Secondary structure and disorder prediction

		1	.	.	.	.	.	.	.	.	10	.	.	.	.	.	.	.	.	.	20	.	.	.	.	.	.	.	.	.	30	.	.	.	.	.	.	.	.	.	40	.	.	.	.	.	.	.	.	.	50	.	.	.	.	.	.	.	.	.	60
Sequence		M	N	R	L	F	S	G	R	S	D	M	P	F	A	L	L	L	L	A	P	S	L	L	L	L	G	G	L	V	A	W	P	M	V	S	N	I	E	I	S	F	L	R	L	P	L	N	P	N	I	E	S	T	F	V	G	V	S	N	Y
Secondary structure
SS confidence
Disorder		?	?	?	?	?	?		?	?																																				?	?	?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	70	.	.	.	.	.	.	.	.	.	80	.	.	.	.	.	.	.	.	.	90	.	.	.	.	.	.	.	.	.	100	.	.	.	.	.	.	.	.	.	110	.	.	.	.	.	.	.	.	.	120
Sequence		V	R	I	L	S	D	P	G	F	W	H	S	L	W	M	T	V	W	Y	T	A	L	V	V	A	G	S	T	V	L	G	L	A	V	A	M	F	F	N	R	E	F	R	L	R	K	T	A	R	S	L	V	I	L	S	Y	V	T	P	S
Secondary structure
SS confidence
Disorder
Disorder confidence
		.	.	.	.	.	.	.	.	.	130	.	.	.	.	.	.	.	.	.	140	.	.	.	.	.	.	.	.	.	150	.	.	.	.	.	.	.	.	.	160	.	.	.	.	.	.	.	.	.	170	.	.	.	.	.	.	.	.	.	180
Sequence		I	S	L	V	F	A	W	K	Y	M	F	N	N	G	Y	G	I	V	N	Y	L	G	V	D	L	L	H	L	Y	E	Q	A	P	L	W	F	D	N	P	G	S	S	F	V	L	V	V	L	F	A	I	W	R	Y	F	P	Y	A	F	I
Secondary structure
SS confidence
Disorder																													?
Disorder confidence
		.	.	.	.	.	.	.	.	.	190	.	.	.	.	.	.	.	.	.	200	.	.	.	.	.	.	.	.	.	210	.	.	.	.	.	.	.	.	.	220	.	.	.	.	.	.	.	.	.	230	.	.	.	.	.	.	.	.	.	240
Sequence		S	F	L	A	I	L	Q	T	I	D	K	S	L	Y	E	A	A	E	M	D	G	A	N	A	W	Q	R	F	R	I	V	T	L	P	A	I	M	P	V	L	A	T	V	V	T	L	R	T	I	W	M	F	Y	M	F	A	D	V	Y	L
Secondary structure
SS confidence
Disorder
Disorder confidence
		.	.	.	.	.	.	.	.	.	250	.	.	.	.	.	.	.	.	.	260	.	.	.	.	.	.	.	.	.	270	.	.	.	.	.	.	.	.	.	280	.	.	.	.	.	.	.	.	.	290	.	.	.
Sequence		L	T	T	K	V	D	I	L	G	V	Y	L	Y	K	T	A	F	A	F	N	D	L	G	K	A	A	A	I	S	V	V	L	F	I	I	I	F	A	V	I	L	L	T	R	K	R	V	N	L	N	G	N	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 3fh6 chain F Region: 9 - 292 Aligned: 281 Modelled: 284 Confidence: 100.0% Identity: 27% 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 F Region: 44 - 282 Aligned: 236 Modelled: 239 Confidence: 100.0% Identity: 29% 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 G domain 1 Region: 9 - 290 Aligned: 264 Modelled: 264 Confidence: 100.0% Identity: 24% Fold: MetI-like Superfamily: MetI-like Family: MetI-like Phyre2 PDB 2onk chain C domain 1 Region: 11 - 288 Aligned: 250 Modelled: 251 Confidence: 100.0% Identity: 18% Fold: MetI-like Superfamily: MetI-like Family: MetI-like Phyre2 PDB 2onk chain C Region: 11 - 288 Aligned: 250 Modelled: 251 Confidence: 100.0% Identity: 18% 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: 57 - 282 Aligned: 223 Modelled: 226 Confidence: 100.0% Identity: 30% Fold: MetI-like Superfamily: MetI-like Family: MetI-like Phyre2 PDB 3d31 chain C domain 1 Region: 15 - 284 Aligned: 245 Modelled: 246 Confidence: 100.0% Identity: 20% Fold: MetI-like Superfamily: MetI-like Family: MetI-like Phyre2 PDB 3d31 chain D Region: 15 - 284 Aligned: 245 Modelled: 246 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 3dhw chain A domain 1 Region: 69 - 282 Aligned: 197 Modelled: 199 Confidence: 99.9% Identity: 18% Fold: MetI-like Superfamily: MetI-like Family: MetI-like Phyre2 PDB 2r6g chain F domain 1 Region: 9 - 69 Aligned: 56 Modelled: 61 Confidence: 95.2% Identity: 20% Fold: MalF N-terminal region-like Superfamily: MalF N-terminal region-like Family: MalF N-terminal region-like Phyre2 PDB 2hx6 chain A Region: 180 - 205 Aligned: 26 Modelled: 26 Confidence: 29.7% Identity: 19% PDB header:hydrolase Chain: A: PDB Molecule:ribonuclease; PDBTitle: solution structure analysis of the phage t42 endoribonuclease regb Phyre2 PDB 1umq chain A Region: 181 - 211 Aligned: 31 Modelled: 31 Confidence: 24.1% 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: 181 - 211 Aligned: 31 Modelled: 31 Confidence: 24.1% Identity: 19% Fold: DNA/RNA-binding 3-helical bundle Superfamily: Homeodomain-like Family: FIS-like Phyre2 PDB 1fip chain A Region: 181 - 211 Aligned: 31 Modelled: 31 Confidence: 22.4% Identity: 19% Fold: DNA/RNA-binding 3-helical bundle Superfamily: Homeodomain-like Family: FIS-like Phyre2 PDB 1eto chain B Region: 181 - 211 Aligned: 31 Modelled: 31 Confidence: 19.0% Identity: 19% Fold: DNA/RNA-binding 3-helical bundle Superfamily: Homeodomain-like Family: FIS-like Phyre2 PDB 1ntc chain A Region: 181 - 211 Aligned: 31 Modelled: 31 Confidence: 18.0% Identity: 19% Fold: DNA/RNA-binding 3-helical bundle Superfamily: Homeodomain-like Family: FIS-like Phyre2 PDB 1etx chain A Region: 181 - 211 Aligned: 31 Modelled: 31 Confidence: 17.6% Identity: 19% Fold: DNA/RNA-binding 3-helical bundle Superfamily: Homeodomain-like Family: FIS-like Phyre2 PDB 1g2h chain A Region: 181 - 211 Aligned: 30 Modelled: 31 Confidence: 17.4% Identity: 10% Fold: DNA/RNA-binding 3-helical bundle Superfamily: Homeodomain-like Family: FIS-like Phyre2 PDB 3e7l chain D Region: 181 - 211 Aligned: 31 Modelled: 31 Confidence: 16.8% Identity: 23% 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 2cw1 chain A Region: 190 - 203 Aligned: 14 Modelled: 14 Confidence: 8.3% Identity: 36% PDB header:de novo protein Chain: A: PDB Molecule:sn4m; PDBTitle: solution structure of the de novo-designed lambda cro fold2 protein Phyre2 1 c3fh6F_ 2 c2r6gF_ 3 d2r6gg1 4 d2onkc1 5 c2onkC_ 6 d2r6gf2 7 d3d31c1 8 c3d31D_ 9 d3dhwa1 10 d2r6gf1 11 c2hx6A_ 12 c1umqA_ 13 d1umqa_ 14 d1fipa_ 15 d1etob_ 16 d1ntca_ 17 d1etxa_ 18 d1g2ha_ 19 c3e7lD_ 20 c2cw1A_ 21 22

Detailed template information

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

1 c3fh6F_ 100.0 27 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 c2r6gF_ 100.0 29 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 3 d2r6gg1 100.0 24 Fold:MetI-like Superfamily:MetI-like Family:MetI-like 4 d2onkc1 100.0 18 Fold:MetI-like Superfamily:MetI-like Family:MetI-like 5 c2onkC_ 100.0 18 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 100.0 30 Fold:MetI-like Superfamily:MetI-like Family:MetI-like 7 d3d31c1 100.0 20 Fold:MetI-like Superfamily:MetI-like Family:MetI-like 8 c3d31D_ 100.0 20 PDB header:transport protein Chain: D: PDB Molecule:sulfate/molybdate abc transporter, permease PDBTitle: modbc from methanosarcina acetivorans 9 d3dhwa1 99.9 18 Fold:MetI-like Superfamily:MetI-like Family:MetI-like 10 d2r6gf1 95.2 20 Fold:MalF N-terminal region-like Superfamily:MalF N-terminal region-like Family:MalF N-terminal region-like 11 c2hx6A_ 29.7 19 PDB header:hydrolase Chain: A: PDB Molecule:ribonuclease; PDBTitle: solution structure analysis of the phage t42 endoribonuclease regb 12 c1umqA_ 24.1 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_ 24.1 19 Fold:DNA/RNA-binding 3-helical bundle Superfamily:Homeodomain-like Family:FIS-like 14 d1fipa_ 22.4 19 Fold:DNA/RNA-binding 3-helical bundle Superfamily:Homeodomain-like Family:FIS-like 15 d1etob_ 19.0 19 Fold:DNA/RNA-binding 3-helical bundle Superfamily:Homeodomain-like Family:FIS-like 16 d1ntca_ 18.0 19 Fold:DNA/RNA-binding 3-helical bundle Superfamily:Homeodomain-like Family:FIS-like 17 d1etxa_ 17.6 19 Fold:DNA/RNA-binding 3-helical bundle Superfamily:Homeodomain-like Family:FIS-like 18 d1g2ha_ 17.4 10 Fold:DNA/RNA-binding 3-helical bundle Superfamily:Homeodomain-like Family:FIS-like 19 c3e7lD_ 16.8 23 PDB header:transcription regulator Chain: D: PDB Molecule:transcriptional regulator (ntrc family); PDBTitle: crystal structure of sigma54 activator ntrc4's dna binding2 domain 20 c2cw1A_ 8.3 36 PDB header:de novo protein Chain: A: PDB Molecule:sn4m; PDBTitle: solution structure of the de novo-designed lambda cro fold2 protein 21 d1cf7a_ not modelled 6.5 24 Fold:DNA/RNA-binding 3-helical bundle Superfamily:"Winged helix" DNA-binding domain Family:Cell cycle transcription factor e2f-dp 22 d1v54g_ not modelled 6.2 21 Fold:Single transmembrane helix Superfamily:Mitochondrial cytochrome c oxidase subunit VIa Family:Mitochondrial cytochrome c oxidase subunit VIa

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