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

R

L

L

I

L

T

L

S

L

I

T

L

A

G

C

T

V

T

R

Q

A

H

V

S

E

V

D

A

A

T

G

I

V

R

L

V

Y

D

Q

A

F

L

Q

H

A

H

T

D

R

Y

V

S

R

G

I

A

D

R

A

Secondary structure

SS confidence

Disorder

?

?

?

?

?

?

?

?

?

?

?

?

?

?

?

?

?

?

?

?

?

?

?

?

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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Sequence

C

Q

Q

E

G

Y

T

H

A

V

P

F

G

Q

P

V

G

N

C

S

L

F

A

G

S

L

C

L

N

T

E

F

T

L

S

Y

Q

C

H

H

S

A

F

P

V

F

L

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 1z8g chain A domain 2 Region: 25 - 73 Aligned: 47 Modelled: 49 Confidence: 47.5% Identity: 13% Fold: SRCR-like Superfamily: SRCR-like Family: Hepsin, N-terminal domain Phyre2 PDB 1z8g chain A Region: 34 - 72 Aligned: 39 Modelled: 39 Confidence: 45.7% Identity: 18% PDB header:hydrolase/hydrolase inhibitor Chain: A: PDB Molecule:serine protease hepsin; PDBTitle: crystal structure of the extracellular region of the transmembrane2 serine protease hepsin with covalently bound preferred substrate. Phyre2 PDB 2ott chain Y Region: 24 - 72 Aligned: 43 Modelled: 49 Confidence: 41.6% Identity: 14% PDB header:immune system Chain: Y: PDB Molecule:t-cell surface glycoprotein cd5; PDBTitle: crystal structure of cd5_diii Phyre2 PDB 2jop chain A Region: 24 - 87 Aligned: 64 Modelled: 64 Confidence: 26.6% Identity: 9% PDB header:immune system Chain: A: PDB Molecule:t-cell surface glycoprotein cd5; PDBTitle: solution structure of the n-terminal extracellular domain2 of the lymphocyte receptor cd5 (cd5 domain 1) Phyre2 PDB 2oya chain A Region: 18 - 72 Aligned: 52 Modelled: 55 Confidence: 24.4% Identity: 13% PDB header:ligand binding protein Chain: A: PDB Molecule:macrophage receptor marco; PDBTitle: crystal structure analysis of the dimeric form of the srcr domain of2 mouse marco Phyre2 PDB 1dx5 chain I domain 1 Region: 95 - 100 Aligned: 6 Modelled: 6 Confidence: 14.4% Identity: 50% Fold: Knottins (small inhibitors, toxins, lectins) Superfamily: EGF/Laminin Family: EGF-type module Phyre2 PDB 2y1b chain A Region: 32 - 105 Aligned: 64 Modelled: 74 Confidence: 14.1% Identity: 19% PDB header:membrane protein Chain: A: PDB Molecule:putative outer membrane protein, signal; PDBTitle: crystal structure of the e. coli outer membrane lipoprotein2 rcsf Phyre2 PDB 1ji8 chain A Region: 39 - 59 Aligned: 21 Modelled: 21 Confidence: 13.5% Identity: 24% Fold: DsrC, the gamma subunit of dissimilatory sulfite reductase Superfamily: DsrC, the gamma subunit of dissimilatory sulfite reductase Family: DsrC, the gamma subunit of dissimilatory sulfite reductase Phyre2 PDB 1yx3 chain A Region: 39 - 59 Aligned: 21 Modelled: 21 Confidence: 11.9% Identity: 14% PDB header:structural genomics, unknown function Chain: A: PDB Molecule:hypothetical protein dsrc; PDBTitle: nmr structure of allochromatium vinosum dsrc: northeast2 structural genomics consortium target op4 Phyre2 PDB 1a0e chain A Region: 64 - 77 Aligned: 14 Modelled: 14 Confidence: 9.4% Identity: 29% Fold: TIM beta/alpha-barrel Superfamily: Xylose isomerase-like Family: Xylose isomerase Phyre2 PDB 1fvi chain A domain 1 Region: 91 - 107 Aligned: 16 Modelled: 17 Confidence: 9.3% Identity: 31% Fold: OB-fold Superfamily: Nucleic acid-binding proteins Family: DNA ligase/mRNA capping enzyme postcatalytic domain Phyre2 PDB 2v4j chain C domain 1 Region: 39 - 60 Aligned: 22 Modelled: 22 Confidence: 8.8% Identity: 9% Fold: DsrC, the gamma subunit of dissimilatory sulfite reductase Superfamily: DsrC, the gamma subunit of dissimilatory sulfite reductase Family: DsrC, the gamma subunit of dissimilatory sulfite reductase Phyre2 PDB 1a0c chain A Region: 64 - 77 Aligned: 14 Modelled: 14 Confidence: 8.5% Identity: 14% Fold: TIM beta/alpha-barrel Superfamily: Xylose isomerase-like Family: Xylose isomerase Phyre2 PDB 2a5w chain C Region: 39 - 57 Aligned: 19 Modelled: 19 Confidence: 8.4% Identity: 32% PDB header:oxidoreductase Chain: C: PDB Molecule:sulfite reductase, desulfoviridin-type subunit gamma PDBTitle: crystal structure of the oxidized gamma-subunit of the dissimilatory2 sulfite reductase (dsrc) from archaeoglobus fulgidus Phyre2 PDB 1by2 chain A Region: 24 - 72 Aligned: 47 Modelled: 49 Confidence: 7.5% Identity: 15% Fold: SRCR-like Superfamily: SRCR-like Family: Scavenger receptor cysteine-rich (SRCR) domain Phyre2 PDB 1xiw chain B Region: 96 - 106 Aligned: 11 Modelled: 11 Confidence: 7.4% Identity: 36% Fold: Immunoglobulin-like beta-sandwich Superfamily: Immunoglobulin Family: I set domains Phyre2 PDB 1xzp chain A domain 3 Region: 93 - 101 Aligned: 9 Modelled: 9 Confidence: 6.6% Identity: 22% Fold: Folate-binding domain Superfamily: Folate-binding domain Family: TrmE formyl-THF-binding domain Phyre2 PDB 1xzq chain B Region: 93 - 101 Aligned: 9 Modelled: 9 Confidence: 6.6% Identity: 22% PDB header:hydrolase Chain: B: PDB Molecule:probable trna modification gtpase trme; PDBTitle: structure of the gtp-binding protein trme from thermotoga2 maritima complexed with 5-formyl-thf Phyre2 PDB 2j8j chain A Region: 31 - 79 Aligned: 49 Modelled: 49 Confidence: 6.5% Identity: 16% PDB header:hydrolase Chain: A: PDB Molecule:coagulation factor xi; PDBTitle: solution structure of the a4 domain of blood coagulation2 factor xi Phyre2 PDB 1sy6 chain A domain 1 Region: 96 - 101 Aligned: 6 Modelled: 6 Confidence: 6.4% Identity: 67% Fold: Immunoglobulin-like beta-sandwich Superfamily: Immunoglobulin Family: I set domains Phyre2 1 d1z8ga2 2 c1z8gA_ 3 c2ottY_ 4 c2jopA_ 5 c2oyaA_ 6 d1dx5i1 7 c2y1bA_ 8 d1ji8a_ 9 c1yx3A_ 10 d1a0ea_ 11 d1fvia1 12 d2v4jc1 13 d1a0ca_ 14 c2a5wC_ 15 d1by2a_ 16 d1xiwb_ 17 d1xzpa3 18 c1xzqB_ 19 c2j8jA_ 20 d1sy6a1 21 22 23

Detailed template information

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

1 d1z8ga2 47.5 13 Fold:SRCR-like Superfamily:SRCR-like Family:Hepsin, N-terminal domain 2 c1z8gA_ 45.7 18 PDB header:hydrolase/hydrolase inhibitor Chain: A: PDB Molecule:serine protease hepsin; PDBTitle: crystal structure of the extracellular region of the transmembrane2 serine protease hepsin with covalently bound preferred substrate. 3 c2ottY_ 41.6 14 PDB header:immune system Chain: Y: PDB Molecule:t-cell surface glycoprotein cd5; PDBTitle: crystal structure of cd5_diii 4 c2jopA_ 26.6 9 PDB header:immune system Chain: A: PDB Molecule:t-cell surface glycoprotein cd5; PDBTitle: solution structure of the n-terminal extracellular domain2 of the lymphocyte receptor cd5 (cd5 domain 1) 5 c2oyaA_ 24.4 13 PDB header:ligand binding protein Chain: A: PDB Molecule:macrophage receptor marco; PDBTitle: crystal structure analysis of the dimeric form of the srcr domain of2 mouse marco 6 d1dx5i1 14.4 50 Fold:Knottins (small inhibitors, toxins, lectins) Superfamily:EGF/Laminin Family:EGF-type module 7 c2y1bA_ 14.1 19 PDB header:membrane protein Chain: A: PDB Molecule:putative outer membrane protein, signal; PDBTitle: crystal structure of the e. coli outer membrane lipoprotein2 rcsf 8 d1ji8a_ 13.5 24 Fold:DsrC, the gamma subunit of dissimilatory sulfite reductase Superfamily:DsrC, the gamma subunit of dissimilatory sulfite reductase Family:DsrC, the gamma subunit of dissimilatory sulfite reductase 9 c1yx3A_ 11.9 14 PDB header:structural genomics, unknown function Chain: A: PDB Molecule:hypothetical protein dsrc; PDBTitle: nmr structure of allochromatium vinosum dsrc: northeast2 structural genomics consortium target op4 10 d1a0ea_ 9.4 29 Fold:TIM beta/alpha-barrel Superfamily:Xylose isomerase-like Family:Xylose isomerase 11 d1fvia1 9.3 31 Fold:OB-fold Superfamily:Nucleic acid-binding proteins Family:DNA ligase/mRNA capping enzyme postcatalytic domain 12 d2v4jc1 8.8 9 Fold:DsrC, the gamma subunit of dissimilatory sulfite reductase Superfamily:DsrC, the gamma subunit of dissimilatory sulfite reductase Family:DsrC, the gamma subunit of dissimilatory sulfite reductase 13 d1a0ca_ 8.5 14 Fold:TIM beta/alpha-barrel Superfamily:Xylose isomerase-like Family:Xylose isomerase 14 c2a5wC_ 8.4 32 PDB header:oxidoreductase Chain: C: PDB Molecule:sulfite reductase, desulfoviridin-type subunit gamma PDBTitle: crystal structure of the oxidized gamma-subunit of the dissimilatory2 sulfite reductase (dsrc) from archaeoglobus fulgidus 15 d1by2a_ 7.5 15 Fold:SRCR-like Superfamily:SRCR-like Family:Scavenger receptor cysteine-rich (SRCR) domain 16 d1xiwb_ 7.4 36 Fold:Immunoglobulin-like beta-sandwich Superfamily:Immunoglobulin Family:I set domains 17 d1xzpa3 6.6 22 Fold:Folate-binding domain Superfamily:Folate-binding domain Family:TrmE formyl-THF-binding domain 18 c1xzqB_ 6.6 22 PDB header:hydrolase Chain: B: PDB Molecule:probable trna modification gtpase trme; PDBTitle: structure of the gtp-binding protein trme from thermotoga2 maritima complexed with 5-formyl-thf 19 c2j8jA_ 6.5 16 PDB header:hydrolase Chain: A: PDB Molecule:coagulation factor xi; PDBTitle: solution structure of the a4 domain of blood coagulation2 factor xi 20 d1sy6a1 6.4 67 Fold:Immunoglobulin-like beta-sandwich Superfamily:Immunoglobulin Family:I set domains 21 d1a0da_ not modelled 6.3 21 Fold:TIM beta/alpha-barrel Superfamily:Xylose isomerase-like Family:Xylose isomerase 22 c2j8jB_ not modelled 6.3 16 PDB header:hydrolase Chain: B: PDB Molecule:coagulation factor xi; PDBTitle: solution structure of the a4 domain of blood coagulation2 factor xi 23 c2j8lA_ not modelled 6.2 16 PDB header:hydrolase Chain: A: PDB Molecule:coagulation factor xi; PDBTitle: fxi apple 4 domain loop-out conformation

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