Secondary structure and disorder prediction

		1	.	.	.	.	.	.	.	.	10	.	.	.	.	.	.	.	.	.	20	.	.	.	.	.	.	.	.	.	30	.	.	.	.	.	.	.	.	.	40	.	.	.	.	.	.	.	.	.	50	.	.	.	.	.	.	.	.	.	60
Sequence		M	A	E	V	T	Q	L	K	R	Y	D	A	R	P	I	N	W	G	K	W	F	L	I	G	I	G	M	L	V	S	A	F	I	L	L	V	P	M	I	Y	I	F	V	Q	A	F	S	K	G	L	M	P	V	L	Q	N	L	A	D	P
Secondary structure
SS confidence
Disorder		?	?	?	?	?	?	?	?	?	?	?	?	?	?	?	?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	70	.	.	.	.	.	.	.	.	.	80	.	.	.	.	.	.	.	.	.	90	.	.	.	.	.	.	.	.	.	100	.	.	.	.	.	.	.	.	.	110	.	.	.	.	.	.	.	.	.	120
Sequence		D	M	L	H	A	I	W	L	T	V	M	I	A	L	I	A	V	P	V	N	L	V	F	G	I	L	L	A	W	L	V	T	R	F	N	F	P	G	R	Q	L	L	L	T	L	L	D	I	P	F	A	V	S	P	V	V	A	G	L	V
Secondary structure
SS confidence
Disorder
Disorder confidence
		.	.	.	.	.	.	.	.	.	130	.	.	.	.	.	.	.	.	.	140	.	.	.	.	.	.	.	.	.	150	.	.	.	.	.	.	.	.	.	160	.	.	.	.	.	.	.	.	.	170	.	.	.	.	.	.	.	.	.	180
Sequence		Y	L	L	F	Y	G	S	N	G	P	L	G	G	W	L	D	E	H	N	L	Q	I	M	F	S	W	P	G	M	V	L	V	T	I	F	V	T	C	P	F	V	V	R	E	L	V	P	V	M	L	S	Q	G	S	Q	E	D	E	A	A
Secondary structure
SS confidence
Disorder																																																				?	?	?		?
Disorder confidence
		.	.	.	.	.	.	.	.	.	190	.	.	.	.	.	.	.	.	.	200	.	.	.	.	.	.	.	.	.	210	.	.	.	.	.	.	.	.	.	220	.	.	.	.	.	.	.	.	.	230	.	.	.	.	.	.	.	.	.	240
Sequence		I	L	L	G	A	S	G	W	Q	M	F	R	R	V	T	L	P	N	I	R	W	A	L	L	Y	G	V	V	L	T	N	A	R	A	I	G	E	F	G	A	V	S	V	V	S	G	S	I	R	G	E	T	L	S	L	P	L	Q	I	E
Secondary structure
SS confidence
Disorder
Disorder confidence
		.	.	.	.	.	.	.	.	.	250	.	.	.	.	.	.	.	.	.	260	.	.	.	.	.	.	.	.	.	270	.	.	.	.	.	.	.	.	.	280	.	.	.	.	.	.	.	.	.	290	.
Sequence		L	L	E	Q	D	Y	N	T	V	G	S	F	T	A	A	A	L	L	T	L	M	A	I	I	T	L	F	L	K	S	M	L	Q	W	R	L	E	N	Q	E	K	R	A	Q	Q	E	E	H	H	E	H
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: 16 - 281 Aligned: 266 Modelled: 266 Confidence: 100.0% Identity: 15% 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 2onk chain C Region: 15 - 272 Aligned: 250 Modelled: 258 Confidence: 100.0% Identity: 24% 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: 15 - 272 Aligned: 250 Modelled: 258 Confidence: 100.0% Identity: 24% Fold: MetI-like Superfamily: MetI-like Family: MetI-like Phyre2 PDB 3d31 chain C domain 1 Region: 21 - 269 Aligned: 244 Modelled: 249 Confidence: 100.0% Identity: 27% Fold: MetI-like Superfamily: MetI-like Family: MetI-like Phyre2 PDB 3d31 chain D Region: 21 - 269 Aligned: 244 Modelled: 249 Confidence: 100.0% Identity: 27% PDB header:transport protein Chain: D: PDB Molecule:sulfate/molybdate abc transporter, permease PDBTitle: modbc from methanosarcina acetivorans Phyre2 PDB 2r6g chain F Region: 49 - 272 Aligned: 224 Modelled: 224 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 G domain 1 Region: 14 - 269 Aligned: 249 Modelled: 256 Confidence: 100.0% Identity: 22% Fold: MetI-like Superfamily: MetI-like Family: MetI-like Phyre2 PDB 2r6g chain F domain 2 Region: 50 - 272 Aligned: 223 Modelled: 223 Confidence: 100.0% Identity: 19% Fold: MetI-like Superfamily: MetI-like Family: MetI-like Phyre2 PDB 3dhw chain A domain 1 Region: 62 - 269 Aligned: 198 Modelled: 208 Confidence: 99.9% Identity: 14% Fold: MetI-like Superfamily: MetI-like Family: MetI-like Phyre2 PDB 2r6g chain F domain 1 Region: 20 - 48 Aligned: 29 Modelled: 29 Confidence: 75.9% Identity: 24% Fold: MalF N-terminal region-like Superfamily: MalF N-terminal region-like Family: MalF N-terminal region-like Phyre2 PDB 1umq chain A Region: 164 - 194 Aligned: 31 Modelled: 31 Confidence: 38.8% Identity: 13% 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: 164 - 194 Aligned: 31 Modelled: 31 Confidence: 38.8% Identity: 13% Fold: DNA/RNA-binding 3-helical bundle Superfamily: Homeodomain-like Family: FIS-like Phyre2 PDB 1ntc chain A Region: 163 - 194 Aligned: 32 Modelled: 32 Confidence: 35.3% Identity: 22% Fold: DNA/RNA-binding 3-helical bundle Superfamily: Homeodomain-like Family: FIS-like Phyre2 PDB 2qks chain A Region: 186 - 291 Aligned: 106 Modelled: 106 Confidence: 31.7% Identity: 8% 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 Phyre2 PDB 1fip chain A Region: 164 - 194 Aligned: 31 Modelled: 31 Confidence: 30.6% Identity: 19% Fold: DNA/RNA-binding 3-helical bundle Superfamily: Homeodomain-like Family: FIS-like Phyre2 PDB 2oar chain A Region: 195 - 290 Aligned: 96 Modelled: 96 Confidence: 27.5% Identity: 10% PDB header:membrane protein Chain: A: PDB Molecule:large-conductance mechanosensitive channel; PDBTitle: mechanosensitive channel of large conductance (mscl) Phyre2 PDB 2oar chain A domain 1 Region: 195 - 290 Aligned: 96 Modelled: 96 Confidence: 26.1% Identity: 10% Fold: Gated mechanosensitive channel Superfamily: Gated mechanosensitive channel Family: Gated mechanosensitive channel Phyre2 PDB 1eto chain B Region: 164 - 194 Aligned: 31 Modelled: 31 Confidence: 25.7% Identity: 19% Fold: DNA/RNA-binding 3-helical bundle Superfamily: Homeodomain-like Family: FIS-like Phyre2 PDB 1etx chain A Region: 164 - 194 Aligned: 31 Modelled: 31 Confidence: 23.6% Identity: 19% Fold: DNA/RNA-binding 3-helical bundle Superfamily: Homeodomain-like Family: FIS-like Phyre2 PDB 1pf4 chain A domain 2 Region: 188 - 291 Aligned: 96 Modelled: 104 Confidence: 19.3% Identity: 14% Fold: ABC transporter transmembrane region Superfamily: ABC transporter transmembrane region Family: ABC transporter transmembrane region Phyre2 1 c3fh6F_ 2 c2onkC_ 3 d2onkc1 4 d3d31c1 5 c3d31D_ 6 c2r6gF_ 7 d2r6gg1 8 d2r6gf2 9 d3dhwa1 10 d2r6gf1 11 c1umqA_ 12 d1umqa_ 13 d1ntca_ 14 c2qksA_ 15 d1fipa_ 16 c2oarA_ 17 d2oara1 18 d1etob_ 19 d1etxa_ 20 d1pf4a2 21 22 23 24 25 26 27 28 29 30 31

Detailed template information

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

1 c3fh6F_ 100.0 15 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 c2onkC_ 100.0 24 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 100.0 24 Fold:MetI-like Superfamily:MetI-like Family:MetI-like 4 d3d31c1 100.0 27 Fold:MetI-like Superfamily:MetI-like Family:MetI-like 5 c3d31D_ 100.0 27 PDB header:transport protein Chain: D: PDB Molecule:sulfate/molybdate abc transporter, permease PDBTitle: modbc from methanosarcina acetivorans 6 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 7 d2r6gg1 100.0 22 Fold:MetI-like Superfamily:MetI-like Family:MetI-like 8 d2r6gf2 100.0 19 Fold:MetI-like Superfamily:MetI-like Family:MetI-like 9 d3dhwa1 99.9 14 Fold:MetI-like Superfamily:MetI-like Family:MetI-like 10 d2r6gf1 75.9 24 Fold:MalF N-terminal region-like Superfamily:MalF N-terminal region-like Family:MalF N-terminal region-like 11 c1umqA_ 38.8 13 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_ 38.8 13 Fold:DNA/RNA-binding 3-helical bundle Superfamily:Homeodomain-like Family:FIS-like 13 d1ntca_ 35.3 22 Fold:DNA/RNA-binding 3-helical bundle Superfamily:Homeodomain-like Family:FIS-like 14 c2qksA_ 31.7 8 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 15 d1fipa_ 30.6 19 Fold:DNA/RNA-binding 3-helical bundle Superfamily:Homeodomain-like Family:FIS-like 16 c2oarA_ 27.5 10 PDB header:membrane protein Chain: A: PDB Molecule:large-conductance mechanosensitive channel; PDBTitle: mechanosensitive channel of large conductance (mscl) 17 d2oara1 26.1 10 Fold:Gated mechanosensitive channel Superfamily:Gated mechanosensitive channel Family:Gated mechanosensitive channel 18 d1etob_ 25.7 19 Fold:DNA/RNA-binding 3-helical bundle Superfamily:Homeodomain-like Family:FIS-like 19 d1etxa_ 23.6 19 Fold:DNA/RNA-binding 3-helical bundle Superfamily:Homeodomain-like Family:FIS-like 20 d1pf4a2 19.3 14 Fold:ABC transporter transmembrane region Superfamily:ABC transporter transmembrane region Family:ABC transporter transmembrane region 21 c3rkoF_ not modelled 18.1 16 PDB header:oxidoreductase Chain: F: PDB Molecule:nadh-quinone oxidoreductase subunit j; PDBTitle: crystal structure of the membrane domain of respiratory complex i from2 e. coli at 3.0 angstrom resolution 22 c2hx6A_ not modelled 16.9 19 PDB header:hydrolase Chain: A: PDB Molecule:ribonuclease; PDBTitle: solution structure analysis of the phage t42 endoribonuclease regb 23 c3e7lD_ not modelled 15.4 9 PDB header:transcription regulator Chain: D: PDB Molecule:transcriptional regulator (ntrc family); PDBTitle: crystal structure of sigma54 activator ntrc4's dna binding2 domain 24 d1g2ha_ not modelled 14.0 17 Fold:DNA/RNA-binding 3-helical bundle Superfamily:Homeodomain-like Family:FIS-like 25 d1fftb2 not modelled 13.8 17 Fold:Transmembrane helix hairpin Superfamily:Cytochrome c oxidase subunit II-like, transmembrane region Family:Cytochrome c oxidase subunit II-like, transmembrane region 26 c2jwaA_ not modelled 12.2 18 PDB header:transferase Chain: A: PDB Molecule:receptor tyrosine-protein kinase erbb-2; PDBTitle: erbb2 transmembrane segment dimer spatial structure 27 c3qnqD_ not modelled 9.0 14 PDB header:membrane protein, transport protein Chain: D: PDB Molecule:pts system, cellobiose-specific iic component; PDBTitle: crystal structure of the transporter chbc, the iic component from the2 n,n'-diacetylchitobiose-specific phosphotransferase system 28 c1p7bB_ not modelled 8.0 7 PDB header:metal transport Chain: B: PDB Molecule:integral membrane channel and cytosolic domains; PDBTitle: crystal structure of an inward rectifier potassium channel 29 c2kncA_ not modelled 6.3 10 PDB header:cell adhesion Chain: A: PDB Molecule:integrin alpha-iib; PDBTitle: platelet integrin alfaiib-beta3 transmembrane-cytoplasmic2 heterocomplex 30 c2cw1A_ not modelled 5.7 33 PDB header:de novo protein Chain: A: PDB Molecule:sn4m; PDBTitle: solution structure of the de novo-designed lambda cro fold2 protein 31 c1ztoA_ not modelled 5.7 33 PDB header:potassium channel Chain: A: PDB Molecule:potassium channel protein rck4; PDBTitle: inactivation gate of potassium channel rck4, nmr, 82 structures

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