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

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L

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V

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R

A

A

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Y

G

A

I

M

A

A

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P

Y

M

Q

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A

D

Y

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M

H

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E

E

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G

A

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L

L

M

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Y

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G

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I

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

P

K

N

R

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K

I

A

R

L

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N

E

R

W

A

D

V

E

P

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L

Q

E

F

F

C

D

N

G

E

E

W

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I

E

E

D

L

A

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V

R

E

K

L

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K

K

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A

A

G

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A

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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

V

Q

A

R

R

S

R

K

E

A

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K

Q

E

R

N

L

T

G

V

Q

T

D

V

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V

V

F

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H

D

V

N

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K

A

T

N

K

D

T

D

K

D

L

K

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D

P

P

L

N

P

P

R

G

N

Secondary structure

SS confidence

Disorder

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Disorder confidence

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190

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200

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210

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220

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230

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240

Sequence

R

G

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K

F

D

P

L

D

I

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L

P

N

W

I

S

V

S

L

W

R

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W

V

E

F

R

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A

L

R

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P

I

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A

N

G

A

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L

E

K

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Q

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Secondary structure

SS confidence

Disorder

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Disorder confidence

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250

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260

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270

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280

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Sequence

Q

V

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R

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S

I

A

N

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Y

Q

G

L

F

A

P

K

G

V

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L

L

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V

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P

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G

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 3kny chain A Region: 176 - 250 Aligned: 62 Modelled: 73 Confidence: 53.1% Identity: 21% PDB header:unknown function Chain: A: PDB Molecule:hypothetical protein bt_3535; PDBTitle: crystal structure of a two domain protein with unknown function2 (bt_3535) from bacteroides thetaiotaomicron vpi-5482 at 2.60 a3 resolution Phyre2 PDB 1pby chain A Region: 31 - 91 Aligned: 61 Modelled: 61 Confidence: 48.8% Identity: 21% PDB header:oxidoreductase Chain: A: PDB Molecule:quinohemoprotein amine dehydrogenase 60 kda PDBTitle: structure of the phenylhydrazine adduct of the2 quinohemoprotein amine dehydrogenase from paracoccus3 denitrificans at 1.7 a resolution Phyre2 PDB 1qmg chain A domain 1 Region: 222 - 256 Aligned: 35 Modelled: 35 Confidence: 45.0% Identity: 20% Fold: 6-phosphogluconate dehydrogenase C-terminal domain-like Superfamily: 6-phosphogluconate dehydrogenase C-terminal domain-like Family: Acetohydroxy acid isomeroreductase (ketol-acid reductoisomerase, KARI) Phyre2 PDB 2v79 chain B Region: 36 - 85 Aligned: 50 Modelled: 50 Confidence: 29.4% Identity: 12% PDB header:dna-binding protein Chain: B: PDB Molecule:dna replication protein dnad; PDBTitle: crystal structure of the n-terminal domain of dnad from2 bacillus subtilis Phyre2 PDB 1khb chain A domain 1 Region: 18 - 33 Aligned: 16 Modelled: 16 Confidence: 27.5% Identity: 31% Fold: PEP carboxykinase-like Superfamily: PEP carboxykinase-like Family: PEP carboxykinase C-terminal domain Phyre2 PDB 2vn2 chain B Region: 36 - 113 Aligned: 77 Modelled: 78 Confidence: 24.5% Identity: 14% PDB header:replication Chain: B: PDB Molecule:chromosome replication initiation protein; PDBTitle: crystal structure of the n-terminal domain of dnad protein2 from geobacillus kaustophilus hta426 Phyre2 PDB 2qey chain A Region: 18 - 33 Aligned: 16 Modelled: 16 Confidence: 23.8% Identity: 31% PDB header:lyase Chain: A: PDB Molecule:phosphoenolpyruvate carboxykinase, cytosolic [gtp]; PDBTitle: rat cytosolic pepck in complex with gtp Phyre2 PDB 2f5u chain A Region: 28 - 61 Aligned: 33 Modelled: 34 Confidence: 20.6% Identity: 30% PDB header:viral protein Chain: A: PDB Molecule:virion protein ul25; PDBTitle: structural characterization of the ul25 dna packaging2 protein from herpes simplex virus type 1 Phyre2 PDB 2jrd chain A Region: 242 - 254 Aligned: 13 Modelled: 13 Confidence: 20.6% Identity: 31% PDB header:viral protein Chain: A: PDB Molecule:hemagglutinin; PDBTitle: influenza hemagglutinin fusion domain mutant f9a Phyre2 PDB 1bdt chain A Region: 18 - 58 Aligned: 41 Modelled: 41 Confidence: 19.1% Identity: 27% Fold: Ribbon-helix-helix Superfamily: Ribbon-helix-helix Family: Arc/Mnt-like phage repressors Phyre2 PDB 2zci chain D Region: 18 - 33 Aligned: 16 Modelled: 16 Confidence: 18.5% Identity: 38% PDB header:signaling protein, lyase Chain: D: PDB Molecule:phosphoenolpyruvate carboxykinase [gtp]; PDBTitle: structure of a gtp-dependent bacterial pep-carboxykinase2 from corynebacterium glutamicum Phyre2 PDB 1t07 chain A Region: 187 - 232 Aligned: 46 Modelled: 46 Confidence: 17.2% Identity: 20% Fold: YggX-like Superfamily: YggX-like Family: YggX-like Phyre2 PDB 1xs8 chain A Region: 187 - 238 Aligned: 52 Modelled: 52 Confidence: 16.1% Identity: 17% Fold: YggX-like Superfamily: YggX-like Family: YggX-like Phyre2 PDB 1jmx chain A Region: 31 - 90 Aligned: 59 Modelled: 60 Confidence: 15.9% Identity: 24% PDB header:oxidoreductase Chain: A: PDB Molecule:amine dehydrogenase; PDBTitle: crystal structure of a quinohemoprotein amine dehydrogenase2 from pseudomonas putida Phyre2 PDB 1sed chain A Region: 225 - 257 Aligned: 30 Modelled: 33 Confidence: 15.9% Identity: 17% Fold: Hypothetical protein YhaI Superfamily: Hypothetical protein YhaI Family: Hypothetical protein YhaI Phyre2 PDB 2fah chain B Region: 18 - 33 Aligned: 16 Modelled: 16 Confidence: 13.2% Identity: 25% PDB header:lyase Chain: B: PDB Molecule:phosphoenolpyruvate carboxykinase; PDBTitle: the structure of mitochondrial pepck, complex with mn and gdp Phyre2 PDB 3bdr chain A Region: 83 - 98 Aligned: 16 Modelled: 16 Confidence: 12.6% Identity: 25% PDB header:structural genomics, unknown function Chain: A: PDB Molecule:ycf58 protein; PDBTitle: crystal structure of fatty acid-binding protein-like ycf582 from thermosynecoccus elongatus. northeast structural3 genomics consortium target ter13. Phyre2 PDB 1pby chain A domain 1 Region: 28 - 51 Aligned: 24 Modelled: 24 Confidence: 12.5% Identity: 29% Fold: Cytochrome c Superfamily: Cytochrome c Family: Quinohemoprotein amine dehydrogenase A chain, domains 1 and 2 Phyre2 PDB 1tw3 chain A Region: 26 - 103 Aligned: 72 Modelled: 78 Confidence: 12.0% Identity: 13% PDB header:transferase Chain: A: PDB Molecule:carminomycin 4-o-methyltransferase; PDBTitle: crystal structure of carminomycin-4-o-methyltransferase2 (dnrk) in complex with s-adenosyl-l-homocystein (sah) and3 4-methoxy-e-rhodomycin t (m-et) Phyre2 PDB 1gjj chain A domain 2 Region: 195 - 236 Aligned: 41 Modelled: 42 Confidence: 11.3% Identity: 17% Fold: LEM/SAP HeH motif Superfamily: LEM domain Family: LEM domain Phyre2 1 c3knyA_ 2 c1pbyA_ 3 d1qmga1 4 c2v79B_ 5 d1khba1 6 c2vn2B_ 7 c2qeyA_ 8 c2f5uA_ 9 c2jrdA_ 10 d1bdta_ 11 c2zciD_ 12 d1t07a_ 13 d1xs8a_ 14 c1jmxA_ 15 d1seda_ 16 c2fahB_ 17 c3bdrA_ 18 d1pbya1 19 c1tw3A_ 20 d1gjja2 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

Detailed template information

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

1 c3knyA_ 53.1 21 PDB header:unknown function Chain: A: PDB Molecule:hypothetical protein bt_3535; PDBTitle: crystal structure of a two domain protein with unknown function2 (bt_3535) from bacteroides thetaiotaomicron vpi-5482 at 2.60 a3 resolution 2 c1pbyA_ 48.8 21 PDB header:oxidoreductase Chain: A: PDB Molecule:quinohemoprotein amine dehydrogenase 60 kda PDBTitle: structure of the phenylhydrazine adduct of the2 quinohemoprotein amine dehydrogenase from paracoccus3 denitrificans at 1.7 a resolution 3 d1qmga1 45.0 20 Fold:6-phosphogluconate dehydrogenase C-terminal domain-like Superfamily:6-phosphogluconate dehydrogenase C-terminal domain-like Family:Acetohydroxy acid isomeroreductase (ketol-acid reductoisomerase, KARI) 4 c2v79B_ 29.4 12 PDB header:dna-binding protein Chain: B: PDB Molecule:dna replication protein dnad; PDBTitle: crystal structure of the n-terminal domain of dnad from2 bacillus subtilis 5 d1khba1 27.5 31 Fold:PEP carboxykinase-like Superfamily:PEP carboxykinase-like Family:PEP carboxykinase C-terminal domain 6 c2vn2B_ 24.5 14 PDB header:replication Chain: B: PDB Molecule:chromosome replication initiation protein; PDBTitle: crystal structure of the n-terminal domain of dnad protein2 from geobacillus kaustophilus hta426 7 c2qeyA_ 23.8 31 PDB header:lyase Chain: A: PDB Molecule:phosphoenolpyruvate carboxykinase, cytosolic [gtp]; PDBTitle: rat cytosolic pepck in complex with gtp 8 c2f5uA_ 20.6 30 PDB header:viral protein Chain: A: PDB Molecule:virion protein ul25; PDBTitle: structural characterization of the ul25 dna packaging2 protein from herpes simplex virus type 1 9 c2jrdA_ 20.6 31 PDB header:viral protein Chain: A: PDB Molecule:hemagglutinin; PDBTitle: influenza hemagglutinin fusion domain mutant f9a 10 d1bdta_ 19.1 27 Fold:Ribbon-helix-helix Superfamily:Ribbon-helix-helix Family:Arc/Mnt-like phage repressors 11 c2zciD_ 18.5 38 PDB header:signaling protein, lyase Chain: D: PDB Molecule:phosphoenolpyruvate carboxykinase [gtp]; PDBTitle: structure of a gtp-dependent bacterial pep-carboxykinase2 from corynebacterium glutamicum 12 d1t07a_ 17.2 20 Fold:YggX-like Superfamily:YggX-like Family:YggX-like 13 d1xs8a_ 16.1 17 Fold:YggX-like Superfamily:YggX-like Family:YggX-like 14 c1jmxA_ 15.9 24 PDB header:oxidoreductase Chain: A: PDB Molecule:amine dehydrogenase; PDBTitle: crystal structure of a quinohemoprotein amine dehydrogenase2 from pseudomonas putida 15 d1seda_ 15.9 17 Fold:Hypothetical protein YhaI Superfamily:Hypothetical protein YhaI Family:Hypothetical protein YhaI 16 c2fahB_ 13.2 25 PDB header:lyase Chain: B: PDB Molecule:phosphoenolpyruvate carboxykinase; PDBTitle: the structure of mitochondrial pepck, complex with mn and gdp 17 c3bdrA_ 12.6 25 PDB header:structural genomics, unknown function Chain: A: PDB Molecule:ycf58 protein; PDBTitle: crystal structure of fatty acid-binding protein-like ycf582 from thermosynecoccus elongatus. northeast structural3 genomics consortium target ter13. 18 d1pbya1 12.5 29 Fold:Cytochrome c Superfamily:Cytochrome c Family:Quinohemoprotein amine dehydrogenase A chain, domains 1 and 2 19 c1tw3A_ 12.0 13 PDB header:transferase Chain: A: PDB Molecule:carminomycin 4-o-methyltransferase; PDBTitle: crystal structure of carminomycin-4-o-methyltransferase2 (dnrk) in complex with s-adenosyl-l-homocystein (sah) and3 4-methoxy-e-rhodomycin t (m-et) 20 d1gjja2 11.3 17 Fold:LEM/SAP HeH motif Superfamily:LEM domain Family:LEM domain 21 d6paxa1 not modelled 11.2 28 Fold:DNA/RNA-binding 3-helical bundle Superfamily:Homeodomain-like Family:Paired domain 22 c1iboA_ not modelled 10.5 31 PDB header:viral protein Chain: A: PDB Molecule:hemagglutinin ha2 chain peptide; PDBTitle: nmr structure of hemagglutinin fusion peptide in dpc2 micelles at ph 7.4 23 c1ibnA_ not modelled 10.5 31 PDB header:viral protein Chain: A: PDB Molecule:hemagglutinin ha2 chain peptide; PDBTitle: nmr structure of hemagglutinin fusion peptide in dpc2 micelles at ph 5 24 d1z5ga1 not modelled 10.2 12 Fold:HAD-like Superfamily:HAD-like Family:Class B acid phosphatase, AphA 25 d1zbsa2 not modelled 9.5 15 Fold:Ribonuclease H-like motif Superfamily:Actin-like ATPase domain Family:BadF/BadG/BcrA/BcrD-like 26 c3chxG_ not modelled 9.3 23 PDB header:membrane protein Chain: G: PDB Molecule:pmoc; PDBTitle: crystal structure of methylosinus trichosporium ob3b2 particulate methane monooxygenase (pmmo) 27 c2kxaA_ not modelled 9.1 23 PDB header:viral protein, immune system Chain: A: PDB Molecule:haemagglutinin ha2 chain peptide; PDBTitle: the hemagglutinin fusion peptide (h1 subtype) at ph 7.4 28 c1gjjA_ not modelled 9.1 33 PDB header:membrane protein Chain: A: PDB Molecule:lap2; PDBTitle: n-terminal constant region of the nuclear envelope protein2 lap2 29 d1b28a_ not modelled 8.8 29 Fold:Ribbon-helix-helix Superfamily:Ribbon-helix-helix Family:Arc/Mnt-like phage repressors 30 d1h9fa_ not modelled 8.2 30 Fold:LEM/SAP HeH motif Superfamily:LEM domain Family:LEM domain 31 d1k78a1 not modelled 7.8 25 Fold:DNA/RNA-binding 3-helical bundle Superfamily:Homeodomain-like Family:Paired domain 32 d1iuqa_ not modelled 7.7 17 Fold:Glycerol-3-phosphate (1)-acyltransferase Superfamily:Glycerol-3-phosphate (1)-acyltransferase Family:Glycerol-3-phosphate (1)-acyltransferase 33 c1yewC_ not modelled 7.0 15 PDB header:oxidoreductase, membrane protein Chain: C: PDB Molecule:particulate methane monooxygenase subunit c2; PDBTitle: crystal structure of particulate methane monooxygenase 34 c2pjwH_ not modelled 6.8 16 PDB header:endocytosis/exocytosis Chain: H: PDB Molecule:uncharacterized protein yhl002w; PDBTitle: the vps27/hse1 complex is a gat domain-based scaffold for2 ubiquitin-dependent sorting 35 c2k1oA_ not modelled 6.7 41 PDB header:gene regulation Chain: A: PDB Molecule:putative; PDBTitle: nmr structure of helicobacter pylori jhp0511 (hp0564). 36 c2pfcA_ not modelled 6.6 22 PDB header:unknown function Chain: A: PDB Molecule:hypothetical protein rv0098/mt0107; PDBTitle: structure of mycobacterium tuberculosis rv0098 37 c1xopA_ not modelled 6.4 31 PDB header:viral protein Chain: A: PDB Molecule:hemagglutinin; PDBTitle: nmr structure of g1v mutant of influenza hemagglutinin2 fusion peptide in dpc micelles at ph 5 38 c1xooA_ not modelled 6.3 31 PDB header:viral protein Chain: A: PDB Molecule:hemagglutinin; PDBTitle: nmr structure of g1s mutant of influenza hemagglutinin2 fusion peptide in dpc micelles at ph 5 39 c3bhwA_ not modelled 6.1 15 PDB header:structural genomics, unknown function Chain: A: PDB Molecule:uncharacterized protein; PDBTitle: crystal structure of an uncharacterized protein from magnetospirillum2 magneticum 40 d1fi6a_ not modelled 5.9 24 Fold:EF Hand-like Superfamily:EF-hand Family:Eps15 homology domain (EH domain) 41 d1c07a_ not modelled 5.7 19 Fold:EF Hand-like Superfamily:EF-hand Family:Eps15 homology domain (EH domain) 42 c2bn5A_ not modelled 5.6 25 PDB header:nuclear protein Chain: A: PDB Molecule:psi; PDBTitle: p-element somatic inhibitor protein complex with u1-70k2 proline-rich peptide 43 c2ia2D_ not modelled 5.5 13 PDB header:transcription Chain: D: PDB Molecule:putative transcriptional regulator; PDBTitle: the crystal structure of a putative transcriptional regulator rha061952 from rhodococcus sp. rha1 44 d2o9aa1 not modelled 5.4 10 Fold:Profilin-like Superfamily:GAF domain-like Family:IclR ligand-binding domain-like 45 d1cmca_ not modelled 5.4 50 Fold:Ribbon-helix-helix Superfamily:Ribbon-helix-helix Family:Met repressor, MetJ (MetR)

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