Secondary structure and disorder prediction

		1	.	.	.	.	.	.	.	.	10	.	.	.	.	.	.	.	.	.	20	.	.	.	.	.	.	.	.	.	30	.	.	.	.	.	.	.	.	.	40	.	.	.	.	.	.	.	.	.	50	.	.	.	.	.	.	.	.	.	60
Sequence		M	G	I	I	A	Q	N	K	I	S	S	L	G	M	L	F	G	A	I	A	L	M	M	G	I	I	H	F	S	F	G	P	F	S	A	P	P	P	T	F	E	S	I	V	A	D	K	T	A	E	I	K	R	G	L	L	A	G	I	K
Secondary structure
SS confidence
Disorder		?	?	?	?	?	?	?																							?	?	?	?	?	?	?	?	?	?																				?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	70	.	.	.	.	.	.	.	.	.	80	.	.	.	.	.	.	.	.	.	90	.	.	.	.	.	.	.	.	.	100	.	.	.	.	.	.	.	.	.	110	.	.	.	.	.	.	.	.	.	120
Sequence		G	E	K	I	T	T	V	E	K	K	E	D	V	D	V	D	K	I	L	N	Q	S	G	I	A	L	A	I	A	A	L	L	C	A	F	I	G	G	M	R	K	E	N	R	W	G	I	R	G	A	L	V	F	G	G	G	T	L	A	F
Secondary structure
SS confidence
Disorder		?	?	?	?	?	?	?	?	?	?	?	?		?																													?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	130	.	.	.	.	.	.	.	.	.	140	.	.	.	.	.	.	.	.	.
Sequence		H	T	L	L	F	G	I	G	I	V	C	S	I	L	L	I	F	L	I	F	S	F	L	T	G	G	S	L	V
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 1eys chain H domain 2 Region: 91 - 105 Aligned: 15 Modelled: 15 Confidence: 40.7% Identity: 20% Fold: Single transmembrane helix Superfamily: Photosystem II reaction centre subunit H, transmembrane region Family: Photosystem II reaction centre subunit H, transmembrane region Phyre2 PDB 1eys chain H Region: 91 - 105 Aligned: 15 Modelled: 15 Confidence: 29.2% Identity: 20% 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 2i5n chain H Region: 89 - 105 Aligned: 17 Modelled: 17 Confidence: 28.9% Identity: 18% PDB header:photosynthesis Chain: H: PDB Molecule:reaction center protein h chain; PDBTitle: 1.96 a x-ray structure of photosynthetic reaction center from2 rhodopseudomonas viridis:crystals grown by microfluidic technique Phyre2 PDB 1k6n chain H Region: 91 - 105 Aligned: 15 Modelled: 15 Confidence: 28.3% Identity: 27% 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 2kic chain A Region: 53 - 71 Aligned: 19 Modelled: 19 Confidence: 20.3% Identity: 11% PDB header:protein binding,metal transport Chain: A: PDB Molecule:nitrogenase gamma subunit; PDBTitle: n-nafy. n-terminal domain of nafy Phyre2 PDB 1hb6 chain A Region: 31 - 67 Aligned: 33 Modelled: 37 Confidence: 16.3% Identity: 18% Fold: Acyl-CoA binding protein-like Superfamily: Acyl-CoA binding protein Family: Acyl-CoA binding protein Phyre2 PDB 3kwr chain A Region: 17 - 37 Aligned: 21 Modelled: 21 Confidence: 13.0% Identity: 33% PDB header:rna binding protein Chain: A: PDB Molecule:putative rna-binding protein; PDBTitle: crystal structure of putative rna-binding protein (np_785364.1) from2 lactobacillus plantarum at 1.45 a resolution Phyre2 PDB 2elo chain A Region: 60 - 80 Aligned: 21 Modelled: 21 Confidence: 12.9% Identity: 10% PDB header:transcription Chain: A: PDB Molecule:zinc finger protein 406; PDBTitle: solution structure of the 12th c2h2 zinc finger of human2 zinc finger protein 406 Phyre2 PDB 3epy chain A Region: 31 - 67 Aligned: 33 Modelled: 37 Confidence: 12.5% Identity: 18% PDB header:lipid binding protein Chain: A: PDB Molecule:acyl-coa-binding domain-containing protein 7; PDBTitle: crystal structure of human acyl-coa binding domain 72 complexed with palmitoyl-coa Phyre2 PDB 1st7 chain A Region: 31 - 67 Aligned: 33 Modelled: 37 Confidence: 9.9% Identity: 18% PDB header:transport protein Chain: A: PDB Molecule:acyl-coa-binding protein; PDBTitle: solution structure of acyl coenzyme a binding protein from2 yeast Phyre2 PDB 2cop chain A Region: 31 - 67 Aligned: 33 Modelled: 37 Confidence: 9.3% Identity: 18% PDB header:lipid binding protein Chain: A: PDB Molecule:acyl-coenzyme a binding domain containing 6; PDBTitle: solution structure of rsgi ruh-040, an acbp domain from2 human cdna Phyre2 PDB 2wh5 chain A Region: 31 - 67 Aligned: 33 Modelled: 37 Confidence: 9.0% Identity: 21% PDB header:lipid binding protein Chain: A: PDB Molecule:acyl-coa-binding domain-containing protein 4; PDBTitle: crystal structure of human acyl-coa binding domain 42 complexed with stearoyl-coa Phyre2 PDB 1hbk chain A Region: 31 - 67 Aligned: 33 Modelled: 37 Confidence: 8.2% Identity: 9% Fold: Acyl-CoA binding protein-like Superfamily: Acyl-CoA binding protein Family: Acyl-CoA binding protein Phyre2 PDB 4a1e chain E Region: 42 - 62 Aligned: 19 Modelled: 21 Confidence: 7.8% Identity: 21% PDB header:ribosome Chain: E: PDB Molecule:60s ribosomal protein l9; PDBTitle: t.thermophila 60s ribosomal subunit in complex with2 initiation factor 6. this file contains 5s rrna, 5.8s rrna3 and proteins of molecule 1 Phyre2 PDB 3iz5 chain F Region: 42 - 62 Aligned: 19 Modelled: 21 Confidence: 7.1% Identity: 21% PDB header:ribosome Chain: F: PDB Molecule:60s ribosomal protein l9 (l6p); PDBTitle: localization of the large subunit ribosomal proteins into a 5.5 a2 cryo-em map of triticum aestivum translating 80s ribosome Phyre2 PDB 2lbb chain A Region: 31 - 67 Aligned: 33 Modelled: 37 Confidence: 6.9% Identity: 15% PDB header:protein binding Chain: A: PDB Molecule:acyl coa binding protein; PDBTitle: solution structure of acyl coa binding protein from babesia bovis t2bo Phyre2 PDB 2iec chain A domain 1 Region: 22 - 60 Aligned: 29 Modelled: 39 Confidence: 6.2% Identity: 24% Fold: MK0786-like Superfamily: MK0786-like Family: MK0786-like Phyre2 PDB 3fp5 chain A Region: 31 - 67 Aligned: 33 Modelled: 37 Confidence: 6.1% Identity: 18% PDB header:lipid binding protein Chain: A: PDB Molecule:acyl-coa binding protein; PDBTitle: crystal structure of acbp from moniliophthora perniciosa Phyre2 PDB 3g80 chain B Region: 51 - 63 Aligned: 13 Modelled: 13 Confidence: 5.7% Identity: 38% PDB header:viral protein Chain: B: PDB Molecule:protein b2; PDBTitle: nodamura virus protein b2, rna-binding domain Phyre2 PDB 1afo chain B Region: 78 - 105 Aligned: 28 Modelled: 28 Confidence: 5.7% Identity: 14% PDB header:integral membrane protein Chain: B: PDB Molecule:glycophorin a; PDBTitle: dimeric transmembrane domain of human glycophorin a, nmr,2 20 structures Phyre2 1 d1eysh2 2 c1eysH_ 3 c2i5nH_ 4 c1k6nH_ 5 c2kicA_ 6 d1hb6a_ 7 c3kwrA_ 8 c2eloA_ 9 c3epyA_ 10 c1st7A_ 11 c2copA_ 12 c2wh5A_ 13 d1hbka_ 14 c4a1eE_ 15 c3iz5F_ 16 c2lbbA_ 17 d2ieca1 18 c3fp5A_ 19 c3g80B_ 20 c1afoB_ 21

Detailed template information

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

1 d1eysh2 40.7 20 Fold:Single transmembrane helix Superfamily:Photosystem II reaction centre subunit H, transmembrane region Family:Photosystem II reaction centre subunit H, transmembrane region 2 c1eysH_ 29.2 20 PDB header:electron transport Chain: H: PDB Molecule:photosynthetic reaction center; PDBTitle: crystal structure of photosynthetic reaction center from a2 thermophilic bacterium, thermochromatium tepidum 3 c2i5nH_ 28.9 18 PDB header:photosynthesis Chain: H: PDB Molecule:reaction center protein h chain; PDBTitle: 1.96 a x-ray structure of photosynthetic reaction center from2 rhodopseudomonas viridis:crystals grown by microfluidic technique 4 c1k6nH_ 28.3 27 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 5 c2kicA_ 20.3 11 PDB header:protein binding,metal transport Chain: A: PDB Molecule:nitrogenase gamma subunit; PDBTitle: n-nafy. n-terminal domain of nafy 6 d1hb6a_ 16.3 18 Fold:Acyl-CoA binding protein-like Superfamily:Acyl-CoA binding protein Family:Acyl-CoA binding protein 7 c3kwrA_ 13.0 33 PDB header:rna binding protein Chain: A: PDB Molecule:putative rna-binding protein; PDBTitle: crystal structure of putative rna-binding protein (np_785364.1) from2 lactobacillus plantarum at 1.45 a resolution 8 c2eloA_ 12.9 10 PDB header:transcription Chain: A: PDB Molecule:zinc finger protein 406; PDBTitle: solution structure of the 12th c2h2 zinc finger of human2 zinc finger protein 406 9 c3epyA_ 12.5 18 PDB header:lipid binding protein Chain: A: PDB Molecule:acyl-coa-binding domain-containing protein 7; PDBTitle: crystal structure of human acyl-coa binding domain 72 complexed with palmitoyl-coa 10 c1st7A_ 9.9 18 PDB header:transport protein Chain: A: PDB Molecule:acyl-coa-binding protein; PDBTitle: solution structure of acyl coenzyme a binding protein from2 yeast 11 c2copA_ 9.3 18 PDB header:lipid binding protein Chain: A: PDB Molecule:acyl-coenzyme a binding domain containing 6; PDBTitle: solution structure of rsgi ruh-040, an acbp domain from2 human cdna 12 c2wh5A_ 9.0 21 PDB header:lipid binding protein Chain: A: PDB Molecule:acyl-coa-binding domain-containing protein 4; PDBTitle: crystal structure of human acyl-coa binding domain 42 complexed with stearoyl-coa 13 d1hbka_ 8.2 9 Fold:Acyl-CoA binding protein-like Superfamily:Acyl-CoA binding protein Family:Acyl-CoA binding protein 14 c4a1eE_ 7.8 21 PDB header:ribosome Chain: E: PDB Molecule:60s ribosomal protein l9; PDBTitle: t.thermophila 60s ribosomal subunit in complex with2 initiation factor 6. this file contains 5s rrna, 5.8s rrna3 and proteins of molecule 1 15 c3iz5F_ 7.1 21 PDB header:ribosome Chain: F: PDB Molecule:60s ribosomal protein l9 (l6p); PDBTitle: localization of the large subunit ribosomal proteins into a 5.5 a2 cryo-em map of triticum aestivum translating 80s ribosome 16 c2lbbA_ 6.9 15 PDB header:protein binding Chain: A: PDB Molecule:acyl coa binding protein; PDBTitle: solution structure of acyl coa binding protein from babesia bovis t2bo 17 d2ieca1 6.2 24 Fold:MK0786-like Superfamily:MK0786-like Family:MK0786-like 18 c3fp5A_ 6.1 18 PDB header:lipid binding protein Chain: A: PDB Molecule:acyl-coa binding protein; PDBTitle: crystal structure of acbp from moniliophthora perniciosa 19 c3g80B_ 5.7 38 PDB header:viral protein Chain: B: PDB Molecule:protein b2; PDBTitle: nodamura virus protein b2, rna-binding domain 20 c1afoB_ 5.7 14 PDB header:integral membrane protein Chain: B: PDB Molecule:glycophorin a; PDBTitle: dimeric transmembrane domain of human glycophorin a, nmr,2 20 structures 21 d1rkla_ not modelled 5.1 20 Fold:Single transmembrane helix Superfamily:Oligosaccharyltransferase subunit ost4p Family:Oligosaccharyltransferase subunit ost4p

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