Secondary structure and disorder prediction

		1	.	.	.	.	.	.	.	.	10	.	.	.	.	.	.	.	.	.	20	.	.	.	.	.	.	.	.	.	30	.	.	.	.	.	.	.	.	.	40	.	.	.	.	.	.	.	.	.	50	.	.	.	.	.	.	.	.	.	60
Sequence		M	F	V	D	R	Q	R	I	D	L	L	N	R	L	I	D	A	R	V	D	L	A	A	Y	V	Q	L	R	K	A	K	G	Y	M	S	V	S	E	S	N	H	L	R	D	N	F	F	K	L	N	R	E	L	H	D	K	S	L	R	L
Secondary structure
SS confidence
Disorder		?	?	?	?																											?				?	?		?																					?
Disorder confidence
		.	.	.	.	.	.	.	.	.	70	.	.	.	.	.	.	.	.	.	80	.	.	.	.	.	.	.	.	.	90	.	.	.	.	.	.	.	.	.	100	.	.	.	.	.	.	.	.	.	110	.	.	.	.	.	.	.	.	.	120
Sequence		N	L	H	L	D	Q	E	E	W	S	A	L	H	H	A	E	E	A	L	A	T	A	A	V	C	L	M	S	G	H	H	D	C	P	T	V	I	T	V	N	A	D	K	L	E	N	C	L	M	S	L	T	L	S	I	Q	S	L	Q	K
Secondary structure
SS confidence
Disorder		?		?																																																	?		?
Disorder confidence
		.	.	.	.	.	.	.
Sequence		H	A	M	L	E	K	A
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 1w07 chain A domain 2 Region: 32 - 70 Aligned: 39 Modelled: 39 Confidence: 33.1% Identity: 8% Fold: Bromodomain-like Superfamily: Acyl-CoA dehydrogenase C-terminal domain-like Family: acyl-CoA oxidase C-terminal domains Phyre2 PDB 2ddh chain A domain 2 Region: 32 - 60 Aligned: 29 Modelled: 29 Confidence: 33.0% Identity: 7% Fold: Bromodomain-like Superfamily: Acyl-CoA dehydrogenase C-terminal domain-like Family: acyl-CoA oxidase C-terminal domains Phyre2 PDB 3iz5 chain K Region: 73 - 103 Aligned: 27 Modelled: 31 Confidence: 20.2% Identity: 22% PDB header:ribosome Chain: K: PDB Molecule:60s ribosomal protein l13a (l13p); PDBTitle: localization of the large subunit ribosomal proteins into a 5.5 a2 cryo-em map of triticum aestivum translating 80s ribosome Phyre2 PDB 2ddh chain A Region: 32 - 70 Aligned: 39 Modelled: 39 Confidence: 15.4% Identity: 8% PDB header:oxidoreductase Chain: A: PDB Molecule:acyl-coa oxidase; PDBTitle: crystal structure of acyl-coa oxidase complexed with 3-oh-dodecanoate Phyre2 PDB 1w07 chain A Region: 32 - 70 Aligned: 39 Modelled: 39 Confidence: 14.3% Identity: 8% PDB header:oxidoreductase Chain: A: PDB Molecule:acyl-coa oxidase; PDBTitle: arabidopsis thaliana acyl-coa oxidase 1 Phyre2 PDB 2fon chain A Region: 32 - 70 Aligned: 39 Modelled: 39 Confidence: 12.8% Identity: 15% PDB header:oxidoreductase Chain: A: PDB Molecule:peroxisomal acyl-coa oxidase 1a; PDBTitle: x-ray crystal structure of leacx1, an acyl-coa oxidase from2 lycopersicon esculentum (tomato) Phyre2 PDB 3hm5 chain A Region: 44 - 52 Aligned: 9 Modelled: 9 Confidence: 11.7% Identity: 44% PDB header:transcription Chain: A: PDB Molecule:dna methyltransferase 1-associated protein 1; PDBTitle: sant domain of human dna methyltransferase 1 associated2 protein 1 Phyre2 PDB 4aco chain A Region: 3 - 76 Aligned: 73 Modelled: 74 Confidence: 9.1% Identity: 30% PDB header:dna binding protein Chain: A: PDB Molecule:centromere dna-binding protein complex cbf3 subunit a; PDBTitle: structure of the budding yeast ndc10 n-terminal domain Phyre2 PDB 3ag5 chain A Region: 61 - 106 Aligned: 46 Modelled: 46 Confidence: 9.0% Identity: 22% PDB header:ligase Chain: A: PDB Molecule:pantothenate synthetase; PDBTitle: crystal structure of pantothenate synthetase from staphylococcus2 aureus Phyre2 PDB 2a6q chain B domain 1 Region: 34 - 72 Aligned: 39 Modelled: 39 Confidence: 8.9% Identity: 15% Fold: YefM-like Superfamily: YefM-like Family: YefM-like Phyre2 PDB 2js5 chain B Region: 22 - 41 Aligned: 20 Modelled: 20 Confidence: 8.8% Identity: 30% PDB header:structural genomics, unknown function Chain: B: PDB Molecule:uncharacterized protein; PDBTitle: nmr structure of protein q60c73_metca. northeast structural2 genomics consortium target mcr1 Phyre2 PDB 1r5t chain A Region: 64 - 102 Aligned: 39 Modelled: 39 Confidence: 8.6% Identity: 13% Fold: Cytidine deaminase-like Superfamily: Cytidine deaminase-like Family: Cytidine deaminase Phyre2 PDB 3las chain A Region: 62 - 93 Aligned: 31 Modelled: 32 Confidence: 8.5% Identity: 23% PDB header:lyase Chain: A: PDB Molecule:putative carbonic anhydrase; PDBTitle: crystal structure of carbonic anhydrase from streptococcus mutans to2 1.4 angstrom resolution Phyre2 PDB 4a1a chain I Region: 73 - 103 Aligned: 27 Modelled: 31 Confidence: 8.5% Identity: 22% PDB header:ribosome Chain: I: PDB Molecule:60s ribosomal protein l13a; PDBTitle: t.thermophila 60s ribosomal subunit in complex with2 initiation factor 6. this file contains 5s rrna,3 5.8s rrna and proteins of molecule 3. Phyre2 PDB 1iyj chain B domain 2 Region: 66 - 75 Aligned: 10 Modelled: 10 Confidence: 7.4% Identity: 40% Fold: BRCA2 tower domain Superfamily: BRCA2 tower domain Family: BRCA2 tower domain Phyre2 PDB 1efv chain A domain 2 Region: 83 - 103 Aligned: 21 Modelled: 21 Confidence: 7.3% Identity: 29% Fold: DHS-like NAD/FAD-binding domain Superfamily: DHS-like NAD/FAD-binding domain Family: C-terminal domain of the electron transfer flavoprotein alpha subunit Phyre2 PDB 2jtv chain A Region: 47 - 69 Aligned: 23 Modelled: 23 Confidence: 7.1% Identity: 30% PDB header:structural genomics Chain: A: PDB Molecule:protein of unknown function; PDBTitle: solution structure of protein rpa3401, northeast structural genomics2 consortium target rpt7, ontario center for structural proteomics3 target rp3384 Phyre2 PDB 1gve chain A Region: 34 - 96 Aligned: 43 Modelled: 63 Confidence: 7.1% Identity: 33% Fold: TIM beta/alpha-barrel Superfamily: NAD(P)-linked oxidoreductase Family: Aldo-keto reductases (NADP) Phyre2 PDB 1v65 chain A Region: 64 - 79 Aligned: 16 Modelled: 16 Confidence: 7.0% Identity: 31% Fold: KRAB domain (Kruppel-associated box) Superfamily: KRAB domain (Kruppel-associated box) Family: KRAB domain (Kruppel-associated box) Phyre2 PDB 2fy8 chain A domain 1 Region: 27 - 76 Aligned: 50 Modelled: 50 Confidence: 6.4% Identity: 16% Fold: NAD(P)-binding Rossmann-fold domains Superfamily: NAD(P)-binding Rossmann-fold domains Family: Potassium channel NAD-binding domain Phyre2 1 d1w07a2 2 d2ddha2 3 c3iz5K_ 4 c2ddhA_ 5 c1w07A_ 6 c2fonA_ 7 c3hm5A_ 8 c4acoA_ 9 c3ag5A_ 10 d2a6qb1 11 c2js5B_ 12 d1r5ta_ 13 c3lasA_ 14 c4a1aI_ 15 d1iyjb2 16 d1efva2 17 c2jtvA_ 18 d1gvea_ 19 d1v65a_ 20 d2fy8a1 21 22

Detailed template information

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

1 d1w07a2 33.1 8 Fold:Bromodomain-like Superfamily:Acyl-CoA dehydrogenase C-terminal domain-like Family:acyl-CoA oxidase C-terminal domains 2 d2ddha2 33.0 7 Fold:Bromodomain-like Superfamily:Acyl-CoA dehydrogenase C-terminal domain-like Family:acyl-CoA oxidase C-terminal domains 3 c3iz5K_ 20.2 22 PDB header:ribosome Chain: K: PDB Molecule:60s ribosomal protein l13a (l13p); PDBTitle: localization of the large subunit ribosomal proteins into a 5.5 a2 cryo-em map of triticum aestivum translating 80s ribosome 4 c2ddhA_ 15.4 8 PDB header:oxidoreductase Chain: A: PDB Molecule:acyl-coa oxidase; PDBTitle: crystal structure of acyl-coa oxidase complexed with 3-oh-dodecanoate 5 c1w07A_ 14.3 8 PDB header:oxidoreductase Chain: A: PDB Molecule:acyl-coa oxidase; PDBTitle: arabidopsis thaliana acyl-coa oxidase 1 6 c2fonA_ 12.8 15 PDB header:oxidoreductase Chain: A: PDB Molecule:peroxisomal acyl-coa oxidase 1a; PDBTitle: x-ray crystal structure of leacx1, an acyl-coa oxidase from2 lycopersicon esculentum (tomato) 7 c3hm5A_ 11.7 44 PDB header:transcription Chain: A: PDB Molecule:dna methyltransferase 1-associated protein 1; PDBTitle: sant domain of human dna methyltransferase 1 associated2 protein 1 8 c4acoA_ 9.1 30 PDB header:dna binding protein Chain: A: PDB Molecule:centromere dna-binding protein complex cbf3 subunit a; PDBTitle: structure of the budding yeast ndc10 n-terminal domain 9 c3ag5A_ 9.0 22 PDB header:ligase Chain: A: PDB Molecule:pantothenate synthetase; PDBTitle: crystal structure of pantothenate synthetase from staphylococcus2 aureus 10 d2a6qb1 8.9 15 Fold:YefM-like Superfamily:YefM-like Family:YefM-like 11 c2js5B_ 8.8 30 PDB header:structural genomics, unknown function Chain: B: PDB Molecule:uncharacterized protein; PDBTitle: nmr structure of protein q60c73_metca. northeast structural2 genomics consortium target mcr1 12 d1r5ta_ 8.6 13 Fold:Cytidine deaminase-like Superfamily:Cytidine deaminase-like Family:Cytidine deaminase 13 c3lasA_ 8.5 23 PDB header:lyase Chain: A: PDB Molecule:putative carbonic anhydrase; PDBTitle: crystal structure of carbonic anhydrase from streptococcus mutans to2 1.4 angstrom resolution 14 c4a1aI_ 8.5 22 PDB header:ribosome Chain: I: PDB Molecule:60s ribosomal protein l13a; PDBTitle: t.thermophila 60s ribosomal subunit in complex with2 initiation factor 6. this file contains 5s rrna,3 5.8s rrna and proteins of molecule 3. 15 d1iyjb2 7.4 40 Fold:BRCA2 tower domain Superfamily:BRCA2 tower domain Family:BRCA2 tower domain 16 d1efva2 7.3 29 Fold:DHS-like NAD/FAD-binding domain Superfamily:DHS-like NAD/FAD-binding domain Family:C-terminal domain of the electron transfer flavoprotein alpha subunit 17 c2jtvA_ 7.1 30 PDB header:structural genomics Chain: A: PDB Molecule:protein of unknown function; PDBTitle: solution structure of protein rpa3401, northeast structural genomics2 consortium target rpt7, ontario center for structural proteomics3 target rp3384 18 d1gvea_ 7.1 33 Fold:TIM beta/alpha-barrel Superfamily:NAD(P)-linked oxidoreductase Family:Aldo-keto reductases (NADP) 19 d1v65a_ 7.0 31 Fold:KRAB domain (Kruppel-associated box) Superfamily:KRAB domain (Kruppel-associated box) Family:KRAB domain (Kruppel-associated box) 20 d2fy8a1 6.4 16 Fold:NAD(P)-binding Rossmann-fold domains Superfamily:NAD(P)-binding Rossmann-fold domains Family:Potassium channel NAD-binding domain 21 d1efpa2 not modelled 6.0 24 Fold:DHS-like NAD/FAD-binding domain Superfamily:DHS-like NAD/FAD-binding domain Family:C-terminal domain of the electron transfer flavoprotein alpha subunit 22 d1poca_ not modelled 5.1 39 Fold:Phospholipase A2, PLA2 Superfamily:Phospholipase A2, PLA2 Family:Insect phospholipase A2

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