Secondary structure and disorder prediction

		1	.	.	.	.	.	.	.	.	10	.	.	.	.	.	.	.	.	.	20	.	.	.	.	.	.	.	.	.	30	.	.	.	.	.	.	.	.	.	40	.	.	.	.	.	.	.	.	.	50	.	.	.	.	.	.	.	.	.	60
Sequence		M	L	L	A	G	S	S	L	L	T	L	L	D	D	I	A	T	L	L	D	D	I	S	V	M	G	K	L	A	A	K	K	T	A	G	V	L	G	D	D	L	S	L	N	A	Q	Q	V	S	G	V	R	A	N	R	E	L	P	V	V
Secondary structure
SS confidence
Disorder		?	?	?	?																									?	?	?																	?	?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	70	.	.	.	.	.	.	.	.	.	80	.	.	.	.	.	.	.	.	.	90	.	.	.	.	.	.	.	.	.	100	.	.	.	.	.	.	.	.	.	110	.	.	.	.	.	.	.	.	.	120
Sequence		W	G	V	A	K	G	S	L	I	N	K	V	I	L	V	P	L	A	L	I	I	S	A	F	I	P	W	A	I	T	P	L	L	M	I	G	G	A	F	L	C	F	E	G	V	E	K	V	L	H	M	L	E	A	R	K	H	K	E	D
Secondary structure
SS confidence
Disorder																																																							?	?	?	?	?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	130	.	.	.	.	.	.	.	.	.	140	.	.	.	.	.	.	.	.	.	150	.	.	.	.	.	.	.	.	.	160	.	.	.	.	.	.	.	.	.	170	.	.	.	.	.	.	.	.	.	180
Sequence		P	A	Q	S	Q	Q	R	L	E	K	L	A	A	Q	D	P	L	K	F	E	K	D	K	I	K	G	A	I	R	T	D	F	I	L	S	A	E	I	V	A	I	T	L	G	I	V	A	E	A	P	L	L	N	Q	V	L	V	L	S	G
Secondary structure
SS confidence
Disorder		?	?	?	?	?	?	?	?	?	?	?	?	?	?	?	?	?																													?	?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	190	.	.	.	.	.	.	.	.	.	200	.	.	.	.	.	.	.	.	.	210	.	.	.	.	.	.	.	.	.	220	.	.	.	.	.	.	.	.	.	230	.	.	.	.	.	.	.	.	.	240
Sequence		I	A	L	V	V	T	V	G	V	Y	G	L	V	G	V	I	V	K	I	D	D	L	G	Y	W	L	A	E	K	S	S	A	L	M	Q	A	L	G	K	G	L	L	I	I	A	P	W	L	M	K	A	L	S	I	V	G	T	L	A	M
Secondary structure
SS confidence
Disorder																														?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	250	.	.	.	.	.	.	.	.	.	260	.	.	.	.	.	.	.	.	.	270	.	.	.	.	.	.	.	.	.	280	.	.	.	.	.	.	.	.	.	290	.	.	.	.	.	.	.	.	.	300
Sequence		F	L	V	G	G	G	I	V	V	H	G	I	A	P	L	H	H	A	I	E	H	F	A	G	Q	Q	S	A	V	V	A	M	I	L	P	T	V	L	N	L	I	L	G	F	I	I	G	G	I	V	V	L	G	V	K	A	V	E	K	M
Secondary structure
SS confidence
Disorder																											?
Disorder confidence
		.	.	.	.	.
Sequence		R	G	Q	A	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 2l9u chain A Region: 88 - 118 Aligned: 25 Modelled: 31 Confidence: 58.6% Identity: 28% PDB header:membrane protein Chain: A: PDB Molecule:receptor tyrosine-protein kinase erbb-3; PDBTitle: spatial structure of dimeric erbb3 transmembrane domain Phyre2 PDB 2end chain A Region: 55 - 71 Aligned: 17 Modelled: 17 Confidence: 37.2% Identity: 41% Fold: T4 endonuclease V Superfamily: T4 endonuclease V Family: T4 endonuclease V Phyre2 PDB 1i7m chain D Region: 102 - 114 Aligned: 13 Modelled: 13 Confidence: 21.8% Identity: 46% PDB header:lyase Chain: D: PDB Molecule:s-adenosylmethionine decarboxylase beta chain; PDBTitle: human s-adenosylmethionine decarboxylase with covalently bound2 pyruvoyl group and complexed with 4-amidinoindan-1-one-2'-3 amidinohydrazone Phyre2 PDB 1nex chain A domain 2 Region: 106 - 121 Aligned: 16 Modelled: 16 Confidence: 16.3% Identity: 25% Fold: POZ domain Superfamily: POZ domain Family: BTB/POZ domain Phyre2 PDB 1msv chain B Region: 102 - 120 Aligned: 19 Modelled: 19 Confidence: 14.1% Identity: 37% PDB header:lyase Chain: B: PDB Molecule:s-adenosylmethionine decarboxylase proenzyme; PDBTitle: the s68a s-adenosylmethionine decarboxylase proenzyme2 processing mutant. Phyre2 PDB 1jl0 chain A Region: 102 - 120 Aligned: 19 Modelled: 19 Confidence: 13.3% Identity: 37% Fold: S-adenosylmethionine decarboxylase Superfamily: S-adenosylmethionine decarboxylase Family: S-adenosylmethionine decarboxylase Phyre2 PDB 2lm4 chain A Region: 114 - 156 Aligned: 43 Modelled: 43 Confidence: 12.8% Identity: 19% PDB header:protein binding Chain: A: PDB Molecule:succinate dehydrogenase assembly factor 2, mitochondrial; PDBTitle: solution nmr structure of mitochondrial succinate dehydrogenase2 assembly factor 2 from saccharomyces cerevisiae, northeast structural3 genomics consortium target yt682a Phyre2 PDB 1cii chain A Region: 219 - 297 Aligned: 75 Modelled: 79 Confidence: 11.7% Identity: 16% PDB header:transmembrane protein Chain: A: PDB Molecule:colicin ia; PDBTitle: colicin ia Phyre2 PDB 1zyb chain A domain 1 Region: 197 - 217 Aligned: 21 Modelled: 21 Confidence: 10.8% Identity: 33% Fold: DNA/RNA-binding 3-helical bundle Superfamily: "Winged helix" DNA-binding domain Family: CAP C-terminal domain-like Phyre2 PDB 1hv2 chain A Region: 106 - 140 Aligned: 35 Modelled: 35 Confidence: 10.0% Identity: 11% Fold: POZ domain Superfamily: POZ domain Family: BTB/POZ domain Phyre2 PDB 1jb0 chain I Region: 84 - 92 Aligned: 9 Modelled: 9 Confidence: 9.7% Identity: 44% Fold: Single transmembrane helix Superfamily: Subunit VIII of photosystem I reaction centre, PsaI Family: Subunit VIII of photosystem I reaction centre, PsaI Phyre2 PDB 3h4c chain A Region: 100 - 119 Aligned: 20 Modelled: 20 Confidence: 8.9% Identity: 30% PDB header:transcription Chain: A: PDB Molecule:transcription factor tfiib-like; PDBTitle: structure of the c-terminal domain of transcription factor iib from2 trypanosoma brucei Phyre2 PDB 2gez chain E Region: 99 - 152 Aligned: 46 Modelled: 54 Confidence: 8.7% Identity: 11% PDB header:hydrolase Chain: E: PDB Molecule:l-asparaginase alpha subunit; PDBTitle: crystal structure of potassium-independent plant asparaginase Phyre2 PDB 2zjs chain E Region: 173 - 193 Aligned: 21 Modelled: 21 Confidence: 8.2% Identity: 33% PDB header:protein transport/immune system Chain: E: PDB Molecule:preprotein translocase sece subunit; PDBTitle: crystal structure of secye translocon from thermus thermophilus with a2 fab fragment Phyre2 PDB 1lgh chain A Region: 51 - 64 Aligned: 14 Modelled: 14 Confidence: 7.6% Identity: 43% Fold: Light-harvesting complex subunits Superfamily: Light-harvesting complex subunits Family: Light-harvesting complex subunits Phyre2 PDB 1kf6 chain D Region: 227 - 286 Aligned: 55 Modelled: 60 Confidence: 7.2% Identity: 11% Fold: Heme-binding four-helical bundle Superfamily: Fumarate reductase respiratory complex transmembrane subunits Family: Succinate dehydrogenase/Fumarate reductase transmembrane subunits (SdhC/FrdC and SdhD/FrdD) Phyre2 PDB 2c9w chain C domain 1 Region: 106 - 123 Aligned: 18 Modelled: 18 Confidence: 7.2% Identity: 11% Fold: POZ domain Superfamily: POZ domain Family: BTB/POZ domain Phyre2 PDB 1rqb chain A domain 1 Region: 234 - 246 Aligned: 13 Modelled: 10 Confidence: 7.0% Identity: 62% Fold: RuvA C-terminal domain-like Superfamily: post-HMGL domain-like Family: Conserved carboxylase domain Phyre2 PDB 2ifo chain A Region: 88 - 113 Aligned: 26 Modelled: 26 Confidence: 7.0% Identity: 35% PDB header:virus Chain: A: PDB Molecule:inovirus; PDBTitle: model-building studies of inovirus: genetic variations on a2 geometric theme Phyre2 PDB 2ksr chain A Region: 208 - 242 Aligned: 35 Modelled: 35 Confidence: 6.4% Identity: 17% PDB header:membrane protein Chain: A: PDB Molecule:neuronal acetylcholine receptor subunit beta-2; PDBTitle: nmr structures of tm domain of the n-acetylcholine receptor b2 subunit Phyre2 1 c2l9uA_ 2 d2enda_ 3 c1i7mD_ 4 d1nexa2 5 c1msvB_ 6 d1jl0a_ 7 c2lm4A_ 8 c1ciiA_ 9 d1zyba1 10 d1hv2a_ 11 d1jb0i_ 12 c3h4cA_ 13 c2gezE_ 14 c2zjsE_ 15 d1lgha_ 16 d1kf6d_ 17 d2c9wc1 18 d1rqba1 19 c2ifoA_ 20 c2ksrA_ 21 22 23 24 25 26

Detailed template information

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

1 c2l9uA_ 58.6 28 PDB header:membrane protein Chain: A: PDB Molecule:receptor tyrosine-protein kinase erbb-3; PDBTitle: spatial structure of dimeric erbb3 transmembrane domain 2 d2enda_ 37.2 41 Fold:T4 endonuclease V Superfamily:T4 endonuclease V Family:T4 endonuclease V 3 c1i7mD_ 21.8 46 PDB header:lyase Chain: D: PDB Molecule:s-adenosylmethionine decarboxylase beta chain; PDBTitle: human s-adenosylmethionine decarboxylase with covalently bound2 pyruvoyl group and complexed with 4-amidinoindan-1-one-2'-3 amidinohydrazone 4 d1nexa2 16.3 25 Fold:POZ domain Superfamily:POZ domain Family:BTB/POZ domain 5 c1msvB_ 14.1 37 PDB header:lyase Chain: B: PDB Molecule:s-adenosylmethionine decarboxylase proenzyme; PDBTitle: the s68a s-adenosylmethionine decarboxylase proenzyme2 processing mutant. 6 d1jl0a_ 13.3 37 Fold:S-adenosylmethionine decarboxylase Superfamily:S-adenosylmethionine decarboxylase Family:S-adenosylmethionine decarboxylase 7 c2lm4A_ 12.8 19 PDB header:protein binding Chain: A: PDB Molecule:succinate dehydrogenase assembly factor 2, mitochondrial; PDBTitle: solution nmr structure of mitochondrial succinate dehydrogenase2 assembly factor 2 from saccharomyces cerevisiae, northeast structural3 genomics consortium target yt682a 8 c1ciiA_ 11.7 16 PDB header:transmembrane protein Chain: A: PDB Molecule:colicin ia; PDBTitle: colicin ia 9 d1zyba1 10.8 33 Fold:DNA/RNA-binding 3-helical bundle Superfamily:"Winged helix" DNA-binding domain Family:CAP C-terminal domain-like 10 d1hv2a_ 10.0 11 Fold:POZ domain Superfamily:POZ domain Family:BTB/POZ domain 11 d1jb0i_ 9.7 44 Fold:Single transmembrane helix Superfamily:Subunit VIII of photosystem I reaction centre, PsaI Family:Subunit VIII of photosystem I reaction centre, PsaI 12 c3h4cA_ 8.9 30 PDB header:transcription Chain: A: PDB Molecule:transcription factor tfiib-like; PDBTitle: structure of the c-terminal domain of transcription factor iib from2 trypanosoma brucei 13 c2gezE_ 8.7 11 PDB header:hydrolase Chain: E: PDB Molecule:l-asparaginase alpha subunit; PDBTitle: crystal structure of potassium-independent plant asparaginase 14 c2zjsE_ 8.2 33 PDB header:protein transport/immune system Chain: E: PDB Molecule:preprotein translocase sece subunit; PDBTitle: crystal structure of secye translocon from thermus thermophilus with a2 fab fragment 15 d1lgha_ 7.6 43 Fold:Light-harvesting complex subunits Superfamily:Light-harvesting complex subunits Family:Light-harvesting complex subunits 16 d1kf6d_ 7.2 11 Fold:Heme-binding four-helical bundle Superfamily:Fumarate reductase respiratory complex transmembrane subunits Family:Succinate dehydrogenase/Fumarate reductase transmembrane subunits (SdhC/FrdC and SdhD/FrdD) 17 d2c9wc1 7.2 11 Fold:POZ domain Superfamily:POZ domain Family:BTB/POZ domain 18 d1rqba1 7.0 62 Fold:RuvA C-terminal domain-like Superfamily:post-HMGL domain-like Family:Conserved carboxylase domain 19 c2ifoA_ 7.0 35 PDB header:virus Chain: A: PDB Molecule:inovirus; PDBTitle: model-building studies of inovirus: genetic variations on a2 geometric theme 20 c2ksrA_ 6.4 17 PDB header:membrane protein Chain: A: PDB Molecule:neuronal acetylcholine receptor subunit beta-2; PDBTitle: nmr structures of tm domain of the n-acetylcholine receptor b2 subunit 21 d1q5za_ not modelled 6.1 29 Fold:Invasion protein A (SipA) , C-terminal actin binding domain Superfamily:Invasion protein A (SipA) , C-terminal actin binding domain Family:Invasion protein A (SipA) , C-terminal actin binding domain 22 c1q5zA_ not modelled 6.1 29 PDB header:cell invasion Chain: A: PDB Molecule:sipa; PDBTitle: crystal structure of the c-terminal actin binding domain of2 salmonella invasion protein a (sipa) 23 d1fs1b2 not modelled 6.0 23 Fold:POZ domain Superfamily:POZ domain Family:BTB/POZ domain 24 c3juiA_ not modelled 5.7 21 PDB header:translation Chain: A: PDB Molecule:translation initiation factor eif-2b subunit epsilon; PDBTitle: crystal structure of the c-terminal domain of human translation2 initiation factor eif2b epsilon subunit 25 c3lw5K_ not modelled 5.6 27 PDB header:photosynthesis Chain: K: PDB Molecule:photosystem i reaction center subunit x psak; PDBTitle: improved model of plant photosystem i 26 c2voyB_ not modelled 5.3 23 PDB header:hydrolase Chain: B: PDB Molecule:sarcoplasmic/endoplasmic reticulum calcium PDBTitle: cryoem model of copa, the copper transporting atpase from2 archaeoglobus fulgidus

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