Secondary structure and disorder prediction

		1	.	.	.	.	.	.	.	.	10	.	.	.	.	.	.	.	.	.	20	.	.	.	.	.	.	.	.	.	30	.	.	.	.	.	.	.	.	.	40	.	.	.	.	.	.	.	.	.	50	.	.	.	.	.	.	.	.	.	60
Sequence		M	S	R	L	S	P	V	N	Q	A	R	W	A	R	F	R	H	N	R	R	G	Y	W	S	L	W	I	F	L	V	L	F	G	L	S	L	C	S	E	L	I	A	N	D	K	P	L	L	V	R	Y	D	G	S	W	Y	F	P	L	L
Secondary structure
SS confidence
Disorder		?	?	?	?	?	?	?																																									?
Disorder confidence
		.	.	.	.	.	.	.	.	.	70	.	.	.	.	.	.	.	.	.	80	.	.	.	.	.	.	.	.	.	90	.	.	.	.	.	.	.	.	.	100	.	.	.	.	.	.	.	.	.	110	.	.	.	.	.	.	.	.	.	120
Sequence		K	N	Y	S	E	S	D	F	G	G	P	L	A	S	Q	A	D	Y	Q	D	P	W	L	K	Q	R	L	E	N	N	G	W	V	L	W	A	P	I	R	F	G	A	T	S	I	N	F	A	T	N	K	P	F	P	S	P	P	S	R	Q
Secondary structure
SS confidence
Disorder																			?	?	?	?					?	?	?	?	?																	?	?	?	?	?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	130	.	.	.	.	.	.	.	.	.	140	.	.	.	.	.	.	.	.	.	150	.	.	.	.	.	.	.	.	.	160	.	.	.	.	.	.	.	.	.	170	.	.	.	.	.	.	.	.	.	180
Sequence		N	W	L	G	T	D	A	N	G	G	D	V	L	A	R	I	L	Y	G	T	R	I	S	V	L	F	G	L	M	L	T	L	C	S	S	V	M	G	V	L	A	G	A	L	Q	G	Y	Y	G	G	K	V	D	L	W	G	Q	R	F	I
Secondary structure
SS confidence
Disorder
Disorder confidence
		.	.	.	.	.	.	.	.	.	190	.	.	.	.	.	.	.	.	.	200	.	.	.	.	.	.	.	.	.	210	.	.	.	.	.	.	.	.	.	220	.	.	.	.	.	.	.	.	.	230	.	.	.	.	.	.	.	.	.	240
Sequence		E	V	W	S	G	M	P	T	L	F	L	I	I	L	L	S	S	V	V	Q	P	N	F	W	W	L	L	A	I	T	V	L	F	G	W	M	S	L	V	G	V	V	R	A	E	F	L	R	T	R	N	F	D	Y	I	R	A	A	Q	A
Secondary structure
SS confidence
Disorder																																																				?
Disorder confidence
		.	.	.	.	.	.	.	.	.	250	.	.	.	.	.	.	.	.	.	260	.	.	.	.	.	.	.	.	.	270	.	.	.	.	.	.	.	.	.	280	.	.	.	.	.	.	.	.	.	290	.	.	.	.	.	.	.	.	.	300
Sequence		L	G	V	S	D	R	S	I	I	L	R	H	M	L	P	N	A	M	V	A	T	L	T	F	L	P	F	I	L	C	S	S	I	T	T	L	T	S	L	D	F	L	G	F	G	L	P	L	G	S	P	S	L	G	E	L	L	L	Q	G
Secondary structure
SS confidence
Disorder																															?
Disorder confidence
		.	.	.	.	.	.	.	.	.	310	.	.	.	.	.	.	.	.	.	320	.	.	.	.	.	.	.	.	.	330	.	.	.	.	.	.	.	.	.	340	.
Sequence		K	N	N	L	Q	A	P	W	L	G	I	T	A	F	L	S	V	A	I	L	L	S	L	L	I	F	I	G	E	A	V	R	D	A	F	D	P	N	K	A	V
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 3dhw chain A domain 1 Region: 136 - 329 Aligned: 187 Modelled: 194 Confidence: 99.9% Identity: 18% Fold: MetI-like Superfamily: MetI-like Family: MetI-like Phyre2 PDB 2onk chain C Region: 134 - 331 Aligned: 192 Modelled: 198 Confidence: 99.8% Identity: 9% 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: 134 - 331 Aligned: 192 Modelled: 198 Confidence: 99.8% Identity: 9% Fold: MetI-like Superfamily: MetI-like Family: MetI-like Phyre2 PDB 3d31 chain D Region: 134 - 327 Aligned: 189 Modelled: 193 Confidence: 99.8% Identity: 16% 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: 134 - 327 Aligned: 189 Modelled: 193 Confidence: 99.8% Identity: 16% Fold: MetI-like Superfamily: MetI-like Family: MetI-like Phyre2 PDB 2r6g chain F domain 2 Region: 118 - 331 Aligned: 208 Modelled: 214 Confidence: 99.7% Identity: 13% Fold: MetI-like Superfamily: MetI-like Family: MetI-like Phyre2 PDB 2r6g chain F Region: 136 - 327 Aligned: 191 Modelled: 192 Confidence: 99.6% Identity: 14% 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 3fh6 chain F Region: 131 - 340 Aligned: 208 Modelled: 210 Confidence: 99.6% Identity: 13% 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: 16 - 329 Aligned: 258 Modelled: 260 Confidence: 99.5% Identity: 14% Fold: MetI-like Superfamily: MetI-like Family: MetI-like Phyre2 PDB 2cw1 chain A Region: 225 - 248 Aligned: 22 Modelled: 24 Confidence: 20.0% Identity: 45% PDB header:de novo protein Chain: A: PDB Molecule:sn4m; PDBTitle: solution structure of the de novo-designed lambda cro fold2 protein Phyre2 PDB 2jwa chain A Region: 142 - 172 Aligned: 31 Modelled: 31 Confidence: 12.0% Identity: 26% PDB header:transferase Chain: A: PDB Molecule:receptor tyrosine-protein kinase erbb-2; PDBTitle: erbb2 transmembrane segment dimer spatial structure Phyre2 PDB 2axt chain K domain 1 Region: 175 - 203 Aligned: 29 Modelled: 29 Confidence: 9.5% Identity: 21% Fold: Single transmembrane helix Superfamily: Photosystem II reaction center protein K, PsbK Family: PsbK-like Phyre2 PDB 3a0b chain K Region: 175 - 203 Aligned: 29 Modelled: 29 Confidence: 8.8% Identity: 17% PDB header:electron transport Chain: K: PDB Molecule:photosystem ii reaction center protein k; PDBTitle: crystal structure of br-substituted photosystem ii complex Phyre2 PDB 3a0b chain K Region: 175 - 203 Aligned: 29 Modelled: 29 Confidence: 8.8% Identity: 17% PDB header:electron transport Chain: K: PDB Molecule:photosystem ii reaction center protein k; PDBTitle: crystal structure of br-substituted photosystem ii complex Phyre2 PDB 1wz4 chain A Region: 332 - 340 Aligned: 9 Modelled: 9 Confidence: 7.8% Identity: 22% PDB header:gene regulation Chain: A: PDB Molecule:major surface antigen; PDBTitle: solution conformation of adr subtype hbv pre-s2 epitope Phyre2 PDB 3hd7 chain A Region: 6 - 37 Aligned: 32 Modelled: 32 Confidence: 7.7% Identity: 3% PDB header:exocytosis Chain: A: PDB Molecule:vesicle-associated membrane protein 2; PDBTitle: helical extension of the neuronal snare complex into the membrane,2 spacegroup c 1 2 1 Phyre2 PDB 2ka2 chain B Region: 144 - 168 Aligned: 25 Modelled: 25 Confidence: 6.7% Identity: 20% 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 Phyre2 PDB 2ka1 chain A Region: 144 - 168 Aligned: 25 Modelled: 25 Confidence: 6.7% Identity: 20% 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 Phyre2 PDB 2ka2 chain A Region: 144 - 168 Aligned: 25 Modelled: 25 Confidence: 6.7% Identity: 20% 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 Phyre2 PDB 2ka1 chain B Region: 144 - 168 Aligned: 25 Modelled: 25 Confidence: 6.7% Identity: 20% 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 Phyre2 1 d3dhwa1 2 c2onkC_ 3 d2onkc1 4 c3d31D_ 5 d3d31c1 6 d2r6gf2 7 c2r6gF_ 8 c3fh6F_ 9 d2r6gg1 10 c2cw1A_ 11 c2jwaA_ 12 d2axtk1 13 c3a0bk_ 14 c3a0bK_ 15 c1wz4A_ 16 c3hd7A_ 17 c2ka2B_ 18 c2ka1A_ 19 c2ka2A_ 20 c2ka1B_ 21 22 23

Detailed template information

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

1 d3dhwa1 99.9 18 Fold:MetI-like Superfamily:MetI-like Family:MetI-like 2 c2onkC_ 99.8 9 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 99.8 9 Fold:MetI-like Superfamily:MetI-like Family:MetI-like 4 c3d31D_ 99.8 16 PDB header:transport protein Chain: D: PDB Molecule:sulfate/molybdate abc transporter, permease PDBTitle: modbc from methanosarcina acetivorans 5 d3d31c1 99.8 16 Fold:MetI-like Superfamily:MetI-like Family:MetI-like 6 d2r6gf2 99.7 13 Fold:MetI-like Superfamily:MetI-like Family:MetI-like 7 c2r6gF_ 99.6 14 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 c3fh6F_ 99.6 13 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 99.5 14 Fold:MetI-like Superfamily:MetI-like Family:MetI-like 10 c2cw1A_ 20.0 45 PDB header:de novo protein Chain: A: PDB Molecule:sn4m; PDBTitle: solution structure of the de novo-designed lambda cro fold2 protein 11 c2jwaA_ 12.0 26 PDB header:transferase Chain: A: PDB Molecule:receptor tyrosine-protein kinase erbb-2; PDBTitle: erbb2 transmembrane segment dimer spatial structure 12 d2axtk1 9.5 21 Fold:Single transmembrane helix Superfamily:Photosystem II reaction center protein K, PsbK Family:PsbK-like 13 c3a0bk_ 8.8 17 PDB header:electron transport Chain: K: PDB Molecule:photosystem ii reaction center protein k; PDBTitle: crystal structure of br-substituted photosystem ii complex 14 c3a0bK_ 8.8 17 PDB header:electron transport Chain: K: PDB Molecule:photosystem ii reaction center protein k; PDBTitle: crystal structure of br-substituted photosystem ii complex 15 c1wz4A_ 7.8 22 PDB header:gene regulation Chain: A: PDB Molecule:major surface antigen; PDBTitle: solution conformation of adr subtype hbv pre-s2 epitope 16 c3hd7A_ 7.7 3 PDB header:exocytosis Chain: A: PDB Molecule:vesicle-associated membrane protein 2; PDBTitle: helical extension of the neuronal snare complex into the membrane,2 spacegroup c 1 2 1 17 c2ka2B_ 6.7 20 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 18 c2ka1A_ 6.7 20 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 19 c2ka2A_ 6.7 20 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 20 c2ka1B_ 6.7 20 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 21 d1g2ha_ not modelled 6.1 44 Fold:DNA/RNA-binding 3-helical bundle Superfamily:Homeodomain-like Family:FIS-like 22 c3a0hk_ not modelled 5.8 17 PDB header:electron transport Chain: K: PDB Molecule:photosystem ii reaction center protein k; PDBTitle: crystal structure of i-substituted photosystem ii complex 23 d1ntca_ not modelled 5.6 19 Fold:DNA/RNA-binding 3-helical bundle Superfamily:Homeodomain-like Family:FIS-like

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

---

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