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

G

G

I

S

I

W

Q

L

L

I

I

A

V

I

V

V

L

L

F

G

T

K

K

L

G

S

I

G

S

D

L

G

A

S

I

K

G

F

K

K

A

M

S

D

D

E

P

K

Q

D

K

T

S

Q

D

A

D

F

T

Secondary structure

SS confidence

Disorder

?

?

?

?

?

?

?

?

?

?

?

?

?

?

?

?

?

?

?

?

?

?

Disorder confidence

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70

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80

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Sequence

A

K

T

I

A

D

K

Q

A

D

T

N

Q

E

Q

A

K

T

E

D

A

K

R

H

D

K

E

Q

V

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: 33% 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 2axt chain I domain 1 Region: 9 - 21 Aligned: 13 Modelled: 13 Confidence: 27.2% Identity: 15% Fold: Single transmembrane helix Superfamily: Photosystem II reaction center protein I, PsbI Family: PsbI-like Phyre2 PDB 3bz2 chain L Region: 7 - 19 Aligned: 13 Modelled: 13 Confidence: 23.7% Identity: 38% 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 2axt chain L Region: 7 - 19 Aligned: 13 Modelled: 13 Confidence: 23.7% Identity: 38% 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 2axt chain L domain 1 Region: 7 - 19 Aligned: 13 Modelled: 13 Confidence: 23.7% Identity: 38% Fold: Single transmembrane helix Superfamily: Photosystem II reaction center protein L, PsbL Family: PsbL-like Phyre2 PDB 3prr chain L Region: 7 - 19 Aligned: 13 Modelled: 13 Confidence: 23.7% Identity: 38% 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 3a0h chain L Region: 7 - 19 Aligned: 13 Modelled: 13 Confidence: 23.7% Identity: 38% 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 L Region: 7 - 19 Aligned: 13 Modelled: 13 Confidence: 23.7% Identity: 38% 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 3arc chain L Region: 7 - 19 Aligned: 13 Modelled: 13 Confidence: 23.7% Identity: 38% 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 1s5l chain L Region: 7 - 19 Aligned: 13 Modelled: 13 Confidence: 23.7% Identity: 38% PDB header:photosynthesis Chain: L: PDB Molecule:photosystem ii reaction center l protein; PDBTitle: architecture of the photosynthetic oxygen evolving center Phyre2 PDB 3kzi chain L Region: 7 - 19 Aligned: 13 Modelled: 13 Confidence: 23.7% Identity: 38% 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 3a0b chain L Region: 7 - 19 Aligned: 13 Modelled: 13 Confidence: 23.7% Identity: 38% 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 3a0b chain L Region: 7 - 19 Aligned: 13 Modelled: 13 Confidence: 23.7% Identity: 38% 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 3bz1 chain L Region: 7 - 19 Aligned: 13 Modelled: 13 Confidence: 23.7% Identity: 38% 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 3a0h chain L Region: 7 - 19 Aligned: 13 Modelled: 13 Confidence: 23.7% Identity: 38% 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 3prq chain L Region: 7 - 19 Aligned: 13 Modelled: 13 Confidence: 23.7% Identity: 38% 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 1s5l chain L Region: 7 - 19 Aligned: 13 Modelled: 13 Confidence: 23.7% Identity: 38% PDB header:photosynthesis Chain: L: PDB Molecule:photosystem ii reaction center l protein; PDBTitle: architecture of the photosynthetic oxygen evolving center Phyre2 PDB 3arc chain L Region: 7 - 19 Aligned: 13 Modelled: 13 Confidence: 21.0% Identity: 38% 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 2kdc chain C Region: 2 - 23 Aligned: 22 Modelled: 22 Confidence: 18.7% Identity: 9% PDB header:transferase Chain: C: PDB Molecule:diacylglycerol kinase; PDBTitle: nmr solution structure of e. coli diacylglycerol kinase2 (dagk) in dpc micelles Phyre2 PDB 2cqq chain A domain 1 Region: 12 - 50 Aligned: 39 Modelled: 39 Confidence: 16.4% Identity: 18% Fold: DNA/RNA-binding 3-helical bundle Superfamily: Homeodomain-like Family: Myb/SANT domain Phyre2 1 c2l16A_ 2 d2axti1 3 c3bz2L_ 4 c2axtL_ 5 d2axtl1 6 c3prrL_ 7 c3a0hl_ 8 c2axtl_ 9 c3arcL_ 10 c1s5lL_ 11 c3kziL_ 12 c3a0bl_ 13 c3a0bL_ 14 c3bz1L_ 15 c3a0hL_ 16 c3prqL_ 17 c1s5ll_ 18 c3arcl_ 19 c2kdcC_ 20 d2cqqa1 21 22 23 24 25 26 27 28 29

Detailed template information

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

1 c2l16A_ 99.8 33 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 d2axti1 27.2 15 Fold:Single transmembrane helix Superfamily:Photosystem II reaction center protein I, PsbI Family:PsbI-like 3 c3bz2L_ 23.7 38 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 4 c2axtL_ 23.7 38 PDB header:electron transport Chain: L: PDB Molecule:photosystem ii reaction center l protein; PDBTitle: crystal structure of photosystem ii from thermosynechococcus elongatus 5 d2axtl1 23.7 38 Fold:Single transmembrane helix Superfamily:Photosystem II reaction center protein L, PsbL Family:PsbL-like 6 c3prrL_ 23.7 38 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 7 c3a0hl_ 23.7 38 PDB header:electron transport Chain: L: PDB Molecule:photosystem ii reaction center protein l; PDBTitle: crystal structure of i-substituted photosystem ii complex 8 c2axtl_ 23.7 38 PDB header:electron transport Chain: L: PDB Molecule:photosystem ii reaction center l protein; PDBTitle: crystal structure of photosystem ii from thermosynechococcus elongatus 9 c3arcL_ 23.7 38 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 10 c1s5lL_ 23.7 38 PDB header:photosynthesis Chain: L: PDB Molecule:photosystem ii reaction center l protein; PDBTitle: architecture of the photosynthetic oxygen evolving center 11 c3kziL_ 23.7 38 PDB header:electron transport Chain: L: PDB Molecule:photosystem ii reaction center protein l; PDBTitle: crystal structure of monomeric form of cyanobacterial photosystem ii 12 c3a0bl_ 23.7 38 PDB header:electron transport Chain: L: PDB Molecule:photosystem ii reaction center protein l; PDBTitle: crystal structure of br-substituted photosystem ii complex 13 c3a0bL_ 23.7 38 PDB header:electron transport Chain: L: PDB Molecule:photosystem ii reaction center protein l; PDBTitle: crystal structure of br-substituted photosystem ii complex 14 c3bz1L_ 23.7 38 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 15 c3a0hL_ 23.7 38 PDB header:electron transport Chain: L: PDB Molecule:photosystem ii reaction center protein l; PDBTitle: crystal structure of i-substituted photosystem ii complex 16 c3prqL_ 23.7 38 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 17 c1s5ll_ 23.7 38 PDB header:photosynthesis Chain: L: PDB Molecule:photosystem ii reaction center l protein; PDBTitle: architecture of the photosynthetic oxygen evolving center 18 c3arcl_ 21.0 38 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 19 c2kdcC_ 18.7 9 PDB header:transferase Chain: C: PDB Molecule:diacylglycerol kinase; PDBTitle: nmr solution structure of e. coli diacylglycerol kinase2 (dagk) in dpc micelles 20 d2cqqa1 16.4 18 Fold:DNA/RNA-binding 3-helical bundle Superfamily:Homeodomain-like Family:Myb/SANT domain 21 c1a92B_ not modelled 15.6 39 PDB header:leucine zipper Chain: B: PDB Molecule:delta antigen; PDBTitle: oligomerization domain of hepatitis delta antigen 22 d2axtj1 not modelled 14.7 14 Fold:Single transmembrane helix Superfamily:Photosystem II reaction center protein J, PsbJ Family:PsbJ-like 23 c1by0A_ not modelled 10.5 42 PDB header:rna binding protein Chain: A: PDB Molecule:protein (hepatitis delta antigen); PDBTitle: n-terminal leucine-repeat region of hepatitis delta antigen 24 d1m56d_ not modelled 9.7 12 Fold:Single transmembrane helix Superfamily:Bacterial aa3 type cytochrome c oxidase subunit IV Family:Bacterial aa3 type cytochrome c oxidase subunit IV 25 d2fbia1 not modelled 8.7 11 Fold:DNA/RNA-binding 3-helical bundle Superfamily:"Winged helix" DNA-binding domain Family:MarR-like transcriptional regulators 26 c2rdpA_ not modelled 8.0 11 PDB header:transcription Chain: A: PDB Molecule:putative transcriptional regulator marr; PDBTitle: the structure of a marr family protein from bacillus2 stearothermophilus 27 c4a1qB_ not modelled 6.7 24 PDB header:viral protein Chain: B: PDB Molecule:orf e73; PDBTitle: solution structure of e73 protein from sulfolobus spindle-2 shaped virus ragged hills, a hyperthermophilic3 crenarchaeal virus from yellowstone national park 28 c2fa5B_ not modelled 5.4 13 PDB header:transcription Chain: B: PDB Molecule:transcriptional regulator marr/emrr family; PDBTitle: the crystal structure of an unliganded multiple antibiotic-2 resistance repressor (marr) from xanthomonas campestris 29 d1cola_ not modelled 5.2 32 Fold:Toxins' membrane translocation domains Superfamily:Colicin Family:Colicin

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