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

P

S

S

S

N

S

R

S

K

G

H

A

K

A

R

R

K

T

R

E

E

L

D

Q

E

A

R

D

R

K

R

Q

K

K

R

R

G

H

A

P

G

S

R

A

A

G

G

N

T

T

S

G

S

K

G

Q

N

A

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

D

P

R

I

G

S

K

T

P

I

P

L

G

V

T

E

K

V

T

K

Q

H

K

P

K

S

E

K

P

M

L

S

P

Q

A

E

L

E

L

L

E

T

D

E

R

L

D

A

L

L

E

R

L

E

A

G

E

T

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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Sequence

L

S

A

E

E

Q

S

W

V

D

A

K

L

D

R

I

D

E

L

M

Q

K

L

G

L

S

Y

D

D

D

E

E

E

E

E

D

E

K

Q

E

D

M

M

R

L

L

R

G

N

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 2k0m chain A Region: 106 - 144 Aligned: 39 Modelled: 39 Confidence: 62.9% Identity: 21% PDB header:structural genomics, unknown function Chain: A: PDB Molecule:uncharacterized protein; PDBTitle: solution nmr structure of the uncharacterized protein from2 rhodospirillum rubrum gene locus rru_a0810. northeast3 structural genomics target rrr43 Phyre2 PDB 8tfv chain A Region: 67 - 75 Aligned: 9 Modelled: 9 Confidence: 61.2% Identity: 56% PDB header:antimicrobial Chain: A: PDB Molecule:protein (thanatin); PDBTitle: insect defense peptide Phyre2 PDB 2wl8 chain D Region: 116 - 166 Aligned: 51 Modelled: 51 Confidence: 54.1% Identity: 14% PDB header:protein transport Chain: D: PDB Molecule:peroxisomal biogenesis factor 19; PDBTitle: x-ray crystal structure of pex19p Phyre2 PDB 2dvz chain A Region: 96 - 149 Aligned: 52 Modelled: 53 Confidence: 52.2% Identity: 15% PDB header:transport protein Chain: A: PDB Molecule:putative exported protein; PDBTitle: structure of a periplasmic transporter Phyre2 PDB 2qpq chain C Region: 123 - 148 Aligned: 26 Modelled: 26 Confidence: 50.8% Identity: 31% PDB header:transport protein Chain: C: PDB Molecule:protein bug27; PDBTitle: structure of bug27 from bordetella pertussis Phyre2 PDB 2xi7 chain B Region: 105 - 150 Aligned: 46 Modelled: 46 Confidence: 38.0% Identity: 24% PDB header:transferase Chain: B: PDB Molecule:rna polymerase l; PDBTitle: n-terminal endonuclease domain of la crosse virus l-protein Phyre2 PDB 2xi5 chain D Region: 105 - 150 Aligned: 46 Modelled: 46 Confidence: 37.9% Identity: 24% PDB header:transferase Chain: D: PDB Molecule:rna polymerase l; PDBTitle: n-terminal endonuclease domain of la crosse virus l-protein Phyre2 PDB 1vp7 chain A Region: 93 - 143 Aligned: 51 Modelled: 51 Confidence: 32.7% Identity: 20% Fold: Spectrin repeat-like Superfamily: XseB-like Family: XseB-like Phyre2 PDB 1vp7 chain B Region: 93 - 153 Aligned: 61 Modelled: 61 Confidence: 30.8% Identity: 18% Fold: Spectrin repeat-like Superfamily: XseB-like Family: XseB-like Phyre2 PDB 2hbp chain A Region: 119 - 131 Aligned: 13 Modelled: 13 Confidence: 28.5% Identity: 31% PDB header:endocytosis, protein binding Chain: A: PDB Molecule:cytoskeleton assembly control protein sla1; PDBTitle: solution structure of sla1 homology domain 1 Phyre2 PDB 1ug8 chain A Region: 122 - 141 Aligned: 20 Modelled: 20 Confidence: 20.3% Identity: 20% Fold: IF3-like Superfamily: R3H domain Family: R3H domain Phyre2 PDB 1tf5 chain A domain 4 Region: 65 - 121 Aligned: 40 Modelled: 40 Confidence: 19.7% Identity: 28% Fold: P-loop containing nucleoside triphosphate hydrolases Superfamily: P-loop containing nucleoside triphosphate hydrolases Family: Tandem AAA-ATPase domain Phyre2 PDB 2cho chain A domain 1 Region: 106 - 143 Aligned: 38 Modelled: 38 Confidence: 18.2% Identity: 13% Fold: Hyaluronidase domain-like Superfamily: Hyaluronidase post-catalytic domain-like Family: Hyaluronidase post-catalytic domain-like Phyre2 PDB 2is9 chain A Region: 104 - 149 Aligned: 36 Modelled: 46 Confidence: 17.8% Identity: 19% PDB header:transcription Chain: A: PDB Molecule:defective in cullin neddylation protein 1; PDBTitle: structure of yeast dcn-1 Phyre2 PDB 1vp7 chain D Region: 94 - 143 Aligned: 50 Modelled: 50 Confidence: 17.8% Identity: 20% PDB header:hydrolase Chain: D: PDB Molecule:exodeoxyribonuclease vii small subunit; PDBTitle: crystal structure of exodeoxyribonuclease vii small subunit2 (np_881400.1) from bordetella pertussis at 2.40 a resolution Phyre2 PDB 2c42 chain A domain 2 Region: 100 - 141 Aligned: 42 Modelled: 42 Confidence: 17.4% Identity: 19% Fold: Thiamin diphosphate-binding fold (THDP-binding) Superfamily: Thiamin diphosphate-binding fold (THDP-binding) Family: PFOR PP module Phyre2 PDB 3h5f chain C Region: 96 - 118 Aligned: 23 Modelled: 23 Confidence: 17.1% Identity: 39% PDB header:de novo protein Chain: C: PDB Molecule:coil ser l16l-pen; PDBTitle: switching the chirality of the metal environment alters the2 coordination mode in designed peptides. Phyre2 PDB 3h5g chain A Region: 96 - 118 Aligned: 23 Modelled: 23 Confidence: 17.1% Identity: 39% PDB header:de novo protein Chain: A: PDB Molecule:coil ser l16d-pen; PDBTitle: switching the chirality of the metal environment alters the2 coordination mode in designed peptides. Phyre2 PDB 3h5g chain B Region: 96 - 118 Aligned: 23 Modelled: 23 Confidence: 17.1% Identity: 39% PDB header:de novo protein Chain: B: PDB Molecule:coil ser l16d-pen; PDBTitle: switching the chirality of the metal environment alters the2 coordination mode in designed peptides. Phyre2 PDB 3h5g chain C Region: 96 - 118 Aligned: 23 Modelled: 23 Confidence: 17.1% Identity: 39% PDB header:de novo protein Chain: C: PDB Molecule:coil ser l16d-pen; PDBTitle: switching the chirality of the metal environment alters the2 coordination mode in designed peptides. Phyre2 1 c2k0mA_ 2 c8tfvA_ 3 c2wl8D_ 4 c2dvzA_ 5 c2qpqC_ 6 c2xi7B_ 7 c2xi5D_ 8 d1vp7a_ 9 d1vp7b_ 10 c2hbpA_ 11 d1ug8a_ 12 d1tf5a4 13 d2choa1 14 c2is9A_ 15 c1vp7D_ 16 d2c42a2 17 c3h5fC_ 18 c3h5gA_ 19 c3h5gB_ 20 c3h5gC_ 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 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66

Detailed template information

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

1 c2k0mA_ 62.9 21 PDB header:structural genomics, unknown function Chain: A: PDB Molecule:uncharacterized protein; PDBTitle: solution nmr structure of the uncharacterized protein from2 rhodospirillum rubrum gene locus rru_a0810. northeast3 structural genomics target rrr43 2 c8tfvA_ 61.2 56 PDB header:antimicrobial Chain: A: PDB Molecule:protein (thanatin); PDBTitle: insect defense peptide 3 c2wl8D_ 54.1 14 PDB header:protein transport Chain: D: PDB Molecule:peroxisomal biogenesis factor 19; PDBTitle: x-ray crystal structure of pex19p 4 c2dvzA_ 52.2 15 PDB header:transport protein Chain: A: PDB Molecule:putative exported protein; PDBTitle: structure of a periplasmic transporter 5 c2qpqC_ 50.8 31 PDB header:transport protein Chain: C: PDB Molecule:protein bug27; PDBTitle: structure of bug27 from bordetella pertussis 6 c2xi7B_ 38.0 24 PDB header:transferase Chain: B: PDB Molecule:rna polymerase l; PDBTitle: n-terminal endonuclease domain of la crosse virus l-protein 7 c2xi5D_ 37.9 24 PDB header:transferase Chain: D: PDB Molecule:rna polymerase l; PDBTitle: n-terminal endonuclease domain of la crosse virus l-protein 8 d1vp7a_ 32.7 20 Fold:Spectrin repeat-like Superfamily:XseB-like Family:XseB-like 9 d1vp7b_ 30.8 18 Fold:Spectrin repeat-like Superfamily:XseB-like Family:XseB-like 10 c2hbpA_ 28.5 31 PDB header:endocytosis, protein binding Chain: A: PDB Molecule:cytoskeleton assembly control protein sla1; PDBTitle: solution structure of sla1 homology domain 1 11 d1ug8a_ 20.3 20 Fold:IF3-like Superfamily:R3H domain Family:R3H domain 12 d1tf5a4 19.7 28 Fold:P-loop containing nucleoside triphosphate hydrolases Superfamily:P-loop containing nucleoside triphosphate hydrolases Family:Tandem AAA-ATPase domain 13 d2choa1 18.2 13 Fold:Hyaluronidase domain-like Superfamily:Hyaluronidase post-catalytic domain-like Family:Hyaluronidase post-catalytic domain-like 14 c2is9A_ 17.8 19 PDB header:transcription Chain: A: PDB Molecule:defective in cullin neddylation protein 1; PDBTitle: structure of yeast dcn-1 15 c1vp7D_ 17.8 20 PDB header:hydrolase Chain: D: PDB Molecule:exodeoxyribonuclease vii small subunit; PDBTitle: crystal structure of exodeoxyribonuclease vii small subunit2 (np_881400.1) from bordetella pertussis at 2.40 a resolution 16 d2c42a2 17.4 19 Fold:Thiamin diphosphate-binding fold (THDP-binding) Superfamily:Thiamin diphosphate-binding fold (THDP-binding) Family:PFOR PP module 17 c3h5fC_ 17.1 39 PDB header:de novo protein Chain: C: PDB Molecule:coil ser l16l-pen; PDBTitle: switching the chirality of the metal environment alters the2 coordination mode in designed peptides. 18 c3h5gA_ 17.1 39 PDB header:de novo protein Chain: A: PDB Molecule:coil ser l16d-pen; PDBTitle: switching the chirality of the metal environment alters the2 coordination mode in designed peptides. 19 c3h5gB_ 17.1 39 PDB header:de novo protein Chain: B: PDB Molecule:coil ser l16d-pen; PDBTitle: switching the chirality of the metal environment alters the2 coordination mode in designed peptides. 20 c3h5gC_ 17.1 39 PDB header:de novo protein Chain: C: PDB Molecule:coil ser l16d-pen; PDBTitle: switching the chirality of the metal environment alters the2 coordination mode in designed peptides. 21 c3h5fB_ not modelled 17.1 39 PDB header:de novo protein Chain: B: PDB Molecule:coil ser l16l-pen; PDBTitle: switching the chirality of the metal environment alters the2 coordination mode in designed peptides. 22 c3h5fA_ not modelled 17.1 39 PDB header:de novo protein Chain: A: PDB Molecule:coil ser l16l-pen; PDBTitle: switching the chirality of the metal environment alters the2 coordination mode in designed peptides. 23 d1uoua1 not modelled 17.0 22 Fold:Methionine synthase domain-like Superfamily:Nucleoside phosphorylase/phosphoribosyltransferase N-terminal domain Family:Nucleoside phosphorylase/phosphoribosyltransferase N-terminal domain 24 d1khda1 not modelled 16.4 24 Fold:Methionine synthase domain-like Superfamily:Nucleoside phosphorylase/phosphoribosyltransferase N-terminal domain Family:Nucleoside phosphorylase/phosphoribosyltransferase N-terminal domain 25 c2c3yA_ not modelled 16.0 20 PDB header:oxidoreductase Chain: A: PDB Molecule:pyruvate-ferredoxin oxidoreductase; PDBTitle: crystal structure of the radical form of2 pyruvate:ferredoxin oxidoreductase from desulfovibrio3 africanus 26 c2xlfA_ not modelled 14.9 28 PDB header:metal binding protein Chain: A: PDB Molecule:sll1785 protein; PDBTitle: structure and metal-loading of a soluble periplasm cupro-protein:2 apo-cuca-closed (semet) 27 c3nr7A_ not modelled 14.6 20 PDB header:dna binding protein Chain: A: PDB Molecule:dna-binding protein h-ns; PDBTitle: crystal structure of s. typhimurium h-ns 1-83 28 d2elca1 not modelled 14.5 32 Fold:Methionine synthase domain-like Superfamily:Nucleoside phosphorylase/phosphoribosyltransferase N-terminal domain Family:Nucleoside phosphorylase/phosphoribosyltransferase N-terminal domain 29 d2ofya1 not modelled 14.3 30 Fold:lambda repressor-like DNA-binding domains Superfamily:lambda repressor-like DNA-binding domains Family:SinR domain-like 30 d1o17a1 not modelled 12.8 18 Fold:Methionine synthase domain-like Superfamily:Nucleoside phosphorylase/phosphoribosyltransferase N-terminal domain Family:Nucleoside phosphorylase/phosphoribosyltransferase N-terminal domain 31 d2acaa1 not modelled 12.2 29 Fold:CYTH-like phosphatases Superfamily:CYTH-like phosphatases Family:CYTH domain 32 d1xp3a1 not modelled 11.9 20 Fold:TIM beta/alpha-barrel Superfamily:Xylose isomerase-like Family:Endonuclease IV 33 c3ovkD_ not modelled 11.7 16 PDB header:hydrolase Chain: D: PDB Molecule:aminopeptidase p, xaa-pro dipeptidase; PDBTitle: crystal structure of an xxa-pro aminopeptidase from streptococcus2 pyogenes 34 c3sp1B_ not modelled 11.0 14 PDB header:ligase Chain: B: PDB Molecule:cysteinyl-trna synthetase; PDBTitle: crystal structure of cysteinyl-trna synthetase (cyss) from borrelia2 burgdorferi 35 d1yg2a_ not modelled 10.8 16 Fold:DNA/RNA-binding 3-helical bundle Superfamily:"Winged helix" DNA-binding domain Family:PadR-like 36 d1h3na3 not modelled 10.6 26 Fold:Adenine nucleotide alpha hydrolase-like Superfamily:Nucleotidylyl transferase Family:Class I aminoacyl-tRNA synthetases (RS), catalytic domain 37 c1u0bB_ not modelled 10.3 19 PDB header:ligase/rna Chain: B: PDB Molecule:cysteinyl trna; PDBTitle: crystal structure of cysteinyl-trna synthetase binary2 complex with trnacys 38 d1tc3c_ not modelled 10.3 45 Fold:DNA/RNA-binding 3-helical bundle Superfamily:Homeodomain-like Family:Recombinase DNA-binding domain 39 c3lutA_ not modelled 9.5 18 PDB header:membrane protein Chain: A: PDB Molecule:voltage-gated potassium channel subunit beta-2; PDBTitle: a structural model for the full-length shaker potassium channel kv1.2 40 d1knza_ not modelled 9.3 38 Fold:NSP3 homodimer Superfamily:NSP3 homodimer Family:NSP3 homodimer 41 d3eaua1 not modelled 9.0 18 Fold:TIM beta/alpha-barrel Superfamily:NAD(P)-linked oxidoreductase Family:Aldo-keto reductases (NADP) 42 d1v8ga1 not modelled 8.7 32 Fold:Methionine synthase domain-like Superfamily:Nucleoside phosphorylase/phosphoribosyltransferase N-terminal domain Family:Nucleoside phosphorylase/phosphoribosyltransferase N-terminal domain 43 c3bq3A_ not modelled 8.5 19 PDB header:cell cycle, ligase Chain: A: PDB Molecule:defective in cullin neddylation protein 1; PDBTitle: crystal structure of s. cerevisiae dcn1 44 c3bm3A_ not modelled 7.8 22 PDB header:hydrolase/dna Chain: A: PDB Molecule:pspgi restriction endonuclease; PDBTitle: restriction endonuclease pspgi-substrate dna complex 45 d1biaa1 not modelled 7.8 38 Fold:DNA/RNA-binding 3-helical bundle Superfamily:"Winged helix" DNA-binding domain Family:Biotin repressor-like 46 c2zi0B_ not modelled 7.4 26 PDB header:gene regulation/rna Chain: B: PDB Molecule:protein 2b; PDBTitle: crystal structure of tav2b/sirna complex 47 c3t76A_ not modelled 7.4 25 PDB header:transcription regulator Chain: A: PDB Molecule:transcriptional regulator vanug; PDBTitle: crystal structure of transcriptional regulator vanug, form ii 48 c2fjtA_ not modelled 7.4 19 PDB header:lyase Chain: A: PDB Molecule:adenylyl cyclase class iv; PDBTitle: adenylyl cyclase class iv from yersinia pestis 49 d1oj7a_ not modelled 7.1 12 Fold:Dehydroquinate synthase-like Superfamily:Dehydroquinate synthase-like Family:Iron-containing alcohol dehydrogenase 50 c3p2fA_ not modelled 7.0 15 PDB header:signaling protein Chain: A: PDB Molecule:ahl synthase; PDBTitle: crystal structure of tofi in an apo form 51 c3au4B_ not modelled 6.9 26 PDB header:motor protein/apoptosis Chain: B: PDB Molecule:netrin receptor dcc; PDBTitle: structure of the human myosin-x myth4-ferm cassette bound to its2 specific cargo, dcc 52 c2l9vA_ not modelled 6.8 24 PDB header:rna binding protein Chain: A: PDB Molecule:pre-mrna-processing factor 40 homolog a; PDBTitle: nmr structure of the ff domain l24a mutant's folding transition state 53 d1dgna_ not modelled 6.8 28 Fold:DEATH domain Superfamily:DEATH domain Family:Caspase recruitment domain, CARD 54 d2outa2 not modelled 6.6 50 Fold:GINS/PriA/YqbF domain Superfamily:PriA/YqbF domain Family:YqbF N-terminal domain-like 55 c3pzdB_ not modelled 6.6 26 PDB header:motor protein/apoptosis Chain: B: PDB Molecule:netrin receptor dcc; PDBTitle: structure of the myosin x myth4-ferm/dcc complex 56 d2jmua1 not modelled 6.6 30 Fold:CYTH-like phosphatases Superfamily:CYTH-like phosphatases Family:CYTH domain 57 d1j99a_ not modelled 6.3 15 Fold:P-loop containing nucleoside triphosphate hydrolases Superfamily:P-loop containing nucleoside triphosphate hydrolases Family:PAPS sulfotransferase 58 c2outA_ not modelled 6.3 50 PDB header:structural genomics, unknown function Chain: A: PDB Molecule:mu-like prophage flumu protein gp35, protein PDBTitle: solution structure of hi1506, a novel two domain protein2 from haemophilus influenzae 59 d1a32a_ not modelled 6.3 50 Fold:S15/NS1 RNA-binding domain Superfamily:S15/NS1 RNA-binding domain Family:Ribosomal protein S15 60 d2tpta1 not modelled 6.2 23 Fold:Methionine synthase domain-like Superfamily:Nucleoside phosphorylase/phosphoribosyltransferase N-terminal domain Family:Nucleoside phosphorylase/phosphoribosyltransferase N-terminal domain 61 c2f5xC_ not modelled 6.2 20 PDB header:transport protein Chain: C: PDB Molecule:bugd; PDBTitle: structure of periplasmic binding protein bugd 62 d1vs5o1 not modelled 5.6 42 Fold:S15/NS1 RNA-binding domain Superfamily:S15/NS1 RNA-binding domain Family:Ribosomal protein S15 63 d1chma1 not modelled 5.5 6 Fold:Ribonuclease H-like motif Superfamily:Creatinase/prolidase N-terminal domain Family:Creatinase/prolidase N-terminal domain 64 c3ulwA_ not modelled 5.4 25 PDB header:ribosomal protein Chain: A: PDB Molecule:30s ribosomal protein s15; PDBTitle: 30s ribosomal protein s15 from campylobacter jejuni 65 d1brwa1 not modelled 5.2 27 Fold:Methionine synthase domain-like Superfamily:Nucleoside phosphorylase/phosphoribosyltransferase N-terminal domain Family:Nucleoside phosphorylase/phosphoribosyltransferase N-terminal domain 66 c3cqxD_ not modelled 5.1 31 PDB header:chaperone Chain: D: PDB Molecule:bag family molecular chaperone regulator 2; PDBTitle: chaperone complex

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