9 c3prrL_ 10 c3arcL_ 11 c3bz2L_ 12 c3a0bl_ 13 c3kziL_ 14 c1s5ll_ 15 c3a0bL_ 16 c1s5lL_ 17 c2axtL_ 18 c3a0hL_ 19 d2axtj1 20 c3arcl_ 21 22 23

Detailed template information

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

1 c2l16A_ 99.8 25 PDB header:protein transport Chain: A: PDB Molecule:sec-independent protein translocase protein tatad; PDBTitle: solution structure of bacillus subtilits tatad protein in dpc micelles 2 d2cqqa1 18.5 12 Fold:DNA/RNA-binding 3-helical bundle Superfamily:Homeodomain-like Family:Myb/SANT domain 3 d2axti1 15.0 23 Fold:Single transmembrane helix Superfamily:Photosystem II reaction center protein I, PsbI Family:PsbI-like 4 d2axtl1 9.2 29 Fold:Single transmembrane helix Superfamily:Photosystem II reaction center protein L, PsbL Family:PsbL-like 5 c3a0hl_ 9.2 29 PDB header:electron transport Chain: L: PDB Molecule:photosystem ii reaction center protein l; PDBTitle: crystal structure of i-substituted photosystem ii complex 6 c3bz1L_ 9.2 29 PDB header:electron transport Chain: L: PDB Molecule:photosystem ii reaction center protein l; PDBTitle: crystal structure of cyanobacterial photosystem ii (part 12 of 2). this file contains first monomer of psii dimer 7 c3prqL_ 9.2 29 PDB header:photosynthesis Chain: L: PDB Molecule:photosystem ii reaction center protein l; PDBTitle: crystal structure of cyanobacterial photosystem ii in complex with2 terbutryn (part 1 of 2). this file contains first monomer of psii3 dimer 8 c2axtl_ 9.2 29 PDB header:electron transport Chain: L: PDB Molecule:photosystem ii reaction center l protein; PDBTitle: crystal structure of photosystem ii from thermosynechococcus elongatus 9 c3prrL_ 9.2 29 PDB header:photosynthesis Chain: L: PDB Molecule:photosystem ii reaction center protein l; PDBTitle: crystal structure of cyanobacterial photosystem ii in complex with2 terbutryn (part 2 of 2). this file contains second monomer of psii3 dimer 10 c3arcL_ 9.2 29 PDB header:electron transport, photosynthesis Chain: L: PDB Molecule:photosystem ii reaction center protein l; PDBTitle: crystal structure of oxygen-evolving photosystem ii at 1.9 angstrom2 resolution 11 c3bz2L_ 9.2 29 PDB header:electron transport Chain: L: PDB Molecule:photosystem ii reaction center protein l; PDBTitle: crystal structure of cyanobacterial photosystem ii (part 22 of 2). this file contains second monomer of psii dimer 12 c3a0bl_ 9.2 29 PDB header:electron transport Chain: L: PDB Molecule:photosystem ii reaction center protein l; PDBTitle: crystal structure of br-substituted photosystem ii complex 13 c3kziL_ 9.2 29 PDB header:electron transport Chain: L: PDB Molecule:photosystem ii reaction center protein l; PDBTitle: crystal structure of monomeric form of cyanobacterial photosystem ii 14 c1s5ll_ 9.2 29 PDB header:photosynthesis Chain: L: PDB Molecule:photosystem ii reaction center l protein; PDBTitle: architecture of the photosynthetic oxygen evolving center 15 c3a0bL_ 9.2 29 PDB header:electron transport Chain: L: PDB Molecule:photosystem ii reaction center protein l; PDBTitle: crystal structure of br-substituted photosystem ii complex 16 c1s5lL_ 9.2 29 PDB header:photosynthesis Chain: L: PDB Molecule:photosystem ii reaction center l protein; PDBTitle: architecture of the photosynthetic oxygen evolving center 17 c2axtL_ 9.2 29 PDB header:electron transport Chain: L: PDB Molecule:photosystem ii reaction center l protein; PDBTitle: crystal structure of photosystem ii from thermosynechococcus elongatus 18 c3a0hL_ 9.2 29 PDB header:electron transport Chain: L: PDB Molecule:photosystem ii reaction center protein l; PDBTitle: crystal structure of i-substituted photosystem ii complex 19 d2axtj1 8.3 14 Fold:Single transmembrane helix Superfamily:Photosystem II reaction center protein J, PsbJ Family:PsbJ-like 20 c3arcl_ 8.1 29 PDB header:electron transport, photosynthesis Chain: L: PDB Molecule:photosystem ii reaction center protein l; PDBTitle: crystal structure of oxygen-evolving photosystem ii at 1.9 angstrom2 resolution 21 c1by0A_ not modelled 8.0 47 PDB header:rna binding protein Chain: A: PDB Molecule:protein (hepatitis delta antigen); PDBTitle: n-terminal leucine-repeat region of hepatitis delta antigen 22 c1a92B_ not modelled 6.3 41 PDB header:leucine zipper Chain: B: PDB Molecule:delta antigen; PDBTitle: oligomerization domain of hepatitis delta antigen 23 c2kdcC_ not modelled 5.9 9 PDB header:transferase Chain: C: PDB Molecule:diacylglycerol kinase; PDBTitle: nmr solution structure of e. coli diacylglycerol kinase2 (dagk) in dpc micelles

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