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

K

L

V

H

M

A

S

G

L

A

V

A

I

A

L

A

A

C

A

D

K

S

A

D

I

Q

T

P

A

P

A

A

N

T

S

I

S

A

T

Q

Q

P

A

I

Q

Q

P

N

V

S

G

T

V

W

I

R

Q

K

V

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

A

L

P

P

D

A

V

L

T

V

T

L

S

D

A

S

L

A

D

A

P

S

K

V

L

A

Q

K

A

V

R

T

E

G

K

Q

S

P

F

S

F

V

L

S

F

N

P

A

D

V

Q

P

N

A

R

I

L

L

S

A

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

T

V

N

D

K

L

V

F

I

T

D

T

V

Q

P

V

I

N

Q

G

G

T

K

A

D

L

T

L

V

P

V

Q

Q

T

A

V

P

V

Q

A

S

G

G

A

T

T

T

V

P

S

T

S

P

T

Q

V

N

P

Secondary structure

SS confidence

Disorder

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Disorder confidence

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190

Sequence

S

S

A

V

P

A

P

T

Q

Y

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 2yjl chain C Region: 49 - 154 Aligned: 97 Modelled: 106 Confidence: 86.4% Identity: 13% PDB header:lipid-binding protein Chain: C: PDB Molecule:exoenzyme s synthesis protein b; PDBTitle: structural characterization of a secretin pilot protein2 from the type iii secretion system (t3ss) of pseudomonas3 aeruginosa Phyre2 PDB 2b9v chain A domain 1 Region: 64 - 119 Aligned: 56 Modelled: 56 Confidence: 74.0% Identity: 18% Fold: Galactose-binding domain-like Superfamily: Galactose-binding domain-like Family: PepX C-terminal domain-like Phyre2 PDB 1ju3 chain A domain 1 Region: 64 - 119 Aligned: 55 Modelled: 56 Confidence: 64.7% Identity: 25% Fold: Galactose-binding domain-like Superfamily: Galactose-binding domain-like Family: PepX C-terminal domain-like Phyre2 PDB 1lns chain A Region: 64 - 119 Aligned: 56 Modelled: 56 Confidence: 56.9% Identity: 9% PDB header:hydrolase Chain: A: PDB Molecule:x-prolyl dipeptidyl aminopetidase; PDBTitle: crystal structure analysis of the x-prolyl dipeptidyl2 aminopeptidase from lactococcus lactis Phyre2 PDB 2b9v chain B Region: 64 - 119 Aligned: 56 Modelled: 56 Confidence: 52.6% Identity: 21% PDB header:hydrolase Chain: B: PDB Molecule:alpha-amino acid ester hydrolase; PDBTitle: acetobacter turbidans alpha-amino acid ester hydrolase Phyre2 PDB 1mpx chain B Region: 64 - 119 Aligned: 56 Modelled: 55 Confidence: 51.9% Identity: 25% PDB header:hydrolase Chain: B: PDB Molecule:alpha-amino acid ester hydrolase; PDBTitle: alpha-amino acid ester hydrolase labeled with selenomethionine Phyre2 PDB 1e5r chain A Region: 125 - 188 Aligned: 60 Modelled: 64 Confidence: 44.1% Identity: 12% Fold: Double-stranded beta-helix Superfamily: Clavaminate synthase-like Family: Type II Proline 3-hydroxylase (proline oxidase) Phyre2 PDB 3cm1 chain C Region: 83 - 127 Aligned: 40 Modelled: 45 Confidence: 43.0% Identity: 20% PDB header:cell cycle Chain: C: PDB Molecule:ssga-like sporulation-specific cell division protein; PDBTitle: crystal structure of ssga-like sporulation-specific cell division2 protein (yp_290167.1) from thermobifida fusca yx-er1 at 2.60 a3 resolution Phyre2 PDB 1l7q chain A Region: 28 - 119 Aligned: 91 Modelled: 92 Confidence: 40.6% Identity: 23% PDB header:hydrolase Chain: A: PDB Molecule:cocaine esterase; PDBTitle: ser117ala mutant of bacterial cocaine esterase coce Phyre2 PDB 1tg7 chain A domain 2 Region: 52 - 127 Aligned: 76 Modelled: 76 Confidence: 38.3% Identity: 8% Fold: Galactose-binding domain-like Superfamily: Galactose-binding domain-like Family: Beta-galactosidase LacA, domains 4 and 5 Phyre2 PDB 2vng chain A domain 1 Region: 86 - 157 Aligned: 72 Modelled: 72 Confidence: 37.7% Identity: 14% Fold: Galactose-binding domain-like Superfamily: Galactose-binding domain-like Family: NPCBM-like Phyre2 PDB 1lns chain A domain 2 Region: 41 - 119 Aligned: 79 Modelled: 79 Confidence: 37.6% Identity: 13% Fold: Galactose-binding domain-like Superfamily: Galactose-binding domain-like Family: PepX C-terminal domain-like Phyre2 PDB 3ib3 chain A Region: 16 - 119 Aligned: 104 Modelled: 104 Confidence: 23.3% Identity: 12% PDB header:hydrolase Chain: A: PDB Molecule:coce/nond family hydrolase; PDBTitle: crystal structure of sacol2612 - coce/nond family hydrolase from2 staphylococcus aureus Phyre2 PDB 2vmh chain A domain 1 Region: 86 - 164 Aligned: 75 Modelled: 77 Confidence: 21.1% Identity: 12% Fold: Galactose-binding domain-like Superfamily: Galactose-binding domain-like Family: NPCBM-like Phyre2 PDB 1wio chain A domain 2 Region: 86 - 135 Aligned: 38 Modelled: 50 Confidence: 19.8% Identity: 26% Fold: Immunoglobulin-like beta-sandwich Superfamily: Immunoglobulin Family: V set domains (antibody variable domain-like) Phyre2 PDB 1ux6 chain A Region: 96 - 136 Aligned: 32 Modelled: 41 Confidence: 16.5% Identity: 13% PDB header:cell adhesion Chain: A: PDB Molecule:thrombospondin-1; PDBTitle: structure of a thrombospondin c-terminal fragment reveals a2 novel calcium core in the type 3 repeats Phyre2 PDB 1mpx chain A domain 1 Region: 64 - 119 Aligned: 56 Modelled: 55 Confidence: 15.4% Identity: 25% Fold: Galactose-binding domain-like Superfamily: Galactose-binding domain-like Family: PepX C-terminal domain-like Phyre2 PDB 1wru chain A Region: 105 - 163 Aligned: 59 Modelled: 59 Confidence: 14.7% Identity: 19% PDB header:structural protein Chain: A: PDB Molecule:43 kda tail protein; PDBTitle: structure of central hub elucidated by x-ray analysis of gene product2 44; baseplate component of bacteriophage mu Phyre2 PDB 2ccl chain A domain 1 Region: 99 - 111 Aligned: 13 Modelled: 13 Confidence: 13.6% Identity: 23% Fold: Common fold of diphtheria toxin/transcription factors/cytochrome f Superfamily: Carbohydrate-binding domain Family: Cellulose-binding domain family III Phyre2 PDB 2icy chain A domain 1 Region: 49 - 69 Aligned: 21 Modelled: 21 Confidence: 12.7% Identity: 29% Fold: Single-stranded left-handed beta-helix Superfamily: Trimeric LpxA-like enzymes Family: GlmU C-terminal domain-like Phyre2 1 c2yjlC_ 2 d2b9va1 3 d1ju3a1 4 c1lnsA_ 5 c2b9vB_ 6 c1mpxB_ 7 d1e5ra_ 8 c3cm1C_ 9 c1l7qA_ 10 d1tg7a2 11 d2vnga1 12 d1lnsa2 13 c3ib3A_ 14 d2vmha1 15 d1wioa2 16 c1ux6A_ 17 d1mpxa1 18 c1wruA_ 19 d2ccla1 20 d2icya1 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46

Detailed template information

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

1 c2yjlC_ 86.4 13 PDB header:lipid-binding protein Chain: C: PDB Molecule:exoenzyme s synthesis protein b; PDBTitle: structural characterization of a secretin pilot protein2 from the type iii secretion system (t3ss) of pseudomonas3 aeruginosa 2 d2b9va1 74.0 18 Fold:Galactose-binding domain-like Superfamily:Galactose-binding domain-like Family:PepX C-terminal domain-like 3 d1ju3a1 64.7 25 Fold:Galactose-binding domain-like Superfamily:Galactose-binding domain-like Family:PepX C-terminal domain-like 4 c1lnsA_ 56.9 9 PDB header:hydrolase Chain: A: PDB Molecule:x-prolyl dipeptidyl aminopetidase; PDBTitle: crystal structure analysis of the x-prolyl dipeptidyl2 aminopeptidase from lactococcus lactis 5 c2b9vB_ 52.6 21 PDB header:hydrolase Chain: B: PDB Molecule:alpha-amino acid ester hydrolase; PDBTitle: acetobacter turbidans alpha-amino acid ester hydrolase 6 c1mpxB_ 51.9 25 PDB header:hydrolase Chain: B: PDB Molecule:alpha-amino acid ester hydrolase; PDBTitle: alpha-amino acid ester hydrolase labeled with selenomethionine 7 d1e5ra_ 44.1 12 Fold:Double-stranded beta-helix Superfamily:Clavaminate synthase-like Family:Type II Proline 3-hydroxylase (proline oxidase) 8 c3cm1C_ 43.0 20 PDB header:cell cycle Chain: C: PDB Molecule:ssga-like sporulation-specific cell division protein; PDBTitle: crystal structure of ssga-like sporulation-specific cell division2 protein (yp_290167.1) from thermobifida fusca yx-er1 at 2.60 a3 resolution 9 c1l7qA_ 40.6 23 PDB header:hydrolase Chain: A: PDB Molecule:cocaine esterase; PDBTitle: ser117ala mutant of bacterial cocaine esterase coce 10 d1tg7a2 38.3 8 Fold:Galactose-binding domain-like Superfamily:Galactose-binding domain-like Family:Beta-galactosidase LacA, domains 4 and 5 11 d2vnga1 37.7 14 Fold:Galactose-binding domain-like Superfamily:Galactose-binding domain-like Family:NPCBM-like 12 d1lnsa2 37.6 13 Fold:Galactose-binding domain-like Superfamily:Galactose-binding domain-like Family:PepX C-terminal domain-like 13 c3ib3A_ 23.3 12 PDB header:hydrolase Chain: A: PDB Molecule:coce/nond family hydrolase; PDBTitle: crystal structure of sacol2612 - coce/nond family hydrolase from2 staphylococcus aureus 14 d2vmha1 21.1 12 Fold:Galactose-binding domain-like Superfamily:Galactose-binding domain-like Family:NPCBM-like 15 d1wioa2 19.8 26 Fold:Immunoglobulin-like beta-sandwich Superfamily:Immunoglobulin Family:V set domains (antibody variable domain-like) 16 c1ux6A_ 16.5 13 PDB header:cell adhesion Chain: A: PDB Molecule:thrombospondin-1; PDBTitle: structure of a thrombospondin c-terminal fragment reveals a2 novel calcium core in the type 3 repeats 17 d1mpxa1 15.4 25 Fold:Galactose-binding domain-like Superfamily:Galactose-binding domain-like Family:PepX C-terminal domain-like 18 c1wruA_ 14.7 19 PDB header:structural protein Chain: A: PDB Molecule:43 kda tail protein; PDBTitle: structure of central hub elucidated by x-ray analysis of gene product2 44; baseplate component of bacteriophage mu 19 d2ccla1 13.6 23 Fold:Common fold of diphtheria toxin/transcription factors/cytochrome f Superfamily:Carbohydrate-binding domain Family:Cellulose-binding domain family III 20 d2icya1 12.7 29 Fold:Single-stranded left-handed beta-helix Superfamily:Trimeric LpxA-like enzymes Family:GlmU C-terminal domain-like 21 c2qeaB_ not modelled 12.7 13 PDB header:oxidoreductase Chain: B: PDB Molecule:putative general stress protein 26; PDBTitle: crystal structure of a putative general stress protein 26 (jann_0955)2 from jannaschia sp. ccs1 at 2.46 a resolution 22 c1yo8A_ not modelled 12.4 6 PDB header:cell adhesion Chain: A: PDB Molecule:thrombospondin-2; PDBTitle: structure of the c-terminal domain of human thrombospondin-2 23 c2giaB_ not modelled 11.2 33 PDB header:translation Chain: B: PDB Molecule:mitochondrial rna-binding protein 1; PDBTitle: crystal structures of trypanosoma bruciei mrp1/mrp2 24 d2giab1 not modelled 11.2 33 Fold:ssDNA-binding transcriptional regulator domain Superfamily:ssDNA-binding transcriptional regulator domain Family:Guide RNA binding protein gBP 25 d1rhoa_ not modelled 11.1 13 Fold:Immunoglobulin-like beta-sandwich Superfamily:E set domains Family:RhoGDI-like 26 d1yq2a3 not modelled 10.2 16 Fold:Galactose-binding domain-like Superfamily:Galactose-binding domain-like Family:beta-Galactosidase/glucuronidase, N-terminal domain 27 c2qv8B_ not modelled 10.2 22 PDB header:transport protein Chain: B: PDB Molecule:general secretion pathway protein h; PDBTitle: structure of the minor pseudopilin epsh from the type 2 secretion2 system of vibrio cholerae 28 d2oz4a1 not modelled 9.8 17 Fold:Immunoglobulin-like beta-sandwich Superfamily:Immunoglobulin Family:C2 set domains 29 d1qhqa_ not modelled 9.1 9 Fold:Cupredoxin-like Superfamily:Cupredoxins Family:Plastocyanin/azurin-like 30 d2vo8a1 not modelled 8.6 8 Fold:Common fold of diphtheria toxin/transcription factors/cytochrome f Superfamily:Carbohydrate-binding domain Family:Cellulose-binding domain family III 31 c3hwjA_ not modelled 8.5 7 PDB header:ligase Chain: A: PDB Molecule:e3 ubiquitin-protein ligase mycbp2; PDBTitle: crystal structure of the second phr domain of mouse myc-2 binding protein 2 (mycbp-2) 32 d2a6va1 not modelled 8.1 20 Fold:Concanavalin A-like lectins/glucanases Superfamily:Concanavalin A-like lectins/glucanases Family:Lectin leg-like 33 c2ov7C_ not modelled 8.1 16 PDB header:ribosomal protein Chain: C: PDB Molecule:50s ribosomal protein l1; PDBTitle: the first domain of the ribosomal protein l1 from thermus2 thermophilus 34 d1cida1 not modelled 8.1 28 Fold:Immunoglobulin-like beta-sandwich Superfamily:Immunoglobulin Family:V set domains (antibody variable domain-like) 35 c1cidA_ not modelled 7.7 32 PDB header:t-cell surface glycoprotein Chain: A: PDB Molecule:t cell surface glycoprotein cd4; PDBTitle: crystal structure of domains 3 & 4 of rat cd4 and their2 relationship to the nh2-terminal domains 36 c1c8uA_ not modelled 7.3 14 PDB header:hydrolase Chain: A: PDB Molecule:acyl-coa thioesterase ii; PDBTitle: crystal structure of the e.coli thioesterase ii, a2 homologue of the human nef-binding enzyme 37 d1c1za5 not modelled 7.1 17 Fold:Complement control module/SCR domain Superfamily:Complement control module/SCR domain Family:Complement control module/SCR domain 38 d1mnga1 not modelled 6.9 27 Fold:Long alpha-hairpin Superfamily:Fe,Mn superoxide dismutase (SOD), N-terminal domain Family:Fe,Mn superoxide dismutase (SOD), N-terminal domain 39 c3r7gB_ not modelled 6.8 18 PDB header:protein binding Chain: B: PDB Molecule:formin-2; PDBTitle: crystal structure of spire kind domain in complex with the tail of2 fmn2 40 c3fbyC_ not modelled 6.4 17 PDB header:cell adhesion Chain: C: PDB Molecule:cartilage oligomeric matrix protein; PDBTitle: the crystal structure of the signature domain of cartilage oligomeric2 matrix protein. 41 d1ux6a1 not modelled 6.1 11 Fold:Concanavalin A-like lectins/glucanases Superfamily:Concanavalin A-like lectins/glucanases Family:Thrombospondin C-terminal domain 42 d1aoha_ not modelled 5.8 31 Fold:Common fold of diphtheria toxin/transcription factors/cytochrome f Superfamily:Carbohydrate-binding domain Family:Cellulose-binding domain family III 43 d2bs2c1 not modelled 5.5 19 Fold:Heme-binding four-helical bundle Superfamily:Fumarate reductase respiratory complex transmembrane subunits Family:Fumarate reductase respiratory complex cytochrome b subunit, FrdC 44 c3bbjA_ not modelled 5.2 0 PDB header:hydrolase Chain: A: PDB Molecule:putative thioesterase ii; PDBTitle: crystal structure of a putative thioesterase ii (tfu_2367) from2 thermobifida fusca yx at 2.45 a resolution 45 d1quba5 not modelled 5.2 17 Fold:Complement control module/SCR domain Superfamily:Complement control module/SCR domain Family:Complement control module/SCR domain 46 d2apsa_ not modelled 5.1 20 Fold:Immunoglobulin-like beta-sandwich Superfamily:Cu,Zn superoxide dismutase-like Family:Cu,Zn superoxide dismutase-like

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

---

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