Secondary structure and disorder prediction

1

.

.

.

.

.

.

.

.

10

.

.

.

.

.

.

.

.

.

20

.

.

.

.

.

.

.

.

.

30

.

.

.

.

.

.

.

.

.

40

.

.

.

.

.

.

.

.

.

50

.

.

.

.

.

.

.

.

.

60

Sequence

M

S

I

D

R

T

S

P

L

K

P

V

S

T

V

Q

P

R

E

T

T

D

A

P

V

T

N

S

R

A

A

K

T

T

A

S

T

S

T

S

V

T

L

S

D

A

Q

A

K

L

M

Q

P

G

S

S

D

I

N

L

Secondary structure

SS confidence

Disorder

?

?

?

?

?

?

?

?

?

?

?

?

?

?

?

?

?

?

?

?

?

?

?

?

?

?

?

?

?

?

?

?

?

?

?

?

?

?

?

?

?

?

?

?

?

?

?

?

?

?

?

Disorder confidence

.

.

.

.

.

.

.

.

.

70

.

.

.

.

.

.

.

.

.

80

.

.

.

.

.

.

.

.

.

90

.

.

.

.

.

.

.

Sequence

E

R

V

E

A

L

K

L

A

I

R

N

G

E

L

K

M

D

T

G

K

I

A

D

A

L

I

N

E

A

Q

Q

D

L

Q

S

N

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 1rp3 chain B Region: 39 - 88 Aligned: 49 Modelled: 50 Confidence: 98.0% Identity: 31% Fold: Non-globular all-alpha subunits of globular proteins Superfamily: Anti-sigma factor FlgM Family: Anti-sigma factor FlgM Phyre2 PDB 3q71 chain A Region: 70 - 97 Aligned: 28 Modelled: 28 Confidence: 40.3% Identity: 25% PDB header:transferase Chain: A: PDB Molecule:poly [adp-ribose] polymerase 14; PDBTitle: human parp14 (artd8) - macro domain 2 in complex with adenosine-5-2 diphosphoribose Phyre2 PDB 2x47 chain A Region: 70 - 97 Aligned: 28 Modelled: 28 Confidence: 40.3% Identity: 14% PDB header:signaling protein Chain: A: PDB Molecule:macro domain-containing protein 1; PDBTitle: crystal structure of human macrod1 Phyre2 PDB 1zr5 chain A domain 1 Region: 70 - 97 Aligned: 28 Modelled: 28 Confidence: 29.3% Identity: 14% Fold: Macro domain-like Superfamily: Macro domain-like Family: Macro domain Phyre2 PDB 1zr5 chain B Region: 70 - 97 Aligned: 28 Modelled: 28 Confidence: 26.3% Identity: 14% PDB header:gene regulation Chain: B: PDB Molecule:h2afy protein; PDBTitle: crystal structure of the macro-domain of human core histone variant2 macroh2a1.2 Phyre2 PDB 2fqx chain A Region: 56 - 78 Aligned: 23 Modelled: 23 Confidence: 25.8% Identity: 17% PDB header:transport protein Chain: A: PDB Molecule:membrane lipoprotein tmpc; PDBTitle: pnra from treponema pallidum complexed with guanosine Phyre2 PDB 1yd9 chain A domain 1 Region: 70 - 97 Aligned: 28 Modelled: 28 Confidence: 25.8% Identity: 14% Fold: Macro domain-like Superfamily: Macro domain-like Family: Macro domain Phyre2 PDB 1spv chain A Region: 70 - 97 Aligned: 28 Modelled: 28 Confidence: 25.6% Identity: 11% Fold: Macro domain-like Superfamily: Macro domain-like Family: Macro domain Phyre2 PDB 3kxe chain D Region: 66 - 86 Aligned: 21 Modelled: 21 Confidence: 24.6% Identity: 14% PDB header:protein binding Chain: D: PDB Molecule:antitoxin protein pard-1; PDBTitle: a conserved mode of protein recognition and binding in a2 pard-pare toxin-antitoxin complex Phyre2 PDB 3s99 chain A Region: 56 - 77 Aligned: 22 Modelled: 22 Confidence: 24.0% Identity: 27% PDB header:lipid binding protein Chain: A: PDB Molecule:basic membrane lipoprotein; PDBTitle: crystal structure of a basic membrane lipoprotein from brucella2 melitensis, iodide soak Phyre2 PDB 3kh6 chain A Region: 70 - 97 Aligned: 28 Modelled: 28 Confidence: 22.5% Identity: 18% PDB header:transferase Chain: A: PDB Molecule:poly [adp-ribose] polymerase 15; PDBTitle: human poly(adp-ribose) polymerase 15, macro domain 2 in2 complex with adenosine-5-diphosphoribose Phyre2 PDB 3q6z chain A Region: 70 - 97 Aligned: 28 Modelled: 28 Confidence: 19.3% Identity: 14% PDB header:transferase Chain: A: PDB Molecule:poly [adp-ribose] polymerase 14; PDBTitle: human parp14 (artd8)-macro domain 1 in complex with adenosine-5-2 diphosphoribose Phyre2 PDB 1vhu chain A Region: 70 - 97 Aligned: 28 Modelled: 28 Confidence: 18.3% Identity: 14% Fold: Macro domain-like Superfamily: Macro domain-like Family: Macro domain Phyre2 PDB 1y0n chain A Region: 60 - 77 Aligned: 18 Modelled: 18 Confidence: 16.0% Identity: 39% Fold: YehU-like Superfamily: YehU-like Family: YehU-like Phyre2 PDB 2xd7 chain B Region: 70 - 97 Aligned: 28 Modelled: 28 Confidence: 15.3% Identity: 7% PDB header:dna-binding protein Chain: B: PDB Molecule:core histone macro-h2a.2; PDBTitle: crystal structure of the macro domain of human core histone2 h2a Phyre2 PDB 2g3b chain A domain 2 Region: 48 - 88 Aligned: 41 Modelled: 38 Confidence: 15.1% Identity: 17% Fold: Tetracyclin repressor-like, C-terminal domain Superfamily: Tetracyclin repressor-like, C-terminal domain Family: Tetracyclin repressor-like, C-terminal domain Phyre2 PDB 1sjp chain A domain 2 Region: 60 - 86 Aligned: 27 Modelled: 27 Confidence: 14.7% Identity: 26% Fold: The "swivelling" beta/beta/alpha domain Superfamily: GroEL apical domain-like Family: GroEL-like chaperone, apical domain Phyre2 PDB 3tqn chain C Region: 63 - 77 Aligned: 15 Modelled: 15 Confidence: 14.2% Identity: 20% PDB header:transcription Chain: C: PDB Molecule:transcriptional regulator, gntr family; PDBTitle: structure of the transcriptional regulator of the gntr family, from2 coxiella burnetii. Phyre2 PDB 1kid chain A Region: 60 - 86 Aligned: 27 Modelled: 27 Confidence: 13.8% Identity: 19% Fold: The "swivelling" beta/beta/alpha domain Superfamily: GroEL apical domain-like Family: GroEL-like chaperone, apical domain Phyre2 PDB 1iok chain A domain 2 Region: 60 - 82 Aligned: 23 Modelled: 23 Confidence: 12.7% Identity: 22% Fold: The "swivelling" beta/beta/alpha domain Superfamily: GroEL apical domain-like Family: GroEL-like chaperone, apical domain Phyre2 1 d1rp3b_ 2 c3q71A_ 3 c2x47A_ 4 d1zr5a1 5 c1zr5B_ 6 c2fqxA_ 7 d1yd9a1 8 d1spva_ 9 c3kxeD_ 10 c3s99A_ 11 c3kh6A_ 12 c3q6zA_ 13 d1vhua_ 14 d1y0na_ 15 c2xd7B_ 16 d2g3ba2 17 d1sjpa2 18 c3tqnC_ 19 d1kida_ 20 d1ioka2 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 46 47 48 49 50

Detailed template information

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

1 d1rp3b_ 98.0 31 Fold:Non-globular all-alpha subunits of globular proteins Superfamily:Anti-sigma factor FlgM Family:Anti-sigma factor FlgM 2 c3q71A_ 40.3 25 PDB header:transferase Chain: A: PDB Molecule:poly [adp-ribose] polymerase 14; PDBTitle: human parp14 (artd8) - macro domain 2 in complex with adenosine-5-2 diphosphoribose 3 c2x47A_ 40.3 14 PDB header:signaling protein Chain: A: PDB Molecule:macro domain-containing protein 1; PDBTitle: crystal structure of human macrod1 4 d1zr5a1 29.3 14 Fold:Macro domain-like Superfamily:Macro domain-like Family:Macro domain 5 c1zr5B_ 26.3 14 PDB header:gene regulation Chain: B: PDB Molecule:h2afy protein; PDBTitle: crystal structure of the macro-domain of human core histone variant2 macroh2a1.2 6 c2fqxA_ 25.8 17 PDB header:transport protein Chain: A: PDB Molecule:membrane lipoprotein tmpc; PDBTitle: pnra from treponema pallidum complexed with guanosine 7 d1yd9a1 25.8 14 Fold:Macro domain-like Superfamily:Macro domain-like Family:Macro domain 8 d1spva_ 25.6 11 Fold:Macro domain-like Superfamily:Macro domain-like Family:Macro domain 9 c3kxeD_ 24.6 14 PDB header:protein binding Chain: D: PDB Molecule:antitoxin protein pard-1; PDBTitle: a conserved mode of protein recognition and binding in a2 pard-pare toxin-antitoxin complex 10 c3s99A_ 24.0 27 PDB header:lipid binding protein Chain: A: PDB Molecule:basic membrane lipoprotein; PDBTitle: crystal structure of a basic membrane lipoprotein from brucella2 melitensis, iodide soak 11 c3kh6A_ 22.5 18 PDB header:transferase Chain: A: PDB Molecule:poly [adp-ribose] polymerase 15; PDBTitle: human poly(adp-ribose) polymerase 15, macro domain 2 in2 complex with adenosine-5-diphosphoribose 12 c3q6zA_ 19.3 14 PDB header:transferase Chain: A: PDB Molecule:poly [adp-ribose] polymerase 14; PDBTitle: human parp14 (artd8)-macro domain 1 in complex with adenosine-5-2 diphosphoribose 13 d1vhua_ 18.3 14 Fold:Macro domain-like Superfamily:Macro domain-like Family:Macro domain 14 d1y0na_ 16.0 39 Fold:YehU-like Superfamily:YehU-like Family:YehU-like 15 c2xd7B_ 15.3 7 PDB header:dna-binding protein Chain: B: PDB Molecule:core histone macro-h2a.2; PDBTitle: crystal structure of the macro domain of human core histone2 h2a 16 d2g3ba2 15.1 17 Fold:Tetracyclin repressor-like, C-terminal domain Superfamily:Tetracyclin repressor-like, C-terminal domain Family:Tetracyclin repressor-like, C-terminal domain 17 d1sjpa2 14.7 26 Fold:The "swivelling" beta/beta/alpha domain Superfamily:GroEL apical domain-like Family:GroEL-like chaperone, apical domain 18 c3tqnC_ 14.2 20 PDB header:transcription Chain: C: PDB Molecule:transcriptional regulator, gntr family; PDBTitle: structure of the transcriptional regulator of the gntr family, from2 coxiella burnetii. 19 d1kida_ 13.8 19 Fold:The "swivelling" beta/beta/alpha domain Superfamily:GroEL apical domain-like Family:GroEL-like chaperone, apical domain 20 d1ioka2 12.7 22 Fold:The "swivelling" beta/beta/alpha domain Superfamily:GroEL apical domain-like Family:GroEL-like chaperone, apical domain 21 c1d8lA_ not modelled 12.1 21 PDB header:gene regulation Chain: A: PDB Molecule:protein (holliday junction dna helicase ruva); PDBTitle: e. coli holliday junction binding protein ruva nh2 region2 lacking domain iii 22 d1we3a2 not modelled 11.8 15 Fold:The "swivelling" beta/beta/alpha domain Superfamily:GroEL apical domain-like Family:GroEL-like chaperone, apical domain 23 d1chda_ not modelled 9.8 21 Fold:Methylesterase CheB, C-terminal domain Superfamily:Methylesterase CheB, C-terminal domain Family:Methylesterase CheB, C-terminal domain 24 d1oela2 not modelled 9.7 22 Fold:The "swivelling" beta/beta/alpha domain Superfamily:GroEL apical domain-like Family:GroEL-like chaperone, apical domain 25 c3eetA_ not modelled 9.1 25 PDB header:transcription regulator Chain: A: PDB Molecule:putative gntr-family transcriptional regulator; PDBTitle: crystal structure of putative gntr-family transcriptional2 regulator 26 c2lciA_ not modelled 9.0 13 PDB header:de novo protein Chain: A: PDB Molecule:protein or36; PDBTitle: solution nmr structure of de novo designed protein, p-loop ntpase2 fold, northeast structural genomics consortium target or36 (casd3 target) 27 c2wv0H_ not modelled 9.0 36 PDB header:transcription Chain: H: PDB Molecule:hth-type transcriptional repressor yvoa; PDBTitle: crystal structure of the gntr-hutc family member yvoa from2 bacillus subtilis 28 c2dx6B_ not modelled 8.9 11 PDB header:structural genomics, unknown function Chain: B: PDB Molecule:hypothetical protein ttha0132; PDBTitle: crystal structure of conserved hypothetical protein, ttha0132 from2 thermus thermophilus hb8 29 d1n7ka_ not modelled 8.3 8 Fold:TIM beta/alpha-barrel Superfamily:Aldolase Family:Class I aldolase 30 d1v4ra1 not modelled 8.1 27 Fold:DNA/RNA-binding 3-helical bundle Superfamily:"Winged helix" DNA-binding domain Family:GntR-like transcriptional regulators 31 d1iq8a1 not modelled 8.1 46 Fold:TIM beta/alpha-barrel Superfamily:tRNA-guanine transglycosylase Family:tRNA-guanine transglycosylase 32 c3ic7A_ not modelled 8.0 13 PDB header:structural genomics, unknown function Chain: A: PDB Molecule:putative transcriptional regulator; PDBTitle: crystal structure of putative transcriptional regulator of gntr family2 from bacteroides thetaiotaomicron 33 d2pgga1 not modelled 7.7 24 Fold:DNA/RNA polymerases Superfamily:DNA/RNA polymerases Family:RNA-dependent RNA-polymerase 34 d1bvsa2 not modelled 7.3 20 Fold:SAM domain-like Superfamily:RuvA domain 2-like Family:DNA helicase RuvA subunit, middle domain 35 d1t95a1 not modelled 6.6 15 Fold:RuvA C-terminal domain-like Superfamily:Hypothetical protein AF0491, middle domain Family:Hypothetical protein AF0491, middle domain 36 c3gqeA_ not modelled 6.6 11 PDB header:viral protein Chain: A: PDB Molecule:non-structural protein 3; PDBTitle: crystal structure of macro domain of venezuelan equine encephalitis2 virus 37 d1rkta2 not modelled 6.4 14 Fold:Tetracyclin repressor-like, C-terminal domain Superfamily:Tetracyclin repressor-like, C-terminal domain Family:Tetracyclin repressor-like, C-terminal domain 38 c3m6cA_ not modelled 6.2 21 PDB header:chaperone Chain: A: PDB Molecule:60 kda chaperonin 1; PDBTitle: crystal structure of mycobacterium tuberculosis groel1 apical domain 39 c1iq8B_ not modelled 6.2 46 PDB header:transferase Chain: B: PDB Molecule:archaeosine trna-guanine transglycosylase; PDBTitle: crystal structure of archaeosine trna-guanine2 transglycosylase from pyrococcus horikoshii 40 c1jrjA_ not modelled 5.9 13 PDB header:hormone/growth factor Chain: A: PDB Molecule:exendin-4; PDBTitle: solution structure of exendin-4 in 30-vol% trifluoroethanol 41 c3dtkA_ not modelled 5.9 23 PDB header:gene regulation Chain: A: PDB Molecule:irre protein; PDBTitle: crystal structure of the irre protein, a central regulator2 of dna damage repair in deinococcaceae 42 c3bwgA_ not modelled 5.7 13 PDB header:transcription regulator Chain: A: PDB Molecule:uncharacterized hth-type transcriptional regulator yydk; PDBTitle: the crystal structure of possible transcriptional regulator yydk from2 bacillus subtilis subsp. subtilis str. 168 43 c3l9vE_ not modelled 5.6 9 PDB header:oxidoreductase Chain: E: PDB Molecule:putative thiol-disulfide isomerase or thioredoxin; PDBTitle: crystal structure of salmonella enterica serovar typhimurium srga 44 d1r5ya_ not modelled 5.6 15 Fold:TIM beta/alpha-barrel Superfamily:tRNA-guanine transglycosylase Family:tRNA-guanine transglycosylase 45 d1w7ca3 not modelled 5.5 21 Fold:Cystatin-like Superfamily:Amine oxidase N-terminal region Family:Amine oxidase N-terminal region 46 c3ng3A_ not modelled 5.5 16 PDB header:lyase Chain: A: PDB Molecule:deoxyribose-phosphate aldolase; PDBTitle: crystal structure of deoxyribose phosphate aldolase from mycobacterium2 avium 104 in a schiff base with an unknown aldehyde 47 d1ub3a_ not modelled 5.5 11 Fold:TIM beta/alpha-barrel Superfamily:Aldolase Family:Class I aldolase 48 d1mzha_ not modelled 5.4 14 Fold:TIM beta/alpha-barrel Superfamily:Aldolase Family:Class I aldolase 49 d1xw3a1 not modelled 5.2 19 Fold:ParB/Sulfiredoxin Superfamily:ParB/Sulfiredoxin Family:Sulfiredoxin-like 50 d1wuea1 not modelled 5.1 21 Fold:TIM beta/alpha-barrel Superfamily:Enolase C-terminal domain-like Family:D-glucarate dehydratase-like

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