Secondary structure and disorder prediction

		1	.	.	.	.	.	.	.	.	10	.	.	.	.	.	.	.	.	.	20	.	.	.	.	.	.	.	.	.	30	.	.	.	.	.	.	.	.	.	40	.	.	.	.	.	.	.	.	.	50	.	.	.	.	.	.	.	.	.	60
Sequence		M	W	F	H	F	L	Q	L	R	S	A	L	N	I	S	S	A	L	R	Q	V	V	H	G	T	R	W	H	A	K	R	K	S	Y	K	V	L	F	W	R	E	I	T	P	L	A	V	P	I	F	M	E	N	A	C	V	L	L	M	G
Secondary structure
SS confidence
Disorder		?	?																		?	?	?	?	?	?	?	?	?	?	?	?	?	?	?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	70	.	.	.	.	.	.	.	.	.	80	.	.	.	.	.	.	.	.	.	90	.	.	.	.	.	.	.	.	.	100	.	.	.	.	.	.	.	.	.	110	.	.	.	.	.	.	.	.	.	120
Sequence		V	L	S	T	F	L	V	S	W	L	G	K	D	A	M	A	G	V	G	L	A	D	S	F	N	M	V	I	M	A	F	F	A	A	I	D	L	G	T	T	V	V	V	A	F	S	L	G	K	R	D	R	R	R	A	R	V	A	T	R
Secondary structure
SS confidence
Disorder																																																		?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	130	.	.	.	.	.	.	.	.	.	140	.	.	.	.	.	.	.	.	.	150	.	.	.	.	.	.	.	.	.	160	.	.	.	.	.	.	.	.	.	170	.	.	.	.	.	.	.	.	.	180
Sequence		Q	S	L	V	I	M	T	L	F	A	V	L	L	A	T	L	I	H	H	F	G	E	Q	I	I	D	F	V	A	G	D	A	T	T	E	V	K	A	L	A	L	T	Y	L	E	L	T	V	L	S	Y	P	A	A	A	I	T	L	I	G
Secondary structure
SS confidence
Disorder
Disorder confidence
		.	.	.	.	.	.	.	.	.	190	.	.	.	.	.	.	.	.	.	200	.	.	.	.	.	.	.	.	.	210	.	.	.	.	.	.	.	.	.	220	.	.	.	.	.	.	.	.	.	230	.	.	.	.	.	.	.	.	.	240
Sequence		S	G	A	L	R	G	A	G	N	T	K	I	P	L	L	I	N	G	S	L	N	I	L	N	I	I	I	S	G	I	L	I	Y	G	L	F	S	W	P	G	L	G	F	V	G	A	G	L	G	L	T	I	S	R	Y	I	G	A	V	A
Secondary structure
SS confidence
Disorder
Disorder confidence
		.	.	.	.	.	.	.	.	.	250	.	.	.	.	.	.	.	.	.	260	.	.	.	.	.	.	.	.	.	270	.	.	.	.	.	.	.	.	.	280	.	.	.	.	.	.	.	.	.	290	.	.	.	.	.	.	.	.	.	300
Sequence		I	L	W	V	L	A	I	G	F	N	P	A	L	R	I	S	L	K	S	Y	F	K	P	L	N	F	S	I	I	W	E	V	M	G	I	G	I	P	A	S	V	E	S	V	L	F	T	S	G	R	L	L	T	Q	M	F	V	A	G	M
Secondary structure
SS confidence
Disorder											?	?	?						?	?	?	?		?
Disorder confidence
		.	.	.	.	.	.	.	.	.	310	.	.	.	.	.	.	.	.	.	320	.	.	.	.	.	.	.	.	.	330	.	.	.	.	.	.	.	.	.	340	.	.	.	.	.	.	.	.	.	350	.	.	.	.	.	.	.	.	.	360
Sequence		G	T	S	V	I	A	G	N	F	I	A	F	S	I	A	A	L	I	N	L	P	G	S	A	L	G	S	A	S	T	I	I	T	G	R	R	L	G	V	G	Q	I	A	Q	A	E	I	Q	L	R	H	V	F	W	L	S	T	L	G	L
Secondary structure
SS confidence
Disorder
Disorder confidence
		.	.	.	.	.	.	.	.	.	370	.	.	.	.	.	.	.	.	.	380	.	.	.	.	.	.	.	.	.	390	.	.	.	.	.	.	.	.	.	400	.	.	.	.	.	.	.	.	.	410	.	.	.	.	.	.	.	.	.	420
Sequence		T	A	I	A	W	L	T	A	P	F	A	G	V	M	A	S	F	Y	T	Q	D	P	Q	V	K	H	V	V	V	I	L	I	W	L	N	A	L	F	M	P	I	W	S	A	S	W	V	L	P	A	G	F	K	G	A	R	D	A	R	Y
Secondary structure
SS confidence
Disorder
Disorder confidence
		.	.	.	.	.	.	.	.	.	430	.	.	.	.	.	.	.	.	.	440	.	.	.	.	.	.	.	.	.	450	.	.	.	.	.	.	.	.	.	460	.	.	.	.	.	.	.	.	.	470	.	.	.	.	.	.	.	.	.	480
Sequence		A	M	W	V	S	M	L	S	M	W	G	C	R	V	V	V	G	Y	V	L	G	I	M	L	G	W	G	V	V	G	V	W	M	G	M	F	A	D	W	A	V	R	A	V	L	F	Y	W	R	M	V	T	G	R	W	L	W	K	Y	P
Secondary structure
SS confidence
Disorder																																																												?
Disorder confidence
		.	.	.	.	.	.	.	.	.	490	.	.	.	.	.
Sequence		R	P	E	P	Q	K	C	E	K	K	P	V	V	S	E
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 3mku chain A Region: 30 - 483 Aligned: 450 Modelled: 450 Confidence: 100.0% Identity: 20% PDB header:transport protein Chain: A: PDB Molecule:multi antimicrobial extrusion protein (na(+)/drug PDBTitle: structure of a cation-bound multidrug and toxin compound extrusion2 (mate) transporter Phyre2 PDB 1pw4 chain A Region: 23 - 483 Aligned: 421 Modelled: 432 Confidence: 88.8% Identity: 10% Fold: MFS general substrate transporter Superfamily: MFS general substrate transporter Family: Glycerol-3-phosphate transporter Phyre2 PDB 1pv7 chain A Region: 40 - 487 Aligned: 411 Modelled: 432 Confidence: 65.7% Identity: 8% Fold: MFS general substrate transporter Superfamily: MFS general substrate transporter Family: LacY-like proton/sugar symporter Phyre2 PDB 3qnq chain D Region: 452 - 490 Aligned: 37 Modelled: 39 Confidence: 36.9% Identity: 11% 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 Phyre2 PDB 2iub chain A domain 2 Region: 419 - 474 Aligned: 47 Modelled: 56 Confidence: 26.7% Identity: 13% Fold: Transmembrane helix hairpin Superfamily: Magnesium transport protein CorA, transmembrane region Family: Magnesium transport protein CorA, transmembrane region Phyre2 PDB 2knc chain A Region: 445 - 490 Aligned: 46 Modelled: 46 Confidence: 15.2% Identity: 15% PDB header:cell adhesion Chain: A: PDB Molecule:integrin alpha-iib; PDBTitle: platelet integrin alfaiib-beta3 transmembrane-cytoplasmic2 heterocomplex Phyre2 PDB 2p09 chain A Region: 471 - 493 Aligned: 23 Modelled: 23 Confidence: 12.2% Identity: 30% PDB header:de novo protein Chain: A: PDB Molecule:a non-biological atp binding protein with two mutations PDBTitle: structural insights into the evolution of a non-biological protein Phyre2 PDB 2oar chain A domain 1 Region: 449 - 490 Aligned: 42 Modelled: 42 Confidence: 11.9% Identity: 12% Fold: Gated mechanosensitive channel Superfamily: Gated mechanosensitive channel Family: Gated mechanosensitive channel Phyre2 PDB 2knc chain B Region: 447 - 490 Aligned: 42 Modelled: 44 Confidence: 10.5% Identity: 12% PDB header:cell adhesion Chain: B: PDB Molecule:integrin beta-3; PDBTitle: platelet integrin alfaiib-beta3 transmembrane-cytoplasmic2 heterocomplex Phyre2 PDB 2oar chain A Region: 449 - 490 Aligned: 42 Modelled: 42 Confidence: 8.3% Identity: 12% PDB header:membrane protein Chain: A: PDB Molecule:large-conductance mechanosensitive channel; PDBTitle: mechanosensitive channel of large conductance (mscl) Phyre2 PDB 1zrt chain D Region: 456 - 482 Aligned: 27 Modelled: 27 Confidence: 6.0% Identity: 4% PDB header:oxidoreductase/metal transport Chain: D: PDB Molecule:cytochrome c1; PDBTitle: rhodobacter capsulatus cytochrome bc1 complex with2 stigmatellin bound Phyre2 PDB 2k2o chain A Region: 471 - 490 Aligned: 20 Modelled: 20 Confidence: 5.7% Identity: 15% PDB header:membrane protein Chain: A: PDB Molecule:myoferlin; PDBTitle: solution structure of the inner dysf domain of human2 myoferlin Phyre2 PDB 3cwb chain Q Region: 455 - 482 Aligned: 28 Modelled: 28 Confidence: 5.7% Identity: 11% PDB header:oxidoreductase Chain: Q: PDB Molecule:mitochondrial cytochrome c1, heme protein; PDBTitle: chicken cytochrome bc1 complex inhibited by an iodinated analogue of2 the polyketide crocacin-d Phyre2 PDB 1p84 chain D Region: 455 - 482 Aligned: 28 Modelled: 28 Confidence: 5.7% Identity: 11% PDB header:oxidoreductase Chain: D: PDB Molecule:cytochrome c1, heme protein; PDBTitle: hdbt inhibited yeast cytochrome bc1 complex Phyre2 PDB 2yiu chain E Region: 455 - 477 Aligned: 23 Modelled: 23 Confidence: 5.0% Identity: 4% PDB header:oxidoreductase Chain: E: PDB Molecule:cytochrome c1, heme protein; PDBTitle: x-ray structure of the dimeric cytochrome bc1 complex from2 the soil bacterium paracoccus denitrificans at 2.73 angstrom resolution Phyre2 PDB 3izs chain Q Region: 472 - 495 Aligned: 24 Modelled: 24 Confidence: 5.0% Identity: 25% PDB header:ribosome Chain: Q: PDB Molecule:60s ribosomal protein rpl5 (l18p); PDBTitle: localization of the large subunit ribosomal proteins into a 6.1 a2 cryo-em map of saccharomyces cerevisiae translating 80s ribosome Phyre2 1 c3mkuA_ 2 d1pw4a_ 3 d1pv7a_ 4 c3qnqD_ 5 d2iuba2 6 c2kncA_ 7 c2p09A_ 8 d2oara1 9 c2kncB_ 10 c2oarA_ 11 c1zrtD_ 12 c2k2oA_ 13 c3cwbQ_ 14 c1p84D_ 15 c2yiuE_ 16 c3izsq_

Detailed template information

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

1 c3mkuA_ 100.0 20 PDB header:transport protein Chain: A: PDB Molecule:multi antimicrobial extrusion protein (na(+)/drug PDBTitle: structure of a cation-bound multidrug and toxin compound extrusion2 (mate) transporter 2 d1pw4a_ 88.8 10 Fold:MFS general substrate transporter Superfamily:MFS general substrate transporter Family:Glycerol-3-phosphate transporter 3 d1pv7a_ 65.7 8 Fold:MFS general substrate transporter Superfamily:MFS general substrate transporter Family:LacY-like proton/sugar symporter 4 c3qnqD_ 36.9 11 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 5 d2iuba2 26.7 13 Fold:Transmembrane helix hairpin Superfamily:Magnesium transport protein CorA, transmembrane region Family:Magnesium transport protein CorA, transmembrane region 6 c2kncA_ 15.2 15 PDB header:cell adhesion Chain: A: PDB Molecule:integrin alpha-iib; PDBTitle: platelet integrin alfaiib-beta3 transmembrane-cytoplasmic2 heterocomplex 7 c2p09A_ 12.2 30 PDB header:de novo protein Chain: A: PDB Molecule:a non-biological atp binding protein with two mutations PDBTitle: structural insights into the evolution of a non-biological protein 8 d2oara1 11.9 12 Fold:Gated mechanosensitive channel Superfamily:Gated mechanosensitive channel Family:Gated mechanosensitive channel 9 c2kncB_ 10.5 12 PDB header:cell adhesion Chain: B: PDB Molecule:integrin beta-3; PDBTitle: platelet integrin alfaiib-beta3 transmembrane-cytoplasmic2 heterocomplex 10 c2oarA_ 8.3 12 PDB header:membrane protein Chain: A: PDB Molecule:large-conductance mechanosensitive channel; PDBTitle: mechanosensitive channel of large conductance (mscl) 11 c1zrtD_ 6.0 4 PDB header:oxidoreductase/metal transport Chain: D: PDB Molecule:cytochrome c1; PDBTitle: rhodobacter capsulatus cytochrome bc1 complex with2 stigmatellin bound 12 c2k2oA_ 5.7 15 PDB header:membrane protein Chain: A: PDB Molecule:myoferlin; PDBTitle: solution structure of the inner dysf domain of human2 myoferlin 13 c3cwbQ_ 5.7 11 PDB header:oxidoreductase Chain: Q: PDB Molecule:mitochondrial cytochrome c1, heme protein; PDBTitle: chicken cytochrome bc1 complex inhibited by an iodinated analogue of2 the polyketide crocacin-d 14 c1p84D_ 5.7 11 PDB header:oxidoreductase Chain: D: PDB Molecule:cytochrome c1, heme protein; PDBTitle: hdbt inhibited yeast cytochrome bc1 complex 15 c2yiuE_ 5.0 4 PDB header:oxidoreductase Chain: E: PDB Molecule:cytochrome c1, heme protein; PDBTitle: x-ray structure of the dimeric cytochrome bc1 complex from2 the soil bacterium paracoccus denitrificans at 2.73 angstrom resolution 16 c3izsq_ 5.0 25 PDB header:ribosome Chain: Q: PDB Molecule:60s ribosomal protein rpl5 (l18p); PDBTitle: localization of the large subunit ribosomal proteins into a 6.1 a2 cryo-em map of saccharomyces cerevisiae translating 80s ribosome

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