Secondary structure and disorder prediction

		1	.	.	.	.	.	.	.	.	10	.	.	.	.	.	.	.	.	.	20	.	.	.	.	.	.	.	.	.	30	.	.	.	.	.	.	.	.	.	40	.	.	.	.	.	.	.	.	.	50	.	.	.	.	.	.	.	.	.	60
Sequence		M	D	M	E	S	Q	K	I	L	F	A	L	S	T	P	M	E	I	R	N	E	C	C	L	P	S	H	S	S	P	K	M	Y	L	G	T	C	F	F	D	L	S	S	S	W	G	I	D	D	R	D	D	L	L	R	T	I	H	R	M
Secondary structure
SS confidence
Disorder		?	?																								?		?			?														?
Disorder confidence
		.	.	.	.	.	.	.	.	.	70	.	.	.	.	.	.	.	.	.	80	.	.	.	.	.	.	.	.	.	90	.	.	.	.	.	.	.	.	.	100	.	.	.	.	.	.	.	.	.	110	.	.	.	.	.	.	.	.	.	120
Sequence		I	D	N	G	H	A	A	R	L	A	G	F	Y	H	R	W	F	R	Y	S	P	C	E	W	R	D	Y	L	A	E	L	N	E	Q	G	Q	A	Y	A	Q	F	V	A	S	T	A	E	C	C	G	E	G	G	I	K	A	W	D	Y	V
Secondary structure
SS confidence
Disorder
Disorder confidence
		.	.	.	.	.	.	.	.	.	130	.	.	.	.	.	.	.	.	.	140	.	.	.	.	.	.	.	.	.	150	.	.	.	.	.	.	.	.	.	160	.	.	.	.	.	.	.	.	.	170	.	.	.	.	.	.	.	.	.	180
Sequence		R	M	G	F	L	S	R	M	G	V	L	N	N	W	L	S	E	E	E	S	L	W	I	Q	S	R	I	H	L	R	A	L	R	Y	Y	S	N	W	R	Q	Y	F	A	G	Y	T	F	G	R	Q	Y	W	Q	S	P	E	D	D	H	L
Secondary structure
SS confidence
Disorder																																																									?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	190	.	.	.	.	.	.	.	.	.	200	.	.	.	.	.	.	.	.	.	210	.	.	.	.	.	.	.	.	.	220	.	.	.	.	.	.	.	.	.	230	.	.	.	.	.
Sequence		P	L	L	R	E	F	L	A	R	K	E	Y	D	D	S	G	N	D	M	F	Y	Q	L	F	A	S	D	D	A	Y	Y	P	T	L	S	W	Q	P	L	A	Y	Y	S	A	C	P	E	T	L	K	D	M	S	D	L
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 3jrk chain G Region: 164 - 211 Aligned: 46 Modelled: 48 Confidence: 29.8% Identity: 17% PDB header:lyase Chain: G: PDB Molecule:tagatose 1,6-diphosphate aldolase 2; PDBTitle: a putative tagatose 1,6-diphosphate aldolase from streptococcus2 pyogenes Phyre2 PDB 2job chain A Region: 124 - 145 Aligned: 22 Modelled: 22 Confidence: 23.7% Identity: 18% PDB header:lipid binding protein Chain: A: PDB Molecule:antilipopolysaccharide factor; PDBTitle: solution structure of an antilipopolysaccharide factor from2 shrimp and its possible lipid a binding site Phyre2 PDB 1tz7 chain A domain 1 Region: 40 - 66 Aligned: 27 Modelled: 27 Confidence: 23.6% Identity: 26% Fold: TIM beta/alpha-barrel Superfamily: (Trans)glycosidases Family: Amylase, catalytic domain Phyre2 PDB 1esw chain A Region: 40 - 66 Aligned: 27 Modelled: 27 Confidence: 21.0% Identity: 11% Fold: TIM beta/alpha-barrel Superfamily: (Trans)glycosidases Family: Amylase, catalytic domain Phyre2 PDB 1jog chain A Region: 124 - 156 Aligned: 33 Modelled: 33 Confidence: 20.1% Identity: 6% Fold: Four-helical up-and-down bundle Superfamily: Nucleotidyltransferase substrate binding subunit/domain Family: Family 1 bi-partite nucleotidyltransferase subunit Phyre2 PDB 1wwp chain A Region: 124 - 156 Aligned: 33 Modelled: 33 Confidence: 17.0% Identity: 15% PDB header:structural genomics, unknown function Chain: A: PDB Molecule:hypothetical protein ttha0636; PDBTitle: crystal structure of ttk003001694 from thermus thermophilus2 hb8 Phyre2 PDB 1wty chain A Region: 124 - 156 Aligned: 33 Modelled: 33 Confidence: 15.2% Identity: 12% Fold: Four-helical up-and-down bundle Superfamily: Nucleotidyltransferase substrate binding subunit/domain Family: Family 1 bi-partite nucleotidyltransferase subunit Phyre2 PDB 2gyk chain B domain 1 Region: 146 - 167 Aligned: 22 Modelled: 22 Confidence: 13.3% Identity: 9% Fold: His-Me finger endonucleases Superfamily: His-Me finger endonucleases Family: HNH-motif Phyre2 PDB 1x1n chain A domain 1 Region: 40 - 66 Aligned: 27 Modelled: 27 Confidence: 10.9% Identity: 15% Fold: TIM beta/alpha-barrel Superfamily: (Trans)glycosidases Family: Amylase, catalytic domain Phyre2 PDB 1e8o chain A Region: 155 - 164 Aligned: 10 Modelled: 10 Confidence: 9.6% Identity: 20% Fold: Signal recognition particle alu RNA binding heterodimer, SRP9/14 Superfamily: Signal recognition particle alu RNA binding heterodimer, SRP9/14 Family: Signal recognition particle alu RNA binding heterodimer, SRP9/14 Phyre2 PDB 1f6v chain A Region: 40 - 54 Aligned: 15 Modelled: 15 Confidence: 7.4% Identity: 20% Fold: C-terminal domain of B transposition protein Superfamily: C-terminal domain of B transposition protein Family: C-terminal domain of B transposition protein Phyre2 PDB 2oa4 chain A domain 1 Region: 108 - 142 Aligned: 34 Modelled: 35 Confidence: 6.8% Identity: 18% Fold: DNA/RNA-binding 3-helical bundle Superfamily: TrpR-like Family: SPO1678-like Phyre2 PDB 1dpu chain A Region: 49 - 65 Aligned: 17 Modelled: 17 Confidence: 6.3% Identity: 12% PDB header:dna binding protein Chain: A: PDB Molecule:replication protein a (rpa32) c-terminal domain; PDBTitle: solution structure of the c-terminal domain of human rpa322 complexed with ung2(73-88) Phyre2 PDB 1dpu chain A Region: 49 - 65 Aligned: 17 Modelled: 17 Confidence: 6.3% Identity: 12% Fold: DNA/RNA-binding 3-helical bundle Superfamily: "Winged helix" DNA-binding domain Family: C-terminal domain of RPA32 Phyre2 PDB 1fsh chain A Region: 46 - 64 Aligned: 19 Modelled: 19 Confidence: 6.0% Identity: 21% Fold: DNA/RNA-binding 3-helical bundle Superfamily: "Winged helix" DNA-binding domain Family: DEP domain Phyre2 PDB 3dkb chain A Region: 45 - 69 Aligned: 25 Modelled: 25 Confidence: 5.9% Identity: 20% PDB header:hydrolase Chain: A: PDB Molecule:tumor necrosis factor, alpha-induced protein 3; PDBTitle: crystal structure of a20, 2.5 angstrom Phyre2 PDB 2p12 chain A domain 1 Region: 128 - 157 Aligned: 30 Modelled: 30 Confidence: 5.9% Identity: 3% Fold: FomD barrel-like Superfamily: FomD-like Family: FomD-like Phyre2 PDB 1jva chain A domain 2 Region: 161 - 181 Aligned: 19 Modelled: 21 Confidence: 5.9% Identity: 16% Fold: Homing endonuclease-like Superfamily: Homing endonucleases Family: Intein endonuclease Phyre2 PDB 2jrt chain A Region: 108 - 142 Aligned: 34 Modelled: 35 Confidence: 5.8% Identity: 18% PDB header:structural genomics, unknown function Chain: A: PDB Molecule:uncharacterized protein; PDBTitle: nmr solution structure of the protein coded by gene2 rhos4_12090 of rhodobacter sphaeroides. northeast3 structural genomics target rhr5 Phyre2 PDB 2gsc chain A domain 1 Region: 119 - 152 Aligned: 34 Modelled: 34 Confidence: 5.8% Identity: 6% Fold: Bromodomain-like Superfamily: IVS-encoded protein-like Family: IVS-encoded protein-like Phyre2 1 c3jrkG_ 2 c2jobA_ 3 d1tz7a1 4 d1eswa_ 5 d1joga_ 6 c1wwpA_ 7 d1wtya_ 8 d2gykb1 9 d1x1na1 10 d1e8oa_ 11 d1f6va_ 12 d2oa4a1 13 c1dpuA_ 14 d1dpua_ 15 d1fsha_ 16 c3dkbA_ 17 d2p12a1 18 d1jvaa2 19 c2jrtA_ 20 d2gsca1 21 22 23 24

Detailed template information

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

1 c3jrkG_ 29.8 17 PDB header:lyase Chain: G: PDB Molecule:tagatose 1,6-diphosphate aldolase 2; PDBTitle: a putative tagatose 1,6-diphosphate aldolase from streptococcus2 pyogenes 2 c2jobA_ 23.7 18 PDB header:lipid binding protein Chain: A: PDB Molecule:antilipopolysaccharide factor; PDBTitle: solution structure of an antilipopolysaccharide factor from2 shrimp and its possible lipid a binding site 3 d1tz7a1 23.6 26 Fold:TIM beta/alpha-barrel Superfamily:(Trans)glycosidases Family:Amylase, catalytic domain 4 d1eswa_ 21.0 11 Fold:TIM beta/alpha-barrel Superfamily:(Trans)glycosidases Family:Amylase, catalytic domain 5 d1joga_ 20.1 6 Fold:Four-helical up-and-down bundle Superfamily:Nucleotidyltransferase substrate binding subunit/domain Family:Family 1 bi-partite nucleotidyltransferase subunit 6 c1wwpA_ 17.0 15 PDB header:structural genomics, unknown function Chain: A: PDB Molecule:hypothetical protein ttha0636; PDBTitle: crystal structure of ttk003001694 from thermus thermophilus2 hb8 7 d1wtya_ 15.2 12 Fold:Four-helical up-and-down bundle Superfamily:Nucleotidyltransferase substrate binding subunit/domain Family:Family 1 bi-partite nucleotidyltransferase subunit 8 d2gykb1 13.3 9 Fold:His-Me finger endonucleases Superfamily:His-Me finger endonucleases Family:HNH-motif 9 d1x1na1 10.9 15 Fold:TIM beta/alpha-barrel Superfamily:(Trans)glycosidases Family:Amylase, catalytic domain 10 d1e8oa_ 9.6 20 Fold:Signal recognition particle alu RNA binding heterodimer, SRP9/14 Superfamily:Signal recognition particle alu RNA binding heterodimer, SRP9/14 Family:Signal recognition particle alu RNA binding heterodimer, SRP9/14 11 d1f6va_ 7.4 20 Fold:C-terminal domain of B transposition protein Superfamily:C-terminal domain of B transposition protein Family:C-terminal domain of B transposition protein 12 d2oa4a1 6.8 18 Fold:DNA/RNA-binding 3-helical bundle Superfamily:TrpR-like Family:SPO1678-like 13 c1dpuA_ 6.3 12 PDB header:dna binding protein Chain: A: PDB Molecule:replication protein a (rpa32) c-terminal domain; PDBTitle: solution structure of the c-terminal domain of human rpa322 complexed with ung2(73-88) 14 d1dpua_ 6.3 12 Fold:DNA/RNA-binding 3-helical bundle Superfamily:"Winged helix" DNA-binding domain Family:C-terminal domain of RPA32 15 d1fsha_ 6.0 21 Fold:DNA/RNA-binding 3-helical bundle Superfamily:"Winged helix" DNA-binding domain Family:DEP domain 16 c3dkbA_ 5.9 20 PDB header:hydrolase Chain: A: PDB Molecule:tumor necrosis factor, alpha-induced protein 3; PDBTitle: crystal structure of a20, 2.5 angstrom 17 d2p12a1 5.9 3 Fold:FomD barrel-like Superfamily:FomD-like Family:FomD-like 18 d1jvaa2 5.9 16 Fold:Homing endonuclease-like Superfamily:Homing endonucleases Family:Intein endonuclease 19 c2jrtA_ 5.8 18 PDB header:structural genomics, unknown function Chain: A: PDB Molecule:uncharacterized protein; PDBTitle: nmr solution structure of the protein coded by gene2 rhos4_12090 of rhodobacter sphaeroides. northeast3 structural genomics target rhr5 20 d2gsca1 5.8 6 Fold:Bromodomain-like Superfamily:IVS-encoded protein-like Family:IVS-encoded protein-like 21 d1q88a_ not modelled 5.6 40 Fold:39 kda initiator binding protein, IBP39, C-terminal domains Superfamily:39 kda initiator binding protein, IBP39, C-terminal domains Family:39 kda initiator binding protein, IBP39, C-terminal domains 22 c3ml6D_ not modelled 5.5 15 PDB header:protein transport Chain: D: PDB Molecule:chimeric complex between protein dishevlled2 homolog dvl-2 PDBTitle: a complex between dishevlled2 and clathrin adaptor ap-2 23 d1jkva_ not modelled 5.5 5 Fold:Ferritin-like Superfamily:Ferritin-like Family:Manganese catalase (T-catalase) 24 d2axte1 not modelled 5.3 7 Fold:Single transmembrane helix Superfamily:Cytochrome b559 subunits Family:Cytochrome b559 subunits

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

---

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