Secondary structure and disorder prediction

		1	.	.	.	.	.	.	.	.	10	.	.	.	.	.	.	.	.	.	20	.	.	.	.	.	.	.	.	.	30	.	.	.	.	.	.	.	.	.	40	.	.	.	.	.	.	.	.	.	50	.	.	.	.	.	.	.	.	.	60
Sequence		M	N	K	E	E	Q	Y	L	L	F	A	L	S	A	P	M	E	I	L	N	Q	G	C	K	P	A	H	D	S	P	K	M	Y	T	G	I	K	E	F	E	L	S	S	S	W	G	I	N	N	R	D	D	L	I	Q	T	I	Y	Q	M
Secondary structure
SS confidence
Disorder		?	?																					?			?
Disorder confidence
		.	.	.	.	.	.	.	.	.	70	.	.	.	.	.	.	.	.	.	80	.	.	.	.	.	.	.	.	.	90	.	.	.	.	.	.	.	.	.	100	.	.	.	.	.	.	.	.	.	110	.	.	.	.	.	.	.	.	.	120
Sequence		T	D	D	G	H	A	N	D	L	A	G	L	Y	L	T	W	H	R	S	S	P	E	E	W	K	A	L	I	A	G	G	S	E	R	G	L	I	Y	T	Q	F	V	A	Q	T	A	M	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	V	G	V	L	N	K	W	L	T	E	E	E	S	L	W	L	Q	S	R	V	Y	V	R	A	H	H	Y	Y	H	S	W	M	H	Y	F	S	A	Y	S	L	G	R	L	Y	W	Q	S	S	Q	C	E	D	N
Secondary structure
SS confidence
Disorder																																																									?	?	?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	190	.	.	.	.	.	.	.	.	.	200	.	.	.	.	.	.	.	.	.	210	.	.	.	.	.	.	.	.	.	220	.	.	.	.	.	.	.	.	.	230	.	.	.	.	.
Sequence		T	S	L	R	E	A	L	T	L	Y	K	Y	D	S	A	G	S	R	M	F	E	E	L	A	A	G	S	D	R	F	Y	A	T	L	P	W	Q	P	L	T	V	Q	S	E	C	P	V	T	L	K	D	V	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 2cwl chain A domain 1 Region: 12 - 77 Aligned: 66 Modelled: 66 Confidence: 34.0% Identity: 8% Fold: Ferritin-like Superfamily: Ferritin-like Family: Manganese catalase (T-catalase) Phyre2 PDB 2job chain A Region: 124 - 145 Aligned: 22 Modelled: 22 Confidence: 25.6% Identity: 14% 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 1jog chain A Region: 124 - 156 Aligned: 33 Modelled: 33 Confidence: 24.7% Identity: 9% Fold: Four-helical up-and-down bundle Superfamily: Nucleotidyltransferase substrate binding subunit/domain Family: Family 1 bi-partite nucleotidyltransferase subunit Phyre2 PDB 1jkv chain A Region: 12 - 78 Aligned: 67 Modelled: 67 Confidence: 23.8% Identity: 4% Fold: Ferritin-like Superfamily: Ferritin-like Family: Manganese catalase (T-catalase) Phyre2 PDB 1wwp chain A Region: 124 - 156 Aligned: 33 Modelled: 33 Confidence: 20.3% Identity: 18% 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: 20.1% Identity: 15% Fold: Four-helical up-and-down bundle Superfamily: Nucleotidyltransferase substrate binding subunit/domain Family: Family 1 bi-partite nucleotidyltransferase subunit Phyre2 PDB 2lhu chain A Region: 29 - 57 Aligned: 24 Modelled: 29 Confidence: 19.0% Identity: 17% PDB header:structural protein Chain: A: PDB Molecule:mybpc3 protein; PDBTitle: structural insight into the unique cardiac myosin binding protein-c2 motif: a partially folded domain Phyre2 PDB 1tz7 chain A domain 1 Region: 40 - 66 Aligned: 27 Modelled: 27 Confidence: 17.0% Identity: 19% 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: 14.9% Identity: 11% Fold: TIM beta/alpha-barrel Superfamily: (Trans)glycosidases Family: Amylase, catalytic domain Phyre2 PDB 2adv chain B Region: 203 - 213 Aligned: 11 Modelled: 11 Confidence: 14.6% Identity: 18% PDB header:hydrolase Chain: B: PDB Molecule:glutaryl 7- aminocephalosporanic acid acylase; PDBTitle: crystal structures of glutaryl 7-aminocephalosporanic acid acylase:2 mutational study of activation mechanism Phyre2 PDB 2oa4 chain A domain 1 Region: 106 - 142 Aligned: 36 Modelled: 37 Confidence: 12.5% Identity: 19% Fold: DNA/RNA-binding 3-helical bundle Superfamily: TrpR-like Family: SPO1678-like Phyre2 PDB 2gyk chain B domain 1 Region: 146 - 167 Aligned: 22 Modelled: 22 Confidence: 12.2% Identity: 14% Fold: His-Me finger endonucleases Superfamily: His-Me finger endonucleases Family: HNH-motif Phyre2 PDB 2jrt chain A Region: 106 - 142 Aligned: 36 Modelled: 37 Confidence: 11.1% Identity: 19% 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 1e8o chain A Region: 155 - 164 Aligned: 10 Modelled: 10 Confidence: 9.9% Identity: 30% 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 2fxh chain B Region: 178 - 235 Aligned: 58 Modelled: 58 Confidence: 7.0% Identity: 17% PDB header:oxidoreductase Chain: B: PDB Molecule:catalase-peroxidase protein; PDBTitle: crystal structure of katg at ph 6.5 Phyre2 PDB 2b2q chain B Region: 178 - 235 Aligned: 58 Modelled: 58 Confidence: 7.0% Identity: 17% PDB header:oxidoreductase Chain: B: PDB Molecule:catalase-peroxidase; PDBTitle: crystal structure of native catalase-peroxidase katg at2 ph7.5 Phyre2 PDB 3rdw chain B Region: 45 - 91 Aligned: 45 Modelled: 47 Confidence: 6.9% Identity: 11% PDB header:oxidoreductase Chain: B: PDB Molecule:putative arsenate reductase; PDBTitle: putative arsenate reductase from yersinia pestis Phyre2 PDB 1x1n chain A domain 1 Region: 40 - 66 Aligned: 27 Modelled: 27 Confidence: 6.8% Identity: 11% Fold: TIM beta/alpha-barrel Superfamily: (Trans)glycosidases Family: Amylase, catalytic domain Phyre2 PDB 2p12 chain A domain 1 Region: 128 - 157 Aligned: 30 Modelled: 30 Confidence: 6.8% Identity: 3% Fold: FomD barrel-like Superfamily: FomD-like Family: FomD-like Phyre2 PDB 2jg6 chain A Region: 103 - 205 Aligned: 103 Modelled: 103 Confidence: 6.2% Identity: 14% PDB header:hydrolase Chain: A: PDB Molecule:dna-3-methyladenine glycosidase; PDBTitle: crystal structure of a 3-methyladenine dna glycosylase i2 from staphylococcus aureus Phyre2 1 d2cwla1 2 c2jobA_ 3 d1joga_ 4 d1jkva_ 5 c1wwpA_ 6 d1wtya_ 7 c2lhuA_ 8 d1tz7a1 9 d1eswa_ 10 c2advB_ 11 d2oa4a1 12 d2gykb1 13 c2jrtA_ 14 d1e8oa_ 15 c2fxhB_ 16 c2b2qB_ 17 c3rdwB_ 18 d1x1na1 19 d2p12a1 20 c2jg6A_ 21 22 23 24 25 26 27 28 29

Detailed template information

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

1 d2cwla1 34.0 8 Fold:Ferritin-like Superfamily:Ferritin-like Family:Manganese catalase (T-catalase) 2 c2jobA_ 25.6 14 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 d1joga_ 24.7 9 Fold:Four-helical up-and-down bundle Superfamily:Nucleotidyltransferase substrate binding subunit/domain Family:Family 1 bi-partite nucleotidyltransferase subunit 4 d1jkva_ 23.8 4 Fold:Ferritin-like Superfamily:Ferritin-like Family:Manganese catalase (T-catalase) 5 c1wwpA_ 20.3 18 PDB header:structural genomics, unknown function Chain: A: PDB Molecule:hypothetical protein ttha0636; PDBTitle: crystal structure of ttk003001694 from thermus thermophilus2 hb8 6 d1wtya_ 20.1 15 Fold:Four-helical up-and-down bundle Superfamily:Nucleotidyltransferase substrate binding subunit/domain Family:Family 1 bi-partite nucleotidyltransferase subunit 7 c2lhuA_ 19.0 17 PDB header:structural protein Chain: A: PDB Molecule:mybpc3 protein; PDBTitle: structural insight into the unique cardiac myosin binding protein-c2 motif: a partially folded domain 8 d1tz7a1 17.0 19 Fold:TIM beta/alpha-barrel Superfamily:(Trans)glycosidases Family:Amylase, catalytic domain 9 d1eswa_ 14.9 11 Fold:TIM beta/alpha-barrel Superfamily:(Trans)glycosidases Family:Amylase, catalytic domain 10 c2advB_ 14.6 18 PDB header:hydrolase Chain: B: PDB Molecule:glutaryl 7- aminocephalosporanic acid acylase; PDBTitle: crystal structures of glutaryl 7-aminocephalosporanic acid acylase:2 mutational study of activation mechanism 11 d2oa4a1 12.5 19 Fold:DNA/RNA-binding 3-helical bundle Superfamily:TrpR-like Family:SPO1678-like 12 d2gykb1 12.2 14 Fold:His-Me finger endonucleases Superfamily:His-Me finger endonucleases Family:HNH-motif 13 c2jrtA_ 11.1 19 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 14 d1e8oa_ 9.9 30 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 15 c2fxhB_ 7.0 17 PDB header:oxidoreductase Chain: B: PDB Molecule:catalase-peroxidase protein; PDBTitle: crystal structure of katg at ph 6.5 16 c2b2qB_ 7.0 17 PDB header:oxidoreductase Chain: B: PDB Molecule:catalase-peroxidase; PDBTitle: crystal structure of native catalase-peroxidase katg at2 ph7.5 17 c3rdwB_ 6.9 11 PDB header:oxidoreductase Chain: B: PDB Molecule:putative arsenate reductase; PDBTitle: putative arsenate reductase from yersinia pestis 18 d1x1na1 6.8 11 Fold:TIM beta/alpha-barrel Superfamily:(Trans)glycosidases Family:Amylase, catalytic domain 19 d2p12a1 6.8 3 Fold:FomD barrel-like Superfamily:FomD-like Family:FomD-like 20 c2jg6A_ 6.2 14 PDB header:hydrolase Chain: A: PDB Molecule:dna-3-methyladenine glycosidase; PDBTitle: crystal structure of a 3-methyladenine dna glycosylase i2 from staphylococcus aureus 21 c1dpuA_ not modelled 6.0 18 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) 22 d1dpua_ not modelled 6.0 18 Fold:DNA/RNA-binding 3-helical bundle Superfamily:"Winged helix" DNA-binding domain Family:C-terminal domain of RPA32 23 c2k5eA_ not modelled 6.0 21 PDB header:structural genomics, unknown function Chain: A: PDB Molecule:uncharacterized protein; PDBTitle: solution structure of putative uncharacterized protein2 gsu1278 from methanocaldococcus jannaschii, northeast3 structural genomics consortium (nesg) target gsr195 24 c3dmlA_ not modelled 5.9 15 PDB header:oxidoreductase Chain: A: PDB Molecule:putative uncharacterized protein; PDBTitle: crystal structure of the periplasmic thioredoxin soxs from2 paracoccus pantotrophus (reduced form) 25 d1jvaa2 not modelled 5.7 32 Fold:Homing endonuclease-like Superfamily:Homing endonucleases Family:Intein endonuclease 26 c3gkxB_ not modelled 5.5 12 PDB header:structural genomics, unknown function Chain: B: PDB Molecule:putative arsc family related protein; PDBTitle: crystal structure of putative arsc family related protein from2 bacteroides fragilis 27 d2gsca1 not modelled 5.5 6 Fold:Bromodomain-like Superfamily:IVS-encoded protein-like Family:IVS-encoded protein-like 28 d1nkua_ not modelled 5.4 6 Fold:DNA-glycosylase Superfamily:DNA-glycosylase Family:3-Methyladenine DNA glycosylase I (Tag) 29 d1fsha_ not modelled 5.2 21 Fold:DNA/RNA-binding 3-helical bundle Superfamily:"Winged helix" DNA-binding domain Family:DEP domain

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