Secondary structure and disorder prediction

		1	.	.	.	.	.	.	.	.	10	.	.	.	.	.	.	.	.	.	20	.	.	.	.	.	.	.	.	.	30	.	.	.	.	.	.	.	.	.	40	.	.	.	.	.	.	.	.	.	50	.	.	.	.	.	.	.	.	.	60
Sequence		M	L	N	Y	V	I	K	R	L	L	G	L	I	P	T	L	F	I	V	S	V	L	V	F	L	F	V	H	M	L	P	G	D	P	A	R	L	I	A	G	P	E	A	D	A	Q	V	I	E	L	V	R	Q	Q	L	G	L	D	Q	P
Secondary structure
SS confidence
Disorder		?
Disorder confidence
		.	.	.	.	.	.	.	.	.	70	.	.	.	.	.	.	.	.	.	80	.	.	.	.	.	.	.	.	.	90	.	.	.	.	.	.	.	.	.	100	.	.	.	.	.	.	.	.	.	110	.	.	.	.	.	.	.	.	.	120
Sequence		L	Y	H	Q	F	W	H	Y	I	S	N	A	V	Q	G	D	F	G	L	S	M	V	S	R	R	P	V	A	D	E	I	A	S	R	F	M	P	T	L	W	L	T	I	T	S	M	V	W	A	V	I	F	G	M	A	A	G	I	I	A
Secondary structure
SS confidence
Disorder
Disorder confidence
		.	.	.	.	.	.	.	.	.	130	.	.	.	.	.	.	.	.	.	140	.	.	.	.	.	.	.	.	.	150	.	.	.	.	.	.	.	.	.	160	.	.	.	.	.	.	.	.	.	170	.	.	.	.	.	.	.	.	.	180
Sequence		A	V	W	R	N	R	W	P	D	R	L	S	M	T	I	A	V	S	G	I	S	F	P	A	F	A	L	G	M	L	L	I	Q	V	F	S	V	E	L	G	W	L	P	T	V	G	A	D	S	W	Q	H	Y	I	L	P	S	L	T	L
Secondary structure
SS confidence
Disorder
Disorder confidence
		.	.	.	.	.	.	.	.	.	190	.	.	.	.	.	.	.	.	.	200	.	.	.	.	.	.	.	.	.	210	.	.	.	.	.	.	.	.	.	220	.	.	.	.	.	.	.	.	.	230	.	.	.	.	.	.	.	.	.	240
Sequence		G	A	A	V	A	A	V	M	A	R	F	T	R	A	S	F	V	D	V	L	S	E	D	Y	M	R	T	A	R	A	K	G	V	S	E	T	W	V	V	L	K	H	G	L	R	N	A	M	I	P	V	V	T	M	M	G	L	Q	F	G
Secondary structure
SS confidence
Disorder
Disorder confidence
		.	.	.	.	.	.	.	.	.	250	.	.	.	.	.	.	.	.	.	260	.	.	.	.	.	.	.	.	.	270	.	.	.	.	.	.	.	.	.	280	.	.	.	.	.	.	.	.	.	290	.	.	.	.	.	.	.	.	.	300
Sequence		F	L	L	G	G	S	I	V	V	E	K	V	F	N	W	P	G	L	G	R	L	L	V	D	S	V	E	M	R	D	Y	P	V	I	Q	A	E	I	L	L	F	S	L	E	F	I	L	I	N	L	V	V	D	V	L	Y	A	A	I	N
Secondary structure
SS confidence
Disorder
Disorder confidence
		.	.	.	.	.	.
Sequence		P	A	I	R	Y	K
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 - 293 Aligned: 195 Modelled: 197 Confidence: 99.9% Identity: 21% Fold: MetI-like Superfamily: MetI-like Family: MetI-like Phyre2 PDB 2onk chain C Region: 8 - 295 Aligned: 248 Modelled: 250 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 2onk chain C domain 1 Region: 8 - 295 Aligned: 248 Modelled: 250 Confidence: 99.9% Identity: 15% Fold: MetI-like Superfamily: MetI-like Family: MetI-like Phyre2 PDB 3d31 chain C domain 1 Region: 89 - 292 Aligned: 202 Modelled: 204 Confidence: 99.9% Identity: 15% Fold: MetI-like Superfamily: MetI-like Family: MetI-like Phyre2 PDB 3d31 chain D Region: 89 - 292 Aligned: 202 Modelled: 204 Confidence: 99.9% Identity: 15% PDB header:transport protein Chain: D: PDB Molecule:sulfate/molybdate abc transporter, permease PDBTitle: modbc from methanosarcina acetivorans Phyre2 PDB 2r6g chain F domain 2 Region: 79 - 291 Aligned: 211 Modelled: 213 Confidence: 99.8% Identity: 14% Fold: MetI-like Superfamily: MetI-like Family: MetI-like Phyre2 PDB 2r6g chain F Region: 68 - 291 Aligned: 221 Modelled: 224 Confidence: 99.8% Identity: 13% 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 - 304 Aligned: 279 Modelled: 286 Confidence: 99.8% Identity: 11% 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: 7 - 292 Aligned: 258 Modelled: 264 Confidence: 99.5% Identity: 13% Fold: MetI-like Superfamily: MetI-like Family: MetI-like Phyre2 PDB 1wz4 chain A Region: 298 - 304 Aligned: 7 Modelled: 7 Confidence: 15.2% Identity: 29% PDB header:gene regulation Chain: A: PDB Molecule:major surface antigen; PDBTitle: solution conformation of adr subtype hbv pre-s2 epitope Phyre2 PDB 1ntc chain A Region: 190 - 222 Aligned: 33 Modelled: 33 Confidence: 14.0% Identity: 15% Fold: DNA/RNA-binding 3-helical bundle Superfamily: Homeodomain-like Family: FIS-like Phyre2 PDB 2cw1 chain A Region: 196 - 218 Aligned: 21 Modelled: 23 Confidence: 12.0% Identity: 38% PDB header:de novo protein Chain: A: PDB Molecule:sn4m; PDBTitle: solution structure of the de novo-designed lambda cro fold2 protein Phyre2 PDB 2ka2 chain B Region: 99 - 123 Aligned: 25 Modelled: 25 Confidence: 11.1% 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 PDB 2ka1 chain A Region: 99 - 123 Aligned: 25 Modelled: 25 Confidence: 11.1% 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 2ka1 chain B Region: 99 - 123 Aligned: 25 Modelled: 25 Confidence: 11.1% 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 Phyre2 PDB 2ka2 chain A Region: 99 - 123 Aligned: 25 Modelled: 25 Confidence: 11.1% 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 with his173-ser172 intermonomer3 hydrogen bond restraints Phyre2 PDB 1umq chain A Region: 190 - 222 Aligned: 33 Modelled: 33 Confidence: 10.8% Identity: 9% Fold: DNA/RNA-binding 3-helical bundle Superfamily: Homeodomain-like Family: FIS-like Phyre2 PDB 1umq chain A Region: 190 - 222 Aligned: 33 Modelled: 33 Confidence: 10.8% Identity: 9% 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 1cii chain A Region: 74 - 131 Aligned: 55 Modelled: 58 Confidence: 10.0% Identity: 15% PDB header:transmembrane protein Chain: A: PDB Molecule:colicin ia; PDBTitle: colicin ia Phyre2 PDB 1fip chain A Region: 190 - 222 Aligned: 33 Modelled: 33 Confidence: 8.9% Identity: 12% Fold: DNA/RNA-binding 3-helical bundle Superfamily: Homeodomain-like Family: FIS-like Phyre2 1 d3dhwa1 2 c2onkC_ 3 d2onkc1 4 d3d31c1 5 c3d31D_ 6 d2r6gf2 7 c2r6gF_ 8 c3fh6F_ 9 d2r6gg1 10 c1wz4A_ 11 d1ntca_ 12 c2cw1A_ 13 c2ka2B_ 14 c2ka1A_ 15 c2ka1B_ 16 c2ka2A_ 17 d1umqa_ 18 c1umqA_ 19 c1ciiA_ 20 d1fipa_ 21 22 23 24 25 26 27

Detailed template information

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

1 d3dhwa1 99.9 21 Fold:MetI-like Superfamily:MetI-like Family:MetI-like 2 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 3 d2onkc1 99.9 15 Fold:MetI-like Superfamily:MetI-like Family:MetI-like 4 d3d31c1 99.9 15 Fold:MetI-like Superfamily:MetI-like Family:MetI-like 5 c3d31D_ 99.9 15 PDB header:transport protein Chain: D: PDB Molecule:sulfate/molybdate abc transporter, permease PDBTitle: modbc from methanosarcina acetivorans 6 d2r6gf2 99.8 14 Fold:MetI-like Superfamily:MetI-like Family:MetI-like 7 c2r6gF_ 99.8 13 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_ 99.8 11 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 13 Fold:MetI-like Superfamily:MetI-like Family:MetI-like 10 c1wz4A_ 15.2 29 PDB header:gene regulation Chain: A: PDB Molecule:major surface antigen; PDBTitle: solution conformation of adr subtype hbv pre-s2 epitope 11 d1ntca_ 14.0 15 Fold:DNA/RNA-binding 3-helical bundle Superfamily:Homeodomain-like Family:FIS-like 12 c2cw1A_ 12.0 38 PDB header:de novo protein Chain: A: PDB Molecule:sn4m; PDBTitle: solution structure of the de novo-designed lambda cro fold2 protein 13 c2ka2B_ 11.1 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 14 c2ka1A_ 11.1 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 15 c2ka1B_ 11.1 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 16 c2ka2A_ 11.1 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 17 d1umqa_ 10.8 9 Fold:DNA/RNA-binding 3-helical bundle Superfamily:Homeodomain-like Family:FIS-like 18 c1umqA_ 10.8 9 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 19 c1ciiA_ 10.0 15 PDB header:transmembrane protein Chain: A: PDB Molecule:colicin ia; PDBTitle: colicin ia 20 d1fipa_ 8.9 12 Fold:DNA/RNA-binding 3-helical bundle Superfamily:Homeodomain-like Family:FIS-like 21 d1etob_ not modelled 8.4 12 Fold:DNA/RNA-binding 3-helical bundle Superfamily:Homeodomain-like Family:FIS-like 22 c2j5dA_ not modelled 8.1 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 23 c2jwaA_ not modelled 7.1 13 PDB header:transferase Chain: A: PDB Molecule:receptor tyrosine-protein kinase erbb-2; PDBTitle: erbb2 transmembrane segment dimer spatial structure 24 c3e7lD_ not modelled 6.8 18 PDB header:transcription regulator Chain: D: PDB Molecule:transcriptional regulator (ntrc family); PDBTitle: crystal structure of sigma54 activator ntrc4's dna binding2 domain 25 c2b9sB_ not modelled 5.8 38 PDB header:isomerase/dna Chain: B: PDB Molecule:dna topoisomerase i-like protein; PDBTitle: crystal structure of heterodimeric l. donovani2 topoisomerase i-vanadate-dna complex 26 d1g2ha_ not modelled 5.6 22 Fold:DNA/RNA-binding 3-helical bundle Superfamily:Homeodomain-like Family:FIS-like 27 d2axtk1 not modelled 5.5 10 Fold:Single transmembrane helix Superfamily:Photosystem II reaction center protein K, PsbK Family:PsbK-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