Secondary structure and disorder prediction

		1	.	.	.	.	.	.	.	.	10	.	.	.	.	.	.	.	.	.	20	.	.	.	.	.	.	.	.	.	30	.	.	.	.	.	.	.	.	.	40	.	.	.	.	.	.	.	.	.	50	.	.	.	.	.	.	.	.	.	60
Sequence		M	C	E	L	D	I	L	H	D	S	L	Y	Q	F	C	P	E	L	H	L	K	R	L	N	S	L	T	L	A	C	H	A	L	L	D	C	K	T	L	T	L	T	E	L	G	R	N	L	P	T	K	A	R	T	K	H	N	I	K	R
Secondary structure
SS confidence
Disorder		?	?																																																		?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	70	.	.	.	.	.	.	.	.	.	80	.	.	.	.	.	.	.	.	.	90	.	.	.	.	.	.	.	.	.	100	.	.	.	.	.	.	.	.	.	110	.	.	.	.	.	.	.	.	.	120
Sequence		I	D	R	L	L	G	N	R	H	L	H	K	E	R	L	A	V	Y	R	W	H	A	S	F	I	C	S	G	N	T	M	P	I	V	L	V	D	W	S	D	I	R	E	Q	K	R	L	M	V	L	R	A	S	V	A	L	H	G	R	S
Secondary structure
SS confidence
Disorder																																																								?
Disorder confidence
		.	.	.	.	.	.	.	.	.	130	.	.	.	.	.	.	.	.	.	140	.	.	.	.	.	.	.	.	.	150	.	.	.	.	.	.	.	.	.	160	.	.	.	.	.	.	.	.	.	170	.	.	.	.	.	.	.	.	.	180
Sequence		V	T	L	Y	E	K	A	F	P	L	S	E	Q	C	S	K	K	A	H	D	Q	F	L	A	D	L	A	S	I	L	P	S	N	T	T	P	L	I	V	S	D	A	G	F	K	V	P	W	Y	K	S	V	E	K	L	G	W	Y	W	L
Secondary structure
SS confidence
Disorder													?	?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	190	.	.	.	.	.	.	.	.	.	200	.	.	.	.	.	.	.	.	.	210	.	.	.	.	.	.	.	.	.	220	.	.	.	.	.	.	.	.	.	230	.	.	.	.	.	.	.	.	.	240
Sequence		S	R	V	R	G	K	V	Q	Y	A	D	L	G	A	E	N	W	K	P	I	S	N	L	H	D	M	S	S	S	H	S	K	T	L	G	Y	K	R	L	T	K	S	N	P	I	S	C	Q	I	L	L	Y	K	S	R	S	K	G	R	K
Secondary structure
SS confidence
Disorder							?	?							?	?										?	?					?																									?	?	?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	250	.	.	.	.	.	.	.	.	.	260	.	.	.	.	.	.	.	.	.	270	.	.	.	.	.	.	.	.	.	280	.	.	.	.	.	.	.	.	.	290	.	.	.	.	.	.	.	.	.	300
Sequence		N	Q	R	S	T	R	T	H	C	H	H	P	S	P	K	I	Y	S	A	S	A	K	E	P	W	I	L	A	T	N	L	P	V	E	I	R	T	P	K	Q	L	V	N	I	Y	S	K	R	M	Q	I	E	E	T	F	R	D	L	K	S
Secondary structure
SS confidence
Disorder				?			?		?	?		?			?		?	?																?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	310	.	.	.	.	.	.	.	.	.	320	.	.	.	.	.	.	.	.	.	330	.	.	.	.	.	.	.	.	.	340	.	.	.	.	.	.	.	.	.	350	.	.	.	.	.	.	.	.	.	360
Sequence		P	A	Y	G	L	G	L	R	H	S	R	T	S	S	S	E	R	F	D	I	M	L	L	I	A	L	M	L	Q	L	T	C	W	L	A	G	V	H	A	Q	K	Q	G	W	D	K	H	F	Q	A	N	T	V	R	N	R	N	V	L	S
Secondary structure
SS confidence
Disorder													?																																	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	370	.	.	.	.	.	.	.	.	.	380	.	.	.	.	.	.	.	.	.	390	.	.	.	.	.	.	.	.	.	400	.	.
Sequence		T	V	R	L	G	M	E	V	L	R	H	S	G	Y	T	I	T	R	E	D	S	L	V	A	A	T	L	L	T	Q	N	L	F	T	H	G	Y	V	L	G	K	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 1mus chain A Region: 19 - 396 Aligned: 364 Modelled: 372 Confidence: 100.0% Identity: 14% Fold: Ribonuclease H-like motif Superfamily: Ribonuclease H-like Family: Transposase inhibitor (Tn5 transposase) Phyre2 PDB 1b7e chain A Region: 76 - 392 Aligned: 304 Modelled: 312 Confidence: 100.0% Identity: 14% Fold: Ribonuclease H-like motif Superfamily: Ribonuclease H-like Family: Transposase inhibitor (Tn5 transposase) Phyre2 PDB 1ovm chain A domain 1 Region: 127 - 181 Aligned: 55 Modelled: 55 Confidence: 25.6% Identity: 13% Fold: DHS-like NAD/FAD-binding domain Superfamily: DHS-like NAD/FAD-binding domain Family: Pyruvate oxidase and decarboxylase, middle domain Phyre2 PDB 1y76 chain B domain 1 Region: 290 - 325 Aligned: 32 Modelled: 36 Confidence: 20.4% Identity: 34% Fold: L27 domain Superfamily: L27 domain Family: L27 domain Phyre2 PDB 2bgw chain A domain 2 Region: 153 - 182 Aligned: 30 Modelled: 30 Confidence: 20.2% Identity: 20% Fold: Restriction endonuclease-like Superfamily: Restriction endonuclease-like Family: XPF/Rad1/Mus81 nuclease Phyre2 PDB 1j1l chain A Region: 290 - 312 Aligned: 21 Modelled: 23 Confidence: 16.1% Identity: 24% Fold: Double-stranded beta-helix Superfamily: RmlC-like cupins Family: Pirin-like Phyre2 PDB 1zpd chain A domain 1 Region: 132 - 181 Aligned: 50 Modelled: 50 Confidence: 13.1% Identity: 8% Fold: DHS-like NAD/FAD-binding domain Superfamily: DHS-like NAD/FAD-binding domain Family: Pyruvate oxidase and decarboxylase, middle domain Phyre2 PDB 2csf chain A domain 1 Region: 57 - 79 Aligned: 21 Modelled: 23 Confidence: 12.4% Identity: 38% Fold: lambda repressor-like DNA-binding domains Superfamily: lambda repressor-like DNA-binding domains Family: CUT domain Phyre2 PDB 2ziu chain A Region: 151 - 182 Aligned: 32 Modelled: 32 Confidence: 11.8% Identity: 16% PDB header:hydrolase Chain: A: PDB Molecule:mus81 protein; PDBTitle: crystal structure of the mus81-eme1 complex Phyre2 PDB 1sko chain A Region: 134 - 163 Aligned: 29 Modelled: 30 Confidence: 11.5% Identity: 21% PDB header:signaling protein Chain: A: PDB Molecule:mitogen-activated protein kinase kinase 1 PDBTitle: mp1-p14 complex Phyre2 PDB 1tty chain A Region: 5 - 68 Aligned: 59 Modelled: 64 Confidence: 11.4% Identity: 25% Fold: DNA/RNA-binding 3-helical bundle Superfamily: Sigma3 and sigma4 domains of RNA polymerase sigma factors Family: Sigma4 domain Phyre2 PDB 2uvp chain B Region: 138 - 172 Aligned: 35 Modelled: 35 Confidence: 9.8% Identity: 14% PDB header:unknown function Chain: B: PDB Molecule:hoba; PDBTitle: crystal structure of hoba (hp1230)from helicobacter pylori Phyre2 PDB 2qkk chain I Region: 89 - 161 Aligned: 73 Modelled: 73 Confidence: 9.8% Identity: 8% PDB header:hydrolase/dna/rna Chain: I: PDB Molecule:ribonuclease h1; PDBTitle: human rnase h catalytic domain mutant d210n in complex with2 14-mer rna/dna hybrid Phyre2 PDB 2aq0 chain A domain 1 Region: 9 - 68 Aligned: 56 Modelled: 60 Confidence: 9.0% Identity: 18% Fold: SAM domain-like Superfamily: RuvA domain 2-like Family: Hef domain-like Phyre2 PDB 1tc3 chain C Region: 29 - 68 Aligned: 34 Modelled: 40 Confidence: 8.7% Identity: 18% Fold: DNA/RNA-binding 3-helical bundle Superfamily: Homeodomain-like Family: Recombinase DNA-binding domain Phyre2 PDB 2gpi chain A domain 1 Region: 288 - 298 Aligned: 11 Modelled: 11 Confidence: 8.5% Identity: 45% Fold: Shew3726-like Superfamily: Shew3726-like Family: Shew3726-like Phyre2 PDB 1smz chain A Region: 394 - 402 Aligned: 9 Modelled: 9 Confidence: 8.2% Identity: 56% PDB header:transport protein Chain: A: PDB Molecule:transportan in bicellar solution with PDBTitle: structure of transportan in phospholipid bicellar solution Phyre2 PDB 1pvd chain A domain 1 Region: 134 - 181 Aligned: 48 Modelled: 48 Confidence: 8.1% Identity: 13% Fold: DHS-like NAD/FAD-binding domain Superfamily: DHS-like NAD/FAD-binding domain Family: Pyruvate oxidase and decarboxylase, middle domain Phyre2 PDB 2zyz chain A Region: 292 - 305 Aligned: 12 Modelled: 14 Confidence: 8.1% Identity: 58% PDB header:splicing Chain: A: PDB Molecule:putative uncharacterized protein pae0789; PDBTitle: pyrobaculum aerophilum splicing endonuclease Phyre2 PDB 2qkl chain B domain 1 Region: 268 - 295 Aligned: 22 Modelled: 28 Confidence: 7.6% Identity: 36% Fold: Dcp2 domain-like Superfamily: Dcp2 domain-like Family: Dcp2 box A domain Phyre2 1 d1musa_ 2 d1b7ea_ 3 d1ovma1 4 d1y76b1 5 d2bgwa2 6 d1j1la_ 7 d1zpda1 8 d2csfa1 9 c2ziuA_ 10 c1skoA_ 11 d1ttya_ 12 c2uvpB_ 13 c2qkkI_ 14 d2aq0a1 15 d1tc3c_ 16 d2gpia1 17 c1smzA_ 18 d1pvda1 19 c2zyzA_ 20 d2qklb1 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44

Detailed template information

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

1 d1musa_ 100.0 14 Fold:Ribonuclease H-like motif Superfamily:Ribonuclease H-like Family:Transposase inhibitor (Tn5 transposase) 2 d1b7ea_ 100.0 14 Fold:Ribonuclease H-like motif Superfamily:Ribonuclease H-like Family:Transposase inhibitor (Tn5 transposase) 3 d1ovma1 25.6 13 Fold:DHS-like NAD/FAD-binding domain Superfamily:DHS-like NAD/FAD-binding domain Family:Pyruvate oxidase and decarboxylase, middle domain 4 d1y76b1 20.4 34 Fold:L27 domain Superfamily:L27 domain Family:L27 domain 5 d2bgwa2 20.2 20 Fold:Restriction endonuclease-like Superfamily:Restriction endonuclease-like Family:XPF/Rad1/Mus81 nuclease 6 d1j1la_ 16.1 24 Fold:Double-stranded beta-helix Superfamily:RmlC-like cupins Family:Pirin-like 7 d1zpda1 13.1 8 Fold:DHS-like NAD/FAD-binding domain Superfamily:DHS-like NAD/FAD-binding domain Family:Pyruvate oxidase and decarboxylase, middle domain 8 d2csfa1 12.4 38 Fold:lambda repressor-like DNA-binding domains Superfamily:lambda repressor-like DNA-binding domains Family:CUT domain 9 c2ziuA_ 11.8 16 PDB header:hydrolase Chain: A: PDB Molecule:mus81 protein; PDBTitle: crystal structure of the mus81-eme1 complex 10 c1skoA_ 11.5 21 PDB header:signaling protein Chain: A: PDB Molecule:mitogen-activated protein kinase kinase 1 PDBTitle: mp1-p14 complex 11 d1ttya_ 11.4 25 Fold:DNA/RNA-binding 3-helical bundle Superfamily:Sigma3 and sigma4 domains of RNA polymerase sigma factors Family:Sigma4 domain 12 c2uvpB_ 9.8 14 PDB header:unknown function Chain: B: PDB Molecule:hoba; PDBTitle: crystal structure of hoba (hp1230)from helicobacter pylori 13 c2qkkI_ 9.8 8 PDB header:hydrolase/dna/rna Chain: I: PDB Molecule:ribonuclease h1; PDBTitle: human rnase h catalytic domain mutant d210n in complex with2 14-mer rna/dna hybrid 14 d2aq0a1 9.0 18 Fold:SAM domain-like Superfamily:RuvA domain 2-like Family:Hef domain-like 15 d1tc3c_ 8.7 18 Fold:DNA/RNA-binding 3-helical bundle Superfamily:Homeodomain-like Family:Recombinase DNA-binding domain 16 d2gpia1 8.5 45 Fold:Shew3726-like Superfamily:Shew3726-like Family:Shew3726-like 17 c1smzA_ 8.2 56 PDB header:transport protein Chain: A: PDB Molecule:transportan in bicellar solution with PDBTitle: structure of transportan in phospholipid bicellar solution 18 d1pvda1 8.1 13 Fold:DHS-like NAD/FAD-binding domain Superfamily:DHS-like NAD/FAD-binding domain Family:Pyruvate oxidase and decarboxylase, middle domain 19 c2zyzA_ 8.1 58 PDB header:splicing Chain: A: PDB Molecule:putative uncharacterized protein pae0789; PDBTitle: pyrobaculum aerophilum splicing endonuclease 20 d2qklb1 7.6 36 Fold:Dcp2 domain-like Superfamily:Dcp2 domain-like Family:Dcp2 box A domain 21 c2ixsB_ not modelled 7.3 13 PDB header:hydrolase Chain: B: PDB Molecule:sdai restriction endonuclease; PDBTitle: structure of sdai restriction endonuclease 22 d1yioa1 not modelled 7.3 20 Fold:DNA/RNA-binding 3-helical bundle Superfamily:C-terminal effector domain of the bipartite response regulators Family:GerE-like (LuxR/UhpA family of transcriptional regulators) 23 c2rpiA_ not modelled 7.1 15 PDB header:hydrolase Chain: A: PDB Molecule:ribonuclease h; PDBTitle: the nmr structure of the submillisecond folding2 intermediate of the thermus thermophilus ribonuclease h 24 d1st6a5 not modelled 6.8 15 Fold:Four-helical up-and-down bundle Superfamily:alpha-catenin/vinculin-like Family:alpha-catenin/vinculin 25 c3e5bB_ not modelled 6.7 10 PDB header:lyase Chain: B: PDB Molecule:isocitrate lyase; PDBTitle: 2.4 a crystal structure of isocitrate lyase from brucella2 melitensis 26 d3cpta1 not modelled 6.7 20 Fold:Profilin-like Superfamily:Roadblock/LC7 domain Family:Roadblock/LC7 domain 27 d1qwia_ not modelled 6.5 13 Fold:OsmC-like Superfamily:OsmC-like Family:Ohr/OsmC resistance proteins 28 d1vf6c_ not modelled 6.2 31 Fold:L27 domain Superfamily:L27 domain Family:L27 domain 29 c1vf6C_ not modelled 6.2 31 PDB header:protein binding/protein transport Chain: C: PDB Molecule:maguk p55 subfamily member 5; PDBTitle: 2.1 angstrom crystal structure of the pals-1-l27n and patj2 l27 heterodimer complex 30 d2hs5a2 not modelled 6.1 18 Fold:GntR ligand-binding domain-like Superfamily:GntR ligand-binding domain-like Family:GntR ligand-binding domain-like 31 c2ejsA_ not modelled 5.9 15 PDB header:ligase Chain: A: PDB Molecule:autocrine motility factor receptor, isoform 2; PDBTitle: solution structure of ruh-076, a human cue domain 32 c2hnhA_ not modelled 5.8 35 PDB header:transferase Chain: A: PDB Molecule:dna polymerase iii alpha subunit; PDBTitle: crystal structure of the catalytic alpha subunit of e. coli2 replicative dna polymerase iii 33 d1st6a3 not modelled 5.7 10 Fold:Four-helical up-and-down bundle Superfamily:alpha-catenin/vinculin-like Family:alpha-catenin/vinculin 34 d1y7la1 not modelled 5.6 10 Fold:Tryptophan synthase beta subunit-like PLP-dependent enzymes Superfamily:Tryptophan synthase beta subunit-like PLP-dependent enzymes Family:Tryptophan synthase beta subunit-like PLP-dependent enzymes 35 c1kyqC_ not modelled 5.6 19 PDB header:oxidoreductase, lyase Chain: C: PDB Molecule:siroheme biosynthesis protein met8; PDBTitle: met8p: a bifunctional nad-dependent dehydrogenase and2 ferrochelatase involved in siroheme synthesis. 36 c3qp5C_ not modelled 5.6 17 PDB header:transcription Chain: C: PDB Molecule:cvir transcriptional regulator; PDBTitle: crystal structure of cvir bound to antagonist chlorolactone (cl) 37 c2zixA_ not modelled 5.6 16 PDB header:hydrolase Chain: A: PDB Molecule:crossover junction endonuclease mus81; PDBTitle: crystal structure of the mus81-eme1 complex 38 d1y1pa1 not modelled 5.5 19 Fold:NAD(P)-binding Rossmann-fold domains Superfamily:NAD(P)-binding Rossmann-fold domains Family:Tyrosine-dependent oxidoreductases 39 d1weya_ not modelled 5.5 18 Fold:Ferredoxin-like Superfamily:RNA-binding domain, RBD Family:Canonical RBD 40 d1xsva_ not modelled 5.4 19 Fold:DNA/RNA-binding 3-helical bundle Superfamily:Sigma3 and sigma4 domains of RNA polymerase sigma factors Family:YlxM/p13-like 41 d1ftha_ not modelled 5.4 12 Fold:4'-phosphopantetheinyl transferase Superfamily:4'-phosphopantetheinyl transferase Family:Holo-(acyl carrier protein) synthase ACPS 42 d1e3oc2 not modelled 5.3 17 Fold:lambda repressor-like DNA-binding domains Superfamily:lambda repressor-like DNA-binding domains Family:POU-specific domain 43 d2fefa1 not modelled 5.2 21 Fold:Bromodomain-like Superfamily:PA2201 N-terminal domain-like Family:PA2201 N-terminal domain-like 44 c3sztB_ not modelled 5.1 22 PDB header:transcription Chain: B: PDB Molecule:quorum-sensing control repressor; PDBTitle: quorum sensing control repressor, qscr, bound to n-3-oxo-dodecanoyl-l-2 homoserine lactone

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