Secondary structure and disorder prediction

		1	.	.	.	.	.	.	.	.	10	.	.	.	.	.	.	.	.	.	20	.	.	.	.	.	.	.	.	.	30	.	.	.	.	.	.	.	.	.	40	.	.	.	.	.	.	.	.	.	50	.	.	.	.	.	.	.	.	.	60
Sequence		M	A	A	T	K	P	A	F	N	P	P	G	K	K	G	D	I	I	F	S	V	L	V	K	L	A	A	L	I	V	L	L	M	L	G	G	I	I	V	S	L	I	I	S	S	W	P	S	I	Q	K	F	G	L	A	F	L	W	T	K
Secondary structure
SS confidence
Disorder		?	?	?	?	?	?	?	?	?	?	?	?																																															?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	70	.	.	.	.	.	.	.	.	.	80	.	.	.	.	.	.	.	.	.	90	.	.	.	.	.	.	.	.	.	100	.	.	.	.	.	.	.	.	.	110	.	.	.	.	.	.	.	.	.	120
Sequence		E	W	D	A	P	N	D	I	Y	G	A	L	V	P	I	Y	G	T	L	V	T	S	F	I	A	L	L	I	A	V	P	V	S	F	G	I	A	L	F	L	T	E	L	A	P	G	W	L	K	R	P	L	G	I	A	I	E	L	L	A
Secondary structure
SS confidence
Disorder		?	?	?	?	?	?	?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	130	.	.	.	.	.	.	.	.	.	140	.	.	.	.	.	.	.	.	.	150	.	.	.	.	.	.	.	.	.	160	.	.	.	.	.	.	.	.	.	170	.	.	.	.	.	.	.	.	.	180
Sequence		A	I	P	S	I	V	Y	G	M	W	G	L	F	I	F	A	P	L	F	A	V	Y	F	Q	E	P	V	G	N	I	M	S	N	I	P	I	V	G	A	L	F	S	G	P	A	F	G	I	G	I	L	A	A	G	V	I	L	A	I	M
Secondary structure
SS confidence
Disorder																																									?		?		?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	190	.	.	.	.	.	.	.	.	.	200	.	.	.	.	.	.	.	.	.	210	.	.	.	.	.	.	.	.	.	220	.	.	.	.	.	.	.	.	.	230	.	.	.	.	.	.	.	.	.	240
Sequence		I	I	P	Y	I	A	A	V	M	R	D	V	F	E	Q	T	P	V	M	M	K	E	S	A	Y	G	I	G	C	T	T	W	E	V	I	W	R	I	V	L	P	F	T	K	N	G	V	I	G	G	I	M	L	G	L	G	R	A	L	G
Secondary structure
SS confidence
Disorder
Disorder confidence
		.	.	.	.	.	.	.	.	.	250	.	.	.	.	.	.	.	.	.	260	.	.	.	.	.	.	.	.	.	270	.	.	.	.	.	.	.	.	.	280	.	.	.	.	.	.	.	.	.	290	.	.	.	.	.	.	.	.	.	300
Sequence		E	T	M	A	V	T	F	I	I	G	N	T	Y	Q	L	D	S	A	S	L	Y	M	P	G	N	S	I	T	S	A	L	A	N	E	F	A	E	A	E	S	G	L	H	V	A	A	L	M	E	L	G	L	I	L	F	V	I	T	F	I
Secondary structure
SS confidence
Disorder												?	?	?	?	?	?	?	?	?	?	?	?	?	?		?
Disorder confidence
		.	.	.	.	.	.	.	.	.	310	.	.	.	.	.	.	.	.	.
Sequence		V	L	A	A	S	K	F	M	I	M	R	L	A	K	N	E	G	A	R
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: 14 - 314 Aligned: 295 Modelled: 301 Confidence: 100.0% Identity: 10% 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: 50 - 304 Aligned: 248 Modelled: 255 Confidence: 100.0% Identity: 11% 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: 59 - 304 Aligned: 239 Modelled: 246 Confidence: 100.0% Identity: 12% Fold: MetI-like Superfamily: MetI-like Family: MetI-like Phyre2 PDB 2onk chain C Region: 16 - 308 Aligned: 249 Modelled: 264 Confidence: 100.0% Identity: 21% 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: 16 - 308 Aligned: 249 Modelled: 264 Confidence: 100.0% Identity: 21% Fold: MetI-like Superfamily: MetI-like Family: MetI-like Phyre2 PDB 3d31 chain C domain 1 Region: 19 - 306 Aligned: 247 Modelled: 252 Confidence: 100.0% Identity: 18% Fold: MetI-like Superfamily: MetI-like Family: MetI-like Phyre2 PDB 3d31 chain D Region: 19 - 306 Aligned: 247 Modelled: 252 Confidence: 100.0% Identity: 18% PDB header:transport protein Chain: D: PDB Molecule:sulfate/molybdate abc transporter, permease PDBTitle: modbc from methanosarcina acetivorans Phyre2 PDB 2r6g chain G domain 1 Region: 10 - 319 Aligned: 276 Modelled: 289 Confidence: 100.0% Identity: 14% Fold: MetI-like Superfamily: MetI-like Family: MetI-like Phyre2 PDB 3dhw chain A domain 1 Region: 71 - 301 Aligned: 192 Modelled: 192 Confidence: 99.9% Identity: 19% Fold: MetI-like Superfamily: MetI-like Family: MetI-like Phyre2 PDB 1ntc chain A Region: 187 - 218 Aligned: 32 Modelled: 32 Confidence: 43.3% Identity: 13% Fold: DNA/RNA-binding 3-helical bundle Superfamily: Homeodomain-like Family: FIS-like Phyre2 PDB 1umq chain A Region: 188 - 218 Aligned: 31 Modelled: 31 Confidence: 42.5% Identity: 10% 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: 188 - 218 Aligned: 31 Modelled: 31 Confidence: 42.5% Identity: 10% Fold: DNA/RNA-binding 3-helical bundle Superfamily: Homeodomain-like Family: FIS-like Phyre2 PDB 1fip chain A Region: 188 - 218 Aligned: 31 Modelled: 31 Confidence: 32.9% Identity: 13% Fold: DNA/RNA-binding 3-helical bundle Superfamily: Homeodomain-like Family: FIS-like Phyre2 PDB 1eto chain B Region: 188 - 218 Aligned: 31 Modelled: 31 Confidence: 25.0% Identity: 13% Fold: DNA/RNA-binding 3-helical bundle Superfamily: Homeodomain-like Family: FIS-like Phyre2 PDB 3e7l chain D Region: 188 - 218 Aligned: 31 Modelled: 31 Confidence: 23.8% Identity: 16% 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: 188 - 218 Aligned: 31 Modelled: 31 Confidence: 22.8% Identity: 13% Fold: DNA/RNA-binding 3-helical bundle Superfamily: Homeodomain-like Family: FIS-like Phyre2 PDB 1g2h chain A Region: 188 - 218 Aligned: 30 Modelled: 31 Confidence: 17.4% Identity: 13% Fold: DNA/RNA-binding 3-helical bundle Superfamily: Homeodomain-like Family: FIS-like Phyre2 PDB 2cw1 chain A Region: 197 - 211 Aligned: 15 Modelled: 15 Confidence: 11.7% Identity: 13% PDB header:de novo protein Chain: A: PDB Molecule:sn4m; PDBTitle: solution structure of the de novo-designed lambda cro fold2 protein Phyre2 PDB 2hx6 chain A Region: 187 - 212 Aligned: 26 Modelled: 26 Confidence: 11.4% Identity: 15% PDB header:hydrolase Chain: A: PDB Molecule:ribonuclease; PDBTitle: solution structure analysis of the phage t42 endoribonuclease regb Phyre2 PDB 2jwa chain A Region: 76 - 109 Aligned: 34 Modelled: 34 Confidence: 7.6% Identity: 9% PDB header:transferase Chain: A: PDB Molecule:receptor tyrosine-protein kinase erbb-2; PDBTitle: erbb2 transmembrane segment dimer spatial structure Phyre2 1 c3fh6F_ 2 c2r6gF_ 3 d2r6gf2 4 c2onkC_ 5 d2onkc1 6 d3d31c1 7 c3d31D_ 8 d2r6gg1 9 d3dhwa1 10 d1ntca_ 11 c1umqA_ 12 d1umqa_ 13 d1fipa_ 14 d1etob_ 15 c3e7lD_ 16 d1etxa_ 17 d1g2ha_ 18 c2cw1A_ 19 c2hx6A_ 20 c2jwaA_ 21 22 23 24 25

Detailed template information

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

1 c3fh6F_ 100.0 10 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 11 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 d2r6gf2 100.0 12 Fold:MetI-like Superfamily:MetI-like Family:MetI-like 4 c2onkC_ 100.0 21 PDB header:membrane protein Chain: C: PDB Molecule:molybdate/tungstate abc transporter, permease PDBTitle: abc transporter modbc in complex with its binding protein2 moda 5 d2onkc1 100.0 21 Fold:MetI-like Superfamily:MetI-like Family:MetI-like 6 d3d31c1 100.0 18 Fold:MetI-like Superfamily:MetI-like Family:MetI-like 7 c3d31D_ 100.0 18 PDB header:transport protein Chain: D: PDB Molecule:sulfate/molybdate abc transporter, permease PDBTitle: modbc from methanosarcina acetivorans 8 d2r6gg1 100.0 14 Fold:MetI-like Superfamily:MetI-like Family:MetI-like 9 d3dhwa1 99.9 19 Fold:MetI-like Superfamily:MetI-like Family:MetI-like 10 d1ntca_ 43.3 13 Fold:DNA/RNA-binding 3-helical bundle Superfamily:Homeodomain-like Family:FIS-like 11 c1umqA_ 42.5 10 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 12 d1umqa_ 42.5 10 Fold:DNA/RNA-binding 3-helical bundle Superfamily:Homeodomain-like Family:FIS-like 13 d1fipa_ 32.9 13 Fold:DNA/RNA-binding 3-helical bundle Superfamily:Homeodomain-like Family:FIS-like 14 d1etob_ 25.0 13 Fold:DNA/RNA-binding 3-helical bundle Superfamily:Homeodomain-like Family:FIS-like 15 c3e7lD_ 23.8 16 PDB header:transcription regulator Chain: D: PDB Molecule:transcriptional regulator (ntrc family); PDBTitle: crystal structure of sigma54 activator ntrc4's dna binding2 domain 16 d1etxa_ 22.8 13 Fold:DNA/RNA-binding 3-helical bundle Superfamily:Homeodomain-like Family:FIS-like 17 d1g2ha_ 17.4 13 Fold:DNA/RNA-binding 3-helical bundle Superfamily:Homeodomain-like Family:FIS-like 18 c2cw1A_ 11.7 13 PDB header:de novo protein Chain: A: PDB Molecule:sn4m; PDBTitle: solution structure of the de novo-designed lambda cro fold2 protein 19 c2hx6A_ 11.4 15 PDB header:hydrolase Chain: A: PDB Molecule:ribonuclease; PDBTitle: solution structure analysis of the phage t42 endoribonuclease regb 20 c2jwaA_ 7.6 9 PDB header:transferase Chain: A: PDB Molecule:receptor tyrosine-protein kinase erbb-2; PDBTitle: erbb2 transmembrane segment dimer spatial structure 21 c1twcF_ not modelled 6.1 21 PDB header:transcription Chain: F: PDB Molecule:dna-directed rna polymerases i, ii, and iii 23 PDBTitle: rna polymerase ii complexed with gtp 22 d1twff_ not modelled 6.1 21 Fold:RPB6/omega subunit-like Superfamily:RPB6/omega subunit-like Family:RPB6 23 c1pyuD_ not modelled 5.9 8 PDB header:lyase Chain: D: PDB Molecule:aspartate 1-decarboxylase alfa chain; PDBTitle: processed aspartate decarboxylase mutant with ser25 mutated to cys 24 c2pmzW_ not modelled 5.9 21 PDB header:translation, transferase Chain: W: PDB Molecule:dna-directed rna polymerase subunit k; PDBTitle: archaeal rna polymerase from sulfolobus solfataricus 25 d1pf4a2 not modelled 5.7 18 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