Secondary structure and disorder prediction

		1	.	.	.	.	.	.	.	.	10	.	.	.	.	.	.	.	.	.	20	.	.	.	.	.	.	.	.	.	30	.	.	.	.	.	.	.	.	.	40	.	.	.	.	.	.	.	.	.	50	.	.	.	.	.	.	.	.	.	60
Sequence		M	L	K	N	L	A	K	L	D	Q	T	E	M	D	K	V	N	V	D	L	A	A	A	G	V	A	F	K	E	R	Y	N	M	P	V	I	A	E	A	V	E	R	E	Q	P	E	H	L	R	S	W	F	R	E	R	L	I	A	H	R
Secondary structure
SS confidence
Disorder		?	?	?	?	?	?	?	?																																			?
Disorder confidence
		.	.	.	.	.	.	.	.	.	70	.	.	.	.	.	.
Sequence		L	A	S	V	N	L	S	R	L	P	Y	E	P	K	L	K
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 2ae9 chain A domain 1 Region: 1 - 76 Aligned: 76 Modelled: 76 Confidence: 100.0% Identity: 100% Fold: DNA polymerase III theta subunit-like Superfamily: DNA polymerase III theta subunit-like Family: DNA polymerase III theta subunit-like Phyre2 PDB 2ido chain B domain 1 Region: 4 - 68 Aligned: 65 Modelled: 65 Confidence: 100.0% Identity: 62% Fold: DNA polymerase III theta subunit-like Superfamily: DNA polymerase III theta subunit-like Family: DNA polymerase III theta subunit-like Phyre2 PDB 1se7 chain A Region: 4 - 66 Aligned: 63 Modelled: 63 Confidence: 100.0% Identity: 63% Fold: DNA polymerase III theta subunit-like Superfamily: DNA polymerase III theta subunit-like Family: DNA polymerase III theta subunit-like Phyre2 PDB 1rrz chain A Region: 17 - 72 Aligned: 56 Modelled: 56 Confidence: 96.8% Identity: 27% PDB header:structural genomics,biosynthetic protein Chain: A: PDB Molecule:glycogen synthesis protein glgs; PDBTitle: solution structure of glgs protein from e. coli Phyre2 PDB 1rrz chain A Region: 17 - 72 Aligned: 56 Modelled: 56 Confidence: 96.8% Identity: 27% Fold: Spectrin repeat-like Superfamily: Glycogen synthesis protein GlgS Family: Glycogen synthesis protein GlgS Phyre2 PDB 2o70 chain A domain 1 Region: 5 - 56 Aligned: 47 Modelled: 52 Confidence: 31.6% Identity: 23% Fold: UraD-like Superfamily: UraD-Like Family: UraD-like Phyre2 PDB 2o8i chain A domain 1 Region: 3 - 56 Aligned: 49 Modelled: 54 Confidence: 28.6% Identity: 20% Fold: UraD-like Superfamily: UraD-Like Family: UraD-like Phyre2 PDB 3o7k chain A Region: 5 - 36 Aligned: 28 Modelled: 32 Confidence: 11.1% Identity: 11% PDB header:lyase Chain: A: PDB Molecule:ohcu decarboxylase; PDBTitle: crystal structure of 2-oxo-4-hydroxy-4-carboxy-5-ureidoimidazoline2 decarboxylase from klebsiella pneumoniae Phyre2 PDB 2qez chain C Region: 3 - 27 Aligned: 25 Modelled: 25 Confidence: 11.0% Identity: 40% PDB header:lyase Chain: C: PDB Molecule:ethanolamine ammonia-lyase heavy chain; PDBTitle: crystal structure of ethanolamine ammonia-lyase heavy chain2 (yp_013784.1) from listeria monocytogenes 4b f2365 at 2.15 a3 resolution Phyre2 PDB 2q37 chain A Region: 5 - 36 Aligned: 28 Modelled: 32 Confidence: 10.7% Identity: 21% PDB header:plant protein, lyase Chain: A: PDB Molecule:ohcu decarboxylase; PDBTitle: crystal structure of ohcu decarboxylase in the presence of2 (s)-allantoin Phyre2 PDB 2q37 chain A domain 1 Region: 5 - 36 Aligned: 28 Modelled: 32 Confidence: 10.7% Identity: 21% Fold: UraD-like Superfamily: UraD-Like Family: UraD-like Phyre2 PDB 3ns6 chain B Region: 32 - 52 Aligned: 21 Modelled: 21 Confidence: 10.7% Identity: 33% PDB header:translation Chain: B: PDB Molecule:eukaryotic translation initiation factor 3 subunit b; PDBTitle: crystal structure of hte rna recognition motif of yeast eif3b residues2 76-170 Phyre2 PDB 2fzt chain A domain 1 Region: 36 - 55 Aligned: 20 Modelled: 20 Confidence: 10.4% Identity: 45% Fold: Methionine synthase domain-like Superfamily: TM0693-like Family: TM0693-like Phyre2 PDB 2gzd chain C Region: 42 - 73 Aligned: 32 Modelled: 32 Confidence: 9.8% Identity: 22% PDB header:protein transport Chain: C: PDB Molecule:rab11 family-interacting protein 2; PDBTitle: crystal structure of rab11 in complex with rab11-fip2 Phyre2 PDB 3ndh chain A Region: 46 - 71 Aligned: 22 Modelled: 26 Confidence: 9.3% Identity: 50% PDB header:hydrolase/dna Chain: A: PDB Molecule:restriction endonuclease thai; PDBTitle: restriction endonuclease in complex with substrate dna Phyre2 PDB 3abq chain A Region: 3 - 27 Aligned: 25 Modelled: 25 Confidence: 8.9% Identity: 32% PDB header:lyase Chain: A: PDB Molecule:ethanolamine ammonia-lyase heavy chain; PDBTitle: crystal structure of ethanolamine ammonia-lyase from escherichia coli2 complexed with cn-cbl and 2-amino-1-propanol Phyre2 PDB 2o8g chain J Region: 5 - 33 Aligned: 29 Modelled: 29 Confidence: 7.9% Identity: 24% PDB header:hydrolase/inhibitor Chain: J: PDB Molecule:protein phosphatase inhibitor 2; PDBTitle: rat pp1c gamma complexed with mouse inhibitor-2 Phyre2 PDB 1fs2 chain B domain 1 Region: 36 - 52 Aligned: 17 Modelled: 17 Confidence: 7.7% Identity: 29% Fold: Skp1 dimerisation domain-like Superfamily: Skp1 dimerisation domain-like Family: Skp1 dimerisation domain-like Phyre2 PDB 1cw5 chain A Region: 24 - 31 Aligned: 8 Modelled: 8 Confidence: 7.6% Identity: 75% PDB header:toxin Chain: A: PDB Molecule:type iia bacteriocin carnobacteriocin b2; PDBTitle: solution structure of carnobacteriocin b2 Phyre2 PDB 1fs1 chain B domain 1 Region: 36 - 52 Aligned: 17 Modelled: 17 Confidence: 7.4% Identity: 29% Fold: Skp1 dimerisation domain-like Superfamily: Skp1 dimerisation domain-like Family: Skp1 dimerisation domain-like Phyre2 1 d2ae9a1 2 d2idob1 3 d1se7a_ 4 c1rrzA_ 5 d1rrza_ 6 d2o70a1 7 d2o8ia1 8 c3o7kA_ 9 c2qezC_ 10 c2q37A_ 11 d2q37a1 12 c3ns6B_ 13 d2fzta1 14 c2gzdC_ 15 c3ndhA_ 16 c3abqA_ 17 c2o8gJ_ 18 d1fs2b1 19 c1cw5A_ 20 d1fs1b1 21 22 23 24 25 26

Detailed template information

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

1 d2ae9a1 100.0 100 Fold:DNA polymerase III theta subunit-like Superfamily:DNA polymerase III theta subunit-like Family:DNA polymerase III theta subunit-like 2 d2idob1 100.0 62 Fold:DNA polymerase III theta subunit-like Superfamily:DNA polymerase III theta subunit-like Family:DNA polymerase III theta subunit-like 3 d1se7a_ 100.0 63 Fold:DNA polymerase III theta subunit-like Superfamily:DNA polymerase III theta subunit-like Family:DNA polymerase III theta subunit-like 4 c1rrzA_ 96.8 27 PDB header:structural genomics,biosynthetic protein Chain: A: PDB Molecule:glycogen synthesis protein glgs; PDBTitle: solution structure of glgs protein from e. coli 5 d1rrza_ 96.8 27 Fold:Spectrin repeat-like Superfamily:Glycogen synthesis protein GlgS Family:Glycogen synthesis protein GlgS 6 d2o70a1 31.6 23 Fold:UraD-like Superfamily:UraD-Like Family:UraD-like 7 d2o8ia1 28.6 20 Fold:UraD-like Superfamily:UraD-Like Family:UraD-like 8 c3o7kA_ 11.1 11 PDB header:lyase Chain: A: PDB Molecule:ohcu decarboxylase; PDBTitle: crystal structure of 2-oxo-4-hydroxy-4-carboxy-5-ureidoimidazoline2 decarboxylase from klebsiella pneumoniae 9 c2qezC_ 11.0 40 PDB header:lyase Chain: C: PDB Molecule:ethanolamine ammonia-lyase heavy chain; PDBTitle: crystal structure of ethanolamine ammonia-lyase heavy chain2 (yp_013784.1) from listeria monocytogenes 4b f2365 at 2.15 a3 resolution 10 c2q37A_ 10.7 21 PDB header:plant protein, lyase Chain: A: PDB Molecule:ohcu decarboxylase; PDBTitle: crystal structure of ohcu decarboxylase in the presence of2 (s)-allantoin 11 d2q37a1 10.7 21 Fold:UraD-like Superfamily:UraD-Like Family:UraD-like 12 c3ns6B_ 10.7 33 PDB header:translation Chain: B: PDB Molecule:eukaryotic translation initiation factor 3 subunit b; PDBTitle: crystal structure of hte rna recognition motif of yeast eif3b residues2 76-170 13 d2fzta1 10.4 45 Fold:Methionine synthase domain-like Superfamily:TM0693-like Family:TM0693-like 14 c2gzdC_ 9.8 22 PDB header:protein transport Chain: C: PDB Molecule:rab11 family-interacting protein 2; PDBTitle: crystal structure of rab11 in complex with rab11-fip2 15 c3ndhA_ 9.3 50 PDB header:hydrolase/dna Chain: A: PDB Molecule:restriction endonuclease thai; PDBTitle: restriction endonuclease in complex with substrate dna 16 c3abqA_ 8.9 32 PDB header:lyase Chain: A: PDB Molecule:ethanolamine ammonia-lyase heavy chain; PDBTitle: crystal structure of ethanolamine ammonia-lyase from escherichia coli2 complexed with cn-cbl and 2-amino-1-propanol 17 c2o8gJ_ 7.9 24 PDB header:hydrolase/inhibitor Chain: J: PDB Molecule:protein phosphatase inhibitor 2; PDBTitle: rat pp1c gamma complexed with mouse inhibitor-2 18 d1fs2b1 7.7 29 Fold:Skp1 dimerisation domain-like Superfamily:Skp1 dimerisation domain-like Family:Skp1 dimerisation domain-like 19 c1cw5A_ 7.6 75 PDB header:toxin Chain: A: PDB Molecule:type iia bacteriocin carnobacteriocin b2; PDBTitle: solution structure of carnobacteriocin b2 20 d1fs1b1 7.4 29 Fold:Skp1 dimerisation domain-like Superfamily:Skp1 dimerisation domain-like Family:Skp1 dimerisation domain-like 21 d1ofcx1 not modelled 7.2 18 Fold:DNA/RNA-binding 3-helical bundle Superfamily:Homeodomain-like Family:Myb/SANT domain 22 d1ryla_ not modelled 6.9 10 Fold:Hypothetical protein yfbM Superfamily:Hypothetical protein yfbM Family:Hypothetical protein yfbM 23 d1vr6a1 not modelled 6.7 21 Fold:TIM beta/alpha-barrel Superfamily:Aldolase Family:Class I DAHP synthetase 24 c3gndC_ not modelled 5.8 14 PDB header:lyase Chain: C: PDB Molecule:aldolase lsrf; PDBTitle: crystal structure of e. coli lsrf in complex with ribulose-5-phosphate 25 c3jsrA_ not modelled 5.7 18 PDB header:structural genomics, unknown function Chain: A: PDB Molecule:all0216 protein; PDBTitle: x-ray structure of all0216 protein from nostoc sp. pcc 7120 at the2 resolution 1.8a. northeast structural genomics consortium target3 nsr236 26 c3i4sB_ not modelled 5.3 17 PDB header:hydrolase Chain: B: PDB Molecule:histidine triad protein; PDBTitle: crystal structure of histidine triad protein blr8122 from2 bradyrhizobium japonicum

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