Secondary structure and disorder prediction

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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

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A

F

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D

G

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M

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T

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L

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F

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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

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K

H

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Y

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N

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E

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T

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M

Y

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N

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G

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I

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D

Q

G

Q

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L

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L

A

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A

A

G

H

Secondary structure

SS confidence

Disorder

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Disorder confidence

Sequence

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 2cbr chain A Region: 4 - 30 Aligned: 27 Modelled: 27 Confidence: 27.6% Identity: 11% Fold: Lipocalins Superfamily: Lipocalins Family: Fatty acid binding protein-like Phyre2 PDB 2fs6 chain A domain 1 Region: 4 - 30 Aligned: 27 Modelled: 27 Confidence: 27.0% Identity: 22% Fold: Lipocalins Superfamily: Lipocalins Family: Fatty acid binding protein-like Phyre2 PDB 1g7n chain A Region: 4 - 30 Aligned: 27 Modelled: 27 Confidence: 22.4% Identity: 15% Fold: Lipocalins Superfamily: Lipocalins Family: Fatty acid binding protein-like Phyre2 PDB 1914 chain A domain 2 Region: 16 - 50 Aligned: 28 Modelled: 35 Confidence: 21.2% Identity: 21% 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 Phyre2 PDB 1e8o chain B Region: 16 - 50 Aligned: 28 Modelled: 35 Confidence: 18.7% Identity: 25% 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 Phyre2 PDB 1fx0 chain A domain 1 Region: 7 - 34 Aligned: 28 Modelled: 28 Confidence: 18.4% Identity: 21% Fold: Left-handed superhelix Superfamily: C-terminal domain of alpha and beta subunits of F1 ATP synthase Family: C-terminal domain of alpha and beta subunits of F1 ATP synthase Phyre2 PDB 1pmp chain A Region: 4 - 27 Aligned: 24 Modelled: 24 Confidence: 18.0% Identity: 21% Fold: Lipocalins Superfamily: Lipocalins Family: Fatty acid binding protein-like Phyre2 PDB 3h4l chain B Region: 10 - 64 Aligned: 52 Modelled: 55 Confidence: 17.8% Identity: 6% PDB header:dna binding protein, protein binding Chain: B: PDB Molecule:dna mismatch repair protein pms1; PDBTitle: crystal structure of n terminal domain of a dna repair protein Phyre2 PDB 2hnx chain A domain 1 Region: 4 - 28 Aligned: 25 Modelled: 25 Confidence: 17.6% Identity: 16% Fold: Lipocalins Superfamily: Lipocalins Family: Fatty acid binding protein-like Phyre2 PDB 3si5 chain X Region: 2 - 20 Aligned: 19 Modelled: 18 Confidence: 16.7% Identity: 37% PDB header:cell cycle Chain: X: PDB Molecule:protein casc5; PDBTitle: kinetochore-bubr1 kinase complex Phyre2 PDB 1fdq chain A Region: 4 - 30 Aligned: 27 Modelled: 27 Confidence: 16.5% Identity: 19% Fold: Lipocalins Superfamily: Lipocalins Family: Fatty acid binding protein-like Phyre2 PDB 1t3b chain A Region: 64 - 112 Aligned: 45 Modelled: 49 Confidence: 16.3% Identity: 18% PDB header:isomerase Chain: A: PDB Molecule:thiol:disulfide interchange protein dsbc; PDBTitle: x-ray structure of dsbc from haemophilus influenzae Phyre2 PDB 3ppt chain A Region: 4 - 30 Aligned: 27 Modelled: 27 Confidence: 15.8% Identity: 15% PDB header:lipid binding protein Chain: A: PDB Molecule:sodium-calcium exchanger; PDBTitle: rep1-nxsq fatty acid transporter Phyre2 PDB 1hms chain A Region: 4 - 26 Aligned: 23 Modelled: 23 Confidence: 15.1% Identity: 13% Fold: Lipocalins Superfamily: Lipocalins Family: Fatty acid binding protein-like Phyre2 PDB 1ftp chain A Region: 4 - 26 Aligned: 23 Modelled: 23 Confidence: 14.8% Identity: 22% Fold: Lipocalins Superfamily: Lipocalins Family: Fatty acid binding protein-like Phyre2 PDB 1yiv chain A domain 1 Region: 4 - 28 Aligned: 25 Modelled: 25 Confidence: 14.4% Identity: 20% Fold: Lipocalins Superfamily: Lipocalins Family: Fatty acid binding protein-like Phyre2 PDB 1opa chain A Region: 4 - 26 Aligned: 23 Modelled: 23 Confidence: 14.0% Identity: 22% Fold: Lipocalins Superfamily: Lipocalins Family: Fatty acid binding protein-like Phyre2 PDB 1mdc chain A Region: 4 - 28 Aligned: 25 Modelled: 25 Confidence: 13.8% Identity: 4% Fold: Lipocalins Superfamily: Lipocalins Family: Fatty acid binding protein-like Phyre2 PDB 1crb chain A Region: 4 - 28 Aligned: 25 Modelled: 25 Confidence: 13.5% Identity: 20% Fold: Lipocalins Superfamily: Lipocalins Family: Fatty acid binding protein-like Phyre2 PDB 2q9s chain A Region: 4 - 27 Aligned: 24 Modelled: 24 Confidence: 13.2% Identity: 17% PDB header:lipid binding protein Chain: A: PDB Molecule:fatty acid-binding protein; PDBTitle: linoleic acid bound to fatty acid binding protein 4 Phyre2 1 d2cbra_ 2 d2fs6a1 3 d1g7na_ 4 d1914a2 5 d1e8ob_ 6 d1fx0a1 7 d1pmpa_ 8 c3h4lB_ 9 d2hnxa1 10 c3si5X_ 11 d1fdqa_ 12 c1t3bA_ 13 c3pptA_ 14 d1hmsa_ 15 d1ftpa_ 16 d1yiva1 17 d1opaa_ 18 d1mdca_ 19 d1crba_ 20 c2q9sA_ 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

Detailed template information

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

1 d2cbra_ 27.6 11 Fold:Lipocalins Superfamily:Lipocalins Family:Fatty acid binding protein-like 2 d2fs6a1 27.0 22 Fold:Lipocalins Superfamily:Lipocalins Family:Fatty acid binding protein-like 3 d1g7na_ 22.4 15 Fold:Lipocalins Superfamily:Lipocalins Family:Fatty acid binding protein-like 4 d1914a2 21.2 21 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 5 d1e8ob_ 18.7 25 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 6 d1fx0a1 18.4 21 Fold:Left-handed superhelix Superfamily:C-terminal domain of alpha and beta subunits of F1 ATP synthase Family:C-terminal domain of alpha and beta subunits of F1 ATP synthase 7 d1pmpa_ 18.0 21 Fold:Lipocalins Superfamily:Lipocalins Family:Fatty acid binding protein-like 8 c3h4lB_ 17.8 6 PDB header:dna binding protein, protein binding Chain: B: PDB Molecule:dna mismatch repair protein pms1; PDBTitle: crystal structure of n terminal domain of a dna repair protein 9 d2hnxa1 17.6 16 Fold:Lipocalins Superfamily:Lipocalins Family:Fatty acid binding protein-like 10 c3si5X_ 16.7 37 PDB header:cell cycle Chain: X: PDB Molecule:protein casc5; PDBTitle: kinetochore-bubr1 kinase complex 11 d1fdqa_ 16.5 19 Fold:Lipocalins Superfamily:Lipocalins Family:Fatty acid binding protein-like 12 c1t3bA_ 16.3 18 PDB header:isomerase Chain: A: PDB Molecule:thiol:disulfide interchange protein dsbc; PDBTitle: x-ray structure of dsbc from haemophilus influenzae 13 c3pptA_ 15.8 15 PDB header:lipid binding protein Chain: A: PDB Molecule:sodium-calcium exchanger; PDBTitle: rep1-nxsq fatty acid transporter 14 d1hmsa_ 15.1 13 Fold:Lipocalins Superfamily:Lipocalins Family:Fatty acid binding protein-like 15 d1ftpa_ 14.8 22 Fold:Lipocalins Superfamily:Lipocalins Family:Fatty acid binding protein-like 16 d1yiva1 14.4 20 Fold:Lipocalins Superfamily:Lipocalins Family:Fatty acid binding protein-like 17 d1opaa_ 14.0 22 Fold:Lipocalins Superfamily:Lipocalins Family:Fatty acid binding protein-like 18 d1mdca_ 13.8 4 Fold:Lipocalins Superfamily:Lipocalins Family:Fatty acid binding protein-like 19 d1crba_ 13.5 20 Fold:Lipocalins Superfamily:Lipocalins Family:Fatty acid binding protein-like 20 c2q9sA_ 13.2 17 PDB header:lipid binding protein Chain: A: PDB Molecule:fatty acid-binding protein; PDBTitle: linoleic acid bound to fatty acid binding protein 4 21 d1kqwa_ not modelled 13.1 17 Fold:Lipocalins Superfamily:Lipocalins Family:Fatty acid binding protein-like 22 d1b56a_ not modelled 12.8 28 Fold:Lipocalins Superfamily:Lipocalins Family:Fatty acid binding protein-like 23 c3na3A_ not modelled 12.7 8 PDB header:protein binding Chain: A: PDB Molecule:dna mismatch repair protein mlh1; PDBTitle: mutl protein homolog 1 isoform 1 from homo sapiens 24 d1bwya_ not modelled 12.3 17 Fold:Lipocalins Superfamily:Lipocalins Family:Fatty acid binding protein-like 25 d1lfoa_ not modelled 12.2 9 Fold:Lipocalins Superfamily:Lipocalins Family:Fatty acid binding protein-like 26 d1o1va_ not modelled 12.2 12 Fold:Lipocalins Superfamily:Lipocalins Family:Fatty acid binding protein-like 27 d1lpja_ not modelled 12.0 17 Fold:Lipocalins Superfamily:Lipocalins Family:Fatty acid binding protein-like 28 d2a0aa1 not modelled 11.8 22 Fold:Lipocalins Superfamily:Lipocalins Family:Fatty acid binding protein-like 29 d2ftba1 not modelled 11.7 9 Fold:Lipocalins Superfamily:Lipocalins Family:Fatty acid binding protein-like 30 d1p6pa_ not modelled 11.6 9 Fold:Lipocalins Superfamily:Lipocalins Family:Fatty acid binding protein-like 31 d1kzwa_ not modelled 11.6 21 Fold:Lipocalins Superfamily:Lipocalins Family:Fatty acid binding protein-like 32 c1b9nA_ not modelled 11.6 14 PDB header:transcription Chain: A: PDB Molecule:protein (mode); PDBTitle: regulator from escherichia coli 33 d1tw4a_ not modelled 11.4 13 Fold:Lipocalins Superfamily:Lipocalins Family:Fatty acid binding protein-like 34 c1914A_ not modelled 11.2 21 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 35 d1eala_ not modelled 11.2 13 Fold:Lipocalins Superfamily:Lipocalins Family:Fatty acid binding protein-like 36 d1vyfa_ not modelled 10.5 22 Fold:Lipocalins Superfamily:Lipocalins Family:Fatty acid binding protein-like 37 d1ifca_ not modelled 9.8 22 Fold:Lipocalins Superfamily:Lipocalins Family:Fatty acid binding protein-like 38 d1h7sa2 not modelled 9.7 13 Fold:ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase Superfamily:ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase Family:DNA gyrase/MutL, N-terminal domain 39 c3gm8A_ not modelled 9.6 26 PDB header:hydrolase Chain: A: PDB Molecule:glycoside hydrolase family 2, candidate beta-glycosidase; PDBTitle: crystal structure of a beta-glycosidase from bacteroides vulgatus 40 c2lbaA_ not modelled 8.7 13 PDB header:lipid binding protein Chain: A: PDB Molecule:babp protein; PDBTitle: solution structure of chicken ileal babp in complex with2 glycochenodeoxycholic acid 41 d1nuba2 not modelled 8.1 53 Fold:Knottins (small inhibitors, toxins, lectins) Superfamily:EGF/Laminin Family:Follistatin (FS) module N-terminal domain, FS-N 42 d2f73a1 not modelled 7.9 13 Fold:Lipocalins Superfamily:Lipocalins Family:Fatty acid binding protein-like 43 c2hbpA_ not modelled 7.9 14 PDB header:endocytosis, protein binding Chain: A: PDB Molecule:cytoskeleton assembly control protein sla1; PDBTitle: solution structure of sla1 homology domain 1 44 c3em0A_ not modelled 7.5 13 PDB header:lipid binding protein Chain: A: PDB Molecule:ileal bile acid-binding protein; PDBTitle: crystal structure of zebrafish ileal bile acid-bindin protein2 complexed with cholic acid (crystal form b). 45 d1ggla_ not modelled 7.3 13 Fold:Lipocalins Superfamily:Lipocalins Family:Fatty acid binding protein-like 46 d2j0na1 not modelled 7.3 28 Fold:IpaD-like Superfamily:IpaD-like Family:IpaD-like 47 d2jdia1 not modelled 7.0 21 Fold:Left-handed superhelix Superfamily:C-terminal domain of alpha and beta subunits of F1 ATP synthase Family:C-terminal domain of alpha and beta subunits of F1 ATP synthase 48 d1o8va_ not modelled 7.0 20 Fold:Lipocalins Superfamily:Lipocalins Family:Fatty acid binding protein-like 49 c3q0bX_ not modelled 6.9 19 PDB header:transferase/dna Chain: X: PDB Molecule:histone-lysine n-methyltransferase, h3 lysine-9 specific PDBTitle: crystal structure of suvh5 sra- fully methylated cg dna complex in2 space group p42212 50 d1t3ba2 not modelled 6.7 17 Fold:Cystatin-like Superfamily:DsbC/DsbG N-terminal domain-like Family:DsbC/DsbG N-terminal domain-like 51 d1ukfa_ not modelled 6.5 13 Fold:Cysteine proteinases Superfamily:Cysteine proteinases Family:Avirulence protein Avrpph3 52 c2kwaA_ not modelled 6.2 20 PDB header:transferase inhibitor Chain: A: PDB Molecule:kinase a inhibitor; PDBTitle: 1h, 13c and 15n backbone and side chain resonance assignments of the2 n-terminal domain of the histidine kinase inhibitor kipi from3 bacillus subtilis 53 d1xrsb2 not modelled 5.9 33 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

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