Secondary structure and disorder prediction

		1	.	.	.	.	.	.	.	.	10	.	.	.	.	.	.	.	.	.	20	.	.	.	.	.	.	.	.	.	30	.	.	.	.	.	.	.	.	.	40	.	.	.	.	.	.	.	.	.	50	.	.	.	.	.	.	.	.	.	60
Sequence		M	Q	K	Y	I	S	E	A	R	L	L	L	A	L	A	I	P	V	I	L	A	Q	I	A	Q	T	A	M	G	F	V	D	T	V	M	A	G	G	Y	S	A	T	D	M	A	A	V	A	I	G	T	S	I	W	L	P	A	I	L	F
Secondary structure
SS confidence
Disorder		?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	70	.	.	.	.	.	.	.	.	.	80	.	.	.	.	.	.	.	.	.	90	.	.	.	.	.	.	.	.	.	100	.	.	.	.	.	.	.	.	.	110	.	.	.	.	.	.	.	.	.	120
Sequence		G	H	G	L	L	L	A	L	T	P	V	I	A	Q	L	N	G	S	G	R	R	E	R	I	A	H	Q	V	R	Q	G	F	W	L	A	G	F	V	S	V	L	I	M	L	V	L	W	N	A	G	Y	I	I	R	S	M	E	N	I	D
Secondary structure
SS confidence
Disorder																			?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	130	.	.	.	.	.	.	.	.	.	140	.	.	.	.	.	.	.	.	.	150	.	.	.	.	.	.	.	.	.	160	.	.	.	.	.	.	.	.	.	170	.	.	.	.	.	.	.	.	.	180
Sequence		P	A	L	A	D	K	A	V	G	Y	L	R	A	L	L	W	G	A	P	G	Y	L	F	F	Q	V	A	R	N	Q	C	E	G	L	A	K	T	K	P	G	M	V	M	G	F	I	G	L	L	V	N	I	P	V	N	Y	I	F	I	Y
Secondary structure
SS confidence
Disorder
Disorder confidence
		.	.	.	.	.	.	.	.	.	190	.	.	.	.	.	.	.	.	.	200	.	.	.	.	.	.	.	.	.	210	.	.	.	.	.	.	.	.	.	220	.	.	.	.	.	.	.	.	.	230	.	.	.	.	.	.	.	.	.	240
Sequence		G	H	F	G	M	P	E	L	G	G	V	G	C	G	V	A	T	A	A	V	Y	W	V	M	F	L	A	M	V	S	Y	I	K	R	A	R	S	M	R	D	I	R	N	E	K	G	T	A	K	P	D	P	A	V	M	K	R	L	I	Q
Secondary structure
SS confidence
Disorder																																							?	?						?	?			?
Disorder confidence
		.	.	.	.	.	.	.	.	.	250	.	.	.	.	.	.	.	.	.	260	.	.	.	.	.	.	.	.	.	270	.	.	.	.	.	.	.	.	.	280	.	.	.	.	.	.	.	.	.	290	.	.	.	.	.	.	.	.	.	300
Sequence		L	G	L	P	I	A	L	A	L	F	F	E	V	T	L	F	A	V	V	A	L	L	V	S	P	L	G	I	V	D	V	A	G	H	Q	I	A	L	N	F	S	S	L	M	F	V	L	P	M	S	L	A	A	A	V	T	I	R	V	G
Secondary structure
SS confidence
Disorder																									?
Disorder confidence
		.	.	.	.	.	.	.	.	.	310	.	.	.	.	.	.	.	.	.	320	.	.	.	.	.	.	.	.	.	330	.	.	.	.	.	.	.	.	.	340	.	.	.	.	.	.	.	.	.	350	.	.	.	.	.	.	.	.	.	360
Sequence		Y	R	L	G	Q	G	S	T	L	D	A	Q	T	A	A	R	T	G	L	M	V	G	V	C	M	A	T	L	T	A	I	F	T	V	S	L	R	E	Q	I	A	L	L	Y	N	D	N	P	E	V	V	T	L	A	A	H	L	M	L	L
Secondary structure
SS confidence
Disorder						?
Disorder confidence
		.	.	.	.	.	.	.	.	.	370	.	.	.	.	.	.	.	.	.	380	.	.	.	.	.	.	.	.	.	390	.	.	.	.	.	.	.	.	.	400	.	.	.	.	.	.	.	.	.	410	.	.	.	.	.	.	.	.	.	420
Sequence		A	A	V	Y	Q	I	S	D	S	I	Q	V	I	G	S	G	I	L	R	G	Y	K	D	T	R	S	I	F	Y	I	T	F	T	A	Y	W	V	L	G	L	P	S	G	Y	I	L	A	L	T	D	L	V	V	E	P	M	G	P	A	G
Secondary structure
SS confidence
Disorder
Disorder confidence
		.	.	.	.	.	.	.	.	.	430	.	.	.	.	.	.	.	.	.	440	.	.	.	.	.	.	.	.	.	450	.	.	.	.	.	.	.
Sequence		F	W	I	G	F	I	I	G	L	T	S	A	A	I	M	M	M	L	R	M	R	F	L	Q	R	L	P	S	A	I	I	L	Q	R	A	S	R
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 3mku chain A Region: 1 - 457 Aligned: 456 Modelled: 456 Confidence: 100.0% Identity: 55% 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 1pw4 chain A Region: 2 - 453 Aligned: 410 Modelled: 420 Confidence: 18.8% Identity: 12% Fold: MFS general substrate transporter Superfamily: MFS general substrate transporter Family: Glycerol-3-phosphate transporter Phyre2 PDB 2iub chain A domain 2 Region: 395 - 444 Aligned: 45 Modelled: 50 Confidence: 10.0% Identity: 18% Fold: Transmembrane helix hairpin Superfamily: Magnesium transport protein CorA, transmembrane region Family: Magnesium transport protein CorA, transmembrane region Phyre2 PDB 3g43 chain F Region: 1 - 24 Aligned: 24 Modelled: 24 Confidence: 9.7% Identity: 8% PDB header:metal binding protein Chain: F: PDB Molecule:voltage-dependent l-type calcium channel subunit PDBTitle: crystal structure of the calmodulin-bound cav1.2 c-terminal2 regulatory domain dimer Phyre2 PDB 1wrg chain A Region: 78 - 114 Aligned: 37 Modelled: 37 Confidence: 9.6% Identity: 11% PDB header:membrane protein Chain: A: PDB Molecule:light-harvesting protein b-880, beta chain; PDBTitle: light-harvesting complex 1 beta subunit from wild-type2 rhodospirillum rubrum Phyre2 PDB 1lgh chain B Region: 78 - 113 Aligned: 36 Modelled: 36 Confidence: 8.8% Identity: 8% Fold: Light-harvesting complex subunits Superfamily: Light-harvesting complex subunits Family: Light-harvesting complex subunits Phyre2 PDB 3ipd chain B Region: 304 - 343 Aligned: 40 Modelled: 40 Confidence: 8.7% Identity: 10% PDB header:exocytosis Chain: B: PDB Molecule:syntaxin-1a; PDBTitle: helical extension of the neuronal snare complex into the2 membrane, spacegroup i 21 21 21 Phyre2 PDB 3hzq chain A Region: 419 - 449 Aligned: 31 Modelled: 31 Confidence: 8.3% Identity: 16% PDB header:membrane protein Chain: A: PDB Molecule:large-conductance mechanosensitive channel; PDBTitle: structure of a tetrameric mscl in an expanded intermediate2 state Phyre2 PDB 2ket chain A Region: 2 - 13 Aligned: 12 Modelled: 12 Confidence: 7.9% Identity: 8% PDB header:antibiotic Chain: A: PDB Molecule:cathelicidin-6; PDBTitle: solution structure of bmap-27 Phyre2 PDB 1m56 chain D Region: 300 - 337 Aligned: 38 Modelled: 38 Confidence: 7.7% Identity: 11% Fold: Single transmembrane helix Superfamily: Bacterial aa3 type cytochrome c oxidase subunit IV Family: Bacterial aa3 type cytochrome c oxidase subunit IV Phyre2 PDB 1nov chain E Region: 4 - 16 Aligned: 13 Modelled: 13 Confidence: 7.5% Identity: 15% PDB header:virus Chain: E: PDB Molecule:nodamura virus coat proteins; PDBTitle: nodamura virus Phyre2 PDB 2z2q chain F Region: 3 - 19 Aligned: 17 Modelled: 17 Confidence: 7.4% Identity: 0% PDB header:virus/rna Chain: F: PDB Molecule:coat protein gamma; PDBTitle: crystal structure of flock house virus Phyre2 PDB 2d5b chain A domain 1 Region: 75 - 123 Aligned: 49 Modelled: 49 Confidence: 7.2% Identity: 8% Fold: Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases Superfamily: Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases Family: Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases Phyre2 PDB 1u61 chain A Region: 292 - 322 Aligned: 31 Modelled: 31 Confidence: 7.1% Identity: 13% Fold: RNase III domain-like Superfamily: RNase III domain-like Family: RNase III catalytic domain-like Phyre2 PDB 1v54 chain C Region: 6 - 101 Aligned: 93 Modelled: 93 Confidence: 6.9% Identity: 10% Fold: Cytochrome c oxidase subunit III-like Superfamily: Cytochrome c oxidase subunit III-like Family: Cytochrome c oxidase subunit III-like Phyre2 PDB 1jo5 chain A Region: 82 - 113 Aligned: 32 Modelled: 32 Confidence: 6.7% Identity: 16% Fold: Light-harvesting complex subunits Superfamily: Light-harvesting complex subunits Family: Light-harvesting complex subunits Phyre2 PDB 2hyd chain B Region: 1 - 315 Aligned: 310 Modelled: 310 Confidence: 6.6% Identity: 11% PDB header:transport protein Chain: B: PDB Molecule:abc transporter homolog; PDBTitle: multidrug abc transporter sav1866 Phyre2 PDB 1w7a chain B domain 4 Region: 1 - 6 Aligned: 6 Modelled: 6 Confidence: 6.3% Identity: 50% Fold: MutS N-terminal domain-like Superfamily: DNA repair protein MutS, domain I Family: DNA repair protein MutS, domain I Phyre2 PDB 2l35 chain A Region: 17 - 60 Aligned: 44 Modelled: 44 Confidence: 6.3% Identity: 7% PDB header:protein binding Chain: A: PDB Molecule:dap12-nkg2c_tm; PDBTitle: structure of the dap12-nkg2c transmembrane heterotrimer Phyre2 PDB 2gsl chain E Region: 292 - 319 Aligned: 28 Modelled: 28 Confidence: 6.3% Identity: 11% PDB header:structural genomics, unknown function Chain: E: PDB Molecule:hypothetical protein; PDBTitle: x-ray crystal structure of protein fn1578 from fusobacterium2 nucleatum. northeast structural genomics consortium target nr1. Phyre2 1 c3mkuA_ 2 d1pw4a_ 3 d2iuba2 4 c3g43F_ 5 c1wrgA_ 6 d1lghb_ 7 c3ipdB_ 8 c3hzqA_ 9 c2ketA_ 10 d1m56d_ 11 c1novE_ 12 c2z2qF_ 13 d2d5ba1 14 d1u61a_ 15 d1v54c_ 16 d1jo5a_ 17 c2hydB_ 18 d1w7ab4 19 c2l35A_ 20 c2gslE_ 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38

Detailed template information

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

1 c3mkuA_ 100.0 55 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 2 d1pw4a_ 18.8 12 Fold:MFS general substrate transporter Superfamily:MFS general substrate transporter Family:Glycerol-3-phosphate transporter 3 d2iuba2 10.0 18 Fold:Transmembrane helix hairpin Superfamily:Magnesium transport protein CorA, transmembrane region Family:Magnesium transport protein CorA, transmembrane region 4 c3g43F_ 9.7 8 PDB header:metal binding protein Chain: F: PDB Molecule:voltage-dependent l-type calcium channel subunit PDBTitle: crystal structure of the calmodulin-bound cav1.2 c-terminal2 regulatory domain dimer 5 c1wrgA_ 9.6 11 PDB header:membrane protein Chain: A: PDB Molecule:light-harvesting protein b-880, beta chain; PDBTitle: light-harvesting complex 1 beta subunit from wild-type2 rhodospirillum rubrum 6 d1lghb_ 8.8 8 Fold:Light-harvesting complex subunits Superfamily:Light-harvesting complex subunits Family:Light-harvesting complex subunits 7 c3ipdB_ 8.7 10 PDB header:exocytosis Chain: B: PDB Molecule:syntaxin-1a; PDBTitle: helical extension of the neuronal snare complex into the2 membrane, spacegroup i 21 21 21 8 c3hzqA_ 8.3 16 PDB header:membrane protein Chain: A: PDB Molecule:large-conductance mechanosensitive channel; PDBTitle: structure of a tetrameric mscl in an expanded intermediate2 state 9 c2ketA_ 7.9 8 PDB header:antibiotic Chain: A: PDB Molecule:cathelicidin-6; PDBTitle: solution structure of bmap-27 10 d1m56d_ 7.7 11 Fold:Single transmembrane helix Superfamily:Bacterial aa3 type cytochrome c oxidase subunit IV Family:Bacterial aa3 type cytochrome c oxidase subunit IV 11 c1novE_ 7.5 15 PDB header:virus Chain: E: PDB Molecule:nodamura virus coat proteins; PDBTitle: nodamura virus 12 c2z2qF_ 7.4 0 PDB header:virus/rna Chain: F: PDB Molecule:coat protein gamma; PDBTitle: crystal structure of flock house virus 13 d2d5ba1 7.2 8 Fold:Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases Superfamily:Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases Family:Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases 14 d1u61a_ 7.1 13 Fold:RNase III domain-like Superfamily:RNase III domain-like Family:RNase III catalytic domain-like 15 d1v54c_ 6.9 10 Fold:Cytochrome c oxidase subunit III-like Superfamily:Cytochrome c oxidase subunit III-like Family:Cytochrome c oxidase subunit III-like 16 d1jo5a_ 6.7 16 Fold:Light-harvesting complex subunits Superfamily:Light-harvesting complex subunits Family:Light-harvesting complex subunits 17 c2hydB_ 6.6 11 PDB header:transport protein Chain: B: PDB Molecule:abc transporter homolog; PDBTitle: multidrug abc transporter sav1866 18 d1w7ab4 6.3 50 Fold:MutS N-terminal domain-like Superfamily:DNA repair protein MutS, domain I Family:DNA repair protein MutS, domain I 19 c2l35A_ 6.3 7 PDB header:protein binding Chain: A: PDB Molecule:dap12-nkg2c_tm; PDBTitle: structure of the dap12-nkg2c transmembrane heterotrimer 20 c2gslE_ 6.3 11 PDB header:structural genomics, unknown function Chain: E: PDB Molecule:hypothetical protein; PDBTitle: x-ray crystal structure of protein fn1578 from fusobacterium2 nucleatum. northeast structural genomics consortium target nr1. 21 c2k6xA_ not modelled 6.2 20 PDB header:transcription Chain: A: PDB Molecule:rna polymerase sigma factor rpod; PDBTitle: autoregulation of a group 1 bacterial sigma factor involves2 the formation of a region 1.1- induced compacted structure 22 d1pf4a2 not modelled 6.0 13 Fold:ABC transporter transmembrane region Superfamily:ABC transporter transmembrane region Family:ABC transporter transmembrane region 23 c1m46B_ not modelled 5.8 22 PDB header:cell cycle protein Chain: B: PDB Molecule:iq4 motif from myo2p, a class v myosin; PDBTitle: crystal structure of mlc1p bound to iq4 of myo2p, a class v2 myosin 24 c1tiiC_ not modelled 5.7 10 PDB header:enterotoxin Chain: C: PDB Molecule:heat labile enterotoxin type iib; PDBTitle: escherichia coli heat labile enterotoxin type iib 25 d1kbhb_ not modelled 5.5 40 Fold:Nuclear receptor coactivator interlocking domain Superfamily:Nuclear receptor coactivator interlocking domain Family:Nuclear receptor coactivator interlocking domain 26 d1eysh2 not modelled 5.4 7 Fold:Single transmembrane helix Superfamily:Photosystem II reaction centre subunit H, transmembrane region Family:Photosystem II reaction centre subunit H, transmembrane region 27 d1nvpb_ not modelled 5.4 17 Fold:Transcription factor IIA (TFIIA), alpha-helical domain Superfamily:Transcription factor IIA (TFIIA), alpha-helical domain Family:Transcription factor IIA (TFIIA), alpha-helical domain 28 c1nvpB_ not modelled 5.4 17 PDB header:transcription/dna Chain: B: PDB Molecule:transcription initiation factor iia alpha chain; PDBTitle: human tfiia/tbp/dna complex 29 c1b9uA_ not modelled 5.4 18 PDB header:hydrolase Chain: A: PDB Molecule:protein (atp synthase); PDBTitle: membrane domain of the subunit b of the e.coli atp synthase 30 d1nkzb_ not modelled 5.2 12 Fold:Light-harvesting complex subunits Superfamily:Light-harvesting complex subunits Family:Light-harvesting complex subunits 31 c1unyA_ not modelled 5.2 15 PDB header:four helix bundle Chain: A: PDB Molecule:general control protein gcn4; PDBTitle: structure based engineering of internal molecular surfaces2 of four helix bundles 32 d1qlec_ not modelled 5.1 13 Fold:Cytochrome c oxidase subunit III-like Superfamily:Cytochrome c oxidase subunit III-like Family:Cytochrome c oxidase subunit III-like 33 d1zoqc1 not modelled 5.1 40 Fold:Nuclear receptor coactivator interlocking domain Superfamily:Nuclear receptor coactivator interlocking domain Family:Nuclear receptor coactivator interlocking domain 34 c2i7uA_ not modelled 5.1 42 PDB header:de novo protein/ligand binding protein Chain: A: PDB Molecule:four-alpha-helix bundle; PDBTitle: structural and dynamical analysis of a four-alpha-helix2 bundle with designed anesthetic binding pockets 35 d2cqna1 not modelled 5.1 23 Fold:Another 3-helical bundle Superfamily:FF domain Family:FF domain 36 c1iojA_ not modelled 5.1 43 PDB header:apolipoprotein Chain: A: PDB Molecule:apoc-i; PDBTitle: human apolipoprotein c-i, nmr, 18 structures 37 c2khgA_ not modelled 5.0 22 PDB header:antimicrobial protein Chain: A: PDB Molecule:plnj; PDBTitle: plantaricin j in tfe 38 c2khfA_ not modelled 5.0 22 PDB header:antimicrobial protein Chain: A: PDB Molecule:plnj; PDBTitle: plantaricin j in dpc-micelles

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