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

N

M

R

N

I

N

V

I

T

V

L

S

V

P

G

K

T

V

S

D

D

F

M

H

A

V

L

S

N

C

A

T

R

I

V

L

P

A

P

E

K

F

G

S

E

S

L

P

D

N

F

N

M

T

A

V

G

V

M

Secondary structure

SS confidence

Disorder

?

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?

?

?

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?

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?

?

?

?

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?

?

?

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?

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?

Disorder confidence

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Sequence

K

N

S

E

I

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 1e9r chain A Region: 3 - 40 Aligned: 38 Modelled: 38 Confidence: 50.1% Identity: 11% Fold: P-loop containing nucleoside triphosphate hydrolases Superfamily: P-loop containing nucleoside triphosphate hydrolases Family: RecA protein-like (ATPase-domain) Phyre2 PDB 2pva chain A Region: 20 - 33 Aligned: 14 Modelled: 14 Confidence: 12.9% Identity: 36% Fold: Ntn hydrolase-like Superfamily: N-terminal nucleophile aminohydrolases (Ntn hydrolases) Family: Penicillin V acylase Phyre2 PDB 2hez chain B Region: 20 - 33 Aligned: 14 Modelled: 14 Confidence: 11.5% Identity: 21% PDB header:hydrolase Chain: B: PDB Molecule:bile salt hydrolase; PDBTitle: bifidobacterium longum bile salt hydrolase Phyre2 PDB 1shz chain F Region: 23 - 30 Aligned: 8 Modelled: 8 Confidence: 10.4% Identity: 13% PDB header:signaling protein Chain: F: PDB Molecule:rho guanine nucleotide exchange factor 1; PDBTitle: crystal structure of the p115rhogef rgrgs domain in a2 complex with galpha(13):galpha(i1) chimera Phyre2 PDB 2bjg chain B Region: 20 - 33 Aligned: 14 Modelled: 14 Confidence: 10.3% Identity: 29% PDB header:hydrolase Chain: B: PDB Molecule:choloylglycine hydrolase; PDBTitle: crystal structure of conjugated bile acid hydrolase from2 clostridium perfringens in complex with reaction products3 taurine and deoxycholate Phyre2 PDB 1iap chain A Region: 23 - 30 Aligned: 8 Modelled: 8 Confidence: 10.3% Identity: 13% Fold: Regulator of G-protein signaling, RGS Superfamily: Regulator of G-protein signaling, RGS Family: Regulator of G-protein signaling, RGS Phyre2 PDB 1htj chain F Region: 23 - 30 Aligned: 8 Modelled: 8 Confidence: 9.2% Identity: 25% Fold: Regulator of G-protein signaling, RGS Superfamily: Regulator of G-protein signaling, RGS Family: Regulator of G-protein signaling, RGS Phyre2 PDB 1htj chain F Region: 23 - 30 Aligned: 8 Modelled: 8 Confidence: 9.2% Identity: 25% PDB header:signaling protein Chain: F: PDB Molecule:kiaa0380; PDBTitle: structure of the rgs-like domain from pdz-rhogef Phyre2 PDB 2jxt chain A domain 1 Region: 4 - 28 Aligned: 25 Modelled: 25 Confidence: 9.0% Identity: 12% Fold: RplX-like Superfamily: RplX-like Family: RplX-like Phyre2 PDB 1tu3 chain J Region: 17 - 25 Aligned: 9 Modelled: 9 Confidence: 8.7% Identity: 33% PDB header:protein transport Chain: J: PDB Molecule:rab gtpase binding effector protein 1; PDBTitle: crystal structure of rab5 complex with rabaptin5 c-terminal2 domain Phyre2 PDB 3aqb chain C Region: 20 - 35 Aligned: 14 Modelled: 16 Confidence: 8.4% Identity: 50% PDB header:transferase Chain: C: PDB Molecule:component a of hexaprenyl diphosphate synthase; PDBTitle: m. luteus b-p 26 heterodimeric hexaprenyl diphosphate synthase in2 complex with magnesium Phyre2 PDB 2f4i chain A domain 1 Region: 39 - 64 Aligned: 26 Modelled: 26 Confidence: 7.4% Identity: 15% Fold: OB-fold Superfamily: TM0957-like Family: TM0957-like Phyre2 PDB 3ipj chain B Region: 28 - 37 Aligned: 10 Modelled: 10 Confidence: 6.6% Identity: 40% PDB header:transferase Chain: B: PDB Molecule:pts system, iiabc component; PDBTitle: the crystal structure of one domain of the pts system, iiabc component2 from clostridium difficile Phyre2 PDB 2oqc chain B Region: 22 - 33 Aligned: 12 Modelled: 12 Confidence: 6.0% Identity: 42% PDB header:hydrolase Chain: B: PDB Molecule:penicillin v acylase; PDBTitle: crystal structure of penicillin v acylase from bacillus subtilis Phyre2 PDB 1iba chain A Region: 28 - 37 Aligned: 10 Modelled: 10 Confidence: 5.9% Identity: 40% PDB header:phoshphotransferase Chain: A: PDB Molecule:glucose permease; PDBTitle: glucose permease (domain iib), nmr, 11 structures Phyre2 PDB 3hbc chain A Region: 22 - 33 Aligned: 12 Modelled: 12 Confidence: 5.6% Identity: 42% PDB header:hydrolase Chain: A: PDB Molecule:choloylglycine hydrolase; PDBTitle: crystal structure of choloylglycine hydrolase from bacteroides2 thetaiotaomicron vpi Phyre2 PDB 3bp8 chain C domain 1 Region: 28 - 37 Aligned: 10 Modelled: 10 Confidence: 5.2% Identity: 40% Fold: Homing endonuclease-like Superfamily: Glucose permease domain IIB Family: Glucose permease domain IIB Phyre2 1 d1e9ra_ 2 d2pvaa_ 3 c2hezB_ 4 c1shzF_ 5 c2bjgB_ 6 d1iapa_ 7 d1htjf_ 8 c1htjF_ 9 d2jxta1 10 c1tu3J_ 11 c3aqbC_ 12 d2f4ia1 13 c3ipjB_ 14 c2oqcB_ 15 c1ibaA_ 16 c3hbcA_ 17 d3bp8c1

Detailed template information

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

1 d1e9ra_ 50.1 11 Fold:P-loop containing nucleoside triphosphate hydrolases Superfamily:P-loop containing nucleoside triphosphate hydrolases Family:RecA protein-like (ATPase-domain) 2 d2pvaa_ 12.9 36 Fold:Ntn hydrolase-like Superfamily:N-terminal nucleophile aminohydrolases (Ntn hydrolases) Family:Penicillin V acylase 3 c2hezB_ 11.5 21 PDB header:hydrolase Chain: B: PDB Molecule:bile salt hydrolase; PDBTitle: bifidobacterium longum bile salt hydrolase 4 c1shzF_ 10.4 13 PDB header:signaling protein Chain: F: PDB Molecule:rho guanine nucleotide exchange factor 1; PDBTitle: crystal structure of the p115rhogef rgrgs domain in a2 complex with galpha(13):galpha(i1) chimera 5 c2bjgB_ 10.3 29 PDB header:hydrolase Chain: B: PDB Molecule:choloylglycine hydrolase; PDBTitle: crystal structure of conjugated bile acid hydrolase from2 clostridium perfringens in complex with reaction products3 taurine and deoxycholate 6 d1iapa_ 10.3 13 Fold:Regulator of G-protein signaling, RGS Superfamily:Regulator of G-protein signaling, RGS Family:Regulator of G-protein signaling, RGS 7 d1htjf_ 9.2 25 Fold:Regulator of G-protein signaling, RGS Superfamily:Regulator of G-protein signaling, RGS Family:Regulator of G-protein signaling, RGS 8 c1htjF_ 9.2 25 PDB header:signaling protein Chain: F: PDB Molecule:kiaa0380; PDBTitle: structure of the rgs-like domain from pdz-rhogef 9 d2jxta1 9.0 12 Fold:RplX-like Superfamily:RplX-like Family:RplX-like 10 c1tu3J_ 8.7 33 PDB header:protein transport Chain: J: PDB Molecule:rab gtpase binding effector protein 1; PDBTitle: crystal structure of rab5 complex with rabaptin5 c-terminal2 domain 11 c3aqbC_ 8.4 50 PDB header:transferase Chain: C: PDB Molecule:component a of hexaprenyl diphosphate synthase; PDBTitle: m. luteus b-p 26 heterodimeric hexaprenyl diphosphate synthase in2 complex with magnesium 12 d2f4ia1 7.4 15 Fold:OB-fold Superfamily:TM0957-like Family:TM0957-like 13 c3ipjB_ 6.6 40 PDB header:transferase Chain: B: PDB Molecule:pts system, iiabc component; PDBTitle: the crystal structure of one domain of the pts system, iiabc component2 from clostridium difficile 14 c2oqcB_ 6.0 42 PDB header:hydrolase Chain: B: PDB Molecule:penicillin v acylase; PDBTitle: crystal structure of penicillin v acylase from bacillus subtilis 15 c1ibaA_ 5.9 40 PDB header:phoshphotransferase Chain: A: PDB Molecule:glucose permease; PDBTitle: glucose permease (domain iib), nmr, 11 structures 16 c3hbcA_ 5.6 42 PDB header:hydrolase Chain: A: PDB Molecule:choloylglycine hydrolase; PDBTitle: crystal structure of choloylglycine hydrolase from bacteroides2 thetaiotaomicron vpi 17 d3bp8c1 5.2 40 Fold:Homing endonuclease-like Superfamily:Glucose permease domain IIB Family:Glucose permease domain IIB

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