Secondary structure and disorder prediction

		1	.	.	.	.	.	.	.	.	10	.	.	.	.	.	.	.	.	.	20	.	.	.	.	.	.	.	.	.	30	.	.	.	.	.	.	.	.	.	40	.	.	.	.	.	.	.	.	.	50	.	.	.	.	.	.	.	.	.	60
Sequence		M	N	F	P	L	I	A	N	I	V	V	F	V	V	L	L	F	A	L	A	Q	T	R	H	K	Q	W	S	L	A	K	K	V	L	V	G	L	V	M	G	V	V	F	G	L	A	L	H	T	I	Y	G	S	D	S	Q	V	L	K	D
Secondary structure
SS confidence
Disorder		?	?	?																			?	?	?	?	?	?																									?	?	?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	70	.	.	.	.	.	.	.	.	.	80	.	.	.	.	.	.	.	.	.	90	.	.	.	.	.	.	.	.	.	100	.	.	.	.	.	.	.	.	.	110	.	.	.	.	.	.	.	.	.	120
Sequence		S	V	Q	W	F	N	I	V	G	N	G	Y	V	Q	L	L	Q	M	I	V	M	P	L	V	F	A	S	I	L	S	A	V	A	R	L	H	N	A	S	Q	L	G	K	I	S	F	L	T	I	G	T	L	L	F	T	T	L	I	A	A
Secondary structure
SS confidence
Disorder																																		?	?	?	?	?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	130	.	.	.	.	.	.	.	.	.	140	.	.	.	.	.	.	.	.	.	150	.	.	.	.	.	.	.	.	.	160	.	.	.	.	.	.	.	.	.	170	.	.	.	.	.	.	.	.	.	180
Sequence		L	V	G	V	L	V	T	N	L	F	G	L	T	A	E	G	L	V	Q	G	G	A	E	T	A	R	L	N	A	I	E	S	N	Y	V	G	K	V	S	D	L	S	V	P	Q	L	V	L	S	F	I	P	K	N	P	F	A	D	L	T
Secondary structure
SS confidence
Disorder														?	?	?	?	?	?	?	?	?	?	?	?	?	?	?	?	?	?	?	?	?	?	?	?	?	?	?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	190	.	.	.	.	.	.	.	.	.	200	.	.	.	.	.	.	.	.	.	210	.	.	.	.	.	.	.	.	.	220	.	.	.	.	.	.	.	.	.	230	.	.	.	.	.	.	.	.	.	240
Sequence		G	A	N	P	T	S	I	I	S	V	V	I	F	A	A	F	L	G	V	A	A	L	K	L	L	K	D	D	A	P	K	G	E	R	V	L	A	A	I	D	T	L	Q	S	W	V	M	K	L	V	R	L	V	M	Q	L	T	P	Y	G
Secondary structure
SS confidence
Disorder		?	?	?																					?	?	?	?	?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	250	.	.	.	.	.	.	.	.	.	260	.	.	.	.	.	.	.	.	.	270	.	.	.	.	.	.	.	.	.	280	.	.	.	.	.	.	.	.	.	290	.	.	.	.	.	.	.	.	.	300
Sequence		V	L	A	L	M	T	K	V	V	A	G	S	N	L	Q	D	I	I	K	L	G	S	F	V	V	A	S	Y	L	G	L	L	I	M	F	A	V	H	G	I	L	L	G	I	N	G	V	S	P	L	K	Y	F	R	K	V	W	P	V	L
Secondary structure
SS confidence
Disorder													?
Disorder confidence
		.	.	.	.	.	.	.	.	.	310	.	.	.	.	.	.	.	.	.	320	.	.	.	.	.	.	.	.	.	330	.	.	.	.	.	.	.	.	.	340	.	.	.	.	.	.	.	.	.	350	.	.	.	.	.	.	.	.	.	360
Sequence		T	F	A	F	T	S	R	S	S	A	A	S	I	P	L	N	V	E	A	Q	T	R	R	L	G	V	P	E	S	I	A	S	F	A	A	S	F	G	A	T	I	G	Q	N	G	C	A	G	L	Y	P	A	M	L	A	V	M	V	A	P
Secondary structure
SS confidence
Disorder
Disorder confidence
		.	.	.	.	.	.	.	.	.	370	.	.	.	.	.	.	.	.	.	380	.	.	.	.	.	.	.	.	.	390	.	.	.	.	.	.	.	.	.	400	.	.	.	.	.	.	.	.	.	410	.	.	.	.	.	.	.	.	.	420
Sequence		T	V	G	I	N	P	L	D	P	M	W	I	A	T	L	V	G	I	V	T	V	S	S	A	G	V	A	G	V	G	G	G	A	T	F	A	A	L	I	V	L	P	A	M	G	L	P	V	T	L	V	A	L	L	I	S	V	E	P	L
Secondary structure
SS confidence
Disorder																									?	?	?	?	?	?															?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	430	.	.	.	.	.	.	.	.	.	440	.	.	.	.	.	.	.	.	.	450	.	.	.	.	.	.	.	.	.	460	.	.	.
Sequence		I	D	M	G	R	T	A	L	N	V	S	G	S	M	T	A	G	T	L	T	S	Q	W	L	K	Q	T	D	K	A	I	L	D	S	E	D	D	A	E	L	A	H	H
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: 29 - 444 Aligned: 394 Modelled: 416 Confidence: 100.0% Identity: 30% Fold: Proton glutamate symport protein Superfamily: Proton glutamate symport protein Family: Proton glutamate symport protein Phyre2 PDB 3qnq chain D Region: 444 - 463 Aligned: 20 Modelled: 20 Confidence: 54.9% Identity: 30% 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 1a77 chain A domain 1 Region: 367 - 405 Aligned: 38 Modelled: 39 Confidence: 18.8% Identity: 11% Fold: SAM domain-like Superfamily: 5' to 3' exonuclease, C-terminal subdomain Family: 5' to 3' exonuclease, C-terminal subdomain Phyre2 PDB 2yvx chain D Region: 21 - 85 Aligned: 65 Modelled: 65 Confidence: 16.1% Identity: 20% PDB header:transport protein Chain: D: PDB Molecule:mg2+ transporter mgte; PDBTitle: crystal structure of magnesium transporter mgte Phyre2 PDB 1x0l chain B Region: 390 - 449 Aligned: 60 Modelled: 60 Confidence: 14.4% Identity: 15% PDB header:oxidoreductase Chain: B: PDB Molecule:homoisocitrate dehydrogenase; PDBTitle: crystal structure of tetrameric homoisocitrate dehydrogenase from an2 extreme thermophile, thermus thermophilus Phyre2 PDB 1o26 chain A Region: 323 - 343 Aligned: 21 Modelled: 21 Confidence: 13.4% Identity: 19% Fold: Thymidylate synthase-complementing protein Thy1 Superfamily: Thymidylate synthase-complementing protein Thy1 Family: Thymidylate synthase-complementing protein Thy1 Phyre2 PDB 3ah5 chain E Region: 322 - 343 Aligned: 22 Modelled: 22 Confidence: 13.0% Identity: 9% 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 3blx chain M Region: 390 - 448 Aligned: 59 Modelled: 59 Confidence: 8.7% Identity: 17% PDB header:oxidoreductase Chain: M: PDB Molecule:isocitrate dehydrogenase [nad] subunit 1; PDBTitle: yeast isocitrate dehydrogenase (apo form) Phyre2 PDB 1ul1 chain X domain 1 Region: 367 - 405 Aligned: 37 Modelled: 39 Confidence: 8.2% Identity: 14% Fold: SAM domain-like Superfamily: 5' to 3' exonuclease, C-terminal subdomain Family: 5' to 3' exonuclease, C-terminal subdomain Phyre2 PDB 1rxw chain A domain 1 Region: 367 - 405 Aligned: 37 Modelled: 39 Confidence: 7.9% Identity: 22% Fold: SAM domain-like Superfamily: 5' to 3' exonuclease, C-terminal subdomain Family: 5' to 3' exonuclease, C-terminal subdomain Phyre2 PDB 2cfa chain B Region: 323 - 339 Aligned: 17 Modelled: 17 Confidence: 7.2% Identity: 18% PDB header:transferase Chain: B: PDB Molecule:thymidylate synthase; PDBTitle: structure of viral flavin-dependant thymidylate synthase2 thyx Phyre2 PDB 1mc8 chain A domain 1 Region: 367 - 405 Aligned: 38 Modelled: 39 Confidence: 7.1% Identity: 18% Fold: SAM domain-like Superfamily: 5' to 3' exonuclease, C-terminal subdomain Family: 5' to 3' exonuclease, C-terminal subdomain Phyre2 PDB 2pxr chain C domain 1 Region: 405 - 454 Aligned: 50 Modelled: 50 Confidence: 7.0% Identity: 16% Fold: Retrovirus capsid protein, N-terminal core domain Superfamily: Retrovirus capsid protein, N-terminal core domain Family: Retrovirus capsid protein, N-terminal core domain Phyre2 PDB 1m9d chain C Region: 405 - 454 Aligned: 50 Modelled: 50 Confidence: 6.9% Identity: 16% Fold: Retrovirus capsid protein, N-terminal core domain Superfamily: Retrovirus capsid protein, N-terminal core domain Family: Retrovirus capsid protein, N-terminal core domain Phyre2 PDB 1m9f chain D Region: 405 - 454 Aligned: 50 Modelled: 50 Confidence: 6.5% Identity: 16% Fold: Retrovirus capsid protein, N-terminal core domain Superfamily: Retrovirus capsid protein, N-terminal core domain Family: Retrovirus capsid protein, N-terminal core domain Phyre2 PDB 1vf5 chain E Region: 31 - 48 Aligned: 18 Modelled: 18 Confidence: 6.4% Identity: 22% PDB header:photosynthesis Chain: E: PDB Molecule:protein pet l; PDBTitle: crystal structure of cytochrome b6f complex from m.laminosus Phyre2 PDB 2e75 chain E Region: 31 - 48 Aligned: 18 Modelled: 18 Confidence: 6.4% Identity: 22% 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: 31 - 48 Aligned: 18 Modelled: 18 Confidence: 6.4% Identity: 22% PDB header:photosynthesis Chain: R: PDB Molecule:protein pet l; PDBTitle: crystal structure of cytochrome b6f complex from m.laminosus Phyre2 PDB 2e76 chain E Region: 31 - 48 Aligned: 18 Modelled: 18 Confidence: 6.4% Identity: 22% 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 Phyre2 PDB 2e74 chain E Region: 31 - 48 Aligned: 18 Modelled: 18 Confidence: 6.4% Identity: 22% 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 1 d2nwwa1 2 c3qnqD_ 3 d1a77a1 4 c2yvxD_ 5 c1x0lB_ 6 d1o26a_ 7 c3ah5E_ 8 c3blxM_ 9 d1ul1x1 10 d1rxwa1 11 c2cfaB_ 12 d1mc8a1 13 d2pxrc1 14 d1m9dc_ 15 d1m9fd_ 16 c1vf5E_ 17 c2e75E_ 18 c1vf5R_ 19 c2e76E_ 20 c2e74E_ 21 22 23 24 25 26 27 28

Detailed template information

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

1 d2nwwa1 100.0 30 Fold:Proton glutamate symport protein Superfamily:Proton glutamate symport protein Family:Proton glutamate symport protein 2 c3qnqD_ 54.9 30 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 3 d1a77a1 18.8 11 Fold:SAM domain-like Superfamily:5' to 3' exonuclease, C-terminal subdomain Family:5' to 3' exonuclease, C-terminal subdomain 4 c2yvxD_ 16.1 20 PDB header:transport protein Chain: D: PDB Molecule:mg2+ transporter mgte; PDBTitle: crystal structure of magnesium transporter mgte 5 c1x0lB_ 14.4 15 PDB header:oxidoreductase Chain: B: PDB Molecule:homoisocitrate dehydrogenase; PDBTitle: crystal structure of tetrameric homoisocitrate dehydrogenase from an2 extreme thermophile, thermus thermophilus 6 d1o26a_ 13.4 19 Fold:Thymidylate synthase-complementing protein Thy1 Superfamily:Thymidylate synthase-complementing protein Thy1 Family:Thymidylate synthase-complementing protein Thy1 7 c3ah5E_ 13.0 9 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 8 c3blxM_ 8.7 17 PDB header:oxidoreductase Chain: M: PDB Molecule:isocitrate dehydrogenase [nad] subunit 1; PDBTitle: yeast isocitrate dehydrogenase (apo form) 9 d1ul1x1 8.2 14 Fold:SAM domain-like Superfamily:5' to 3' exonuclease, C-terminal subdomain Family:5' to 3' exonuclease, C-terminal subdomain 10 d1rxwa1 7.9 22 Fold:SAM domain-like Superfamily:5' to 3' exonuclease, C-terminal subdomain Family:5' to 3' exonuclease, C-terminal subdomain 11 c2cfaB_ 7.2 18 PDB header:transferase Chain: B: PDB Molecule:thymidylate synthase; PDBTitle: structure of viral flavin-dependant thymidylate synthase2 thyx 12 d1mc8a1 7.1 18 Fold:SAM domain-like Superfamily:5' to 3' exonuclease, C-terminal subdomain Family:5' to 3' exonuclease, C-terminal subdomain 13 d2pxrc1 7.0 16 Fold:Retrovirus capsid protein, N-terminal core domain Superfamily:Retrovirus capsid protein, N-terminal core domain Family:Retrovirus capsid protein, N-terminal core domain 14 d1m9dc_ 6.9 16 Fold:Retrovirus capsid protein, N-terminal core domain Superfamily:Retrovirus capsid protein, N-terminal core domain Family:Retrovirus capsid protein, N-terminal core domain 15 d1m9fd_ 6.5 16 Fold:Retrovirus capsid protein, N-terminal core domain Superfamily:Retrovirus capsid protein, N-terminal core domain Family:Retrovirus capsid protein, N-terminal core domain 16 c1vf5E_ 6.4 22 PDB header:photosynthesis Chain: E: PDB Molecule:protein pet l; PDBTitle: crystal structure of cytochrome b6f complex from m.laminosus 17 c2e75E_ 6.4 22 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 18 c1vf5R_ 6.4 22 PDB header:photosynthesis Chain: R: PDB Molecule:protein pet l; PDBTitle: crystal structure of cytochrome b6f complex from m.laminosus 19 c2e76E_ 6.4 22 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 20 c2e74E_ 6.4 22 PDB header:photosynthesis Chain: E: PDB Molecule:cytochrome b6-f complex subunit 6; PDBTitle: crystal structure of the cytochrome b6f complex from m.laminosus 21 d2e74e1 not modelled 6.4 22 Fold:Single transmembrane helix Superfamily:PetL subunit of the cytochrome b6f complex Family:PetL subunit of the cytochrome b6f complex 22 c2wlvA_ not modelled 6.3 16 PDB header:virus protein Chain: A: PDB Molecule:gag polyprotein; PDBTitle: structure of the n-terminal capsid domain of hiv-2 23 c2jwaA_ not modelled 6.2 38 PDB header:transferase Chain: A: PDB Molecule:receptor tyrosine-protein kinase erbb-2; PDBTitle: erbb2 transmembrane segment dimer spatial structure 24 d1b43a1 not modelled 6.1 18 Fold:SAM domain-like Superfamily:5' to 3' exonuclease, C-terminal subdomain Family:5' to 3' exonuclease, C-terminal subdomain 25 d1hqsa_ not modelled 6.1 12 Fold:Isocitrate/Isopropylmalate dehydrogenase-like Superfamily:Isocitrate/Isopropylmalate dehydrogenase-like Family:Dimeric isocitrate & isopropylmalate dehydrogenases 26 d1xo1a1 not modelled 6.1 18 Fold:SAM domain-like Superfamily:5' to 3' exonuclease, C-terminal subdomain Family:5' to 3' exonuclease, C-terminal subdomain 27 d1ku2a1 not modelled 5.9 17 Fold:DNA/RNA-binding 3-helical bundle Superfamily:Sigma3 and sigma4 domains of RNA polymerase sigma factors Family:Sigma3 domain 28 d1uxca_ not modelled 5.8 24 Fold:lambda repressor-like DNA-binding domains Superfamily:lambda repressor-like DNA-binding domains Family:GalR/LacI-like bacterial regulator

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