Secondary structure and disorder prediction

		1	.	.	.	.	.	.	.	.	10	.	.	.	.	.	.	.	.	.	20	.	.	.	.	.	.	.	.	.	30	.	.	.	.	.	.	.	.	.	40	.	.	.	.	.	.	.	.	.	50	.	.	.	.	.	.	.	.	.	60
Sequence		M	S	Q	A	K	S	N	K	M	G	V	V	Q	L	T	I	L	T	M	V	N	M	M	G	S	G	I	I	M	L	P	T	K	L	A	E	V	G	T	I	S	I	I	S	W	L	V	T	A	V	G	S	M	A	L	A	W	A	F	A
Secondary structure
SS confidence
Disorder		?	?	?	?	?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	70	.	.	.	.	.	.	.	.	.	80	.	.	.	.	.	.	.	.	.	90	.	.	.	.	.	.	.	.	.	100	.	.	.	.	.	.	.	.	.	110	.	.	.	.	.	.	.	.	.	120
Sequence		K	C	G	M	F	S	R	K	S	G	G	M	G	G	Y	A	E	Y	A	F	G	K	S	G	N	F	M	A	N	Y	T	Y	G	V	S	L	L	I	A	N	V	A	I	A	I	S	A	V	G	Y	G	T	E	L	L	G	A	S	L	S
Secondary structure
SS confidence
Disorder
Disorder confidence
		.	.	.	.	.	.	.	.	.	130	.	.	.	.	.	.	.	.	.	140	.	.	.	.	.	.	.	.	.	150	.	.	.	.	.	.	.	.	.	160	.	.	.	.	.	.	.	.	.	170	.	.	.	.	.	.	.	.	.	180
Sequence		P	V	Q	I	G	L	A	T	I	G	V	L	W	I	C	T	V	A	N	F	G	G	A	R	I	T	G	Q	I	S	S	I	T	V	W	G	V	I	I	P	V	V	G	L	C	I	I	G	W	F	W	F	S	P	T	L	Y	V	D	S
Secondary structure
SS confidence
Disorder																																																												?
Disorder confidence
		.	.	.	.	.	.	.	.	.	190	.	.	.	.	.	.	.	.	.	200	.	.	.	.	.	.	.	.	.	210	.	.	.	.	.	.	.	.	.	220	.	.	.	.	.	.	.	.	.	230	.	.	.	.	.	.	.	.	.	240
Sequence		W	N	P	H	H	A	P	F	F	S	A	V	G	S	S	I	A	M	T	L	W	A	F	L	G	L	E	S	A	C	A	N	T	D	V	V	E	N	P	E	R	N	V	P	I	A	V	L	G	G	T	L	G	A	A	V	I	Y	I	V
Secondary structure
SS confidence
Disorder				?	?	?	?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	250	.	.	.	.	.	.	.	.	.	260	.	.	.	.	.	.	.	.	.	270	.	.	.	.	.	.	.	.	.	280	.	.	.	.	.	.	.	.	.	290	.	.	.	.	.	.	.	.	.	300
Sequence		S	T	N	V	I	A	G	I	V	P	N	M	E	L	A	N	S	T	A	P	F	G	L	A	F	A	Q	M	F	T	P	E	V	G	K	V	I	M	A	L	M	V	M	S	C	C	G	S	L	L	G	W	Q	F	T	I	A	Q	V	F
Secondary structure
SS confidence
Disorder															?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	310	.	.	.	.	.	.	.	.	.	320	.	.	.	.	.	.	.	.	.	330	.	.	.	.	.	.	.	.	.	340	.	.	.	.	.	.	.	.	.	350	.	.	.	.	.	.	.	.	.	360
Sequence		K	S	S	S	D	E	G	Y	F	P	K	I	F	S	R	V	T	K	V	D	A	P	V	Q	G	M	L	T	I	V	I	I	Q	S	G	L	A	L	M	T	I	S	P	S	L	N	S	Q	F	N	V	L	V	N	L	A	V	V	T	N
Secondary structure
SS confidence
Disorder																																										?	?	?	?	?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	370	.	.	.	.	.	.	.	.	.	380	.	.	.	.	.	.	.	.	.	390	.	.	.	.	.	.	.	.	.	400	.	.	.	.	.	.	.	.	.	410	.	.	.	.	.	.	.	.	.	420
Sequence		I	I	P	Y	I	L	S	M	A	A	L	V	I	I	Q	K	V	A	N	V	P	P	S	K	A	K	V	A	N	F	V	A	F	V	G	A	M	Y	S	F	Y	A	L	Y	S	S	G	E	E	A	M	L	Y	G	S	I	V	T	F	L
Secondary structure
SS confidence
Disorder																				?
Disorder confidence
		.	.	.	.	.	.	.	.	.	430	.	.	.	.	.	.	.	.	.
Sequence		G	W	T	L	Y	G	L	V	S	P	R	F	E	L	K	N	K	H	G
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 3gia chain A Region: 5 - 439 Aligned: 423 Modelled: 423 Confidence: 100.0% Identity: 16% PDB header:transport protein Chain: A: PDB Molecule:uncharacterized protein mj0609; PDBTitle: crystal structure of apct transporter Phyre2 PDB 3lrc chain C Region: 5 - 435 Aligned: 409 Modelled: 409 Confidence: 100.0% Identity: 33% PDB header:transport protein Chain: C: PDB Molecule:arginine/agmatine antiporter; PDBTitle: structure of e. coli adic (p1) Phyre2 PDB 2jln chain A Region: 2 - 439 Aligned: 425 Modelled: 427 Confidence: 100.0% Identity: 10% PDB header:membrane protein Chain: A: PDB Molecule:mhp1; PDBTitle: structure of mhp1, a nucleobase-cation-symport-1 family2 transporter Phyre2 PDB 2xq2 chain A Region: 7 - 435 Aligned: 425 Modelled: 425 Confidence: 99.4% Identity: 11% PDB header:transport protein Chain: A: PDB Molecule:sodium/glucose cotransporter; PDBTitle: structure of the k294a mutant of vsglt Phyre2 PDB 3dh4 chain A Region: 7 - 438 Aligned: 421 Modelled: 421 Confidence: 99.4% Identity: 10% PDB header:transport protein Chain: A: PDB Molecule:sodium/glucose cotransporter; PDBTitle: crystal structure of sodium/sugar symporter with bound galactose from2 vibrio parahaemolyticus Phyre2 PDB 2a65 chain A domain 1 Region: 10 - 436 Aligned: 418 Modelled: 418 Confidence: 98.5% Identity: 13% Fold: SNF-like Superfamily: SNF-like Family: SNF-like Phyre2 PDB 2w8a chain C Region: 2 - 379 Aligned: 366 Modelled: 376 Confidence: 97.6% Identity: 13% 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 3hfx chain A Region: 4 - 381 Aligned: 369 Modelled: 369 Confidence: 83.2% Identity: 11% PDB header:transport protein Chain: A: PDB Molecule:l-carnitine/gamma-butyrobetaine antiporter; PDBTitle: crystal structure of carnitine transporter Phyre2 PDB 2l2t chain A Region: 411 - 437 Aligned: 27 Modelled: 27 Confidence: 8.6% Identity: 15% PDB header:membrane protein Chain: A: PDB Molecule:receptor tyrosine-protein kinase erbb-4; PDBTitle: solution nmr structure of the erbb4 dimeric membrane domain Phyre2 PDB 1lfb chain A Region: 423 - 438 Aligned: 16 Modelled: 16 Confidence: 8.4% Identity: 19% Fold: DNA/RNA-binding 3-helical bundle Superfamily: Homeodomain-like Family: Homeodomain Phyre2 PDB 1r3j chain C Region: 349 - 438 Aligned: 90 Modelled: 90 Confidence: 8.4% Identity: 19% Fold: Voltage-gated potassium channels Superfamily: Voltage-gated potassium channels Family: Voltage-gated potassium channels Phyre2 PDB 2gli chain A domain 5 Region: 429 - 439 Aligned: 11 Modelled: 11 Confidence: 8.2% Identity: 45% Fold: beta-beta-alpha zinc fingers Superfamily: beta-beta-alpha zinc fingers Family: Classic zinc finger, C2H2 Phyre2 PDB 2iub chain A domain 2 Region: 383 - 432 Aligned: 50 Modelled: 50 Confidence: 7.8% Identity: 2% Fold: Transmembrane helix hairpin Superfamily: Magnesium transport protein CorA, transmembrane region Family: Magnesium transport protein CorA, transmembrane region Phyre2 PDB 2rdd chain B Region: 417 - 437 Aligned: 21 Modelled: 21 Confidence: 6.6% 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 3rko chain F Region: 319 - 438 Aligned: 120 Modelled: 120 Confidence: 6.5% Identity: 9% PDB header:oxidoreductase Chain: F: PDB Molecule:nadh-quinone oxidoreductase subunit j; PDBTitle: crystal structure of the membrane domain of respiratory complex i from2 e. coli at 3.0 angstrom resolution Phyre2 PDB 2klu chain A Region: 413 - 436 Aligned: 24 Modelled: 24 Confidence: 6.0% Identity: 17% 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 1fft chain B domain 2 Region: 344 - 411 Aligned: 68 Modelled: 68 Confidence: 5.9% Identity: 9% Fold: Transmembrane helix hairpin Superfamily: Cytochrome c oxidase subunit II-like, transmembrane region Family: Cytochrome c oxidase subunit II-like, transmembrane region Phyre2 PDB 3og0 chain 2 Region: 431 - 439 Aligned: 9 Modelled: 9 Confidence: 5.9% Identity: 22% PDB header:ribosome Chain: 2: PDB Molecule:50s ribosomal protein l34; PDBTitle: crystal structure of the e. coli ribosome bound to clindamycin. this2 file contains the 50s subunit of the second 70s ribosome. Phyre2 PDB 1vt2 chain 2 Region: 431 - 439 Aligned: 9 Modelled: 9 Confidence: 5.9% Identity: 22% PDB header:ribosome Chain: 2: PDB Molecule:50s ribosomal protein l34; PDBTitle: crystal structure of the e. coli ribosome bound to cem-101. this file2 contains the 50s subunit of the second 70s ribosome. Phyre2 PDB 3ofd chain 2 Region: 431 - 439 Aligned: 9 Modelled: 9 Confidence: 5.9% Identity: 22% PDB header:ribosome Chain: 2: PDB Molecule:50s ribosomal protein l34; PDBTitle: crystal structure of the e. coli ribosome bound to chloramphenicol.2 this file contains the 50s subunit of the second 70s ribosome. Phyre2 1 c3giaA_ 2 c3lrcC_ 3 c2jlnA_ 4 c2xq2A_ 5 c3dh4A_ 6 d2a65a1 7 c2w8aC_ 8 c3hfxA_ 9 c2l2tA_ 10 d1lfba_ 11 d1r3jc_ 12 d2glia5 13 d2iuba2 14 c2rddB_ 15 c3rkoF_ 16 c2kluA_ 17 d1fftb2 18 c3og02_ 19 c1vt22_ 20 c3ofd2_ 21 22 23

Detailed template information

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

1 c3giaA_ 100.0 16 PDB header:transport protein Chain: A: PDB Molecule:uncharacterized protein mj0609; PDBTitle: crystal structure of apct transporter 2 c3lrcC_ 100.0 33 PDB header:transport protein Chain: C: PDB Molecule:arginine/agmatine antiporter; PDBTitle: structure of e. coli adic (p1) 3 c2jlnA_ 100.0 10 PDB header:membrane protein Chain: A: PDB Molecule:mhp1; PDBTitle: structure of mhp1, a nucleobase-cation-symport-1 family2 transporter 4 c2xq2A_ 99.4 11 PDB header:transport protein Chain: A: PDB Molecule:sodium/glucose cotransporter; PDBTitle: structure of the k294a mutant of vsglt 5 c3dh4A_ 99.4 10 PDB header:transport protein Chain: A: PDB Molecule:sodium/glucose cotransporter; PDBTitle: crystal structure of sodium/sugar symporter with bound galactose from2 vibrio parahaemolyticus 6 d2a65a1 98.5 13 Fold:SNF-like Superfamily:SNF-like Family:SNF-like 7 c2w8aC_ 97.6 13 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 8 c3hfxA_ 83.2 11 PDB header:transport protein Chain: A: PDB Molecule:l-carnitine/gamma-butyrobetaine antiporter; PDBTitle: crystal structure of carnitine transporter 9 c2l2tA_ 8.6 15 PDB header:membrane protein Chain: A: PDB Molecule:receptor tyrosine-protein kinase erbb-4; PDBTitle: solution nmr structure of the erbb4 dimeric membrane domain 10 d1lfba_ 8.4 19 Fold:DNA/RNA-binding 3-helical bundle Superfamily:Homeodomain-like Family:Homeodomain 11 d1r3jc_ 8.4 19 Fold:Voltage-gated potassium channels Superfamily:Voltage-gated potassium channels Family:Voltage-gated potassium channels 12 d2glia5 8.2 45 Fold:beta-beta-alpha zinc fingers Superfamily:beta-beta-alpha zinc fingers Family:Classic zinc finger, C2H2 13 d2iuba2 7.8 2 Fold:Transmembrane helix hairpin Superfamily:Magnesium transport protein CorA, transmembrane region Family:Magnesium transport protein CorA, transmembrane region 14 c2rddB_ 6.6 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. 15 c3rkoF_ 6.5 9 PDB header:oxidoreductase Chain: F: PDB Molecule:nadh-quinone oxidoreductase subunit j; PDBTitle: crystal structure of the membrane domain of respiratory complex i from2 e. coli at 3.0 angstrom resolution 16 c2kluA_ 6.0 17 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 d1fftb2 5.9 9 Fold:Transmembrane helix hairpin Superfamily:Cytochrome c oxidase subunit II-like, transmembrane region Family:Cytochrome c oxidase subunit II-like, transmembrane region 18 c3og02_ 5.9 22 PDB header:ribosome Chain: 2: PDB Molecule:50s ribosomal protein l34; PDBTitle: crystal structure of the e. coli ribosome bound to clindamycin. this2 file contains the 50s subunit of the second 70s ribosome. 19 c1vt22_ 5.9 22 PDB header:ribosome Chain: 2: PDB Molecule:50s ribosomal protein l34; PDBTitle: crystal structure of the e. coli ribosome bound to cem-101. this file2 contains the 50s subunit of the second 70s ribosome. 20 c3ofd2_ 5.9 22 PDB header:ribosome Chain: 2: PDB Molecule:50s ribosomal protein l34; PDBTitle: crystal structure of the e. coli ribosome bound to chloramphenicol.2 this file contains the 50s subunit of the second 70s ribosome. 21 c2ftcQ_ not modelled 5.5 71 PDB header:ribosome Chain: Q: PDB Molecule:39s ribosomal protein l34, mitochondrial; PDBTitle: structural model for the large subunit of the mammalian mitochondrial2 ribosome 22 c1m57H_ not modelled 5.2 10 PDB header:oxidoreductase Chain: H: PDB Molecule:cytochrome c oxidase; PDBTitle: structure of cytochrome c oxidase from rhodobacter2 sphaeroides (eq(i-286) mutant)) 23 c1ar1B_ not modelled 5.0 12 PDB header:complex (oxidoreductase/antibody) Chain: B: PDB Molecule:cytochrome c oxidase; PDBTitle: structure at 2.7 angstrom resolution of the paracoccus2 denitrificans two-subunit cytochrome c oxidase complexed3 with an antibody fv fragment

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