Secondary structure and disorder prediction

		1	.	.	.	.	.	.	.	.	10	.	.	.	.	.	.	.	.	.	20	.	.	.	.	.	.	.	.	.	30	.	.	.	.	.	.	.	.	.	40	.	.	.	.	.	.	.	.	.	50	.	.	.	.	.	.	.	.	.	60
Sequence		M	K	K	W	A	V	I	I	S	A	V	G	L	A	F	A	V	S	G	C	S	S	D	Y	V	M	A	T	K	D	G	R	M	I	L	T	D	G	K	P	E	I	D	D	D	T	G	L	V	S	Y	H	D	Q	Q	G	N	A	M	Q
Secondary structure
SS confidence
Disorder		?	?	?	?																																	?	?	?																	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	70	.	.
Sequence		I	N	R	D	D	V	S	Q	I	I	E	R
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 2rb6 chain A domain 1 Region: 21 - 72 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: 21 - 71 Aligned: 51 Modelled: 51 Confidence: 99.9% Identity: 27% Fold: Sm-like fold Superfamily: Sm-like ribonucleoproteins Family: YgdI/YgdR-like Phyre2 PDB 3bdu chain A domain 1 Region: 21 - 71 Aligned: 51 Modelled: 51 Confidence: 99.9% Identity: 51% Fold: Sm-like fold Superfamily: Sm-like ribonucleoproteins Family: YgdI/YgdR-like Phyre2 PDB 2jn0 chain A domain 1 Region: 23 - 72 Aligned: 50 Modelled: 50 Confidence: 99.9% Identity: 100% Fold: Sm-like fold Superfamily: Sm-like ribonucleoproteins Family: YgdI/YgdR-like Phyre2 PDB 2rd1 chain A domain 1 Region: 22 - 71 Aligned: 50 Modelled: 50 Confidence: 99.9% Identity: 50% Fold: Sm-like fold Superfamily: Sm-like ribonucleoproteins Family: YgdI/YgdR-like Phyre2 PDB 2ra2 chain A domain 1 Region: 22 - 71 Aligned: 50 Modelled: 47 Confidence: 99.9% Identity: 54% Fold: Sm-like fold Superfamily: Sm-like ribonucleoproteins Family: YgdI/YgdR-like Phyre2 PDB 2npt chain A domain 1 Region: 43 - 65 Aligned: 23 Modelled: 23 Confidence: 45.3% Identity: 22% Fold: beta-Grasp (ubiquitin-like) Superfamily: CAD & PB1 domains Family: PB1 domain Phyre2 PDB 1wi0 chain A Region: 43 - 65 Aligned: 23 Modelled: 23 Confidence: 35.6% Identity: 22% Fold: beta-Grasp (ubiquitin-like) Superfamily: CAD & PB1 domains Family: PB1 domain Phyre2 PDB 2h2w chain A Region: 24 - 46 Aligned: 23 Modelled: 23 Confidence: 24.6% Identity: 48% 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 3dso chain A Region: 25 - 38 Aligned: 14 Modelled: 14 Confidence: 23.8% 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 2ghr chain A domain 1 Region: 23 - 46 Aligned: 24 Modelled: 24 Confidence: 22.6% Identity: 25% Fold: Flavodoxin-like Superfamily: Class I glutamine amidotransferase-like Family: HTS-like Phyre2 PDB 2ktr chain A Region: 40 - 65 Aligned: 26 Modelled: 26 Confidence: 20.1% Identity: 15% 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 1br2 chain A domain 1 Region: 54 - 69 Aligned: 16 Modelled: 16 Confidence: 16.6% Identity: 19% Fold: SH3-like barrel Superfamily: Myosin S1 fragment, N-terminal domain Family: Myosin S1 fragment, N-terminal domain Phyre2 PDB 2kdk chain A Region: 24 - 58 Aligned: 35 Modelled: 35 Confidence: 15.6% 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 1gvi chain A domain 2 Region: 43 - 65 Aligned: 23 Modelled: 23 Confidence: 15.2% Identity: 39% Fold: Glycosyl hydrolase domain Superfamily: Glycosyl hydrolase domain Family: alpha-Amylases, C-terminal beta-sheet domain Phyre2 PDB 1h6l chain A Region: 43 - 60 Aligned: 17 Modelled: 18 Confidence: 11.5% Identity: 24% Fold: 6-bladed beta-propeller Superfamily: Thermostable phytase (3-phytase) Family: Thermostable phytase (3-phytase) Phyre2 PDB 2k5w chain A domain 1 Region: 33 - 61 Aligned: 29 Modelled: 29 Confidence: 9.4% Identity: 34% Fold: OB-fold Superfamily: BC4932-like Family: BC4932-like Phyre2 PDB 2pxg chain A Region: 17 - 31 Aligned: 15 Modelled: 15 Confidence: 9.3% Identity: 20% PDB header:membrane protein Chain: A: PDB Molecule:outer membrane protein; PDBTitle: nmr solution structure of omla Phyre2 PDB 1w0n chain A Region: 15 - 30 Aligned: 16 Modelled: 16 Confidence: 9.1% Identity: 38% Fold: Galactose-binding domain-like Superfamily: Galactose-binding domain-like Family: Family 36 carbohydrate binding module, CBM36 Phyre2 PDB 2b38 chain A Region: 18 - 32 Aligned: 15 Modelled: 15 Confidence: 9.0% Identity: 47% PDB header:plant protein Chain: A: PDB Molecule:kalata b8; PDBTitle: solution structure of kalata b8 Phyre2 1 d2rb6a1 2 d2k57a1 3 d3bdua1 4 d2jn0a1 5 d2rd1a1 6 d2ra2a1 7 d2npta1 8 d1wi0a_ 9 c2h2wA_ 10 c3dsoA_ 11 d2ghra1 12 c2ktrA_ 13 d1br2a1 14 c2kdkA_ 15 d1gvia2 16 d1h6la_ 17 d2k5wa1 18 c2pxgA_ 19 d1w0na_ 20 c2b38A_ 21 22 23 24 25 26 27 28

Detailed template information

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

1 d2rb6a1 99.9 48 Fold:Sm-like fold Superfamily:Sm-like ribonucleoproteins Family:YgdI/YgdR-like 2 d2k57a1 99.9 27 Fold:Sm-like fold Superfamily:Sm-like ribonucleoproteins Family:YgdI/YgdR-like 3 d3bdua1 99.9 51 Fold:Sm-like fold Superfamily:Sm-like ribonucleoproteins Family:YgdI/YgdR-like 4 d2jn0a1 99.9 100 Fold:Sm-like fold Superfamily:Sm-like ribonucleoproteins Family:YgdI/YgdR-like 5 d2rd1a1 99.9 50 Fold:Sm-like fold Superfamily:Sm-like ribonucleoproteins Family:YgdI/YgdR-like 6 d2ra2a1 99.9 54 Fold:Sm-like fold Superfamily:Sm-like ribonucleoproteins Family:YgdI/YgdR-like 7 d2npta1 45.3 22 Fold:beta-Grasp (ubiquitin-like) Superfamily:CAD & PB1 domains Family:PB1 domain 8 d1wi0a_ 35.6 22 Fold:beta-Grasp (ubiquitin-like) Superfamily:CAD & PB1 domains Family:PB1 domain 9 c2h2wA_ 24.6 48 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 c3dsoA_ 23.8 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 11 d2ghra1 22.6 25 Fold:Flavodoxin-like Superfamily:Class I glutamine amidotransferase-like Family:HTS-like 12 c2ktrA_ 20.1 15 PDB header:signaling protein, transport protein Chain: A: PDB Molecule:sequestosome-1; PDBTitle: nmr structure of p62 pb1 dimer determined based on pcs 13 d1br2a1 16.6 19 Fold:SH3-like barrel Superfamily:Myosin S1 fragment, N-terminal domain Family:Myosin S1 fragment, N-terminal domain 14 c2kdkA_ 15.6 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 15 d1gvia2 15.2 39 Fold:Glycosyl hydrolase domain Superfamily:Glycosyl hydrolase domain Family:alpha-Amylases, C-terminal beta-sheet domain 16 d1h6la_ 11.5 24 Fold:6-bladed beta-propeller Superfamily:Thermostable phytase (3-phytase) Family:Thermostable phytase (3-phytase) 17 d2k5wa1 9.4 34 Fold:OB-fold Superfamily:BC4932-like Family:BC4932-like 18 c2pxgA_ 9.3 20 PDB header:membrane protein Chain: A: PDB Molecule:outer membrane protein; PDBTitle: nmr solution structure of omla 19 d1w0na_ 9.1 38 Fold:Galactose-binding domain-like Superfamily:Galactose-binding domain-like Family:Family 36 carbohydrate binding module, CBM36 20 c2b38A_ 9.0 47 PDB header:plant protein Chain: A: PDB Molecule:kalata b8; PDBTitle: solution structure of kalata b8 21 d1wmha_ not modelled 8.1 12 Fold:beta-Grasp (ubiquitin-like) Superfamily:CAD & PB1 domains Family:PB1 domain 22 d1wzaa1 not modelled 7.0 23 Fold:Glycosyl hydrolase domain Superfamily:Glycosyl hydrolase domain Family:alpha-Amylases, C-terminal beta-sheet domain 23 d2bkfa1 not modelled 6.9 24 Fold:beta-Grasp (ubiquitin-like) Superfamily:CAD & PB1 domains Family:PB1 domain 24 d1u5sa1 not modelled 6.6 11 Fold:SH3-like barrel Superfamily:SH3-domain Family:SH3-domain 25 d1wj6a_ not modelled 6.6 24 Fold:beta-Grasp (ubiquitin-like) Superfamily:CAD & PB1 domains Family:PB1 domain 26 d1sg5a1 not modelled 5.9 11 Fold:Rof/RNase P subunit-like Superfamily:Rof/RNase P subunit-like Family:Rof-like 27 c1tr8A_ not modelled 5.5 21 PDB header:chaperone Chain: A: PDB Molecule:conserved protein (mth177); PDBTitle: crystal structure of archaeal nascent polypeptide-associated complex2 (aenac) 28 c3uc0B_ not modelled 5.3 36 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

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