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

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N

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Y

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G

I

G

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L

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M

G

L

A

A

C

D

D

K

D

T

N

A

T

A

Q

G

S

V

A

E

S

N

A

T

G

N

P

V

N

L

L

D

G

K

L

S

F

S

L

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A

D

M

T

D

Secondary structure

SS confidence

Disorder

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Disorder confidence

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70

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80

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90

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100

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110

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120

Sequence

Q

S

G

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L

G

T

Q

A

N

N

M

H

V

W

S

D

A

T

G

Q

K

A

V

I

V

I

M

G

D

D

P

K

E

D

L

A

V

L

A

K

R

L

E

D

Q

Q

R

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R

D

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Q

V

V

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N

K

Secondary structure

SS confidence

Disorder

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Disorder confidence

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130

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140

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150

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160

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170

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180

Sequence

A

I

E

L

K

G

H

K

M

Q

Q

L

D

S

I

I

S

A

K

G

Q

T

A

Y

S

S

V

I

L

G

N

V

G

N

Q

L

L

T

M

Q

I

T

L

P

A

D

D

Q

Q

K

A

Q

T

T

A

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N

I

I

N

Secondary structure

SS confidence

Disorder

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Disorder confidence

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Sequence

T

L

V

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Q

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 1tu1 chain A Region: 44 - 185 Aligned: 131 Modelled: 142 Confidence: 99.0% Identity: 16% Fold: Mog1p/PsbP-like Superfamily: Mog1p/PsbP-like Family: PA0094-like Phyre2 PDB 2xb3 chain A Region: 47 - 184 Aligned: 134 Modelled: 138 Confidence: 97.7% Identity: 13% PDB header:photosynthesis Chain: A: PDB Molecule:psbp protein; PDBTitle: the structure of cyanobacterial psbp Phyre2 PDB 1v2b chain A Region: 43 - 184 Aligned: 139 Modelled: 142 Confidence: 89.6% Identity: 10% Fold: Mog1p/PsbP-like Superfamily: Mog1p/PsbP-like Family: PsbP-like Phyre2 PDB 2vu4 chain A Region: 47 - 184 Aligned: 133 Modelled: 138 Confidence: 89.3% Identity: 10% PDB header:photosynthesis Chain: A: PDB Molecule:oxygen-evolving enhancer protein 2; PDBTitle: structure of psbp protein from spinacia oleracea at 1.98 a2 resolution Phyre2 PDB 2jx5 chain A Region: 43 - 81 Aligned: 39 Modelled: 39 Confidence: 45.6% Identity: 26% PDB header:ribosomal protein Chain: A: PDB Molecule:glub(s27a); PDBTitle: solution structure of the ubiquitin domain n-terminal to2 the s27a ribosomal subunit of giardia lamblia Phyre2 PDB 1qho chain A domain 3 Region: 40 - 57 Aligned: 18 Modelled: 18 Confidence: 31.1% Identity: 33% Fold: Glycosyl hydrolase domain Superfamily: Glycosyl hydrolase domain Family: alpha-Amylases, C-terminal beta-sheet domain Phyre2 PDB 1ji1 chain A domain 2 Region: 39 - 56 Aligned: 18 Modelled: 18 Confidence: 30.2% Identity: 17% Fold: Glycosyl hydrolase domain Superfamily: Glycosyl hydrolase domain Family: alpha-Amylases, C-terminal beta-sheet domain Phyre2 PDB 3orj chain A Region: 49 - 76 Aligned: 28 Modelled: 28 Confidence: 24.0% Identity: 18% PDB header:sugar binding protein Chain: A: PDB Molecule:sugar-binding protein; PDBTitle: crystal structure of a sugar-binding protein (bacova_04391) from2 bacteroides ovatus at 2.16 a resolution Phyre2 PDB 2c7f chain A domain 1 Region: 17 - 56 Aligned: 36 Modelled: 40 Confidence: 22.0% Identity: 28% Fold: Glycosyl hydrolase domain Superfamily: Glycosyl hydrolase domain Family: Composite domain of glycosyl hydrolase families 5, 30, 39 and 51 Phyre2 PDB 1jhs chain A Region: 42 - 86 Aligned: 44 Modelled: 45 Confidence: 21.9% Identity: 23% Fold: Mog1p/PsbP-like Superfamily: Mog1p/PsbP-like Family: Ran-binding protein mog1p Phyre2 PDB 1cgt chain A domain 3 Region: 40 - 57 Aligned: 18 Modelled: 18 Confidence: 20.9% Identity: 33% Fold: Glycosyl hydrolase domain Superfamily: Glycosyl hydrolase domain Family: alpha-Amylases, C-terminal beta-sheet domain Phyre2 PDB 1qw9 chain A domain 1 Region: 17 - 56 Aligned: 38 Modelled: 40 Confidence: 16.9% Identity: 29% Fold: Glycosyl hydrolase domain Superfamily: Glycosyl hydrolase domain Family: Composite domain of glycosyl hydrolase families 5, 30, 39 and 51 Phyre2 PDB 1wzl chain A domain 2 Region: 39 - 56 Aligned: 18 Modelled: 18 Confidence: 16.5% Identity: 33% Fold: Glycosyl hydrolase domain Superfamily: Glycosyl hydrolase domain Family: alpha-Amylases, C-terminal beta-sheet domain Phyre2 PDB 3lyd chain A Region: 102 - 185 Aligned: 84 Modelled: 84 Confidence: 13.1% Identity: 13% PDB header:structural genomics, unknown function Chain: A: PDB Molecule:uncharacterized protein; PDBTitle: crystal structure of putative uncharacterized protein from jonesia2 denitrificans Phyre2 PDB 3iz5 chain W Region: 63 - 111 Aligned: 47 Modelled: 49 Confidence: 12.3% Identity: 30% PDB header:ribosome Chain: W: PDB Molecule:60s ribosomal protein l22 (l22e); PDBTitle: localization of the large subunit ribosomal proteins into a 5.5 a2 cryo-em map of triticum aestivum translating 80s ribosome Phyre2 PDB 1xrs chain B domain 2 Region: 50 - 55 Aligned: 6 Modelled: 6 Confidence: 12.3% Identity: 83% Fold: Dodecin subunit-like Superfamily: D-lysine 5,6-aminomutase beta subunit KamE, N-terminal domain Family: D-lysine 5,6-aminomutase beta subunit KamE, N-terminal domain Phyre2 PDB 3bmv chain A domain 3 Region: 47 - 57 Aligned: 11 Modelled: 11 Confidence: 12.1% Identity: 45% Fold: Glycosyl hydrolase domain Superfamily: Glycosyl hydrolase domain Family: alpha-Amylases, C-terminal beta-sheet domain Phyre2 PDB 1bag chain A Region: 40 - 57 Aligned: 18 Modelled: 18 Confidence: 10.7% Identity: 28% PDB header:alpha-amylase Chain: A: PDB Molecule:alpha-1,4-glucan-4-glucanohydrolase; PDBTitle: alpha-amylase from bacillus subtilis complexed with2 maltopentaose Phyre2 PDB 2j98 chain A Region: 54 - 93 Aligned: 40 Modelled: 40 Confidence: 10.6% Identity: 13% PDB header:rna-binding protein Chain: A: PDB Molecule:replicase polyprotein 1ab; PDBTitle: human coronavirus 229e non structural protein 9 cys69ala2 mutant (nsp9) Phyre2 PDB 4a1d chain M Region: 62 - 111 Aligned: 48 Modelled: 50 Confidence: 9.7% Identity: 27% PDB header:ribosome Chain: M: PDB Molecule:ribosomal protein l22; PDBTitle: t.thermophila 60s ribosomal subunit in complex with initiation2 factor 6. this file contains 26s rrna and proteins of3 molecule 4. Phyre2 1 d1tu1a_ 2 c2xb3A_ 3 d1v2ba_ 4 c2vu4A_ 5 c2jx5A_ 6 d1qhoa3 7 d1ji1a2 8 c3orjA_ 9 d2c7fa1 10 d1jhsa_ 11 d1cgta3 12 d1qw9a1 13 d1wzla2 14 c3lydA_ 15 c3iz5W_ 16 d1xrsb2 17 d3bmva3 18 c1bagA_ 19 c2j98A_ 20 c4a1dM_ 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37

Detailed template information

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

1 d1tu1a_ 99.0 16 Fold:Mog1p/PsbP-like Superfamily:Mog1p/PsbP-like Family:PA0094-like 2 c2xb3A_ 97.7 13 PDB header:photosynthesis Chain: A: PDB Molecule:psbp protein; PDBTitle: the structure of cyanobacterial psbp 3 d1v2ba_ 89.6 10 Fold:Mog1p/PsbP-like Superfamily:Mog1p/PsbP-like Family:PsbP-like 4 c2vu4A_ 89.3 10 PDB header:photosynthesis Chain: A: PDB Molecule:oxygen-evolving enhancer protein 2; PDBTitle: structure of psbp protein from spinacia oleracea at 1.98 a2 resolution 5 c2jx5A_ 45.6 26 PDB header:ribosomal protein Chain: A: PDB Molecule:glub(s27a); PDBTitle: solution structure of the ubiquitin domain n-terminal to2 the s27a ribosomal subunit of giardia lamblia 6 d1qhoa3 31.1 33 Fold:Glycosyl hydrolase domain Superfamily:Glycosyl hydrolase domain Family:alpha-Amylases, C-terminal beta-sheet domain 7 d1ji1a2 30.2 17 Fold:Glycosyl hydrolase domain Superfamily:Glycosyl hydrolase domain Family:alpha-Amylases, C-terminal beta-sheet domain 8 c3orjA_ 24.0 18 PDB header:sugar binding protein Chain: A: PDB Molecule:sugar-binding protein; PDBTitle: crystal structure of a sugar-binding protein (bacova_04391) from2 bacteroides ovatus at 2.16 a resolution 9 d2c7fa1 22.0 28 Fold:Glycosyl hydrolase domain Superfamily:Glycosyl hydrolase domain Family:Composite domain of glycosyl hydrolase families 5, 30, 39 and 51 10 d1jhsa_ 21.9 23 Fold:Mog1p/PsbP-like Superfamily:Mog1p/PsbP-like Family:Ran-binding protein mog1p 11 d1cgta3 20.9 33 Fold:Glycosyl hydrolase domain Superfamily:Glycosyl hydrolase domain Family:alpha-Amylases, C-terminal beta-sheet domain 12 d1qw9a1 16.9 29 Fold:Glycosyl hydrolase domain Superfamily:Glycosyl hydrolase domain Family:Composite domain of glycosyl hydrolase families 5, 30, 39 and 51 13 d1wzla2 16.5 33 Fold:Glycosyl hydrolase domain Superfamily:Glycosyl hydrolase domain Family:alpha-Amylases, C-terminal beta-sheet domain 14 c3lydA_ 13.1 13 PDB header:structural genomics, unknown function Chain: A: PDB Molecule:uncharacterized protein; PDBTitle: crystal structure of putative uncharacterized protein from jonesia2 denitrificans 15 c3iz5W_ 12.3 30 PDB header:ribosome Chain: W: PDB Molecule:60s ribosomal protein l22 (l22e); PDBTitle: localization of the large subunit ribosomal proteins into a 5.5 a2 cryo-em map of triticum aestivum translating 80s ribosome 16 d1xrsb2 12.3 83 Fold:Dodecin subunit-like Superfamily:D-lysine 5,6-aminomutase beta subunit KamE, N-terminal domain Family:D-lysine 5,6-aminomutase beta subunit KamE, N-terminal domain 17 d3bmva3 12.1 45 Fold:Glycosyl hydrolase domain Superfamily:Glycosyl hydrolase domain Family:alpha-Amylases, C-terminal beta-sheet domain 18 c1bagA_ 10.7 28 PDB header:alpha-amylase Chain: A: PDB Molecule:alpha-1,4-glucan-4-glucanohydrolase; PDBTitle: alpha-amylase from bacillus subtilis complexed with2 maltopentaose 19 c2j98A_ 10.6 13 PDB header:rna-binding protein Chain: A: PDB Molecule:replicase polyprotein 1ab; PDBTitle: human coronavirus 229e non structural protein 9 cys69ala2 mutant (nsp9) 20 c4a1dM_ 9.7 27 PDB header:ribosome Chain: M: PDB Molecule:ribosomal protein l22; PDBTitle: t.thermophila 60s ribosomal subunit in complex with initiation2 factor 6. this file contains 26s rrna and proteins of3 molecule 4. 21 d1lmia_ not modelled 8.2 22 Fold:Immunoglobulin-like beta-sandwich Superfamily:Antigen MPT63/MPB63 (immunoprotective extracellular protein) Family:Antigen MPT63/MPB63 (immunoprotective extracellular protein) 22 d1ni2a3 not modelled 8.2 23 Fold:beta-Grasp (ubiquitin-like) Superfamily:Ubiquitin-like Family:First domain of FERM 23 c3es1A_ not modelled 7.9 23 PDB header:structural genomics, unknown function Chain: A: PDB Molecule:cupin 2, conserved barrel domain protein; PDBTitle: crystal structure of protein with a cupin-like fold and unknown2 function (yp_001165807.1) from novosphingobium aromaticivorans dsm3 12444 at 1.91 a resolution 24 c3mx7A_ not modelled 6.8 18 PDB header:apoptosis Chain: A: PDB Molecule:fas apoptotic inhibitory molecule 1; PDBTitle: crystal structure analysis of human faim-ntd 25 d1szwa_ not modelled 6.8 44 Fold:Pseudouridine synthase Superfamily:Pseudouridine synthase Family:tRNA pseudouridine synthase TruD 26 c1bplB_ not modelled 6.6 18 PDB header:glycosyltransferase Chain: B: PDB Molecule:alpha-1,4-glucan-4-glucanohydrolase; PDBTitle: glycosyltransferase 27 c1z2zB_ not modelled 6.5 44 PDB header:lyase Chain: B: PDB Molecule:probable trna pseudouridine synthase d; PDBTitle: crystal structure of the putative trna pseudouridine2 synthase d (trud) from methanosarcina mazei, northeast3 structural genomics target mar1 28 d1s21a_ not modelled 6.4 42 Fold:ADP-ribosylation Superfamily:ADP-ribosylation Family:AvrPphF ORF2, a type III effector 29 c1s21A_ not modelled 6.4 42 PDB header:chaperone Chain: A: PDB Molecule:orf2; PDBTitle: crystal structure of avrpphf orf2, a type iii effector from2 p. syringae 30 c2gs8A_ not modelled 6.2 14 PDB header:lyase Chain: A: PDB Molecule:mevalonate pyrophosphate decarboxylase; PDBTitle: structure of mevalonate pyrophosphate decarboxylase from streptococcus2 pyogenes 31 c1sb7A_ not modelled 6.2 44 PDB header:lyase Chain: A: PDB Molecule:trna pseudouridine synthase d; PDBTitle: crystal structure of the e.coli pseudouridine synthase trud 32 d2bsya1 not modelled 5.6 17 Fold:beta-clip Superfamily:dUTPase-like Family:dUTPase-like 33 d1zupa1 not modelled 5.6 28 Fold:Ribonuclease H-like motif Superfamily:Ribonuclease H-like Family:TM1739-like 34 c2zt9E_ not modelled 5.5 42 PDB header:photosynthesis Chain: E: PDB Molecule:cytochrome b6-f complex subunit 6; PDBTitle: crystal structure of the cytochrome b6f complex from nostoc sp. pcc2 7120 35 d1ua7a1 not modelled 5.4 26 Fold:Glycosyl hydrolase domain Superfamily:Glycosyl hydrolase domain Family:alpha-Amylases, C-terminal beta-sheet domain 36 d1x38a2 not modelled 5.3 15 Fold:Flavodoxin-like Superfamily:Beta-D-glucan exohydrolase, C-terminal domain Family:Beta-D-glucan exohydrolase, C-terminal domain 37 d1cxla3 not modelled 5.3 45 Fold:Glycosyl hydrolase domain Superfamily:Glycosyl hydrolase domain Family:alpha-Amylases, C-terminal beta-sheet domain

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