Secondary structure and disorder prediction

		1	.	.	.	.	.	.	.	.	10	.	.	.	.	.	.	.	.	.	20	.	.	.	.	.	.	.	.	.	30	.	.	.	.	.	.	.	.	.	40	.	.	.	.	.	.	.	.	.	50	.	.	.	.	.	.	.	.	.	60
Sequence		M	K	K	T	A	A	I	I	S	A	C	M	L	T	F	A	L	S	A	C	S	G	S	N	Y	V	M	H	T	N	D	G	R	T	I	V	S	D	G	K	P	Q	T	D	N	D	T	G	M	I	S	Y	K	D	A	N	G	N	K	Q
Secondary structure
SS confidence
Disorder		?	?	?	?																																				?																		?
Disorder confidence
		.	.	.	.	.	.	.	.	.	70	.	.	.	.	.
Sequence		Q	I	N	R	T	D	V	K	E	M	V	E	L	D	Q
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 2rd1 chain A domain 1 Region: 23 - 74 Aligned: 52 Modelled: 52 Confidence: 99.9% Identity: 48% Fold: Sm-like fold Superfamily: Sm-like ribonucleoproteins Family: YgdI/YgdR-like Phyre2 PDB 2k57 chain A domain 1 Region: 22 - 73 Aligned: 52 Modelled: 52 Confidence: 99.9% Identity: 31% Fold: Sm-like fold Superfamily: Sm-like ribonucleoproteins Family: YgdI/YgdR-like Phyre2 PDB 2ra2 chain A domain 1 Region: 23 - 74 Aligned: 52 Modelled: 52 Confidence: 99.9% Identity: 85% Fold: Sm-like fold Superfamily: Sm-like ribonucleoproteins Family: YgdI/YgdR-like Phyre2 PDB 2rb6 chain A domain 1 Region: 22 - 72 Aligned: 51 Modelled: 51 Confidence: 99.9% Identity: 39% Fold: Sm-like fold Superfamily: Sm-like ribonucleoproteins Family: YgdI/YgdR-like Phyre2 PDB 3bdu chain A domain 1 Region: 22 - 73 Aligned: 52 Modelled: 52 Confidence: 99.9% Identity: 63% Fold: Sm-like fold Superfamily: Sm-like ribonucleoproteins Family: YgdI/YgdR-like Phyre2 PDB 2jn0 chain A domain 1 Region: 24 - 72 Aligned: 49 Modelled: 49 Confidence: 99.8% Identity: 57% Fold: Sm-like fold Superfamily: Sm-like ribonucleoproteins Family: YgdI/YgdR-like Phyre2 PDB 2npt chain A domain 1 Region: 44 - 66 Aligned: 23 Modelled: 23 Confidence: 39.2% Identity: 17% Fold: beta-Grasp (ubiquitin-like) Superfamily: CAD & PB1 domains Family: PB1 domain Phyre2 PDB 1wi0 chain A Region: 44 - 66 Aligned: 23 Modelled: 23 Confidence: 31.0% Identity: 17% Fold: beta-Grasp (ubiquitin-like) Superfamily: CAD & PB1 domains Family: PB1 domain Phyre2 PDB 2h2w chain A Region: 24 - 47 Aligned: 24 Modelled: 24 Confidence: 29.8% Identity: 33% PDB header:transferase Chain: A: PDB Molecule:homoserine o-succinyltransferase; PDBTitle: crystal structure of homoserine o-succinyltransferase (ec 2.3.1.46)2 (homoserine o-transsuccinylase) (hts) (tm0881) from thermotoga3 maritima at 2.52 a resolution Phyre2 PDB 2ghr chain A domain 1 Region: 24 - 47 Aligned: 24 Modelled: 24 Confidence: 27.6% Identity: 21% Fold: Flavodoxin-like Superfamily: Class I glutamine amidotransferase-like Family: HTS-like Phyre2 PDB 3dso chain A Region: 26 - 39 Aligned: 14 Modelled: 14 Confidence: 24.5% Identity: 50% PDB header:metal binding protein Chain: A: PDB Molecule:putative uncharacterized protein copk; PDBTitle: crystal structure of cu(i) bound copper resistance protein copk Phyre2 PDB 2ktr chain A Region: 41 - 66 Aligned: 26 Modelled: 26 Confidence: 16.7% Identity: 12% PDB header:signaling protein, transport protein Chain: A: PDB Molecule:sequestosome-1; PDBTitle: nmr structure of p62 pb1 dimer determined based on pcs Phyre2 PDB 2kdk chain A Region: 25 - 59 Aligned: 35 Modelled: 35 Confidence: 16.2% Identity: 23% PDB header:transcription regulator Chain: A: PDB Molecule:aryl hydrocarbon receptor nuclear translocator-like protein PDBTitle: structure of human circadian clock protein bmal2 c-terminal pas domain Phyre2 PDB 1br2 chain A domain 1 Region: 55 - 70 Aligned: 16 Modelled: 16 Confidence: 14.1% Identity: 31% Fold: SH3-like barrel Superfamily: Myosin S1 fragment, N-terminal domain Family: Myosin S1 fragment, N-terminal domain Phyre2 PDB 1gjw chain A domain 1 Region: 49 - 62 Aligned: 13 Modelled: 14 Confidence: 9.5% Identity: 54% Fold: Glycosyl hydrolase domain Superfamily: Glycosyl hydrolase domain Family: alpha-Amylases, C-terminal beta-sheet domain Phyre2 PDB 2k5w chain A domain 1 Region: 34 - 62 Aligned: 29 Modelled: 29 Confidence: 8.6% Identity: 28% Fold: OB-fold Superfamily: BC4932-like Family: BC4932-like Phyre2 PDB 2b38 chain A Region: 19 - 33 Aligned: 15 Modelled: 15 Confidence: 8.1% Identity: 33% PDB header:plant protein Chain: A: PDB Molecule:kalata b8; PDBTitle: solution structure of kalata b8 Phyre2 PDB 1wj6 chain A Region: 50 - 66 Aligned: 17 Modelled: 17 Confidence: 7.4% Identity: 29% Fold: beta-Grasp (ubiquitin-like) Superfamily: CAD & PB1 domains Family: PB1 domain Phyre2 PDB 3uc0 chain B Region: 34 - 44 Aligned: 11 Modelled: 11 Confidence: 6.4% Identity: 45% PDB header:viral protein/immune system Chain: B: PDB Molecule:envelope protein; PDBTitle: crystal structure of domain i of the envelope glycoprotein ectodomain2 from dengue virus serotype 4 in complex with the fab fragment of the3 chimpanzee monoclonal antibody 5h2 Phyre2 PDB 2bkf chain A domain 1 Region: 50 - 66 Aligned: 17 Modelled: 17 Confidence: 6.1% Identity: 29% Fold: beta-Grasp (ubiquitin-like) Superfamily: CAD & PB1 domains Family: PB1 domain Phyre2 1 d2rd1a1 2 d2k57a1 3 d2ra2a1 4 d2rb6a1 5 d3bdua1 6 d2jn0a1 7 d2npta1 8 d1wi0a_ 9 c2h2wA_ 10 d2ghra1 11 c3dsoA_ 12 c2ktrA_ 13 c2kdkA_ 14 d1br2a1 15 d1gjwa1 16 d2k5wa1 17 c2b38A_ 18 d1wj6a_ 19 c3uc0B_ 20 d2bkfa1 21 22 23 24 25

Detailed template information

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

1 d2rd1a1 99.9 48 Fold:Sm-like fold Superfamily:Sm-like ribonucleoproteins Family:YgdI/YgdR-like 2 d2k57a1 99.9 31 Fold:Sm-like fold Superfamily:Sm-like ribonucleoproteins Family:YgdI/YgdR-like 3 d2ra2a1 99.9 85 Fold:Sm-like fold Superfamily:Sm-like ribonucleoproteins Family:YgdI/YgdR-like 4 d2rb6a1 99.9 39 Fold:Sm-like fold Superfamily:Sm-like ribonucleoproteins Family:YgdI/YgdR-like 5 d3bdua1 99.9 63 Fold:Sm-like fold Superfamily:Sm-like ribonucleoproteins Family:YgdI/YgdR-like 6 d2jn0a1 99.8 57 Fold:Sm-like fold Superfamily:Sm-like ribonucleoproteins Family:YgdI/YgdR-like 7 d2npta1 39.2 17 Fold:beta-Grasp (ubiquitin-like) Superfamily:CAD & PB1 domains Family:PB1 domain 8 d1wi0a_ 31.0 17 Fold:beta-Grasp (ubiquitin-like) Superfamily:CAD & PB1 domains Family:PB1 domain 9 c2h2wA_ 29.8 33 PDB header:transferase Chain: A: PDB Molecule:homoserine o-succinyltransferase; PDBTitle: crystal structure of homoserine o-succinyltransferase (ec 2.3.1.46)2 (homoserine o-transsuccinylase) (hts) (tm0881) from thermotoga3 maritima at 2.52 a resolution 10 d2ghra1 27.6 21 Fold:Flavodoxin-like Superfamily:Class I glutamine amidotransferase-like Family:HTS-like 11 c3dsoA_ 24.5 50 PDB header:metal binding protein Chain: A: PDB Molecule:putative uncharacterized protein copk; PDBTitle: crystal structure of cu(i) bound copper resistance protein copk 12 c2ktrA_ 16.7 12 PDB header:signaling protein, transport protein Chain: A: PDB Molecule:sequestosome-1; PDBTitle: nmr structure of p62 pb1 dimer determined based on pcs 13 c2kdkA_ 16.2 23 PDB header:transcription regulator Chain: A: PDB Molecule:aryl hydrocarbon receptor nuclear translocator-like protein PDBTitle: structure of human circadian clock protein bmal2 c-terminal pas domain 14 d1br2a1 14.1 31 Fold:SH3-like barrel Superfamily:Myosin S1 fragment, N-terminal domain Family:Myosin S1 fragment, N-terminal domain 15 d1gjwa1 9.5 54 Fold:Glycosyl hydrolase domain Superfamily:Glycosyl hydrolase domain Family:alpha-Amylases, C-terminal beta-sheet domain 16 d2k5wa1 8.6 28 Fold:OB-fold Superfamily:BC4932-like Family:BC4932-like 17 c2b38A_ 8.1 33 PDB header:plant protein Chain: A: PDB Molecule:kalata b8; PDBTitle: solution structure of kalata b8 18 d1wj6a_ 7.4 29 Fold:beta-Grasp (ubiquitin-like) Superfamily:CAD & PB1 domains Family:PB1 domain 19 c3uc0B_ 6.4 45 PDB header:viral protein/immune system Chain: B: PDB Molecule:envelope protein; PDBTitle: crystal structure of domain i of the envelope glycoprotein ectodomain2 from dengue virus serotype 4 in complex with the fab fragment of the3 chimpanzee monoclonal antibody 5h2 20 d2bkfa1 6.1 29 Fold:beta-Grasp (ubiquitin-like) Superfamily:CAD & PB1 domains Family:PB1 domain 21 d1ip9a_ not modelled 5.7 22 Fold:beta-Grasp (ubiquitin-like) Superfamily:CAD & PB1 domains Family:PB1 domain 22 d1wmha_ not modelled 5.2 17 Fold:beta-Grasp (ubiquitin-like) Superfamily:CAD & PB1 domains Family:PB1 domain 23 d1epwa2 not modelled 5.2 20 Fold:beta-Trefoil Superfamily:STI-like Family:Clostridium neurotoxins, C-terminal domain 24 d1f53a_ not modelled 5.1 33 Fold:gamma-Crystallin-like Superfamily:gamma-Crystallin-like Family:Killer toxin-like protein SKLP 25 d1p97a_ not modelled 5.0 14 Fold:Profilin-like Superfamily:PYP-like sensor domain (PAS domain) Family:Hypoxia-inducible factor Hif2a, C-terminal 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

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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