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

A

K

G

Q

S

L

Q

D

P

F

L

N

A

L

R

R

E

R

V

P

V

S

I

Y

L

V

N

G

I

K

L

Q

G

Q

I

E

S

F

D

Q

F

V

I

L

L

K

N

T

V

S

Q

M

V

Y

K

H

A

I

S

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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Sequence

T

V

V

P

S

R

P

V

S

H

H

S

N

N

A

G

G

G

T

S

S

N

Y

H

H

G

S

S

A

Q

N

T

S

A

Q

Q

D

S

E

E

T

E

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 3qhs chain D Region: 5 - 72 Aligned: 68 Modelled: 68 Confidence: 100.0% Identity: 100% PDB header:rna binding protein Chain: D: PDB Molecule:protein hfq; PDBTitle: crystal structure of full-length hfq from escherichia coli Phyre2 PDB 1u1s chain A domain 1 Region: 6 - 70 Aligned: 65 Modelled: 65 Confidence: 100.0% Identity: 92% Fold: Sm-like fold Superfamily: Sm-like ribonucleoproteins Family: Pleiotropic translational regulator Hfq Phyre2 PDB 1hk9 chain A Region: 6 - 69 Aligned: 64 Modelled: 64 Confidence: 100.0% Identity: 100% Fold: Sm-like fold Superfamily: Sm-like ribonucleoproteins Family: Pleiotropic translational regulator Hfq Phyre2 PDB 3hsb chain B Region: 6 - 70 Aligned: 65 Modelled: 65 Confidence: 100.0% Identity: 45% PDB header:rna binding protein/rna Chain: B: PDB Molecule:protein hfq; PDBTitle: crystal structure of ymah (hfq) from bacillus subtilis in complex with2 an rna aptamer Phyre2 PDB 1kq1 chain W Region: 6 - 65 Aligned: 60 Modelled: 60 Confidence: 100.0% Identity: 32% PDB header:translation Chain: W: PDB Molecule:host factor for q beta; PDBTitle: 1.55 a crystal structure of the pleiotropic translational2 regulator, hfq Phyre2 PDB 1kq1 chain A Region: 6 - 63 Aligned: 58 Modelled: 58 Confidence: 100.0% Identity: 33% Fold: Sm-like fold Superfamily: Sm-like ribonucleoproteins Family: Pleiotropic translational regulator Hfq Phyre2 PDB 2qtx chain L Region: 16 - 62 Aligned: 47 Modelled: 47 Confidence: 97.4% Identity: 30% PDB header:rna binding protein Chain: L: PDB Molecule:uncharacterized protein mj1435; PDBTitle: crystal structure of an hfq-like protein from methanococcus2 jannaschii Phyre2 PDB 3hfo chain C Region: 11 - 66 Aligned: 56 Modelled: 56 Confidence: 96.8% Identity: 29% PDB header:rna binding protein Chain: C: PDB Molecule:ssr3341 protein; PDBTitle: crystal structure of an hfq protein from synechocystis sp. Phyre2 PDB 3hfn chain A Region: 11 - 64 Aligned: 53 Modelled: 54 Confidence: 96.5% Identity: 26% PDB header:rna binding protein Chain: A: PDB Molecule:asl2047 protein; PDBTitle: crystal structure of an hfq protein from anabaena sp. Phyre2 PDB 1b34 chain B Region: 10 - 43 Aligned: 34 Modelled: 34 Confidence: 96.0% Identity: 26% Fold: Sm-like fold Superfamily: Sm-like ribonucleoproteins Family: Sm motif of small nuclear ribonucleoproteins, SNRNP Phyre2 PDB 1b34 chain B Region: 10 - 43 Aligned: 34 Modelled: 34 Confidence: 96.0% Identity: 26% PDB header:rna binding protein Chain: B: PDB Molecule:protein (small nuclear ribonucleoprotein sm d2); PDBTitle: crystal structure of the d1d2 sub-complex from the human snrnp core2 domain Phyre2 PDB 3cw1 chain W Region: 16 - 43 Aligned: 28 Modelled: 28 Confidence: 92.3% Identity: 29% PDB header:splicing Chain: W: PDB Molecule:small nuclear ribonucleoprotein e; PDBTitle: crystal structure of human spliceosomal u1 snrnp Phyre2 PDB 2x4j chain A Region: 18 - 57 Aligned: 38 Modelled: 40 Confidence: 91.2% Identity: 29% PDB header:viral protein Chain: A: PDB Molecule:hypothetical protein orf137; PDBTitle: crystal structure of orf137 from pyrobaculum spherical2 virus Phyre2 PDB 1th7 chain A domain 1 Region: 10 - 43 Aligned: 32 Modelled: 34 Confidence: 91.0% Identity: 22% Fold: Sm-like fold Superfamily: Sm-like ribonucleoproteins Family: Sm motif of small nuclear ribonucleoproteins, SNRNP Phyre2 PDB 1h64 chain 1 Region: 10 - 43 Aligned: 32 Modelled: 34 Confidence: 90.8% Identity: 16% Fold: Sm-like fold Superfamily: Sm-like ribonucleoproteins Family: Sm motif of small nuclear ribonucleoproteins, SNRNP Phyre2 PDB 2fwk chain B Region: 10 - 42 Aligned: 31 Modelled: 33 Confidence: 90.6% Identity: 10% PDB header:dna binding protein Chain: B: PDB Molecule:u6 snrna-associated sm-like protein lsm5; PDBTitle: crystal structure of cryptosporidium parvum u6 snrna-associated sm-2 like protein lsm5 Phyre2 PDB 3swn chain A Region: 10 - 43 Aligned: 32 Modelled: 34 Confidence: 90.4% Identity: 13% PDB header:rna binding protein Chain: A: PDB Molecule:u6 snrna-associated sm-like protein lsm5; PDBTitle: structure of the lsm657 complex: an assembly intermediate of the lsm12 7 and lsm2 8 rings Phyre2 PDB 1d3b chain A Region: 10 - 43 Aligned: 32 Modelled: 34 Confidence: 90.0% Identity: 16% Fold: Sm-like fold Superfamily: Sm-like ribonucleoproteins Family: Sm motif of small nuclear ribonucleoproteins, SNRNP Phyre2 PDB 1jbm chain A Region: 6 - 43 Aligned: 38 Modelled: 38 Confidence: 89.8% Identity: 26% Fold: Sm-like fold Superfamily: Sm-like ribonucleoproteins Family: Sm motif of small nuclear ribonucleoproteins, SNRNP Phyre2 PDB 1i4k chain 1 Region: 10 - 43 Aligned: 32 Modelled: 34 Confidence: 89.6% Identity: 25% Fold: Sm-like fold Superfamily: Sm-like ribonucleoproteins Family: Sm motif of small nuclear ribonucleoproteins, SNRNP Phyre2 1 c3qhsD_ 2 d1u1sa1 3 d1hk9a_ 4 c3hsbB_ 5 c1kq1W_ 6 d1kq1a_ 7 c2qtxL_ 8 c3hfoC_ 9 c3hfnA_ 10 d1b34b_ 11 c1b34B_ 12 c3cw1W_ 13 c2x4jA_ 14 d1th7a1 15 d1h641_ 16 c2fwkB_ 17 c3swnA_ 18 d1d3ba_ 19 d1jbma_ 20 d1i4k1_ 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 67 68 69 70 71

Detailed template information

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

1 c3qhsD_ 100.0 100 PDB header:rna binding protein Chain: D: PDB Molecule:protein hfq; PDBTitle: crystal structure of full-length hfq from escherichia coli 2 d1u1sa1 100.0 92 Fold:Sm-like fold Superfamily:Sm-like ribonucleoproteins Family:Pleiotropic translational regulator Hfq 3 d1hk9a_ 100.0 100 Fold:Sm-like fold Superfamily:Sm-like ribonucleoproteins Family:Pleiotropic translational regulator Hfq 4 c3hsbB_ 100.0 45 PDB header:rna binding protein/rna Chain: B: PDB Molecule:protein hfq; PDBTitle: crystal structure of ymah (hfq) from bacillus subtilis in complex with2 an rna aptamer 5 c1kq1W_ 100.0 32 PDB header:translation Chain: W: PDB Molecule:host factor for q beta; PDBTitle: 1.55 a crystal structure of the pleiotropic translational2 regulator, hfq 6 d1kq1a_ 100.0 33 Fold:Sm-like fold Superfamily:Sm-like ribonucleoproteins Family:Pleiotropic translational regulator Hfq 7 c2qtxL_ 97.4 30 PDB header:rna binding protein Chain: L: PDB Molecule:uncharacterized protein mj1435; PDBTitle: crystal structure of an hfq-like protein from methanococcus2 jannaschii 8 c3hfoC_ 96.8 29 PDB header:rna binding protein Chain: C: PDB Molecule:ssr3341 protein; PDBTitle: crystal structure of an hfq protein from synechocystis sp. 9 c3hfnA_ 96.5 26 PDB header:rna binding protein Chain: A: PDB Molecule:asl2047 protein; PDBTitle: crystal structure of an hfq protein from anabaena sp. 10 d1b34b_ 96.0 26 Fold:Sm-like fold Superfamily:Sm-like ribonucleoproteins Family:Sm motif of small nuclear ribonucleoproteins, SNRNP 11 c1b34B_ 96.0 26 PDB header:rna binding protein Chain: B: PDB Molecule:protein (small nuclear ribonucleoprotein sm d2); PDBTitle: crystal structure of the d1d2 sub-complex from the human snrnp core2 domain 12 c3cw1W_ 92.3 29 PDB header:splicing Chain: W: PDB Molecule:small nuclear ribonucleoprotein e; PDBTitle: crystal structure of human spliceosomal u1 snrnp 13 c2x4jA_ 91.2 29 PDB header:viral protein Chain: A: PDB Molecule:hypothetical protein orf137; PDBTitle: crystal structure of orf137 from pyrobaculum spherical2 virus 14 d1th7a1 91.0 22 Fold:Sm-like fold Superfamily:Sm-like ribonucleoproteins Family:Sm motif of small nuclear ribonucleoproteins, SNRNP 15 d1h641_ 90.8 16 Fold:Sm-like fold Superfamily:Sm-like ribonucleoproteins Family:Sm motif of small nuclear ribonucleoproteins, SNRNP 16 c2fwkB_ 90.6 10 PDB header:dna binding protein Chain: B: PDB Molecule:u6 snrna-associated sm-like protein lsm5; PDBTitle: crystal structure of cryptosporidium parvum u6 snrna-associated sm-2 like protein lsm5 17 c3swnA_ 90.4 13 PDB header:rna binding protein Chain: A: PDB Molecule:u6 snrna-associated sm-like protein lsm5; PDBTitle: structure of the lsm657 complex: an assembly intermediate of the lsm12 7 and lsm2 8 rings 18 d1d3ba_ 90.0 16 Fold:Sm-like fold Superfamily:Sm-like ribonucleoproteins Family:Sm motif of small nuclear ribonucleoproteins, SNRNP 19 d1jbma_ 89.8 26 Fold:Sm-like fold Superfamily:Sm-like ribonucleoproteins Family:Sm motif of small nuclear ribonucleoproteins, SNRNP 20 d1i4k1_ 89.6 25 Fold:Sm-like fold Superfamily:Sm-like ribonucleoproteins Family:Sm motif of small nuclear ribonucleoproteins, SNRNP 21 d1ljoa_ not modelled 88.9 13 Fold:Sm-like fold Superfamily:Sm-like ribonucleoproteins Family:Sm motif of small nuclear ribonucleoproteins, SNRNP 22 c3cw1Z_ not modelled 88.0 38 PDB header:splicing Chain: Z: PDB Molecule:small nuclear ribonucleoprotein f; PDBTitle: crystal structure of human spliceosomal u1 snrnp 23 d1mgqa_ not modelled 87.6 29 Fold:Sm-like fold Superfamily:Sm-like ribonucleoproteins Family:Sm motif of small nuclear ribonucleoproteins, SNRNP 24 d2fwka1 not modelled 87.4 10 Fold:Sm-like fold Superfamily:Sm-like ribonucleoproteins Family:Sm motif of small nuclear ribonucleoproteins, SNRNP 25 c3swnT_ not modelled 85.9 29 PDB header:rna binding protein Chain: T: PDB Molecule:u6 snrna-associated sm-like protein lsm6; PDBTitle: structure of the lsm657 complex: an assembly intermediate of the lsm12 7 and lsm2 8 rings 26 d1i8fa_ not modelled 85.6 32 Fold:Sm-like fold Superfamily:Sm-like ribonucleoproteins Family:Sm motif of small nuclear ribonucleoproteins, SNRNP 27 c3cw15_ not modelled 85.5 30 PDB header:splicing Chain: 5: PDB Molecule:small nuclear ribonucleoprotein g; PDB Fragment:residues 1-215; PDBTitle: crystal structure of human spliceosomal u1 snrnp 28 d1n9sc_ not modelled 84.8 25 Fold:Sm-like fold Superfamily:Sm-like ribonucleoproteins Family:Sm motif of small nuclear ribonucleoproteins, SNRNP 29 c1n9sH_ not modelled 83.8 25 PDB header:translation Chain: H: PDB Molecule:small nuclear ribonucleoprotein f; PDBTitle: crystal structure of yeast smf in spacegroup p43212 30 d1n9ra_ not modelled 83.7 25 Fold:Sm-like fold Superfamily:Sm-like ribonucleoproteins Family:Sm motif of small nuclear ribonucleoproteins, SNRNP 31 c3bw1A_ not modelled 83.5 29 PDB header:rna binding protein Chain: A: PDB Molecule:u6 snrna-associated sm-like protein lsm3; PDBTitle: crystal structure of homomeric yeast lsm3 exhibiting novel octameric2 ring organisation 32 c3swnC_ not modelled 82.4 20 PDB header:rna binding protein Chain: C: PDB Molecule:u6 snrna-associated sm-like protein lsm7; PDBTitle: structure of the lsm657 complex: an assembly intermediate of the lsm12 7 and lsm2 8 rings 33 d1b34a_ not modelled 81.5 33 Fold:Sm-like fold Superfamily:Sm-like ribonucleoproteins Family:Sm motif of small nuclear ribonucleoproteins, SNRNP 34 c1b34A_ not modelled 81.5 33 PDB header:rna binding protein Chain: A: PDB Molecule:protein (small nuclear ribonucleoprotein sm d1); PDBTitle: crystal structure of the d1d2 sub-complex from the human snrnp core2 domain 35 d1d3bl_ not modelled 80.0 21 Fold:Sm-like fold Superfamily:Sm-like ribonucleoproteins Family:Sm motif of small nuclear ribonucleoproteins, SNRNP 36 d1m5q1_ not modelled 78.7 24 Fold:Sm-like fold Superfamily:Sm-like ribonucleoproteins Family:Sm motif of small nuclear ribonucleoproteins, SNRNP 37 d1d3bb_ not modelled 77.3 21 Fold:Sm-like fold Superfamily:Sm-like ribonucleoproteins Family:Sm motif of small nuclear ribonucleoproteins, SNRNP 38 c3cw1D_ not modelled 75.5 16 PDB header:splicing Chain: D: PDB Molecule:small nuclear ribonucleoprotein sm d3; PDBTitle: crystal structure of human spliceosomal u1 snrnp 39 c3pgwQ_ not modelled 75.2 20 PDB header:splicing/dna/rna Chain: Q: PDB Molecule:sm b; PDBTitle: crystal structure of human u1 snrnp 40 c3cw1A_ not modelled 71.8 20 PDB header:splicing Chain: A: PDB Molecule:small nuclear ribonucleoprotein-associated proteins b and PDBTitle: crystal structure of human spliceosomal u1 snrnp 41 c1y96C_ not modelled 64.2 23 PDB header:rna binding protein Chain: C: PDB Molecule:gem-associated protein 6; PDBTitle: crystal structure of the gemin6/gemin7 heterodimer from the2 human smn complex 42 d2bo9b2 not modelled 60.5 24 Fold:Cystatin-like Superfamily:Cystatin/monellin Family:Latexin-like 43 c3pgwB_ not modelled 60.0 21 PDB header:splicing/dna/rna Chain: B: PDB Molecule:sm b; PDBTitle: crystal structure of human u1 snrnp 44 c2bo9B_ not modelled 54.2 24 PDB header:hydrolase Chain: B: PDB Molecule:human latexin; PDBTitle: human carboxypeptidase a4 in complex with human latexin. 45 d1ycya1 not modelled 41.4 46 Fold:Sm-like fold Superfamily:Sm-like ribonucleoproteins Family:PF1955-like 46 d1914a2 not modelled 33.4 35 Fold:Signal recognition particle alu RNA binding heterodimer, SRP9/14 Superfamily:Signal recognition particle alu RNA binding heterodimer, SRP9/14 Family:Signal recognition particle alu RNA binding heterodimer, SRP9/14 47 d1f15a_ not modelled 18.5 19 Fold:Nucleoplasmin-like/VP (viral coat and capsid proteins) Superfamily:Positive stranded ssRNA viruses Family:Bromoviridae-like VP 48 d2diga1 not modelled 16.8 33 Fold:SH3-like barrel Superfamily:Tudor/PWWP/MBT Family:Tudor domain 49 d1e8ob_ not modelled 16.2 40 Fold:Signal recognition particle alu RNA binding heterodimer, SRP9/14 Superfamily:Signal recognition particle alu RNA binding heterodimer, SRP9/14 Family:Signal recognition particle alu RNA binding heterodimer, SRP9/14 50 d1wlfa1 not modelled 14.1 22 Fold:Cdc48 domain 2-like Superfamily:Cdc48 domain 2-like Family:Cdc48 domain 2-like 51 d1tpna_ not modelled 11.6 21 Fold:FnI-like domain Superfamily:FnI-like domain Family:Fibronectin type I module 52 d1g40a1 not modelled 11.4 23 Fold:Complement control module/SCR domain Superfamily:Complement control module/SCR domain Family:Complement control module/SCR domain 53 c1vjqB_ not modelled 11.3 29 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. 54 c2kcmA_ not modelled 9.7 20 PDB header:nucleic acid binding protein Chain: A: PDB Molecule:cold shock domain family protein; PDBTitle: solution nmr structure of the n-terminal ob-domain of so_1732 from2 shewanella oneidensis. northeast structural genomics consortium3 target sor210a. 55 c1f15C_ not modelled 8.9 31 PDB header:virus Chain: C: PDB Molecule:coat protein; PDBTitle: cucumber mosaic virus (strain fny) 56 d1sg5a1 not modelled 8.0 19 Fold:Rof/RNase P subunit-like Superfamily:Rof/RNase P subunit-like Family:Rof-like 57 d1f15b_ not modelled 8.0 31 Fold:Nucleoplasmin-like/VP (viral coat and capsid proteins) Superfamily:Positive stranded ssRNA viruses Family:Bromoviridae-like VP 58 d2c71a1 not modelled 7.8 21 Fold:7-stranded beta/alpha barrel Superfamily:Glycoside hydrolase/deacetylase Family:NodB-like polysaccharide deacetylase 59 c2gtiA_ not modelled 7.4 18 PDB header:viral protein Chain: A: PDB Molecule:replicase polyprotein 1ab; PDBTitle: mutation of mhv coronavirus non-structural protein nsp15 (f307l) 60 c3lf4B_ not modelled 7.1 17 PDB header:fluorescent protein Chain: B: PDB Molecule:fluorescent timer precursor blue102; PDBTitle: crystal structure of fluorescent timer precursor blue102 61 d2j13a1 not modelled 6.4 21 Fold:7-stranded beta/alpha barrel Superfamily:Glycoside hydrolase/deacetylase Family:NodB-like polysaccharide deacetylase 62 d1g6pa_ not modelled 6.4 30 Fold:OB-fold Superfamily:Nucleic acid-binding proteins Family:Cold shock DNA-binding domain-like 63 d1rqpa1 not modelled 6.1 31 Fold:Bacterial fluorinating enzyme, C-terminal domain Superfamily:Bacterial fluorinating enzyme, C-terminal domain Family:Bacterial fluorinating enzyme, C-terminal domain 64 c2g3dB_ not modelled 6.0 14 PDB header:luminescent protein Chain: B: PDB Molecule:green fluorescent protein; PDBTitle: structure of s65g y66a gfp variant after spontaneous2 peptide hydrolysis 65 c1914A_ not modelled 5.7 35 PDB header:alu domain Chain: A: PDB Molecule:signal recognition particle 9/14 fusion protein; PDBTitle: signal recognition particle alu rna binding heterodimer, srp9/14 66 d1j5ya2 not modelled 5.5 21 Fold:HPr-like Superfamily:Putative transcriptional regulator TM1602, C-terminal domain Family:Putative transcriptional regulator TM1602, C-terminal domain 67 c1wlfA_ not modelled 5.3 23 PDB header:protein transport Chain: A: PDB Molecule:peroxisome biogenesis factor 1; PDBTitle: structure of the n-terminal domain of pex1 aaa-atpase:2 characterization of a putative adaptor-binding domain 68 d2iuwa1 not modelled 5.2 17 Fold:Double-stranded beta-helix Superfamily:Clavaminate synthase-like Family:AlkB-like 69 c2iuwA_ not modelled 5.2 17 PDB header:oxidoreductase Chain: A: PDB Molecule:alkylated repair protein alkb homolog 3; PDBTitle: crystal structure of human abh3 in complex with iron ion2 and 2-oxoglutarate 70 c3iv4A_ not modelled 5.2 23 PDB header:oxidoreductase Chain: A: PDB Molecule:putative oxidoreductase; PDBTitle: a putative oxidoreductase with a thioredoxin fold 71 d2g9hd2 not modelled 5.1 19 Fold:beta-Grasp (ubiquitin-like) Superfamily:Superantigen toxins, C-terminal domain Family:Superantigen toxins, C-terminal domain

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