Secondary structure and disorder prediction

1

.

.

.

.

.

.

.

.

10

.

.

.

.

.

.

.

.

.

20

.

.

.

.

.

.

.

.

.

30

.

.

.

.

.

.

.

.

.

40

.

.

.

.

.

.

.

.

.

50

.

.

.

.

.

.

.

.

.

60

Sequence

M

A

K

E

Q

T

D

R

T

T

L

D

L

F

A

H

E

R

R

P

G

R

P

K

T

N

P

L

S

R

D

E

Q

L

R

I

N

K

R

N

Q

L

K

R

D

K

V

R

G

L

K

R

V

E

L

K

L

N

A

E

Secondary structure

SS confidence

Disorder

?

?

?

?

?

?

?

?

?

?

?

?

?

?

?

?

?

?

?

?

?

?

?

?

?

?

?

?

?

?

Disorder confidence

.

.

.

.

.

.

.

.

.

70

.

.

.

.

.

.

.

.

.

80

.

.

.

.

.

.

.

.

.

90

.

.

.

.

.

.

.

Sequence

A

V

E

A

L

N

E

L

A

E

S

R

N

M

S

R

S

E

L

I

E

E

M

L

M

Q

Q

L

A

A

L

R

S

Q

G

I

V

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 1q5v chain B Region: 50 - 89 Aligned: 40 Modelled: 40 Confidence: 95.3% Identity: 35% PDB header:transcription Chain: B: PDB Molecule:nickel responsive regulator; PDBTitle: apo-nikr Phyre2 PDB 2bj3 chain D Region: 50 - 89 Aligned: 40 Modelled: 40 Confidence: 95.2% Identity: 20% PDB header:transcription Chain: D: PDB Molecule:nickel responsive regulator; PDBTitle: nikr-apo Phyre2 PDB 2bj7 chain A domain 1 Region: 50 - 89 Aligned: 40 Modelled: 40 Confidence: 95.2% Identity: 20% Fold: Ribbon-helix-helix Superfamily: Ribbon-helix-helix Family: CopG-like Phyre2 PDB 2ca9 chain B Region: 50 - 92 Aligned: 43 Modelled: 43 Confidence: 94.6% Identity: 23% PDB header:transcriptional regulation Chain: B: PDB Molecule:putative nickel-responsive regulator; PDBTitle: apo-nikr from helicobacter pylori in closed trans-2 conformation Phyre2 PDB 2hza chain A domain 1 Region: 51 - 89 Aligned: 39 Modelled: 39 Confidence: 93.1% Identity: 36% Fold: Ribbon-helix-helix Superfamily: Ribbon-helix-helix Family: CopG-like Phyre2 PDB 2hza chain B domain 1 Region: 51 - 89 Aligned: 39 Modelled: 39 Confidence: 92.8% Identity: 36% Fold: Ribbon-helix-helix Superfamily: Ribbon-helix-helix Family: CopG-like Phyre2 PDB 2k5j chain B Region: 50 - 89 Aligned: 40 Modelled: 40 Confidence: 89.9% Identity: 33% PDB header:structural genomics, unknown function Chain: B: PDB Molecule:uncharacterized protein yiif; PDBTitle: solution structure of protein yiif from shigella flexneri2 serotype 5b (strain 8401) . northeast structural genomics3 consortium target sft1 Phyre2 PDB 2cpg chain A Region: 51 - 88 Aligned: 38 Modelled: 38 Confidence: 72.3% Identity: 26% Fold: Ribbon-helix-helix Superfamily: Ribbon-helix-helix Family: CopG-like Phyre2 PDB 1y9b chain A domain 1 Region: 52 - 80 Aligned: 29 Modelled: 29 Confidence: 29.3% Identity: 14% Fold: Ribbon-helix-helix Superfamily: Ribbon-helix-helix Family: VCA0319-like Phyre2 PDB 2kwp chain A Region: 58 - 92 Aligned: 35 Modelled: 35 Confidence: 25.7% Identity: 14% PDB header:transcription Chain: A: PDB Molecule:transcription elongation protein nusa; PDBTitle: solution structure of the aminoterminal domain of e. coli nusa Phyre2 PDB 3kk4 chain B Region: 55 - 90 Aligned: 36 Modelled: 36 Confidence: 22.3% Identity: 19% PDB header:structural genomics, unknown function Chain: B: PDB Molecule:uncharacterized protein bp1543; PDBTitle: uncharacterized protein bp1543 from bordetella pertussis tohama i Phyre2 PDB 2kkm chain A Region: 17 - 50 Aligned: 30 Modelled: 34 Confidence: 18.9% Identity: 37% PDB header:translation Chain: A: PDB Molecule:translation machinery-associated protein 16; PDBTitle: solution nmr structure of yeast protein yor252w [residues2 38-178]: northeast structural genomics consortium target3 yt654 Phyre2 PDB 1svm chain A Region: 67 - 92 Aligned: 26 Modelled: 26 Confidence: 17.5% Identity: 12% Fold: P-loop containing nucleoside triphosphate hydrolases Superfamily: P-loop containing nucleoside triphosphate hydrolases Family: Extended AAA-ATPase domain Phyre2 PDB 2k29 chain A Region: 50 - 89 Aligned: 40 Modelled: 40 Confidence: 15.4% Identity: 18% PDB header:transcription Chain: A: PDB Molecule:antitoxin relb; PDBTitle: structure of the dbd domain of e. coli antitoxin relb Phyre2 PDB 1l2f chain A Region: 58 - 92 Aligned: 35 Modelled: 35 Confidence: 14.7% Identity: 31% PDB header:transcription Chain: A: PDB Molecule:n utilization substance protein a; PDBTitle: crystal structure of nusa from thermotoga maritima: a2 structure-based role of the n-terminal domain Phyre2 PDB 2k9i chain B Region: 57 - 89 Aligned: 33 Modelled: 33 Confidence: 12.9% Identity: 21% PDB header:dna binding protein Chain: B: PDB Molecule:plasmid prn1, complete sequence; PDBTitle: nmr structure of plasmid copy control protein orf56 from2 sulfolobus islandicus Phyre2 PDB 1t6s chain A domain 2 Region: 56 - 81 Aligned: 26 Modelled: 26 Confidence: 12.5% Identity: 19% Fold: DNA/RNA-binding 3-helical bundle Superfamily: "Winged helix" DNA-binding domain Family: ScpB/YpuH-like Phyre2 PDB 1qx8 chain A Region: 61 - 71 Aligned: 11 Modelled: 11 Confidence: 11.8% Identity: 55% Fold: ROP-like Superfamily: ROP protein Family: ROP protein Phyre2 PDB 2keb chain A Region: 55 - 96 Aligned: 41 Modelled: 42 Confidence: 11.6% Identity: 17% PDB header:dna binding protein Chain: A: PDB Molecule:dna polymerase subunit alpha b; PDBTitle: nmr solution structure of the n-terminal domain of the dna polymerase2 alpha p68 subunit Phyre2 PDB 2rbf chain B Region: 52 - 93 Aligned: 42 Modelled: 42 Confidence: 10.8% Identity: 19% PDB header:oxidoreductase/dna Chain: B: PDB Molecule:bifunctional protein puta; PDBTitle: structure of the ribbon-helix-helix domain of escherichia coli puta2 (puta52) complexed with operator dna (o2) Phyre2 1 c1q5vB_ 2 c2bj3D_ 3 d2bj7a1 4 c2ca9B_ 5 d2hzaa1 6 d2hzab1 7 c2k5jB_ 8 d2cpga_ 9 d1y9ba1 10 c2kwpA_ 11 c3kk4B_ 12 c2kkmA_ 13 d1svma_ 14 c2k29A_ 15 c1l2fA_ 16 c2k9iB_ 17 d1t6sa2 18 d1qx8a_ 19 c2kebA_ 20 c2rbfB_ 21 22 23 24 25 26 27 28 29 30 31 32

Detailed template information

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

1 c1q5vB_ 95.3 35 PDB header:transcription Chain: B: PDB Molecule:nickel responsive regulator; PDBTitle: apo-nikr 2 c2bj3D_ 95.2 20 PDB header:transcription Chain: D: PDB Molecule:nickel responsive regulator; PDBTitle: nikr-apo 3 d2bj7a1 95.2 20 Fold:Ribbon-helix-helix Superfamily:Ribbon-helix-helix Family:CopG-like 4 c2ca9B_ 94.6 23 PDB header:transcriptional regulation Chain: B: PDB Molecule:putative nickel-responsive regulator; PDBTitle: apo-nikr from helicobacter pylori in closed trans-2 conformation 5 d2hzaa1 93.1 36 Fold:Ribbon-helix-helix Superfamily:Ribbon-helix-helix Family:CopG-like 6 d2hzab1 92.8 36 Fold:Ribbon-helix-helix Superfamily:Ribbon-helix-helix Family:CopG-like 7 c2k5jB_ 89.9 33 PDB header:structural genomics, unknown function Chain: B: PDB Molecule:uncharacterized protein yiif; PDBTitle: solution structure of protein yiif from shigella flexneri2 serotype 5b (strain 8401) . northeast structural genomics3 consortium target sft1 8 d2cpga_ 72.3 26 Fold:Ribbon-helix-helix Superfamily:Ribbon-helix-helix Family:CopG-like 9 d1y9ba1 29.3 14 Fold:Ribbon-helix-helix Superfamily:Ribbon-helix-helix Family:VCA0319-like 10 c2kwpA_ 25.7 14 PDB header:transcription Chain: A: PDB Molecule:transcription elongation protein nusa; PDBTitle: solution structure of the aminoterminal domain of e. coli nusa 11 c3kk4B_ 22.3 19 PDB header:structural genomics, unknown function Chain: B: PDB Molecule:uncharacterized protein bp1543; PDBTitle: uncharacterized protein bp1543 from bordetella pertussis tohama i 12 c2kkmA_ 18.9 37 PDB header:translation Chain: A: PDB Molecule:translation machinery-associated protein 16; PDBTitle: solution nmr structure of yeast protein yor252w [residues2 38-178]: northeast structural genomics consortium target3 yt654 13 d1svma_ 17.5 12 Fold:P-loop containing nucleoside triphosphate hydrolases Superfamily:P-loop containing nucleoside triphosphate hydrolases Family:Extended AAA-ATPase domain 14 c2k29A_ 15.4 18 PDB header:transcription Chain: A: PDB Molecule:antitoxin relb; PDBTitle: structure of the dbd domain of e. coli antitoxin relb 15 c1l2fA_ 14.7 31 PDB header:transcription Chain: A: PDB Molecule:n utilization substance protein a; PDBTitle: crystal structure of nusa from thermotoga maritima: a2 structure-based role of the n-terminal domain 16 c2k9iB_ 12.9 21 PDB header:dna binding protein Chain: B: PDB Molecule:plasmid prn1, complete sequence; PDBTitle: nmr structure of plasmid copy control protein orf56 from2 sulfolobus islandicus 17 d1t6sa2 12.5 19 Fold:DNA/RNA-binding 3-helical bundle Superfamily:"Winged helix" DNA-binding domain Family:ScpB/YpuH-like 18 d1qx8a_ 11.8 55 Fold:ROP-like Superfamily:ROP protein Family:ROP protein 19 c2kebA_ 11.6 17 PDB header:dna binding protein Chain: A: PDB Molecule:dna polymerase subunit alpha b; PDBTitle: nmr solution structure of the n-terminal domain of the dna polymerase2 alpha p68 subunit 20 c2rbfB_ 10.8 19 PDB header:oxidoreductase/dna Chain: B: PDB Molecule:bifunctional protein puta; PDBTitle: structure of the ribbon-helix-helix domain of escherichia coli puta2 (puta52) complexed with operator dna (o2) 21 c2jvdA_ not modelled 10.6 30 PDB header:structural genomics, unknown function Chain: A: PDB Molecule:upf0291 protein ynzc; PDBTitle: solution nmr structure of the folded n-terminal fragment of2 upf0291 protein ynzc from bacillus subtilis. northeast3 structural genomics target sr384-1-46 22 c2x7lP_ not modelled 9.1 33 PDB header:immune system Chain: P: PDB Molecule:hiv rev; PDBTitle: implications of the hiv-1 rev dimer structure at 3.2a2 resolution for multimeric binding to the rev response3 element 23 d1myla_ not modelled 8.7 20 Fold:Ribbon-helix-helix Superfamily:Ribbon-helix-helix Family:Arc/Mnt-like phage repressors 24 d1mnta_ not modelled 8.3 16 Fold:Ribbon-helix-helix Superfamily:Ribbon-helix-helix Family:Arc/Mnt-like phage repressors 25 c3h87D_ not modelled 8.1 27 PDB header:toxin/antitoxin Chain: D: PDB Molecule:putative uncharacterized protein; PDBTitle: rv0301 rv0300 toxin antitoxin complex from mycobacterium tuberculosis 26 c2hepA_ not modelled 7.4 29 PDB header:structural genomics, unknown function Chain: A: PDB Molecule:upf0291 protein ynzc; PDBTitle: solution nmr structure of the upf0291 protein ynzc from2 bacillus subtilis. northeast structural genomics target3 sr384. 27 d2hepa1 not modelled 7.4 29 Fold:Long alpha-hairpin Superfamily:YnzC-like Family:YznC-like 28 c3lphD_ not modelled 6.8 33 PDB header:viral protein Chain: D: PDB Molecule:protein rev; PDBTitle: crystal structure of the hiv-1 rev dimer 29 d1b28a_ not modelled 6.5 19 Fold:Ribbon-helix-helix Superfamily:Ribbon-helix-helix Family:Arc/Mnt-like phage repressors 30 c2a8vA_ not modelled 6.1 24 PDB header:protein/rna Chain: A: PDB Molecule:rna binding domain of rho transcription PDBTitle: rho transcription termination factor/rna complex 31 d2cz4a1 not modelled 5.4 19 Fold:Ferredoxin-like Superfamily:GlnB-like Family:Prokaryotic signal transducing protein 32 c2r0vB_ not modelled 5.1 31 PDB header:transcription Chain: B: PDB Molecule:chromatin structure-remodeling complex protein PDBTitle: structure of the rsc4 tandem bromodomain acetylated at k25

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