Secondary structure and disorder prediction

		1	.	.	.	.	.	.	.	.	10	.	.	.	.	.	.	.	.	.	20	.	.	.	.	.	.	.	.	.	30	.	.	.	.	.	.	.	.	.	40	.	.	.	.	.	.	.	.	.	50	.	.	.	.	.	.	.	.	.	60
Sequence		M	L	N	R	Y	P	L	W	K	Y	V	M	L	I	V	V	I	V	I	G	L	L	Y	A	L	P	N	L	F	G	E	D	P	A	V	Q	I	T	G	A	R	G	V	A	A	S	E	Q	T	L	I	Q	V	Q	K	T	L	Q	E	E
Secondary structure
SS confidence
Disorder		?	?	?	?	?																																			?	?	?	?		?	?														?
Disorder confidence
		.	.	.	.	.	.	.	.	.	70	.	.	.	.	.	.	.	.	.	80	.	.	.	.	.	.	.	.	.	90	.	.	.	.	.	.	.	.	.	100	.	.	.	.	.	.	.	.	.	110	.	.	.	.	.	.	.	.	.	120
Sequence		K	I	T	A	K	S	V	A	L	E	E	G	A	I	L	A	R	F	D	S	T	D	T	Q	L	R	A	R	E	A	L	M	G	V	M	G	D	K	Y	V	V	A	L	N	L	A	P	A	T	P	R	W	L	A	A	I	H	A	E	P
Secondary structure
SS confidence
Disorder					?	?	?	?	?	?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	130	.	.	.	.	.	.	.	.	.	140	.	.	.	.	.	.	.	.	.	150	.	.	.	.	.	.	.	.	.	160	.	.	.	.	.	.	.	.	.	170	.	.	.	.	.	.	.	.	.	180
Sequence		M	K	L	G	L	D	L	R	G	G	V	H	F	L	M	E	V	D	M	D	T	A	L	G	K	L	Q	E	Q	N	I	D	S	L	R	S	D	L	R	E	K	G	I	P	Y	T	T	V	R	K	E	N	N	Y	G	L	S	I	T	F
Secondary structure
SS confidence
Disorder																			?																							?	?		?	?	?	?	?	?	?	?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	190	.	.	.	.	.	.	.	.	.	200	.	.	.	.	.	.	.	.	.	210	.	.	.	.	.	.	.	.	.	220	.	.	.	.	.	.	.	.	.	230	.	.	.	.	.	.	.	.	.	240
Sequence		R	D	A	K	A	R	D	E	A	I	A	Y	L	S	K	R	H	P	D	L	V	I	S	S	Q	G	S	N	Q	L	R	A	V	M	S	D	A	R	L	S	E	A	R	E	Y	A	V	Q	Q	N	I	N	I	L	R	N	R	V	N	Q
Secondary structure
SS confidence
Disorder				?	?	?										?	?	?	?	?	?	?		?		?	?	?								?	?	?	?	?	?	?	?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	250	.	.	.	.	.	.	.	.	.	260	.	.	.	.	.	.	.	.	.	270	.	.	.	.	.	.	.	.	.	280	.	.	.	.	.	.	.	.	.	290	.	.	.	.	.	.	.	.	.	300
Sequence		L	G	V	A	E	P	V	V	Q	R	Q	G	A	D	R	I	V	V	E	L	P	G	I	Q	D	T	A	R	A	K	E	I	L	G	A	T	A	T	L	E	F	R	L	V	N	T	N	V	D	Q	A	A	A	A	S	G	R	V	P	G
Secondary structure
SS confidence
Disorder		?	?	?	?	?	?	?	?		?	?	?	?	?		?	?				?	?	?	?	?								?													?					?		?		?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	310	.	.	.	.	.	.	.	.	.	320	.	.	.	.	.	.	.	.	.	330	.	.	.	.	.	.	.	.	.	340	.	.	.	.	.	.	.	.	.	350	.	.	.	.	.	.	.	.	.	360
Sequence		D	S	E	V	K	Q	T	R	E	G	Q	P	V	V	L	Y	K	R	V	I	L	T	G	D	H	I	T	D	S	T	S	S	Q	D	E	Y	N	Q	P	Q	V	N	I	S	L	D	S	A	G	G	N	I	M	S	N	F	T	K	D	N
Secondary structure
SS confidence
Disorder											?						?			?	?	?	?					?	?	?	?	?	?	?	?	?	?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	370	.	.	.	.	.	.	.	.	.	380	.	.	.	.	.	.	.	.	.	390	.	.	.	.	.	.	.	.	.	400	.	.	.	.	.	.	.	.	.	410	.	.	.	.	.	.	.	.	.	420
Sequence		I	G	K	P	M	A	T	L	F	V	E	Y	K	D	S	G	K	K	D	A	N	G	R	A	V	L	V	K	Q	E	E	V	I	N	I	A	N	I	Q	S	R	L	G	N	S	F	R	I	T	G	I	N	N	P	N	E	A	R	Q	L
Secondary structure
SS confidence
Disorder						?		?		?	?	?	?	?	?	?	?		?	?	?	?	?									?			?	?	?	?	?	?	?	?	?	?	?	?				?	?	?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	430	.	.	.	.	.	.	.	.	.	440	.	.	.	.	.	.	.	.	.	450	.	.	.	.	.	.	.	.	.	460	.	.	.	.	.	.	.	.	.	470	.	.	.	.	.	.	.	.	.	480
Sequence		S	L	L	L	R	A	G	A	L	I	A	P	I	Q	I	V	E	E	R	T	I	G	P	T	L	G	M	Q	N	I	E	Q	G	L	E	A	C	L	A	G	L	L	V	S	I	L	F	M	I	I	F	Y	K	K	F	G	L	I	A	T
Secondary structure
SS confidence
Disorder						?	?	?	?	?	?	?	?	?		?	?	?	?	?	?	?	?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	490	.	.	.	.	.	.	.	.	.	500	.	.	.	.	.	.	.	.	.	510	.	.	.	.	.	.	.	.	.	520	.	.	.	.	.	.	.	.	.	530	.	.	.	.	.	.	.	.	.	540
Sequence		S	A	L	I	A	N	L	I	L	I	V	G	I	M	S	L	L	P	G	A	T	L	S	M	P	G	I	A	G	I	V	L	T	L	A	V	A	V	D	A	N	V	L	I	N	E	R	I	K	E	E	L	S	N	G	R	T	V	Q	Q
Secondary structure
SS confidence
Disorder																							?																																?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	550	.	.	.	.	.	.	.	.	.	560	.	.	.	.	.	.	.	.	.	570	.	.	.	.	.	.	.	.	.	580	.	.	.	.	.	.	.	.	.	590	.	.	.	.	.	.	.	.	.	600
Sequence		A	I	D	E	G	Y	R	G	A	F	S	S	I	F	D	A	N	I	T	T	L	I	K	V	I	I	L	Y	A	V	G	T	G	A	I	K	G	F	A	I	T	T	G	I	G	V	A	T	S	M	F	T	A	I	V	G	T	R	A	I
Secondary structure
SS confidence
Disorder																																	?	?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	610	.	.	.	.	.
Sequence		V	N	L	L	Y	G	G	K	R	V	K	K	L	S	I
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 3k07 chain A Region: 13 - 605 Aligned: 563 Modelled: 593 Confidence: 100.0% Identity: 10% PDB header:transport protein Chain: A: PDB Molecule:cation efflux system protein cusa; PDBTitle: crystal structure of cusa Phyre2 PDB 1oy8 chain A Region: 13 - 611 Aligned: 553 Modelled: 584 Confidence: 100.0% Identity: 13% PDB header:membrane protein Chain: A: PDB Molecule:acriflavine resistance protein b; PDBTitle: structural basis of multiple drug binding capacity of the acrb2 multidrug efflux pump Phyre2 PDB 3aqp chain B Region: 96 - 614 Aligned: 419 Modelled: 420 Confidence: 100.0% Identity: 36% PDB header:membrane protein Chain: B: PDB Molecule:probable secdf protein-export membrane protein; PDBTitle: crystal structure of secdf, a translocon-associated membrane protein,2 from thermus thrmophilus Phyre2 PDB 1iwg chain A domain 8 Region: 411 - 611 Aligned: 200 Modelled: 201 Confidence: 100.0% Identity: 17% Fold: Multidrug efflux transporter AcrB transmembrane domain Superfamily: Multidrug efflux transporter AcrB transmembrane domain Family: Multidrug efflux transporter AcrB transmembrane domain Phyre2 PDB 1iwg chain A domain 7 Region: 410 - 606 Aligned: 194 Modelled: 197 Confidence: 99.9% Identity: 15% Fold: Multidrug efflux transporter AcrB transmembrane domain Superfamily: Multidrug efflux transporter AcrB transmembrane domain Family: Multidrug efflux transporter AcrB transmembrane domain Phyre2 PDB 3aqo chain D Region: 216 - 441 Aligned: 207 Modelled: 207 Confidence: 99.7% Identity: 34% PDB header:membrane protein Chain: D: PDB Molecule:probable secdf protein-export membrane protein; PDBTitle: structure and function of a membrane component secdf that enhances2 protein export Phyre2 PDB 1iwg chain A domain 6 Region: 292 - 382 Aligned: 88 Modelled: 91 Confidence: 98.7% Identity: 6% Fold: Multidrug efflux transporter AcrB TolC docking domain; DN and DC subdomains Superfamily: Multidrug efflux transporter AcrB TolC docking domain; DN and DC subdomains Family: Multidrug efflux transporter AcrB TolC docking domain; DN and DC subdomains Phyre2 PDB 1iwg chain A domain 5 Region: 293 - 382 Aligned: 89 Modelled: 90 Confidence: 95.8% Identity: 8% Fold: Multidrug efflux transporter AcrB TolC docking domain; DN and DC subdomains Superfamily: Multidrug efflux transporter AcrB TolC docking domain; DN and DC subdomains Family: Multidrug efflux transporter AcrB TolC docking domain; DN and DC subdomains Phyre2 PDB 1iwg chain A domain 4 Region: 371 - 437 Aligned: 59 Modelled: 67 Confidence: 95.2% Identity: 10% Fold: Ferredoxin-like Superfamily: Multidrug efflux transporter AcrB pore domain; PN1, PN2, PC1 and PC2 subdomains Family: Multidrug efflux transporter AcrB pore domain; PN1, PN2, PC1 and PC2 subdomains Phyre2 PDB 1iwg chain A domain 2 Region: 340 - 440 Aligned: 94 Modelled: 101 Confidence: 94.5% Identity: 6% Fold: Ferredoxin-like Superfamily: Multidrug efflux transporter AcrB pore domain; PN1, PN2, PC1 and PC2 subdomains Family: Multidrug efflux transporter AcrB pore domain; PN1, PN2, PC1 and PC2 subdomains Phyre2 PDB 1iwg chain A domain 1 Region: 139 - 207 Aligned: 69 Modelled: 69 Confidence: 59.5% Identity: 7% Fold: Ferredoxin-like Superfamily: Multidrug efflux transporter AcrB pore domain; PN1, PN2, PC1 and PC2 subdomains Family: Multidrug efflux transporter AcrB pore domain; PN1, PN2, PC1 and PC2 subdomains Phyre2 PDB 1cii chain A Region: 488 - 523 Aligned: 36 Modelled: 36 Confidence: 41.1% Identity: 19% PDB header:transmembrane protein Chain: A: PDB Molecule:colicin ia; PDBTitle: colicin ia Phyre2 PDB 2bbj chain B Region: 517 - 609 Aligned: 86 Modelled: 93 Confidence: 34.8% Identity: 8% PDB header:metal transport/membrane protein Chain: B: PDB Molecule:divalent cation transport-related protein; PDBTitle: crystal structure of the cora mg2+ transporter Phyre2 PDB 2r6g chain F domain 1 Region: 8 - 34 Aligned: 26 Modelled: 27 Confidence: 15.4% Identity: 19% Fold: MalF N-terminal region-like Superfamily: MalF N-terminal region-like Family: MalF N-terminal region-like Phyre2 PDB 2yvx chain D Region: 476 - 615 Aligned: 137 Modelled: 140 Confidence: 14.7% Identity: 13% PDB header:transport protein Chain: D: PDB Molecule:mg2+ transporter mgte; PDBTitle: crystal structure of magnesium transporter mgte Phyre2 PDB 2qts chain A Region: 487 - 511 Aligned: 23 Modelled: 25 Confidence: 10.9% Identity: 30% PDB header:membrane protein Chain: A: PDB Molecule:acid-sensing ion channel; PDBTitle: structure of an acid-sensing ion channel 1 at 1.9 a resolution and low2 ph Phyre2 PDB 2iub chain A domain 2 Region: 564 - 609 Aligned: 35 Modelled: 46 Confidence: 8.3% Identity: 11% Fold: Transmembrane helix hairpin Superfamily: Magnesium transport protein CorA, transmembrane region Family: Magnesium transport protein CorA, transmembrane region Phyre2 PDB 1pby chain C Region: 1 - 8 Aligned: 8 Modelled: 8 Confidence: 7.0% Identity: 63% Fold: Non-globular all-alpha subunits of globular proteins Superfamily: Quinohemoprotein amine dehydrogenase C chain Family: Quinohemoprotein amine dehydrogenase C chain Phyre2 PDB 1xme chain B domain 2 Region: 449 - 471 Aligned: 23 Modelled: 23 Confidence: 6.8% Identity: 22% Fold: Transmembrane helix hairpin Superfamily: Cytochrome c oxidase subunit II-like, transmembrane region Family: Cytochrome c oxidase subunit II-like, transmembrane region Phyre2 PDB 1jmx chain G Region: 1 - 8 Aligned: 8 Modelled: 8 Confidence: 6.3% Identity: 38% Fold: Non-globular all-alpha subunits of globular proteins Superfamily: Quinohemoprotein amine dehydrogenase C chain Family: Quinohemoprotein amine dehydrogenase C chain Phyre2 1 c3k07A_ 2 c1oy8A_ 3 c3aqpB_ 4 d1iwga8 5 d1iwga7 6 c3aqoD_ 7 d1iwga6 8 d1iwga5 9 d1iwga4 10 d1iwga2 11 d1iwga1 12 c1ciiA_ 13 c2bbjB_ 14 d2r6gf1 15 c2yvxD_ 16 c2qtsA_ 17 d2iuba2 18 d1pbyc_ 19 d1xmeb2 20 d1jmxg_ 21 22

Detailed template information

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

1 c3k07A_ 100.0 10 PDB header:transport protein Chain: A: PDB Molecule:cation efflux system protein cusa; PDBTitle: crystal structure of cusa 2 c1oy8A_ 100.0 13 PDB header:membrane protein Chain: A: PDB Molecule:acriflavine resistance protein b; PDBTitle: structural basis of multiple drug binding capacity of the acrb2 multidrug efflux pump 3 c3aqpB_ 100.0 36 PDB header:membrane protein Chain: B: PDB Molecule:probable secdf protein-export membrane protein; PDBTitle: crystal structure of secdf, a translocon-associated membrane protein,2 from thermus thrmophilus 4 d1iwga8 100.0 17 Fold:Multidrug efflux transporter AcrB transmembrane domain Superfamily:Multidrug efflux transporter AcrB transmembrane domain Family:Multidrug efflux transporter AcrB transmembrane domain 5 d1iwga7 99.9 15 Fold:Multidrug efflux transporter AcrB transmembrane domain Superfamily:Multidrug efflux transporter AcrB transmembrane domain Family:Multidrug efflux transporter AcrB transmembrane domain 6 c3aqoD_ 99.7 34 PDB header:membrane protein Chain: D: PDB Molecule:probable secdf protein-export membrane protein; PDBTitle: structure and function of a membrane component secdf that enhances2 protein export 7 d1iwga6 98.7 6 Fold:Multidrug efflux transporter AcrB TolC docking domain; DN and DC subdomains Superfamily:Multidrug efflux transporter AcrB TolC docking domain; DN and DC subdomains Family:Multidrug efflux transporter AcrB TolC docking domain; DN and DC subdomains 8 d1iwga5 95.8 8 Fold:Multidrug efflux transporter AcrB TolC docking domain; DN and DC subdomains Superfamily:Multidrug efflux transporter AcrB TolC docking domain; DN and DC subdomains Family:Multidrug efflux transporter AcrB TolC docking domain; DN and DC subdomains 9 d1iwga4 95.2 10 Fold:Ferredoxin-like Superfamily:Multidrug efflux transporter AcrB pore domain; PN1, PN2, PC1 and PC2 subdomains Family:Multidrug efflux transporter AcrB pore domain; PN1, PN2, PC1 and PC2 subdomains 10 d1iwga2 94.5 6 Fold:Ferredoxin-like Superfamily:Multidrug efflux transporter AcrB pore domain; PN1, PN2, PC1 and PC2 subdomains Family:Multidrug efflux transporter AcrB pore domain; PN1, PN2, PC1 and PC2 subdomains 11 d1iwga1 59.5 7 Fold:Ferredoxin-like Superfamily:Multidrug efflux transporter AcrB pore domain; PN1, PN2, PC1 and PC2 subdomains Family:Multidrug efflux transporter AcrB pore domain; PN1, PN2, PC1 and PC2 subdomains 12 c1ciiA_ 41.1 19 PDB header:transmembrane protein Chain: A: PDB Molecule:colicin ia; PDBTitle: colicin ia 13 c2bbjB_ 34.8 8 PDB header:metal transport/membrane protein Chain: B: PDB Molecule:divalent cation transport-related protein; PDBTitle: crystal structure of the cora mg2+ transporter 14 d2r6gf1 15.4 19 Fold:MalF N-terminal region-like Superfamily:MalF N-terminal region-like Family:MalF N-terminal region-like 15 c2yvxD_ 14.7 13 PDB header:transport protein Chain: D: PDB Molecule:mg2+ transporter mgte; PDBTitle: crystal structure of magnesium transporter mgte 16 c2qtsA_ 10.9 30 PDB header:membrane protein Chain: A: PDB Molecule:acid-sensing ion channel; PDBTitle: structure of an acid-sensing ion channel 1 at 1.9 a resolution and low2 ph 17 d2iuba2 8.3 11 Fold:Transmembrane helix hairpin Superfamily:Magnesium transport protein CorA, transmembrane region Family:Magnesium transport protein CorA, transmembrane region 18 d1pbyc_ 7.0 63 Fold:Non-globular all-alpha subunits of globular proteins Superfamily:Quinohemoprotein amine dehydrogenase C chain Family:Quinohemoprotein amine dehydrogenase C chain 19 d1xmeb2 6.8 22 Fold:Transmembrane helix hairpin Superfamily:Cytochrome c oxidase subunit II-like, transmembrane region Family:Cytochrome c oxidase subunit II-like, transmembrane region 20 d1jmxg_ 6.3 38 Fold:Non-globular all-alpha subunits of globular proteins Superfamily:Quinohemoprotein amine dehydrogenase C chain Family:Quinohemoprotein amine dehydrogenase C chain 21 c2xznC_ not modelled 6.2 13 PDB header:ribosome Chain: C: PDB Molecule:kh domain containing protein; PDBTitle: crystal structure of the eukaryotic 40s ribosomal2 subunit in complex with initiation factor 1. this file3 contains the 40s subunit and initiation factor for4 molecule 2 22 d2axte1 not modelled 6.2 12 Fold:Single transmembrane helix Superfamily:Cytochrome b559 subunits Family:Cytochrome b559 subunits

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