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

D

E

F

K

P

E

D

E

L

K

P

D

P

S

D

R

R

T

G

R

S

R

Q

S

S

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R

S

E

R

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E

R

G

E

P

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I

N

F

D

D

I

E

L

D

D

T

D

D

R

R

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T

R

A

Q

K

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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100

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110

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120

Sequence

R

N

E

E

P

E

I

E

E

E

I

D

E

S

E

D

E

T

V

D

E

E

R

V

E

R

R

P

R

K

R

K

K

A

A

S

K

P

A

S

R

Q

Y

M

M

M

G

V

G

I

L

V

L

L

L

L

I

I

G

I

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

G

S

A

L

K

A

P

S

T

T

S

S

D

Q

T

A

S

G

E

K

S

I

D

L

A

G

N

A

T

D

Q

A

N

G

V

Q

P

A

P

G

T

T

S

A

E

N

T

Q

Q

D

V

S

L

P

P

I

S

S

T

P

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

T

Q

G

Q

T

P

V

A

T

D

G

Q

Q

R

V

E

V

Q

G

D

L

N

N

A

L

T

Q

P

Q

N

Q

Q

Q

L

N

N

V

A

V

N

S

T

L

P

T

E

P

A

T

V

A

P

V

R

N

G

N

A

S

R

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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290

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300

Sequence

D

T

A

K

T

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T

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R

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S

T

T

R

P

A

R

Q

Q

A

V

I

E

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K

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A

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R

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A

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A

A

Secondary structure

SS confidence

Disorder

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Disorder confidence

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310

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320

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330

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340

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350

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360

Sequence

T

S

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T

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A

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A

A

G

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K

T

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G

N

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G

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S

H

Y

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D

N

Secondary structure

SS confidence

Disorder

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Disorder confidence

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370

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380

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390

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400

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410

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420

Sequence

L

N

G

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A

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K

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N

L

K

N

Y

V

V

Y

E

T

T

R

N

G

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W

Y

V

L

V

S

G

V

Y

A

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K

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E

A

K

K

A

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A

D

V

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A

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N

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W

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L

Secondary structure

SS confidence

Disorder

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Disorder confidence

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Sequence

R

Q

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Q

A

D

L

K

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 1uta chain A Region: 344 - 406 Aligned: 61 Modelled: 63 Confidence: 98.0% Identity: 18% Fold: Ferredoxin-like Superfamily: Sporulation related repeat Family: Sporulation related repeat Phyre2 PDB 1x60 chain A Region: 341 - 406 Aligned: 64 Modelled: 64 Confidence: 97.9% Identity: 20% PDB header:hydrolase Chain: A: PDB Molecule:sporulation-specific n-acetylmuramoyl-l-alanine PDBTitle: solution structure of the peptidoglycan binding domain of2 b. subtilis cell wall lytic enzyme cwlc Phyre2 PDB 3g5o chain A Region: 359 - 427 Aligned: 65 Modelled: 69 Confidence: 32.8% Identity: 23% PDB header:toxin/antitoxin Chain: A: PDB Molecule:uncharacterized protein rv2865; PDBTitle: the crystal structure of the toxin-antitoxin complex relbe2 (rv2865-2 2866) from mycobacterium tuberculosis Phyre2 PDB 3kgk chain A Region: 347 - 398 Aligned: 47 Modelled: 52 Confidence: 25.3% Identity: 13% PDB header:chaperone Chain: A: PDB Molecule:arsenical resistance operon trans-acting repressor arsd; PDBTitle: crystal structure of arsd Phyre2 PDB 3ktb chain D Region: 347 - 398 Aligned: 47 Modelled: 52 Confidence: 24.3% Identity: 13% PDB header:transcription regulator Chain: D: PDB Molecule:arsenical resistance operon trans-acting repressor; PDBTitle: crystal structure of arsenical resistance operon trans-acting2 repressor from bacteroides vulgatus atcc 8482 Phyre2 PDB 1xrs chain B domain 2 Region: 358 - 392 Aligned: 35 Modelled: 35 Confidence: 20.0% Identity: 17% 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 2k49 chain A domain 1 Region: 377 - 406 Aligned: 30 Modelled: 30 Confidence: 19.1% Identity: 20% Fold: YegP-like Superfamily: YegP-like Family: YegP-like Phyre2 PDB 1qqk chain A Region: 364 - 392 Aligned: 29 Modelled: 29 Confidence: 15.8% Identity: 14% Fold: beta-Trefoil Superfamily: Cytokine Family: Fibroblast growth factors (FGF) Phyre2 PDB 2odk chain D Region: 376 - 399 Aligned: 24 Modelled: 24 Confidence: 13.6% Identity: 29% PDB header:structural genomics, unknown function Chain: D: PDB Molecule:hypothetical protein; PDBTitle: putative prevent-host-death protein from nitrosomonas europaea Phyre2 PDB 1ywl chain A Region: 359 - 401 Aligned: 43 Modelled: 43 Confidence: 12.5% Identity: 14% PDB header:structural genomics, unknown function Chain: A: PDB Molecule:hypothetical upf0213 protein ef2693; PDBTitle: solution nmr structure of the protein ef2693 from e.2 faecalis: northeast structural genomics consortium target3 efr36 Phyre2 PDB 2odk chain A domain 1 Region: 376 - 399 Aligned: 24 Modelled: 24 Confidence: 12.5% Identity: 29% Fold: YefM-like Superfamily: YefM-like Family: YefM-like Phyre2 PDB 2jvr chain A Region: 344 - 406 Aligned: 60 Modelled: 63 Confidence: 12.5% Identity: 20% PDB header:rna binding protein Chain: A: PDB Molecule:nucleolar protein 3; PDBTitle: segmental isotope labeling of npl3p Phyre2 PDB 2a6q chain A domain 1 Region: 358 - 405 Aligned: 48 Modelled: 48 Confidence: 12.4% Identity: 21% Fold: YefM-like Superfamily: YefM-like Family: YefM-like Phyre2 PDB 2cqi chain A domain 1 Region: 340 - 406 Aligned: 65 Modelled: 67 Confidence: 11.7% Identity: 12% Fold: Ferredoxin-like Superfamily: RNA-binding domain, RBD Family: Canonical RBD Phyre2 PDB 1tua chain A domain 2 Region: 386 - 406 Aligned: 21 Modelled: 21 Confidence: 11.6% Identity: 33% Fold: Eukaryotic type KH-domain (KH-domain type I) Superfamily: Eukaryotic type KH-domain (KH-domain type I) Family: Eukaryotic type KH-domain (KH-domain type I) Phyre2 PDB 2osr chain A Region: 342 - 406 Aligned: 62 Modelled: 65 Confidence: 11.2% Identity: 19% PDB header:rna binding protein Chain: A: PDB Molecule:nucleolar protein 3; PDBTitle: nmr structure of rrm-2 of yeast npl3 protein Phyre2 PDB 2k7i chain A domain 1 Region: 364 - 406 Aligned: 41 Modelled: 43 Confidence: 10.5% Identity: 17% Fold: YegP-like Superfamily: YegP-like Family: YegP-like Phyre2 PDB 2k7i chain B Region: 364 - 406 Aligned: 41 Modelled: 43 Confidence: 10.5% Identity: 17% PDB header:structural genomics, unknown function Chain: B: PDB Molecule:upf0339 protein atu0232; PDBTitle: solution nmr structure of protein atu0232 from agrobacterium2 tumefaciens. northeast structural genomics consortium (nesg) target3 att3. ontario center for structural proteomics target atc0223. Phyre2 PDB 1x5s chain A domain 1 Region: 344 - 406 Aligned: 63 Modelled: 63 Confidence: 10.1% Identity: 21% Fold: Ferredoxin-like Superfamily: RNA-binding domain, RBD Family: Canonical RBD Phyre2 PDB 2dnz chain A Region: 344 - 406 Aligned: 63 Modelled: 63 Confidence: 9.7% Identity: 17% PDB header:rna binding protein Chain: A: PDB Molecule:probable rna-binding protein 23; PDBTitle: solution structure of the second rna binding domain of rna2 binding motif protein 23 Phyre2 1 d1utaa_ 2 c1x60A_ 3 c3g5oA_ 4 c3kgkA_ 5 c3ktbD_ 6 d1xrsb2 7 d2k49a1 8 d1qqka_ 9 c2odkD_ 10 c1ywlA_ 11 d2odka1 12 c2jvrA_ 13 d2a6qa1 14 d2cqia1 15 d1tuaa2 16 c2osrA_ 17 d2k7ia1 18 c2k7iB_ 19 d1x5sa1 20 c2dnzA_ 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43

Detailed template information

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

1 d1utaa_ 98.0 18 Fold:Ferredoxin-like Superfamily:Sporulation related repeat Family:Sporulation related repeat 2 c1x60A_ 97.9 20 PDB header:hydrolase Chain: A: PDB Molecule:sporulation-specific n-acetylmuramoyl-l-alanine PDBTitle: solution structure of the peptidoglycan binding domain of2 b. subtilis cell wall lytic enzyme cwlc 3 c3g5oA_ 32.8 23 PDB header:toxin/antitoxin Chain: A: PDB Molecule:uncharacterized protein rv2865; PDBTitle: the crystal structure of the toxin-antitoxin complex relbe2 (rv2865-2 2866) from mycobacterium tuberculosis 4 c3kgkA_ 25.3 13 PDB header:chaperone Chain: A: PDB Molecule:arsenical resistance operon trans-acting repressor arsd; PDBTitle: crystal structure of arsd 5 c3ktbD_ 24.3 13 PDB header:transcription regulator Chain: D: PDB Molecule:arsenical resistance operon trans-acting repressor; PDBTitle: crystal structure of arsenical resistance operon trans-acting2 repressor from bacteroides vulgatus atcc 8482 6 d1xrsb2 20.0 17 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 7 d2k49a1 19.1 20 Fold:YegP-like Superfamily:YegP-like Family:YegP-like 8 d1qqka_ 15.8 14 Fold:beta-Trefoil Superfamily:Cytokine Family:Fibroblast growth factors (FGF) 9 c2odkD_ 13.6 29 PDB header:structural genomics, unknown function Chain: D: PDB Molecule:hypothetical protein; PDBTitle: putative prevent-host-death protein from nitrosomonas europaea 10 c1ywlA_ 12.5 14 PDB header:structural genomics, unknown function Chain: A: PDB Molecule:hypothetical upf0213 protein ef2693; PDBTitle: solution nmr structure of the protein ef2693 from e.2 faecalis: northeast structural genomics consortium target3 efr36 11 d2odka1 12.5 29 Fold:YefM-like Superfamily:YefM-like Family:YefM-like 12 c2jvrA_ 12.5 20 PDB header:rna binding protein Chain: A: PDB Molecule:nucleolar protein 3; PDBTitle: segmental isotope labeling of npl3p 13 d2a6qa1 12.4 21 Fold:YefM-like Superfamily:YefM-like Family:YefM-like 14 d2cqia1 11.7 12 Fold:Ferredoxin-like Superfamily:RNA-binding domain, RBD Family:Canonical RBD 15 d1tuaa2 11.6 33 Fold:Eukaryotic type KH-domain (KH-domain type I) Superfamily:Eukaryotic type KH-domain (KH-domain type I) Family:Eukaryotic type KH-domain (KH-domain type I) 16 c2osrA_ 11.2 19 PDB header:rna binding protein Chain: A: PDB Molecule:nucleolar protein 3; PDBTitle: nmr structure of rrm-2 of yeast npl3 protein 17 d2k7ia1 10.5 17 Fold:YegP-like Superfamily:YegP-like Family:YegP-like 18 c2k7iB_ 10.5 17 PDB header:structural genomics, unknown function Chain: B: PDB Molecule:upf0339 protein atu0232; PDBTitle: solution nmr structure of protein atu0232 from agrobacterium2 tumefaciens. northeast structural genomics consortium (nesg) target3 att3. ontario center for structural proteomics target atc0223. 19 d1x5sa1 10.1 21 Fold:Ferredoxin-like Superfamily:RNA-binding domain, RBD Family:Canonical RBD 20 c2dnzA_ 9.7 17 PDB header:rna binding protein Chain: A: PDB Molecule:probable rna-binding protein 23; PDBTitle: solution structure of the second rna binding domain of rna2 binding motif protein 23 21 d1ihka_ not modelled 8.6 17 Fold:beta-Trefoil Superfamily:Cytokine Family:Fibroblast growth factors (FGF) 22 c3jtzA_ not modelled 8.3 19 PDB header:dna binding protein Chain: A: PDB Molecule:integrase; PDBTitle: structure of the arm-type binding domain of hpi integrase 23 c3ju0A_ not modelled 8.3 20 PDB header:dna binding protein Chain: A: PDB Molecule:phage integrase; PDBTitle: structure of the arm-type binding domain of hai7 integrase 24 c2dnmA_ not modelled 8.0 15 PDB header:rna binding protein Chain: A: PDB Molecule:srp46 splicing factor; PDBTitle: solution structure of rna binding domain in srp46 splicing2 factor 25 c2wbrA_ not modelled 7.9 24 PDB header:dna-binding protein Chain: A: PDB Molecule:gw182; PDBTitle: the rrm domain in gw182 proteins contributes to mirna-2 mediated gene silencing 26 c2dh9A_ not modelled 7.6 13 PDB header:rna binding protein Chain: A: PDB Molecule:heterogeneous nuclear ribonucleoprotein m; PDBTitle: solution structure of the c-terminal rna binding domain in2 heterogeneous nuclear ribonucleoprotein m 27 c1vjqB_ not modelled 7.3 27 PDB header:structural genomics, de novo protein Chain: B: PDB Molecule:designed protein; PDBTitle: designed protein based on backbone conformation of2 procarboxypeptidase-a (1aye) with sidechains chosen for maximal3 predicted stability. 28 c2oq8A_ not modelled 6.8 33 PDB header:dna binding protein Chain: A: PDB Molecule:hypothetical protein; PDBTitle: structure of orf 157 from acidianus filamentous virus 1 29 d3e2ba1 not modelled 6.5 18 Fold:DLC Superfamily:DLC Family:DLC 30 c3femB_ not modelled 6.5 15 PDB header:biosynthetic protein, transferase Chain: B: PDB Molecule:pyridoxine biosynthesis protein snz1; PDBTitle: structure of the synthase subunit pdx1.1 (snz1) of plp synthase from2 saccharomyces cerevisiae 31 c2k49A_ not modelled 6.4 12 PDB header:structural genomics, unknown function Chain: A: PDB Molecule:upf0339 protein so_3888; PDBTitle: solution nmr structure of upf0339 protein so3888 from shewanella2 oneidensis. northeast structural genomics consortium target sor190 32 d1vkwa_ not modelled 6.4 31 Fold:FMN-dependent nitroreductase-like Superfamily:FMN-dependent nitroreductase-like Family:Putative nitroreductase TM1586 33 c3qbtH_ not modelled 6.3 16 PDB header:protein transport/hydrolase Chain: H: PDB Molecule:inositol polyphosphate 5-phosphatase ocrl-1; PDBTitle: crystal structure of ocrl1 540-678 in complex with rab8a:gppnhp 34 d1kr4a_ not modelled 6.0 25 Fold:Ferredoxin-like Superfamily:GlnB-like Family:Divalent ion tolerance proteins CutA (CutA1) 35 c2rneA_ not modelled 5.8 10 PDB header:rna binding protein Chain: A: PDB Molecule:tia1 protein; PDBTitle: solution structure of the second rna recognition motif2 (rrm) of tia-1 36 d2cq3a1 not modelled 5.7 14 Fold:Ferredoxin-like Superfamily:RNA-binding domain, RBD Family:Canonical RBD 37 d1nuna_ not modelled 5.6 24 Fold:beta-Trefoil Superfamily:Cytokine Family:Fibroblast growth factors (FGF) 38 c3i6pF_ not modelled 5.6 20 PDB header:structural protein Chain: F: PDB Molecule:ethanolamine utilization protein eutm; PDBTitle: ethanolamine utilization microcompartment shell subunit, eutm 39 c3o4aC_ not modelled 5.6 5 PDB header:de novo protein Chain: C: PDB Molecule:de novo designed beta-trefoil architecture with symmetric PDBTitle: crystal structure of symfoil-2: de novo designed beta-trefoil2 architecture with symmetric primary structure 40 c3ngkA_ not modelled 5.5 25 PDB header:unknown function Chain: A: PDB Molecule:propanediol utilization protein pdua; PDBTitle: pdua from salmonella enterica typhimurium 41 d1r89a3 not modelled 5.3 12 Fold:Ferredoxin-like Superfamily:PAP/Archaeal CCA-adding enzyme, C-terminal domain Family:Archaeal tRNA CCA-adding enzyme 42 d2ewha1 not modelled 5.2 20 Fold:Ferredoxin-like Superfamily:CcmK-like Family:CcmK-like 43 d1rk8a_ not modelled 5.2 14 Fold:Ferredoxin-like Superfamily:RNA-binding domain, RBD Family:Canonical RBD

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

Transmembrane helix prediction

Transmembrane helices have been predicted in your sequence to adopt the topology shown below

---

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