Secondary structure and disorder prediction

		1	.	.	.	.	.	.	.	.	10	.	.	.	.	.	.	.	.	.	20	.	.	.	.	.	.	.	.	.	30	.	.	.	.	.	.	.	.	.	40	.	.	.	.	.	.	.	.	.	50	.	.	.	.	.	.	.	.	.	60
Sequence		M	P	L	L	N	D	L	L	D	F	S	D	H	P	L	M	P	P	P	S	A	Q	L	F	A	E	H	L	P	T	E	W	I	Q	H	C	L	T	L	S	A	H	A	T	V	R	R	R	R	L	P	G	D	M	V	I	W	M	V	V
Secondary structure
SS confidence
Disorder		?	?	?	?										?	?	?	?	?	?																								?		?
Disorder confidence
		.	.	.	.	.	.	.	.	.	70	.	.	.	.	.	.	.	.	.	80	.	.	.	.	.	.	.	.	.	90	.	.	.	.	.	.	.	.	.	100	.	.	.	.	.	.	.	.	.	110	.	.	.	.	.	.	.	.	.	120
Sequence		Q	N	E	P	I	T	D	V	V	R	R	L	N	L	S	A	D	G	E	A	G	M	N	L	L	A	R	S	A	V	T	Q	A	R	Q	R	V	G	A	A	P	V	E	W	L	F	R	Q	T	A	Q	D	R	G	A	E	R	Y	L	K
Secondary structure
SS confidence
Disorder																				?	?	?	?	?		?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	130	.	.	.	.	.	.	.	.	.	140	.	.	.	.	.	.	.	.	.	150	.	.	.	.	.	.	.	.	.	160	.	.	.	.	.	.	.	.	.	170	.	.	.	.	.	.	.	.	.	180
Sequence		D	D	W	H	G	L	Q	L	F	A	I	D	G	A	Q	F	R	T	P	D	K	P	E	L	R	E	Y	Y	G	S	A	N	T	S	T	K	R	Q	N	A	Y	P	V	M	R	L	V	A	L	M	N	L	G	S	H	I	L	L	N	A
Secondary structure
SS confidence
Disorder																																	?	?	?	?	?	?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	190	.	.	.	.	.	.	.	.	.	200	.	.	.	.	.	.	.	.	.	210	.	.	.	.	.	.	.	.	.	220	.	.	.	.	.	.	.	.	.	230	.	.	.	.	.	.	.	.	.	240
Sequence		V	T	A	P	Y	R	Q	S	E	T	V	L	A	H	S	M	L	A	T	I	P	D	N	S	I	T	L	F	D	K	L	F	Y	S	E	D	L	L	L	T	L	N	Q	K	G	C	N	R	H	W	L	L	P	A	W	K	N	I	A	S
Secondary structure
SS confidence
Disorder
Disorder confidence
		.	.	.	.	.	.	.	.	.	250	.	.	.	.	.	.	.	.	.	260	.	.	.	.	.	.	.	.	.	270	.	.	.	.	.	.	.	.	.	280	.	.	.	.	.	.	.	.	.	290	.	.	.	.	.	.	.	.	.
Sequence		E	M	I	E	L	G	N	T	A	S	P	G	T	I	P	K	R	L	E	H	L	R	G	A	L	E	V	V	F	I	T	K	R	P	R	P	S	R	P	R	S	V	K	I	S	K	T	R	Y	P	V	K	H	S	A	A	P	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 1mus chain A Region: 31 - 237 Aligned: 182 Modelled: 206 Confidence: 98.6% Identity: 15% Fold: Ribonuclease H-like motif Superfamily: Ribonuclease H-like Family: Transposase inhibitor (Tn5 transposase) Phyre2 PDB 1b7e chain A Region: 190 - 241 Aligned: 50 Modelled: 52 Confidence: 97.3% Identity: 10% Fold: Ribonuclease H-like motif Superfamily: Ribonuclease H-like Family: Transposase inhibitor (Tn5 transposase) Phyre2 PDB 1yoc chain A domain 1 Region: 88 - 184 Aligned: 79 Modelled: 93 Confidence: 49.5% Identity: 22% Fold: Thioesterase/thiol ester dehydrase-isomerase Superfamily: Thioesterase/thiol ester dehydrase-isomerase Family: PaaI/YdiI-like Phyre2 PDB 1wb9 chain A domain 2 Region: 152 - 209 Aligned: 56 Modelled: 58 Confidence: 46.7% Identity: 27% Fold: P-loop containing nucleoside triphosphate hydrolases Superfamily: P-loop containing nucleoside triphosphate hydrolases Family: ABC transporter ATPase domain-like Phyre2 PDB 3thx chain B Region: 152 - 209 Aligned: 56 Modelled: 58 Confidence: 32.6% Identity: 18% PDB header:dna binding protein/dna Chain: B: PDB Molecule:dna mismatch repair protein msh3; PDBTitle: human mutsbeta complexed with an idl of 3 bases (loop3) and adp Phyre2 PDB 1d5y chain D Region: 3 - 104 Aligned: 91 Modelled: 92 Confidence: 26.2% Identity: 20% PDB header:transcription/dna Chain: D: PDB Molecule:rob transcription factor; PDBTitle: crystal structure of the e. coli rob transcription factor2 in complex with dna Phyre2 PDB 1ewq chain A Region: 152 - 209 Aligned: 56 Modelled: 58 Confidence: 20.7% Identity: 21% PDB header:replication/dna Chain: A: PDB Molecule:dna mismatch repair protein muts; PDBTitle: crystal structure taq muts complexed with a heteroduplex2 dna at 2.2 a resolution Phyre2 PDB 1wbd chain A Region: 152 - 209 Aligned: 56 Modelled: 58 Confidence: 16.6% Identity: 27% PDB header:dna-binding Chain: A: PDB Molecule:dna mismatch repair protein muts; PDBTitle: crystal structure of e. coli dna mismatch repair enzyme2 muts, e38q mutant, in complex with a g.t mismatch Phyre2 PDB 1u35 chain C domain 1 Region: 32 - 78 Aligned: 47 Modelled: 47 Confidence: 12.2% Identity: 17% Fold: Histone-fold Superfamily: Histone-fold Family: Nucleosome core histones Phyre2 PDB 2o8b chain A Region: 152 - 209 Aligned: 56 Modelled: 58 Confidence: 12.0% Identity: 18% PDB header:dna binding protein/dna Chain: A: PDB Molecule:dna mismatch repair protein msh2; PDBTitle: human mutsalpha (msh2/msh6) bound to adp and a g t mispair Phyre2 PDB 2o8d chain B Region: 152 - 209 Aligned: 56 Modelled: 58 Confidence: 11.6% Identity: 21% PDB header:dna binding protein/dna Chain: B: PDB Molecule:dna mismatch repair protein msh6; PDBTitle: human mutsalpha (msh2/msh6) bound to adp and a g du mispair Phyre2 PDB 3pco chain D Region: 210 - 279 Aligned: 57 Modelled: 70 Confidence: 11.2% Identity: 26% PDB header:ligase Chain: D: PDB Molecule:phenylalanyl-trna synthetase, beta chain; PDBTitle: crystal structure of e. coli phenylalanine-trna synthetase complexed2 with phenylalanine and amp Phyre2 PDB 2jfg chain A domain 2 Region: 190 - 225 Aligned: 36 Modelled: 36 Confidence: 10.7% Identity: 14% Fold: MurD-like peptide ligases, peptide-binding domain Superfamily: MurD-like peptide ligases, peptide-binding domain Family: MurCDEF C-terminal domain Phyre2 PDB 2f8n chain K Region: 32 - 78 Aligned: 47 Modelled: 47 Confidence: 8.9% Identity: 17% PDB header:structural protein/dna Chain: K: PDB Molecule:histone h2a type 1; PDBTitle: 2.9 angstrom x-ray structure of hybrid macroh2a nucleosomes Phyre2 PDB 2hmh chain A Region: 190 - 279 Aligned: 90 Modelled: 90 Confidence: 8.8% Identity: 11% PDB header:cytokine regulator Chain: A: PDB Molecule:suppressor of cytokine signaling 3; PDBTitle: crystal structure of socs3 in complex with gp130(ptyr757)2 phosphopeptide. Phyre2 PDB 3czp chain A Region: 192 - 214 Aligned: 23 Modelled: 23 Confidence: 8.8% Identity: 26% PDB header:transferase Chain: A: PDB Molecule:putative polyphosphate kinase 2; PDBTitle: crystal structure of putative polyphosphate kinase 2 from pseudomonas2 aeruginosa pa01 Phyre2 PDB 1k8k chain E Region: 87 - 126 Aligned: 34 Modelled: 40 Confidence: 8.8% Identity: 24% Fold: Arp2/3 complex 21 kDa subunit ARPC3 Superfamily: Arp2/3 complex 21 kDa subunit ARPC3 Family: Arp2/3 complex 21 kDa subunit ARPC3 Phyre2 PDB 1ewq chain A domain 2 Region: 152 - 209 Aligned: 58 Modelled: 58 Confidence: 8.4% Identity: 14% Fold: P-loop containing nucleoside triphosphate hydrolases Superfamily: P-loop containing nucleoside triphosphate hydrolases Family: ABC transporter ATPase domain-like Phyre2 PDB 1id3 chain C Region: 32 - 78 Aligned: 47 Modelled: 47 Confidence: 7.7% Identity: 13% Fold: Histone-fold Superfamily: Histone-fold Family: Nucleosome core histones Phyre2 PDB 1eqz chain A Region: 32 - 78 Aligned: 47 Modelled: 47 Confidence: 7.7% Identity: 15% Fold: Histone-fold Superfamily: Histone-fold Family: Nucleosome core histones Phyre2 1 d1musa_ 2 d1b7ea_ 3 d1yoca1 4 d1wb9a2 5 c3thxB_ 6 c1d5yD_ 7 c1ewqA_ 8 c1wbdA_ 9 d1u35c1 10 c2o8bA_ 11 c2o8dB_ 12 c3pcoD_ 13 d2jfga2 14 c2f8nK_ 15 c2hmhA_ 16 c3czpA_ 17 d1k8ke_ 18 d1ewqa2 19 d1id3c_ 20 d1eqza_ 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38

Detailed template information

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

1 d1musa_ 98.6 15 Fold:Ribonuclease H-like motif Superfamily:Ribonuclease H-like Family:Transposase inhibitor (Tn5 transposase) 2 d1b7ea_ 97.3 10 Fold:Ribonuclease H-like motif Superfamily:Ribonuclease H-like Family:Transposase inhibitor (Tn5 transposase) 3 d1yoca1 49.5 22 Fold:Thioesterase/thiol ester dehydrase-isomerase Superfamily:Thioesterase/thiol ester dehydrase-isomerase Family:PaaI/YdiI-like 4 d1wb9a2 46.7 27 Fold:P-loop containing nucleoside triphosphate hydrolases Superfamily:P-loop containing nucleoside triphosphate hydrolases Family:ABC transporter ATPase domain-like 5 c3thxB_ 32.6 18 PDB header:dna binding protein/dna Chain: B: PDB Molecule:dna mismatch repair protein msh3; PDBTitle: human mutsbeta complexed with an idl of 3 bases (loop3) and adp 6 c1d5yD_ 26.2 20 PDB header:transcription/dna Chain: D: PDB Molecule:rob transcription factor; PDBTitle: crystal structure of the e. coli rob transcription factor2 in complex with dna 7 c1ewqA_ 20.7 21 PDB header:replication/dna Chain: A: PDB Molecule:dna mismatch repair protein muts; PDBTitle: crystal structure taq muts complexed with a heteroduplex2 dna at 2.2 a resolution 8 c1wbdA_ 16.6 27 PDB header:dna-binding Chain: A: PDB Molecule:dna mismatch repair protein muts; PDBTitle: crystal structure of e. coli dna mismatch repair enzyme2 muts, e38q mutant, in complex with a g.t mismatch 9 d1u35c1 12.2 17 Fold:Histone-fold Superfamily:Histone-fold Family:Nucleosome core histones 10 c2o8bA_ 12.0 18 PDB header:dna binding protein/dna Chain: A: PDB Molecule:dna mismatch repair protein msh2; PDBTitle: human mutsalpha (msh2/msh6) bound to adp and a g t mispair 11 c2o8dB_ 11.6 21 PDB header:dna binding protein/dna Chain: B: PDB Molecule:dna mismatch repair protein msh6; PDBTitle: human mutsalpha (msh2/msh6) bound to adp and a g du mispair 12 c3pcoD_ 11.2 26 PDB header:ligase Chain: D: PDB Molecule:phenylalanyl-trna synthetase, beta chain; PDBTitle: crystal structure of e. coli phenylalanine-trna synthetase complexed2 with phenylalanine and amp 13 d2jfga2 10.7 14 Fold:MurD-like peptide ligases, peptide-binding domain Superfamily:MurD-like peptide ligases, peptide-binding domain Family:MurCDEF C-terminal domain 14 c2f8nK_ 8.9 17 PDB header:structural protein/dna Chain: K: PDB Molecule:histone h2a type 1; PDBTitle: 2.9 angstrom x-ray structure of hybrid macroh2a nucleosomes 15 c2hmhA_ 8.8 11 PDB header:cytokine regulator Chain: A: PDB Molecule:suppressor of cytokine signaling 3; PDBTitle: crystal structure of socs3 in complex with gp130(ptyr757)2 phosphopeptide. 16 c3czpA_ 8.8 26 PDB header:transferase Chain: A: PDB Molecule:putative polyphosphate kinase 2; PDBTitle: crystal structure of putative polyphosphate kinase 2 from pseudomonas2 aeruginosa pa01 17 d1k8ke_ 8.8 24 Fold:Arp2/3 complex 21 kDa subunit ARPC3 Superfamily:Arp2/3 complex 21 kDa subunit ARPC3 Family:Arp2/3 complex 21 kDa subunit ARPC3 18 d1ewqa2 8.4 14 Fold:P-loop containing nucleoside triphosphate hydrolases Superfamily:P-loop containing nucleoside triphosphate hydrolases Family:ABC transporter ATPase domain-like 19 d1id3c_ 7.7 13 Fold:Histone-fold Superfamily:Histone-fold Family:Nucleosome core histones 20 d1eqza_ 7.7 15 Fold:Histone-fold Superfamily:Histone-fold Family:Nucleosome core histones 21 c3btpA_ not modelled 7.6 20 PDB header:dna binding protein, chaperone Chain: A: PDB Molecule:single-strand dna-binding protein; PDBTitle: crystal structure of agrobacterium tumefaciens vire2 in complex with2 its chaperone vire1: a novel fold and implications for dna binding 22 c3tdqB_ not modelled 7.6 36 PDB header:cell adhesion Chain: B: PDB Molecule:pily2 protein; PDBTitle: crystal structure of a fimbrial biogenesis protein pily22 (pily2_pa4555) from pseudomonas aeruginosa pao1 at 2.10 a resolution 23 c2vzaD_ not modelled 7.4 18 PDB header:cell adhesion Chain: D: PDB Molecule:cell filamentation protein; PDBTitle: type iv secretion system effector protein bepa 24 d1tzya_ not modelled 7.0 15 Fold:Histone-fold Superfamily:Histone-fold Family:Nucleosome core histones 25 d1dk7a_ not modelled 6.9 43 Fold:The "swivelling" beta/beta/alpha domain Superfamily:GroEL apical domain-like Family:GroEL-like chaperone, apical domain 26 d1sjpa2 not modelled 6.6 57 Fold:The "swivelling" beta/beta/alpha domain Superfamily:GroEL apical domain-like Family:GroEL-like chaperone, apical domain 27 c3rhfB_ not modelled 6.5 21 PDB header:transferase Chain: B: PDB Molecule:putative polyphosphate kinase 2 family protein; PDBTitle: crystal structure of polyphosphate kinase 2 from arthrobacter2 aurescens tc1 28 d1srva_ not modelled 6.4 57 Fold:The "swivelling" beta/beta/alpha domain Superfamily:GroEL apical domain-like Family:GroEL-like chaperone, apical domain 29 d1ioka2 not modelled 6.2 43 Fold:The "swivelling" beta/beta/alpha domain Superfamily:GroEL apical domain-like Family:GroEL-like chaperone, apical domain 30 d1aoic_ not modelled 6.1 19 Fold:Histone-fold Superfamily:Histone-fold Family:Nucleosome core histones 31 d1ikpa3 not modelled 6.0 69 Fold:Toxins' membrane translocation domains Superfamily:Exotoxin A, middle domain Family:Exotoxin A, middle domain 32 c2vifA_ not modelled 6.0 23 PDB header:signaling protein Chain: A: PDB Molecule:suppressor of cytokine signalling 6; PDBTitle: crystal structure of socs6 sh2 domain in complex with a c-kit2 phosphopeptide 33 c3ld9D_ not modelled 5.9 13 PDB header:transferase Chain: D: PDB Molecule:thymidylate kinase; PDBTitle: crystal structure of thymidylate kinase from ehrlichia chaffeensis at2 2.15a resolution 34 d1oela2 not modelled 5.7 43 Fold:The "swivelling" beta/beta/alpha domain Superfamily:GroEL apical domain-like Family:GroEL-like chaperone, apical domain 35 d1kx3c_ not modelled 5.7 19 Fold:Histone-fold Superfamily:Histone-fold Family:Nucleosome core histones 36 c3pjvD_ not modelled 5.5 50 PDB header:lyase Chain: D: PDB Molecule:cyclic dimeric gmp binding protein; PDBTitle: structure of pseudomonas fluorescence lapd periplasmic domain 37 d1pvda3 not modelled 5.5 2 Fold:Thiamin diphosphate-binding fold (THDP-binding) Superfamily:Thiamin diphosphate-binding fold (THDP-binding) Family:Pyruvate oxidase and decarboxylase PP module 38 d1sjpa3 not modelled 5.3 0 Fold:GroEL-intermediate domain like Superfamily:GroEL-intermediate domain like Family:GroEL-like chaperone, intermediate 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