Secondary structure and disorder prediction

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Sequence		M	I	M	A	K	L	K	S	A	K	G	K	K	F	L	F	G	L	L	A	V	F	I	I	A	A	S	V	V	T	R	A	T	I	G	G	V	I	E	Q	Y	N	I	P	L	S	E	W	T	T	S	M	Y	V	I	Q	S	S	M	I
Secondary structure
SS confidence
Disorder		?	?				?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	70	.	.	.	.	.	.	.	.	.	80	.	.	.	.	.
Sequence		F	V	Y	S	L	V	F	T	V	L	L	A	I	P	L	G	I	Y	F	L	G	G	E	E	Q
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 2ka1 chain B Region: 53 - 78 Aligned: 26 Modelled: 26 Confidence: 28.4% Identity: 42% PDB header:membrane protein Chain: B: PDB Molecule:bcl2/adenovirus e1b 19 kda protein-interacting PDBTitle: solution nmr structure of bnip3 transmembrane peptide dimer2 in detergent micelles Phyre2 PDB 2ka2 chain A Region: 53 - 78 Aligned: 26 Modelled: 26 Confidence: 28.4% Identity: 42% PDB header:membrane protein Chain: A: PDB Molecule:bcl2/adenovirus e1b 19 kda protein-interacting PDBTitle: solution nmr structure of bnip3 transmembrane peptide dimer2 in detergent micelles with his173-ser172 intermonomer3 hydrogen bond restraints Phyre2 PDB 2ka1 chain A Region: 53 - 78 Aligned: 26 Modelled: 26 Confidence: 24.9% Identity: 42% PDB header:membrane protein Chain: A: PDB Molecule:bcl2/adenovirus e1b 19 kda protein-interacting PDBTitle: solution nmr structure of bnip3 transmembrane peptide dimer2 in detergent micelles Phyre2 PDB 2ka2 chain B Region: 53 - 78 Aligned: 26 Modelled: 26 Confidence: 24.9% Identity: 42% PDB header:membrane protein Chain: B: PDB Molecule:bcl2/adenovirus e1b 19 kda protein-interacting PDBTitle: solution nmr structure of bnip3 transmembrane peptide dimer2 in detergent micelles with his173-ser172 intermonomer3 hydrogen bond restraints Phyre2 PDB 2o35 chain A Region: 35 - 48 Aligned: 14 Modelled: 14 Confidence: 22.0% Identity: 29% PDB header:structural genomics, unknown function Chain: A: PDB Molecule:hypothetical protein duf1244; PDBTitle: protein of unknown function (duf1244) from sinorhizobium meliloti Phyre2 PDB 2o35 chain A domain 1 Region: 35 - 48 Aligned: 14 Modelled: 14 Confidence: 22.0% Identity: 29% Fold: SMc04008-like Superfamily: SMc04008-like Family: SMc04008-like Phyre2 PDB 3fyb chain A Region: 35 - 48 Aligned: 14 Modelled: 14 Confidence: 21.4% Identity: 36% PDB header:structural genomics, unknown function Chain: A: PDB Molecule:protein of unknown function (duf1244); PDBTitle: crystal structure of a protein of unknown function (duf1244) from2 alcanivorax borkumensis Phyre2 PDB 2j5d chain A Region: 56 - 78 Aligned: 23 Modelled: 23 Confidence: 17.6% Identity: 48% PDB header:membrane protein Chain: A: PDB Molecule:bcl2/adenovirus e1b 19 kda protein-interacting PDBTitle: nmr structure of bnip3 transmembrane domain in lipid2 bicelles Phyre2 PDB 3r45 chain C Region: 32 - 47 Aligned: 16 Modelled: 16 Confidence: 13.8% Identity: 31% PDB header:nuclear protein Chain: C: PDB Molecule:holliday junction recognition protein; PDBTitle: structure of a cenp-a-histone h4 heterodimer in complex with chaperone2 hjurp Phyre2 PDB 1vzj chain B Region: 33 - 52 Aligned: 20 Modelled: 19 Confidence: 12.4% Identity: 15% PDB header:hydrolase Chain: B: PDB Molecule:acetylcholinesterase; PDBTitle: structure of the tetramerization domain of2 acetylcholinesterase: four-fold interaction of a www motif3 with a left-handed polyproline helix Phyre2 PDB 1g4u chain S domain 1 Region: 43 - 50 Aligned: 8 Modelled: 8 Confidence: 8.9% Identity: 38% Fold: Four-helical up-and-down bundle Superfamily: Bacterial GAP domain Family: Bacterial GAP domain Phyre2 PDB 2ksd chain A Region: 64 - 80 Aligned: 17 Modelled: 17 Confidence: 8.7% Identity: 41% PDB header:transferase Chain: A: PDB Molecule:aerobic respiration control sensor protein arcb; PDBTitle: backbone structure of the membrane domain of e. coli2 histidine kinase receptor arcb, center for structures of3 membrane proteins (csmp) target 4310c Phyre2 PDB 3mk7 chain F Region: 38 - 63 Aligned: 26 Modelled: 26 Confidence: 7.5% Identity: 27% PDB header:oxidoreductase Chain: F: PDB Molecule:cytochrome c oxidase, cbb3-type, subunit p; PDBTitle: the structure of cbb3 cytochrome oxidase Phyre2 PDB 1pk1 chain C domain 1 Region: 44 - 51 Aligned: 8 Modelled: 8 Confidence: 7.2% Identity: 38% Fold: SAM domain-like Superfamily: SAM/Pointed domain Family: SAM (sterile alpha motif) domain Phyre2 PDB 1he1 chain A Region: 43 - 50 Aligned: 8 Modelled: 8 Confidence: 7.1% Identity: 50% Fold: Four-helical up-and-down bundle Superfamily: Bacterial GAP domain Family: Bacterial GAP domain Phyre2 PDB 1te7 chain A Region: 39 - 47 Aligned: 9 Modelled: 9 Confidence: 6.7% Identity: 56% Fold: PUA domain-like Superfamily: PUA domain-like Family: yqfB-like Phyre2 PDB 2l35 chain B Region: 58 - 81 Aligned: 22 Modelled: 24 Confidence: 6.5% Identity: 59% PDB header:protein binding Chain: B: PDB Molecule:tyro protein tyrosine kinase-binding protein; PDBTitle: structure of the dap12-nkg2c transmembrane heterotrimer Phyre2 PDB 1hy5 chain A Region: 43 - 50 Aligned: 8 Modelled: 8 Confidence: 6.5% Identity: 63% Fold: Four-helical up-and-down bundle Superfamily: Bacterial GAP domain Family: Bacterial GAP domain Phyre2 PDB 2ido chain B domain 1 Region: 39 - 44 Aligned: 6 Modelled: 6 Confidence: 6.1% Identity: 67% Fold: DNA polymerase III theta subunit-like Superfamily: DNA polymerase III theta subunit-like Family: DNA polymerase III theta subunit-like Phyre2 PDB 2l34 chain B Region: 58 - 81 Aligned: 22 Modelled: 24 Confidence: 6.0% Identity: 59% PDB header:protein binding Chain: B: PDB Molecule:tyro protein tyrosine kinase-binding protein; PDBTitle: structure of the dap12 transmembrane homodimer Phyre2 1 c2ka1B_ 2 c2ka2A_ 3 c2ka1A_ 4 c2ka2B_ 5 c2o35A_ 6 d2o35a1 7 c3fybA_ 8 c2j5dA_ 9 c3r45C_ 10 c1vzjB_ 11 d1g4us1 12 c2ksdA_ 13 c3mk7F_ 14 d1pk1c1 15 d1he1a_ 16 d1te7a_ 17 c2l35B_ 18 d1hy5a_ 19 d2idob1 20 c2l34B_ 21 22 23 24 25

Detailed template information

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

1 c2ka1B_ 28.4 42 PDB header:membrane protein Chain: B: PDB Molecule:bcl2/adenovirus e1b 19 kda protein-interacting PDBTitle: solution nmr structure of bnip3 transmembrane peptide dimer2 in detergent micelles 2 c2ka2A_ 28.4 42 PDB header:membrane protein Chain: A: PDB Molecule:bcl2/adenovirus e1b 19 kda protein-interacting PDBTitle: solution nmr structure of bnip3 transmembrane peptide dimer2 in detergent micelles with his173-ser172 intermonomer3 hydrogen bond restraints 3 c2ka1A_ 24.9 42 PDB header:membrane protein Chain: A: PDB Molecule:bcl2/adenovirus e1b 19 kda protein-interacting PDBTitle: solution nmr structure of bnip3 transmembrane peptide dimer2 in detergent micelles 4 c2ka2B_ 24.9 42 PDB header:membrane protein Chain: B: PDB Molecule:bcl2/adenovirus e1b 19 kda protein-interacting PDBTitle: solution nmr structure of bnip3 transmembrane peptide dimer2 in detergent micelles with his173-ser172 intermonomer3 hydrogen bond restraints 5 c2o35A_ 22.0 29 PDB header:structural genomics, unknown function Chain: A: PDB Molecule:hypothetical protein duf1244; PDBTitle: protein of unknown function (duf1244) from sinorhizobium meliloti 6 d2o35a1 22.0 29 Fold:SMc04008-like Superfamily:SMc04008-like Family:SMc04008-like 7 c3fybA_ 21.4 36 PDB header:structural genomics, unknown function Chain: A: PDB Molecule:protein of unknown function (duf1244); PDBTitle: crystal structure of a protein of unknown function (duf1244) from2 alcanivorax borkumensis 8 c2j5dA_ 17.6 48 PDB header:membrane protein Chain: A: PDB Molecule:bcl2/adenovirus e1b 19 kda protein-interacting PDBTitle: nmr structure of bnip3 transmembrane domain in lipid2 bicelles 9 c3r45C_ 13.8 31 PDB header:nuclear protein Chain: C: PDB Molecule:holliday junction recognition protein; PDBTitle: structure of a cenp-a-histone h4 heterodimer in complex with chaperone2 hjurp 10 c1vzjB_ 12.4 15 PDB header:hydrolase Chain: B: PDB Molecule:acetylcholinesterase; PDBTitle: structure of the tetramerization domain of2 acetylcholinesterase: four-fold interaction of a www motif3 with a left-handed polyproline helix 11 d1g4us1 8.9 38 Fold:Four-helical up-and-down bundle Superfamily:Bacterial GAP domain Family:Bacterial GAP domain 12 c2ksdA_ 8.7 41 PDB header:transferase Chain: A: PDB Molecule:aerobic respiration control sensor protein arcb; PDBTitle: backbone structure of the membrane domain of e. coli2 histidine kinase receptor arcb, center for structures of3 membrane proteins (csmp) target 4310c 13 c3mk7F_ 7.5 27 PDB header:oxidoreductase Chain: F: PDB Molecule:cytochrome c oxidase, cbb3-type, subunit p; PDBTitle: the structure of cbb3 cytochrome oxidase 14 d1pk1c1 7.2 38 Fold:SAM domain-like Superfamily:SAM/Pointed domain Family:SAM (sterile alpha motif) domain 15 d1he1a_ 7.1 50 Fold:Four-helical up-and-down bundle Superfamily:Bacterial GAP domain Family:Bacterial GAP domain 16 d1te7a_ 6.7 56 Fold:PUA domain-like Superfamily:PUA domain-like Family:yqfB-like 17 c2l35B_ 6.5 59 PDB header:protein binding Chain: B: PDB Molecule:tyro protein tyrosine kinase-binding protein; PDBTitle: structure of the dap12-nkg2c transmembrane heterotrimer 18 d1hy5a_ 6.5 63 Fold:Four-helical up-and-down bundle Superfamily:Bacterial GAP domain Family:Bacterial GAP domain 19 d2idob1 6.1 67 Fold:DNA polymerase III theta subunit-like Superfamily:DNA polymerase III theta subunit-like Family:DNA polymerase III theta subunit-like 20 c2l34B_ 6.0 59 PDB header:protein binding Chain: B: PDB Molecule:tyro protein tyrosine kinase-binding protein; PDBTitle: structure of the dap12 transmembrane homodimer 21 c2l34A_ not modelled 6.0 59 PDB header:protein binding Chain: A: PDB Molecule:tyro protein tyrosine kinase-binding protein; PDBTitle: structure of the dap12 transmembrane homodimer 22 d2ae9a1 not modelled 6.0 67 Fold:DNA polymerase III theta subunit-like Superfamily:DNA polymerase III theta subunit-like Family:DNA polymerase III theta subunit-like 23 c1m56G_ not modelled 5.5 33 PDB header:oxidoreductase Chain: G: PDB Molecule:cytochrome c oxidase; PDBTitle: structure of cytochrome c oxidase from rhodobactor2 sphaeroides (wild type) 24 c3bq7A_ not modelled 5.5 38 PDB header:transferase Chain: A: PDB Molecule:diacylglycerol kinase delta; PDBTitle: sam domain of diacylglycerol kinase delta1 (e35g) 25 d1se7a_ not modelled 5.4 67 Fold:DNA polymerase III theta subunit-like Superfamily:DNA polymerase III theta subunit-like Family:DNA polymerase III theta subunit-like

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