Secondary structure and disorder prediction

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Sequence

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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 2kvt chain A Region: 1 - 63 Aligned: 63 Modelled: 63 Confidence: 100.0% Identity: 100% PDB header:structural genomics, unknown function Chain: A: PDB Molecule:uncharacterized protein yaia; PDBTitle: solution nmr structure of yaia from escherichia eoli. northeast2 structural genomics target er244 Phyre2 PDB 2krx chain A Region: 21 - 36 Aligned: 16 Modelled: 16 Confidence: 27.8% Identity: 25% PDB header:structural genomics, unknown function Chain: A: PDB Molecule:asl3597 protein; PDBTitle: solution nmr structure of asl3597 from nostoc sp. pcc7120.2 northeast structural genomics consortium target id nsr244. Phyre2 PDB 2gsk chain B domain 1 Region: 4 - 57 Aligned: 50 Modelled: 54 Confidence: 27.0% Identity: 22% Fold: TolA/TonB C-terminal domain Superfamily: TolA/TonB C-terminal domain Family: TonB Phyre2 PDB 1j6w chain A Region: 4 - 40 Aligned: 34 Modelled: 37 Confidence: 25.9% Identity: 32% Fold: LuxS/MPP-like metallohydrolase Superfamily: LuxS/MPP-like metallohydrolase Family: Autoinducer-2 production protein LuxS Phyre2 PDB 1j98 chain A Region: 4 - 40 Aligned: 34 Modelled: 37 Confidence: 25.8% Identity: 18% Fold: LuxS/MPP-like metallohydrolase Superfamily: LuxS/MPP-like metallohydrolase Family: Autoinducer-2 production protein LuxS Phyre2 PDB 2grx chain C Region: 4 - 57 Aligned: 50 Modelled: 54 Confidence: 22.6% Identity: 22% PDB header:metal transport Chain: C: PDB Molecule:protein tonb; PDBTitle: crystal structure of tonb in complex with fhua, e. coli2 outer membrane receptor for ferrichrome Phyre2 PDB 2qqd chain G Region: 7 - 42 Aligned: 36 Modelled: 36 Confidence: 15.3% Identity: 31% PDB header:lyase Chain: G: PDB Molecule:pyruvoyl-dependent arginine decarboxylase (ec PDBTitle: n47a mutant of pyruvoyl-dependent arginine decarboxylase2 from methanococcus jannashii Phyre2 PDB 1u07 chain A Region: 3 - 33 Aligned: 27 Modelled: 31 Confidence: 14.9% Identity: 26% Fold: TolA/TonB C-terminal domain Superfamily: TolA/TonB C-terminal domain Family: TonB Phyre2 PDB 3t6o chain A Region: 38 - 53 Aligned: 16 Modelled: 16 Confidence: 12.1% Identity: 38% PDB header:transport protein Chain: A: PDB Molecule:sulfate transporter/antisigma-factor antagonist stas; PDBTitle: the structure of an anti-sigma-factor antagonist (stas) domain protein2 from planctomyces limnophilus. Phyre2 PDB 1xx3 chain A Region: 4 - 57 Aligned: 50 Modelled: 54 Confidence: 11.9% Identity: 22% PDB header:transport protein Chain: A: PDB Molecule:tonb protein; PDBTitle: solution structure of escherichia coli tonb-ctd Phyre2 PDB 1jj2 chain H Region: 4 - 30 Aligned: 23 Modelled: 27 Confidence: 11.5% Identity: 43% Fold: alpha/beta-Hammerhead Superfamily: Ribosomal protein L16p/L10e Family: Ribosomal protein L10e Phyre2 PDB 1n13 chain J Region: 7 - 42 Aligned: 36 Modelled: 36 Confidence: 11.2% Identity: 31% PDB header:lyase Chain: J: PDB Molecule:pyruvoyl-dependent arginine decarboxylase alpha PDBTitle: the crystal structure of pyruvoyl-dependent arginine2 decarboxylase from methanococcus jannashii Phyre2 PDB 4a1a chain H Region: 4 - 30 Aligned: 23 Modelled: 27 Confidence: 9.1% Identity: 30% PDB header:ribosome Chain: H: PDB Molecule:60s ribosomal protein l10; PDBTitle: t.thermophila 60s ribosomal subunit in complex with2 initiation factor 6. this file contains 5s rrna,3 5.8s rrna and proteins of molecule 3. Phyre2 PDB 1j6x chain A Region: 12 - 40 Aligned: 29 Modelled: 28 Confidence: 6.7% Identity: 28% Fold: LuxS/MPP-like metallohydrolase Superfamily: LuxS/MPP-like metallohydrolase Family: Autoinducer-2 production protein LuxS Phyre2 PDB 2zkd chain A domain 1 Region: 12 - 44 Aligned: 33 Modelled: 33 Confidence: 6.2% Identity: 36% Fold: PUA domain-like Superfamily: PUA domain-like Family: SRA domain-like Phyre2 PDB 2pb7 chain A Region: 16 - 37 Aligned: 22 Modelled: 22 Confidence: 6.0% Identity: 50% PDB header:ligase Chain: A: PDB Molecule:e3 ubiquitin-protein ligase uhrf1; PDBTitle: crystal structure of the sra domain of the human uhrf12 protein Phyre2 PDB 3k6q chain B Region: 40 - 53 Aligned: 14 Modelled: 14 Confidence: 5.5% Identity: 21% PDB header:ligand binding protein Chain: B: PDB Molecule:putative ligand binding protein; PDBTitle: crystal structure of an antitoxin part of a putative toxin/antitoxin2 system (swol_0700) from syntrophomonas wolfei subsp. wolfei at 1.80 a3 resolution Phyre2 PDB 3bi7 chain A domain 1 Region: 16 - 43 Aligned: 28 Modelled: 28 Confidence: 5.3% Identity: 43% Fold: PUA domain-like Superfamily: PUA domain-like Family: SRA domain-like Phyre2 PDB 1ffk chain F Region: 4 - 30 Aligned: 23 Modelled: 27 Confidence: 5.0% Identity: 43% Fold: alpha/beta-Hammerhead Superfamily: Ribosomal protein L16p/L10e Family: Ribosomal protein L10e Phyre2 1 c2kvtA_ 2 c2krxA_ 3 d2gskb1 4 d1j6wa_ 5 d1j98a_ 6 c2grxC_ 7 c2qqdG_ 8 d1u07a_ 9 c3t6oA_ 10 c1xx3A_ 11 d1jj2h_ 12 c1n13J_ 13 c4a1aH_ 14 d1j6xa_ 15 d2zkda1 16 c2pb7A_ 17 c3k6qB_ 18 d3bi7a1 19 d1ffkf_

Detailed template information

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

1 c2kvtA_ 100.0 100 PDB header:structural genomics, unknown function Chain: A: PDB Molecule:uncharacterized protein yaia; PDBTitle: solution nmr structure of yaia from escherichia eoli. northeast2 structural genomics target er244 2 c2krxA_ 27.8 25 PDB header:structural genomics, unknown function Chain: A: PDB Molecule:asl3597 protein; PDBTitle: solution nmr structure of asl3597 from nostoc sp. pcc7120.2 northeast structural genomics consortium target id nsr244. 3 d2gskb1 27.0 22 Fold:TolA/TonB C-terminal domain Superfamily:TolA/TonB C-terminal domain Family:TonB 4 d1j6wa_ 25.9 32 Fold:LuxS/MPP-like metallohydrolase Superfamily:LuxS/MPP-like metallohydrolase Family:Autoinducer-2 production protein LuxS 5 d1j98a_ 25.8 18 Fold:LuxS/MPP-like metallohydrolase Superfamily:LuxS/MPP-like metallohydrolase Family:Autoinducer-2 production protein LuxS 6 c2grxC_ 22.6 22 PDB header:metal transport Chain: C: PDB Molecule:protein tonb; PDBTitle: crystal structure of tonb in complex with fhua, e. coli2 outer membrane receptor for ferrichrome 7 c2qqdG_ 15.3 31 PDB header:lyase Chain: G: PDB Molecule:pyruvoyl-dependent arginine decarboxylase (ec PDBTitle: n47a mutant of pyruvoyl-dependent arginine decarboxylase2 from methanococcus jannashii 8 d1u07a_ 14.9 26 Fold:TolA/TonB C-terminal domain Superfamily:TolA/TonB C-terminal domain Family:TonB 9 c3t6oA_ 12.1 38 PDB header:transport protein Chain: A: PDB Molecule:sulfate transporter/antisigma-factor antagonist stas; PDBTitle: the structure of an anti-sigma-factor antagonist (stas) domain protein2 from planctomyces limnophilus. 10 c1xx3A_ 11.9 22 PDB header:transport protein Chain: A: PDB Molecule:tonb protein; PDBTitle: solution structure of escherichia coli tonb-ctd 11 d1jj2h_ 11.5 43 Fold:alpha/beta-Hammerhead Superfamily:Ribosomal protein L16p/L10e Family:Ribosomal protein L10e 12 c1n13J_ 11.2 31 PDB header:lyase Chain: J: PDB Molecule:pyruvoyl-dependent arginine decarboxylase alpha PDBTitle: the crystal structure of pyruvoyl-dependent arginine2 decarboxylase from methanococcus jannashii 13 c4a1aH_ 9.1 30 PDB header:ribosome Chain: H: PDB Molecule:60s ribosomal protein l10; PDBTitle: t.thermophila 60s ribosomal subunit in complex with2 initiation factor 6. this file contains 5s rrna,3 5.8s rrna and proteins of molecule 3. 14 d1j6xa_ 6.7 28 Fold:LuxS/MPP-like metallohydrolase Superfamily:LuxS/MPP-like metallohydrolase Family:Autoinducer-2 production protein LuxS 15 d2zkda1 6.2 36 Fold:PUA domain-like Superfamily:PUA domain-like Family:SRA domain-like 16 c2pb7A_ 6.0 50 PDB header:ligase Chain: A: PDB Molecule:e3 ubiquitin-protein ligase uhrf1; PDBTitle: crystal structure of the sra domain of the human uhrf12 protein 17 c3k6qB_ 5.5 21 PDB header:ligand binding protein Chain: B: PDB Molecule:putative ligand binding protein; PDBTitle: crystal structure of an antitoxin part of a putative toxin/antitoxin2 system (swol_0700) from syntrophomonas wolfei subsp. wolfei at 1.80 a3 resolution 18 d3bi7a1 5.3 43 Fold:PUA domain-like Superfamily:PUA domain-like Family:SRA domain-like 19 d1ffkf_ 5.0 43 Fold:alpha/beta-Hammerhead Superfamily:Ribosomal protein L16p/L10e Family:Ribosomal protein L10e

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