Secondary structure and disorder prediction

		1	.	.	.	.	.	.	.	.	10	.	.	.	.	.	.	.	.	.	20	.	.	.	.	.	.	.	.	.	30	.	.	.	.	.	.	.	.	.	40	.	.	.	.	.	.	.	.	.	50	.	.	.	.	.	.	.	.	.	60
Sequence		M	L	A	F	L	N	Q	V	R	K	P	T	L	D	L	P	L	E	V	R	R	K	M	W	F	K	P	F	M	Q	S	Y	L	V	V	F	I	G	Y	L	T	M	Y	L	I	R	K	N	F	N	I	A	Q	N	D	M	I	S	T	Y
Secondary structure
SS confidence
Disorder		?	?	?	?	?	?	?	?	?	?	?	?	?	?	?	?	?	?	?	?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	70	.	.	.	.	.	.	.	.	.	80	.	.	.	.	.	.	.	.	.	90	.	.	.	.	.	.	.	.	.	100	.	.	.	.	.	.	.	.	.	110	.	.	.	.	.	.	.	.	.	120
Sequence		G	L	S	M	T	Q	L	G	M	I	G	L	G	F	S	I	T	Y	G	V	G	K	T	L	V	S	Y	Y	A	D	G	K	N	T	K	Q	F	L	P	F	M	L	I	L	S	A	I	C	M	L	G	F	S	A	S	M	G	S	G	S
Secondary structure
SS confidence
Disorder
Disorder confidence
		.	.	.	.	.	.	.	.	.	130	.	.	.	.	.	.	.	.	.	140	.	.	.	.	.	.	.	.	.	150	.	.	.	.	.	.	.	.	.	160	.	.	.	.	.	.	.	.	.	170	.	.	.	.	.	.	.	.	.	180
Sequence		V	S	L	F	L	M	I	A	F	Y	A	L	S	G	F	F	Q	S	T	G	G	S	C	S	Y	S	T	I	T	K	W	T	P	R	R	K	R	G	T	F	L	G	F	W	N	I	S	H	N	L	G	G	A	G	A	A	G	V	A	L
Secondary structure
SS confidence
Disorder
Disorder confidence
		.	.	.	.	.	.	.	.	.	190	.	.	.	.	.	.	.	.	.	200	.	.	.	.	.	.	.	.	.	210	.	.	.	.	.	.	.	.	.	220	.	.	.	.	.	.	.	.	.	230	.	.	.	.	.	.	.	.	.	240
Sequence		F	G	A	N	Y	L	F	D	G	H	V	I	G	M	F	I	F	P	S	I	I	A	L	I	V	G	F	I	G	L	R	Y	G	S	D	S	P	E	S	Y	G	L	G	K	A	E	E	L	F	G	E	E	I	S	E	E	D	K	E	T
Secondary structure
SS confidence
Disorder																																										?									?	?	?	?	?	?	?	?	?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	250	.	.	.	.	.	.	.	.	.	260	.	.	.	.	.	.	.	.	.	270	.	.	.	.	.	.	.	.	.	280	.	.	.	.	.	.	.	.	.	290	.	.	.	.	.	.	.	.	.	300
Sequence		E	S	T	D	M	T	K	W	Q	I	F	V	E	Y	V	L	K	N	K	V	I	W	L	L	C	F	A	N	I	F	L	Y	V	V	R	I	G	I	D	Q	W	S	T	V	Y	A	F	Q	E	L	K	L	S	K	A	V	A	I	Q	G
Secondary structure
SS confidence
Disorder		?	?	?	?	?	?	?	?	?																																										?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	310	.	.	.	.	.	.	.	.	.	320	.	.	.	.	.	.	.	.	.	330	.	.	.	.	.	.	.	.	.	340	.	.	.	.	.	.	.	.	.	350	.	.	.	.	.	.	.	.	.	360
Sequence		F	T	L	F	E	A	G	A	L	V	G	T	L	L	W	G	W	L	S	D	L	A	N	G	R	R	G	L	V	A	C	I	A	L	A	L	I	I	A	T	L	G	V	Y	Q	H	A	S	N	E	Y	I	Y	L	A	S	L	F	A	L
Secondary structure
SS confidence
Disorder
Disorder confidence
		.	.	.	.	.	.	.	.	.	370	.	.	.	.	.	.	.	.	.	380	.	.	.	.	.	.	.	.	.	390	.	.	.	.	.	.	.	.	.	400	.	.	.	.	.	.	.	.	.	410	.	.	.	.	.	.	.	.	.	420
Sequence		G	F	L	V	F	G	P	Q	L	L	I	G	V	A	A	V	G	F	V	P	K	K	A	I	G	A	A	D	G	I	K	G	T	F	A	Y	L	I	G	D	S	F	A	K	L	G	L	G	M	I	A	D	G	T	P	V	F	G	L	T
Secondary structure
SS confidence
Disorder																				?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	430	.	.	.	.	.	.	.	.	.	440	.	.	.	.	.	.	.	.	.	450	.	.	.	.	.	.	.	.	.	460	.	.	.
Sequence		G	W	A	G	T	F	A	A	L	D	I	A	A	I	G	C	I	C	L	M	A	I	V	A	V	M	E	E	R	K	I	R	R	E	K	K	I	Q	Q	L	T	V	A
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: 7 - 456 Aligned: 426 Modelled: 434 Confidence: 100.0% Identity: 30% Fold: MFS general substrate transporter Superfamily: MFS general substrate transporter Family: Glycerol-3-phosphate transporter Phyre2 PDB 1pv7 chain A Region: 24 - 461 Aligned: 416 Modelled: 424 Confidence: 100.0% Identity: 9% Fold: MFS general substrate transporter Superfamily: MFS general substrate transporter Family: LacY-like proton/sugar symporter Phyre2 PDB 3o7p chain A Region: 26 - 441 Aligned: 399 Modelled: 410 Confidence: 100.0% Identity: 10% 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 2gfp chain A Region: 31 - 438 Aligned: 370 Modelled: 383 Confidence: 100.0% Identity: 13% 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: 30 - 445 Aligned: 411 Modelled: 416 Confidence: 100.0% Identity: 10% 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 3qnq chain D Region: 417 - 461 Aligned: 45 Modelled: 45 Confidence: 81.2% Identity: 16% 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 3mku chain A Region: 19 - 460 Aligned: 440 Modelled: 440 Confidence: 35.2% Identity: 10% 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 3hd6 chain A Region: 305 - 461 Aligned: 152 Modelled: 157 Confidence: 34.9% Identity: 10% PDB header:membrane protein, transport protein Chain: A: PDB Molecule:ammonium transporter rh type c; PDBTitle: crystal structure of the human rhesus glycoprotein rhcg Phyre2 PDB 2oar chain A domain 1 Region: 387 - 461 Aligned: 75 Modelled: 75 Confidence: 26.3% Identity: 7% Fold: Gated mechanosensitive channel Superfamily: Gated mechanosensitive channel Family: Gated mechanosensitive channel Phyre2 PDB 2oar chain A Region: 387 - 461 Aligned: 75 Modelled: 75 Confidence: 15.7% Identity: 8% PDB header:membrane protein Chain: A: PDB Molecule:large-conductance mechanosensitive channel; PDBTitle: mechanosensitive channel of large conductance (mscl) Phyre2 PDB 2w2e chain A Region: 2 - 85 Aligned: 84 Modelled: 84 Confidence: 12.4% Identity: 13% PDB header:membrane protein Chain: A: PDB Molecule:aquaporin; PDBTitle: 1.15 angstrom crystal structure of p.pastoris aquaporin,2 aqy1, in a closed conformation at ph 3.5 Phyre2 PDB 3pro chain C domain 1 Region: 52 - 93 Aligned: 42 Modelled: 42 Confidence: 10.9% Identity: 12% Fold: Alpha-lytic protease prodomain-like Superfamily: Alpha-lytic protease prodomain Family: Alpha-lytic protease prodomain Phyre2 PDB 2g9p chain A Region: 84 - 97 Aligned: 14 Modelled: 14 Confidence: 9.3% Identity: 14% 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 2e6i chain A Region: 4 - 24 Aligned: 21 Modelled: 21 Confidence: 7.6% Identity: 33% PDB header:transferase Chain: A: PDB Molecule:tyrosine-protein kinase itk/tsk; PDBTitle: solution structure of the btk motif of tyrosine-protein2 kinase itk from human Phyre2 PDB 2knc chain A Region: 422 - 461 Aligned: 40 Modelled: 40 Confidence: 7.1% Identity: 15% PDB header:cell adhesion Chain: A: PDB Molecule:integrin alpha-iib; PDBTitle: platelet integrin alfaiib-beta3 transmembrane-cytoplasmic2 heterocomplex Phyre2 PDB 1qfq chain B Region: 448 - 463 Aligned: 16 Modelled: 16 Confidence: 7.1% Identity: 38% PDB header:transcription/rna Chain: B: PDB Molecule:36-mer n-terminal peptide of the n protein; PDBTitle: bacteriophage lambda n-protein-nutboxb-rna complex Phyre2 PDB 2rdd chain B Region: 426 - 460 Aligned: 35 Modelled: 35 Confidence: 6.9% Identity: 6% 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 2xse chain A Region: 447 - 460 Aligned: 14 Modelled: 13 Confidence: 6.1% Identity: 21% PDB header:oxidoreductase Chain: A: PDB Molecule:thymine dioxygenase jbp1; PDBTitle: the structural basis for recognition of j-base containing2 dna by a novel dna-binding domain in jbp1 Phyre2 1 d1pw4a_ 2 d1pv7a_ 3 c3o7pA_ 4 c2gfpA_ 5 c2xutC_ 6 c3qnqD_ 7 c3mkuA_ 8 c3hd6A_ 9 d2oara1 10 c2oarA_ 11 c2w2eA_ 12 d3proc1 13 c2g9pA_ 14 c2e6iA_ 15 c2kncA_ 16 c1qfqB_ 17 c2rddB_ 18 c2xseA_

Detailed template information

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

1 d1pw4a_ 100.0 30 Fold:MFS general substrate transporter Superfamily:MFS general substrate transporter Family:Glycerol-3-phosphate transporter 2 d1pv7a_ 100.0 9 Fold:MFS general substrate transporter Superfamily:MFS general substrate transporter Family:LacY-like proton/sugar symporter 3 c3o7pA_ 100.0 10 PDB header:transport protein Chain: A: PDB Molecule:l-fucose-proton symporter; PDBTitle: crystal structure of the e.coli fucose:proton symporter, fucp (n162a) 4 c2gfpA_ 100.0 13 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 10 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 c3qnqD_ 81.2 16 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 7 c3mkuA_ 35.2 10 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 8 c3hd6A_ 34.9 10 PDB header:membrane protein, transport protein Chain: A: PDB Molecule:ammonium transporter rh type c; PDBTitle: crystal structure of the human rhesus glycoprotein rhcg 9 d2oara1 26.3 7 Fold:Gated mechanosensitive channel Superfamily:Gated mechanosensitive channel Family:Gated mechanosensitive channel 10 c2oarA_ 15.7 8 PDB header:membrane protein Chain: A: PDB Molecule:large-conductance mechanosensitive channel; PDBTitle: mechanosensitive channel of large conductance (mscl) 11 c2w2eA_ 12.4 13 PDB header:membrane protein Chain: A: PDB Molecule:aquaporin; PDBTitle: 1.15 angstrom crystal structure of p.pastoris aquaporin,2 aqy1, in a closed conformation at ph 3.5 12 d3proc1 10.9 12 Fold:Alpha-lytic protease prodomain-like Superfamily:Alpha-lytic protease prodomain Family:Alpha-lytic protease prodomain 13 c2g9pA_ 9.3 14 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 14 c2e6iA_ 7.6 33 PDB header:transferase Chain: A: PDB Molecule:tyrosine-protein kinase itk/tsk; PDBTitle: solution structure of the btk motif of tyrosine-protein2 kinase itk from human 15 c2kncA_ 7.1 15 PDB header:cell adhesion Chain: A: PDB Molecule:integrin alpha-iib; PDBTitle: platelet integrin alfaiib-beta3 transmembrane-cytoplasmic2 heterocomplex 16 c1qfqB_ 7.1 38 PDB header:transcription/rna Chain: B: PDB Molecule:36-mer n-terminal peptide of the n protein; PDBTitle: bacteriophage lambda n-protein-nutboxb-rna complex 17 c2rddB_ 6.9 6 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. 18 c2xseA_ 6.1 21 PDB header:oxidoreductase Chain: A: PDB Molecule:thymine dioxygenase jbp1; PDBTitle: the structural basis for recognition of j-base containing2 dna by a novel dna-binding domain in jbp1

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