Secondary structure and disorder prediction

		1	.	.	.	.	.	.	.	.	10	.	.	.	.	.	.	.	.	.	20	.	.	.	.	.	.	.	.	.	30	.	.	.	.	.	.	.	.	.	40	.	.	.	.	.	.	.	.	.	50	.	.	.	.	.	.	.	.	.	60
Sequence		M	T	I	T	P	Q	N	L	I	A	L	L	P	L	L	I	V	G	L	T	V	V	V	V	M	L	S	I	A	W	R	R	N	H	F	L	N	A	T	L	S	V	I	G	L	N	A	A	L	V	S	L	W	F	V	G	Q	A	G	A
Secondary structure
SS confidence
Disorder		?	?	?	?																									?		?	?																										?		?
Disorder confidence
		.	.	.	.	.	.	.	.	.	70	.	.	.	.	.	.	.	.	.	80	.	.	.	.	.	.	.	.	.	90	.	.	.	.	.	.	.	.	.	100	.	.	.	.	.	.	.	.	.	110	.	.	.	.	.	.	.	.	.	120
Sequence		M	D	V	T	P	L	M	R	V	D	G	F	A	M	L	Y	T	G	L	V	L	L	A	S	L	A	T	C	T	F	A	Y	P	W	L	E	G	Y	N	D	N	K	D	E	F	Y	L	L	V	L	I	A	A	L	G	G	I	L	L	A
Secondary structure
SS confidence
Disorder																																					?	?	?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	130	.	.	.	.	.	.	.	.	.	140	.	.	.	.	.	.	.	.	.	150	.	.	.	.	.	.	.	.	.	160	.	.	.	.	.	.	.	.	.	170	.	.	.	.	.	.	.	.	.	180
Sequence		N	A	N	H	L	A	S	L	F	L	G	I	E	L	I	S	L	P	L	F	G	L	V	G	Y	A	F	R	Q	K	R	S	L	E	A	S	I	K	Y	T	I	L	S	A	A	A	S	S	F	L	L	F	G	M	A	L	V	Y	A	Q
Secondary structure
SS confidence
Disorder
Disorder confidence
		.	.	.	.	.	.	.	.	.	190	.	.	.	.	.	.	.	.	.	200	.	.	.	.	.	.	.	.	.	210	.	.	.	.	.	.	.	.	.	220	.	.	.	.	.	.	.	.	.	230	.	.	.	.	.	.	.	.	.	240
Sequence		S	G	D	L	S	F	V	A	L	G	K	N	L	G	D	G	M	L	N	E	P	L	L	L	A	G	F	G	L	M	I	V	G	L	G	F	K	L	S	L	V	P	F	H	L	W	T	P	D	V	Y	Q	G	A	P	A	P	V	S	T
Secondary structure
SS confidence
Disorder														?	?	?	?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	250	.	.	.	.	.	.	.	.	.	260	.	.	.	.	.	.	.	.	.	270	.	.	.	.	.	.	.	.	.	280	.	.	.	.	.	.	.	.	.	290	.	.	.	.	.	.	.	.	.	300
Sequence		F	L	A	T	A	S	K	I	A	I	F	G	V	V	M	R	L	F	L	Y	A	P	V	G	D	S	E	A	I	R	V	V	L	A	I	I	A	F	A	S	I	I	F	G	N	L	M	A	L	S	Q	T	N	I	K	R	L	L	G	Y
Secondary structure
SS confidence
Disorder
Disorder confidence
		.	.	.	.	.	.	.	.	.	310	.	.	.	.	.	.	.	.	.	320	.	.	.	.	.	.	.	.	.	330	.	.	.	.	.	.	.	.	.	340	.	.	.	.	.	.	.	.	.	350	.	.	.	.	.	.	.	.	.	360
Sequence		S	S	I	S	H	L	G	Y	L	L	V	A	L	I	A	L	Q	T	G	E	M	S	M	E	A	V	G	V	Y	L	A	G	Y	L	F	S	S	L	G	A	F	G	V	V	S	L	M	S	S	P	Y	R	G	P	D	A	D	S	L	F
Secondary structure
SS confidence
Disorder																	?		?	?	?																													?		?			?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	370	.	.	.	.	.	.	.	.	.	380	.	.	.	.	.	.	.	.	.	390	.	.	.	.	.	.	.	.	.	400	.	.	.	.	.	.	.	.	.	410	.	.	.	.	.	.	.	.	.	420
Sequence		S	Y	R	G	L	F	W	H	R	P	I	L	A	A	V	M	T	V	M	M	L	S	L	A	G	I	P	M	T	L	G	F	I	G	K	F	Y	V	L	A	V	G	V	Q	A	H	L	W	W	L	V	G	A	V	V	V	G	S	A	I
Secondary structure
SS confidence
Disorder																								?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	430	.	.	.	.	.	.	.	.	.	440	.	.	.	.	.	.	.	.	.	450	.	.	.	.	.	.	.	.	.	460	.	.	.	.	.	.	.	.	.	470	.	.	.	.	.	.	.	.	.	480
Sequence		G	L	Y	Y	Y	L	R	V	A	V	S	L	Y	L	H	A	P	E	Q	P	G	R	D	A	P	S	N	W	Q	Y	S	A	G	G	I	V	V	L	I	S	A	L	L	V	L	V	L	G	V	W	P	Q	P	L	I	S	I	V	R	L
Secondary structure
SS confidence
Disorder																				?	?	?	?	?	?	?	?	?	?	?	?	?	?	?
Disorder confidence
		.	.	.	.	.
Sequence		A	M	P	L	M
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 3rko chain N Region: 1 - 485 Aligned: 473 Modelled: 485 Confidence: 100.0% Identity: 99% PDB header:oxidoreductase Chain: N: PDB Molecule:nadh-quinone oxidoreductase subunit n; PDBTitle: crystal structure of the membrane domain of respiratory complex i from2 e. coli at 3.0 angstrom resolution Phyre2 PDB 3rko chain L Region: 3 - 473 Aligned: 457 Modelled: 471 Confidence: 100.0% Identity: 19% PDB header:oxidoreductase Chain: L: PDB Molecule:nadh-quinone oxidoreductase subunit l; PDBTitle: crystal structure of the membrane domain of respiratory complex i from2 e. coli at 3.0 angstrom resolution Phyre2 PDB 3rko chain M Region: 8 - 483 Aligned: 467 Modelled: 476 Confidence: 100.0% Identity: 20% PDB header:oxidoreductase Chain: M: PDB Molecule:nadh-quinone oxidoreductase subunit m; PDBTitle: crystal structure of the membrane domain of respiratory complex i from2 e. coli at 3.0 angstrom resolution Phyre2 PDB 3rko chain K Region: 102 - 188 Aligned: 87 Modelled: 87 Confidence: 54.7% Identity: 21% PDB header:oxidoreductase Chain: K: PDB Molecule:nadh-quinone oxidoreductase subunit k; PDBTitle: crystal structure of the membrane domain of respiratory complex i from2 e. coli at 3.0 angstrom resolution Phyre2 PDB 1a6q chain A domain 1 Region: 371 - 405 Aligned: 35 Modelled: 35 Confidence: 39.8% Identity: 11% Fold: Another 3-helical bundle Superfamily: Protein serine/threonine phosphatase 2C, C-terminal domain Family: Protein serine/threonine phosphatase 2C, C-terminal domain Phyre2 PDB 2l3i chain A Region: 288 - 300 Aligned: 13 Modelled: 13 Confidence: 21.6% Identity: 46% PDB header:antimicrobial protein Chain: A: PDB Molecule:aoxki4a, antimicrobial peptide in spider venom; PDBTitle: oxki4a, spider derived antimicrobial peptide Phyre2 PDB 3mes chain B Region: 215 - 227 Aligned: 13 Modelled: 13 Confidence: 8.8% Identity: 15% PDB header:transferase Chain: B: PDB Molecule:choline kinase; PDBTitle: crystal structure of choline kinase from cryptosporidium2 parvum iowa ii, cgd3_2030 Phyre2 PDB 1fft chain B domain 2 Region: 402 - 481 Aligned: 80 Modelled: 80 Confidence: 8.0% Identity: 10% Fold: Transmembrane helix hairpin Superfamily: Cytochrome c oxidase subunit II-like, transmembrane region Family: Cytochrome c oxidase subunit II-like, transmembrane region Phyre2 PDB 2knc chain A Region: 404 - 448 Aligned: 45 Modelled: 45 Confidence: 7.2% Identity: 13% PDB header:cell adhesion Chain: A: PDB Molecule:integrin alpha-iib; PDBTitle: platelet integrin alfaiib-beta3 transmembrane-cytoplasmic2 heterocomplex Phyre2 PDB 1r6r chain A Region: 370 - 396 Aligned: 27 Modelled: 27 Confidence: 6.8% Identity: 26% PDB header:viral protein Chain: A: PDB Molecule:genome polyprotein; PDBTitle: solution structure of dengue virus capsid protein reveals a2 new fold Phyre2 PDB 1r6r chain A Region: 370 - 396 Aligned: 27 Modelled: 27 Confidence: 6.8% Identity: 26% Fold: Flavivirus capsid protein C Superfamily: Flavivirus capsid protein C Family: Flavivirus capsid protein C Phyre2 PDB 1ceu chain A Region: 222 - 233 Aligned: 12 Modelled: 12 Confidence: 6.6% Identity: 25% PDB header:viral protein Chain: A: PDB Molecule:protein (hiv-1 regulatory protein n-terminal PDBTitle: nmr structure of the (1-51) n-terminal domain of the hiv-12 regulatory protein Phyre2 PDB 1n9w chain A domain 2 Region: 385 - 392 Aligned: 8 Modelled: 8 Confidence: 6.5% Identity: 50% Fold: Class II aaRS and biotin synthetases Superfamily: Class II aaRS and biotin synthetases Family: Class II aminoacyl-tRNA synthetase (aaRS)-like, catalytic domain Phyre2 PDB 3r24 chain A Region: 224 - 232 Aligned: 9 Modelled: 9 Confidence: 6.5% Identity: 44% PDB header:transferase, viral protein Chain: A: PDB Molecule:2'-o-methyl transferase; PDBTitle: crystal structure of nsp10/nsp16 complex of sars coronavirus" if2 possible Phyre2 PDB 3c25 chain A Region: 223 - 228 Aligned: 6 Modelled: 6 Confidence: 6.3% Identity: 67% PDB header:hydrolase/dna Chain: A: PDB Molecule:noti restriction endonuclease; PDBTitle: crystal structure of noti restriction endonuclease bound to cognate2 dna Phyre2 PDB 1n9w chain A Region: 385 - 392 Aligned: 8 Modelled: 8 Confidence: 6.2% Identity: 50% PDB header:biosynthetic protein Chain: A: PDB Molecule:aspartyl-trna synthetase 2; PDBTitle: crystal structure of the non-discriminating and archaeal-2 type aspartyl-trna synthetase from thermus thermophilus Phyre2 PDB 3dtu chain B domain 2 Region: 384 - 465 Aligned: 77 Modelled: 82 Confidence: 6.1% 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 3bju chain B Region: 385 - 392 Aligned: 8 Modelled: 8 Confidence: 5.8% Identity: 50% PDB header:ligase Chain: B: PDB Molecule:lysyl-trna synthetase; PDBTitle: crystal structure of tetrameric form of human lysyl-trna2 synthetase Phyre2 PDB 1b8a chain B Region: 385 - 392 Aligned: 8 Modelled: 8 Confidence: 5.4% Identity: 50% PDB header:ligase Chain: B: PDB Molecule:protein (aspartyl-trna synthetase); PDBTitle: aspartyl-trna synthetase Phyre2 PDB 2xte chain H Region: 469 - 483 Aligned: 15 Modelled: 15 Confidence: 5.3% Identity: 40% PDB header:transcription Chain: H: PDB Molecule:f-box-like/wd repeat-containing protein tbl1x; PDBTitle: structure of the tbl1 tetramerisation domain Phyre2 1 c3rkoN_ 2 c3rkoL_ 3 c3rkoM_ 4 c3rkoK_ 5 d1a6qa1 6 c2l3iA_ 7 c3mesB_ 8 d1fftb2 9 c2kncA_ 10 c1r6rA_ 11 d1r6ra_ 12 c1ceuA_ 13 d1n9wa2 14 c3r24A_ 15 c3c25A_ 16 c1n9wA_ 17 d3dtub2 18 c3bjuB_ 19 c1b8aB_ 20 c2xteH_ 21 22

Detailed template information

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

1 c3rkoN_ 100.0 99 PDB header:oxidoreductase Chain: N: PDB Molecule:nadh-quinone oxidoreductase subunit n; PDBTitle: crystal structure of the membrane domain of respiratory complex i from2 e. coli at 3.0 angstrom resolution 2 c3rkoL_ 100.0 19 PDB header:oxidoreductase Chain: L: PDB Molecule:nadh-quinone oxidoreductase subunit l; PDBTitle: crystal structure of the membrane domain of respiratory complex i from2 e. coli at 3.0 angstrom resolution 3 c3rkoM_ 100.0 20 PDB header:oxidoreductase Chain: M: PDB Molecule:nadh-quinone oxidoreductase subunit m; PDBTitle: crystal structure of the membrane domain of respiratory complex i from2 e. coli at 3.0 angstrom resolution 4 c3rkoK_ 54.7 21 PDB header:oxidoreductase Chain: K: PDB Molecule:nadh-quinone oxidoreductase subunit k; PDBTitle: crystal structure of the membrane domain of respiratory complex i from2 e. coli at 3.0 angstrom resolution 5 d1a6qa1 39.8 11 Fold:Another 3-helical bundle Superfamily:Protein serine/threonine phosphatase 2C, C-terminal domain Family:Protein serine/threonine phosphatase 2C, C-terminal domain 6 c2l3iA_ 21.6 46 PDB header:antimicrobial protein Chain: A: PDB Molecule:aoxki4a, antimicrobial peptide in spider venom; PDBTitle: oxki4a, spider derived antimicrobial peptide 7 c3mesB_ 8.8 15 PDB header:transferase Chain: B: PDB Molecule:choline kinase; PDBTitle: crystal structure of choline kinase from cryptosporidium2 parvum iowa ii, cgd3_2030 8 d1fftb2 8.0 10 Fold:Transmembrane helix hairpin Superfamily:Cytochrome c oxidase subunit II-like, transmembrane region Family:Cytochrome c oxidase subunit II-like, transmembrane region 9 c2kncA_ 7.2 13 PDB header:cell adhesion Chain: A: PDB Molecule:integrin alpha-iib; PDBTitle: platelet integrin alfaiib-beta3 transmembrane-cytoplasmic2 heterocomplex 10 c1r6rA_ 6.8 26 PDB header:viral protein Chain: A: PDB Molecule:genome polyprotein; PDBTitle: solution structure of dengue virus capsid protein reveals a2 new fold 11 d1r6ra_ 6.8 26 Fold:Flavivirus capsid protein C Superfamily:Flavivirus capsid protein C Family:Flavivirus capsid protein C 12 c1ceuA_ 6.6 25 PDB header:viral protein Chain: A: PDB Molecule:protein (hiv-1 regulatory protein n-terminal PDBTitle: nmr structure of the (1-51) n-terminal domain of the hiv-12 regulatory protein 13 d1n9wa2 6.5 50 Fold:Class II aaRS and biotin synthetases Superfamily:Class II aaRS and biotin synthetases Family:Class II aminoacyl-tRNA synthetase (aaRS)-like, catalytic domain 14 c3r24A_ 6.5 44 PDB header:transferase, viral protein Chain: A: PDB Molecule:2'-o-methyl transferase; PDBTitle: crystal structure of nsp10/nsp16 complex of sars coronavirus" if2 possible 15 c3c25A_ 6.3 67 PDB header:hydrolase/dna Chain: A: PDB Molecule:noti restriction endonuclease; PDBTitle: crystal structure of noti restriction endonuclease bound to cognate2 dna 16 c1n9wA_ 6.2 50 PDB header:biosynthetic protein Chain: A: PDB Molecule:aspartyl-trna synthetase 2; PDBTitle: crystal structure of the non-discriminating and archaeal-2 type aspartyl-trna synthetase from thermus thermophilus 17 d3dtub2 6.1 9 Fold:Transmembrane helix hairpin Superfamily:Cytochrome c oxidase subunit II-like, transmembrane region Family:Cytochrome c oxidase subunit II-like, transmembrane region 18 c3bjuB_ 5.8 50 PDB header:ligase Chain: B: PDB Molecule:lysyl-trna synthetase; PDBTitle: crystal structure of tetrameric form of human lysyl-trna2 synthetase 19 c1b8aB_ 5.4 50 PDB header:ligase Chain: B: PDB Molecule:protein (aspartyl-trna synthetase); PDBTitle: aspartyl-trna synthetase 20 c2xteH_ 5.3 40 PDB header:transcription Chain: H: PDB Molecule:f-box-like/wd repeat-containing protein tbl1x; PDBTitle: structure of the tbl1 tetramerisation domain 21 c1wydB_ not modelled 5.2 50 PDB header:ligase Chain: B: PDB Molecule:hypothetical aspartyl-trna synthetase; PDBTitle: crystal structure of aspartyl-trna synthetase from sulfolobus tokodaii 22 c2jwaA_ not modelled 5.1 21 PDB header:transferase Chain: A: PDB Molecule:receptor tyrosine-protein kinase erbb-2; PDBTitle: erbb2 transmembrane segment dimer spatial structure

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

Transmembrane helix prediction

Transmembrane helices have been predicted in your sequence to adopt the topology shown below

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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