Secondary structure and disorder prediction

		1	.	.	.	.	.	.	.	.	10	.	.	.	.	.	.	.	.	.	20	.	.	.	.	.	.	.	.	.	30	.	.	.	.	.	.	.	.	.	40	.	.	.	.	.	.	.	.	.	50	.	.	.	.	.	.	.	.	.	60
Sequence		M	G	K	H	H	W	K	I	E	K	Q	P	E	W	Y	V	K	A	V	R	K	T	I	A	A	L	P	S	G	Y	A	E	A	A	D	W	L	D	V	T	E	N	A	L	F	N	R	L	R	A	D	G	D	Q	I	F	P	L	G	W
Secondary structure
SS confidence
Disorder		?	?	?	?	?	?	?	?	?																																										?	?	?	?	?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	70	.	.	.	.	.	.	.	.	.	80	.	.	.	.	.	.	.	.	.	90	.	.	.	.	.	.	.	.	.	100	.	.	.	.	.	.	.	.	.	110	.	.	.	.	.	.	.	.	.	120
Sequence		A	M	V	L	Q	R	A	G	G	T	H	F	I	A	D	A	V	A	Q	S	A	N	G	V	F	V	S	L	P	D	V	E	D	V	D	N	A	D	I	N	Q	R	L	L	E	V	I	E	Q	I	G	S	Y	S	K	Q	I	R	S	A
Secondary structure
SS confidence
Disorder																															?	?	?	?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	130	.	.	.	.	.	.	.	.	.	140	.	.	.	.	.	.	.	.	.	150	.	.	.	.	.	.	.	.	.	160	.	.	.	.	.	.	.	.	.	170	.	.	.	.	.	.	.	.	.	180
Sequence		I	E	D	G	V	V	E	P	H	E	K	T	A	I	N	D	E	L	Y	L	S	I	S	K	L	Q	E	H	A	A	L	V	Y	K	I	F	C	I	S	E	S	N	D	A	R	E	C	A	A	P	G	V	V	A	S	I	A	S	G	C
Secondary structure
SS confidence
Disorder						?																																		?	?	?																	?	?	?
Disorder confidence
		.	.	.	.	.
Sequence		G	E	T	N	A
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 1rzs chain A Region: 20 - 69 Aligned: 44 Modelled: 50 Confidence: 89.1% Identity: 16% Fold: lambda repressor-like DNA-binding domains Superfamily: lambda repressor-like DNA-binding domains Family: Phage repressors Phyre2 PDB 1fip chain A Region: 17 - 52 Aligned: 36 Modelled: 36 Confidence: 88.7% Identity: 14% Fold: DNA/RNA-binding 3-helical bundle Superfamily: Homeodomain-like Family: FIS-like Phyre2 PDB 3bd1 chain B Region: 16 - 69 Aligned: 50 Modelled: 54 Confidence: 87.8% Identity: 20% PDB header:transcription Chain: B: PDB Molecule:cro protein; PDBTitle: structure of the cro protein from putative prophage element xfaso 1 in2 xylella fastidiosa strain ann-1 Phyre2 PDB 1etx chain A Region: 17 - 52 Aligned: 36 Modelled: 36 Confidence: 86.7% Identity: 14% Fold: DNA/RNA-binding 3-helical bundle Superfamily: Homeodomain-like Family: FIS-like Phyre2 PDB 3e7l chain D Region: 17 - 52 Aligned: 36 Modelled: 36 Confidence: 84.3% Identity: 6% PDB header:transcription regulator Chain: D: PDB Molecule:transcriptional regulator (ntrc family); PDBTitle: crystal structure of sigma54 activator ntrc4's dna binding2 domain Phyre2 PDB 1g2h chain A Region: 17 - 52 Aligned: 35 Modelled: 36 Confidence: 83.4% Identity: 23% Fold: DNA/RNA-binding 3-helical bundle Superfamily: Homeodomain-like Family: FIS-like Phyre2 PDB 1eto chain B Region: 17 - 52 Aligned: 36 Modelled: 36 Confidence: 83.2% Identity: 14% Fold: DNA/RNA-binding 3-helical bundle Superfamily: Homeodomain-like Family: FIS-like Phyre2 PDB 3trb chain A Region: 11 - 80 Aligned: 66 Modelled: 70 Confidence: 82.8% Identity: 17% PDB header:dna binding protein Chain: A: PDB Molecule:virulence-associated protein i; PDBTitle: structure of an addiction module antidote protein of a higa (higa)2 family from coxiella burnetii Phyre2 PDB 1umq chain A Region: 17 - 54 Aligned: 38 Modelled: 38 Confidence: 82.8% Identity: 13% Fold: DNA/RNA-binding 3-helical bundle Superfamily: Homeodomain-like Family: FIS-like Phyre2 PDB 1umq chain A Region: 17 - 54 Aligned: 38 Modelled: 38 Confidence: 82.8% Identity: 13% PDB header:dna-binding protein Chain: A: PDB Molecule:photosynthetic apparatus regulatory protein; PDBTitle: solution structure and dna binding of the effector domain2 from the global regulator prra(rega) from r. sphaeroides:3 insights into dna binding specificity Phyre2 PDB 2fjr chain B Region: 16 - 71 Aligned: 53 Modelled: 56 Confidence: 82.2% Identity: 21% PDB header:transcription regulator Chain: B: PDB Molecule:repressor protein ci; PDBTitle: crystal structure of bacteriophage 186 Phyre2 PDB 1ntc chain A Region: 17 - 48 Aligned: 32 Modelled: 32 Confidence: 81.1% Identity: 19% Fold: DNA/RNA-binding 3-helical bundle Superfamily: Homeodomain-like Family: FIS-like Phyre2 PDB 3cec chain A Region: 17 - 71 Aligned: 53 Modelled: 55 Confidence: 80.3% Identity: 17% PDB header:transcription Chain: A: PDB Molecule:putative antidote protein of plasmid maintenance system; PDBTitle: crystal structure of a putative antidote protein of plasmid2 maintenance system (npun_f2943) from nostoc punctiforme pcc 73102 at3 1.60 a resolution Phyre2 PDB 2ou3 chain A domain 1 Region: 109 - 141 Aligned: 33 Modelled: 33 Confidence: 74.8% Identity: 21% Fold: TerB-like Superfamily: TerB-like Family: COG3793-like Phyre2 PDB 3onq chain B Region: 10 - 49 Aligned: 39 Modelled: 40 Confidence: 70.1% Identity: 21% PDB header:structural genomics, unknown function Chain: B: PDB Molecule:regulator of polyketide synthase expression; PDBTitle: crystal structure of regulator of polyketide synthase expression2 bad_0249 from bifidobacterium adolescentis Phyre2 PDB 3omt chain A Region: 30 - 71 Aligned: 40 Modelled: 42 Confidence: 66.3% Identity: 13% PDB header:structural genomics, unknown function Chain: A: PDB Molecule:uncharacterized protein; PDBTitle: putative antitoxin component, chu_2935 protein, from xre family from2 prevotella buccae. Phyre2 PDB 1vz0 chain A domain 1 Region: 18 - 49 Aligned: 31 Modelled: 32 Confidence: 61.2% Identity: 16% Fold: DNA/RNA-binding 3-helical bundle Superfamily: KorB DNA-binding domain-like Family: KorB DNA-binding domain-like Phyre2 PDB 2jxu chain A Region: 108 - 139 Aligned: 32 Modelled: 32 Confidence: 58.9% Identity: 22% PDB header:unknown function Chain: A: PDB Molecule:terb; PDBTitle: nmr solution structure of kp-terb, a tellurite resistance2 protein from klebsiella pneumoniae Phyre2 PDB 3mn2 chain B Region: 13 - 83 Aligned: 71 Modelled: 71 Confidence: 58.3% Identity: 14% PDB header:transcription regulator Chain: B: PDB Molecule:probable arac family transcriptional regulator; PDBTitle: the crystal structure of a probable arac family transcriptional2 regulator from rhodopseudomonas palustris cga009 Phyre2 PDB 3bdn chain B Region: 13 - 71 Aligned: 57 Modelled: 59 Confidence: 57.7% Identity: 12% PDB header:transcription/dna Chain: B: PDB Molecule:lambda repressor; PDBTitle: crystal structure of the lambda repressor Phyre2 PDB 2a61 chain A domain 1 Region: 10 - 148 Aligned: 134 Modelled: 134 Confidence: 54.0% Identity: 17% Fold: DNA/RNA-binding 3-helical bundle Superfamily: "Winged helix" DNA-binding domain Family: MarR-like transcriptional regulators Phyre2 1 d1rzsa_ 2 d1fipa_ 3 c3bd1B_ 4 d1etxa_ 5 c3e7lD_ 6 d1g2ha_ 7 d1etob_ 8 c3trbA_ 9 d1umqa_ 10 c1umqA_ 11 c2fjrB_ 12 d1ntca_ 13 c3cecA_ 14 d2ou3a1 15 c3onqB_ 16 c3omtA_ 17 d1vz0a1 18 c2jxuA_ 19 c3mn2B_ 20 c3bdnB_ 21 22 23 24 25 26 27 d2a61a1 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 99 100 101 102 103 104 105 106 107 108

Detailed template information

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

1 d1rzsa_ 89.1 16 Fold:lambda repressor-like DNA-binding domains Superfamily:lambda repressor-like DNA-binding domains Family:Phage repressors 2 d1fipa_ 88.7 14 Fold:DNA/RNA-binding 3-helical bundle Superfamily:Homeodomain-like Family:FIS-like 3 c3bd1B_ 87.8 20 PDB header:transcription Chain: B: PDB Molecule:cro protein; PDBTitle: structure of the cro protein from putative prophage element xfaso 1 in2 xylella fastidiosa strain ann-1 4 d1etxa_ 86.7 14 Fold:DNA/RNA-binding 3-helical bundle Superfamily:Homeodomain-like Family:FIS-like 5 c3e7lD_ 84.3 6 PDB header:transcription regulator Chain: D: PDB Molecule:transcriptional regulator (ntrc family); PDBTitle: crystal structure of sigma54 activator ntrc4's dna binding2 domain 6 d1g2ha_ 83.4 23 Fold:DNA/RNA-binding 3-helical bundle Superfamily:Homeodomain-like Family:FIS-like 7 d1etob_ 83.2 14 Fold:DNA/RNA-binding 3-helical bundle Superfamily:Homeodomain-like Family:FIS-like 8 c3trbA_ 82.8 17 PDB header:dna binding protein Chain: A: PDB Molecule:virulence-associated protein i; PDBTitle: structure of an addiction module antidote protein of a higa (higa)2 family from coxiella burnetii 9 d1umqa_ 82.8 13 Fold:DNA/RNA-binding 3-helical bundle Superfamily:Homeodomain-like Family:FIS-like 10 c1umqA_ 82.8 13 PDB header:dna-binding protein Chain: A: PDB Molecule:photosynthetic apparatus regulatory protein; PDBTitle: solution structure and dna binding of the effector domain2 from the global regulator prra(rega) from r. sphaeroides:3 insights into dna binding specificity 11 c2fjrB_ 82.2 21 PDB header:transcription regulator Chain: B: PDB Molecule:repressor protein ci; PDBTitle: crystal structure of bacteriophage 186 12 d1ntca_ 81.1 19 Fold:DNA/RNA-binding 3-helical bundle Superfamily:Homeodomain-like Family:FIS-like 13 c3cecA_ 80.3 17 PDB header:transcription Chain: A: PDB Molecule:putative antidote protein of plasmid maintenance system; PDBTitle: crystal structure of a putative antidote protein of plasmid2 maintenance system (npun_f2943) from nostoc punctiforme pcc 73102 at3 1.60 a resolution 14 d2ou3a1 74.8 21 Fold:TerB-like Superfamily:TerB-like Family:COG3793-like 15 c3onqB_ 70.1 21 PDB header:structural genomics, unknown function Chain: B: PDB Molecule:regulator of polyketide synthase expression; PDBTitle: crystal structure of regulator of polyketide synthase expression2 bad_0249 from bifidobacterium adolescentis 16 c3omtA_ 66.3 13 PDB header:structural genomics, unknown function Chain: A: PDB Molecule:uncharacterized protein; PDBTitle: putative antitoxin component, chu_2935 protein, from xre family from2 prevotella buccae. 17 d1vz0a1 61.2 16 Fold:DNA/RNA-binding 3-helical bundle Superfamily:KorB DNA-binding domain-like Family:KorB DNA-binding domain-like 18 c2jxuA_ 58.9 22 PDB header:unknown function Chain: A: PDB Molecule:terb; PDBTitle: nmr solution structure of kp-terb, a tellurite resistance2 protein from klebsiella pneumoniae 19 c3mn2B_ 58.3 14 PDB header:transcription regulator Chain: B: PDB Molecule:probable arac family transcriptional regulator; PDBTitle: the crystal structure of a probable arac family transcriptional2 regulator from rhodopseudomonas palustris cga009 20 c3bdnB_ 57.7 12 PDB header:transcription/dna Chain: B: PDB Molecule:lambda repressor; PDBTitle: crystal structure of the lambda repressor 21 d1utxa_ not modelled 57.4 14 Fold:lambda repressor-like DNA-binding domains Superfamily:lambda repressor-like DNA-binding domains Family:SinR domain-like 22 c3bs3A_ not modelled 56.8 10 PDB header:dna binding protein Chain: A: PDB Molecule:putative dna-binding protein; PDBTitle: crystal structure of a putative dna-binding protein from bacteroides2 fragilis 23 c3mklB_ not modelled 55.3 22 PDB header:transcription regulator Chain: B: PDB Molecule:hth-type transcriptional regulator gadx; PDBTitle: crystal structure of dna-binding transcriptional dual regulator from2 escherichia coli k-12 24 d2cg4a1 not modelled 54.8 18 Fold:DNA/RNA-binding 3-helical bundle Superfamily:"Winged helix" DNA-binding domain Family:Lrp/AsnC-like transcriptional regulator N-terminal domain 25 d2icta1 not modelled 54.8 14 Fold:lambda repressor-like DNA-binding domains Superfamily:lambda repressor-like DNA-binding domains Family:SinR domain-like 26 d1ctda_ not modelled 54.4 24 Fold:EF Hand-like Superfamily:EF-hand Family:Calmodulin-like 27 d2a61a1 54.0 17 Fold:DNA/RNA-binding 3-helical bundle Superfamily:"Winged helix" DNA-binding domain Family:MarR-like transcriptional regulators 28 c3mkyP_ not modelled 53.5 7 PDB header:dna binding protein/dna Chain: P: PDB Molecule:protein sopb; PDBTitle: structure of sopb(155-323)-18mer dna complex, i23 form 29 c3eusB_ not modelled 51.8 15 PDB header:dna binding protein Chain: B: PDB Molecule:dna-binding protein; PDBTitle: the crystal structure of the dna binding protein from silicibacter2 pomeroyi 30 d2cfxa1 not modelled 51.4 9 Fold:DNA/RNA-binding 3-helical bundle Superfamily:"Winged helix" DNA-binding domain Family:Lrp/AsnC-like transcriptional regulator N-terminal domain 31 d2cyya1 not modelled 50.4 15 Fold:DNA/RNA-binding 3-helical bundle Superfamily:"Winged helix" DNA-binding domain Family:Lrp/AsnC-like transcriptional regulator N-terminal domain 32 c3lisB_ not modelled 50.4 12 PDB header:transcription Chain: B: PDB Molecule:csp231i c protein; PDBTitle: crystal structure of the restriction-modification controller protein2 c.csp231i (monoclinic form) 33 c1nh2D_ not modelled 49.0 12 PDB header:transcription/dna Chain: D: PDB Molecule:transcription initiation factor iia small chain; PDBTitle: crystal structure of a yeast tfiia/tbp/dna complex 34 c3op9A_ not modelled 47.7 13 PDB header:transcription regulator Chain: A: PDB Molecule:pli0006 protein; PDBTitle: crystal structure of transcriptional regulator from listeria innocua 35 c2l4aA_ not modelled 47.6 9 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 36 d1i1ga1 not modelled 45.8 18 Fold:DNA/RNA-binding 3-helical bundle Superfamily:"Winged helix" DNA-binding domain Family:Lrp/AsnC-like transcriptional regulator N-terminal domain 37 c3f6wE_ not modelled 44.3 15 PDB header:dna binding protein Chain: E: PDB Molecule:xre-family like protein; PDBTitle: xre-family like protein from pseudomonas syringae pv. tomato str.2 dc3000 38 d2p12a1 not modelled 44.1 12 Fold:FomD barrel-like Superfamily:FomD-like Family:FomD-like 39 d1y9qa1 not modelled 43.5 7 Fold:lambda repressor-like DNA-binding domains Superfamily:lambda repressor-like DNA-binding domains Family:Probable transcriptional regulator VC1968, N-terminal domain 40 c2o38A_ not modelled 43.5 16 PDB header:structural genomics, unknown function Chain: A: PDB Molecule:hypothetical protein; PDBTitle: putative xre family transcriptional regulator 41 d2o38a1 not modelled 43.5 16 Fold:lambda repressor-like DNA-binding domains Superfamily:lambda repressor-like DNA-binding domains Family:NE1354 42 c2kpjA_ not modelled 43.2 18 PDB header:transcription regulator Chain: A: PDB Molecule:sos-response transcriptional repressor, lexa; PDBTitle: solution structure of protein sos-response transcriptional2 repressor, lexa from eubacterium rectale. northeast3 structural genomics consortium target err9a 43 c3mkzU_ not modelled 43.1 6 PDB header:dna-binding protein/dna Chain: U: PDB Molecule:protein sopb; PDBTitle: structure of sopb(155-272)-18mer complex, p21 form 44 c1vkoA_ not modelled 42.2 21 PDB header:isomerase Chain: A: PDB Molecule:inositol-3-phosphate synthase; PDBTitle: crystal structure of inositol-3-phosphate synthase (ce21227) from2 caenorhabditis elegans at 2.30 a resolution 45 c3b7hA_ not modelled 40.8 7 PDB header:structural protein Chain: A: PDB Molecule:prophage lp1 protein 11; PDBTitle: crystal structure of the prophage lp1 protein 11 46 c2dbbA_ not modelled 40.4 24 PDB header:transcriptional regulator Chain: A: PDB Molecule:putative hth-type transcriptional regulator ph0061; PDBTitle: crystal structure of ph0061 47 c3lsgD_ not modelled 39.8 9 PDB header:transcription regulator Chain: D: PDB Molecule:two-component response regulator yesn; PDBTitle: the crystal structure of the c-terminal domain of the two-2 component response regulator yesn from fusobacterium3 nucleatum subsp. nucleatum atcc 25586 48 d1rp3a1 not modelled 39.0 23 Fold:DNA/RNA-binding 3-helical bundle Superfamily:Sigma3 and sigma4 domains of RNA polymerase sigma factors Family:Sigma3 domain 49 c2ebyA_ not modelled 38.9 16 PDB header:transcription Chain: A: PDB Molecule:putative hth-type transcriptional regulator ybaq; PDBTitle: crystal structure of a hypothetical protein from e. coli 50 c3f52A_ not modelled 38.4 20 PDB header:transcription activator Chain: A: PDB Molecule:clp gene regulator (clgr); PDBTitle: crystal structure of the clp gene regulator clgr from c. glutamicum 51 d1e6yb1 not modelled 35.9 27 Fold:Methyl-coenzyme M reductase alpha and beta chain C-terminal domain Superfamily:Methyl-coenzyme M reductase alpha and beta chain C-terminal domain Family:Methyl-coenzyme M reductase alpha and beta chain C-terminal domain 52 c3oioA_ not modelled 35.9 15 PDB header:transcription regulator Chain: A: PDB Molecule:transcriptional regulator (arac-type dna-binding domain- PDBTitle: crystal structure of transcriptional regulator (arac-type dna-binding2 domain-containing proteins) from chromobacterium violaceum 53 c3k2zA_ not modelled 35.5 18 PDB header:hydrolase Chain: A: PDB Molecule:lexa repressor; PDBTitle: crystal structure of a lexa protein from thermotoga maritima 54 c1r71B_ not modelled 35.2 6 PDB header:transcription/dna Chain: B: PDB Molecule:transcriptional repressor protein korb; PDBTitle: crystal structure of the dna binding domain of korb in2 complex with the operator dna 55 d1ttya_ not modelled 35.2 10 Fold:DNA/RNA-binding 3-helical bundle Superfamily:Sigma3 and sigma4 domains of RNA polymerase sigma factors Family:Sigma4 domain 56 c2e1cA_ not modelled 34.3 15 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 57 c3exmA_ not modelled 33.4 11 PDB header:hydrolase Chain: A: PDB Molecule:phosphatase sc4828; PDBTitle: crystal structure of the phosphatase sc4828 with the non-hydrolyzable2 nucleotide gpcp 58 d2r1jl1 not modelled 32.5 13 Fold:lambda repressor-like DNA-binding domains Superfamily:lambda repressor-like DNA-binding domains Family:Phage repressors 59 d3ygsp_ not modelled 32.4 13 Fold:DEATH domain Superfamily:DEATH domain Family:Caspase recruitment domain, CARD 60 c2p6tH_ not modelled 30.8 12 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 61 c2q9lA_ not modelled 30.0 21 PDB header:hydrolase Chain: A: PDB Molecule:hypothetical protein; PDBTitle: crystal structure of imazg from vibrio dat 722: ctag-imazg (p43212) 62 c2vbzA_ not modelled 28.8 24 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 63 d1e6vb1 not modelled 28.3 22 Fold:Methyl-coenzyme M reductase alpha and beta chain C-terminal domain Superfamily:Methyl-coenzyme M reductase alpha and beta chain C-terminal domain Family:Methyl-coenzyme M reductase alpha and beta chain C-terminal domain 64 d1llib_ not modelled 27.3 12 Fold:lambda repressor-like DNA-binding domains Superfamily:lambda repressor-like DNA-binding domains Family:Phage repressors 65 d2b5aa1 not modelled 26.5 16 Fold:lambda repressor-like DNA-binding domains Superfamily:lambda repressor-like DNA-binding domains Family:SinR domain-like 66 d2f2ea1 not modelled 26.5 28 Fold:DNA/RNA-binding 3-helical bundle Superfamily:"Winged helix" DNA-binding domain Family:HxlR-like 67 d1z0xa1 not modelled 26.3 17 Fold:DNA/RNA-binding 3-helical bundle Superfamily:Homeodomain-like Family:Tetracyclin repressor-like, N-terminal domain 68 d1ui5a1 not modelled 26.3 20 Fold:DNA/RNA-binding 3-helical bundle Superfamily:Homeodomain-like Family:Tetracyclin repressor-like, N-terminal domain 69 d2vcha1 not modelled 25.9 6 Fold:UDP-Glycosyltransferase/glycogen phosphorylase Superfamily:UDP-Glycosyltransferase/glycogen phosphorylase Family:UDPGT-like 70 d1r71a_ not modelled 25.7 6 Fold:DNA/RNA-binding 3-helical bundle Superfamily:KorB DNA-binding domain-like Family:KorB DNA-binding domain-like 71 c3hugJ_ not modelled 25.7 10 PDB header:transcription/membrane protein Chain: J: PDB Molecule:probable conserved membrane protein; PDBTitle: crystal structure of mycobacterium tuberculosis anti-sigma factor rsla2 in complex with -35 promoter binding domain of sigl 72 c3kxaD_ not modelled 25.5 15 PDB header:structural genomics, unknown function Chain: D: PDB Molecule:putative uncharacterized protein; PDBTitle: crystal structure of ngo0477 from neisseria gonorrhoeae 73 d1or7a1 not modelled 25.3 25 Fold:DNA/RNA-binding 3-helical bundle Superfamily:Sigma3 and sigma4 domains of RNA polymerase sigma factors Family:Sigma4 domain 74 d2jn6a1 not modelled 25.1 20 Fold:DNA/RNA-binding 3-helical bundle Superfamily:Homeodomain-like Family:Cgl2762-like 75 c3clcC_ not modelled 25.0 4 PDB header:transcription regulator/dna Chain: C: PDB Molecule:regulatory protein; PDBTitle: crystal structure of the restriction-modification controller protein2 c.esp1396i tetramer in complex with its natural 35 base-pair operator 76 c3bhqB_ not modelled 24.8 10 PDB header:transcription Chain: B: PDB Molecule:transcriptional regulator; PDBTitle: crystal structure of a putative tetr-family transcriptional regulator2 (mlr_4833) from mesorhizobium loti maff303099 at 1.54 a resolution 77 c1nvpD_ not modelled 24.8 9 PDB header:transcription/dna Chain: D: PDB Molecule:transcription initiation factor iia gamma chain; PDBTitle: human tfiia/tbp/dna complex 78 d1adra_ not modelled 24.6 15 Fold:lambda repressor-like DNA-binding domains Superfamily:lambda repressor-like DNA-binding domains Family:Phage repressors 79 c3k0lA_ not modelled 24.6 15 PDB header:transcription regulator Chain: A: PDB Molecule:repressor protein; PDBTitle: crystal structure of putative marr family transcriptional2 regulator from acinetobacter sp. adp 80 c3mlfC_ not modelled 24.3 12 PDB header:transcription regulator Chain: C: PDB Molecule:transcriptional regulator; PDBTitle: putative transcriptional regulator from staphylococcus aureus. 81 d1kl7a_ not modelled 23.8 16 Fold:Tryptophan synthase beta subunit-like PLP-dependent enzymes Superfamily:Tryptophan synthase beta subunit-like PLP-dependent enzymes Family:Tryptophan synthase beta subunit-like PLP-dependent enzymes 82 c1e6yE_ not modelled 23.7 29 PDB header:oxidoreductase Chain: E: PDB Molecule:methyl-coenzyme m reductase i beta subunit; PDBTitle: methyl-coenzyme m reductase from methanosarcina barkeri 83 d1nh2d1 not modelled 23.7 12 Fold:Transcription factor IIA (TFIIA), alpha-helical domain Superfamily:Transcription factor IIA (TFIIA), alpha-helical domain Family:Transcription factor IIA (TFIIA), alpha-helical domain 84 d1lmb3_ not modelled 23.6 11 Fold:lambda repressor-like DNA-binding domains Superfamily:lambda repressor-like DNA-binding domains Family:Phage repressors 85 c2cfxD_ not modelled 23.6 9 PDB header:transcription Chain: D: PDB Molecule:hth-type transcriptional regulator lrpc; PDBTitle: structure of b.subtilis lrpc 86 c2k9sA_ not modelled 23.4 10 PDB header:transcription Chain: A: PDB Molecule:arabinose operon regulatory protein; PDBTitle: solution structure of dna binding domain of e. coli arac 87 c2ia0A_ not modelled 23.1 15 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) 88 c2gqqB_ not modelled 22.9 9 PDB header:transcription Chain: B: PDB Molecule:leucine-responsive regulatory protein; PDBTitle: crystal structure of e. coli leucine-responsive regulatory protein2 (lrp) 89 c1i1gA_ not modelled 22.8 18 PDB header:transcription Chain: A: PDB Molecule:transcriptional regulator lrpa; PDBTitle: crystal structure of the lrp-like transcriptional regulator from the2 archaeon pyrococcus furiosus 90 c2p8tA_ not modelled 22.3 26 PDB header:structural genomics, unknown function Chain: A: PDB Molecule:hypothetical protein ph0730; PDBTitle: hypothetical protein ph0730 from pyrococcus horikoshii ot3 91 d2h5na1 not modelled 22.2 26 Fold:TerB-like Superfamily:TerB-like Family:PG1108-like 92 c3mzyA_ not modelled 22.2 25 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 93 d1in4a1 not modelled 22.1 19 Fold:DNA/RNA-binding 3-helical bundle Superfamily:"Winged helix" DNA-binding domain Family:Helicase DNA-binding domain 94 c3oouA_ not modelled 22.1 10 PDB header:structural genomics, unknown function Chain: A: PDB Molecule:lin2118 protein; PDBTitle: the structure of a protein with unkown function from listeria innocua 95 d1sq8a_ not modelled 22.0 20 Fold:lambda repressor-like DNA-binding domains Superfamily:lambda repressor-like DNA-binding domains Family:Phage repressors 96 c2nz7A_ not modelled 21.9 8 PDB header:apoptosis Chain: A: PDB Molecule:caspase recruitment domain-containing protein 4; PDBTitle: crystal structure analysis of caspase-recruitment domain2 (card) of nod1 97 d1b0na2 not modelled 21.8 9 Fold:lambda repressor-like DNA-binding domains Superfamily:lambda repressor-like DNA-binding domains Family:SinR domain-like 98 c1bl0A_ not modelled 21.7 6 PDB header:transcription/dna Chain: A: PDB Molecule:protein (multiple antibiotic resistance protein); PDBTitle: multiple antibiotic resistance protein (mara)/dna complex 99 d1r69a_ not modelled 21.7 17 Fold:lambda repressor-like DNA-binding domains Superfamily:lambda repressor-like DNA-binding domains Family:Phage repressors 100 c3katA_ not modelled 21.6 7 PDB header:apoptosis Chain: A: PDB Molecule:nacht, lrr and pyd domains-containing protein 1; PDBTitle: crystal structure of the card domain of the human nlrp12 protein, northeast structural genomics consortium target3 hr3486e 101 c3b6aC_ not modelled 21.5 15 PDB header:transcription Chain: C: PDB Molecule:actr protein; PDBTitle: crystal structure of the streptomyces coelicolor tetr2 family protein actr in complex with actinorhodin 102 d2fq4a1 not modelled 21.4 9 Fold:DNA/RNA-binding 3-helical bundle Superfamily:Homeodomain-like Family:Tetracyclin repressor-like, N-terminal domain 103 c2b1wA_ not modelled 20.9 8 PDB header:apoptosis Chain: A: PDB Molecule:caspase recruitment domain protein 4; PDBTitle: solution structure of the nod1 caspase activating and recruitment2 domain 104 d1uxca_ not modelled 20.3 8 Fold:lambda repressor-like DNA-binding domains Superfamily:lambda repressor-like DNA-binding domains Family:GalR/LacI-like bacterial regulator 105 c1zljE_ not modelled 20.3 20 PDB header:transcription Chain: E: PDB Molecule:dormancy survival regulator; PDBTitle: crystal structure of the mycobacterium tuberculosis hypoxic2 response regulator dosr c-terminal domain 106 c4a5mH_ not modelled 20.2 19 PDB header:transcription Chain: H: PDB Molecule:uncharacterized hth-type transcriptional regulator yybr; PDBTitle: redox regulator hypr in its oxidized form 107 d1ixrc1 not modelled 20.1 17 Fold:DNA/RNA-binding 3-helical bundle Superfamily:"Winged helix" DNA-binding domain Family:Helicase DNA-binding domain 108 c3t76A_ not modelled 20.1 8 PDB header:transcription regulator Chain: A: PDB Molecule:transcriptional regulator vanug; PDBTitle: crystal structure of transcriptional regulator vanug, form ii

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