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

T

T

Y

D

R

N

R

N

A

I

T

T

G

S

R

V

M

V

S

G

T

G

H

T

G

K

I

L

S

I

D

T

E

G

L

T

A

E

Q

I

R

R

G

K

T

V

V

V

E

G

C

E

E

K

L

A

P

L

D

Secondary structure

SS confidence

Disorder

?

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?

?

?

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?

?

?

?

?

?

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?

?

?

?

?

Disorder confidence

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Sequence

L

I

R

L

G

M

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 2hqh chain A domain 1 Region: 10 - 31 Aligned: 22 Modelled: 22 Confidence: 22.3% Identity: 41% Fold: SH3-like barrel Superfamily: Cap-Gly domain Family: Cap-Gly domain Phyre2 PDB 2coy chain A domain 1 Region: 5 - 31 Aligned: 27 Modelled: 27 Confidence: 22.3% Identity: 33% Fold: SH3-like barrel Superfamily: Cap-Gly domain Family: Cap-Gly domain Phyre2 PDB 1w4x chain A domain 2 Region: 13 - 27 Aligned: 15 Modelled: 15 Confidence: 19.0% Identity: 53% Fold: FAD/NAD(P)-binding domain Superfamily: FAD/NAD(P)-binding domain Family: FAD/NAD-linked reductases, N-terminal and central domains Phyre2 PDB 3iz6 chain D Region: 10 - 31 Aligned: 22 Modelled: 22 Confidence: 16.3% Identity: 45% PDB header:ribosome Chain: D: PDB Molecule:40s ribosomal protein s4 (s4e); PDBTitle: localization of the small subunit ribosomal proteins into a 5.5 a2 cryo-em map of triticum aestivum translating 80s ribosome Phyre2 PDB 2xzm chain W Region: 10 - 31 Aligned: 22 Modelled: 22 Confidence: 16.1% Identity: 27% PDB header:ribosome Chain: W: PDB Molecule:40s ribosomal protein s4; PDBTitle: crystal structure of the eukaryotic 40s ribosomal2 subunit in complex with initiation factor 1. this file3 contains the 40s subunit and initiation factor for4 molecule 1 Phyre2 PDB 3uvz chain B Region: 10 - 26 Aligned: 17 Modelled: 17 Confidence: 16.1% Identity: 29% PDB header:lyase Chain: B: PDB Molecule:phosphoribosylaminoimidazole carboxylase, atpase subunit; PDBTitle: crystal structure of phosphoribosylaminoimidazole carboxylase, atpase2 subunit from burkholderia ambifaria Phyre2 PDB 1q1r chain A domain 2 Region: 4 - 27 Aligned: 24 Modelled: 24 Confidence: 15.0% Identity: 25% Fold: FAD/NAD(P)-binding domain Superfamily: FAD/NAD(P)-binding domain Family: FAD/NAD-linked reductases, N-terminal and central domains Phyre2 PDB 1g7s chain A domain 2 Region: 11 - 50 Aligned: 40 Modelled: 40 Confidence: 14.4% Identity: 23% Fold: Reductase/isomerase/elongation factor common domain Superfamily: Translation proteins Family: Elongation factors Phyre2 PDB 3kbg chain A Region: 10 - 31 Aligned: 22 Modelled: 21 Confidence: 13.8% Identity: 27% PDB header:ribosomal protein Chain: A: PDB Molecule:30s ribosomal protein s4e; PDBTitle: crystal structure of the 30s ribosomal protein s4e from2 thermoplasma acidophilum. northeast structural genomics3 consortium target tar28. Phyre2 PDB 1zun chain B domain 1 Region: 10 - 54 Aligned: 45 Modelled: 41 Confidence: 13.6% Identity: 24% Fold: Reductase/isomerase/elongation factor common domain Superfamily: Translation proteins Family: Elongation factors Phyre2 PDB 3orq chain A Region: 7 - 26 Aligned: 20 Modelled: 20 Confidence: 13.3% Identity: 30% PDB header:ligase,biosynthetic protein Chain: A: PDB Molecule:n5-carboxyaminoimidazole ribonucleotide synthetase; PDBTitle: crystal structure of n5-carboxyaminoimidazole synthetase from2 staphylococcus aureus complexed with adp Phyre2 PDB 1whk chain A Region: 10 - 31 Aligned: 22 Modelled: 22 Confidence: 11.8% Identity: 14% Fold: SH3-like barrel Superfamily: Cap-Gly domain Family: Cap-Gly domain Phyre2 PDB 2zc6 chain A Region: 2 - 13 Aligned: 11 Modelled: 12 Confidence: 11.4% Identity: 36% PDB header:biosynthetic protein Chain: A: PDB Molecule:penicillin-binding protein 1a; PDBTitle: penicillin-binding protein 1a (pbp 1a) acyl-enzyme complex2 (tebipenem) from streptococcus pneumoniae Phyre2 PDB 2zc6 chain C Region: 2 - 13 Aligned: 11 Modelled: 12 Confidence: 11.4% Identity: 36% PDB header:biosynthetic protein Chain: C: PDB Molecule:penicillin-binding protein 1a; PDBTitle: penicillin-binding protein 1a (pbp 1a) acyl-enzyme complex2 (tebipenem) from streptococcus pneumoniae Phyre2 PDB 2zc5 chain C Region: 2 - 13 Aligned: 11 Modelled: 12 Confidence: 11.4% Identity: 36% PDB header:biosynthetic protein Chain: C: PDB Molecule:penicillin-binding protein 1a; PDBTitle: penicillin-binding protein 1a (pbp 1a) acyl-enzyme complex2 (biapenem) from streptococcus pneumoniae Phyre2 PDB 2zc5 chain A Region: 2 - 13 Aligned: 11 Modelled: 12 Confidence: 11.4% Identity: 36% PDB header:biosynthetic protein Chain: A: PDB Molecule:penicillin-binding protein 1a; PDBTitle: penicillin-binding protein 1a (pbp 1a) acyl-enzyme complex2 (biapenem) from streptococcus pneumoniae Phyre2 PDB 2v2f chain A Region: 2 - 13 Aligned: 11 Modelled: 12 Confidence: 11.4% Identity: 36% PDB header:transferase Chain: A: PDB Molecule:penicillin binding protein 1a; PDBTitle: crystal structure of pbp1a from drug-resistant strain 52042 from streptococcus pneumoniae Phyre2 PDB 1li4 chain A domain 1 Region: 6 - 26 Aligned: 21 Modelled: 21 Confidence: 10.5% Identity: 29% Fold: NAD(P)-binding Rossmann-fold domains Superfamily: NAD(P)-binding Rossmann-fold domains Family: Formate/glycerate dehydrogenases, NAD-domain Phyre2 PDB 1l7d chain A domain 1 Region: 13 - 26 Aligned: 14 Modelled: 14 Confidence: 9.5% Identity: 43% Fold: NAD(P)-binding Rossmann-fold domains Superfamily: NAD(P)-binding Rossmann-fold domains Family: Formate/glycerate dehydrogenases, NAD-domain Phyre2 PDB 3epm chain B Region: 13 - 25 Aligned: 13 Modelled: 13 Confidence: 9.2% Identity: 38% PDB header:biosynthetic protein Chain: B: PDB Molecule:thiamine biosynthesis protein thic; PDBTitle: crystal structure of caulobacter crescentus thic Phyre2 1 d2hqha1 2 d2coya1 3 d1w4xa2 4 c3iz6D_ 5 c2xzmW_ 6 c3uvzB_ 7 d1q1ra2 8 d1g7sa2 9 c3kbgA_ 10 d1zunb1 11 c3orqA_ 12 d1whka_ 13 c2zc6A_ 14 c2zc6C_ 15 c2zc5C_ 16 c2zc5A_ 17 c2v2fA_ 18 d1li4a1 19 d1l7da1 20 c3epmB_ 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

Detailed template information

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

1 d2hqha1 22.3 41 Fold:SH3-like barrel Superfamily:Cap-Gly domain Family:Cap-Gly domain 2 d2coya1 22.3 33 Fold:SH3-like barrel Superfamily:Cap-Gly domain Family:Cap-Gly domain 3 d1w4xa2 19.0 53 Fold:FAD/NAD(P)-binding domain Superfamily:FAD/NAD(P)-binding domain Family:FAD/NAD-linked reductases, N-terminal and central domains 4 c3iz6D_ 16.3 45 PDB header:ribosome Chain: D: PDB Molecule:40s ribosomal protein s4 (s4e); PDBTitle: localization of the small subunit ribosomal proteins into a 5.5 a2 cryo-em map of triticum aestivum translating 80s ribosome 5 c2xzmW_ 16.1 27 PDB header:ribosome Chain: W: PDB Molecule:40s ribosomal protein s4; PDBTitle: crystal structure of the eukaryotic 40s ribosomal2 subunit in complex with initiation factor 1. this file3 contains the 40s subunit and initiation factor for4 molecule 1 6 c3uvzB_ 16.1 29 PDB header:lyase Chain: B: PDB Molecule:phosphoribosylaminoimidazole carboxylase, atpase subunit; PDBTitle: crystal structure of phosphoribosylaminoimidazole carboxylase, atpase2 subunit from burkholderia ambifaria 7 d1q1ra2 15.0 25 Fold:FAD/NAD(P)-binding domain Superfamily:FAD/NAD(P)-binding domain Family:FAD/NAD-linked reductases, N-terminal and central domains 8 d1g7sa2 14.4 23 Fold:Reductase/isomerase/elongation factor common domain Superfamily:Translation proteins Family:Elongation factors 9 c3kbgA_ 13.8 27 PDB header:ribosomal protein Chain: A: PDB Molecule:30s ribosomal protein s4e; PDBTitle: crystal structure of the 30s ribosomal protein s4e from2 thermoplasma acidophilum. northeast structural genomics3 consortium target tar28. 10 d1zunb1 13.6 24 Fold:Reductase/isomerase/elongation factor common domain Superfamily:Translation proteins Family:Elongation factors 11 c3orqA_ 13.3 30 PDB header:ligase,biosynthetic protein Chain: A: PDB Molecule:n5-carboxyaminoimidazole ribonucleotide synthetase; PDBTitle: crystal structure of n5-carboxyaminoimidazole synthetase from2 staphylococcus aureus complexed with adp 12 d1whka_ 11.8 14 Fold:SH3-like barrel Superfamily:Cap-Gly domain Family:Cap-Gly domain 13 c2zc6A_ 11.4 36 PDB header:biosynthetic protein Chain: A: PDB Molecule:penicillin-binding protein 1a; PDBTitle: penicillin-binding protein 1a (pbp 1a) acyl-enzyme complex2 (tebipenem) from streptococcus pneumoniae 14 c2zc6C_ 11.4 36 PDB header:biosynthetic protein Chain: C: PDB Molecule:penicillin-binding protein 1a; PDBTitle: penicillin-binding protein 1a (pbp 1a) acyl-enzyme complex2 (tebipenem) from streptococcus pneumoniae 15 c2zc5C_ 11.4 36 PDB header:biosynthetic protein Chain: C: PDB Molecule:penicillin-binding protein 1a; PDBTitle: penicillin-binding protein 1a (pbp 1a) acyl-enzyme complex2 (biapenem) from streptococcus pneumoniae 16 c2zc5A_ 11.4 36 PDB header:biosynthetic protein Chain: A: PDB Molecule:penicillin-binding protein 1a; PDBTitle: penicillin-binding protein 1a (pbp 1a) acyl-enzyme complex2 (biapenem) from streptococcus pneumoniae 17 c2v2fA_ 11.4 36 PDB header:transferase Chain: A: PDB Molecule:penicillin binding protein 1a; PDBTitle: crystal structure of pbp1a from drug-resistant strain 52042 from streptococcus pneumoniae 18 d1li4a1 10.5 29 Fold:NAD(P)-binding Rossmann-fold domains Superfamily:NAD(P)-binding Rossmann-fold domains Family:Formate/glycerate dehydrogenases, NAD-domain 19 d1l7da1 9.5 43 Fold:NAD(P)-binding Rossmann-fold domains Superfamily:NAD(P)-binding Rossmann-fold domains Family:Formate/glycerate dehydrogenases, NAD-domain 20 c3epmB_ 9.2 38 PDB header:biosynthetic protein Chain: B: PDB Molecule:thiamine biosynthesis protein thic; PDBTitle: crystal structure of caulobacter crescentus thic 21 c2d7gD_ not modelled 8.4 22 PDB header:hydrolase Chain: D: PDB Molecule:primosomal protein n; PDBTitle: crystal structure of the aa complex of the n-terminal2 domain of pria 22 c3gvpB_ not modelled 8.2 26 PDB header:hydrolase Chain: B: PDB Molecule:adenosylhomocysteinase 3; PDBTitle: human sahh-like domain of human adenosylhomocysteinase 3 23 d1stma_ not modelled 8.1 38 Fold:Nucleoplasmin-like/VP (viral coat and capsid proteins) Superfamily:Satellite viruses Family:Satellite viruses 24 c3q2oB_ not modelled 7.8 26 PDB header:lyase Chain: B: PDB Molecule:phosphoribosylaminoimidazole carboxylase, atpase subunit; PDBTitle: crystal structure of purk: n5-carboxyaminoimidazole ribonucleotide2 synthetase 25 d1d7ya2 not modelled 7.5 25 Fold:FAD/NAD(P)-binding domain Superfamily:FAD/NAD(P)-binding domain Family:FAD/NAD-linked reductases, N-terminal and central domains 26 d1fcda1 not modelled 7.3 40 Fold:FAD/NAD(P)-binding domain Superfamily:FAD/NAD(P)-binding domain Family:FAD/NAD-linked reductases, N-terminal and central domains 27 d1wb1a1 not modelled 7.3 18 Fold:Reductase/isomerase/elongation factor common domain Superfamily:Translation proteins Family:Elongation factors 28 d1g47a1 not modelled 7.1 36 Fold:Glucocorticoid receptor-like (DNA-binding domain) Superfamily:Glucocorticoid receptor-like (DNA-binding domain) Family:LIM domain 29 d1muga_ not modelled 6.8 33 Fold:Uracil-DNA glycosylase-like Superfamily:Uracil-DNA glycosylase-like Family:Mug-like 30 c2xz2A_ not modelled 6.6 21 PDB header:rna-binding protein Chain: A: PDB Molecule:cstf-50, isoform b; PDBTitle: crystal structure of cstf-50 homodimerization domain 31 d1d1ta2 not modelled 6.5 31 Fold:NAD(P)-binding Rossmann-fold domains Superfamily:NAD(P)-binding Rossmann-fold domains Family:Alcohol dehydrogenase-like, C-terminal domain 32 c1zfnA_ not modelled 6.2 35 PDB header:transferase Chain: A: PDB Molecule:adenylyltransferase thif; PDBTitle: structural analysis of escherichia coli thif 33 d1pjqa1 not modelled 6.2 12 Fold:NAD(P)-binding Rossmann-fold domains Superfamily:NAD(P)-binding Rossmann-fold domains Family:Siroheme synthase N-terminal domain-like 34 c2yyyB_ not modelled 6.1 36 PDB header:oxidoreductase Chain: B: PDB Molecule:glyceraldehyde-3-phosphate dehydrogenase; PDBTitle: crystal structure of glyceraldehyde-3-phosphate2 dehydrogenase 35 c2gzaB_ not modelled 6.1 31 PDB header:hydrolase Chain: B: PDB Molecule:type iv secretion system protein virb11; PDBTitle: crystal structure of the virb11 atpase from the brucella suis type iv2 secretion system in complex with sulphate 36 d2czca2 not modelled 6.1 45 Fold:NAD(P)-binding Rossmann-fold domains Superfamily:NAD(P)-binding Rossmann-fold domains Family:Glyceraldehyde-3-phosphate dehydrogenase-like, N-terminal domain 37 d1kola2 not modelled 6.0 35 Fold:NAD(P)-binding Rossmann-fold domains Superfamily:NAD(P)-binding Rossmann-fold domains Family:Alcohol dehydrogenase-like, C-terminal domain 38 d1v8ba1 not modelled 5.8 29 Fold:NAD(P)-binding Rossmann-fold domains Superfamily:NAD(P)-binding Rossmann-fold domains Family:Formate/glycerate dehydrogenases, NAD-domain 39 c1cf2Q_ not modelled 5.7 33 PDB header:oxidoreductase Chain: Q: PDB Molecule:protein (glyceraldehyde-3-phosphate PDBTitle: three-dimensional structure of d-glyceraldehyde-3-phosphate2 dehydrogenase from the hyperthermophilic archaeon3 methanothermus fervidus 40 c1gpjA_ not modelled 5.5 30 PDB header:reductase Chain: A: PDB Molecule:glutamyl-trna reductase; PDBTitle: glutamyl-trna reductase from methanopyrus kandleri 41 c3s5wB_ not modelled 5.5 8 PDB header:oxidoreductase Chain: B: PDB Molecule:l-ornithine 5-monooxygenase; PDBTitle: ornithine hydroxylase (pvda) from pseudomonas aeruginosa 42 d1gpja2 not modelled 5.5 38 Fold:NAD(P)-binding Rossmann-fold domains Superfamily:NAD(P)-binding Rossmann-fold domains Family:Aminoacid dehydrogenase-like, C-terminal domain 43 d1pyya3 not modelled 5.3 50 Fold:Penicillin binding protein dimerisation domain Superfamily:Penicillin binding protein dimerisation domain Family:Penicillin binding protein dimerisation domain 44 c1w4xA_ not modelled 5.3 25 PDB header:oxygenase Chain: A: PDB Molecule:phenylacetone monooxygenase; PDBTitle: phenylacetone monooxygenase, a baeyer-villiger2 monooxygenase 45 d1dssg1 not modelled 5.3 33 Fold:NAD(P)-binding Rossmann-fold domains Superfamily:NAD(P)-binding Rossmann-fold domains Family:Glyceraldehyde-3-phosphate dehydrogenase-like, N-terminal domain 46 d1leha1 not modelled 5.1 36 Fold:NAD(P)-binding Rossmann-fold domains Superfamily:NAD(P)-binding Rossmann-fold domains Family:Aminoacid dehydrogenase-like, 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

Transmembrane helix prediction

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

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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