Secondary structure and disorder prediction

		1	.	.	.	.	.	.	.	.	10	.	.	.	.	.	.	.	.	.	20	.	.	.	.	.	.	.	.	.	30	.	.	.	.	.	.	.	.	.	40	.	.	.	.	.	.	.	.	.	50	.	.	.	.	.	.	.	.	.	60
Sequence		M	N	L	L	T	V	S	T	D	L	I	S	I	F	L	F	T	T	L	F	L	F	F	A	R	K	V	A	K	K	V	G	L	V	D	K	P	N	F	R	K	R	H	Q	G	L	I	P	L	V	G	G	I	S	V	Y	A	G	I	C
Secondary structure
SS confidence
Disorder		?	?																																					?	?	?	?	?	?			?
Disorder confidence
		.	.	.	.	.	.	.	.	.	70	.	.	.	.	.	.	.	.	.	80	.	.	.	.	.	.	.	.	.	90	.	.	.	.	.	.	.	.	.	100	.	.	.	.	.	.	.	.	.	110	.	.	.	.	.	.	.	.	.	120
Sequence		F	T	F	G	I	V	D	Y	Y	I	P	H	A	S	L	Y	L	A	C	A	G	V	L	V	F	I	G	A	L	D	D	R	F	D	I	S	V	K	I	R	A	T	I	Q	A	A	V	G	I	V	M	M	V	F	G	K	L	Y	L	S
Secondary structure
SS confidence
Disorder											?
Disorder confidence
		.	.	.	.	.	.	.	.	.	130	.	.	.	.	.	.	.	.	.	140	.	.	.	.	.	.	.	.	.	150	.	.	.	.	.	.	.	.	.	160	.	.	.	.	.	.	.	.	.	170	.	.	.	.	.	.	.	.	.	180
Sequence		S	L	G	Y	I	F	G	S	W	E	M	V	L	G	P	F	G	Y	F	L	T	L	F	A	V	W	A	A	I	N	A	F	N	M	V	D	G	I	D	G	L	L	G	G	L	S	C	V	S	F	A	A	I	G	M	I	L	W	F	D
Secondary structure
SS confidence
Disorder							?		?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	190	.	.	.	.	.	.	.	.	.	200	.	.	.	.	.	.	.	.	.	210	.	.	.	.	.	.	.	.	.	220	.	.	.	.	.	.	.	.	.	230	.	.	.	.	.	.	.	.	.	240
Sequence		G	Q	T	S	L	A	I	W	C	F	A	M	I	A	A	I	L	P	Y	I	M	L	N	L	G	I	L	G	R	R	Y	K	V	F	M	G	D	A	G	S	T	L	I	G	F	T	V	I	W	I	L	L	E	T	T	Q	G	K	T	H
Secondary structure
SS confidence
Disorder																											?	?																														?		?
Disorder confidence
		.	.	.	.	.	.	.	.	.	250	.	.	.	.	.	.	.	.	.	260	.	.	.	.	.	.	.	.	.	270	.	.	.	.	.	.	.	.	.	280	.	.	.	.	.	.	.	.	.	290	.	.	.	.	.	.	.	.	.	300
Sequence		P	I	S	P	V	T	A	L	W	I	I	A	I	P	L	M	D	M	V	A	I	M	Y	R	R	L	R	K	G	M	S	P	F	S	P	D	R	Q	H	I	H	H	L	I	M	R	A	G	F	T	S	R	Q	A	F	V	L	I	T	L
Secondary structure
SS confidence
Disorder																																	?		?
Disorder confidence
		.	.	.	.	.	.	.	.	.	310	.	.	.	.	.	.	.	.	.	320	.	.	.	.	.	.	.	.	.	330	.	.	.	.	.	.	.	.	.	340	.	.	.	.	.	.	.	.	.	350	.	.	.	.	.	.	.	.	.	360
Sequence		A	A	A	L	L	A	S	I	G	V	L	A	E	Y	S	H	F	V	P	E	W	V	M	L	V	L	F	L	L	A	F	F	L	Y	G	Y	C	I	K	R	A	W	K	V	A	R	F	I	K	R	V	K	R	R	L	R	R	N	R	G
Secondary structure
SS confidence
Disorder																																												?	?		?							?				?	?	?	?
Disorder confidence
		.	.	.	.	.	.	.
Sequence		G	S	P	N	L	T	K
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 3aqp chain B Region: 220 - 364 Aligned: 136 Modelled: 145 Confidence: 23.3% Identity: 15% PDB header:membrane protein Chain: B: PDB Molecule:probable secdf protein-export membrane protein; PDBTitle: crystal structure of secdf, a translocon-associated membrane protein,2 from thermus thrmophilus Phyre2 PDB 3k07 chain A Region: 184 - 357 Aligned: 167 Modelled: 174 Confidence: 12.3% Identity: 11% PDB header:transport protein Chain: A: PDB Molecule:cation efflux system protein cusa; PDBTitle: crystal structure of cusa Phyre2 PDB 3izc chain Q Region: 345 - 362 Aligned: 18 Modelled: 18 Confidence: 9.5% Identity: 33% PDB header:ribosome Chain: Q: PDB Molecule:60s ribosomal protein rpl5 (l18p); PDBTitle: localization of the large subunit ribosomal proteins into a 6.1 a2 cryo-em map of saccharomyces cerevisiae translating 80s ribosome Phyre2 PDB 3u5i chain N Region: 345 - 362 Aligned: 18 Modelled: 18 Confidence: 9.5% Identity: 33% PDB header:ribosome Chain: N: PDB Molecule:60s ribosomal protein l15-a; PDBTitle: the structure of the eukaryotic ribosome at 3.0 a resolution Phyre2 PDB 3u5e chain N Region: 345 - 362 Aligned: 18 Modelled: 18 Confidence: 9.5% Identity: 33% PDB header:ribosome Chain: N: PDB Molecule:60s ribosomal protein l15-a; PDBTitle: the structure of the eukaryotic ribosome at 3.0 resolution Phyre2 PDB 3izs chain Q Region: 345 - 362 Aligned: 18 Modelled: 18 Confidence: 9.5% Identity: 33% PDB header:ribosome Chain: Q: PDB Molecule:60s ribosomal protein rpl5 (l18p); PDBTitle: localization of the large subunit ribosomal proteins into a 6.1 a2 cryo-em map of saccharomyces cerevisiae translating 80s ribosome Phyre2 PDB 2knc chain A Region: 315 - 362 Aligned: 48 Modelled: 48 Confidence: 7.9% Identity: 23% PDB header:cell adhesion Chain: A: PDB Molecule:integrin alpha-iib; PDBTitle: platelet integrin alfaiib-beta3 transmembrane-cytoplasmic2 heterocomplex Phyre2 PDB 1uou chain A domain 1 Region: 262 - 303 Aligned: 42 Modelled: 42 Confidence: 6.1% Identity: 12% Fold: Methionine synthase domain-like Superfamily: Nucleoside phosphorylase/phosphoribosyltransferase N-terminal domain Family: Nucleoside phosphorylase/phosphoribosyltransferase N-terminal domain Phyre2 PDB 2cpw chain A domain 1 Region: 265 - 299 Aligned: 34 Modelled: 35 Confidence: 5.7% Identity: 15% Fold: RuvA C-terminal domain-like Superfamily: UBA-like Family: UBA domain Phyre2 PDB 2rmz chain A Region: 316 - 353 Aligned: 38 Modelled: 38 Confidence: 5.2% Identity: 24% PDB header:cell adhesion Chain: A: PDB Molecule:integrin beta-3; PDBTitle: bicelle-embedded integrin beta3 transmembrane segment Phyre2 PDB 3iz5 chain Q Region: 345 - 362 Aligned: 18 Modelled: 18 Confidence: 5.1% Identity: 33% PDB header:ribosome Chain: Q: PDB Molecule:60s ribosomal protein l5 (l18p); PDBTitle: localization of the large subunit ribosomal proteins into a 5.5 a2 cryo-em map of triticum aestivum translating 80s ribosome Phyre2 1 c3aqpB_ 2 c3k07A_ 3 c3izcq_ 4 c3u5in_ 5 c3u5en_ 6 c3izsq_ 7 c2kncA_ 8 d1uoua1 9 d2cpwa1 10 c2rmzA_ 11 c3iz5q_

Detailed template information

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

1 c3aqpB_ 23.3 15 PDB header:membrane protein Chain: B: PDB Molecule:probable secdf protein-export membrane protein; PDBTitle: crystal structure of secdf, a translocon-associated membrane protein,2 from thermus thrmophilus 2 c3k07A_ 12.3 11 PDB header:transport protein Chain: A: PDB Molecule:cation efflux system protein cusa; PDBTitle: crystal structure of cusa 3 c3izcq_ 9.5 33 PDB header:ribosome Chain: Q: PDB Molecule:60s ribosomal protein rpl5 (l18p); PDBTitle: localization of the large subunit ribosomal proteins into a 6.1 a2 cryo-em map of saccharomyces cerevisiae translating 80s ribosome 4 c3u5in_ 9.5 33 PDB header:ribosome Chain: N: PDB Molecule:60s ribosomal protein l15-a; PDBTitle: the structure of the eukaryotic ribosome at 3.0 a resolution 5 c3u5en_ 9.5 33 PDB header:ribosome Chain: N: PDB Molecule:60s ribosomal protein l15-a; PDBTitle: the structure of the eukaryotic ribosome at 3.0 resolution 6 c3izsq_ 9.5 33 PDB header:ribosome Chain: Q: PDB Molecule:60s ribosomal protein rpl5 (l18p); PDBTitle: localization of the large subunit ribosomal proteins into a 6.1 a2 cryo-em map of saccharomyces cerevisiae translating 80s ribosome 7 c2kncA_ 7.9 23 PDB header:cell adhesion Chain: A: PDB Molecule:integrin alpha-iib; PDBTitle: platelet integrin alfaiib-beta3 transmembrane-cytoplasmic2 heterocomplex 8 d1uoua1 6.1 12 Fold:Methionine synthase domain-like Superfamily:Nucleoside phosphorylase/phosphoribosyltransferase N-terminal domain Family:Nucleoside phosphorylase/phosphoribosyltransferase N-terminal domain 9 d2cpwa1 5.7 15 Fold:RuvA C-terminal domain-like Superfamily:UBA-like Family:UBA domain 10 c2rmzA_ 5.2 24 PDB header:cell adhesion Chain: A: PDB Molecule:integrin beta-3; PDBTitle: bicelle-embedded integrin beta3 transmembrane segment 11 c3iz5q_ 5.1 33 PDB header:ribosome Chain: Q: PDB Molecule:60s ribosomal protein l5 (l18p); PDBTitle: localization of the large subunit ribosomal proteins into a 5.5 a2 cryo-em map of triticum aestivum translating 80s ribosome

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