Secondary structure and disorder prediction

		1	.	.	.	.	.	.	.	.	10	.	.	.	.	.	.	.	.	.	20	.	.	.	.	.	.	.	.	.	30	.	.	.	.	.	.	.	.	.	40	.	.	.	.	.	.	.	.	.	50	.	.	.	.	.	.	.	.	.	60
Sequence		M	L	K	F	I	L	R	R	C	L	E	A	I	P	T	L	F	I	L	I	T	I	S	F	F	M	M	R	L	A	P	G	S	P	F	T	G	E	R	T	L	P	P	E	V	M	A	N	I	E	A	K	Y	H	L	N	D	P	I	M
Secondary structure
SS confidence
Disorder		?																																		?	?	?	?	?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	70	.	.	.	.	.	.	.	.	.	80	.	.	.	.	.	.	.	.	.	90	.	.	.	.	.	.	.	.	.	100	.	.	.	.	.	.	.	.	.	110	.	.	.	.	.	.	.	.	.	120
Sequence		T	Q	Y	F	S	Y	L	K	Q	L	A	H	G	D	F	G	P	S	F	K	Y	K	D	Y	S	V	N	D	L	V	A	S	S	F	P	V	S	A	K	L	G	A	A	A	F	F	L	A	V	I	L	G	V	S	A	G	V	I	A	A
Secondary structure
SS confidence
Disorder																										?
Disorder confidence
		.	.	.	.	.	.	.	.	.	130	.	.	.	.	.	.	.	.	.	140	.	.	.	.	.	.	.	.	.	150	.	.	.	.	.	.	.	.	.	160	.	.	.	.	.	.	.	.	.	170	.	.	.	.	.	.	.	.	.	180
Sequence		L	K	Q	N	T	K	W	D	Y	T	V	M	G	L	A	M	T	G	V	V	I	P	S	F	V	V	A	P	L	L	V	M	I	F	A	I	I	L	H	W	L	P	G	G	G	W	N	G	G	A	L	K	F	M	I	L	P	M	V	A
Secondary structure
SS confidence
Disorder
Disorder confidence
		.	.	.	.	.	.	.	.	.	190	.	.	.	.	.	.	.	.	.	200	.	.	.	.	.	.	.	.	.	210	.	.	.	.	.	.	.	.	.	220	.	.	.	.	.	.	.	.	.	230	.	.	.	.	.	.	.	.	.	240
Sequence		L	S	L	A	Y	I	A	S	I	A	R	I	T	R	G	S	M	I	E	V	L	H	S	N	F	I	R	T	A	R	A	K	G	L	P	M	R	R	I	I	L	R	H	A	L	K	P	A	L	L	P	V	L	S	Y	M	G	P	A	F
Secondary structure
SS confidence
Disorder
Disorder confidence
		.	.	.	.	.	.	.	.	.	250	.	.	.	.	.	.	.	.	.	260	.	.	.	.	.	.	.	.	.	270	.	.	.	.	.	.	.	.	.	280	.	.	.	.	.	.	.	.	.	290	.	.	.	.	.	.	.	.	.	300
Sequence		V	G	I	I	T	G	S	M	V	I	E	T	I	Y	G	L	P	G	I	G	Q	L	F	V	N	G	A	L	N	R	D	Y	S	L	V	L	S	L	T	I	L	V	G	A	L	T	I	L	F	N	A	I	V	D	V	L	Y	A	V	I
Secondary structure
SS confidence
Disorder
Disorder confidence
		.	.	.	.	.	.
Sequence		D	P	K	I	R	Y
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 3dhw chain A domain 1 Region: 89 - 294 Aligned: 194 Modelled: 196 Confidence: 99.9% Identity: 17% Fold: MetI-like Superfamily: MetI-like Family: MetI-like Phyre2 PDB 3d31 chain D Region: 88 - 293 Aligned: 204 Modelled: 206 Confidence: 99.9% Identity: 18% PDB header:transport protein Chain: D: PDB Molecule:sulfate/molybdate abc transporter, permease PDBTitle: modbc from methanosarcina acetivorans Phyre2 PDB 3d31 chain C domain 1 Region: 88 - 293 Aligned: 204 Modelled: 206 Confidence: 99.9% Identity: 18% Fold: MetI-like Superfamily: MetI-like Family: MetI-like Phyre2 PDB 2onk chain C domain 1 Region: 88 - 296 Aligned: 205 Modelled: 209 Confidence: 99.9% Identity: 15% Fold: MetI-like Superfamily: MetI-like Family: MetI-like Phyre2 PDB 2onk chain C Region: 88 - 296 Aligned: 205 Modelled: 209 Confidence: 99.9% Identity: 15% PDB header:membrane protein Chain: C: PDB Molecule:molybdate/tungstate abc transporter, permease PDBTitle: abc transporter modbc in complex with its binding protein2 moda Phyre2 PDB 2r6g chain F domain 2 Region: 82 - 292 Aligned: 210 Modelled: 211 Confidence: 99.8% Identity: 13% Fold: MetI-like Superfamily: MetI-like Family: MetI-like Phyre2 PDB 2r6g chain F Region: 90 - 292 Aligned: 201 Modelled: 203 Confidence: 99.7% Identity: 12% PDB header:hydrolase/transport protein Chain: F: PDB Molecule:maltose transport system permease protein malf; PDBTitle: the crystal structure of the e. coli maltose transporter Phyre2 PDB 3fh6 chain F Region: 1 - 305 Aligned: 285 Modelled: 287 Confidence: 99.7% Identity: 12% PDB header:transport protein Chain: F: PDB Molecule:maltose transport system permease protein malf; PDBTitle: crystal structure of the resting state maltose transporter from e.2 coli Phyre2 PDB 2r6g chain G domain 1 Region: 6 - 293 Aligned: 255 Modelled: 263 Confidence: 99.5% Identity: 15% Fold: MetI-like Superfamily: MetI-like Family: MetI-like Phyre2 PDB 1ntc chain A Region: 191 - 223 Aligned: 33 Modelled: 33 Confidence: 24.7% Identity: 12% Fold: DNA/RNA-binding 3-helical bundle Superfamily: Homeodomain-like Family: FIS-like Phyre2 PDB 1wz4 chain A Region: 297 - 305 Aligned: 9 Modelled: 9 Confidence: 23.7% Identity: 44% PDB header:gene regulation Chain: A: PDB Molecule:major surface antigen; PDBTitle: solution conformation of adr subtype hbv pre-s2 epitope Phyre2 PDB 1umq chain A Region: 191 - 222 Aligned: 32 Modelled: 32 Confidence: 17.7% Identity: 19% PDB header:dna-binding protein Chain: A: PDB Molecule:photosynthetic apparatus regulatory protein; PDBTitle: solution structure and dna binding of the effector domain2 from the global regulator prra(rega) from r. sphaeroides:3 insights into dna binding specificity Phyre2 PDB 1umq chain A Region: 191 - 222 Aligned: 32 Modelled: 32 Confidence: 17.7% Identity: 19% Fold: DNA/RNA-binding 3-helical bundle Superfamily: Homeodomain-like Family: FIS-like Phyre2 PDB 1n0u chain A domain 5 Region: 30 - 65 Aligned: 35 Modelled: 36 Confidence: 17.3% Identity: 11% Fold: Ferredoxin-like Superfamily: EF-G C-terminal domain-like Family: EF-G/eEF-2 domains III and V Phyre2 PDB 1fip chain A Region: 191 - 223 Aligned: 33 Modelled: 33 Confidence: 13.9% Identity: 12% Fold: DNA/RNA-binding 3-helical bundle Superfamily: Homeodomain-like Family: FIS-like Phyre2 PDB 1eto chain B Region: 191 - 223 Aligned: 33 Modelled: 33 Confidence: 13.8% Identity: 12% Fold: DNA/RNA-binding 3-helical bundle Superfamily: Homeodomain-like Family: FIS-like Phyre2 PDB 2cw1 chain A Region: 202 - 219 Aligned: 18 Modelled: 18 Confidence: 11.0% Identity: 39% PDB header:de novo protein Chain: A: PDB Molecule:sn4m; PDBTitle: solution structure of the de novo-designed lambda cro fold2 protein Phyre2 PDB 3e7l chain D Region: 191 - 223 Aligned: 33 Modelled: 33 Confidence: 10.7% Identity: 15% PDB header:transcription regulator Chain: D: PDB Molecule:transcriptional regulator (ntrc family); PDBTitle: crystal structure of sigma54 activator ntrc4's dna binding2 domain Phyre2 PDB 2ka1 chain A Region: 98 - 122 Aligned: 25 Modelled: 25 Confidence: 9.8% Identity: 16% 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: 98 - 122 Aligned: 25 Modelled: 25 Confidence: 9.8% Identity: 16% 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 1 d3dhwa1 2 c3d31D_ 3 d3d31c1 4 d2onkc1 5 c2onkC_ 6 d2r6gf2 7 c2r6gF_ 8 c3fh6F_ 9 d2r6gg1 10 d1ntca_ 11 c1wz4A_ 12 c1umqA_ 13 d1umqa_ 14 d1n0ua5 15 d1fipa_ 16 d1etob_ 17 c2cw1A_ 18 c3e7lD_ 19 c2ka1A_ 20 c2ka2B_ 21 22 23 24 25 26 27 28 29

Detailed template information

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

1 d3dhwa1 99.9 17 Fold:MetI-like Superfamily:MetI-like Family:MetI-like 2 c3d31D_ 99.9 18 PDB header:transport protein Chain: D: PDB Molecule:sulfate/molybdate abc transporter, permease PDBTitle: modbc from methanosarcina acetivorans 3 d3d31c1 99.9 18 Fold:MetI-like Superfamily:MetI-like Family:MetI-like 4 d2onkc1 99.9 15 Fold:MetI-like Superfamily:MetI-like Family:MetI-like 5 c2onkC_ 99.9 15 PDB header:membrane protein Chain: C: PDB Molecule:molybdate/tungstate abc transporter, permease PDBTitle: abc transporter modbc in complex with its binding protein2 moda 6 d2r6gf2 99.8 13 Fold:MetI-like Superfamily:MetI-like Family:MetI-like 7 c2r6gF_ 99.7 12 PDB header:hydrolase/transport protein Chain: F: PDB Molecule:maltose transport system permease protein malf; PDBTitle: the crystal structure of the e. coli maltose transporter 8 c3fh6F_ 99.7 12 PDB header:transport protein Chain: F: PDB Molecule:maltose transport system permease protein malf; PDBTitle: crystal structure of the resting state maltose transporter from e.2 coli 9 d2r6gg1 99.5 15 Fold:MetI-like Superfamily:MetI-like Family:MetI-like 10 d1ntca_ 24.7 12 Fold:DNA/RNA-binding 3-helical bundle Superfamily:Homeodomain-like Family:FIS-like 11 c1wz4A_ 23.7 44 PDB header:gene regulation Chain: A: PDB Molecule:major surface antigen; PDBTitle: solution conformation of adr subtype hbv pre-s2 epitope 12 c1umqA_ 17.7 19 PDB header:dna-binding protein Chain: A: PDB Molecule:photosynthetic apparatus regulatory protein; PDBTitle: solution structure and dna binding of the effector domain2 from the global regulator prra(rega) from r. sphaeroides:3 insights into dna binding specificity 13 d1umqa_ 17.7 19 Fold:DNA/RNA-binding 3-helical bundle Superfamily:Homeodomain-like Family:FIS-like 14 d1n0ua5 17.3 11 Fold:Ferredoxin-like Superfamily:EF-G C-terminal domain-like Family:EF-G/eEF-2 domains III and V 15 d1fipa_ 13.9 12 Fold:DNA/RNA-binding 3-helical bundle Superfamily:Homeodomain-like Family:FIS-like 16 d1etob_ 13.8 12 Fold:DNA/RNA-binding 3-helical bundle Superfamily:Homeodomain-like Family:FIS-like 17 c2cw1A_ 11.0 39 PDB header:de novo protein Chain: A: PDB Molecule:sn4m; PDBTitle: solution structure of the de novo-designed lambda cro fold2 protein 18 c3e7lD_ 10.7 15 PDB header:transcription regulator Chain: D: PDB Molecule:transcriptional regulator (ntrc family); PDBTitle: crystal structure of sigma54 activator ntrc4's dna binding2 domain 19 c2ka1A_ 9.8 16 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 20 c2ka2B_ 9.8 16 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 21 c2ka1B_ not modelled 9.8 16 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 22 c2ka2A_ not modelled 9.8 16 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 23 d1wpga4 not modelled 9.4 22 Fold:Calcium ATPase, transmembrane domain M Superfamily:Calcium ATPase, transmembrane domain M Family:Calcium ATPase, transmembrane domain M 24 c2jwaA_ not modelled 8.5 27 PDB header:transferase Chain: A: PDB Molecule:receptor tyrosine-protein kinase erbb-2; PDBTitle: erbb2 transmembrane segment dimer spatial structure 25 d1g2ha_ not modelled 8.1 9 Fold:DNA/RNA-binding 3-helical bundle Superfamily:Homeodomain-like Family:FIS-like 26 d1etxa_ not modelled 7.7 12 Fold:DNA/RNA-binding 3-helical bundle Superfamily:Homeodomain-like Family:FIS-like 27 c2j5dA_ not modelled 7.7 16 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 28 c1ciiA_ not modelled 7.0 15 PDB header:transmembrane protein Chain: A: PDB Molecule:colicin ia; PDBTitle: colicin ia 29 d1tdpa_ not modelled 6.9 5 Fold:Bromodomain-like Superfamily:Bacteriocin immunity protein-like Family:Carnobacteriocin B2 immunity protein

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