Secondary structure and disorder prediction

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10

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20

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40

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50

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60

Sequence

M

D

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L

A

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Y

W

W

I

L

V

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F

L

V

G

V

L

L

N

V

I

K

D

L

K

R

V

D

H

K

K

F

L

A

N

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P

E

L

P

P

H

R

D

F

N

D

K

W

D

D

D

D

D

W

P

K

Secondary structure

SS confidence

Disorder

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Disorder confidence

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Sequence

K

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Q

P

K

K

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 2knc chain A Region: 8 - 44 Aligned: 37 Modelled: 37 Confidence: 23.9% Identity: 30% PDB header:cell adhesion Chain: A: PDB Molecule:integrin alpha-iib; PDBTitle: platelet integrin alfaiib-beta3 transmembrane-cytoplasmic2 heterocomplex Phyre2 PDB 2axt chain L domain 1 Region: 8 - 21 Aligned: 14 Modelled: 14 Confidence: 18.6% Identity: 14% Fold: Single transmembrane helix Superfamily: Photosystem II reaction center protein L, PsbL Family: PsbL-like Phyre2 PDB 3a0b chain L Region: 8 - 21 Aligned: 14 Modelled: 14 Confidence: 18.6% Identity: 14% 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 3prr chain L Region: 8 - 21 Aligned: 14 Modelled: 14 Confidence: 18.6% Identity: 14% 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 1s5l chain L Region: 8 - 21 Aligned: 14 Modelled: 14 Confidence: 18.6% Identity: 14% 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: 8 - 21 Aligned: 14 Modelled: 14 Confidence: 18.6% Identity: 14% 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 2axt chain L Region: 8 - 21 Aligned: 14 Modelled: 14 Confidence: 18.6% Identity: 14% 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 3bz2 chain L Region: 8 - 21 Aligned: 14 Modelled: 14 Confidence: 18.6% Identity: 14% 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 1s5l chain L Region: 8 - 21 Aligned: 14 Modelled: 14 Confidence: 18.6% Identity: 14% PDB header:photosynthesis Chain: L: PDB Molecule:photosystem ii reaction center l protein; PDBTitle: architecture of the photosynthetic oxygen evolving center Phyre2 PDB 3a0h chain L Region: 8 - 21 Aligned: 14 Modelled: 14 Confidence: 18.6% Identity: 14% 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 3kzi chain L Region: 8 - 21 Aligned: 14 Modelled: 14 Confidence: 18.6% Identity: 14% 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 3prq chain L Region: 8 - 21 Aligned: 14 Modelled: 14 Confidence: 18.6% Identity: 14% 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 3bz1 chain L Region: 8 - 21 Aligned: 14 Modelled: 14 Confidence: 18.6% Identity: 14% 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: 8 - 21 Aligned: 14 Modelled: 14 Confidence: 18.6% Identity: 14% 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 3arc chain L Region: 8 - 21 Aligned: 14 Modelled: 14 Confidence: 18.6% Identity: 14% 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 2axt chain L Region: 8 - 21 Aligned: 14 Modelled: 14 Confidence: 18.6% Identity: 14% 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 3aa6 chain C Region: 34 - 46 Aligned: 13 Modelled: 13 Confidence: 10.1% Identity: 38% PDB header:protein binding Chain: C: PDB Molecule:23mer peptide from cd2-associated protein; PDBTitle: crystal structure of actin capping protein in complex with the cp-2 binding motif derived from cd2ap Phyre2 PDB 2k1a chain A Region: 8 - 24 Aligned: 17 Modelled: 17 Confidence: 8.9% Identity: 35% PDB header:cell adhesion Chain: A: PDB Molecule:integrin alpha-iib; PDBTitle: bicelle-embedded integrin alpha(iib) transmembrane segment Phyre2 PDB 1fft chain B domain 2 Region: 3 - 32 Aligned: 30 Modelled: 30 Confidence: 8.3% Identity: 10% Fold: Transmembrane helix hairpin Superfamily: Cytochrome c oxidase subunit II-like, transmembrane region Family: Cytochrome c oxidase subunit II-like, transmembrane region Phyre2 PDB 2j0s chain C domain 1 Region: 53 - 64 Aligned: 12 Modelled: 12 Confidence: 8.2% Identity: 42% Fold: Mago nashi protein Superfamily: Mago nashi protein Family: Mago nashi protein Phyre2 1 c2kncA_ 2 d2axtl1 3 c3a0bl_ 4 c3prrL_ 5 c1s5lL_ 6 c3a0bL_ 7 c2axtL_ 8 c3bz2L_ 9 c1s5ll_ 10 c3a0hl_ 11 c3kziL_ 12 c3prqL_ 13 c3bz1L_ 14 c3a0hL_ 15 c3arcL_ 16 c2axtl_ 17 c3aa6C_ 18 c2k1aA_ 19 d1fftb2 20 d2j0sc1 21 22 23 24 25

Detailed template information

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

1 c2kncA_ 23.9 30 PDB header:cell adhesion Chain: A: PDB Molecule:integrin alpha-iib; PDBTitle: platelet integrin alfaiib-beta3 transmembrane-cytoplasmic2 heterocomplex 2 d2axtl1 18.6 14 Fold:Single transmembrane helix Superfamily:Photosystem II reaction center protein L, PsbL Family:PsbL-like 3 c3a0bl_ 18.6 14 PDB header:electron transport Chain: L: PDB Molecule:photosystem ii reaction center protein l; PDBTitle: crystal structure of br-substituted photosystem ii complex 4 c3prrL_ 18.6 14 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 5 c1s5lL_ 18.6 14 PDB header:photosynthesis Chain: L: PDB Molecule:photosystem ii reaction center l protein; PDBTitle: architecture of the photosynthetic oxygen evolving center 6 c3a0bL_ 18.6 14 PDB header:electron transport Chain: L: PDB Molecule:photosystem ii reaction center protein l; PDBTitle: crystal structure of br-substituted photosystem ii complex 7 c2axtL_ 18.6 14 PDB header:electron transport Chain: L: PDB Molecule:photosystem ii reaction center l protein; PDBTitle: crystal structure of photosystem ii from thermosynechococcus elongatus 8 c3bz2L_ 18.6 14 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 9 c1s5ll_ 18.6 14 PDB header:photosynthesis Chain: L: PDB Molecule:photosystem ii reaction center l protein; PDBTitle: architecture of the photosynthetic oxygen evolving center 10 c3a0hl_ 18.6 14 PDB header:electron transport Chain: L: PDB Molecule:photosystem ii reaction center protein l; PDBTitle: crystal structure of i-substituted photosystem ii complex 11 c3kziL_ 18.6 14 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 c3prqL_ 18.6 14 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 13 c3bz1L_ 18.6 14 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 14 c3a0hL_ 18.6 14 PDB header:electron transport Chain: L: PDB Molecule:photosystem ii reaction center protein l; PDBTitle: crystal structure of i-substituted photosystem ii complex 15 c3arcL_ 18.6 14 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 16 c2axtl_ 18.6 14 PDB header:electron transport Chain: L: PDB Molecule:photosystem ii reaction center l protein; PDBTitle: crystal structure of photosystem ii from thermosynechococcus elongatus 17 c3aa6C_ 10.1 38 PDB header:protein binding Chain: C: PDB Molecule:23mer peptide from cd2-associated protein; PDBTitle: crystal structure of actin capping protein in complex with the cp-2 binding motif derived from cd2ap 18 c2k1aA_ 8.9 35 PDB header:cell adhesion Chain: A: PDB Molecule:integrin alpha-iib; PDBTitle: bicelle-embedded integrin alpha(iib) transmembrane segment 19 d1fftb2 8.3 10 Fold:Transmembrane helix hairpin Superfamily:Cytochrome c oxidase subunit II-like, transmembrane region Family:Cytochrome c oxidase subunit II-like, transmembrane region 20 d2j0sc1 8.2 42 Fold:Mago nashi protein Superfamily:Mago nashi protein Family:Mago nashi protein 21 d1rk8b_ not modelled 7.2 36 Fold:Mago nashi protein Superfamily:Mago nashi protein Family:Mago nashi protein 22 c2fd4A_ not modelled 7.0 57 PDB header:ligase Chain: A: PDB Molecule:avirulence protein avrptob; PDBTitle: crystal structure of avrptob (436-553) 23 d2b9va2 not modelled 7.0 32 Fold:alpha/beta-Hydrolases Superfamily:alpha/beta-Hydrolases Family:PepX catalytic domain-like 24 c2gidP_ not modelled 6.4 42 PDB header:translation Chain: P: PDB Molecule:mitochondrial rna-binding protein 2; PDBTitle: crystal structures of trypanosoma bruciei mrp1/mrp2 25 c1z65A_ not modelled 6.2 26 PDB header:unknown function Chain: A: PDB Molecule:prion-like protein doppel; PDBTitle: mouse doppel 1-30 peptide

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