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

K

L

S

T

C

C

A

A

L

L

L

A

L

A

S

P

A

V

L

A

A

P

G

S

C

E

R

I

Q

S

D

I

S

Q

R

I

I

N

N

G

V

P

E

S

S

F

T

L

S

I

V

P

N

D

Q

V

D

Q

P

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

D

S

Q

V

V

G

H

C

A

N

D

T

H

K

I

L

Y

T

R

T

T

S

G

N

V

S

A

P

A

Q

S

S

Q

D

G

A

P

A

E

P

Q

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 2wy3 chain B Region: 68 - 76 Aligned: 9 Modelled: 9 Confidence: 28.6% Identity: 56% PDB header:immune system/viral protein Chain: B: PDB Molecule:uncharacterized protein ul16; PDBTitle: structure of the hcmv ul16-micb complex elucidates select2 binding of a viral immunoevasin to diverse nkg2d ligands Phyre2 PDB 2jna chain A domain 1 Region: 1 - 50 Aligned: 48 Modelled: 50 Confidence: 27.6% Identity: 35% Fold: Dodecin subunit-like Superfamily: YdgH-like Family: YdgH-like Phyre2 PDB 2y69 chain S Region: 51 - 85 Aligned: 31 Modelled: 35 Confidence: 17.3% Identity: 23% PDB header:electron transport Chain: S: PDB Molecule:cytochrome c oxidase subunit 5b; PDBTitle: bovine heart cytochrome c oxidase re-refined with molecular2 oxygen Phyre2 PDB 2dhm chain A Region: 29 - 55 Aligned: 27 Modelled: 27 Confidence: 16.4% Identity: 26% PDB header:protein binding Chain: A: PDB Molecule:protein bola; PDBTitle: solution structure of the bola protein from escherichia coli Phyre2 PDB 1v54 chain F Region: 51 - 85 Aligned: 31 Modelled: 35 Confidence: 15.7% Identity: 23% Fold: Rubredoxin-like Superfamily: Rubredoxin-like Family: Cytochrome c oxidase Subunit F Phyre2 PDB 3k2t chain A Region: 69 - 83 Aligned: 15 Modelled: 15 Confidence: 12.5% Identity: 20% PDB header:structural genomics, unknown function Chain: A: PDB Molecule:lmo2511 protein; PDBTitle: crystal structure of lmo2511 protein from listeria2 monocytogenes, northeast structural genomics consortium3 target lkr84a Phyre2 PDB 2fz5 chain A domain 1 Region: 24 - 68 Aligned: 45 Modelled: 45 Confidence: 11.0% Identity: 20% Fold: Flavodoxin-like Superfamily: Flavoproteins Family: Flavodoxin-related Phyre2 PDB 3ka5 chain A Region: 69 - 83 Aligned: 15 Modelled: 15 Confidence: 9.8% Identity: 13% PDB header:chaperone Chain: A: PDB Molecule:ribosome-associated protein y (psrp-1); PDBTitle: crystal structure of ribosome-associated protein y (psrp-1)2 from clostridium acetobutylicum. northeast structural3 genomics consortium target id car123a Phyre2 PDB 1xs3 chain A Region: 30 - 55 Aligned: 26 Modelled: 26 Confidence: 9.7% Identity: 19% PDB header:structural genomics, unknown function Chain: A: PDB Molecule:hypothetical protein xc975; PDBTitle: solution structure analysis of the xc975 protein Phyre2 PDB 1ea9 chain C domain 2 Region: 67 - 83 Aligned: 17 Modelled: 17 Confidence: 8.2% Identity: 18% Fold: Glycosyl hydrolase domain Superfamily: Glycosyl hydrolase domain Family: alpha-Amylases, C-terminal beta-sheet domain Phyre2 PDB 5nul chain A Region: 24 - 68 Aligned: 45 Modelled: 45 Confidence: 8.1% Identity: 24% Fold: Flavodoxin-like Superfamily: Flavoproteins Family: Flavodoxin-related Phyre2 PDB 1v60 chain A Region: 29 - 55 Aligned: 25 Modelled: 25 Confidence: 7.9% Identity: 20% PDB header:structural genomics, unknown function Chain: A: PDB Molecule:riken cdna 1810037g04; PDBTitle: solution structure of bola1 protein from mus musculus Phyre2 PDB 1u9d chain A Region: 35 - 61 Aligned: 25 Modelled: 27 Confidence: 7.6% Identity: 8% Fold: Tautomerase/MIF Superfamily: Tautomerase/MIF Family: VC0714-like Phyre2 PDB 1pqs chain A Region: 16 - 55 Aligned: 40 Modelled: 40 Confidence: 7.6% Identity: 10% Fold: beta-Grasp (ubiquitin-like) Superfamily: CAD & PB1 domains Family: PB1 domain Phyre2 PDB 1xrs chain B domain 2 Region: 46 - 79 Aligned: 34 Modelled: 34 Confidence: 7.3% Identity: 18% Fold: Dodecin subunit-like Superfamily: D-lysine 5,6-aminomutase beta subunit KamE, N-terminal domain Family: D-lysine 5,6-aminomutase beta subunit KamE, N-terminal domain Phyre2 PDB 1q90 chain L Region: 5 - 16 Aligned: 12 Modelled: 12 Confidence: 7.1% Identity: 25% PDB header:photosynthesis Chain: L: PDB Molecule:cytochrome b6f complex subunit petl; PDBTitle: structure of the cytochrome b6f (plastohydroquinone : plastocyanin2 oxidoreductase) from chlamydomonas reinhardtii Phyre2 PDB 1q90 chain L Region: 5 - 16 Aligned: 12 Modelled: 12 Confidence: 7.1% Identity: 25% Fold: Single transmembrane helix Superfamily: PetL subunit of the cytochrome b6f complex Family: PetL subunit of the cytochrome b6f complex Phyre2 PDB 1go3 chain E domain 2 Region: 27 - 78 Aligned: 50 Modelled: 52 Confidence: 6.7% Identity: 18% Fold: Dodecin subunit-like Superfamily: N-terminal, heterodimerisation domain of RBP7 (RpoE) Family: N-terminal, heterodimerisation domain of RBP7 (RpoE) Phyre2 PDB 2k8s chain A Region: 39 - 52 Aligned: 14 Modelled: 14 Confidence: 6.5% Identity: 36% PDB header:oxidoreductase Chain: A: PDB Molecule:thioredoxin; PDBTitle: solution nmr structure of dimeric thioredoxin-like protein2 ne0084 from nitrosomonas europea: northeast structural3 genomics target net6 Phyre2 PDB 2jo1 chain A Region: 5 - 46 Aligned: 36 Modelled: 42 Confidence: 6.5% Identity: 25% PDB header:hydrolase regulator Chain: A: PDB Molecule:phospholemman; PDBTitle: structure of the na,k-atpase regulatory protein fxyd1 in2 micelles Phyre2 1 c2wy3B_ 2 d2jnaa1 3 c2y69S_ 4 c2dhmA_ 5 d1v54f_ 6 c3k2tA_ 7 d2fz5a1 8 c3ka5A_ 9 c1xs3A_ 10 d1ea9c2 11 d5nula_ 12 c1v60A_ 13 d1u9da_ 14 d1pqsa_ 15 d1xrsb2 16 c1q90L_ 17 d1q90l_ 18 d1go3e2 19 c2k8sA_ 20 c2jo1A_ 21 22 23 24 25 26 27 28

Detailed template information

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

1 c2wy3B_ 28.6 56 PDB header:immune system/viral protein Chain: B: PDB Molecule:uncharacterized protein ul16; PDBTitle: structure of the hcmv ul16-micb complex elucidates select2 binding of a viral immunoevasin to diverse nkg2d ligands 2 d2jnaa1 27.6 35 Fold:Dodecin subunit-like Superfamily:YdgH-like Family:YdgH-like 3 c2y69S_ 17.3 23 PDB header:electron transport Chain: S: PDB Molecule:cytochrome c oxidase subunit 5b; PDBTitle: bovine heart cytochrome c oxidase re-refined with molecular2 oxygen 4 c2dhmA_ 16.4 26 PDB header:protein binding Chain: A: PDB Molecule:protein bola; PDBTitle: solution structure of the bola protein from escherichia coli 5 d1v54f_ 15.7 23 Fold:Rubredoxin-like Superfamily:Rubredoxin-like Family:Cytochrome c oxidase Subunit F 6 c3k2tA_ 12.5 20 PDB header:structural genomics, unknown function Chain: A: PDB Molecule:lmo2511 protein; PDBTitle: crystal structure of lmo2511 protein from listeria2 monocytogenes, northeast structural genomics consortium3 target lkr84a 7 d2fz5a1 11.0 20 Fold:Flavodoxin-like Superfamily:Flavoproteins Family:Flavodoxin-related 8 c3ka5A_ 9.8 13 PDB header:chaperone Chain: A: PDB Molecule:ribosome-associated protein y (psrp-1); PDBTitle: crystal structure of ribosome-associated protein y (psrp-1)2 from clostridium acetobutylicum. northeast structural3 genomics consortium target id car123a 9 c1xs3A_ 9.7 19 PDB header:structural genomics, unknown function Chain: A: PDB Molecule:hypothetical protein xc975; PDBTitle: solution structure analysis of the xc975 protein 10 d1ea9c2 8.2 18 Fold:Glycosyl hydrolase domain Superfamily:Glycosyl hydrolase domain Family:alpha-Amylases, C-terminal beta-sheet domain 11 d5nula_ 8.1 24 Fold:Flavodoxin-like Superfamily:Flavoproteins Family:Flavodoxin-related 12 c1v60A_ 7.9 20 PDB header:structural genomics, unknown function Chain: A: PDB Molecule:riken cdna 1810037g04; PDBTitle: solution structure of bola1 protein from mus musculus 13 d1u9da_ 7.6 8 Fold:Tautomerase/MIF Superfamily:Tautomerase/MIF Family:VC0714-like 14 d1pqsa_ 7.6 10 Fold:beta-Grasp (ubiquitin-like) Superfamily:CAD & PB1 domains Family:PB1 domain 15 d1xrsb2 7.3 18 Fold:Dodecin subunit-like Superfamily:D-lysine 5,6-aminomutase beta subunit KamE, N-terminal domain Family:D-lysine 5,6-aminomutase beta subunit KamE, N-terminal domain 16 c1q90L_ 7.1 25 PDB header:photosynthesis Chain: L: PDB Molecule:cytochrome b6f complex subunit petl; PDBTitle: structure of the cytochrome b6f (plastohydroquinone : plastocyanin2 oxidoreductase) from chlamydomonas reinhardtii 17 d1q90l_ 7.1 25 Fold:Single transmembrane helix Superfamily:PetL subunit of the cytochrome b6f complex Family:PetL subunit of the cytochrome b6f complex 18 d1go3e2 6.7 18 Fold:Dodecin subunit-like Superfamily:N-terminal, heterodimerisation domain of RBP7 (RpoE) Family:N-terminal, heterodimerisation domain of RBP7 (RpoE) 19 c2k8sA_ 6.5 36 PDB header:oxidoreductase Chain: A: PDB Molecule:thioredoxin; PDBTitle: solution nmr structure of dimeric thioredoxin-like protein2 ne0084 from nitrosomonas europea: northeast structural3 genomics target net6 20 c2jo1A_ 6.5 25 PDB header:hydrolase regulator Chain: A: PDB Molecule:phospholemman; PDBTitle: structure of the na,k-atpase regulatory protein fxyd1 in2 micelles 21 d2cu6a1 not modelled 6.3 12 Fold:Alpha-lytic protease prodomain-like Superfamily:Fe-S cluster assembly (FSCA) domain-like Family:PaaD-like 22 d1l7da2 not modelled 6.1 7 Fold:Flavodoxin-like Superfamily:Formate/glycerate dehydrogenase catalytic domain-like Family:L-alanine dehydrogenase-like 23 d1pjca2 not modelled 6.0 9 Fold:Flavodoxin-like Superfamily:Formate/glycerate dehydrogenase catalytic domain-like Family:L-alanine dehydrogenase-like 24 d1r17a1 not modelled 6.0 22 Fold:Common fold of diphtheria toxin/transcription factors/cytochrome f Superfamily:Bacterial adhesins Family:Fibrinogen-binding domain 25 c1ib8A_ not modelled 5.8 15 PDB header:nucleic acid binding protein Chain: A: PDB Molecule:conserved protein sp14.3; PDBTitle: solution structure and function of a conserved protein2 sp14.3 encoded by an essential streptococcus pneumoniae3 gene 26 d1ylea1 not modelled 5.7 27 Fold:Acyl-CoA N-acyltransferases (Nat) Superfamily:Acyl-CoA N-acyltransferases (Nat) Family:AstA-like 27 c3hyjD_ not modelled 5.5 21 PDB header:transcription regulator Chain: D: PDB Molecule:protein duf199/whia; PDBTitle: crystal structure of the n-terminal laglidadg domain of duf199/whia 28 c2kdnA_ not modelled 5.5 30 PDB header:unknown function Chain: A: PDB Molecule:putative uncharacterized protein pfe0790c; PDBTitle: solution structure of pfe0790c, a putative bola-like2 protein from the protozoan parasite plasmodium falciparum.

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