Secondary structure and disorder prediction

		1	.	.	.	.	.	.	.	.	10	.	.	.	.	.	.	.	.	.	20	.	.	.	.	.	.	.	.	.	30	.	.	.	.	.	.	.	.	.	40	.	.	.	.	.	.	.	.	.	50	.	.	.	.	.	.	.	.	.	60
Sequence		M	E	Q	Y	D	Q	I	G	A	R	L	D	R	L	P	L	A	R	F	H	Y	R	I	F	G	I	I	S	F	S	L	L	L	T	G	F	L	S	Y	S	G	N	V	V	L	A	K	L	V	S	N	G	W	S	N	N	F	L	N	A
Secondary structure
SS confidence
Disorder		?	?	?	?	?	?																																														?
Disorder confidence
		.	.	.	.	.	.	.	.	.	70	.	.	.	.	.	.	.	.	.	80	.	.	.	.	.	.	.	.	.	90	.	.	.	.	.	.	.	.	.	100	.	.	.	.	.	.	.	.	.	110	.	.	.	.	.	.	.	.	.	120
Sequence		A	F	T	S	A	L	M	F	G	Y	F	I	G	S	L	T	G	G	F	I	G	D	Y	F	G	R	R	R	A	F	R	I	N	L	L	I	V	G	I	A	A	T	G	A	A	F	V	P	D	M	Y	W	L	I	F	F	R	F	L	M
Secondary structure
SS confidence
Disorder
Disorder confidence
		.	.	.	.	.	.	.	.	.	130	.	.	.	.	.	.	.	.	.	140	.	.	.	.	.	.	.	.	.	150	.	.	.	.	.	.	.	.	.	160	.	.	.	.	.	.	.	.	.	170	.	.	.	.	.	.	.	.	.	180
Sequence		G	T	G	M	G	A	L	I	M	V	G	Y	A	S	F	T	E	F	I	P	A	T	V	R	G	K	W	S	A	R	L	S	F	V	G	N	W	S	P	M	L	S	A	A	I	G	V	V	V	I	A	F	F	S	W	R	I	M	F	L
Secondary structure
SS confidence
Disorder
Disorder confidence
		.	.	.	.	.	.	.	.	.	190	.	.	.	.	.	.	.	.	.	200	.	.	.	.	.	.	.	.	.	210	.	.	.	.	.	.	.	.	.	220	.	.	.	.	.	.	.	.	.	230	.	.	.	.	.	.	.	.	.	240
Sequence		L	G	G	I	G	I	L	L	A	W	F	L	S	G	K	Y	F	I	E	S	P	R	W	L	A	G	K	G	Q	I	A	G	A	E	C	Q	L	R	E	V	E	Q	Q	I	E	R	E	K	S	I	R	L	P	P	L	T	S	Y	Q	S
Secondary structure
SS confidence
Disorder																																											?	?	?	?	?	?	?	?	?	?	?	?	?	?	?	?	?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	250	.	.	.	.	.	.	.	.	.	260	.	.	.	.	.	.	.	.	.	270	.	.	.	.	.	.	.	.	.	280	.	.	.	.	.	.	.	.	.	290	.	.	.	.	.	.	.	.	.	300
Sequence		N	S	K	V	K	V	I	K	G	T	F	W	L	L	F	K	G	E	M	L	R	R	T	L	V	A	I	T	V	L	I	A	M	N	I	S	L	Y	T	I	T	V	W	I	P	T	I	F	V	N	S	G	I	D	V	D	K	S	I	L
Secondary structure
SS confidence
Disorder		?	?	?	?	?	?	?	?	?	?																																									?	?	?		?
Disorder confidence
		.	.	.	.	.	.	.	.	.	310	.	.	.	.	.	.	.	.	.	320	.	.	.	.	.	.	.	.	.	330	.	.	.	.	.	.	.	.	.	340	.	.	.	.	.	.	.	.	.	350	.	.	.	.	.	.	.	.	.	360
Sequence		M	T	A	V	I	M	I	G	A	P	V	G	I	F	I	A	A	L	I	I	D	H	F	P	R	R	L	F	G	S	T	L	L	I	I	I	A	V	L	G	Y	I	Y	S	I	Q	T	T	E	W	A	I	L	I	Y	G	L	V	M	I
Secondary structure
SS confidence
Disorder
Disorder confidence
		.	.	.	.	.	.	.	.	.	370	.	.	.	.	.	.	.	.	.	380	.	.	.	.	.	.	.	.	.	390	.	.	.	.	.	.	.	.	.	400	.	.	.	.	.	.	.	.	.	410	.	.	.	.	.	.	.	.	.	420
Sequence		F	F	L	Y	M	Y	V	C	F	A	S	A	V	Y	I	P	E	L	W	P	T	H	L	R	L	R	G	S	G	F	V	N	A	V	G	R	I	V	A	V	F	T	P	Y	G	V	A	A	L	L	T	H	Y	G	S	I	T	V	F	M
Secondary structure
SS confidence
Disorder
Disorder confidence
		.	.	.	.	.	.	.	.	.	430	.	.	.	.	.	.	.	.	.	440	.	.	.	.	.	.	.	.	.	450	.	.
Sequence		V	L	G	V	M	L	L	L	C	A	L	V	L	S	I	F	G	I	E	T	R	K	V	S	L	E	E	I	S	E	V	N
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 1pw4 chain A Region: 3 - 451 Aligned: 417 Modelled: 418 Confidence: 100.0% Identity: 13% Fold: MFS general substrate transporter Superfamily: MFS general substrate transporter Family: Glycerol-3-phosphate transporter Phyre2 PDB 3o7p chain A Region: 18 - 440 Aligned: 407 Modelled: 417 Confidence: 100.0% Identity: 11% PDB header:transport protein Chain: A: PDB Molecule:l-fucose-proton symporter; PDBTitle: crystal structure of the e.coli fucose:proton symporter, fucp (n162a) Phyre2 PDB 1pv7 chain A Region: 16 - 451 Aligned: 412 Modelled: 412 Confidence: 100.0% Identity: 10% Fold: MFS general substrate transporter Superfamily: MFS general substrate transporter Family: LacY-like proton/sugar symporter Phyre2 PDB 2gfp chain A Region: 23 - 429 Aligned: 369 Modelled: 370 Confidence: 100.0% Identity: 14% PDB header:membrane protein Chain: A: PDB Molecule:multidrug resistance protein d; PDBTitle: structure of the multidrug transporter emrd from2 escherichia coli Phyre2 PDB 2xut chain C Region: 25 - 437 Aligned: 413 Modelled: 413 Confidence: 100.0% Identity: 11% PDB header:transport protein Chain: C: PDB Molecule:proton/peptide symporter family protein; PDBTitle: crystal structure of a proton dependent oligopeptide (pot)2 family transporter. Phyre2 PDB 3b9y chain A Region: 10 - 243 Aligned: 226 Modelled: 234 Confidence: 40.3% Identity: 10% PDB header:transport protein Chain: A: PDB Molecule:ammonium transporter family rh-like protein; PDBTitle: crystal structure of the nitrosomonas europaea rh protein Phyre2 PDB 3qnq chain D Region: 403 - 450 Aligned: 48 Modelled: 48 Confidence: 17.5% Identity: 19% 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 1wfz chain A Region: 426 - 452 Aligned: 27 Modelled: 27 Confidence: 13.5% Identity: 11% Fold: SufE/NifU Superfamily: SufE/NifU Family: NifU/IscU domain Phyre2 PDB 2g9p chain A Region: 76 - 89 Aligned: 14 Modelled: 14 Confidence: 13.4% Identity: 29% PDB header:antimicrobial protein Chain: A: PDB Molecule:antimicrobial peptide latarcin 2a; PDBTitle: nmr structure of a novel antimicrobial peptide, latarcin 2a,2 from spider (lachesana tarabaevi) venom Phyre2 PDB 1fs1 chain B domain 1 Region: 441 - 451 Aligned: 11 Modelled: 11 Confidence: 13.1% Identity: 27% Fold: Skp1 dimerisation domain-like Superfamily: Skp1 dimerisation domain-like Family: Skp1 dimerisation domain-like Phyre2 PDB 2rdd chain B Region: 424 - 451 Aligned: 28 Modelled: 28 Confidence: 12.2% Identity: 14% PDB header:membrane protein/transport protein Chain: B: PDB Molecule:upf0092 membrane protein yajc; PDBTitle: x-ray crystal structure of acrb in complex with a novel2 transmembrane helix. Phyre2 PDB 1r9p chain A Region: 426 - 452 Aligned: 27 Modelled: 27 Confidence: 9.2% Identity: 19% Fold: SufE/NifU Superfamily: SufE/NifU Family: NifU/IscU domain Phyre2 PDB 2hsg chain A domain 1 Region: 438 - 452 Aligned: 15 Modelled: 15 Confidence: 8.8% Identity: 40% Fold: lambda repressor-like DNA-binding domains Superfamily: lambda repressor-like DNA-binding domains Family: GalR/LacI-like bacterial regulator Phyre2 PDB 1ofc chain X domain 1 Region: 439 - 450 Aligned: 12 Modelled: 12 Confidence: 8.6% Identity: 25% Fold: DNA/RNA-binding 3-helical bundle Superfamily: Homeodomain-like Family: Myb/SANT domain Phyre2 PDB 1xjs chain A Region: 426 - 451 Aligned: 26 Modelled: 26 Confidence: 8.3% Identity: 8% Fold: SufE/NifU Superfamily: SufE/NifU Family: NifU/IscU domain Phyre2 PDB 3mmy chain F Region: 436 - 448 Aligned: 13 Modelled: 13 Confidence: 8.1% Identity: 38% PDB header:nuclear protein Chain: F: PDB Molecule:nuclear pore complex protein nup98; PDBTitle: structural and functional analysis of the interaction between the2 nucleoporin nup98 and the mrna export factor rae1 Phyre2 PDB 1uxd chain A Region: 438 - 452 Aligned: 15 Modelled: 15 Confidence: 7.7% Identity: 20% Fold: lambda repressor-like DNA-binding domains Superfamily: lambda repressor-like DNA-binding domains Family: GalR/LacI-like bacterial regulator Phyre2 PDB 1qpz chain A domain 1 Region: 438 - 452 Aligned: 15 Modelled: 15 Confidence: 7.4% Identity: 33% Fold: lambda repressor-like DNA-binding domains Superfamily: lambda repressor-like DNA-binding domains Family: GalR/LacI-like bacterial regulator Phyre2 PDB 1fs2 chain B domain 1 Region: 441 - 451 Aligned: 11 Modelled: 11 Confidence: 7.1% Identity: 27% Fold: Skp1 dimerisation domain-like Superfamily: Skp1 dimerisation domain-like Family: Skp1 dimerisation domain-like Phyre2 PDB 3ff5 chain B Region: 439 - 450 Aligned: 12 Modelled: 12 Confidence: 7.1% Identity: 25% PDB header:protein transport Chain: B: PDB Molecule:peroxisomal biogenesis factor 14; PDBTitle: crystal structure of the conserved n-terminal domain of the2 peroxisomal matrix-protein-import receptor, pex14p Phyre2 1 d1pw4a_ 2 c3o7pA_ 3 d1pv7a_ 4 c2gfpA_ 5 c2xutC_ 6 c3b9yA_ 7 c3qnqD_ 8 d1wfza_ 9 c2g9pA_ 10 d1fs1b1 11 c2rddB_ 12 d1r9pa_ 13 d2hsga1 14 d1ofcx1 15 d1xjsa_ 16 c3mmyF_ 17 d1uxda_ 18 d1qpza1 19 d1fs2b1 20 c3ff5B_ 21 22 23 24 25 26 27 28 29 30 31

Detailed template information

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

1 d1pw4a_ 100.0 13 Fold:MFS general substrate transporter Superfamily:MFS general substrate transporter Family:Glycerol-3-phosphate transporter 2 c3o7pA_ 100.0 11 PDB header:transport protein Chain: A: PDB Molecule:l-fucose-proton symporter; PDBTitle: crystal structure of the e.coli fucose:proton symporter, fucp (n162a) 3 d1pv7a_ 100.0 10 Fold:MFS general substrate transporter Superfamily:MFS general substrate transporter Family:LacY-like proton/sugar symporter 4 c2gfpA_ 100.0 14 PDB header:membrane protein Chain: A: PDB Molecule:multidrug resistance protein d; PDBTitle: structure of the multidrug transporter emrd from2 escherichia coli 5 c2xutC_ 100.0 11 PDB header:transport protein Chain: C: PDB Molecule:proton/peptide symporter family protein; PDBTitle: crystal structure of a proton dependent oligopeptide (pot)2 family transporter. 6 c3b9yA_ 40.3 10 PDB header:transport protein Chain: A: PDB Molecule:ammonium transporter family rh-like protein; PDBTitle: crystal structure of the nitrosomonas europaea rh protein 7 c3qnqD_ 17.5 19 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 8 d1wfza_ 13.5 11 Fold:SufE/NifU Superfamily:SufE/NifU Family:NifU/IscU domain 9 c2g9pA_ 13.4 29 PDB header:antimicrobial protein Chain: A: PDB Molecule:antimicrobial peptide latarcin 2a; PDBTitle: nmr structure of a novel antimicrobial peptide, latarcin 2a,2 from spider (lachesana tarabaevi) venom 10 d1fs1b1 13.1 27 Fold:Skp1 dimerisation domain-like Superfamily:Skp1 dimerisation domain-like Family:Skp1 dimerisation domain-like 11 c2rddB_ 12.2 14 PDB header:membrane protein/transport protein Chain: B: PDB Molecule:upf0092 membrane protein yajc; PDBTitle: x-ray crystal structure of acrb in complex with a novel2 transmembrane helix. 12 d1r9pa_ 9.2 19 Fold:SufE/NifU Superfamily:SufE/NifU Family:NifU/IscU domain 13 d2hsga1 8.8 40 Fold:lambda repressor-like DNA-binding domains Superfamily:lambda repressor-like DNA-binding domains Family:GalR/LacI-like bacterial regulator 14 d1ofcx1 8.6 25 Fold:DNA/RNA-binding 3-helical bundle Superfamily:Homeodomain-like Family:Myb/SANT domain 15 d1xjsa_ 8.3 8 Fold:SufE/NifU Superfamily:SufE/NifU Family:NifU/IscU domain 16 c3mmyF_ 8.1 38 PDB header:nuclear protein Chain: F: PDB Molecule:nuclear pore complex protein nup98; PDBTitle: structural and functional analysis of the interaction between the2 nucleoporin nup98 and the mrna export factor rae1 17 d1uxda_ 7.7 20 Fold:lambda repressor-like DNA-binding domains Superfamily:lambda repressor-like DNA-binding domains Family:GalR/LacI-like bacterial regulator 18 d1qpza1 7.4 33 Fold:lambda repressor-like DNA-binding domains Superfamily:lambda repressor-like DNA-binding domains Family:GalR/LacI-like bacterial regulator 19 d1fs2b1 7.1 27 Fold:Skp1 dimerisation domain-like Superfamily:Skp1 dimerisation domain-like Family:Skp1 dimerisation domain-like 20 c3ff5B_ 7.1 25 PDB header:protein transport Chain: B: PDB Molecule:peroxisomal biogenesis factor 14; PDBTitle: crystal structure of the conserved n-terminal domain of the2 peroxisomal matrix-protein-import receptor, pex14p 21 c2l8nA_ not modelled 6.9 27 PDB header:transcription regulator Chain: A: PDB Molecule:transcriptional repressor cytr; PDBTitle: nmr structure of the cytidine repressor dna binding domain in presence2 of operator half-site dna 22 c2z7eB_ not modelled 6.6 7 PDB header:biosynthetic protein Chain: B: PDB Molecule:nifu-like protein; PDBTitle: crystal structure of aquifex aeolicus iscu with bound [2fe-2 2s] cluster 23 c2lcvA_ not modelled 6.2 27 PDB header:transcription regulator Chain: A: PDB Molecule:hth-type transcriptional repressor cytr; PDBTitle: structure of the cytidine repressor dna-binding domain; an alternate2 calculation 24 c2f9jP_ not modelled 6.1 36 PDB header:rna binding protein Chain: P: PDB Molecule:splicing factor 3b subunit 1; PDBTitle: 3.0 angstrom resolution structure of a y22m mutant of the spliceosomal2 protein p14 bound to a region of sf3b155 25 d1uxca_ not modelled 6.1 20 Fold:lambda repressor-like DNA-binding domains Superfamily:lambda repressor-like DNA-binding domains Family:GalR/LacI-like bacterial regulator 26 d1su0b_ not modelled 5.8 15 Fold:SufE/NifU Superfamily:SufE/NifU Family:NifU/IscU domain 27 d2bjca1 not modelled 5.7 27 Fold:lambda repressor-like DNA-binding domains Superfamily:lambda repressor-like DNA-binding domains Family:GalR/LacI-like bacterial regulator 28 d1nexa1 not modelled 5.7 45 Fold:Skp1 dimerisation domain-like Superfamily:Skp1 dimerisation domain-like Family:Skp1 dimerisation domain-like 29 d1efaa1 not modelled 5.6 27 Fold:lambda repressor-like DNA-binding domains Superfamily:lambda repressor-like DNA-binding domains Family:GalR/LacI-like bacterial regulator 30 d1xeqa1 not modelled 5.1 50 Fold:S15/NS1 RNA-binding domain Superfamily:S15/NS1 RNA-binding domain Family:N-terminal, RNA-binding domain of nonstructural protein NS1 31 d2ovra1 not modelled 5.1 27 Fold:Skp1 dimerisation domain-like Superfamily:Skp1 dimerisation domain-like Family:Skp1 dimerisation domain-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

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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