Secondary structure and disorder prediction

		1	.	.	.	.	.	.	.	.	10	.	.	.	.	.	.	.	.	.	20	.	.	.	.	.	.	.	.	.	30	.	.	.	.	.	.	.	.	.	40	.	.	.	.	.	.	.	.	.	50	.	.	.	.	.	.	.	.	.	60
Sequence		M	N	N	L	P	V	V	R	S	P	W	R	I	V	I	L	L	L	G	F	T	F	L	Y	A	P	M	L	M	L	V	I	Y	S	F	N	S	S	K	L	V	T	V	W	A	G	W	S	T	R	W	Y	G	E	L	L	R	D	D	A
Secondary structure
SS confidence
Disorder		?	?	?	?	?	?	?	?																														?	?	?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	70	.	.	.	.	.	.	.	.	.	80	.	.	.	.	.	.	.	.	.	90	.	.	.	.	.	.	.	.	.	100	.	.	.	.	.	.	.	.	.	110	.	.	.	.	.	.	.	.	.	120
Sequence		M	M	S	A	V	G	L	S	L	T	I	A	A	C	A	A	T	A	A	A	I	L	G	T	I	A	A	V	V	L	V	R	F	G	R	F	R	G	S	N	G	F	A	F	M	I	T	A	P	L	V	M	P	D	V	I	T	G	L	S
Secondary structure
SS confidence
Disorder																																																						?
Disorder confidence
		.	.	.	.	.	.	.	.	.	130	.	.	.	.	.	.	.	.	.	140	.	.	.	.	.	.	.	.	.	150	.	.	.	.	.	.	.	.	.	160	.	.	.	.	.	.	.	.	.	170	.	.	.	.	.	.	.	.	.	180
Sequence		L	L	L	L	F	V	A	L	A	H	A	I	G	W	P	A	D	R	G	M	L	T	I	W	L	A	H	V	T	F	C	T	A	Y	V	A	V	V	I	S	S	R	L	R	E	L	D	R	S	I	E	E	A	A	M	D	L	G	A	T
Secondary structure
SS confidence
Disorder									?	?	?	?	?	?	?	?	?	?	?																										?
Disorder confidence
		.	.	.	.	.	.	.	.	.	190	.	.	.	.	.	.	.	.	.	200	.	.	.	.	.	.	.	.	.	210	.	.	.	.	.	.	.	.	.	220	.	.	.	.	.	.	.	.	.	230	.	.	.	.	.	.	.	.	.	240
Sequence		P	L	K	V	F	F	V	I	T	L	P	M	I	M	P	A	I	I	S	G	W	L	L	A	F	T	L	S	L	D	D	L	V	I	A	S	F	V	S	G	P	G	A	T	T	L	P	M	L	V	F	S	S	V	R	M	G	V	N	P
Secondary structure
SS confidence
Disorder																																												?												?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	250	.	.	.	.	.	.	.	.	.	260	.	.	.	.	.	.	.	.	.	270	.	.	.	.	.	.	.	.	.	280	.
Sequence		E	I	N	A	L	A	T	L	I	L	G	A	V	G	I	V	G	F	I	A	W	Y	L	M	A	R	A	E	K	Q	R	I	R	D	I	Q	R	A	R	R	G
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 3fh6 chain F Region: 4 - 269 Aligned: 266 Modelled: 265 Confidence: 100.0% Identity: 18% 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: 3 - 266 Aligned: 262 Modelled: 264 Confidence: 100.0% Identity: 21% Fold: MetI-like Superfamily: MetI-like Family: MetI-like Phyre2 PDB 2onk chain C Region: 9 - 264 Aligned: 243 Modelled: 256 Confidence: 100.0% Identity: 19% 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: 9 - 264 Aligned: 243 Modelled: 256 Confidence: 100.0% Identity: 19% Fold: MetI-like Superfamily: MetI-like Family: MetI-like Phyre2 PDB 3d31 chain C domain 1 Region: 11 - 261 Aligned: 239 Modelled: 251 Confidence: 100.0% Identity: 20% Fold: MetI-like Superfamily: MetI-like Family: MetI-like Phyre2 PDB 3d31 chain D Region: 11 - 261 Aligned: 239 Modelled: 251 Confidence: 100.0% Identity: 20% PDB header:transport protein Chain: D: PDB Molecule:sulfate/molybdate abc transporter, permease PDBTitle: modbc from methanosarcina acetivorans Phyre2 PDB 2r6g chain F Region: 42 - 259 Aligned: 217 Modelled: 218 Confidence: 100.0% Identity: 20% 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 2r6g chain F domain 2 Region: 49 - 259 Aligned: 210 Modelled: 210 Confidence: 100.0% Identity: 21% Fold: MetI-like Superfamily: MetI-like Family: MetI-like Phyre2 PDB 3dhw chain A domain 1 Region: 61 - 260 Aligned: 197 Modelled: 200 Confidence: 99.9% Identity: 15% Fold: MetI-like Superfamily: MetI-like Family: MetI-like Phyre2 PDB 2r6g chain F domain 1 Region: 4 - 45 Aligned: 42 Modelled: 42 Confidence: 87.7% Identity: 10% Fold: MalF N-terminal region-like Superfamily: MalF N-terminal region-like Family: MalF N-terminal region-like Phyre2 PDB 1ntc chain A Region: 158 - 188 Aligned: 31 Modelled: 31 Confidence: 48.8% Identity: 23% Fold: DNA/RNA-binding 3-helical bundle Superfamily: Homeodomain-like Family: FIS-like Phyre2 PDB 1umq chain A Region: 158 - 188 Aligned: 31 Modelled: 31 Confidence: 46.3% Identity: 19% Fold: DNA/RNA-binding 3-helical bundle Superfamily: Homeodomain-like Family: FIS-like Phyre2 PDB 1umq chain A Region: 158 - 188 Aligned: 31 Modelled: 31 Confidence: 46.3% 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 1fip chain A Region: 158 - 188 Aligned: 31 Modelled: 31 Confidence: 37.2% Identity: 10% Fold: DNA/RNA-binding 3-helical bundle Superfamily: Homeodomain-like Family: FIS-like Phyre2 PDB 1eto chain B Region: 158 - 188 Aligned: 31 Modelled: 31 Confidence: 34.2% Identity: 10% Fold: DNA/RNA-binding 3-helical bundle Superfamily: Homeodomain-like Family: FIS-like Phyre2 PDB 3e7l chain D Region: 158 - 188 Aligned: 31 Modelled: 31 Confidence: 30.9% Identity: 26% 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 1etx chain A Region: 158 - 188 Aligned: 31 Modelled: 31 Confidence: 26.0% Identity: 10% Fold: DNA/RNA-binding 3-helical bundle Superfamily: Homeodomain-like Family: FIS-like Phyre2 PDB 1bct chain A Region: 5 - 31 Aligned: 27 Modelled: 27 Confidence: 22.7% Identity: 19% PDB header:photoreceptor Chain: A: PDB Molecule:bacteriorhodopsin; PDBTitle: three-dimensional structure of proteolytic fragment 163-2312 of bacterioopsin determined from nuclear magnetic3 resonance data in solution Phyre2 PDB 1g2h chain A Region: 158 - 188 Aligned: 30 Modelled: 31 Confidence: 18.6% Identity: 20% Fold: DNA/RNA-binding 3-helical bundle Superfamily: Homeodomain-like Family: FIS-like Phyre2 PDB 1etf chain B Region: 265 - 279 Aligned: 15 Modelled: 15 Confidence: 15.6% Identity: 40% PDB header:viral protein/rna Chain: B: PDB Molecule:rev peptide; PDBTitle: rev response element (rre) rna complexed with rev peptide,2 nmr, minimized average structure Phyre2 1 c3fh6F_ 2 d2r6gg1 3 c2onkC_ 4 d2onkc1 5 d3d31c1 6 c3d31D_ 7 c2r6gF_ 8 d2r6gf2 9 d3dhwa1 10 d2r6gf1 11 d1ntca_ 12 d1umqa_ 13 c1umqA_ 14 d1fipa_ 15 d1etob_ 16 c3e7lD_ 17 d1etxa_ 18 c1bctA_ 19 d1g2ha_ 20 c1etfB_ 21 22 23 24 25 26 27 28 29

Detailed template information

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

1 c3fh6F_ 100.0 18 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 2 d2r6gg1 100.0 21 Fold:MetI-like Superfamily:MetI-like Family:MetI-like 3 c2onkC_ 100.0 19 PDB header:membrane protein Chain: C: PDB Molecule:molybdate/tungstate abc transporter, permease PDBTitle: abc transporter modbc in complex with its binding protein2 moda 4 d2onkc1 100.0 19 Fold:MetI-like Superfamily:MetI-like Family:MetI-like 5 d3d31c1 100.0 20 Fold:MetI-like Superfamily:MetI-like Family:MetI-like 6 c3d31D_ 100.0 20 PDB header:transport protein Chain: D: PDB Molecule:sulfate/molybdate abc transporter, permease PDBTitle: modbc from methanosarcina acetivorans 7 c2r6gF_ 100.0 20 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 d2r6gf2 100.0 21 Fold:MetI-like Superfamily:MetI-like Family:MetI-like 9 d3dhwa1 99.9 15 Fold:MetI-like Superfamily:MetI-like Family:MetI-like 10 d2r6gf1 87.7 10 Fold:MalF N-terminal region-like Superfamily:MalF N-terminal region-like Family:MalF N-terminal region-like 11 d1ntca_ 48.8 23 Fold:DNA/RNA-binding 3-helical bundle Superfamily:Homeodomain-like Family:FIS-like 12 d1umqa_ 46.3 19 Fold:DNA/RNA-binding 3-helical bundle Superfamily:Homeodomain-like Family:FIS-like 13 c1umqA_ 46.3 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 14 d1fipa_ 37.2 10 Fold:DNA/RNA-binding 3-helical bundle Superfamily:Homeodomain-like Family:FIS-like 15 d1etob_ 34.2 10 Fold:DNA/RNA-binding 3-helical bundle Superfamily:Homeodomain-like Family:FIS-like 16 c3e7lD_ 30.9 26 PDB header:transcription regulator Chain: D: PDB Molecule:transcriptional regulator (ntrc family); PDBTitle: crystal structure of sigma54 activator ntrc4's dna binding2 domain 17 d1etxa_ 26.0 10 Fold:DNA/RNA-binding 3-helical bundle Superfamily:Homeodomain-like Family:FIS-like 18 c1bctA_ 22.7 19 PDB header:photoreceptor Chain: A: PDB Molecule:bacteriorhodopsin; PDBTitle: three-dimensional structure of proteolytic fragment 163-2312 of bacterioopsin determined from nuclear magnetic3 resonance data in solution 19 d1g2ha_ 18.6 20 Fold:DNA/RNA-binding 3-helical bundle Superfamily:Homeodomain-like Family:FIS-like 20 c1etfB_ 15.6 40 PDB header:viral protein/rna Chain: B: PDB Molecule:rev peptide; PDBTitle: rev response element (rre) rna complexed with rev peptide,2 nmr, minimized average structure 21 c1etgB_ not modelled 15.6 40 PDB header:viral protein/rna Chain: B: PDB Molecule:rev peptide; PDBTitle: rev response element (rre) rna complexed with rev peptide,2 nmr, 19 structures 22 c2hx6A_ not modelled 13.6 23 PDB header:hydrolase Chain: A: PDB Molecule:ribonuclease; PDBTitle: solution structure analysis of the phage t42 endoribonuclease regb 23 c2x7lP_ not modelled 7.7 36 PDB header:immune system Chain: P: PDB Molecule:hiv rev; PDBTitle: implications of the hiv-1 rev dimer structure at 3.2a2 resolution for multimeric binding to the rev response3 element 24 c2jwaA_ not modelled 6.0 15 PDB header:transferase Chain: A: PDB Molecule:receptor tyrosine-protein kinase erbb-2; PDBTitle: erbb2 transmembrane segment dimer spatial structure 25 d1cf7a_ not modelled 5.9 24 Fold:DNA/RNA-binding 3-helical bundle Superfamily:"Winged helix" DNA-binding domain Family:Cell cycle transcription factor e2f-dp 26 c3lphD_ not modelled 5.8 33 PDB header:viral protein Chain: D: PDB Molecule:protein rev; PDBTitle: crystal structure of the hiv-1 rev dimer 27 c2qksA_ not modelled 5.6 11 PDB header:metal transport Chain: A: PDB Molecule:kir3.1-prokaryotic kir channel chimera; PDBTitle: crystal structure of a kir3.1-prokaryotic kir channel chimera 28 c2kluA_ not modelled 5.5 22 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 29 d1pf4a2 not modelled 5.3 6 Fold:ABC transporter transmembrane region Superfamily:ABC transporter transmembrane region Family:ABC transporter transmembrane region

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