Secondary structure and disorder prediction

		1	.	.	.	.	.	.	.	.	10	.	.	.	.	.	.	.	.	.	20	.	.	.	.	.	.	.	.	.	30	.	.	.	.	.	.	.	.	.	40	.	.	.	.	.	.	.	.	.	50	.	.	.	.	.	.	.	.	.	60
Sequence		M	A	E	T	A	V	I	N	H	K	K	R	K	N	S	P	R	I	V	Q	S	N	D	L	T	E	A	A	Y	S	L	S	R	D	Q	K	R	M	L	Y	L	F	V	D	Q	I	R	K	S	D	G	T	L	Q	E	H	D	G	I	C
Secondary structure
SS confidence
Disorder		?	?	?	?	?	?	?	?	?	?	?	?	?	?	?	?																																?	?	?	?	?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	70	.	.	.	.	.	.	.	.	.	80	.	.	.	.	.	.	.	.	.	90	.	.	.	.	.	.	.	.	.	100	.	.	.	.	.	.	.	.	.	110	.	.	.	.	.	.	.	.	.	120
Sequence		E	I	H	V	A	K	Y	A	E	I	F	G	L	T	S	A	E	A	S	K	D	I	R	Q	A	L	K	S	F	A	G	K	E	V	V	F	Y	R	P	E	E	D	A	G	D	E	K	G	Y	E	S	F	P	W	F	I	K	R	A	H
Secondary structure
SS confidence
Disorder																																									?	?	?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	130	.	.	.	.	.	.	.	.	.	140	.	.	.	.	.	.	.	.	.	150	.	.	.	.	.	.	.	.	.	160	.	.	.	.	.	.	.	.	.	170	.	.	.	.	.	.	.	.	.	180
Sequence		S	P	S	R	G	L	Y	S	V	H	I	N	P	Y	L	I	P	F	F	I	G	L	Q	N	R	F	T	Q	F	R	L	S	E	T	K	E	I	T	N	P	Y	A	M	R	L	Y	E	S	L	C	Q	Y	R	K	P	D	G	S	G	I
Secondary structure
SS confidence
Disorder																																					?	?																		?	?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	190	.	.	.	.	.	.	.	.	.	200	.	.	.	.	.	.	.	.	.	210	.	.	.	.	.	.	.	.	.	220	.	.	.	.	.	.	.	.	.	230	.	.	.	.	.	.	.	.	.	240
Sequence		V	S	L	K	I	D	W	I	I	E	R	Y	Q	L	P	Q	S	Y	Q	R	M	P	D	F	R	R	R	F	L	Q	V	C	V	N	E	I	N	S	R	T	P	M	R	L	S	Y	I	E	K	K	K	G	R	Q	T	T	H	I	V	F
Secondary structure
SS confidence
Disorder																																																				?
Disorder confidence
		.	.	.	.	.	.	.	.	.	250	.
Sequence		S	F	R	D	I	T	S	M	T	T	G
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 2z9o chain B Region: 20 - 247 Aligned: 218 Modelled: 228 Confidence: 100.0% Identity: 99% PDB header:replication/dna Chain: B: PDB Molecule:replication initiation protein; PDBTitle: crystal structure of the dimeric form of repe in complex with the repe2 operator dna Phyre2 PDB 2nra chain C Region: 14 - 247 Aligned: 232 Modelled: 234 Confidence: 100.0% Identity: 19% PDB header:replication/dna Chain: C: PDB Molecule:pi protein; PDBTitle: crystal structure of pi initiator protein in complex with iteron dna Phyre2 PDB 1rep chain C domain 2 Region: 144 - 246 Aligned: 103 Modelled: 103 Confidence: 100.0% Identity: 100% Fold: DNA/RNA-binding 3-helical bundle Superfamily: "Winged helix" DNA-binding domain Family: Replication initiation protein Phyre2 PDB 2nra chain C domain 2 Region: 143 - 247 Aligned: 105 Modelled: 105 Confidence: 100.0% Identity: 21% Fold: DNA/RNA-binding 3-helical bundle Superfamily: "Winged helix" DNA-binding domain Family: Replication initiation protein Phyre2 PDB 1hkq chain A Region: 20 - 152 Aligned: 125 Modelled: 127 Confidence: 99.9% Identity: 22% Fold: DNA/RNA-binding 3-helical bundle Superfamily: "Winged helix" DNA-binding domain Family: Replication initiation protein Phyre2 PDB 2nra chain C domain 1 Region: 13 - 144 Aligned: 130 Modelled: 132 Confidence: 99.9% Identity: 18% Fold: DNA/RNA-binding 3-helical bundle Superfamily: "Winged helix" DNA-binding domain Family: Replication initiation protein Phyre2 PDB 1rep chain C domain 1 Region: 15 - 143 Aligned: 111 Modelled: 129 Confidence: 99.9% Identity: 99% Fold: DNA/RNA-binding 3-helical bundle Superfamily: "Winged helix" DNA-binding domain Family: Replication initiation protein Phyre2 PDB 1jhf chain A domain 1 Region: 30 - 92 Aligned: 51 Modelled: 63 Confidence: 86.4% Identity: 27% Fold: DNA/RNA-binding 3-helical bundle Superfamily: "Winged helix" DNA-binding domain Family: LexA repressor, N-terminal DNA-binding domain Phyre2 PDB 3r0a chain B Region: 19 - 113 Aligned: 79 Modelled: 95 Confidence: 73.7% Identity: 14% PDB header:transcription regulator Chain: B: PDB Molecule:putative transcriptional regulator; PDBTitle: possible transcriptional regulator from methanosarcina mazei go1 (gi2 21227196) Phyre2 PDB 2v79 chain B Region: 18 - 88 Aligned: 62 Modelled: 71 Confidence: 68.5% Identity: 13% PDB header:dna-binding protein Chain: B: PDB Molecule:dna replication protein dnad; PDBTitle: crystal structure of the n-terminal domain of dnad from2 bacillus subtilis Phyre2 PDB 1stz chain A domain 1 Region: 30 - 92 Aligned: 51 Modelled: 63 Confidence: 67.8% Identity: 20% Fold: DNA/RNA-binding 3-helical bundle Superfamily: "Winged helix" DNA-binding domain Family: Heat-inducible transcription repressor HrcA, N-terminal domain Phyre2 PDB 2cg4 chain A domain 1 Region: 29 - 88 Aligned: 46 Modelled: 46 Confidence: 60.1% Identity: 13% Fold: DNA/RNA-binding 3-helical bundle Superfamily: "Winged helix" DNA-binding domain Family: Lrp/AsnC-like transcriptional regulator N-terminal domain Phyre2 PDB 2d1h chain A domain 1 Region: 15 - 88 Aligned: 61 Modelled: 0 Confidence: 58.1% Identity: 15% Fold: DNA/RNA-binding 3-helical bundle Superfamily: "Winged helix" DNA-binding domain Family: TrmB-like Phyre2 PDB 2vn2 chain B Region: 18 - 88 Aligned: 62 Modelled: 71 Confidence: 52.8% Identity: 18% PDB header:replication Chain: B: PDB Molecule:chromosome replication initiation protein; PDBTitle: crystal structure of the n-terminal domain of dnad protein2 from geobacillus kaustophilus hta426 Phyre2 PDB 1x3u chain A Region: 20 - 89 Aligned: 54 Modelled: 54 Confidence: 51.1% Identity: 15% PDB header:transcription Chain: A: PDB Molecule:transcriptional regulatory protein fixj; PDBTitle: solution structure of the c-terminal transcriptional2 activator domain of fixj from sinorhizobium melilot Phyre2 PDB 1a04 chain A domain 1 Region: 29 - 89 Aligned: 45 Modelled: 45 Confidence: 50.2% Identity: 18% 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 1ku3 chain A Region: 23 - 91 Aligned: 58 Modelled: 69 Confidence: 46.8% Identity: 21% Fold: DNA/RNA-binding 3-helical bundle Superfamily: Sigma3 and sigma4 domains of RNA polymerase sigma factors Family: Sigma4 domain Phyre2 PDB 1ku7 chain A Region: 21 - 91 Aligned: 60 Modelled: 71 Confidence: 46.5% Identity: 22% Fold: DNA/RNA-binding 3-helical bundle Superfamily: Sigma3 and sigma4 domains of RNA polymerase sigma factors Family: Sigma4 domain Phyre2 PDB 1zlj chain E Region: 30 - 90 Aligned: 45 Modelled: 45 Confidence: 45.5% Identity: 16% PDB header:transcription Chain: E: PDB Molecule:dormancy survival regulator; PDBTitle: crystal structure of the mycobacterium tuberculosis hypoxic2 response regulator dosr c-terminal domain Phyre2 PDB 1s7o chain A Region: 22 - 91 Aligned: 55 Modelled: 55 Confidence: 41.8% Identity: 25% Fold: DNA/RNA-binding 3-helical bundle Superfamily: Sigma3 and sigma4 domains of RNA polymerase sigma factors Family: YlxM/p13-like Phyre2 1 c2z9oB_ 2 c2nraC_ 3 d1repc2 4 d2nrac2 5 d1hkqa_ 6 d2nrac1 7 d1repc1 8 d1jhfa1 9 c3r0aB_ 10 c2v79B_ 11 d1stza1 12 d2cg4a1 13 d2d1ha1 14 c2vn2B_ 15 c1x3uA_ 16 d1a04a1 17 d1ku3a_ 18 d1ku7a_ 19 c1zljE_ 20 d1s7oa_ 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 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99

Detailed template information

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

1 c2z9oB_ 100.0 99 PDB header:replication/dna Chain: B: PDB Molecule:replication initiation protein; PDBTitle: crystal structure of the dimeric form of repe in complex with the repe2 operator dna 2 c2nraC_ 100.0 19 PDB header:replication/dna Chain: C: PDB Molecule:pi protein; PDBTitle: crystal structure of pi initiator protein in complex with iteron dna 3 d1repc2 100.0 100 Fold:DNA/RNA-binding 3-helical bundle Superfamily:"Winged helix" DNA-binding domain Family:Replication initiation protein 4 d2nrac2 100.0 21 Fold:DNA/RNA-binding 3-helical bundle Superfamily:"Winged helix" DNA-binding domain Family:Replication initiation protein 5 d1hkqa_ 99.9 22 Fold:DNA/RNA-binding 3-helical bundle Superfamily:"Winged helix" DNA-binding domain Family:Replication initiation protein 6 d2nrac1 99.9 18 Fold:DNA/RNA-binding 3-helical bundle Superfamily:"Winged helix" DNA-binding domain Family:Replication initiation protein 7 d1repc1 99.9 99 Fold:DNA/RNA-binding 3-helical bundle Superfamily:"Winged helix" DNA-binding domain Family:Replication initiation protein 8 d1jhfa1 86.4 27 Fold:DNA/RNA-binding 3-helical bundle Superfamily:"Winged helix" DNA-binding domain Family:LexA repressor, N-terminal DNA-binding domain 9 c3r0aB_ 73.7 14 PDB header:transcription regulator Chain: B: PDB Molecule:putative transcriptional regulator; PDBTitle: possible transcriptional regulator from methanosarcina mazei go1 (gi2 21227196) 10 c2v79B_ 68.5 13 PDB header:dna-binding protein Chain: B: PDB Molecule:dna replication protein dnad; PDBTitle: crystal structure of the n-terminal domain of dnad from2 bacillus subtilis 11 d1stza1 67.8 20 Fold:DNA/RNA-binding 3-helical bundle Superfamily:"Winged helix" DNA-binding domain Family:Heat-inducible transcription repressor HrcA, N-terminal domain 12 d2cg4a1 60.1 13 Fold:DNA/RNA-binding 3-helical bundle Superfamily:"Winged helix" DNA-binding domain Family:Lrp/AsnC-like transcriptional regulator N-terminal domain 13 d2d1ha1 58.1 15 Fold:DNA/RNA-binding 3-helical bundle Superfamily:"Winged helix" DNA-binding domain Family:TrmB-like 14 c2vn2B_ 52.8 18 PDB header:replication Chain: B: PDB Molecule:chromosome replication initiation protein; PDBTitle: crystal structure of the n-terminal domain of dnad protein2 from geobacillus kaustophilus hta426 15 c1x3uA_ 51.1 15 PDB header:transcription Chain: A: PDB Molecule:transcriptional regulatory protein fixj; PDBTitle: solution structure of the c-terminal transcriptional2 activator domain of fixj from sinorhizobium melilot 16 d1a04a1 50.2 18 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 d1ku3a_ 46.8 21 Fold:DNA/RNA-binding 3-helical bundle Superfamily:Sigma3 and sigma4 domains of RNA polymerase sigma factors Family:Sigma4 domain 18 d1ku7a_ 46.5 22 Fold:DNA/RNA-binding 3-helical bundle Superfamily:Sigma3 and sigma4 domains of RNA polymerase sigma factors Family:Sigma4 domain 19 c1zljE_ 45.5 16 PDB header:transcription Chain: E: PDB Molecule:dormancy survival regulator; PDBTitle: crystal structure of the mycobacterium tuberculosis hypoxic2 response regulator dosr c-terminal domain 20 d1s7oa_ 41.8 25 Fold:DNA/RNA-binding 3-helical bundle Superfamily:Sigma3 and sigma4 domains of RNA polymerase sigma factors Family:YlxM/p13-like 21 d2p7vb1 not modelled 41.4 13 Fold:DNA/RNA-binding 3-helical bundle Superfamily:Sigma3 and sigma4 domains of RNA polymerase sigma factors Family:Sigma4 domain 22 d1ttya_ not modelled 41.0 13 Fold:DNA/RNA-binding 3-helical bundle Superfamily:Sigma3 and sigma4 domains of RNA polymerase sigma factors Family:Sigma4 domain 23 d1sfxa_ not modelled 40.7 22 Fold:DNA/RNA-binding 3-helical bundle Superfamily:"Winged helix" DNA-binding domain Family:TrmB-like 24 d1yioa1 not modelled 40.6 16 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) 25 c3nqoB_ not modelled 38.9 13 PDB header:transcription Chain: B: PDB Molecule:marr-family transcriptional regulator; PDBTitle: crystal structure of a marr family transcriptional regulator (cd1569)2 from clostridium difficile 630 at 2.20 a resolution 26 d1fsea_ not modelled 37.6 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) 27 d2etha1 not modelled 36.8 14 Fold:DNA/RNA-binding 3-helical bundle Superfamily:"Winged helix" DNA-binding domain Family:MarR-like transcriptional regulators 28 c2rnjA_ not modelled 36.1 14 PDB header:transcription Chain: A: PDB Molecule:response regulator protein vrar; PDBTitle: nmr structure of the s. aureus vrar dna binding domain 29 d2cyya1 not modelled 35.5 23 Fold:DNA/RNA-binding 3-helical bundle Superfamily:"Winged helix" DNA-binding domain Family:Lrp/AsnC-like transcriptional regulator N-terminal domain 30 d1i1ga1 not modelled 33.9 11 Fold:DNA/RNA-binding 3-helical bundle Superfamily:"Winged helix" DNA-binding domain Family:Lrp/AsnC-like transcriptional regulator N-terminal domain 31 d2cfxa1 not modelled 32.8 11 Fold:DNA/RNA-binding 3-helical bundle Superfamily:"Winged helix" DNA-binding domain Family:Lrp/AsnC-like transcriptional regulator N-terminal domain 32 c2l4aA_ not modelled 32.8 20 PDB header:dna binding protein Chain: A: PDB Molecule:leucine responsive regulatory protein; PDBTitle: nmr structure of the dna-binding domain of e.coli lrp 33 d1l3la1 not modelled 32.6 22 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 d1fnna1 not modelled 32.2 16 Fold:DNA/RNA-binding 3-helical bundle Superfamily:"Winged helix" DNA-binding domain Family:Helicase DNA-binding domain 35 d1or7a1 not modelled 31.3 7 Fold:DNA/RNA-binding 3-helical bundle Superfamily:Sigma3 and sigma4 domains of RNA polymerase sigma factors Family:Sigma4 domain 36 c2krfB_ not modelled 30.8 9 PDB header:transcription Chain: B: PDB Molecule:transcriptional regulatory protein coma; PDBTitle: nmr solution structure of the dna binding domain of competence protein2 a 37 c2fxaB_ not modelled 29.0 8 PDB header:transcription Chain: B: PDB Molecule:protease production regulatory protein hpr; PDBTitle: structure of the protease production regulatory protein hpr from2 bacillus subtilis. 38 c3iwfA_ not modelled 28.3 9 PDB header:transcription regulator Chain: A: PDB Molecule:transcription regulator rpir family; PDBTitle: the crystal structure of the n-terminal domain of a rpir2 transcriptional regulator from staphylococcus epidermidis to 1.4a 39 d1xsva_ not modelled 27.5 13 Fold:DNA/RNA-binding 3-helical bundle Superfamily:Sigma3 and sigma4 domains of RNA polymerase sigma factors Family:YlxM/p13-like 40 d1p4wa_ not modelled 27.4 20 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) 41 c3hugA_ not modelled 26.1 9 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 42 c2wteB_ not modelled 25.7 13 PDB header:antiviral protein Chain: B: PDB Molecule:csa3; PDBTitle: the structure of the crispr-associated protein, csa3, from2 sulfolobus solfataricus at 1.8 angstrom resolution. 43 c2qwwB_ not modelled 25.0 15 PDB header:transcription Chain: B: PDB Molecule:transcriptional regulator, marr family; PDBTitle: crystal structure of multiple antibiotic-resistance repressor (marr)2 (yp_013417.1) from listeria monocytogenes 4b f2365 at 2.07 a3 resolution 44 c3k2zA_ not modelled 24.6 26 PDB header:hydrolase Chain: A: PDB Molecule:lexa repressor; PDBTitle: crystal structure of a lexa protein from thermotoga maritima 45 d1rp3a2 not modelled 24.6 12 Fold:DNA/RNA-binding 3-helical bundle Superfamily:Sigma3 and sigma4 domains of RNA polymerase sigma factors Family:Sigma4 domain 46 c2o8xA_ not modelled 24.0 7 PDB header:transcription Chain: A: PDB Molecule:probable rna polymerase sigma-c factor; PDBTitle: crystal structure of the "-35 element" promoter recognition domain of2 mycobacterium tuberculosis sigc 47 d1hsja1 not modelled 23.8 11 Fold:DNA/RNA-binding 3-helical bundle Superfamily:"Winged helix" DNA-binding domain Family:MarR-like transcriptional regulators 48 d2fbia1 not modelled 23.2 16 Fold:DNA/RNA-binding 3-helical bundle Superfamily:"Winged helix" DNA-binding domain Family:MarR-like transcriptional regulators 49 c2cg4B_ not modelled 22.8 13 PDB header:transcription Chain: B: PDB Molecule:regulatory protein asnc; PDBTitle: structure of e.coli asnc 50 d2oz6a1 not modelled 21.6 11 Fold:DNA/RNA-binding 3-helical bundle Superfamily:"Winged helix" DNA-binding domain Family:CAP C-terminal domain-like 51 c2q0oA_ not modelled 21.2 16 PDB header:transcription Chain: A: PDB Molecule:probable transcriptional activator protein trar; PDBTitle: crystal structure of an anti-activation complex in bacterial quorum2 sensing 52 c3qp5C_ not modelled 20.0 11 PDB header:transcription Chain: C: PDB Molecule:cvir transcriptional regulator; PDBTitle: crystal structure of cvir bound to antagonist chlorolactone (cl) 53 d1dpua_ not modelled 19.0 21 Fold:DNA/RNA-binding 3-helical bundle Superfamily:"Winged helix" DNA-binding domain Family:C-terminal domain of RPA32 54 c1dpuA_ not modelled 19.0 21 PDB header:dna binding protein Chain: A: PDB Molecule:replication protein a (rpa32) c-terminal domain; PDBTitle: solution structure of the c-terminal domain of human rpa322 complexed with ung2(73-88) 55 d1ku9a_ not modelled 18.6 9 Fold:DNA/RNA-binding 3-helical bundle Superfamily:"Winged helix" DNA-binding domain Family:DNA-binding protein Mj223 56 d1i5za1 not modelled 18.6 9 Fold:DNA/RNA-binding 3-helical bundle Superfamily:"Winged helix" DNA-binding domain Family:CAP C-terminal domain-like 57 d2gaua1 not modelled 18.1 7 Fold:DNA/RNA-binding 3-helical bundle Superfamily:"Winged helix" DNA-binding domain Family:CAP C-terminal domain-like 58 d2frha1 not modelled 17.5 13 Fold:DNA/RNA-binding 3-helical bundle Superfamily:"Winged helix" DNA-binding domain Family:MarR-like transcriptional regulators 59 d1smyf2 not modelled 17.2 27 Fold:DNA/RNA-binding 3-helical bundle Superfamily:Sigma3 and sigma4 domains of RNA polymerase sigma factors Family:Sigma4 domain 60 c3sztB_ not modelled 17.2 16 PDB header:transcription Chain: B: PDB Molecule:quorum-sensing control repressor; PDBTitle: quorum sensing control repressor, qscr, bound to n-3-oxo-dodecanoyl-l-2 homoserine lactone 61 c2k9lA_ not modelled 16.1 10 PDB header:transcription Chain: A: PDB Molecule:rna polymerase sigma factor rpon; PDBTitle: structure of the core binding domain of sigma54 62 c2l3iA_ not modelled 16.0 18 PDB header:antimicrobial protein Chain: A: PDB Molecule:aoxki4a, antimicrobial peptide in spider venom; PDBTitle: oxki4a, spider derived antimicrobial peptide 63 d2dt5a1 not modelled 15.9 11 Fold:DNA/RNA-binding 3-helical bundle Superfamily:"Winged helix" DNA-binding domain Family:Transcriptional repressor Rex, N-terminal domain 64 c1h0mD_ not modelled 14.1 20 PDB header:transcription/dna Chain: D: PDB Molecule:transcriptional activator protein trar; PDBTitle: three-dimensional structure of the quorum sensing protein2 trar bound to its autoinducer and to its target dna 65 c1hsjA_ not modelled 12.8 10 PDB header:transcription/sugar binding protein Chain: A: PDB Molecule:fusion protein consisting of staphylococcus PDBTitle: sarr mbp fusion structure 66 c3cloC_ not modelled 12.4 16 PDB header:transcription regulator Chain: C: PDB Molecule:transcriptional regulator; PDBTitle: crystal structure of putative transcriptional regulator containing a2 luxr dna binding domain (np_811094.1) from bacteroides3 thetaiotaomicron vpi-5482 at 2.04 a resolution 67 c2e1cA_ not modelled 12.1 22 PDB header:transcription/dna Chain: A: PDB Molecule:putative hth-type transcriptional regulator ph1519; PDBTitle: structure of putative hth-type transcriptional regulator ph1519/dna2 complex 68 d1p4xa2 not modelled 12.0 12 Fold:DNA/RNA-binding 3-helical bundle Superfamily:"Winged helix" DNA-binding domain Family:MarR-like transcriptional regulators 69 c3mzyA_ not modelled 11.9 13 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 70 d2coha1 not modelled 11.9 11 Fold:DNA/RNA-binding 3-helical bundle Superfamily:"Winged helix" DNA-binding domain Family:CAP C-terminal domain-like 71 d2o8ra1 not modelled 11.0 19 Fold:Spectrin repeat-like Superfamily:PPK N-terminal domain-like Family:PPK N-terminal domain-like 72 d1lnwa_ not modelled 10.6 13 Fold:DNA/RNA-binding 3-helical bundle Superfamily:"Winged helix" DNA-binding domain Family:MarR-like transcriptional regulators 73 c1p4xA_ not modelled 10.5 9 PDB header:transcription Chain: A: PDB Molecule:staphylococcal accessory regulator a homologue; PDBTitle: crystal structure of sars protein from staphylococcus aureus 74 d2o3fa1 not modelled 10.5 10 Fold:DNA/RNA-binding 3-helical bundle Superfamily:Homeodomain-like Family:RpiR-like 75 c2o3fC_ not modelled 10.4 10 PDB header:transcription Chain: C: PDB Molecule:putative hth-type transcriptional regulator ybbh; PDBTitle: structural genomics, the crystal structure of the n-2 terminal domain of the putative transcriptional regulator3 ybbh from bacillus subtilis subsp. subtilis str. 168. 76 d1j5ya1 not modelled 10.4 21 Fold:DNA/RNA-binding 3-helical bundle Superfamily:"Winged helix" DNA-binding domain Family:Biotin repressor-like 77 d3broa1 not modelled 10.4 15 Fold:DNA/RNA-binding 3-helical bundle Superfamily:"Winged helix" DNA-binding domain Family:MarR-like transcriptional regulators 78 d1p4xa1 not modelled 9.8 12 Fold:DNA/RNA-binding 3-helical bundle Superfamily:"Winged helix" DNA-binding domain Family:MarR-like transcriptional regulators 79 d1xdpa1 not modelled 9.6 25 Fold:Spectrin repeat-like Superfamily:PPK N-terminal domain-like Family:PPK N-terminal domain-like 80 d1d5ya1 not modelled 9.3 9 Fold:DNA/RNA-binding 3-helical bundle Superfamily:Homeodomain-like Family:AraC type transcriptional activator 81 c1wsuA_ not modelled 9.3 19 PDB header:translation/rna Chain: A: PDB Molecule:selenocysteine-specific elongation factor; PDBTitle: c-terminal domain of elongation factor selb complexed with2 secis rna 82 c2vbzA_ not modelled 8.5 16 PDB header:dna-binding protein Chain: A: PDB Molecule:transcriptional regulatory protein; PDBTitle: feast or famine regulatory protein (rv3291c)from m.2 tuberculosis complexed with l-tryptophan 83 c2e7xA_ not modelled 8.5 14 PDB header:transcription regulator Chain: A: PDB Molecule:150aa long hypothetical transcriptional regulator; PDBTitle: structure of the lrp/asnc like transcriptional regulator from2 sulfolobus tokodaii 7 complexed with its cognate ligand 84 d1fs2b1 not modelled 8.2 7 Fold:Skp1 dimerisation domain-like Superfamily:Skp1 dimerisation domain-like Family:Skp1 dimerisation domain-like 85 c2gqqB_ not modelled 8.0 20 PDB header:transcription Chain: B: PDB Molecule:leucine-responsive regulatory protein; PDBTitle: crystal structure of e. coli leucine-responsive regulatory protein2 (lrp) 86 c2ia0A_ not modelled 7.9 11 PDB header:structural genomics, unknown function Chain: A: PDB Molecule:putative hth-type transcriptional regulator pf0864; PDBTitle: transcriptional regulatory protein pf0864 from pyrococcus furiosus a2 member of the asnc family (pf0864) 87 d2aq0a1 not modelled 7.8 10 Fold:SAM domain-like Superfamily:RuvA domain 2-like Family:Hef domain-like 88 d1jt6a1 not modelled 7.5 5 Fold:DNA/RNA-binding 3-helical bundle Superfamily:Homeodomain-like Family:Tetracyclin repressor-like, N-terminal domain 89 c2rdpA_ not modelled 7.4 16 PDB header:transcription Chain: A: PDB Molecule:putative transcriptional regulator marr; PDBTitle: the structure of a marr family protein from bacillus2 stearothermophilus 90 d2a61a1 not modelled 7.3 14 Fold:DNA/RNA-binding 3-helical bundle Superfamily:"Winged helix" DNA-binding domain Family:MarR-like transcriptional regulators 91 c2k9mA_ not modelled 7.3 10 PDB header:transcription Chain: A: PDB Molecule:rna polymerase sigma factor rpon; PDBTitle: structure of the core binding domain of sigma54 92 c2p6tH_ not modelled 7.3 16 PDB header:transcription Chain: H: PDB Molecule:transcriptional regulator, lrp/asnc family; PDBTitle: crystal structure of transcriptional regulator nmb0573 and l-leucine2 complex from neisseria meningitidis 93 d2g3ba1 not modelled 6.9 16 Fold:DNA/RNA-binding 3-helical bundle Superfamily:Homeodomain-like Family:Tetracyclin repressor-like, N-terminal domain 94 d2ovra1 not modelled 6.8 12 Fold:Skp1 dimerisation domain-like Superfamily:Skp1 dimerisation domain-like Family:Skp1 dimerisation domain-like 95 d1biaa1 not modelled 6.8 19 Fold:DNA/RNA-binding 3-helical bundle Superfamily:"Winged helix" DNA-binding domain Family:Biotin repressor-like 96 c3boqB_ not modelled 6.7 13 PDB header:transcription regulator Chain: B: PDB Molecule:transcriptional regulator, marr family; PDBTitle: crystal structure of marr family transcriptional regulator from2 silicibacter pomeroyi 97 d2fxaa1 not modelled 6.6 11 Fold:DNA/RNA-binding 3-helical bundle Superfamily:"Winged helix" DNA-binding domain Family:MarR-like transcriptional regulators 98 c2plyB_ not modelled 6.5 19 PDB header:translation/rna Chain: B: PDB Molecule:selenocysteine-specific elongation factor; PDBTitle: structure of the mrna binding fragment of elongation factor2 selb in complex with secis rna. 99 c3bpxB_ not modelled 6.5 12 PDB header:transcription regulator Chain: B: PDB Molecule:transcriptional regulator; PDBTitle: crystal structure of marr

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