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

F

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V

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A

L

L

A

V

L

L

L

S

A

N

T

W

A

A

I

E

I

N

N

H

Q

A

R

N

M

D

D

V

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S

L

G

V

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Y

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N

F

A

T

E

S

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A

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A

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N

E

E

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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Sequence

T

D

A

Q

G

A

T

Y

Y

H

V

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L

M

R

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P

G

S

N

G

N

M

H

A

S

A

D

I

Y

R

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 2jna chain A domain 1 Region: 1 - 91 Aligned: 88 Modelled: 91 Confidence: 100.0% Identity: 32% Fold: Dodecin subunit-like Superfamily: YdgH-like Family: YdgH-like Phyre2 PDB 2noc chain A domain 1 Region: 1 - 91 Aligned: 87 Modelled: 88 Confidence: 99.9% Identity: 22% Fold: Dodecin subunit-like Superfamily: YdgH-like Family: YdgH-like Phyre2 PDB 3b9n chain B Region: 47 - 72 Aligned: 26 Modelled: 26 Confidence: 32.1% Identity: 8% PDB header:oxidoreductase Chain: B: PDB Molecule:alkane monoxygenase; PDBTitle: crystal structure of long-chain alkane monooxygenase (lada) Phyre2 PDB 2y1b chain A Region: 25 - 73 Aligned: 48 Modelled: 49 Confidence: 22.5% Identity: 13% 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 1hl8 chain B Region: 55 - 78 Aligned: 24 Modelled: 24 Confidence: 20.7% Identity: 21% PDB header:hydrolase Chain: B: PDB Molecule:putative alpha-l-fucosidase; PDBTitle: crystal structure of thermotoga maritima alpha-fucosidase Phyre2 PDB 1luc chain A Region: 44 - 71 Aligned: 28 Modelled: 28 Confidence: 20.3% Identity: 18% Fold: TIM beta/alpha-barrel Superfamily: Bacterial luciferase-like Family: Bacterial luciferase (alkanal monooxygenase) Phyre2 PDB 3sdo chain B Region: 46 - 71 Aligned: 26 Modelled: 26 Confidence: 19.7% Identity: 12% PDB header:oxidoreductase Chain: B: PDB Molecule:nitrilotriacetate monooxygenase; PDBTitle: structure of a nitrilotriacetate monooxygenase from burkholderia2 pseudomallei Phyre2 PDB 1oy8 chain A Region: 2 - 64 Aligned: 61 Modelled: 63 Confidence: 18.7% Identity: 10% PDB header:membrane protein Chain: A: PDB Molecule:acriflavine resistance protein b; PDBTitle: structural basis of multiple drug binding capacity of the acrb2 multidrug efflux pump Phyre2 PDB 3qkb chain B Region: 51 - 89 Aligned: 39 Modelled: 39 Confidence: 16.0% Identity: 15% PDB header:structural genomics, unknown function Chain: B: PDB Molecule:uncharacterized protein; PDBTitle: crystal structure of a protein with unknown function which belongs to2 pfam duf74 family (pepe_0654) from pediococcus pentosaceus atcc 257453 at 2.73 a resolution Phyre2 PDB 3eyp chain B Region: 55 - 78 Aligned: 24 Modelled: 24 Confidence: 15.9% Identity: 13% PDB header:structural genomics, unknown function Chain: B: PDB Molecule:putative alpha-l-fucosidase; PDBTitle: crystal structure of putative alpha-l-fucosidase from bacteroides2 thetaiotaomicron Phyre2 PDB 3mo4 chain B Region: 55 - 78 Aligned: 24 Modelled: 24 Confidence: 15.3% Identity: 13% PDB header:hydrolase Chain: B: PDB Molecule:alpha-1,3/4-fucosidase; PDBTitle: the crystal structure of an alpha-(1-3,4)-fucosidase from2 bifidobacterium longum subsp. infantis atcc 15697 Phyre2 PDB 2fiq chain A domain 1 Region: 47 - 83 Aligned: 37 Modelled: 35 Confidence: 13.0% Identity: 16% Fold: TIM beta/alpha-barrel Superfamily: Aldolase Family: GatZ-like Phyre2 PDB 1luc chain B Region: 48 - 71 Aligned: 24 Modelled: 24 Confidence: 11.1% Identity: 25% Fold: TIM beta/alpha-barrel Superfamily: Bacterial luciferase-like Family: Bacterial luciferase (alkanal monooxygenase) Phyre2 PDB 1hl9 chain A domain 2 Region: 55 - 78 Aligned: 24 Modelled: 24 Confidence: 10.6% Identity: 21% Fold: TIM beta/alpha-barrel Superfamily: (Trans)glycosidases Family: Putative alpha-L-fucosidase, catalytic domain Phyre2 PDB 1kqf chain B Region: 46 - 86 Aligned: 41 Modelled: 41 Confidence: 9.8% Identity: 22% PDB header:oxidoreductase Chain: B: PDB Molecule:formate dehydrogenase, nitrate-inducible, iron-sulfur PDBTitle: formate dehydrogenase n from e. coli Phyre2 PDB 2wvs chain D Region: 55 - 78 Aligned: 24 Modelled: 24 Confidence: 9.6% Identity: 13% PDB header:hydrolase Chain: D: PDB Molecule:alpha-l-fucosidase; PDBTitle: crystal structure of an alpha-l-fucosidase gh29 trapped2 covalent intermediate from bacteroides thetaiotaomicron in3 complex with 2-fluoro-fucosyl fluoride using an e288q4 mutant Phyre2 PDB 1xn9 chain A Region: 40 - 91 Aligned: 51 Modelled: 52 Confidence: 9.3% Identity: 14% Fold: Ribosomal proteins S24e, L23 and L15e Superfamily: Ribosomal proteins S24e, L23 and L15e Family: Ribosomal protein S24e Phyre2 PDB 1z69 chain D Region: 48 - 71 Aligned: 23 Modelled: 24 Confidence: 9.2% Identity: 13% PDB header:oxidoreductase Chain: D: PDB Molecule:coenzyme f420-dependent n(5),n(10)- PDBTitle: crystal structure of methylenetetrahydromethanopterin2 reductase (mer) in complex with coenzyme f420 Phyre2 PDB 3etj chain A domain 1 Region: 33 - 68 Aligned: 34 Modelled: 36 Confidence: 8.9% Identity: 12% Fold: Barrel-sandwich hybrid Superfamily: Rudiment single hybrid motif Family: BC C-terminal domain-like Phyre2 PDB 3k07 chain A Region: 2 - 89 Aligned: 86 Modelled: 88 Confidence: 8.1% Identity: 9% PDB header:transport protein Chain: A: PDB Molecule:cation efflux system protein cusa; PDBTitle: crystal structure of cusa Phyre2 1 d2jnaa1 2 d2noca1 3 c3b9nB_ 4 c2y1bA_ 5 c1hl8B_ 6 d1luca_ 7 c3sdoB_ 8 c1oy8A_ 9 c3qkbB_ 10 c3eypB_ 11 c3mo4B_ 12 d2fiqa1 13 d1lucb_ 14 d1hl9a2 15 c1kqfB_ 16 c2wvsD_ 17 d1xn9a_ 18 c1z69D_ 19 d3etja1 20 c3k07A_ 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36

Detailed template information

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

1 d2jnaa1 100.0 32 Fold:Dodecin subunit-like Superfamily:YdgH-like Family:YdgH-like 2 d2noca1 99.9 22 Fold:Dodecin subunit-like Superfamily:YdgH-like Family:YdgH-like 3 c3b9nB_ 32.1 8 PDB header:oxidoreductase Chain: B: PDB Molecule:alkane monoxygenase; PDBTitle: crystal structure of long-chain alkane monooxygenase (lada) 4 c2y1bA_ 22.5 13 PDB header:membrane protein Chain: A: PDB Molecule:putative outer membrane protein, signal; PDBTitle: crystal structure of the e. coli outer membrane lipoprotein2 rcsf 5 c1hl8B_ 20.7 21 PDB header:hydrolase Chain: B: PDB Molecule:putative alpha-l-fucosidase; PDBTitle: crystal structure of thermotoga maritima alpha-fucosidase 6 d1luca_ 20.3 18 Fold:TIM beta/alpha-barrel Superfamily:Bacterial luciferase-like Family:Bacterial luciferase (alkanal monooxygenase) 7 c3sdoB_ 19.7 12 PDB header:oxidoreductase Chain: B: PDB Molecule:nitrilotriacetate monooxygenase; PDBTitle: structure of a nitrilotriacetate monooxygenase from burkholderia2 pseudomallei 8 c1oy8A_ 18.7 10 PDB header:membrane protein Chain: A: PDB Molecule:acriflavine resistance protein b; PDBTitle: structural basis of multiple drug binding capacity of the acrb2 multidrug efflux pump 9 c3qkbB_ 16.0 15 PDB header:structural genomics, unknown function Chain: B: PDB Molecule:uncharacterized protein; PDBTitle: crystal structure of a protein with unknown function which belongs to2 pfam duf74 family (pepe_0654) from pediococcus pentosaceus atcc 257453 at 2.73 a resolution 10 c3eypB_ 15.9 13 PDB header:structural genomics, unknown function Chain: B: PDB Molecule:putative alpha-l-fucosidase; PDBTitle: crystal structure of putative alpha-l-fucosidase from bacteroides2 thetaiotaomicron 11 c3mo4B_ 15.3 13 PDB header:hydrolase Chain: B: PDB Molecule:alpha-1,3/4-fucosidase; PDBTitle: the crystal structure of an alpha-(1-3,4)-fucosidase from2 bifidobacterium longum subsp. infantis atcc 15697 12 d2fiqa1 13.0 16 Fold:TIM beta/alpha-barrel Superfamily:Aldolase Family:GatZ-like 13 d1lucb_ 11.1 25 Fold:TIM beta/alpha-barrel Superfamily:Bacterial luciferase-like Family:Bacterial luciferase (alkanal monooxygenase) 14 d1hl9a2 10.6 21 Fold:TIM beta/alpha-barrel Superfamily:(Trans)glycosidases Family:Putative alpha-L-fucosidase, catalytic domain 15 c1kqfB_ 9.8 22 PDB header:oxidoreductase Chain: B: PDB Molecule:formate dehydrogenase, nitrate-inducible, iron-sulfur PDBTitle: formate dehydrogenase n from e. coli 16 c2wvsD_ 9.6 13 PDB header:hydrolase Chain: D: PDB Molecule:alpha-l-fucosidase; PDBTitle: crystal structure of an alpha-l-fucosidase gh29 trapped2 covalent intermediate from bacteroides thetaiotaomicron in3 complex with 2-fluoro-fucosyl fluoride using an e288q4 mutant 17 d1xn9a_ 9.3 14 Fold:Ribosomal proteins S24e, L23 and L15e Superfamily:Ribosomal proteins S24e, L23 and L15e Family:Ribosomal protein S24e 18 c1z69D_ 9.2 13 PDB header:oxidoreductase Chain: D: PDB Molecule:coenzyme f420-dependent n(5),n(10)- PDBTitle: crystal structure of methylenetetrahydromethanopterin2 reductase (mer) in complex with coenzyme f420 19 d3etja1 8.9 12 Fold:Barrel-sandwich hybrid Superfamily:Rudiment single hybrid motif Family:BC C-terminal domain-like 20 c3k07A_ 8.1 9 PDB header:transport protein Chain: A: PDB Molecule:cation efflux system protein cusa; PDBTitle: crystal structure of cusa 21 c1tvlA_ not modelled 8.1 15 PDB header:oxidoreductase Chain: A: PDB Molecule:protein ytnj; PDBTitle: structure of ytnj from bacillus subtilis 22 d1tvla_ not modelled 8.1 15 Fold:TIM beta/alpha-barrel Superfamily:Bacterial luciferase-like Family:Ssud-like monoxygenases 23 c3ir9A_ not modelled 7.7 19 PDB header:structural genomics, unknown function Chain: A: PDB Molecule:peptide chain release factor subunit 1; PDBTitle: c-terminal domain of peptide chain release factor from2 methanosarcina mazei. 24 c2k38A_ not modelled 7.0 25 PDB header:antimicrobial protein Chain: A: PDB Molecule:cupiennin-1a; PDBTitle: cupiennin 1a, nmr, minimized average structure 25 c2jz7A_ not modelled 6.4 17 PDB header:selenium-binding protein Chain: A: PDB Molecule:selenium binding protein; PDBTitle: solution nmr structure of selenium-binding protein from2 methanococcus vannielii 26 c1f02T_ not modelled 6.3 7 PDB header:cell adhesion Chain: T: PDB Molecule:translocated intimin receptor; PDBTitle: crystal structure of c-terminal 282-residue fragment of2 intimin in complex with translocated intimin receptor3 (tir) intimin-binding domain 27 d1f07a_ not modelled 6.3 20 Fold:TIM beta/alpha-barrel Superfamily:Bacterial luciferase-like Family:F420 dependent oxidoreductases 28 c3gzaB_ not modelled 6.3 17 PDB header:hydrolase Chain: B: PDB Molecule:putative alpha-l-fucosidase; PDBTitle: crystal structure of putative alpha-l-fucosidase (np_812709.1) from2 bacteroides thetaiotaomicron vpi-5482 at 1.60 a resolution 29 d1wu7a1 not modelled 6.2 22 Fold:Anticodon-binding domain-like Superfamily:Class II aaRS ABD-related Family:Anticodon-binding domain of Class II aaRS 30 c2i7gA_ not modelled 6.2 0 PDB header:oxidoreductase Chain: A: PDB Molecule:monooxygenase; PDBTitle: crystal structure of monooxygenase from agrobacterium tumefaciens 31 c2k4qA_ not modelled 6.2 19 PDB header:viral protein Chain: A: PDB Molecule:major tail protein v; PDBTitle: the solution structure of gpv, the major tail protein from2 bacteriophage lambda 32 c3dfeA_ not modelled 5.8 23 PDB header:signaling protein Chain: A: PDB Molecule:putative pii-like signaling protein; PDBTitle: crystal structure of a putative pii-like signaling protein2 (yp_323533.1) from anabaena variabilis atcc 29413 at 2.35 a3 resolution 33 d1ywxa1 not modelled 5.8 18 Fold:Ribosomal proteins S24e, L23 and L15e Superfamily:Ribosomal proteins S24e, L23 and L15e Family:Ribosomal protein S24e 34 d1kjqa1 not modelled 5.4 17 Fold:Barrel-sandwich hybrid Superfamily:Rudiment single hybrid motif Family:BC C-terminal domain-like 35 c2wgkA_ not modelled 5.3 9 PDB header:oxidoreductase Chain: A: PDB Molecule:3,6-diketocamphane 1,6 monooxygenase; PDBTitle: type ii baeyer-villiger monooxygenase oxygenating2 constituent of 3,6-diketocamphane 1,6 monooxygenase from3 pseudomonas putida 36 d1nqka_ not modelled 5.2 13 Fold:TIM beta/alpha-barrel Superfamily:Bacterial luciferase-like Family:Ssud-like monoxygenases

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