Secondary structure and disorder prediction

		1	.	.	.	.	.	.	.	.	10	.	.	.	.	.	.	.	.	.	20	.	.	.	.	.	.	.	.	.	30	.	.	.	.	.	.	.	.	.	40	.	.	.	.	.	.	.	.	.	50	.	.	.	.	.	.	.	.	.	60
Sequence		M	S	L	D	I	N	Q	I	A	L	H	Q	L	I	K	R	D	E	Q	N	L	E	L	V	L	R	D	S	L	L	E	P	T	E	T	V	V	E	M	V	A	E	L	H	R	V	Y	S	A	K	N	K	A	Y	G	L	F	S	E	E
Secondary structure
SS confidence
Disorder		?	?	?	?	?														?	?		?					?		?	?	?	?																		?	?	?						?
Disorder confidence
		.	.	.	.	.	.	.	.	.	70	.	.	.	.	.	.	.	.	.	80	.	.	.	.	.	.	.	.	.	90	.	.	.	.	.	.	.	.	.	100	.	.	.	.	.	.	.	.	.	110	.	.	.	.	.	.	.	.	.	120
Sequence		S	E	L	A	Q	T	L	R	L	Q	R	Q	G	E	E	D	F	L	A	F	S	R	A	A	T	G	R	L	R	D	E	L	A	K	Y	P	F	A	D	G	G	F	V	L	F	C	H	Y	R	Y	L	A	V	E	Y	L	L	V	A	V
Secondary structure
SS confidence
Disorder																																			?		?
Disorder confidence
		.	.	.	.	.	.	.	.	.	130	.	.	.	.	.	.	.	.	.	140	.	.	.	.	.	.	.	.	.	150	.	.	.	.	.	.	.	.	.	160	.	.	.	.	.	.	.	.	.	170	.	.	.	.	.	.	.	.	.	180
Sequence		L	S	N	L	S	S	M	R	V	N	E	N	L	D	I	N	P	T	H	Y	L	D	I	N	H	A	D	I	V	A	R	I	D	L	T	E	W	E	T	N	P	E	S	T	R	Y	L	T	F	L	K	G	R	V	G	R	K	V	A	D
Secondary structure
SS confidence
Disorder						?					?								?	?		?																?	?															?		?
Disorder confidence
		.	.	.	.	.	.	.	.	.	190	.	.	.	.	.	.	.	.	.	200	.	.	.	.	.	.	.	.	.	210	.	.	.	.	.	.	.	.	.	220	.	.	.	.	.	.	.	.	.	230	.	.	.	.	.	.	.	.	.	240
Sequence		F	F	M	D	F	L	G	A	S	E	G	L	N	A	K	A	Q	N	R	G	L	L	Q	A	V	D	D	F	T	A	E	A	Q	L	D	K	A	E	R	Q	N	V	R	Q	Q	V	Y	S	Y	C	N	E	Q	L	Q	A	G	E	E	I
Secondary structure
SS confidence
Disorder									?	?			?	?																				?	?																					?	?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	250	.	.	.	.	.	.	.	.	.	260	.	.	.	.	.	.	.	.	.	270	.	.	.	.	.	.	.	.	.	280	.	.	.	.	.	.	.	.	.	290	.	.	.	.	.	.	.	.	.	300
Sequence		E	L	K	S	L	S	K	E	L	A	G	V	S	E	V	S	F	T	E	F	A	A	E	K	G	Y	E	L	E	E	S	F	P	A	D	R	S	T	L	R	Q	L	T	K	F	A	G	S	G	G	G	L	T	I	N	F	D	A	M	L
Secondary structure
SS confidence
Disorder													?	?	?									?	?	?	?	?	?	?	?	?	?	?	?	?				?									?		?
Disorder confidence
		.	.	.	.	.	.	.	.	.	310	.	.	.	.	.	.	.	.	.	320	.	.	.	.	.	.	.	.	.	330	.	.	.	.	.
Sequence		L	G	E	R	I	F	W	D	P	A	T	D	T	L	T	I	K	G	T	P	P	N	L	R	D	Q	L	Q	R	R	T	S	G	G	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 2bsq chain E domain 1 Region: 313 - 334 Aligned: 22 Modelled: 22 Confidence: 63.6% Identity: 9% Fold: Ribbon-helix-helix Superfamily: Ribbon-helix-helix Family: Trafficking protein A-like Phyre2 PDB 1mul chain A Region: 203 - 245 Aligned: 43 Modelled: 43 Confidence: 46.0% Identity: 21% Fold: IHF-like DNA-binding proteins Superfamily: IHF-like DNA-binding proteins Family: Prokaryotic DNA-bending protein Phyre2 PDB 1huu chain A Region: 203 - 245 Aligned: 43 Modelled: 43 Confidence: 36.5% Identity: 16% Fold: IHF-like DNA-binding proteins Superfamily: IHF-like DNA-binding proteins Family: Prokaryotic DNA-bending protein Phyre2 PDB 3c4i chain A Region: 203 - 245 Aligned: 43 Modelled: 43 Confidence: 34.9% Identity: 12% PDB header:dna binding protein Chain: A: PDB Molecule:dna-binding protein hu homolog; PDBTitle: crystal structure analysis of n terminal region containing the2 dimerization domain and dna binding domain of hu protein(histone like3 protein-dna binding) from mycobacterium tuberculosis [h37rv] Phyre2 PDB 1p71 chain A Region: 203 - 245 Aligned: 43 Modelled: 43 Confidence: 34.3% Identity: 19% Fold: IHF-like DNA-binding proteins Superfamily: IHF-like DNA-binding proteins Family: Prokaryotic DNA-bending protein Phyre2 PDB 1owf chain A Region: 203 - 245 Aligned: 43 Modelled: 43 Confidence: 33.9% Identity: 14% Fold: IHF-like DNA-binding proteins Superfamily: IHF-like DNA-binding proteins Family: Prokaryotic DNA-bending protein Phyre2 PDB 2iif chain A Region: 203 - 245 Aligned: 43 Modelled: 43 Confidence: 33.2% Identity: 16% PDB header:recombination/dna Chain: A: PDB Molecule:integration host factor; PDBTitle: single chain integration host factor mutant protein (scihf2-2 k45ae) in complex with dna Phyre2 PDB 1exe chain A Region: 203 - 245 Aligned: 43 Modelled: 43 Confidence: 28.9% Identity: 9% Fold: IHF-like DNA-binding proteins Superfamily: IHF-like DNA-binding proteins Family: Prokaryotic DNA-bending protein Phyre2 PDB 1b8z chain A Region: 203 - 242 Aligned: 40 Modelled: 40 Confidence: 28.3% Identity: 18% Fold: IHF-like DNA-binding proteins Superfamily: IHF-like DNA-binding proteins Family: Prokaryotic DNA-bending protein Phyre2 PDB 2k42 chain A Region: 305 - 329 Aligned: 24 Modelled: 25 Confidence: 19.4% Identity: 29% PDB header:signaling protein Chain: A: PDB Molecule:wiskott-aldrich syndrome protein; PDBTitle: solution structure of the gtpase binding domain of wasp in2 complex with espfu, an ehec effector Phyre2 PDB 2kl8 chain A Region: 301 - 332 Aligned: 32 Modelled: 32 Confidence: 19.0% Identity: 19% PDB header:de novo protein Chain: A: PDB Molecule:or15; PDBTitle: solution nmr structure of de novo designed ferredoxin-like2 fold protein, northeast structural genomics consortium3 target or15 Phyre2 PDB 3gr5 chain A Region: 302 - 332 Aligned: 30 Modelled: 31 Confidence: 18.5% Identity: 7% PDB header:membrane protein Chain: A: PDB Molecule:escc; PDBTitle: periplasmic domain of the outer membrane secretin escc from2 enteropathogenic e.coli (epec) Phyre2 PDB 2y9k chain G Region: 304 - 332 Aligned: 28 Modelled: 29 Confidence: 18.2% Identity: 18% PDB header:protein transport Chain: G: PDB Molecule:protein invg; PDBTitle: three-dimensional model of salmonella's needle complex at2 subnanometer resolution Phyre2 PDB 1owf chain B Region: 203 - 245 Aligned: 43 Modelled: 43 Confidence: 17.5% Identity: 9% Fold: IHF-like DNA-binding proteins Superfamily: IHF-like DNA-binding proteins Family: Prokaryotic DNA-bending protein Phyre2 PDB 1mnt chain A Region: 319 - 335 Aligned: 17 Modelled: 17 Confidence: 16.4% Identity: 24% Fold: Ribbon-helix-helix Superfamily: Ribbon-helix-helix Family: Arc/Mnt-like phage repressors Phyre2 PDB 1f3m chain B Region: 305 - 329 Aligned: 23 Modelled: 25 Confidence: 16.2% Identity: 30% PDB header:transferase Chain: B: PDB Molecule:serine/threonine-protein kinase pak-alpha; PDBTitle: crystal structure of human serine/threonine kinase pak1 Phyre2 PDB 2xfl chain B Region: 305 - 331 Aligned: 27 Modelled: 27 Confidence: 16.1% Identity: 26% PDB header:hydrolase Chain: B: PDB Molecule:dyne7; PDBTitle: induced-fit and allosteric effects upon polyene binding2 revealed by crystal structures of the dynemicin3 thioesterase Phyre2 PDB 1cee chain B Region: 305 - 329 Aligned: 24 Modelled: 25 Confidence: 15.0% Identity: 29% PDB header:structural protein regulation Chain: B: PDB Molecule:wiskott-aldrich syndrome protein wasp; PDBTitle: solution structure of cdc42 in complex with the gtpase2 binding domain of wasp Phyre2 PDB 2y3m chain A Region: 302 - 332 Aligned: 30 Modelled: 31 Confidence: 14.6% Identity: 17% PDB header:transport protein Chain: A: PDB Molecule:protein transport protein hofq; PDBTitle: structure of the extra-membranous domain of the secretin2 hofq from actinobacillus actinomycetemcomitans Phyre2 PDB 1ej5 chain A Region: 307 - 329 Aligned: 22 Modelled: 23 Confidence: 14.5% Identity: 32% Fold: Wiscott-Aldrich syndrome protein, WASP, C-terminal domain Superfamily: Wiscott-Aldrich syndrome protein, WASP, C-terminal domain Family: Wiscott-Aldrich syndrome protein, WASP, C-terminal domain Phyre2 1 d2bsqe1 2 d1mula_ 3 d1huua_ 4 c3c4iA_ 5 d1p71a_ 6 d1owfa_ 7 c2iifA_ 8 d1exea_ 9 d1b8za_ 10 c2k42A_ 11 c2kl8A_ 12 c3gr5A_ 13 c2y9kG_ 14 d1owfb_ 15 d1mnta_ 16 c1f3mB_ 17 c2xflB_ 18 c1ceeB_ 19 c2y3mA_ 20 d1ej5a_ 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41

Detailed template information

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

1 d2bsqe1 63.6 9 Fold:Ribbon-helix-helix Superfamily:Ribbon-helix-helix Family:Trafficking protein A-like 2 d1mula_ 46.0 21 Fold:IHF-like DNA-binding proteins Superfamily:IHF-like DNA-binding proteins Family:Prokaryotic DNA-bending protein 3 d1huua_ 36.5 16 Fold:IHF-like DNA-binding proteins Superfamily:IHF-like DNA-binding proteins Family:Prokaryotic DNA-bending protein 4 c3c4iA_ 34.9 12 PDB header:dna binding protein Chain: A: PDB Molecule:dna-binding protein hu homolog; PDBTitle: crystal structure analysis of n terminal region containing the2 dimerization domain and dna binding domain of hu protein(histone like3 protein-dna binding) from mycobacterium tuberculosis [h37rv] 5 d1p71a_ 34.3 19 Fold:IHF-like DNA-binding proteins Superfamily:IHF-like DNA-binding proteins Family:Prokaryotic DNA-bending protein 6 d1owfa_ 33.9 14 Fold:IHF-like DNA-binding proteins Superfamily:IHF-like DNA-binding proteins Family:Prokaryotic DNA-bending protein 7 c2iifA_ 33.2 16 PDB header:recombination/dna Chain: A: PDB Molecule:integration host factor; PDBTitle: single chain integration host factor mutant protein (scihf2-2 k45ae) in complex with dna 8 d1exea_ 28.9 9 Fold:IHF-like DNA-binding proteins Superfamily:IHF-like DNA-binding proteins Family:Prokaryotic DNA-bending protein 9 d1b8za_ 28.3 18 Fold:IHF-like DNA-binding proteins Superfamily:IHF-like DNA-binding proteins Family:Prokaryotic DNA-bending protein 10 c2k42A_ 19.4 29 PDB header:signaling protein Chain: A: PDB Molecule:wiskott-aldrich syndrome protein; PDBTitle: solution structure of the gtpase binding domain of wasp in2 complex with espfu, an ehec effector 11 c2kl8A_ 19.0 19 PDB header:de novo protein Chain: A: PDB Molecule:or15; PDBTitle: solution nmr structure of de novo designed ferredoxin-like2 fold protein, northeast structural genomics consortium3 target or15 12 c3gr5A_ 18.5 7 PDB header:membrane protein Chain: A: PDB Molecule:escc; PDBTitle: periplasmic domain of the outer membrane secretin escc from2 enteropathogenic e.coli (epec) 13 c2y9kG_ 18.2 18 PDB header:protein transport Chain: G: PDB Molecule:protein invg; PDBTitle: three-dimensional model of salmonella's needle complex at2 subnanometer resolution 14 d1owfb_ 17.5 9 Fold:IHF-like DNA-binding proteins Superfamily:IHF-like DNA-binding proteins Family:Prokaryotic DNA-bending protein 15 d1mnta_ 16.4 24 Fold:Ribbon-helix-helix Superfamily:Ribbon-helix-helix Family:Arc/Mnt-like phage repressors 16 c1f3mB_ 16.2 30 PDB header:transferase Chain: B: PDB Molecule:serine/threonine-protein kinase pak-alpha; PDBTitle: crystal structure of human serine/threonine kinase pak1 17 c2xflB_ 16.1 26 PDB header:hydrolase Chain: B: PDB Molecule:dyne7; PDBTitle: induced-fit and allosteric effects upon polyene binding2 revealed by crystal structures of the dynemicin3 thioesterase 18 c1ceeB_ 15.0 29 PDB header:structural protein regulation Chain: B: PDB Molecule:wiskott-aldrich syndrome protein wasp; PDBTitle: solution structure of cdc42 in complex with the gtpase2 binding domain of wasp 19 c2y3mA_ 14.6 17 PDB header:transport protein Chain: A: PDB Molecule:protein transport protein hofq; PDBTitle: structure of the extra-membranous domain of the secretin2 hofq from actinobacillus actinomycetemcomitans 20 d1ej5a_ 14.5 32 Fold:Wiscott-Aldrich syndrome protein, WASP, C-terminal domain Superfamily:Wiscott-Aldrich syndrome protein, WASP, C-terminal domain Family:Wiscott-Aldrich syndrome protein, WASP, C-terminal domain 21 c3fwcO_ not modelled 14.3 7 PDB header:cell cycle, transcription Chain: O: PDB Molecule:protein sus1; PDBTitle: sac3:sus1:cdc31 complex 22 d1ucra_ not modelled 13.2 26 Fold:DNA/RNA-binding 3-helical bundle Superfamily:"Winged helix" DNA-binding domain Family:Dissimilatory sulfite reductase DsvD 23 c1u9pA_ not modelled 12.3 12 PDB header:unknown function Chain: A: PDB Molecule:parc; PDBTitle: permuted single-chain arc 24 d2o97b1 not modelled 11.1 25 Fold:IHF-like DNA-binding proteins Superfamily:IHF-like DNA-binding proteins Family:Prokaryotic DNA-bending protein 25 c3eudE_ not modelled 9.5 23 PDB header:nuclear protein Chain: E: PDB Molecule:protein shq1; PDBTitle: structure of the cs domain of the essential h/aca rnp2 assembly protein shq1p 26 d1d5ya1 not modelled 8.4 7 Fold:DNA/RNA-binding 3-helical bundle Superfamily:Homeodomain-like Family:AraC type transcriptional activator 27 c2ptvA_ not modelled 8.1 12 PDB header:immune system Chain: A: PDB Molecule:cd48 antigen; PDBTitle: structure of nk cell receptor ligand cd48 28 c3ossD_ not modelled 7.8 7 PDB header:protein transport Chain: D: PDB Molecule:type 2 secretion system, secretin gspd; PDBTitle: the crystal structure of enterotoxigenic escherichia coli gspc-gspd2 complex from the type ii secretion system 29 d2o4ta1 not modelled 7.8 14 Fold:Left-handed superhelix Superfamily:BH3980-like Family:BH3980-like 30 d1d6za4 not modelled 7.4 20 Fold:N domain of copper amine oxidase-like Superfamily:Copper amine oxidase, domain N Family:Copper amine oxidase, domain N 31 d1d8ja_ not modelled 6.6 19 Fold:DNA/RNA-binding 3-helical bundle Superfamily:"Winged helix" DNA-binding domain Family:The central core domain of TFIIE beta 32 d2qi2a1 not modelled 6.6 31 Fold:Sm-like fold Superfamily:Dom34/Pelota N-terminal domain-like Family:Dom34/Pelota N-terminal domain-like 33 d2b0ga1 not modelled 6.6 13 Fold:Ferredoxin-like Superfamily:RNA-binding domain, RBD Family:Canonical RBD 34 c3kf8D_ not modelled 6.4 25 PDB header:structural protein Chain: D: PDB Molecule:protein ten1; PDBTitle: crystal structure of c. tropicalis stn1-ten1 complex 35 c2edoA_ not modelled 6.0 26 PDB header:cell adhesion Chain: A: PDB Molecule:cd48 antigen; PDBTitle: solution structure of the first ig-like domain from human2 cd48 antigen 36 c1e0aB_ not modelled 5.8 24 PDB header:signalling protein Chain: B: PDB Molecule:serine/threonine-protein kinase pak-alpha; PDBTitle: cdc42 complexed with the gtpase binding domain of p212 activated kinase 37 c2np2B_ not modelled 5.6 21 PDB header:dna binding protein/dna Chain: B: PDB Molecule:hbb; PDBTitle: hbb-dna complex 38 d1rxta1 not modelled 5.6 31 Fold:Acyl-CoA N-acyltransferases (Nat) Superfamily:Acyl-CoA N-acyltransferases (Nat) Family:N-myristoyl transferase, NMT 39 c3aqjQ_ not modelled 5.6 38 PDB header:metal binding protein Chain: Q: PDB Molecule:baseplate assembly protein v; PDBTitle: crystal structure of a c-terminal domain of the bacteriophage p2 tail2 spike protein, gpv 40 d1qa9b_ not modelled 5.3 26 Fold:Immunoglobulin-like beta-sandwich Superfamily:Immunoglobulin Family:V set domains (antibody variable domain-like) 41 c2o37A_ not modelled 5.1 18 PDB header:chaperone Chain: A: PDB Molecule:protein sis1; PDBTitle: j-domain of sis1 protein, hsp40 co-chaperone from2 saccharomyces cerevisiae.

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