Secondary structure and disorder prediction

		1	.	.	.	.	.	.	.	.	10	.	.	.	.	.	.	.	.	.	20	.	.	.	.	.	.	.	.	.	30	.	.	.	.	.	.	.	.	.	40	.	.	.	.	.	.	.	.	.	50	.	.	.	.	.	.	.	.	.	60
Sequence		M	T	T	Q	R	S	P	G	L	F	R	R	L	A	H	G	S	L	V	K	Q	I	L	V	G	L	V	L	G	I	L	L	A	W	I	S	K	P	A	A	E	A	V	G	L	L	G	T	L	F	V	G	A	L	K	A	V	A	P	I
Secondary structure
SS confidence
Disorder		?	?	?	?	?	?	?								?	?		?
Disorder confidence
		.	.	.	.	.	.	.	.	.	70	.	.	.	.	.	.	.	.	.	80	.	.	.	.	.	.	.	.	.	90	.	.	.	.	.	.	.	.	.	100	.	.	.	.	.	.	.	.	.	110	.	.	.	.	.	.	.	.	.	120
Sequence		L	V	L	M	L	V	M	A	S	I	A	N	H	Q	H	G	Q	K	T	N	I	R	P	I	L	F	L	Y	L	L	G	T	F	S	A	A	L	A	A	V	V	F	S	F	A	F	P	S	T	L	H	L	S	S	S	A	G	D	I	S
Secondary structure
SS confidence
Disorder												?	?	?	?	?	?	?	?	?																											?	?	?	?	?	?	?	?	?	?	?	?	?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	130	.	.	.	.	.	.	.	.	.	140	.	.	.	.	.	.	.	.	.	150	.	.	.	.	.	.	.	.	.	160	.	.	.	.	.	.	.	.	.	170	.	.	.	.	.	.	.	.	.	180
Sequence		P	P	S	G	I	V	E	V	M	R	G	L	V	M	S	M	V	S	N	P	I	D	A	L	L	K	G	N	Y	I	G	I	L	V	W	A	I	G	L	G	F	A	L	R	H	G	N	E	T	T	K	N	L	V	N	D	M	S	N	A
Secondary structure
SS confidence
Disorder		?	?	?	?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	190	.	.	.	.	.	.	.	.	.	200	.	.	.	.	.	.	.	.	.	210	.	.	.	.	.	.	.	.	.	220	.	.	.	.	.	.	.	.	.	230	.	.	.	.	.	.	.	.	.	240
Sequence		V	T	F	M	V	K	L	V	I	R	F	A	P	I	G	I	F	G	L	V	S	S	T	L	A	T	T	G	F	S	T	L	W	G	Y	A	Q	L	L	V	V	L	V	G	C	M	L	L	V	A	L	V	V	N	P	L	L	V	W	W
Secondary structure
SS confidence
Disorder																												?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	250	.	.	.	.	.	.	.	.	.	260	.	.	.	.	.	.	.	.	.	270	.	.	.	.	.	.	.	.	.	280	.	.	.	.	.	.	.	.	.	290	.	.	.	.	.	.	.	.	.	300
Sequence		K	I	R	R	N	P	F	P	L	V	L	L	C	L	R	E	S	G	V	Y	A	F	F	T	R	S	S	A	A	N	I	P	V	N	M	A	L	C	E	K	L	N	L	D	R	D	T	Y	S	V	S	I	P	L	G	A	T	I	N	M
Secondary structure
SS confidence
Disorder
Disorder confidence
		.	.	.	.	.	.	.	.	.	310	.	.	.	.	.	.	.	.	.	320	.	.	.	.	.	.	.	.	.	330	.	.	.	.	.	.	.	.	.	340	.	.	.	.	.	.	.	.	.	350	.	.	.	.	.	.	.	.	.	360
Sequence		A	G	A	A	I	T	I	T	V	L	T	L	A	A	V	N	T	L	G	I	P	V	D	L	P	T	A	L	L	L	S	V	V	A	S	L	C	A	C	G	A	S	G	V	A	G	G	S	L	L	L	I	P	L	A	C	N	M	F	G
Secondary structure
SS confidence
Disorder																																								?	?	?	?		?
Disorder confidence
		.	.	.	.	.	.	.	.	.	370	.	.	.	.	.	.	.	.	.	380	.	.	.	.	.	.	.	.	.	390	.	.	.	.	.	.	.	.	.	400	.	.	.	.	.	.	.	.	.	410	.	.	.	.
Sequence		I	S	N	D	I	A	M	Q	V	V	A	V	G	F	I	I	G	V	L	Q	D	S	C	E	T	A	L	N	S	S	T	D	V	L	F	T	A	A	A	C	Q	A	E	D	D	R	L	A	N	S	A	L	R	N
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 2nww chain A domain 1 Region: 18 - 403 Aligned: 384 Modelled: 386 Confidence: 100.0% Identity: 26% Fold: Proton glutamate symport protein Superfamily: Proton glutamate symport protein Family: Proton glutamate symport protein Phyre2 PDB 1iwg chain A domain 8 Region: 148 - 246 Aligned: 99 Modelled: 99 Confidence: 58.6% Identity: 14% Fold: Multidrug efflux transporter AcrB transmembrane domain Superfamily: Multidrug efflux transporter AcrB transmembrane domain Family: Multidrug efflux transporter AcrB transmembrane domain Phyre2 PDB 1a77 chain A domain 1 Region: 322 - 360 Aligned: 38 Modelled: 39 Confidence: 22.0% Identity: 11% Fold: SAM domain-like Superfamily: 5' to 3' exonuclease, C-terminal subdomain Family: 5' to 3' exonuclease, C-terminal subdomain Phyre2 PDB 1oy8 chain A Region: 148 - 258 Aligned: 111 Modelled: 111 Confidence: 18.9% Identity: 13% PDB header:membrane protein Chain: A: PDB Molecule:acriflavine resistance protein b; PDBTitle: structural basis of multiple drug binding capacity of the acrb2 multidrug efflux pump Phyre2 PDB 3ah5 chain E Region: 276 - 296 Aligned: 21 Modelled: 21 Confidence: 18.7% Identity: 19% PDB header:transferase Chain: E: PDB Molecule:thymidylate synthase thyx; PDBTitle: crystal structure of flavin dependent thymidylate synthase thyx from2 helicobacter pylori complexed with fad and dump Phyre2 PDB 1o26 chain A Region: 276 - 296 Aligned: 21 Modelled: 21 Confidence: 16.0% Identity: 14% Fold: Thymidylate synthase-complementing protein Thy1 Superfamily: Thymidylate synthase-complementing protein Thy1 Family: Thymidylate synthase-complementing protein Thy1 Phyre2 PDB 1bbo chain A domain 1 Region: 5 - 15 Aligned: 11 Modelled: 11 Confidence: 12.3% Identity: 9% Fold: beta-beta-alpha zinc fingers Superfamily: beta-beta-alpha zinc fingers Family: Classic zinc finger, C2H2 Phyre2 PDB 3k07 chain A Region: 148 - 241 Aligned: 94 Modelled: 94 Confidence: 10.4% Identity: 15% PDB header:transport protein Chain: A: PDB Molecule:cation efflux system protein cusa; PDBTitle: crystal structure of cusa Phyre2 PDB 1mc8 chain A domain 1 Region: 322 - 360 Aligned: 38 Modelled: 39 Confidence: 9.2% Identity: 11% Fold: SAM domain-like Superfamily: 5' to 3' exonuclease, C-terminal subdomain Family: 5' to 3' exonuclease, C-terminal subdomain Phyre2 PDB 2cmy chain B Region: 3 - 16 Aligned: 14 Modelled: 14 Confidence: 8.9% Identity: 50% PDB header:hydrolase Chain: B: PDB Molecule:veronica hederifolia trypsin inhibitor; PDBTitle: crystal complex between bovine trypsin and veronica2 hederifolia trypsin inhibitor Phyre2 PDB 2cmy chain B domain 1 Region: 3 - 16 Aligned: 14 Modelled: 14 Confidence: 8.9% Identity: 50% Fold: Toxic hairpin Superfamily: VhTI-like Family: VhTI-like Phyre2 PDB 1rxw chain A domain 1 Region: 322 - 360 Aligned: 37 Modelled: 39 Confidence: 8.6% Identity: 11% Fold: SAM domain-like Superfamily: 5' to 3' exonuclease, C-terminal subdomain Family: 5' to 3' exonuclease, C-terminal subdomain Phyre2 PDB 1kyz chain A domain 1 Region: 266 - 289 Aligned: 24 Modelled: 24 Confidence: 8.4% Identity: 21% Fold: DNA/RNA-binding 3-helical bundle Superfamily: "Winged helix" DNA-binding domain Family: Plant O-methyltransferase, N-terminal domain Phyre2 PDB 2cfa chain B Region: 276 - 296 Aligned: 21 Modelled: 21 Confidence: 8.3% Identity: 10% PDB header:transferase Chain: B: PDB Molecule:thymidylate synthase; PDBTitle: structure of viral flavin-dependant thymidylate synthase2 thyx Phyre2 PDB 1ul1 chain X domain 1 Region: 322 - 360 Aligned: 37 Modelled: 39 Confidence: 8.2% Identity: 5% Fold: SAM domain-like Superfamily: 5' to 3' exonuclease, C-terminal subdomain Family: 5' to 3' exonuclease, C-terminal subdomain Phyre2 PDB 2e75 chain E Region: 147 - 164 Aligned: 18 Modelled: 18 Confidence: 8.1% Identity: 28% PDB header:photosynthesis Chain: E: PDB Molecule:cytochrome b6-f complex subunit 6; PDBTitle: crystal structure of the cytochrome b6f complex with 2-nonyl-4-2 hydroxyquinoline n-oxide (nqno) from m.laminosus Phyre2 PDB 1vf5 chain R Region: 147 - 164 Aligned: 18 Modelled: 18 Confidence: 8.1% Identity: 28% PDB header:photosynthesis Chain: R: PDB Molecule:protein pet l; PDBTitle: crystal structure of cytochrome b6f complex from m.laminosus Phyre2 PDB 2e74 chain E Region: 147 - 164 Aligned: 18 Modelled: 18 Confidence: 8.1% Identity: 28% PDB header:photosynthesis Chain: E: PDB Molecule:cytochrome b6-f complex subunit 6; PDBTitle: crystal structure of the cytochrome b6f complex from m.laminosus Phyre2 PDB 1vf5 chain E Region: 147 - 164 Aligned: 18 Modelled: 18 Confidence: 8.1% Identity: 28% PDB header:photosynthesis Chain: E: PDB Molecule:protein pet l; PDBTitle: crystal structure of cytochrome b6f complex from m.laminosus Phyre2 PDB 2e74 chain E domain 1 Region: 147 - 164 Aligned: 18 Modelled: 18 Confidence: 8.1% Identity: 28% Fold: Single transmembrane helix Superfamily: PetL subunit of the cytochrome b6f complex Family: PetL subunit of the cytochrome b6f complex Phyre2 1 d2nwwa1 2 d1iwga8 3 d1a77a1 4 c1oy8A_ 5 c3ah5E_ 6 d1o26a_ 7 d1bboa1 8 c3k07A_ 9 d1mc8a1 10 c2cmyB_ 11 d2cmyb1 12 d1rxwa1 13 d1kyza1 14 c2cfaB_ 15 d1ul1x1 16 c2e75E_ 17 c1vf5R_ 18 c2e74E_ 19 c1vf5E_ 20 d2e74e1 21 22 23 24 25 26 27 28 29 30 31 32 33 34

Detailed template information

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

1 d2nwwa1 100.0 26 Fold:Proton glutamate symport protein Superfamily:Proton glutamate symport protein Family:Proton glutamate symport protein 2 d1iwga8 58.6 14 Fold:Multidrug efflux transporter AcrB transmembrane domain Superfamily:Multidrug efflux transporter AcrB transmembrane domain Family:Multidrug efflux transporter AcrB transmembrane domain 3 d1a77a1 22.0 11 Fold:SAM domain-like Superfamily:5' to 3' exonuclease, C-terminal subdomain Family:5' to 3' exonuclease, C-terminal subdomain 4 c1oy8A_ 18.9 13 PDB header:membrane protein Chain: A: PDB Molecule:acriflavine resistance protein b; PDBTitle: structural basis of multiple drug binding capacity of the acrb2 multidrug efflux pump 5 c3ah5E_ 18.7 19 PDB header:transferase Chain: E: PDB Molecule:thymidylate synthase thyx; PDBTitle: crystal structure of flavin dependent thymidylate synthase thyx from2 helicobacter pylori complexed with fad and dump 6 d1o26a_ 16.0 14 Fold:Thymidylate synthase-complementing protein Thy1 Superfamily:Thymidylate synthase-complementing protein Thy1 Family:Thymidylate synthase-complementing protein Thy1 7 d1bboa1 12.3 9 Fold:beta-beta-alpha zinc fingers Superfamily:beta-beta-alpha zinc fingers Family:Classic zinc finger, C2H2 8 c3k07A_ 10.4 15 PDB header:transport protein Chain: A: PDB Molecule:cation efflux system protein cusa; PDBTitle: crystal structure of cusa 9 d1mc8a1 9.2 11 Fold:SAM domain-like Superfamily:5' to 3' exonuclease, C-terminal subdomain Family:5' to 3' exonuclease, C-terminal subdomain 10 c2cmyB_ 8.9 50 PDB header:hydrolase Chain: B: PDB Molecule:veronica hederifolia trypsin inhibitor; PDBTitle: crystal complex between bovine trypsin and veronica2 hederifolia trypsin inhibitor 11 d2cmyb1 8.9 50 Fold:Toxic hairpin Superfamily:VhTI-like Family:VhTI-like 12 d1rxwa1 8.6 11 Fold:SAM domain-like Superfamily:5' to 3' exonuclease, C-terminal subdomain Family:5' to 3' exonuclease, C-terminal subdomain 13 d1kyza1 8.4 21 Fold:DNA/RNA-binding 3-helical bundle Superfamily:"Winged helix" DNA-binding domain Family:Plant O-methyltransferase, N-terminal domain 14 c2cfaB_ 8.3 10 PDB header:transferase Chain: B: PDB Molecule:thymidylate synthase; PDBTitle: structure of viral flavin-dependant thymidylate synthase2 thyx 15 d1ul1x1 8.2 5 Fold:SAM domain-like Superfamily:5' to 3' exonuclease, C-terminal subdomain Family:5' to 3' exonuclease, C-terminal subdomain 16 c2e75E_ 8.1 28 PDB header:photosynthesis Chain: E: PDB Molecule:cytochrome b6-f complex subunit 6; PDBTitle: crystal structure of the cytochrome b6f complex with 2-nonyl-4-2 hydroxyquinoline n-oxide (nqno) from m.laminosus 17 c1vf5R_ 8.1 28 PDB header:photosynthesis Chain: R: PDB Molecule:protein pet l; PDBTitle: crystal structure of cytochrome b6f complex from m.laminosus 18 c2e74E_ 8.1 28 PDB header:photosynthesis Chain: E: PDB Molecule:cytochrome b6-f complex subunit 6; PDBTitle: crystal structure of the cytochrome b6f complex from m.laminosus 19 c1vf5E_ 8.1 28 PDB header:photosynthesis Chain: E: PDB Molecule:protein pet l; PDBTitle: crystal structure of cytochrome b6f complex from m.laminosus 20 d2e74e1 8.1 28 Fold:Single transmembrane helix Superfamily:PetL subunit of the cytochrome b6f complex Family:PetL subunit of the cytochrome b6f complex 21 c2e76E_ not modelled 8.1 28 PDB header:photosynthesis Chain: E: PDB Molecule:cytochrome b6-f complex subunit 6; PDBTitle: crystal structure of the cytochrome b6f complex with tridecyl-2 stigmatellin (tds) from m.laminosus 22 d1xo1a1 not modelled 8.0 18 Fold:SAM domain-like Superfamily:5' to 3' exonuclease, C-terminal subdomain Family:5' to 3' exonuclease, C-terminal subdomain 23 d1fp1d1 not modelled 7.2 15 Fold:DNA/RNA-binding 3-helical bundle Superfamily:"Winged helix" DNA-binding domain Family:Plant O-methyltransferase, N-terminal domain 24 d2eiaa2 not modelled 7.1 10 Fold:Retrovirus capsid protein, N-terminal core domain Superfamily:Retrovirus capsid protein, N-terminal core domain Family:Retrovirus capsid protein, N-terminal core domain 25 d1b43a1 not modelled 6.8 11 Fold:SAM domain-like Superfamily:5' to 3' exonuclease, C-terminal subdomain Family:5' to 3' exonuclease, C-terminal subdomain 26 c1tujA_ not modelled 6.5 22 PDB header:transport protein Chain: A: PDB Molecule:odorant binding protein asp2; PDBTitle: solution structure of the honey bee general odorant binding2 protein asp2 in complex with trimethylsilyl-d4 propionate 27 c3dl8D_ not modelled 6.4 13 PDB header:protein transport Chain: D: PDB Molecule:sece; PDBTitle: structure of the complex of aquifex aeolicus secyeg and2 bacillus subtilis seca 28 c2crnA_ not modelled 6.3 10 PDB header:immune system Chain: A: PDB Molecule:ubash3a protein; PDBTitle: solution structure of the uba domain of human ubash3a2 protein 29 d1iwga7 not modelled 6.1 11 Fold:Multidrug efflux transporter AcrB transmembrane domain Superfamily:Multidrug efflux transporter AcrB transmembrane domain Family:Multidrug efflux transporter AcrB transmembrane domain 30 c2wlvA_ not modelled 5.5 15 PDB header:virus protein Chain: A: PDB Molecule:gag polyprotein; PDBTitle: structure of the n-terminal capsid domain of hiv-2 31 d1m9dc_ not modelled 5.4 15 Fold:Retrovirus capsid protein, N-terminal core domain Superfamily:Retrovirus capsid protein, N-terminal core domain Family:Retrovirus capsid protein, N-terminal core domain 32 c2pcoA_ not modelled 5.4 38 PDB header:toxin Chain: A: PDB Molecule:latarcin-1; PDBTitle: spatial structure and membrane permeabilization for2 latarcin-1, a spider antimicrobial peptide 33 d2pxrc1 not modelled 5.4 15 Fold:Retrovirus capsid protein, N-terminal core domain Superfamily:Retrovirus capsid protein, N-terminal core domain Family:Retrovirus capsid protein, N-terminal core domain 34 c2jwaA_ not modelled 5.1 8 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

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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