Secondary structure and disorder prediction

		1	.	.	.	.	.	.	.	.	10	.	.	.	.	.	.	.	.	.	20	.	.	.	.	.	.	.	.	.	30	.	.	.	.	.	.	.	.	.	40	.	.	.	.	.	.	.	.	.	50	.	.	.	.	.	.	.	.	.	60
Sequence		M	K	T	T	A	K	L	S	F	M	M	F	V	E	W	F	I	W	G	A	W	F	V	P	L	W	L	W	L	S	K	S	G	F	S	A	G	E	I	G	W	S	Y	A	C	T	A	I	A	A	I	L	S	P	I	L	V	G	S	I
Secondary structure
SS confidence
Disorder		?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	70	.	.	.	.	.	.	.	.	.	80	.	.	.	.	.	.	.	.	.	90	.	.	.	.	.	.	.	.	.	100	.	.	.	.	.	.	.	.	.	110	.	.	.	.	.	.	.	.	.	120
Sequence		T	D	R	F	F	S	A	Q	K	V	L	A	V	L	M	F	A	G	A	L	L	M	Y	F	A	A	Q	Q	T	T	F	A	G	F	F	P	L	L	L	A	Y	S	L	T	Y	M	P	T	I	A	L	T	N	S	I	A	F	A	N	V
Secondary structure
SS confidence
Disorder
Disorder confidence
		.	.	.	.	.	.	.	.	.	130	.	.	.	.	.	.	.	.	.	140	.	.	.	.	.	.	.	.	.	150	.	.	.	.	.	.	.	.	.	160	.	.	.	.	.	.	.	.	.	170	.	.	.	.	.	.	.	.	.	180
Sequence		P	D	V	E	R	D	F	P	R	I	R	V	M	G	T	I	G	W	I	A	S	G	L	A	C	G	F	L	P	Q	I	L	G	Y	A	D	I	S	P	T	N	I	P	L	L	I	T	A	G	S	S	A	L	L	G	V	F	A	F	F
Secondary structure
SS confidence
Disorder		?	?	?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	190	.	.	.	.	.	.	.	.	.	200	.	.	.	.	.	.	.	.	.	210	.	.	.	.	.	.	.	.	.	220	.	.	.	.	.	.	.	.	.	230	.	.	.	.	.	.	.	.	.	240
Sequence		L	P	D	T	P	P	K	S	T	G	K	M	D	I	K	V	M	L	G	L	D	A	L	I	L	L	R	D	K	N	F	L	V	F	F	F	C	S	F	L	F	A	M	P	L	A	F	Y	Y	I	F	A	N	G	Y	L	T	E	V	G
Secondary structure
SS confidence
Disorder				?	?	?	?	?	?	?	?	?	?	?	?	?	?	?	?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	250	.	.	.	.	.	.	.	.	.	260	.	.	.	.	.	.	.	.	.	270	.	.	.	.	.	.	.	.	.	280	.	.	.	.	.	.	.	.	.	290	.	.	.	.	.	.	.	.	.	300
Sequence		M	K	N	A	T	G	W	M	T	L	G	Q	F	S	E	I	F	F	M	L	A	L	P	F	F	T	K	R	F	G	I	K	K	V	L	L	L	G	L	V	T	A	A	I	R	Y	G	F	F	I	Y	G	S	A	D	E	Y	F	T	Y
Secondary structure
SS confidence
Disorder
Disorder confidence
		.	.	.	.	.	.	.	.	.	310	.	.	.	.	.	.	.	.	.	320	.	.	.	.	.	.	.	.	.	330	.	.	.	.	.	.	.	.	.	340	.	.	.	.	.	.	.	.	.	350	.	.	.	.	.	.	.	.	.	360
Sequence		A	L	L	F	L	G	I	L	L	H	G	V	S	Y	D	F	Y	Y	V	T	A	Y	I	Y	V	D	K	K	A	P	V	H	M	R	T	A	A	Q	G	L	I	T	L	C	C	Q	G	F	G	S	L	L	G	Y	R	L	G	G	V	M
Secondary structure
SS confidence
Disorder																														?
Disorder confidence
		.	.	.	.	.	.	.	.	.	370	.	.	.	.	.	.	.	.	.	380	.	.	.	.	.	.	.	.	.	390	.	.	.	.	.	.	.	.	.	400	.	.	.	.	.	.	.	.	.	410	.	.	.	.	.	.	.	.	.	420
Sequence		M	E	K	M	F	A	Y	Q	E	P	V	N	G	L	T	F	N	W	S	G	M	W	T	F	G	A	V	M	I	A	I	I	A	V	L	F	M	I	F	F	R	E	S	D	N	E	I	T	A	I	K	V	D	D	R	D	I	A	L	T
Secondary structure
SS confidence
Disorder							?		?		?																																?	?	?	?	?	?	?	?	?	?	?	?	?	?	?	?	?	?	?
Disorder confidence
		.	.	.	.	.
Sequence		Q	G	E	V	K
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 1pv7 chain A Region: 2 - 417 Aligned: 403 Modelled: 416 Confidence: 100.0% Identity: 12% Fold: MFS general substrate transporter Superfamily: MFS general substrate transporter Family: LacY-like proton/sugar symporter Phyre2 PDB 1pw4 chain A Region: 7 - 413 Aligned: 394 Modelled: 395 Confidence: 100.0% Identity: 14% Fold: MFS general substrate transporter Superfamily: MFS general substrate transporter Family: Glycerol-3-phosphate transporter Phyre2 PDB 2gfp chain A Region: 5 - 394 Aligned: 368 Modelled: 377 Confidence: 100.0% Identity: 10% PDB header:membrane protein Chain: A: PDB Molecule:multidrug resistance protein d; PDBTitle: structure of the multidrug transporter emrd from2 escherichia coli Phyre2 PDB 3o7p chain A Region: 2 - 403 Aligned: 385 Modelled: 400 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 2xut chain C Region: 7 - 395 Aligned: 388 Modelled: 389 Confidence: 99.9% Identity: 13% 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: 348 - 418 Aligned: 71 Modelled: 71 Confidence: 85.1% 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 3mku chain A Region: 1 - 414 Aligned: 414 Modelled: 414 Confidence: 51.3% Identity: 6% 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: 199 - 423 Aligned: 216 Modelled: 225 Confidence: 31.1% Identity: 9% 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 2w8a chain C Region: 385 - 423 Aligned: 39 Modelled: 39 Confidence: 26.0% Identity: 3% PDB header:membrane protein Chain: C: PDB Molecule:glycine betaine transporter betp; PDBTitle: crystal structure of the sodium-coupled glycine betaine2 symporter betp from corynebacterium glutamicum with bound3 substrate Phyre2 PDB 2knc chain A Region: 378 - 415 Aligned: 38 Modelled: 38 Confidence: 18.0% Identity: 8% PDB header:cell adhesion Chain: A: PDB Molecule:integrin alpha-iib; PDBTitle: platelet integrin alfaiib-beta3 transmembrane-cytoplasmic2 heterocomplex Phyre2 PDB 1j4n chain A Region: 313 - 414 Aligned: 102 Modelled: 102 Confidence: 11.9% Identity: 14% Fold: Aquaporin-like Superfamily: Aquaporin-like Family: Aquaporin-like Phyre2 PDB 1zza chain A Region: 365 - 425 Aligned: 59 Modelled: 61 Confidence: 8.9% Identity: 12% PDB header:membrane protein Chain: A: PDB Molecule:stannin; PDBTitle: solution nmr structure of the membrane protein stannin Phyre2 PDB 3a0b chain T Region: 383 - 405 Aligned: 23 Modelled: 23 Confidence: 7.7% Identity: 30% PDB header:electron transport Chain: T: PDB Molecule:photosystem ii reaction center protein t; PDBTitle: crystal structure of br-substituted photosystem ii complex Phyre2 PDB 3arc chain T Region: 383 - 405 Aligned: 23 Modelled: 23 Confidence: 7.7% Identity: 30% PDB header:electron transport, photosynthesis Chain: T: PDB Molecule:photosystem ii reaction center protein t; PDBTitle: crystal structure of oxygen-evolving photosystem ii at 1.9 angstrom2 resolution Phyre2 PDB 2jln chain A Region: 381 - 416 Aligned: 36 Modelled: 36 Confidence: 7.5% Identity: 11% PDB header:membrane protein Chain: A: PDB Molecule:mhp1; PDBTitle: structure of mhp1, a nucleobase-cation-symport-1 family2 transporter Phyre2 PDB 2klu chain A Region: 386 - 423 Aligned: 38 Modelled: 38 Confidence: 7.4% Identity: 13% PDB header:immune system, membrane protein Chain: A: PDB Molecule:t-cell surface glycoprotein cd4; PDBTitle: nmr structure of the transmembrane and cytoplasmic domains2 of human cd4 Phyre2 PDB 1ymg chain A domain 1 Region: 313 - 416 Aligned: 104 Modelled: 104 Confidence: 7.1% Identity: 13% Fold: Aquaporin-like Superfamily: Aquaporin-like Family: Aquaporin-like Phyre2 PDB 1ymg chain A Region: 313 - 416 Aligned: 104 Modelled: 104 Confidence: 7.1% Identity: 13% PDB header:membrane protein Chain: A: PDB Molecule:lens fiber major intrinsic protein; PDBTitle: the channel architecture of aquaporin o at 2.2 angstrom resolution Phyre2 PDB 2rdd chain B Region: 388 - 412 Aligned: 25 Modelled: 25 Confidence: 7.0% Identity: 8% 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 3b9y chain A Region: 15 - 208 Aligned: 194 Modelled: 194 Confidence: 6.9% Identity: 11% PDB header:transport protein Chain: A: PDB Molecule:ammonium transporter family rh-like protein; PDBTitle: crystal structure of the nitrosomonas europaea rh protein Phyre2 1 d1pv7a_ 2 d1pw4a_ 3 c2gfpA_ 4 c3o7pA_ 5 c2xutC_ 6 c3qnqD_ 7 c3mkuA_ 8 c3hd6A_ 9 c2w8aC_ 10 c2kncA_ 11 d1j4na_ 12 c1zzaA_ 13 c3a0bT_ 14 c3arct_ 15 c2jlnA_ 16 c2kluA_ 17 d1ymga1 18 c1ymgA_ 19 c2rddB_ 20 c3b9yA_ 21 22 23 24

Detailed template information

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

1 d1pv7a_ 100.0 12 Fold:MFS general substrate transporter Superfamily:MFS general substrate transporter Family:LacY-like proton/sugar symporter 2 d1pw4a_ 100.0 14 Fold:MFS general substrate transporter Superfamily:MFS general substrate transporter Family:Glycerol-3-phosphate transporter 3 c2gfpA_ 100.0 10 PDB header:membrane protein Chain: A: PDB Molecule:multidrug resistance protein d; PDBTitle: structure of the multidrug transporter emrd from2 escherichia coli 4 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) 5 c2xutC_ 99.9 13 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_ 85.1 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 7 c3mkuA_ 51.3 6 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_ 31.1 9 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 c2w8aC_ 26.0 3 PDB header:membrane protein Chain: C: PDB Molecule:glycine betaine transporter betp; PDBTitle: crystal structure of the sodium-coupled glycine betaine2 symporter betp from corynebacterium glutamicum with bound3 substrate 10 c2kncA_ 18.0 8 PDB header:cell adhesion Chain: A: PDB Molecule:integrin alpha-iib; PDBTitle: platelet integrin alfaiib-beta3 transmembrane-cytoplasmic2 heterocomplex 11 d1j4na_ 11.9 14 Fold:Aquaporin-like Superfamily:Aquaporin-like Family:Aquaporin-like 12 c1zzaA_ 8.9 12 PDB header:membrane protein Chain: A: PDB Molecule:stannin; PDBTitle: solution nmr structure of the membrane protein stannin 13 c3a0bT_ 7.7 30 PDB header:electron transport Chain: T: PDB Molecule:photosystem ii reaction center protein t; PDBTitle: crystal structure of br-substituted photosystem ii complex 14 c3arct_ 7.7 30 PDB header:electron transport, photosynthesis Chain: T: PDB Molecule:photosystem ii reaction center protein t; PDBTitle: crystal structure of oxygen-evolving photosystem ii at 1.9 angstrom2 resolution 15 c2jlnA_ 7.5 11 PDB header:membrane protein Chain: A: PDB Molecule:mhp1; PDBTitle: structure of mhp1, a nucleobase-cation-symport-1 family2 transporter 16 c2kluA_ 7.4 13 PDB header:immune system, membrane protein Chain: A: PDB Molecule:t-cell surface glycoprotein cd4; PDBTitle: nmr structure of the transmembrane and cytoplasmic domains2 of human cd4 17 d1ymga1 7.1 13 Fold:Aquaporin-like Superfamily:Aquaporin-like Family:Aquaporin-like 18 c1ymgA_ 7.1 13 PDB header:membrane protein Chain: A: PDB Molecule:lens fiber major intrinsic protein; PDBTitle: the channel architecture of aquaporin o at 2.2 angstrom resolution 19 c2rddB_ 7.0 8 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. 20 c3b9yA_ 6.9 11 PDB header:transport protein Chain: A: PDB Molecule:ammonium transporter family rh-like protein; PDBTitle: crystal structure of the nitrosomonas europaea rh protein 21 c2g9pA_ not modelled 6.4 25 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 22 d2fnoa1 not modelled 6.3 29 Fold:GST C-terminal domain-like Superfamily:GST C-terminal domain-like Family:Glutathione S-transferase (GST), C-terminal domain 23 c2rm9A_ not modelled 6.0 19 PDB header:neuropeptide Chain: A: PDB Molecule:astressin2b; PDBTitle: astressin2b 24 c3rl0j_ not modelled 5.8 27 PDB header:membrane protein/exocytosis Chain: J: PDB Molecule:syntaxin-1a; PDBTitle: truncated snare complex with complexin (p1)

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