Secondary structure and disorder prediction

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60

Sequence

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D

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P

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L

Secondary structure

SS confidence

Disorder

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Disorder confidence

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Sequence

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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 2jra chain B Region: 1 - 63 Aligned: 63 Modelled: 63 Confidence: 99.8% Identity: 32% PDB header:structural genomics, unknown function Chain: B: PDB Molecule:protein rpa2121; PDBTitle: a novel domain-swapped solution nmr structure of protein rpa2121 from2 rhodopseudomonas palustris. northeast structural genomics target rpt6 Phyre2 PDB 1t1u chain A domain 1 Region: 36 - 60 Aligned: 25 Modelled: 25 Confidence: 29.5% Identity: 16% Fold: CoA-dependent acyltransferases Superfamily: CoA-dependent acyltransferases Family: Choline/Carnitine O-acyltransferase Phyre2 PDB 1xl7 chain A domain 1 Region: 35 - 60 Aligned: 26 Modelled: 26 Confidence: 28.7% Identity: 12% Fold: CoA-dependent acyltransferases Superfamily: CoA-dependent acyltransferases Family: Choline/Carnitine O-acyltransferase Phyre2 PDB 1qqr chain A Region: 1 - 51 Aligned: 51 Modelled: 51 Confidence: 22.7% Identity: 20% Fold: beta-Grasp (ubiquitin-like) Superfamily: Staphylokinase/streptokinase Family: Staphylokinase/streptokinase Phyre2 PDB 1q6x chain A Region: 36 - 60 Aligned: 25 Modelled: 25 Confidence: 17.4% Identity: 16% PDB header:transferase Chain: A: PDB Molecule:choline o-acetyltransferase; PDBTitle: crystal structure of rat choline acetyltransferase Phyre2 PDB 1nm8 chain A domain 1 Region: 35 - 62 Aligned: 28 Modelled: 28 Confidence: 14.4% Identity: 21% Fold: CoA-dependent acyltransferases Superfamily: CoA-dependent acyltransferases Family: Choline/Carnitine O-acyltransferase Phyre2 PDB 1t7q chain A Region: 35 - 62 Aligned: 28 Modelled: 28 Confidence: 12.7% Identity: 21% PDB header:transferase Chain: A: PDB Molecule:carnitine acetyltransferase; PDBTitle: crystal structure of the f565a mutant of murine carnitine2 acetyltransferase in complex with carnitine and coa Phyre2 PDB 1ndb chain A domain 1 Region: 35 - 62 Aligned: 28 Modelled: 28 Confidence: 12.3% Identity: 21% Fold: CoA-dependent acyltransferases Superfamily: CoA-dependent acyltransferases Family: Choline/Carnitine O-acyltransferase Phyre2 PDB 1xl8 chain B Region: 35 - 60 Aligned: 26 Modelled: 26 Confidence: 10.0% Identity: 12% PDB header:transferase Chain: B: PDB Molecule:peroxisomal carnitine o-octanoyltransferase; PDBTitle: crystal structure of mouse carnitine octanoyltransferase in2 complex with octanoylcarnitine Phyre2 PDB 1dcj chain A Region: 22 - 57 Aligned: 36 Modelled: 36 Confidence: 9.8% Identity: 19% Fold: IF3-like Superfamily: SirA-like Family: SirA-like Phyre2 PDB 3tq8 chain A Region: 32 - 63 Aligned: 32 Modelled: 32 Confidence: 9.6% Identity: 22% PDB header:oxidoreductase/oxidoreductase inhibitor Chain: A: PDB Molecule:dihydrofolate reductase; PDBTitle: structure of the dihydrofolate reductase (fola) from coxiella burnetii2 in complex with trimethoprim Phyre2 PDB 3lyd chain A Region: 33 - 54 Aligned: 22 Modelled: 22 Confidence: 9.3% Identity: 9% PDB header:structural genomics, unknown function Chain: A: PDB Molecule:uncharacterized protein; PDBTitle: crystal structure of putative uncharacterized protein from jonesia2 denitrificans Phyre2 PDB 2fy2 chain A Region: 36 - 60 Aligned: 25 Modelled: 25 Confidence: 9.0% Identity: 16% PDB header:transferase Chain: A: PDB Molecule:choline o-acetyltransferase; PDBTitle: structures of ligand bound human choline acetyltransferase2 provide insight into regulation of acetylcholine synthesis Phyre2 PDB 3f0u chain X Region: 14 - 63 Aligned: 50 Modelled: 50 Confidence: 8.5% Identity: 10% PDB header:oxidoreductase Chain: X: PDB Molecule:trimethoprim-sensitive dihydrofolate reductase; PDBTitle: staphylococcus aureus f98y mutant dihydrofolate reductase2 complexed with nadph and 2,4-diamino-5-[3-(3-methoxy-5-3 phenylphenyl)but-1-ynyl]-6-methylpyrimidine Phyre2 PDB 1kv7 chain A domain 2 Region: 33 - 57 Aligned: 25 Modelled: 25 Confidence: 8.1% Identity: 12% Fold: Cupredoxin-like Superfamily: Cupredoxins Family: Multidomain cupredoxins Phyre2 PDB 2xzm chain W Region: 39 - 63 Aligned: 25 Modelled: 25 Confidence: 8.1% Identity: 16% 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 3iz6 chain D Region: 39 - 63 Aligned: 25 Modelled: 25 Confidence: 7.5% Identity: 24% 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 2zjr chain 3 domain 1 Region: 50 - 60 Aligned: 11 Modelled: 11 Confidence: 7.0% Identity: 27% Fold: L35p-like Superfamily: L35p-like Family: Ribosomal protein L35p Phyre2 PDB 1v10 chain A domain 2 Region: 35 - 57 Aligned: 23 Modelled: 23 Confidence: 6.5% Identity: 13% Fold: Cupredoxin-like Superfamily: Cupredoxins Family: Multidomain cupredoxins Phyre2 PDB 2hsi chain B Region: 21 - 51 Aligned: 31 Modelled: 31 Confidence: 5.9% Identity: 13% PDB header:structural genomics, unknown function Chain: B: PDB Molecule:putative peptidase m23; PDBTitle: crystal structure of putative peptidase m23 from2 pseudomonas aeruginosa, new york structural genomics3 consortium Phyre2 1 c2jraB_ 2 d1t1ua1 3 d1xl7a1 4 d1qqra_ 5 c1q6xA_ 6 d1nm8a1 7 c1t7qA_ 8 d1ndba1 9 c1xl8B_ 10 d1dcja_ 11 c3tq8A_ 12 c3lydA_ 13 c2fy2A_ 14 c3f0uX_ 15 d1kv7a2 16 c2xzmW_ 17 c3iz6D_ 18 d2zjr31 19 d1v10a2 20 c2hsiB_ 21 22

Detailed template information

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

1 c2jraB_ 99.8 32 PDB header:structural genomics, unknown function Chain: B: PDB Molecule:protein rpa2121; PDBTitle: a novel domain-swapped solution nmr structure of protein rpa2121 from2 rhodopseudomonas palustris. northeast structural genomics target rpt6 2 d1t1ua1 29.5 16 Fold:CoA-dependent acyltransferases Superfamily:CoA-dependent acyltransferases Family:Choline/Carnitine O-acyltransferase 3 d1xl7a1 28.7 12 Fold:CoA-dependent acyltransferases Superfamily:CoA-dependent acyltransferases Family:Choline/Carnitine O-acyltransferase 4 d1qqra_ 22.7 20 Fold:beta-Grasp (ubiquitin-like) Superfamily:Staphylokinase/streptokinase Family:Staphylokinase/streptokinase 5 c1q6xA_ 17.4 16 PDB header:transferase Chain: A: PDB Molecule:choline o-acetyltransferase; PDBTitle: crystal structure of rat choline acetyltransferase 6 d1nm8a1 14.4 21 Fold:CoA-dependent acyltransferases Superfamily:CoA-dependent acyltransferases Family:Choline/Carnitine O-acyltransferase 7 c1t7qA_ 12.7 21 PDB header:transferase Chain: A: PDB Molecule:carnitine acetyltransferase; PDBTitle: crystal structure of the f565a mutant of murine carnitine2 acetyltransferase in complex with carnitine and coa 8 d1ndba1 12.3 21 Fold:CoA-dependent acyltransferases Superfamily:CoA-dependent acyltransferases Family:Choline/Carnitine O-acyltransferase 9 c1xl8B_ 10.0 12 PDB header:transferase Chain: B: PDB Molecule:peroxisomal carnitine o-octanoyltransferase; PDBTitle: crystal structure of mouse carnitine octanoyltransferase in2 complex with octanoylcarnitine 10 d1dcja_ 9.8 19 Fold:IF3-like Superfamily:SirA-like Family:SirA-like 11 c3tq8A_ 9.6 22 PDB header:oxidoreductase/oxidoreductase inhibitor Chain: A: PDB Molecule:dihydrofolate reductase; PDBTitle: structure of the dihydrofolate reductase (fola) from coxiella burnetii2 in complex with trimethoprim 12 c3lydA_ 9.3 9 PDB header:structural genomics, unknown function Chain: A: PDB Molecule:uncharacterized protein; PDBTitle: crystal structure of putative uncharacterized protein from jonesia2 denitrificans 13 c2fy2A_ 9.0 16 PDB header:transferase Chain: A: PDB Molecule:choline o-acetyltransferase; PDBTitle: structures of ligand bound human choline acetyltransferase2 provide insight into regulation of acetylcholine synthesis 14 c3f0uX_ 8.5 10 PDB header:oxidoreductase Chain: X: PDB Molecule:trimethoprim-sensitive dihydrofolate reductase; PDBTitle: staphylococcus aureus f98y mutant dihydrofolate reductase2 complexed with nadph and 2,4-diamino-5-[3-(3-methoxy-5-3 phenylphenyl)but-1-ynyl]-6-methylpyrimidine 15 d1kv7a2 8.1 12 Fold:Cupredoxin-like Superfamily:Cupredoxins Family:Multidomain cupredoxins 16 c2xzmW_ 8.1 16 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 17 c3iz6D_ 7.5 24 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 18 d2zjr31 7.0 27 Fold:L35p-like Superfamily:L35p-like Family:Ribosomal protein L35p 19 d1v10a2 6.5 13 Fold:Cupredoxin-like Superfamily:Cupredoxins Family:Multidomain cupredoxins 20 c2hsiB_ 5.9 13 PDB header:structural genomics, unknown function Chain: B: PDB Molecule:putative peptidase m23; PDBTitle: crystal structure of putative peptidase m23 from2 pseudomonas aeruginosa, new york structural genomics3 consortium 21 d1u0la1 not modelled 5.9 13 Fold:OB-fold Superfamily:Nucleic acid-binding proteins Family:Cold shock DNA-binding domain-like 22 c3ia5A_ not modelled 5.5 25 PDB header:oxidoreductase Chain: A: PDB Molecule:dihydrofolate reductase; PDBTitle: moritella profunda dihydrofolate reductase (dhfr)

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