Secondary structure and disorder prediction

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Sequence

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A

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M

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K

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H

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N

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M

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I

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L

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Y

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H

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P

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 1eys chain H domain 2 Region: 21 - 35 Aligned: 15 Modelled: 15 Confidence: 22.1% Identity: 27% Fold: Single transmembrane helix Superfamily: Photosystem II reaction centre subunit H, transmembrane region Family: Photosystem II reaction centre subunit H, transmembrane region Phyre2 PDB 3qq5 chain A Region: 21 - 33 Aligned: 13 Modelled: 13 Confidence: 21.8% Identity: 31% PDB header:oxidoreductase Chain: A: PDB Molecule:small gtp-binding protein; PDBTitle: crystal structure of the [fefe]-hydrogenase maturation protein hydf Phyre2 PDB 1v54 chain L Region: 19 - 48 Aligned: 30 Modelled: 30 Confidence: 18.4% Identity: 27% Fold: Single transmembrane helix Superfamily: Mitochondrial cytochrome c oxidase subunit VIIc (aka VIIIa) Family: Mitochondrial cytochrome c oxidase subunit VIIc (aka VIIIa) Phyre2 PDB 1rzh chain H domain 2 Region: 25 - 35 Aligned: 11 Modelled: 11 Confidence: 18.1% Identity: 45% Fold: Single transmembrane helix Superfamily: Photosystem II reaction centre subunit H, transmembrane region Family: Photosystem II reaction centre subunit H, transmembrane region Phyre2 PDB 1l9b chain H domain 2 Region: 25 - 35 Aligned: 11 Modelled: 11 Confidence: 16.5% Identity: 45% Fold: Single transmembrane helix Superfamily: Photosystem II reaction centre subunit H, transmembrane region Family: Photosystem II reaction centre subunit H, transmembrane region Phyre2 PDB 2rcr chain H domain 2 Region: 25 - 35 Aligned: 11 Modelled: 11 Confidence: 13.1% Identity: 45% Fold: Single transmembrane helix Superfamily: Photosystem II reaction centre subunit H, transmembrane region Family: Photosystem II reaction centre subunit H, transmembrane region Phyre2 PDB 1adu chain B Region: 25 - 38 Aligned: 14 Modelled: 14 Confidence: 11.5% Identity: 29% PDB header:dna-binding protein Chain: B: PDB Molecule:adenovirus single-stranded dna-binding protein; PDBTitle: early e2a dna-binding protein Phyre2 PDB 1afo chain B Region: 20 - 28 Aligned: 9 Modelled: 9 Confidence: 8.1% Identity: 44% PDB header:integral membrane protein Chain: B: PDB Molecule:glycophorin a; PDBTitle: dimeric transmembrane domain of human glycophorin a, nmr,2 20 structures Phyre2 PDB 1k6n chain H Region: 21 - 35 Aligned: 15 Modelled: 15 Confidence: 7.9% Identity: 33% PDB header:photosynthesis Chain: H: PDB Molecule:photosynthetic reaction center h subunit; PDBTitle: e(l212)a,d(l213)a double mutant structure of photosynthetic reaction2 center from rhodobacter sphaeroides Phyre2 PDB 1p2z chain A domain 1 Region: 38 - 56 Aligned: 19 Modelled: 19 Confidence: 7.5% Identity: 26% Fold: Nucleoplasmin-like/VP (viral coat and capsid proteins) Superfamily: Group II dsDNA viruses VP Family: Adenovirus hexon Phyre2 PDB 2klu chain A Region: 15 - 30 Aligned: 16 Modelled: 16 Confidence: 6.9% Identity: 25% PDB header:immune system, membrane protein Chain: A: PDB Molecule:t-cell surface glycoprotein cd4; PDBTitle: nmr structure of the transmembrane and cytoplasmic domains2 of human cd4 Phyre2 PDB 1p30 chain A domain 1 Region: 38 - 56 Aligned: 19 Modelled: 19 Confidence: 6.9% Identity: 26% Fold: Nucleoplasmin-like/VP (viral coat and capsid proteins) Superfamily: Group II dsDNA viruses VP Family: Adenovirus hexon Phyre2 PDB 3o0r chain C Region: 13 - 54 Aligned: 42 Modelled: 42 Confidence: 6.8% Identity: 14% PDB header:immune system/oxidoreductase Chain: C: PDB Molecule:nitric oxide reductase subunit c; PDBTitle: crystal structure of nitric oxide reductase from pseudomonas2 aeruginosa in complex with antibody fragment Phyre2 PDB 1eys chain H Region: 21 - 35 Aligned: 15 Modelled: 15 Confidence: 6.6% Identity: 27% PDB header:electron transport Chain: H: PDB Molecule:photosynthetic reaction center; PDBTitle: crystal structure of photosynthetic reaction center from a2 thermophilic bacterium, thermochromatium tepidum Phyre2 PDB 1adt chain A domain 1 Region: 25 - 38 Aligned: 14 Modelled: 14 Confidence: 6.6% Identity: 29% Fold: Domain of early E2A DNA-binding protein, ADDBP Superfamily: Domain of early E2A DNA-binding protein, ADDBP Family: Domain of early E2A DNA-binding protein, ADDBP Phyre2 PDB 1l4t chain A Region: 24 - 30 Aligned: 7 Modelled: 7 Confidence: 5.8% Identity: 57% PDB header:hormone/growth factor receptor Chain: A: PDB Molecule:gastrin/cholecystokinin type b receptor; PDBTitle: solution nmr structure of the cck2e3 Phyre2 PDB 2fef chain B Region: 20 - 32 Aligned: 13 Modelled: 13 Confidence: 5.5% Identity: 8% PDB header:structural genomics, unknown function Chain: B: PDB Molecule:hypothetical protein pa2201; PDBTitle: the crystal structure of protein pa2201 from pseudomonas aeruginosa Phyre2 PDB 2iny chain A Region: 38 - 56 Aligned: 19 Modelled: 19 Confidence: 5.4% Identity: 26% PDB header:viral protein Chain: A: PDB Molecule:hexon protein; PDBTitle: nanoporous crystals of chicken embryo lethal orphan (celo) adenovirus2 major coat protein, hexon Phyre2 1 d1eysh2 2 c3qq5A_ 3 d1v54l_ 4 d1rzhh2 5 d1l9bh2 6 d2rcrh2 7 c1aduB_ 8 c1afoB_ 9 c1k6nH_ 10 d1p2za1 11 c2kluA_ 12 d1p30a1 13 c3o0rC_ 14 c1eysH_ 15 d1adta1 16 c1l4tA_ 17 c2fefB_ 18 c2inyA_

Detailed template information

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

1 d1eysh2 22.1 27 Fold:Single transmembrane helix Superfamily:Photosystem II reaction centre subunit H, transmembrane region Family:Photosystem II reaction centre subunit H, transmembrane region 2 c3qq5A_ 21.8 31 PDB header:oxidoreductase Chain: A: PDB Molecule:small gtp-binding protein; PDBTitle: crystal structure of the [fefe]-hydrogenase maturation protein hydf 3 d1v54l_ 18.4 27 Fold:Single transmembrane helix Superfamily:Mitochondrial cytochrome c oxidase subunit VIIc (aka VIIIa) Family:Mitochondrial cytochrome c oxidase subunit VIIc (aka VIIIa) 4 d1rzhh2 18.1 45 Fold:Single transmembrane helix Superfamily:Photosystem II reaction centre subunit H, transmembrane region Family:Photosystem II reaction centre subunit H, transmembrane region 5 d1l9bh2 16.5 45 Fold:Single transmembrane helix Superfamily:Photosystem II reaction centre subunit H, transmembrane region Family:Photosystem II reaction centre subunit H, transmembrane region 6 d2rcrh2 13.1 45 Fold:Single transmembrane helix Superfamily:Photosystem II reaction centre subunit H, transmembrane region Family:Photosystem II reaction centre subunit H, transmembrane region 7 c1aduB_ 11.5 29 PDB header:dna-binding protein Chain: B: PDB Molecule:adenovirus single-stranded dna-binding protein; PDBTitle: early e2a dna-binding protein 8 c1afoB_ 8.1 44 PDB header:integral membrane protein Chain: B: PDB Molecule:glycophorin a; PDBTitle: dimeric transmembrane domain of human glycophorin a, nmr,2 20 structures 9 c1k6nH_ 7.9 33 PDB header:photosynthesis Chain: H: PDB Molecule:photosynthetic reaction center h subunit; PDBTitle: e(l212)a,d(l213)a double mutant structure of photosynthetic reaction2 center from rhodobacter sphaeroides 10 d1p2za1 7.5 26 Fold:Nucleoplasmin-like/VP (viral coat and capsid proteins) Superfamily:Group II dsDNA viruses VP Family:Adenovirus hexon 11 c2kluA_ 6.9 25 PDB header:immune system, membrane protein Chain: A: PDB Molecule:t-cell surface glycoprotein cd4; PDBTitle: nmr structure of the transmembrane and cytoplasmic domains2 of human cd4 12 d1p30a1 6.9 26 Fold:Nucleoplasmin-like/VP (viral coat and capsid proteins) Superfamily:Group II dsDNA viruses VP Family:Adenovirus hexon 13 c3o0rC_ 6.8 14 PDB header:immune system/oxidoreductase Chain: C: PDB Molecule:nitric oxide reductase subunit c; PDBTitle: crystal structure of nitric oxide reductase from pseudomonas2 aeruginosa in complex with antibody fragment 14 c1eysH_ 6.6 27 PDB header:electron transport Chain: H: PDB Molecule:photosynthetic reaction center; PDBTitle: crystal structure of photosynthetic reaction center from a2 thermophilic bacterium, thermochromatium tepidum 15 d1adta1 6.6 29 Fold:Domain of early E2A DNA-binding protein, ADDBP Superfamily:Domain of early E2A DNA-binding protein, ADDBP Family:Domain of early E2A DNA-binding protein, ADDBP 16 c1l4tA_ 5.8 57 PDB header:hormone/growth factor receptor Chain: A: PDB Molecule:gastrin/cholecystokinin type b receptor; PDBTitle: solution nmr structure of the cck2e3 17 c2fefB_ 5.5 8 PDB header:structural genomics, unknown function Chain: B: PDB Molecule:hypothetical protein pa2201; PDBTitle: the crystal structure of protein pa2201 from pseudomonas aeruginosa 18 c2inyA_ 5.4 26 PDB header:viral protein Chain: A: PDB Molecule:hexon protein; PDBTitle: nanoporous crystals of chicken embryo lethal orphan (celo) adenovirus2 major coat protein, hexon

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