Secondary structure and disorder prediction

1

.

.

.

.

.

.

.

.

10

.

.

.

.

.

.

.

.

.

20

.

.

.

.

.

.

.

.

.

30

.

.

.

.

.

.

.

.

.

40

.

.

.

.

.

.

.

.

.

50

.

.

.

.

.

.

.

Sequence

M

K

K

L

A

L

I

L

F

M

G

T

L

V

S

F

Y

A

D

A

G

R

K

P

C

S

G

S

K

G

G

I

S

H

C

T

A

G

G

K

F

V

C

N

D

G

S

I

S

A

S

K

K

T

C

T

N

Secondary structure

SS confidence

Disorder

?

?

?

?

?

?

?

?

?

?

?

?

?

?

?

?

?

?

?

?

?

?

?

?

?

?

?

?

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 1tih chain A Region: 25 - 56 Aligned: 31 Modelled: 32 Confidence: 81.2% Identity: 35% Fold: Plant proteinase inhibitors Superfamily: Plant proteinase inhibitors Family: Plant proteinase inhibitors Phyre2 PDB 1pju chain A domain 1 Region: 25 - 56 Aligned: 31 Modelled: 32 Confidence: 80.7% Identity: 39% Fold: Plant proteinase inhibitors Superfamily: Plant proteinase inhibitors Family: Plant proteinase inhibitors Phyre2 PDB 1fyb chain A domain 1 Region: 25 - 56 Aligned: 31 Modelled: 32 Confidence: 80.1% Identity: 39% Fold: Plant proteinase inhibitors Superfamily: Plant proteinase inhibitors Family: Plant proteinase inhibitors Phyre2 PDB 4sgb chain I Region: 25 - 56 Aligned: 31 Modelled: 32 Confidence: 77.6% Identity: 35% Fold: Plant proteinase inhibitors Superfamily: Plant proteinase inhibitors Family: Plant proteinase inhibitors Phyre2 PDB 1oyv chain I Region: 25 - 56 Aligned: 31 Modelled: 32 Confidence: 71.6% Identity: 39% Fold: Plant proteinase inhibitors Superfamily: Plant proteinase inhibitors Family: Plant proteinase inhibitors Phyre2 PDB 1fyb chain A Region: 25 - 56 Aligned: 31 Modelled: 31 Confidence: 69.3% Identity: 39% PDB header:hydrolase inhibitor Chain: A: PDB Molecule:proteinase inhibitor; PDBTitle: solution structure of c1-t1, a two-domain proteinase2 inhibitor derived from the circular precursor protein na-3 propi from nicotiana alata Phyre2 PDB 1ce3 chain A Region: 25 - 47 Aligned: 22 Modelled: 23 Confidence: 50.6% Identity: 41% Fold: Plant proteinase inhibitors Superfamily: Plant proteinase inhibitors Family: Plant proteinase inhibitors Phyre2 PDB 1pju chain A domain 2 Region: 25 - 47 Aligned: 22 Modelled: 23 Confidence: 35.9% Identity: 45% Fold: Plant proteinase inhibitors Superfamily: Plant proteinase inhibitors Family: Plant proteinase inhibitors Phyre2 PDB 2d3j chain A Region: 24 - 33 Aligned: 10 Modelled: 10 Confidence: 13.3% Identity: 40% PDB header:signaling protein inhibitor Chain: A: PDB Molecule:wnt inhibitory factor-1; PDBTitle: nmr structure of the wif domain from human wif-1 Phyre2 PDB 2e3e chain A Region: 27 - 45 Aligned: 16 Modelled: 19 Confidence: 12.5% Identity: 38% PDB header:antimicrobial protein Chain: A: PDB Molecule:defensin, mutant def-bbb; PDBTitle: nmr structure of def-bbb, a mutant of anopheles defensin2 def-aaa Phyre2 PDB 2jna chain A domain 1 Region: 1 - 23 Aligned: 23 Modelled: 23 Confidence: 11.9% Identity: 30% Fold: Dodecin subunit-like Superfamily: YdgH-like Family: YdgH-like Phyre2 PDB 2e2f chain A Region: 29 - 44 Aligned: 15 Modelled: 16 Confidence: 10.2% Identity: 40% PDB header:antifungal protein Chain: A: PDB Molecule:diapausin; PDBTitle: solution structure of dsp Phyre2 PDB 1zue chain A domain 1 Region: 21 - 47 Aligned: 16 Modelled: 27 Confidence: 9.6% Identity: 56% Fold: Defensin-like Superfamily: Defensin-like Family: Defensin Phyre2 PDB 1xfe chain A Region: 30 - 46 Aligned: 17 Modelled: 17 Confidence: 9.5% Identity: 35% PDB header:lipid transport, endocytosis/exocytosis Chain: A: PDB Molecule:low-density lipoprotein receptor; PDBTitle: solution structure of the la7-egfa pair from the ldl2 receptor Phyre2 PDB 2cup chain A domain 2 Region: 34 - 48 Aligned: 15 Modelled: 15 Confidence: 9.5% Identity: 40% Fold: Glucocorticoid receptor-like (DNA-binding domain) Superfamily: Glucocorticoid receptor-like (DNA-binding domain) Family: LIM domain Phyre2 PDB 1e43 chain A domain 1 Region: 39 - 49 Aligned: 11 Modelled: 11 Confidence: 8.3% Identity: 55% Fold: Glycosyl hydrolase domain Superfamily: Glycosyl hydrolase domain Family: alpha-Amylases, C-terminal beta-sheet domain Phyre2 PDB 1bgv chain A domain 2 Region: 7 - 32 Aligned: 26 Modelled: 26 Confidence: 8.2% Identity: 31% Fold: Aminoacid dehydrogenase-like, N-terminal domain Superfamily: Aminoacid dehydrogenase-like, N-terminal domain Family: Aminoacid dehydrogenases Phyre2 PDB 1ud2 chain A domain 1 Region: 39 - 49 Aligned: 11 Modelled: 11 Confidence: 8.2% Identity: 55% Fold: Glycosyl hydrolase domain Superfamily: Glycosyl hydrolase domain Family: alpha-Amylases, C-terminal beta-sheet domain Phyre2 PDB 2d3n chain A domain 1 Region: 39 - 49 Aligned: 11 Modelled: 11 Confidence: 8.0% Identity: 55% Fold: Glycosyl hydrolase domain Superfamily: Glycosyl hydrolase domain Family: alpha-Amylases, C-terminal beta-sheet domain Phyre2 PDB 2gjp chain A domain 1 Region: 39 - 49 Aligned: 11 Modelled: 11 Confidence: 7.8% Identity: 45% Fold: Glycosyl hydrolase domain Superfamily: Glycosyl hydrolase domain Family: alpha-Amylases, C-terminal beta-sheet domain Phyre2 1 d1tiha_ 2 d1pjua1 3 d1fyba1 4 d4sgbi_ 5 d1oyvi_ 6 c1fybA_ 7 d1ce3a_ 8 d1pjua2 9 c2d3jA_ 10 c2e3eA_ 11 d2jnaa1 12 c2e2fA_ 13 d1zuea1 14 c1xfeA_ 15 d2cupa2 16 d1e43a1 17 d1bgva2 18 d1ud2a1 19 d2d3na1 20 d2gjpa1 21 22 23 24 25 26 27 28 29 30 31 32 33 34

Detailed template information

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

1 d1tiha_ 81.2 35 Fold:Plant proteinase inhibitors Superfamily:Plant proteinase inhibitors Family:Plant proteinase inhibitors 2 d1pjua1 80.7 39 Fold:Plant proteinase inhibitors Superfamily:Plant proteinase inhibitors Family:Plant proteinase inhibitors 3 d1fyba1 80.1 39 Fold:Plant proteinase inhibitors Superfamily:Plant proteinase inhibitors Family:Plant proteinase inhibitors 4 d4sgbi_ 77.6 35 Fold:Plant proteinase inhibitors Superfamily:Plant proteinase inhibitors Family:Plant proteinase inhibitors 5 d1oyvi_ 71.6 39 Fold:Plant proteinase inhibitors Superfamily:Plant proteinase inhibitors Family:Plant proteinase inhibitors 6 c1fybA_ 69.3 39 PDB header:hydrolase inhibitor Chain: A: PDB Molecule:proteinase inhibitor; PDBTitle: solution structure of c1-t1, a two-domain proteinase2 inhibitor derived from the circular precursor protein na-3 propi from nicotiana alata 7 d1ce3a_ 50.6 41 Fold:Plant proteinase inhibitors Superfamily:Plant proteinase inhibitors Family:Plant proteinase inhibitors 8 d1pjua2 35.9 45 Fold:Plant proteinase inhibitors Superfamily:Plant proteinase inhibitors Family:Plant proteinase inhibitors 9 c2d3jA_ 13.3 40 PDB header:signaling protein inhibitor Chain: A: PDB Molecule:wnt inhibitory factor-1; PDBTitle: nmr structure of the wif domain from human wif-1 10 c2e3eA_ 12.5 38 PDB header:antimicrobial protein Chain: A: PDB Molecule:defensin, mutant def-bbb; PDBTitle: nmr structure of def-bbb, a mutant of anopheles defensin2 def-aaa 11 d2jnaa1 11.9 30 Fold:Dodecin subunit-like Superfamily:YdgH-like Family:YdgH-like 12 c2e2fA_ 10.2 40 PDB header:antifungal protein Chain: A: PDB Molecule:diapausin; PDBTitle: solution structure of dsp 13 d1zuea1 9.6 56 Fold:Defensin-like Superfamily:Defensin-like Family:Defensin 14 c1xfeA_ 9.5 35 PDB header:lipid transport, endocytosis/exocytosis Chain: A: PDB Molecule:low-density lipoprotein receptor; PDBTitle: solution structure of the la7-egfa pair from the ldl2 receptor 15 d2cupa2 9.5 40 Fold:Glucocorticoid receptor-like (DNA-binding domain) Superfamily:Glucocorticoid receptor-like (DNA-binding domain) Family:LIM domain 16 d1e43a1 8.3 55 Fold:Glycosyl hydrolase domain Superfamily:Glycosyl hydrolase domain Family:alpha-Amylases, C-terminal beta-sheet domain 17 d1bgva2 8.2 31 Fold:Aminoacid dehydrogenase-like, N-terminal domain Superfamily:Aminoacid dehydrogenase-like, N-terminal domain Family:Aminoacid dehydrogenases 18 d1ud2a1 8.2 55 Fold:Glycosyl hydrolase domain Superfamily:Glycosyl hydrolase domain Family:alpha-Amylases, C-terminal beta-sheet domain 19 d2d3na1 8.0 55 Fold:Glycosyl hydrolase domain Superfamily:Glycosyl hydrolase domain Family:alpha-Amylases, C-terminal beta-sheet domain 20 d2gjpa1 7.8 45 Fold:Glycosyl hydrolase domain Superfamily:Glycosyl hydrolase domain Family:alpha-Amylases, C-terminal beta-sheet domain 21 d1eoka_ not modelled 7.3 33 Fold:TIM beta/alpha-barrel Superfamily:(Trans)glycosidases Family:Type II chitinase 22 c1ozbI_ not modelled 6.1 67 PDB header:protein transport Chain: I: PDB Molecule:preprotein translocase seca subunit; PDBTitle: crystal structure of secb complexed with seca c-terminus 23 d1ozbi_ not modelled 6.1 67 Fold:Sec-C motif Superfamily:Sec-C motif Family:Sec-C motif 24 c1ozbJ_ not modelled 6.1 67 PDB header:protein transport Chain: J: PDB Molecule:preprotein translocase seca subunit; PDBTitle: crystal structure of secb complexed with seca c-terminus 25 c1d2jA_ not modelled 6.0 26 PDB header:signaling protein Chain: A: PDB Molecule:low-density lipoprotein receptor; PDBTitle: ldl receptor ligand-binding module 6 26 d1hvxa1 not modelled 5.9 55 Fold:Glycosyl hydrolase domain Superfamily:Glycosyl hydrolase domain Family:alpha-Amylases, C-terminal beta-sheet domain 27 c4a1eT_ not modelled 5.9 36 PDB header:ribosome Chain: T: PDB Molecule:rpl24; PDBTitle: t.thermophila 60s ribosomal subunit in complex with2 initiation factor 6. this file contains 5s rrna, 5.8s rrna3 and proteins of molecule 1 28 d1v9la2 not modelled 5.8 19 Fold:Aminoacid dehydrogenase-like, N-terminal domain Superfamily:Aminoacid dehydrogenase-like, N-terminal domain Family:Aminoacid dehydrogenases 29 d1g26a_ not modelled 5.7 38 Fold:Knottins (small inhibitors, toxins, lectins) Superfamily:Granulin repeat Family:Granulin repeat 30 c2i1pA_ not modelled 5.7 43 PDB header:ligand binding protein Chain: A: PDB Molecule:low-density lipoprotein receptor-related protein PDBTitle: solution structure of the twelfth cysteine-rich ligand-2 binding repeat in rat megalin 31 d1euza2 not modelled 5.6 27 Fold:Aminoacid dehydrogenase-like, N-terminal domain Superfamily:Aminoacid dehydrogenase-like, N-terminal domain Family:Aminoacid dehydrogenases 32 d1hwxa2 not modelled 5.6 19 Fold:Aminoacid dehydrogenase-like, N-terminal domain Superfamily:Aminoacid dehydrogenase-like, N-terminal domain Family:Aminoacid dehydrogenases 33 d1tm6a_ not modelled 5.5 67 Fold:Sec-C motif Superfamily:Sec-C motif Family:Sec-C motif 34 c1tm6A_ not modelled 5.5 67 PDB header:protein transport Chain: A: PDB Molecule:preprotein translocase seca subunit; PDBTitle: nmr structure of the free zinc binding c-terminal domain of2 seca

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