Secondary structure and disorder prediction

		1	.	.	.	.	.	.	.	.	10	.	.	.	.	.	.	.	.	.	20	.	.	.	.	.	.	.	.	.	30	.	.	.	.	.	.	.	.	.	40	.	.	.	.	.	.	.	.	.	50	.	.	.	.	.	.	.	.	.	60
Sequence		M	N	L	L	I	D	N	W	I	P	V	R	P	R	N	G	G	K	V	Q	I	I	N	L	Q	S	L	Y	C	S	R	D	Q	W	R	L	S	L	P	R	D	D	M	E	L	A	A	L	A	L	L	V	C	I	G	Q	I	I	A	P
Secondary structure
SS confidence
Disorder		?	?	?	?	?	?									?	?	?		?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	70	.	.	.	.	.	.	.	.	.	80	.	.	.	.	.	.	.	.	.	90	.	.	.	.	.	.	.	.	.	100	.	.	.	.	.	.	.	.	.	110	.	.	.	.	.	.	.	.	.	120
Sequence		A	K	D	D	V	E	F	R	H	R	I	M	N	P	L	T	E	D	E	F	Q	Q	L	I	A	P	W	I	D	M	F	Y	L	N	H	A	E	H	P	F	M	Q	T	K	G	V	K	A	N	D	V	T	P	M	E	K	L	L	A	G
Secondary structure
SS confidence
Disorder																																																?		?	?	?	?	?						?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	130	.	.	.	.	.	.	.	.	.	140	.	.	.	.	.	.	.	.	.	150	.	.	.	.	.	.	.	.	.	160	.	.	.	.	.	.	.	.	.	170	.	.	.	.	.	.	.	.	.	180
Sequence		V	S	G	A	T	N	C	A	F	V	N	Q	P	G	Q	G	E	A	L	C	G	G	C	T	A	I	A	L	F	N	Q	A	N	Q	A	P	G	F	G	G	G	F	K	S	G	L	R	G	G	T	P	V	T	T	F	V	R	G	I	D
Secondary structure
SS confidence
Disorder		?																																			?		?	?	?	?	?	?	?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	190	.	.	.	.	.	.	.	.	.	200	.	.	.	.	.	.	.	.	.	210	.	.	.	.	.	.	.	.	.	220	.	.	.	.	.	.	.	.	.	230	.	.	.	.	.	.	.	.	.	240
Sequence		L	R	S	T	V	L	L	N	V	L	T	L	P	R	L	Q	K	Q	F	P	N	E	S	H	T	E	N	Q	P	T	W	I	K	P	I	K	S	N	E	S	I	P	A	S	S	I	G	F	V	R	G	L	F	W	Q	P	A	H	I	E
Secondary structure
SS confidence
Disorder																?	?																			?	?	?	?	?	?	?	?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	250	.	.	.	.	.	.	.	.	.	260	.	.	.	.	.	.	.	.	.	270	.	.	.	.	.	.	.	.	.	280	.	.	.	.	.	.	.	.	.	290	.	.	.	.	.	.	.	.	.	300
Sequence		L	C	D	P	I	G	I	G	K	C	S	C	C	G	Q	E	S	N	L	R	Y	T	G	F	L	K	E	K	F	T	F	T	V	N	G	L	W	P	H	P	H	S	P	C	L	V	T	V	K	K	G	E	V	E	E	K	F	L	A	F
Secondary structure
SS confidence
Disorder																													?				?															?	?	?	?	?		?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	310	.	.	.	.	.	.	.	.	.	320	.	.	.	.	.	.	.	.	.	330	.	.	.	.	.	.	.	.	.	340	.	.	.	.	.	.	.	.	.	350	.	.	.	.	.	.	.	.	.	360
Sequence		T	T	S	A	P	S	W	T	Q	I	S	R	V	V	V	D	K	I	I	Q	N	E	N	G	N	R	V	A	A	V	V	N	Q	F	R	N	I	A	P	Q	S	P	L	E	L	I	M	G	G	Y	R	N	N	Q	A	S	I	L	E	R
Secondary structure
SS confidence
Disorder			?			?	?	?									?	?	?	?	?	?	?	?	?													?	?		?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	370	.	.	.	.	.	.	.	.	.	380	.	.	.	.	.	.	.	.	.	390	.	.	.	.	.	.	.	.	.	400	.	.	.	.	.	.	.	.	.	410	.	.	.	.	.	.	.	.	.	420
Sequence		R	H	D	V	L	M	F	N	Q	G	W	Q	Q	Y	G	N	V	I	N	E	I	V	T	V	G	L	G	Y	K	T	A	L	R	K	A	L	Y	T	F	A	E	G	F	K	N	K	D	F	K	G	A	G	V	S	V	H	E	T	A	E
Secondary structure
SS confidence
Disorder								?	?	?	?	?																											?		?		?	?	?	?	?			?		?
Disorder confidence
		.	.	.	.	.	.	.	.	.	430	.	.	.	.	.	.	.	.	.	440	.	.	.	.	.	.	.	.	.	450	.	.	.	.	.	.	.	.	.	460	.	.	.	.	.	.	.	.	.	470	.	.	.	.	.	.	.	.	.	480
Sequence		R	H	F	Y	R	Q	S	E	L	L	I	P	D	V	L	A	N	V	N	F	S	Q	A	D	E	V	I	A	D	L	R	D	K	L	H	Q	L	C	E	M	L	F	N	Q	S	V	A	P	Y	A	H	H	P	K	L	I	S	T	L	A
Secondary structure
SS confidence
Disorder																		?
Disorder confidence
		.	.	.	.	.	.	.	.	.	490	.	.	.	.	.	.	.	.	.	500	.	.
Sequence		L	A	R	A	T	L	Y	K	H	L	R	E	L	K	P	Q	G	G	P	S	N	G
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 1fip chain A Region: 425 - 494 Aligned: 68 Modelled: 70 Confidence: 20.8% Identity: 12% Fold: DNA/RNA-binding 3-helical bundle Superfamily: Homeodomain-like Family: FIS-like Phyre2 PDB 2ns0 chain A domain 1 Region: 128 - 148 Aligned: 21 Modelled: 21 Confidence: 20.5% Identity: 19% Fold: DNA/RNA-binding 3-helical bundle Superfamily: "Winged helix" DNA-binding domain Family: RHA1 ro06458-like Phyre2 PDB 3k6q chain B Region: 78 - 94 Aligned: 17 Modelled: 17 Confidence: 19.0% Identity: 12% PDB header:ligand binding protein Chain: B: PDB Molecule:putative ligand binding protein; PDBTitle: crystal structure of an antitoxin part of a putative toxin/antitoxin2 system (swol_0700) from syntrophomonas wolfei subsp. wolfei at 1.80 a3 resolution Phyre2 PDB 1w36 chain C domain 2 Region: 9 - 131 Aligned: 123 Modelled: 123 Confidence: 17.7% Identity: 9% Fold: P-loop containing nucleoside triphosphate hydrolases Superfamily: P-loop containing nucleoside triphosphate hydrolases Family: Tandem AAA-ATPase domain Phyre2 PDB 1etx chain A Region: 425 - 494 Aligned: 64 Modelled: 70 Confidence: 14.3% Identity: 14% Fold: DNA/RNA-binding 3-helical bundle Superfamily: Homeodomain-like Family: FIS-like Phyre2 PDB 1nj1 chain A domain 2 Region: 239 - 266 Aligned: 28 Modelled: 28 Confidence: 14.0% Identity: 29% Fold: IF3-like Superfamily: C-terminal domain of ProRS Family: C-terminal domain of ProRS Phyre2 PDB 2ak3 chain A domain 2 Region: 238 - 260 Aligned: 23 Modelled: 23 Confidence: 11.0% Identity: 26% Fold: Rubredoxin-like Superfamily: Microbial and mitochondrial ADK, insert "zinc finger" domain Family: Microbial and mitochondrial ADK, insert "zinc finger" domain Phyre2 PDB 1e4v chain A domain 2 Region: 238 - 260 Aligned: 23 Modelled: 23 Confidence: 10.4% Identity: 30% Fold: Rubredoxin-like Superfamily: Microbial and mitochondrial ADK, insert "zinc finger" domain Family: Microbial and mitochondrial ADK, insert "zinc finger" domain Phyre2 PDB 1p3j chain A domain 2 Region: 238 - 260 Aligned: 23 Modelled: 23 Confidence: 10.3% Identity: 30% Fold: Rubredoxin-like Superfamily: Microbial and mitochondrial ADK, insert "zinc finger" domain Family: Microbial and mitochondrial ADK, insert "zinc finger" domain Phyre2 PDB 1t6s chain A domain 1 Region: 47 - 92 Aligned: 46 Modelled: 46 Confidence: 10.3% Identity: 11% Fold: DNA/RNA-binding 3-helical bundle Superfamily: "Winged helix" DNA-binding domain Family: ScpB/YpuH-like Phyre2 PDB 1zin chain A domain 2 Region: 238 - 260 Aligned: 23 Modelled: 23 Confidence: 10.2% Identity: 35% Fold: Rubredoxin-like Superfamily: Microbial and mitochondrial ADK, insert "zinc finger" domain Family: Microbial and mitochondrial ADK, insert "zinc finger" domain Phyre2 PDB 1s3g chain A domain 2 Region: 238 - 260 Aligned: 23 Modelled: 23 Confidence: 9.4% Identity: 35% Fold: Rubredoxin-like Superfamily: Microbial and mitochondrial ADK, insert "zinc finger" domain Family: Microbial and mitochondrial ADK, insert "zinc finger" domain Phyre2 PDB 1aky chain A domain 2 Region: 238 - 260 Aligned: 23 Modelled: 23 Confidence: 8.9% Identity: 22% Fold: Rubredoxin-like Superfamily: Microbial and mitochondrial ADK, insert "zinc finger" domain Family: Microbial and mitochondrial ADK, insert "zinc finger" domain Phyre2 PDB 1poi chain A Region: 48 - 109 Aligned: 60 Modelled: 62 Confidence: 7.6% Identity: 8% Fold: NagB/RpiA/CoA transferase-like Superfamily: NagB/RpiA/CoA transferase-like Family: CoA transferase alpha subunit-like Phyre2 PDB 1g2h chain A Region: 435 - 494 Aligned: 53 Modelled: 60 Confidence: 7.5% Identity: 15% Fold: DNA/RNA-binding 3-helical bundle Superfamily: Homeodomain-like Family: FIS-like Phyre2 PDB 1xx6 chain A domain 1 Region: 321 - 367 Aligned: 46 Modelled: 44 Confidence: 7.4% Identity: 15% Fold: P-loop containing nucleoside triphosphate hydrolases Superfamily: P-loop containing nucleoside triphosphate hydrolases Family: Type II thymidine kinase Phyre2 PDB 1qhh chain B Region: 9 - 77 Aligned: 68 Modelled: 69 Confidence: 6.9% Identity: 13% PDB header:hydrolase Chain: B: PDB Molecule:protein (pcra (subunit)); PDBTitle: structure of dna helicase with adpnp Phyre2 PDB 2qfa chain C Region: 422 - 462 Aligned: 36 Modelled: 41 Confidence: 5.9% Identity: 17% PDB header:cell cycle/cell cycle/cell cycle Chain: C: PDB Molecule:inner centromere protein; PDBTitle: crystal structure of a survivin-borealin-incenp core complex Phyre2 PDB 3ndh chain A Region: 76 - 93 Aligned: 18 Modelled: 18 Confidence: 5.9% Identity: 22% PDB header:hydrolase/dna Chain: A: PDB Molecule:restriction endonuclease thai; PDBTitle: restriction endonuclease in complex with substrate dna Phyre2 PDB 2wdt chain A Region: 76 - 157 Aligned: 76 Modelled: 82 Confidence: 5.8% Identity: 9% PDB header:hydrolase/protein binding Chain: A: PDB Molecule:ubiquitin carboxyl-terminal hydrolase l3; PDBTitle: crystal structure of plasmodium falciparum uchl3 in complex2 with the suicide inhibitor ubvme Phyre2 1 d1fipa_ 2 d2ns0a1 3 c3k6qB_ 4 d1w36c2 5 d1etxa_ 6 d1nj1a2 7 d2ak3a2 8 d1e4va2 9 d1p3ja2 10 d1t6sa1 11 d1zina2 12 d1s3ga2 13 d1akya2 14 d1poia_ 15 d1g2ha_ 16 d1xx6a1 17 c1qhhB_ 18 c2qfaC_ 19 c3ndhA_ 20 c2wdtA_ 21 22 23 24 25

Detailed template information

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

1 d1fipa_ 20.8 12 Fold:DNA/RNA-binding 3-helical bundle Superfamily:Homeodomain-like Family:FIS-like 2 d2ns0a1 20.5 19 Fold:DNA/RNA-binding 3-helical bundle Superfamily:"Winged helix" DNA-binding domain Family:RHA1 ro06458-like 3 c3k6qB_ 19.0 12 PDB header:ligand binding protein Chain: B: PDB Molecule:putative ligand binding protein; PDBTitle: crystal structure of an antitoxin part of a putative toxin/antitoxin2 system (swol_0700) from syntrophomonas wolfei subsp. wolfei at 1.80 a3 resolution 4 d1w36c2 17.7 9 Fold:P-loop containing nucleoside triphosphate hydrolases Superfamily:P-loop containing nucleoside triphosphate hydrolases Family:Tandem AAA-ATPase domain 5 d1etxa_ 14.3 14 Fold:DNA/RNA-binding 3-helical bundle Superfamily:Homeodomain-like Family:FIS-like 6 d1nj1a2 14.0 29 Fold:IF3-like Superfamily:C-terminal domain of ProRS Family:C-terminal domain of ProRS 7 d2ak3a2 11.0 26 Fold:Rubredoxin-like Superfamily:Microbial and mitochondrial ADK, insert "zinc finger" domain Family:Microbial and mitochondrial ADK, insert "zinc finger" domain 8 d1e4va2 10.4 30 Fold:Rubredoxin-like Superfamily:Microbial and mitochondrial ADK, insert "zinc finger" domain Family:Microbial and mitochondrial ADK, insert "zinc finger" domain 9 d1p3ja2 10.3 30 Fold:Rubredoxin-like Superfamily:Microbial and mitochondrial ADK, insert "zinc finger" domain Family:Microbial and mitochondrial ADK, insert "zinc finger" domain 10 d1t6sa1 10.3 11 Fold:DNA/RNA-binding 3-helical bundle Superfamily:"Winged helix" DNA-binding domain Family:ScpB/YpuH-like 11 d1zina2 10.2 35 Fold:Rubredoxin-like Superfamily:Microbial and mitochondrial ADK, insert "zinc finger" domain Family:Microbial and mitochondrial ADK, insert "zinc finger" domain 12 d1s3ga2 9.4 35 Fold:Rubredoxin-like Superfamily:Microbial and mitochondrial ADK, insert "zinc finger" domain Family:Microbial and mitochondrial ADK, insert "zinc finger" domain 13 d1akya2 8.9 22 Fold:Rubredoxin-like Superfamily:Microbial and mitochondrial ADK, insert "zinc finger" domain Family:Microbial and mitochondrial ADK, insert "zinc finger" domain 14 d1poia_ 7.6 8 Fold:NagB/RpiA/CoA transferase-like Superfamily:NagB/RpiA/CoA transferase-like Family:CoA transferase alpha subunit-like 15 d1g2ha_ 7.5 15 Fold:DNA/RNA-binding 3-helical bundle Superfamily:Homeodomain-like Family:FIS-like 16 d1xx6a1 7.4 15 Fold:P-loop containing nucleoside triphosphate hydrolases Superfamily:P-loop containing nucleoside triphosphate hydrolases Family:Type II thymidine kinase 17 c1qhhB_ 6.9 13 PDB header:hydrolase Chain: B: PDB Molecule:protein (pcra (subunit)); PDBTitle: structure of dna helicase with adpnp 18 c2qfaC_ 5.9 17 PDB header:cell cycle/cell cycle/cell cycle Chain: C: PDB Molecule:inner centromere protein; PDBTitle: crystal structure of a survivin-borealin-incenp core complex 19 c3ndhA_ 5.9 22 PDB header:hydrolase/dna Chain: A: PDB Molecule:restriction endonuclease thai; PDBTitle: restriction endonuclease in complex with substrate dna 20 c2wdtA_ 5.8 9 PDB header:hydrolase/protein binding Chain: A: PDB Molecule:ubiquitin carboxyl-terminal hydrolase l3; PDBTitle: crystal structure of plasmodium falciparum uchl3 in complex2 with the suicide inhibitor ubvme 21 d2f7fa2 not modelled 5.7 50 Fold:alpha/beta-Hammerhead Superfamily:Nicotinate/Quinolinate PRTase N-terminal domain-like Family:NadC N-terminal domain-like 22 d1nbwa1 not modelled 5.4 22 Fold:The "swivelling" beta/beta/alpha domain Superfamily:Swiveling domain of dehydratase reactivase alpha subunit Family:Swiveling domain of dehydratase reactivase alpha subunit 23 c3e2iA_ not modelled 5.3 11 PDB header:transferase Chain: A: PDB Molecule:thymidine kinase; PDBTitle: crystal structure of thymidine kinase from s. aureus 24 d1etob_ not modelled 5.3 11 Fold:DNA/RNA-binding 3-helical bundle Superfamily:Homeodomain-like Family:FIS-like 25 c1nj2A_ not modelled 5.2 29 PDB header:ligase Chain: A: PDB Molecule:proline-trna synthetase; PDBTitle: crystal structure of prolyl-trna synthetase from methanothermobacter2 thermautotrophicus

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