Secondary structure and disorder prediction

		1	.	.	.	.	.	.	.	.	10	.	.	.	.	.	.	.	.	.	20	.	.	.	.	.	.	.	.	.	30	.	.	.	.	.	.	.	.	.	40	.	.	.	.	.	.	.	.	.	50	.	.	.	.	.	.	.	.	.	60
Sequence		M	A	D	Q	N	N	P	W	D	T	T	P	A	A	D	S	A	A	Q	S	A	D	A	W	G	T	P	T	T	A	P	T	D	G	G	G	A	D	W	L	T	S	T	P	A	P	N	V	E	H	F	N	I	L	D	P	F	H	K	T
Secondary structure
SS confidence
Disorder		?	?	?	?	?	?	?	?	?	?	?	?	?	?	?	?	?	?	?	?	?	?	?	?	?	?	?	?	?	?	?	?	?												?	?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	70	.	.	.	.	.	.	.	.	.	80	.	.	.	.	.	.	.	.	.	90	.	.	.	.	.	.	.	.	.	100	.	.	.	.	.	.	.	.	.	110	.	.	.	.	.	.	.	.	.	120
Sequence		L	I	P	L	D	S	W	V	T	E	G	I	D	W	V	V	T	H	F	R	P	V	F	Q	G	V	R	V	P	V	D	Y	I	L	N	G	F	Q	Q	L	L	L	G	M	P	A	P	V	A	I	I	V	F	A	L	I	A	W	Q	I
Secondary structure
SS confidence
Disorder		?
Disorder confidence
		.	.	.	.	.	.	.	.	.	130	.	.	.	.	.	.	.	.	.	140	.	.	.	.	.	.	.	.	.	150	.	.	.	.	.	.	.	.	.	160	.	.	.	.	.	.	.	.	.	170	.	.	.	.	.	.	.	.	.	180
Sequence		S	G	V	G	M	G	V	A	T	L	V	S	L	I	A	I	G	A	I	G	A	W	S	Q	A	M	V	T	L	A	L	V	L	T	A	L	L	F	C	I	V	I	G	L	P	L	G	I	W	L	A	R	S	P	R	A	A	K	I	I
Secondary structure
SS confidence
Disorder			?	?	?	?	?	?	?	?	?						?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	190	.	.	.	.	.	.	.	.	.	200	.	.	.	.	.	.	.	.	.	210	.	.	.	.	.	.	.	.	.	220	.	.	.	.	.	.	.	.	.	230	.	.	.	.	.	.	.	.	.	240
Sequence		R	P	L	L	D	A	M	Q	T	T	P	A	F	V	Y	L	V	P	I	V	M	L	F	G	I	G	N	V	P	G	V	V	V	T	I	I	F	A	L	P	P	I	I	R	L	T	I	L	G	I	N	Q	V	P	A	D	L	I	E	A
Secondary structure
SS confidence
Disorder
Disorder confidence
		.	.	.	.	.	.	.	.	.	250	.	.	.	.	.	.	.	.	.	260	.	.	.	.	.	.	.	.	.	270	.	.	.	.	.	.	.	.	.	280	.	.	.	.	.	.	.	.	.	290	.	.	.	.	.	.	.	.	.	300
Sequence		S	R	S	F	G	A	S	P	R	Q	M	L	F	K	V	Q	L	P	L	A	M	P	T	I	M	A	G	V	N	Q	T	L	M	L	A	L	S	M	V	V	I	A	S	M	I	A	V	G	G	L	G	Q	M	V	L	R	G	I	G	R
Secondary structure
SS confidence
Disorder
Disorder confidence
		.	.	.	.	.	.	.	.	.	310	.	.	.	.	.	.	.	.	.	320	.	.	.	.	.	.	.	.	.	330	.	.	.	.	.	.	.	.	.	340	.	.	.	.	.	.	.	.	.	350	.	.	.	.
Sequence		L	D	M	G	L	A	T	V	G	G	V	G	I	V	I	L	A	I	I	L	D	R	L	T	Q	A	V	G	R	D	S	R	S	R	G	N	R	R	W	Y	T	T	G	P	V	G	L	L	T	R	P	F	I	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 2onk chain C Region: 94 - 327 Aligned: 233 Modelled: 234 Confidence: 99.9% 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: 94 - 327 Aligned: 233 Modelled: 234 Confidence: 99.9% Identity: 19% Fold: MetI-like Superfamily: MetI-like Family: MetI-like Phyre2 PDB 3d31 chain D Region: 105 - 325 Aligned: 221 Modelled: 221 Confidence: 99.9% Identity: 20% PDB header:transport protein Chain: D: PDB Molecule:sulfate/molybdate abc transporter, permease PDBTitle: modbc from methanosarcina acetivorans Phyre2 PDB 3d31 chain C domain 1 Region: 105 - 325 Aligned: 221 Modelled: 221 Confidence: 99.9% Identity: 20% Fold: MetI-like Superfamily: MetI-like Family: MetI-like Phyre2 PDB 3dhw chain A domain 1 Region: 141 - 323 Aligned: 183 Modelled: 183 Confidence: 99.9% Identity: 27% Fold: MetI-like Superfamily: MetI-like Family: MetI-like Phyre2 PDB 2r6g chain F Region: 140 - 323 Aligned: 184 Modelled: 184 Confidence: 99.9% Identity: 25% 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: 140 - 323 Aligned: 184 Modelled: 184 Confidence: 99.9% Identity: 24% Fold: MetI-like Superfamily: MetI-like Family: MetI-like Phyre2 PDB 3fh6 chain F Region: 140 - 333 Aligned: 194 Modelled: 194 Confidence: 99.9% Identity: 24% 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: 140 - 338 Aligned: 199 Modelled: 199 Confidence: 99.8% Identity: 19% Fold: MetI-like Superfamily: MetI-like Family: MetI-like Phyre2 PDB 1ntc chain A Region: 224 - 255 Aligned: 32 Modelled: 32 Confidence: 36.5% Identity: 19% Fold: DNA/RNA-binding 3-helical bundle Superfamily: Homeodomain-like Family: FIS-like Phyre2 PDB 1umq chain A Region: 225 - 255 Aligned: 31 Modelled: 31 Confidence: 29.5% Identity: 10% Fold: DNA/RNA-binding 3-helical bundle Superfamily: Homeodomain-like Family: FIS-like Phyre2 PDB 1umq chain A Region: 225 - 255 Aligned: 31 Modelled: 31 Confidence: 29.5% 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 1fip chain A Region: 225 - 255 Aligned: 31 Modelled: 31 Confidence: 18.6% Identity: 13% Fold: DNA/RNA-binding 3-helical bundle Superfamily: Homeodomain-like Family: FIS-like Phyre2 PDB 2gqb chain A domain 1 Region: 2 - 57 Aligned: 56 Modelled: 56 Confidence: 17.7% Identity: 11% Fold: RPA2825-like Superfamily: RPA2825-like Family: RPA2825-like Phyre2 PDB 1eto chain B Region: 225 - 255 Aligned: 31 Modelled: 31 Confidence: 17.2% Identity: 13% Fold: DNA/RNA-binding 3-helical bundle Superfamily: Homeodomain-like Family: FIS-like Phyre2 PDB 3e7l chain D Region: 224 - 255 Aligned: 32 Modelled: 32 Confidence: 15.6% Identity: 13% 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: 225 - 255 Aligned: 31 Modelled: 31 Confidence: 14.7% Identity: 13% Fold: DNA/RNA-binding 3-helical bundle Superfamily: Homeodomain-like Family: FIS-like Phyre2 PDB 3hzq chain A Region: 256 - 334 Aligned: 79 Modelled: 79 Confidence: 12.6% Identity: 16% PDB header:membrane protein Chain: A: PDB Molecule:large-conductance mechanosensitive channel; PDBTitle: structure of a tetrameric mscl in an expanded intermediate2 state Phyre2 PDB 3bjr chain A Region: 58 - 78 Aligned: 21 Modelled: 21 Confidence: 11.4% Identity: 19% PDB header:hydrolase Chain: A: PDB Molecule:putative carboxylesterase; PDBTitle: crystal structure of a putative carboxylesterase (lp_1002) from2 lactobacillus plantarum wcfs1 at 2.09 a resolution Phyre2 PDB 3a0b chain K Region: 172 - 201 Aligned: 30 Modelled: 30 Confidence: 9.8% Identity: 27% PDB header:electron transport Chain: K: PDB Molecule:photosystem ii reaction center protein k; PDBTitle: crystal structure of br-substituted photosystem ii complex Phyre2 1 c2onkC_ 2 d2onkc1 3 c3d31D_ 4 d3d31c1 5 d3dhwa1 6 c2r6gF_ 7 d2r6gf2 8 c3fh6F_ 9 d2r6gg1 10 d1ntca_ 11 d1umqa_ 12 c1umqA_ 13 d1fipa_ 14 d2gqba1 15 d1etob_ 16 c3e7lD_ 17 d1etxa_ 18 c3hzqA_ 19 c3bjrA_ 20 c3a0bk_ 21 22 23 24 25 26 27 28 29 30 31 32 33 34

Detailed template information

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

1 c2onkC_ 99.9 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 2 d2onkc1 99.9 19 Fold:MetI-like Superfamily:MetI-like Family:MetI-like 3 c3d31D_ 99.9 20 PDB header:transport protein Chain: D: PDB Molecule:sulfate/molybdate abc transporter, permease PDBTitle: modbc from methanosarcina acetivorans 4 d3d31c1 99.9 20 Fold:MetI-like Superfamily:MetI-like Family:MetI-like 5 d3dhwa1 99.9 27 Fold:MetI-like Superfamily:MetI-like Family:MetI-like 6 c2r6gF_ 99.9 25 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 d2r6gf2 99.9 24 Fold:MetI-like Superfamily:MetI-like Family:MetI-like 8 c3fh6F_ 99.9 24 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 99.8 19 Fold:MetI-like Superfamily:MetI-like Family:MetI-like 10 d1ntca_ 36.5 19 Fold:DNA/RNA-binding 3-helical bundle Superfamily:Homeodomain-like Family:FIS-like 11 d1umqa_ 29.5 10 Fold:DNA/RNA-binding 3-helical bundle Superfamily:Homeodomain-like Family:FIS-like 12 c1umqA_ 29.5 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 13 d1fipa_ 18.6 13 Fold:DNA/RNA-binding 3-helical bundle Superfamily:Homeodomain-like Family:FIS-like 14 d2gqba1 17.7 11 Fold:RPA2825-like Superfamily:RPA2825-like Family:RPA2825-like 15 d1etob_ 17.2 13 Fold:DNA/RNA-binding 3-helical bundle Superfamily:Homeodomain-like Family:FIS-like 16 c3e7lD_ 15.6 13 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_ 14.7 13 Fold:DNA/RNA-binding 3-helical bundle Superfamily:Homeodomain-like Family:FIS-like 18 c3hzqA_ 12.6 16 PDB header:membrane protein Chain: A: PDB Molecule:large-conductance mechanosensitive channel; PDBTitle: structure of a tetrameric mscl in an expanded intermediate2 state 19 c3bjrA_ 11.4 19 PDB header:hydrolase Chain: A: PDB Molecule:putative carboxylesterase; PDBTitle: crystal structure of a putative carboxylesterase (lp_1002) from2 lactobacillus plantarum wcfs1 at 2.09 a resolution 20 c3a0bk_ 9.8 27 PDB header:electron transport Chain: K: PDB Molecule:photosystem ii reaction center protein k; PDBTitle: crystal structure of br-substituted photosystem ii complex 21 c3a0bK_ not modelled 9.8 27 PDB header:electron transport Chain: K: PDB Molecule:photosystem ii reaction center protein k; PDBTitle: crystal structure of br-substituted photosystem ii complex 22 c2jwaA_ not modelled 9.6 21 PDB header:transferase Chain: A: PDB Molecule:receptor tyrosine-protein kinase erbb-2; PDBTitle: erbb2 transmembrane segment dimer spatial structure 23 d1g2ha_ not modelled 9.3 17 Fold:DNA/RNA-binding 3-helical bundle Superfamily:Homeodomain-like Family:FIS-like 24 c3k3gA_ not modelled 8.7 14 PDB header:transport protein Chain: A: PDB Molecule:urea transporter; PDBTitle: crystal structure of the urea transporter from desulfovibrio vulgaris2 bound to 1,3-dimethylurea 25 c3a0hk_ not modelled 8.4 27 PDB header:electron transport Chain: K: PDB Molecule:photosystem ii reaction center protein k; PDBTitle: crystal structure of i-substituted photosystem ii complex 26 d2axtk1 not modelled 6.6 25 Fold:Single transmembrane helix Superfamily:Photosystem II reaction center protein K, PsbK Family:PsbK-like 27 c2ka1B_ not modelled 6.5 32 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 28 c2ka1A_ not modelled 6.5 32 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 29 c2ka2A_ not modelled 6.5 32 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 30 c2ka2B_ not modelled 6.5 32 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 31 c2x7lP_ not modelled 6.2 33 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 32 d1iwga8 not modelled 5.9 14 Fold:Multidrug efflux transporter AcrB transmembrane domain Superfamily:Multidrug efflux transporter AcrB transmembrane domain Family:Multidrug efflux transporter AcrB transmembrane domain 33 c1p58C_ not modelled 5.6 16 PDB header:virus Chain: C: PDB Molecule:major envelope protein e; PDBTitle: complex organization of dengue virus membrane proteins as revealed by2 9.5 angstrom cryo-em reconstruction 34 c2j5dA_ not modelled 5.4 32 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

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