Secondary structure and disorder prediction

		1	.	.	.	.	.	.	.	.	10	.	.	.	.	.	.	.	.	.	20	.	.	.	.	.	.	.	.	.	30	.	.	.	.	.	.	.	.	.	40	.	.	.	.	.	.	.	.	.	50	.	.	.	.	.	.	.	.	.	60
Sequence		M	E	H	G	A	R	L	S	T	S	R	V	M	A	I	A	F	I	F	M	S	V	L	I	V	L	S	L	S	V	N	V	I	Q	G	V	N	N	Y	R	L	Q	N	E	Q	R	T	A	V	T	P	M	A	F	N	A	P	F	A	V
Secondary structure
SS confidence
Disorder		?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	70	.	.	.	.	.	.	.	.	.	80	.	.	.	.	.	.	.	.	.	90	.	.	.	.	.	.	.	.	.	100	.	.	.	.	.	.	.	.	.	110	.	.	.	.	.	.	.	.	.	120
Sequence		S	Q	N	S	A	D	A	S	Y	L	Q	Q	M	A	L	S	F	I	A	L	R	L	N	V	S	S	E	T	V	D	A	S	H	Q	A	L	L	Q	Y	I	R	P	G	A	Q	N	Q	M	K	V	I	L	A	E	E	A	K	R	I	K
Secondary structure
SS confidence
Disorder		?
Disorder confidence
		.	.	.	.	.	.	.	.	.	130	.	.	.	.	.	.	.	.	.	140	.	.	.	.	.	.	.	.	.	150	.	.	.	.	.	.	.	.	.	160	.	.	.	.	.	.	.	.	.	170	.	.	.	.	.	.	.	.	.	180
Sequence		N	D	N	V	N	S	A	F	F	Q	T	S	V	R	V	W	P	Q	Y	G	R	V	E	I	R	G	V	L	K	T	W	I	G	D	S	K	P	F	T	D	I	K	H	Y	I	L	I	L	K	R	E	N	G	V	T	W	L	D	N	F
Secondary structure
SS confidence
Disorder					?							?								?	?													?	?	?	?		?			?
Disorder confidence
		.	.	.	.	.	.	.	.
Sequence		G	E	T	D	D	E	K	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 2l0k chain A Region: 82 - 113 Aligned: 32 Modelled: 32 Confidence: 25.5% Identity: 34% PDB header:transcription Chain: A: PDB Molecule:stage iii sporulation protein d; PDBTitle: nmr solution structure of a transcription factor spoiiid in complex2 with dna Phyre2 PDB 1ug2 chain A Region: 77 - 104 Aligned: 28 Modelled: 28 Confidence: 23.3% Identity: 14% Fold: DNA/RNA-binding 3-helical bundle Superfamily: Homeodomain-like Family: Myb/SANT domain Phyre2 PDB 2cc3 chain A domain 1 Region: 64 - 171 Aligned: 107 Modelled: 108 Confidence: 21.2% Identity: 8% Fold: Cystatin-like Superfamily: NTF2-like Family: VirB8-like Phyre2 PDB 3rgg chain D Region: 85 - 123 Aligned: 39 Modelled: 39 Confidence: 18.8% Identity: 10% PDB header:lyase Chain: D: PDB Molecule:phosphoribosylaminoimidazole carboxylase, pure protein; PDBTitle: crystal structure of treponema denticola pure bound to air Phyre2 PDB 2ix0 chain A domain 3 Region: 122 - 154 Aligned: 33 Modelled: 33 Confidence: 16.9% Identity: 27% Fold: OB-fold Superfamily: Nucleic acid-binding proteins Family: Cold shock DNA-binding domain-like Phyre2 PDB 1u11 chain A Region: 86 - 124 Aligned: 39 Modelled: 39 Confidence: 15.8% Identity: 10% Fold: Flavodoxin-like Superfamily: N5-CAIR mutase (phosphoribosylaminoimidazole carboxylase, PurE) Family: N5-CAIR mutase (phosphoribosylaminoimidazole carboxylase, PurE) Phyre2 PDB 1l3l chain A domain 1 Region: 69 - 114 Aligned: 46 Modelled: 46 Confidence: 15.3% Identity: 9% Fold: DNA/RNA-binding 3-helical bundle Superfamily: C-terminal effector domain of the bipartite response regulators Family: GerE-like (LuxR/UhpA family of transcriptional regulators) Phyre2 PDB 2hsg chain A domain 1 Region: 73 - 114 Aligned: 41 Modelled: 42 Confidence: 15.0% Identity: 15% Fold: lambda repressor-like DNA-binding domains Superfamily: lambda repressor-like DNA-binding domains Family: GalR/LacI-like bacterial regulator Phyre2 PDB 2fw9 chain A Region: 86 - 124 Aligned: 39 Modelled: 39 Confidence: 14.5% Identity: 10% PDB header:lyase Chain: A: PDB Molecule:n5-carboxyaminoimidazole ribonucleotide mutase; PDBTitle: structure of pure (n5-carboxyaminoimidazole ribonucleotide mutase)2 h59f from the acidophilic bacterium acetobacter aceti, at ph 8 Phyre2 PDB 3mzy chain A Region: 69 - 115 Aligned: 39 Modelled: 47 Confidence: 14.4% Identity: 21% PDB header:rna binding protein Chain: A: PDB Molecule:rna polymerase sigma-h factor; PDBTitle: the crystal structure of the rna polymerase sigma-h factor from2 fusobacterium nucleatum to 2.5a Phyre2 PDB 3l1e chain A Region: 128 - 178 Aligned: 51 Modelled: 51 Confidence: 13.9% Identity: 22% PDB header:chaperone Chain: A: PDB Molecule:alpha-crystallin a chain; PDBTitle: bovine alphaa crystallin zinc bound Phyre2 PDB 1yio chain A domain 1 Region: 69 - 114 Aligned: 46 Modelled: 46 Confidence: 12.6% Identity: 13% Fold: DNA/RNA-binding 3-helical bundle Superfamily: C-terminal effector domain of the bipartite response regulators Family: GerE-like (LuxR/UhpA family of transcriptional regulators) Phyre2 PDB 2krf chain B Region: 69 - 114 Aligned: 46 Modelled: 46 Confidence: 11.8% Identity: 15% PDB header:transcription Chain: B: PDB Molecule:transcriptional regulatory protein coma; PDBTitle: nmr solution structure of the dna binding domain of competence protein2 a Phyre2 PDB 2wj7 chain D Region: 128 - 168 Aligned: 41 Modelled: 41 Confidence: 11.5% Identity: 12% PDB header:chaperone Chain: D: PDB Molecule:alpha-crystallin b chain; PDBTitle: human alphab crystallin Phyre2 PDB 1dgr chain W Region: 52 - 95 Aligned: 42 Modelled: 44 Confidence: 11.4% Identity: 14% PDB header:plant protein Chain: W: PDB Molecule:canavalin; PDBTitle: refined crystal structure of canavalin from jack bean Phyre2 PDB 1p4w chain A Region: 69 - 114 Aligned: 46 Modelled: 46 Confidence: 11.3% Identity: 15% Fold: DNA/RNA-binding 3-helical bundle Superfamily: C-terminal effector domain of the bipartite response regulators Family: GerE-like (LuxR/UhpA family of transcriptional regulators) Phyre2 PDB 1qcz chain A Region: 86 - 123 Aligned: 38 Modelled: 38 Confidence: 11.3% Identity: 3% Fold: Flavodoxin-like Superfamily: N5-CAIR mutase (phosphoribosylaminoimidazole carboxylase, PurE) Family: N5-CAIR mutase (phosphoribosylaminoimidazole carboxylase, PurE) Phyre2 PDB 3eip chain A Region: 154 - 173 Aligned: 20 Modelled: 20 Confidence: 11.1% Identity: 10% Fold: FKBP-like Superfamily: Colicin E3 immunity protein Family: Colicin E3 immunity protein Phyre2 PDB 2jpc chain A Region: 78 - 108 Aligned: 31 Modelled: 31 Confidence: 11.1% Identity: 16% PDB header:dna binding protein Chain: A: PDB Molecule:ssrb; PDBTitle: ssrb dna binding protein Phyre2 PDB 2ywx chain A Region: 85 - 123 Aligned: 39 Modelled: 39 Confidence: 11.1% Identity: 8% PDB header:lyase Chain: A: PDB Molecule:phosphoribosylaminoimidazole carboxylase catalytic subunit; PDBTitle: crystal structure of phosphoribosylaminoimidazole carboxylase2 catalytic subunit from methanocaldococcus jannaschii Phyre2 1 c2l0kA_ 2 d1ug2a_ 3 d2cc3a1 4 c3rggD_ 5 d2ix0a3 6 d1u11a_ 7 d1l3la1 8 d2hsga1 9 c2fw9A_ 10 c3mzyA_ 11 c3l1eA_ 12 d1yioa1 13 c2krfB_ 14 c2wj7D_ 15 c1dgrW_ 16 d1p4wa_ 17 d1qcza_ 18 d3eipa_ 19 c2jpcA_ 20 c2ywxA_ 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54

Detailed template information

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

1 c2l0kA_ 25.5 34 PDB header:transcription Chain: A: PDB Molecule:stage iii sporulation protein d; PDBTitle: nmr solution structure of a transcription factor spoiiid in complex2 with dna 2 d1ug2a_ 23.3 14 Fold:DNA/RNA-binding 3-helical bundle Superfamily:Homeodomain-like Family:Myb/SANT domain 3 d2cc3a1 21.2 8 Fold:Cystatin-like Superfamily:NTF2-like Family:VirB8-like 4 c3rggD_ 18.8 10 PDB header:lyase Chain: D: PDB Molecule:phosphoribosylaminoimidazole carboxylase, pure protein; PDBTitle: crystal structure of treponema denticola pure bound to air 5 d2ix0a3 16.9 27 Fold:OB-fold Superfamily:Nucleic acid-binding proteins Family:Cold shock DNA-binding domain-like 6 d1u11a_ 15.8 10 Fold:Flavodoxin-like Superfamily:N5-CAIR mutase (phosphoribosylaminoimidazole carboxylase, PurE) Family:N5-CAIR mutase (phosphoribosylaminoimidazole carboxylase, PurE) 7 d1l3la1 15.3 9 Fold:DNA/RNA-binding 3-helical bundle Superfamily:C-terminal effector domain of the bipartite response regulators Family:GerE-like (LuxR/UhpA family of transcriptional regulators) 8 d2hsga1 15.0 15 Fold:lambda repressor-like DNA-binding domains Superfamily:lambda repressor-like DNA-binding domains Family:GalR/LacI-like bacterial regulator 9 c2fw9A_ 14.5 10 PDB header:lyase Chain: A: PDB Molecule:n5-carboxyaminoimidazole ribonucleotide mutase; PDBTitle: structure of pure (n5-carboxyaminoimidazole ribonucleotide mutase)2 h59f from the acidophilic bacterium acetobacter aceti, at ph 8 10 c3mzyA_ 14.4 21 PDB header:rna binding protein Chain: A: PDB Molecule:rna polymerase sigma-h factor; PDBTitle: the crystal structure of the rna polymerase sigma-h factor from2 fusobacterium nucleatum to 2.5a 11 c3l1eA_ 13.9 22 PDB header:chaperone Chain: A: PDB Molecule:alpha-crystallin a chain; PDBTitle: bovine alphaa crystallin zinc bound 12 d1yioa1 12.6 13 Fold:DNA/RNA-binding 3-helical bundle Superfamily:C-terminal effector domain of the bipartite response regulators Family:GerE-like (LuxR/UhpA family of transcriptional regulators) 13 c2krfB_ 11.8 15 PDB header:transcription Chain: B: PDB Molecule:transcriptional regulatory protein coma; PDBTitle: nmr solution structure of the dna binding domain of competence protein2 a 14 c2wj7D_ 11.5 12 PDB header:chaperone Chain: D: PDB Molecule:alpha-crystallin b chain; PDBTitle: human alphab crystallin 15 c1dgrW_ 11.4 14 PDB header:plant protein Chain: W: PDB Molecule:canavalin; PDBTitle: refined crystal structure of canavalin from jack bean 16 d1p4wa_ 11.3 15 Fold:DNA/RNA-binding 3-helical bundle Superfamily:C-terminal effector domain of the bipartite response regulators Family:GerE-like (LuxR/UhpA family of transcriptional regulators) 17 d1qcza_ 11.3 3 Fold:Flavodoxin-like Superfamily:N5-CAIR mutase (phosphoribosylaminoimidazole carboxylase, PurE) Family:N5-CAIR mutase (phosphoribosylaminoimidazole carboxylase, PurE) 18 d3eipa_ 11.1 10 Fold:FKBP-like Superfamily:Colicin E3 immunity protein Family:Colicin E3 immunity protein 19 c2jpcA_ 11.1 16 PDB header:dna binding protein Chain: A: PDB Molecule:ssrb; PDBTitle: ssrb dna binding protein 20 c2ywxA_ 11.1 8 PDB header:lyase Chain: A: PDB Molecule:phosphoribosylaminoimidazole carboxylase catalytic subunit; PDBTitle: crystal structure of phosphoribosylaminoimidazole carboxylase2 catalytic subunit from methanocaldococcus jannaschii 21 c3lp6D_ not modelled 10.2 8 PDB header:lyase Chain: D: PDB Molecule:phosphoribosylaminoimidazole carboxylase catalytic subunit; PDBTitle: crystal structure of rv3275c-e60a from mycobacterium tuberculosis at2 1.7a resolution 22 d1fsea_ not modelled 10.2 24 Fold:DNA/RNA-binding 3-helical bundle Superfamily:C-terminal effector domain of the bipartite response regulators Family:GerE-like (LuxR/UhpA family of transcriptional regulators) 23 c3glaA_ not modelled 10.0 18 PDB header:chaperone Chain: A: PDB Molecule:low molecular weight heat shock protein; PDBTitle: crystal structure of the hspa from xanthomonas axonopodis 24 d1dgwa_ not modelled 9.6 15 Fold:Double-stranded beta-helix Superfamily:RmlC-like cupins Family:Germin/Seed storage 7S protein 25 c3trhI_ not modelled 9.3 3 PDB header:lyase Chain: I: PDB Molecule:phosphoribosylaminoimidazole carboxylase PDBTitle: structure of a phosphoribosylaminoimidazole carboxylase catalytic2 subunit (pure) from coxiella burnetii 26 d1qpza1 not modelled 9.3 25 Fold:lambda repressor-like DNA-binding domains Superfamily:lambda repressor-like DNA-binding domains Family:GalR/LacI-like bacterial regulator 27 d1uija1 not modelled 9.2 19 Fold:Double-stranded beta-helix Superfamily:RmlC-like cupins Family:Germin/Seed storage 7S protein 28 d2phla1 not modelled 9.2 24 Fold:Double-stranded beta-helix Superfamily:RmlC-like cupins Family:Germin/Seed storage 7S protein 29 c3orsD_ not modelled 8.9 5 PDB header:isomerase,biosynthetic protein Chain: D: PDB Molecule:n5-carboxyaminoimidazole ribonucleotide mutase; PDBTitle: crystal structure of n5-carboxyaminoimidazole ribonucleotide mutase2 from staphylococcus aureus 30 c3q9qB_ not modelled 8.0 35 PDB header:chaperone Chain: B: PDB Molecule:heat shock protein beta-1; PDBTitle: hspb1 fragment second crystal form 31 c2jtwA_ not modelled 7.9 50 PDB header:membrane protein Chain: A: PDB Molecule:transmembrane helix 7 of yeast vatpase; PDBTitle: solution structure of tm7 bound to dpc micelles 32 d1t3ua_ not modelled 7.5 7 Fold:Cell division protein ZapA-like Superfamily:Cell division protein ZapA-like Family:Cell division protein ZapA-like 33 d1a04a1 not modelled 7.5 24 Fold:DNA/RNA-binding 3-helical bundle Superfamily:C-terminal effector domain of the bipartite response regulators Family:GerE-like (LuxR/UhpA family of transcriptional regulators) 34 d2bjca1 not modelled 7.3 19 Fold:lambda repressor-like DNA-binding domains Superfamily:lambda repressor-like DNA-binding domains Family:GalR/LacI-like bacterial regulator 35 c2nvjA_ not modelled 7.3 42 PDB header:hydrolase Chain: A: PDB Molecule:25mer peptide from vacuolar atp synthase subunit PDBTitle: nmr structures of transmembrane segment from subunit a from2 the yeast proton v-atpase 36 c2bolA_ not modelled 6.6 15 PDB header:heat shock protein Chain: A: PDB Molecule:small heat shock protein; PDBTitle: crystal structure and assembly of tsp36, a metazoan small2 heat shock protein 37 d1fpoa1 not modelled 6.4 11 Fold:Long alpha-hairpin Superfamily:Chaperone J-domain Family:Chaperone J-domain 38 d1efaa1 not modelled 6.3 19 Fold:lambda repressor-like DNA-binding domains Superfamily:lambda repressor-like DNA-binding domains Family:GalR/LacI-like bacterial regulator 39 c2rnjA_ not modelled 6.3 16 PDB header:transcription Chain: A: PDB Molecule:response regulator protein vrar; PDBTitle: nmr structure of the s. aureus vrar dna binding domain 40 c1zljE_ not modelled 6.0 26 PDB header:transcription Chain: E: PDB Molecule:dormancy survival regulator; PDBTitle: crystal structure of the mycobacterium tuberculosis hypoxic2 response regulator dosr c-terminal domain 41 c2l8nA_ not modelled 6.0 22 PDB header:transcription regulator Chain: A: PDB Molecule:transcriptional repressor cytr; PDBTitle: nmr structure of the cytidine repressor dna binding domain in presence2 of operator half-site dna 42 c2bhmE_ not modelled 5.9 15 PDB header:bacterial protein Chain: E: PDB Molecule:type iv secretion system protein virb8; PDBTitle: crystal structure of virb8 from brucella suis 43 d1lcda_ not modelled 5.8 19 Fold:lambda repressor-like DNA-binding domains Superfamily:lambda repressor-like DNA-binding domains Family:GalR/LacI-like bacterial regulator 44 d1uxda_ not modelled 5.7 19 Fold:lambda repressor-like DNA-binding domains Superfamily:lambda repressor-like DNA-binding domains Family:GalR/LacI-like bacterial regulator 45 d1uika1 not modelled 5.7 20 Fold:Double-stranded beta-helix Superfamily:RmlC-like cupins Family:Germin/Seed storage 7S protein 46 d1ik9a1 not modelled 5.6 13 Fold:XRCC4, N-terminal domain Superfamily:XRCC4, N-terminal domain Family:XRCC4, N-terminal domain 47 c3o0lB_ not modelled 5.6 10 PDB header:structural genomics, unknown function Chain: B: PDB Molecule:uncharacterized protein; PDBTitle: crystal structure of a pfam duf1425 family member (shew_1734) from2 shewanella sp. pv-4 at 1.81 a resolution 48 d2p81a1 not modelled 5.6 14 Fold:DNA/RNA-binding 3-helical bundle Superfamily:Homeodomain-like Family:Homeodomain 49 c3bw8B_ not modelled 5.6 20 PDB header:transferase Chain: B: PDB Molecule:mono-adp-ribosyltransferase c3; PDBTitle: crystal structure of the clostridium limosum c3 exoenzyme 50 d1xsva_ not modelled 5.5 33 Fold:DNA/RNA-binding 3-helical bundle Superfamily:Sigma3 and sigma4 domains of RNA polymerase sigma factors Family:YlxM/p13-like 51 c3hugA_ not modelled 5.5 21 PDB header:transcription/membrane protein Chain: A: PDB Molecule:rna polymerase sigma factor; PDBTitle: crystal structure of mycobacterium tuberculosis anti-sigma factor rsla2 in complex with -35 promoter binding domain of sigl 52 d1o4va_ not modelled 5.4 8 Fold:Flavodoxin-like Superfamily:N5-CAIR mutase (phosphoribosylaminoimidazole carboxylase, PurE) Family:N5-CAIR mutase (phosphoribosylaminoimidazole carboxylase, PurE) 53 c3guzB_ not modelled 5.3 19 PDB header:ligase Chain: B: PDB Molecule:pantothenate synthetase; PDBTitle: structural and substrate-binding studies of pantothenate2 synthenate (ps)provide insights into homotropic inhibition3 by pantoate in ps's 54 d1go3f_ not modelled 5.1 10 Fold:SAM domain-like Superfamily:HRDC-like Family:RNA polymerase II subunit RBP4 (RpoF)

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