Secondary structure and disorder prediction

		1	.	.	.	.	.	.	.	.	10	.	.	.	.	.	.	.	.	.	20	.	.	.	.	.	.	.	.	.	30	.	.	.	.	.	.	.	.	.	40	.	.	.	.	.	.	.	.	.	50	.	.	.	.	.	.	.	.	.	60
Sequence		M	E	T	P	Q	P	D	K	T	G	M	H	I	L	L	K	L	A	S	L	V	V	I	L	A	G	I	H	A	A	A	D	I	I	V	Q	L	L	L	A	L	F	F	A	I	V	L	N	P	L	V	T	W	F	I	R	R	G	V	Q
Secondary structure
SS confidence
Disorder		?	?	?	?	?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	70	.	.	.	.	.	.	.	.	.	80	.	.	.	.	.	.	.	.	.	90	.	.	.	.	.	.	.	.	.	100	.	.	.	.	.	.	.	.	.	110	.	.	.	.	.	.	.	.	.	120
Sequence		R	P	V	A	I	T	I	V	V	V	V	M	L	I	A	L	T	A	L	V	G	V	L	A	A	S	F	N	E	F	I	S	M	L	P	K	F	N	K	E	L	T	R	K	L	F	K	L	Q	E	M	L	P	F	L	N	L	H	M	S
Secondary structure
SS confidence
Disorder																																																							?	?	?	?	?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	130	.	.	.	.	.	.	.	.	.	140	.	.	.	.	.	.	.	.	.	150	.	.	.	.	.	.	.	.	.	160	.	.	.	.	.	.	.	.	.	170	.	.	.	.	.	.	.	.	.	180
Sequence		P	E	R	M	L	Q	R	M	D	S	E	K	V	V	T	F	T	T	A	L	M	T	G	L	S	G	A	M	A	S	V	L	L	L	V	M	T	V	V	F	M	L	F	E	V	R	H	V	P	Y	K	M	R	F	A	L	N	N	P	Q
Secondary structure
SS confidence
Disorder									?																																																		?
Disorder confidence
		.	.	.	.	.	.	.	.	.	190	.	.	.	.	.	.	.	.	.	200	.	.	.	.	.	.	.	.	.	210	.	.	.	.	.	.	.	.	.	220	.	.	.	.	.	.	.	.	.	230	.	.	.	.	.	.	.	.	.	240
Sequence		I	H	I	A	G	L	H	R	A	L	K	G	V	S	H	Y	L	A	L	K	T	L	L	S	L	W	T	G	V	I	V	W	L	G	L	E	L	M	G	V	Q	F	A	L	M	W	A	V	L	A	F	L	L	N	Y	V	P	N	I	G
Secondary structure
SS confidence
Disorder
Disorder confidence
		.	.	.	.	.	.	.	.	.	250	.	.	.	.	.	.	.	.	.	260	.	.	.	.	.	.	.	.	.	270	.	.	.	.	.	.	.	.	.	280	.	.	.	.	.	.	.	.	.	290	.	.	.	.	.	.	.	.	.	300
Sequence		A	V	I	S	A	V	P	P	M	I	Q	V	L	L	F	N	G	V	Y	E	C	I	L	V	G	A	L	F	L	V	V	H	M	V	I	G	N	I	L	E	P	R	M	M	G	H	R	L	G	M	S	T	M	V	V	F	L	S	L	L
Secondary structure
SS confidence
Disorder																																												?		?	?		?
Disorder confidence
		.	.	.	.	.	.	.	.	.	310	.	.	.	.	.	.	.	.	.	320	.	.	.	.	.	.	.	.	.	330	.	.	.	.	.	.	.	.	.	340	.	.	.	.	.	.	.	.	.
Sequence		I	W	G	W	L	L	G	P	V	G	M	L	L	S	V	P	L	T	S	V	C	K	I	W	M	E	T	T	K	G	G	S	K	L	A	I	L	L	G	P	G	R	P	K	S	R	L	P	G
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 2oar chain A Region: 142 - 195 Aligned: 54 Modelled: 54 Confidence: 24.9% Identity: 13% PDB header:membrane protein Chain: A: PDB Molecule:large-conductance mechanosensitive channel; PDBTitle: mechanosensitive channel of large conductance (mscl) Phyre2 PDB 1ppj chain C domain 2 Region: 180 - 248 Aligned: 69 Modelled: 69 Confidence: 18.4% Identity: 13% Fold: Heme-binding four-helical bundle Superfamily: Transmembrane di-heme cytochromes Family: Cytochrome b of cytochrome bc1 complex (Ubiquinol-cytochrome c reductase) Phyre2 PDB 3rlb chain A Region: 223 - 341 Aligned: 109 Modelled: 119 Confidence: 18.1% Identity: 26% PDB header:thiamine-binding protein Chain: A: PDB Molecule:thit; PDBTitle: crystal structure at 2.0 a of the s-component for thiamin from an ecf-2 type abc transporter Phyre2 PDB 1bcc chain C domain 3 Region: 180 - 247 Aligned: 68 Modelled: 68 Confidence: 11.4% Identity: 13% Fold: Heme-binding four-helical bundle Superfamily: Transmembrane di-heme cytochromes Family: Cytochrome b of cytochrome bc1 complex (Ubiquinol-cytochrome c reductase) Phyre2 PDB 1kkx chain A Region: 281 - 345 Aligned: 64 Modelled: 65 Confidence: 10.7% Identity: 6% Fold: DNA/RNA-binding 3-helical bundle Superfamily: ARID-like Family: ARID domain Phyre2 PDB 3cwb chain C Region: 180 - 248 Aligned: 69 Modelled: 69 Confidence: 10.2% Identity: 13% PDB header:oxidoreductase Chain: C: PDB Molecule:cytochrome b; PDBTitle: chicken cytochrome bc1 complex inhibited by an iodinated analogue of2 the polyketide crocacin-d Phyre2 PDB 2oar chain A domain 1 Region: 142 - 189 Aligned: 48 Modelled: 48 Confidence: 10.2% Identity: 15% Fold: Gated mechanosensitive channel Superfamily: Gated mechanosensitive channel Family: Gated mechanosensitive channel Phyre2 PDB 2r6g chain F domain 1 Region: 12 - 89 Aligned: 78 Modelled: 78 Confidence: 7.9% Identity: 12% Fold: MalF N-terminal region-like Superfamily: MalF N-terminal region-like Family: MalF N-terminal region-like Phyre2 PDB 1r11 chain A domain 3 Region: 285 - 307 Aligned: 23 Modelled: 23 Confidence: 6.0% Identity: 13% Fold: MutS N-terminal domain-like Superfamily: tRNA-intron endonuclease N-terminal domain-like Family: tRNA-intron endonuclease N-terminal domain-like Phyre2 PDB 3ixz chain B Region: 244 - 286 Aligned: 41 Modelled: 41 Confidence: 5.9% Identity: 12% PDB header:hydrolase Chain: B: PDB Molecule:potassium-transporting atpase subunit beta; PDBTitle: pig gastric h+/k+-atpase complexed with aluminium fluoride Phyre2 PDB 2axt chain J domain 1 Region: 296 - 313 Aligned: 18 Modelled: 18 Confidence: 5.9% Identity: 11% Fold: Single transmembrane helix Superfamily: Photosystem II reaction center protein J, PsbJ Family: PsbJ-like Phyre2 PDB 3cx5 chain C domain 2 Region: 195 - 248 Aligned: 54 Modelled: 54 Confidence: 5.7% Identity: 13% Fold: Heme-binding four-helical bundle Superfamily: Transmembrane di-heme cytochromes Family: Cytochrome b of cytochrome bc1 complex (Ubiquinol-cytochrome c reductase) Phyre2 PDB 2qjk chain M Region: 195 - 248 Aligned: 54 Modelled: 54 Confidence: 5.5% Identity: 13% PDB header:electron transport Chain: M: PDB Molecule:cytochrome b; PDBTitle: crystal structure analysis of mutant rhodobacter2 sphaeroides bc1 with stigmatellin and antimycin Phyre2 PDB 2e74 chain A domain 1 Region: 195 - 248 Aligned: 54 Modelled: 54 Confidence: 5.3% Identity: 11% Fold: Heme-binding four-helical bundle Superfamily: Transmembrane di-heme cytochromes Family: Cytochrome b of cytochrome bc1 complex (Ubiquinol-cytochrome c reductase) Phyre2 1 c2oarA_ 2 d1ppjc2 3 c3rlbA_ 4 d1bccc3 5 d1kkxa_ 6 c3cwbC_ 7 d2oara1 8 d2r6gf1 9 d1r11a3 10 c3ixzB_ 11 d2axtj1 12 d3cx5c2 13 c2qjkM_ 14 d2e74a1

Detailed template information

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

1 c2oarA_ 24.9 13 PDB header:membrane protein Chain: A: PDB Molecule:large-conductance mechanosensitive channel; PDBTitle: mechanosensitive channel of large conductance (mscl) 2 d1ppjc2 18.4 13 Fold:Heme-binding four-helical bundle Superfamily:Transmembrane di-heme cytochromes Family:Cytochrome b of cytochrome bc1 complex (Ubiquinol-cytochrome c reductase) 3 c3rlbA_ 18.1 26 PDB header:thiamine-binding protein Chain: A: PDB Molecule:thit; PDBTitle: crystal structure at 2.0 a of the s-component for thiamin from an ecf-2 type abc transporter 4 d1bccc3 11.4 13 Fold:Heme-binding four-helical bundle Superfamily:Transmembrane di-heme cytochromes Family:Cytochrome b of cytochrome bc1 complex (Ubiquinol-cytochrome c reductase) 5 d1kkxa_ 10.7 6 Fold:DNA/RNA-binding 3-helical bundle Superfamily:ARID-like Family:ARID domain 6 c3cwbC_ 10.2 13 PDB header:oxidoreductase Chain: C: PDB Molecule:cytochrome b; PDBTitle: chicken cytochrome bc1 complex inhibited by an iodinated analogue of2 the polyketide crocacin-d 7 d2oara1 10.2 15 Fold:Gated mechanosensitive channel Superfamily:Gated mechanosensitive channel Family:Gated mechanosensitive channel 8 d2r6gf1 7.9 12 Fold:MalF N-terminal region-like Superfamily:MalF N-terminal region-like Family:MalF N-terminal region-like 9 d1r11a3 6.0 13 Fold:MutS N-terminal domain-like Superfamily:tRNA-intron endonuclease N-terminal domain-like Family:tRNA-intron endonuclease N-terminal domain-like 10 c3ixzB_ 5.9 12 PDB header:hydrolase Chain: B: PDB Molecule:potassium-transporting atpase subunit beta; PDBTitle: pig gastric h+/k+-atpase complexed with aluminium fluoride 11 d2axtj1 5.9 11 Fold:Single transmembrane helix Superfamily:Photosystem II reaction center protein J, PsbJ Family:PsbJ-like 12 d3cx5c2 5.7 13 Fold:Heme-binding four-helical bundle Superfamily:Transmembrane di-heme cytochromes Family:Cytochrome b of cytochrome bc1 complex (Ubiquinol-cytochrome c reductase) 13 c2qjkM_ 5.5 13 PDB header:electron transport Chain: M: PDB Molecule:cytochrome b; PDBTitle: crystal structure analysis of mutant rhodobacter2 sphaeroides bc1 with stigmatellin and antimycin 14 d2e74a1 5.3 11 Fold:Heme-binding four-helical bundle Superfamily:Transmembrane di-heme cytochromes Family:Cytochrome b of cytochrome bc1 complex (Ubiquinol-cytochrome c reductase)

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