Secondary structure and disorder prediction

		1	.	.	.	.	.	.	.	.	10	.	.	.	.	.	.	.	.	.	20	.	.	.	.	.	.	.	.	.	30	.	.	.	.	.	.	.	.	.	40	.	.	.	.	.	.	.	.	.	50	.	.	.	.	.	.	.	.	.	60
Sequence		M	A	G	W	H	L	D	T	K	M	A	Q	D	I	V	A	R	T	M	R	I	I	D	T	N	I	N	V	M	D	A	R	G	R	I	I	G	S	G	D	R	E	R	I	G	E	L	H	E	G	A	L	L	V	L	S	Q	G	R	V
Secondary structure
SS confidence
Disorder		?	?	?	?	?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	70	.	.	.	.	.	.	.	.	.	80	.	.	.	.	.	.	.	.	.	90	.	.	.	.	.	.	.	.	.	100	.	.	.	.	.	.	.	.	.	110	.	.	.	.	.	.	.	.	.	120
Sequence		V	D	I	D	D	A	V	A	R	H	L	H	G	V	R	Q	G	I	N	L	P	L	R	L	E	G	E	I	V	G	V	I	G	L	T	G	E	P	E	N	L	R	K	Y	G	E	L	V	C	M	T	A	E	M	M	L	E	Q	S	R
Secondary structure
SS confidence
Disorder									?	?																																?
Disorder confidence
		.	.	.	.	.	.	.	.	.	130	.	.	.	.	.	.	.	.	.	140	.	.	.	.	.	.	.	.	.	150	.	.	.	.	.	.	.	.	.	160	.	.	.	.	.	.	.	.	.	170	.	.	.	.	.	.	.	.	.	180
Sequence		L	M	H	L	L	A	Q	D	S	R	L	R	E	E	L	V	M	N	L	I	Q	A	E	E	N	T	P	A	L	T	E	W	A	Q	R	L	G	I	D	L	N	Q	P	R	V	V	A	I	V	E	V	D	S	G	Q	L	G	V	D	S
Secondary structure
SS confidence
Disorder																																																							?	?	?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	190	.	.	.	.	.	.	.	.	.	200	.	.	.	.	.	.	.	.	.	210	.	.	.	.	.	.	.	.	.	220	.	.	.	.	.	.	.	.	.	230	.	.	.	.	.	.	.	.	.	240
Sequence		A	M	A	E	L	Q	Q	L	Q	N	A	L	T	T	P	E	R	N	N	L	V	A	I	V	S	L	T	E	M	V	V	L	K	P	A	L	N	S	F	G	R	W	D	A	E	D	H	R	K	R	V	E	Q	L	I	T	R	M	K	E
Secondary structure
SS confidence
Disorder																																						?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	250	.	.	.	.	.	.	.	.	.	260	.	.	.	.	.	.	.	.	.	270	.	.	.	.	.	.	.	.	.	280	.	.	.	.	.	.	.	.	.	290	.	.	.	.	.	.	.	.	.	300
Sequence		Y	G	Q	L	R	F	R	V	S	L	G	N	Y	F	T	G	P	G	S	I	A	R	S	Y	R	T	A	K	T	T	M	V	V	G	K	Q	R	M	P	E	S	R	C	Y	F	Y	Q	D	L	M	L	P	V	L	L	D	S	L	R	G
Secondary structure
SS confidence
Disorder
Disorder confidence
		.	.	.	.	.	.	.	.	.	310	.	.	.	.	.	.	.	.	.	320	.	.	.	.	.	.	.	.	.	330	.	.	.	.	.	.	.	.	.	340	.	.	.	.	.	.	.	.	.	350	.	.	.	.	.	.	.	.	.	360
Sequence		D	W	Q	A	N	E	L	A	R	P	L	A	R	L	K	T	M	D	N	N	G	L	L	R	R	T	L	A	A	W	F	R	H	N	V	Q	P	L	A	T	S	K	A	L	F	I	H	R	N	T	L	E	Y	R	L	N	R	I	S	E
Secondary structure
SS confidence
Disorder																	?		?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	370	.	.	.	.	.	.	.	.	.	380	.	.	.	.	.
Sequence		L	T	G	L	D	L	G	N	F	D	D	R	L	L	L	Y	V	A	L	Q	L	D	E	E	R
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 3onq chain B Region: 128 - 385 Aligned: 240 Modelled: 242 Confidence: 100.0% Identity: 16% 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 2gx5 chain B Region: 6 - 124 Aligned: 119 Modelled: 119 Confidence: 98.8% Identity: 16% PDB header:transcription Chain: B: PDB Molecule:gtp-sensing transcriptional pleiotropic repressor cody; PDBTitle: n-terminal gaf domain of transcriptional pleiotropic repressor cody Phyre2 PDB 2w1r chain A Region: 10 - 116 Aligned: 106 Modelled: 107 Confidence: 97.8% Identity: 14% PDB header:transcription Chain: A: PDB Molecule:stage v sporulation protein t; PDBTitle: crystal structure of the c-terminal domain of b. subtilis2 spovt Phyre2 PDB 3ezu chain A Region: 110 - 284 Aligned: 173 Modelled: 175 Confidence: 97.3% Identity: 14% PDB header:signaling protein Chain: A: PDB Molecule:ggdef domain protein; PDBTitle: crystal structure of multidomain protein of unknown function with2 ggdef-domain (np_951600.1) from geobacter sulfurreducens at 1.95 a3 resolution Phyre2 PDB 1fip chain A Region: 327 - 357 Aligned: 31 Modelled: 31 Confidence: 97.3% Identity: 16% Fold: DNA/RNA-binding 3-helical bundle Superfamily: Homeodomain-like Family: FIS-like Phyre2 PDB 1ntc chain A Region: 326 - 359 Aligned: 34 Modelled: 34 Confidence: 97.2% Identity: 15% Fold: DNA/RNA-binding 3-helical bundle Superfamily: Homeodomain-like Family: FIS-like Phyre2 PDB 1eto chain B Region: 300 - 357 Aligned: 58 Modelled: 58 Confidence: 97.1% Identity: 26% Fold: DNA/RNA-binding 3-helical bundle Superfamily: Homeodomain-like Family: FIS-like Phyre2 PDB 1umq chain A Region: 322 - 357 Aligned: 36 Modelled: 36 Confidence: 97.1% Identity: 19% Fold: DNA/RNA-binding 3-helical bundle Superfamily: Homeodomain-like Family: FIS-like Phyre2 PDB 1umq chain A Region: 322 - 357 Aligned: 36 Modelled: 36 Confidence: 97.1% Identity: 19% 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 1etx chain A Region: 327 - 357 Aligned: 31 Modelled: 31 Confidence: 97.0% Identity: 16% Fold: DNA/RNA-binding 3-helical bundle Superfamily: Homeodomain-like Family: FIS-like Phyre2 PDB 2w1t chain B Region: 8 - 121 Aligned: 113 Modelled: 114 Confidence: 97.0% Identity: 13% PDB header:transcription Chain: B: PDB Molecule:stage v sporulation protein t; PDBTitle: crystal structure of b. subtilis spovt Phyre2 PDB 1p0z chain A Region: 7 - 94 Aligned: 85 Modelled: 88 Confidence: 96.8% Identity: 18% Fold: Profilin-like Superfamily: Sensory domain-like Family: Sensory domain of two-component sensor kinase Phyre2 PDB 1g2h chain A Region: 325 - 357 Aligned: 33 Modelled: 33 Confidence: 96.7% Identity: 9% Fold: DNA/RNA-binding 3-helical bundle Superfamily: Homeodomain-like Family: FIS-like Phyre2 PDB 2esn chain C Region: 320 - 366 Aligned: 46 Modelled: 47 Confidence: 96.6% Identity: 20% PDB header:structural genomics, unknown function Chain: C: PDB Molecule:probable transcriptional regulator; PDBTitle: the crystal structure of probable transcriptional regulator pa04772 from pseudomonas aeruginosa Phyre2 PDB 1iz1 chain B Region: 320 - 366 Aligned: 46 Modelled: 47 Confidence: 96.4% Identity: 13% PDB header:dna binding protein Chain: B: PDB Molecule:lysr-type regulatory protein; PDBTitle: crystal structure of cbnr, a lysr family transcriptional2 regulator Phyre2 PDB 3m1e chain A Region: 320 - 366 Aligned: 46 Modelled: 47 Confidence: 96.4% Identity: 17% PDB header:transcription regulator Chain: A: PDB Molecule:hth-type transcriptional regulator benm; PDBTitle: crystal structure of benm_dbd Phyre2 PDB 2esn chain A domain 1 Region: 322 - 366 Aligned: 44 Modelled: 45 Confidence: 96.3% Identity: 20% Fold: DNA/RNA-binding 3-helical bundle Superfamily: "Winged helix" DNA-binding domain Family: LysR-like transcriptional regulators Phyre2 PDB 3e7l chain D Region: 327 - 357 Aligned: 31 Modelled: 31 Confidence: 96.2% Identity: 10% 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 3t1b chain B Region: 320 - 366 Aligned: 46 Modelled: 47 Confidence: 96.2% Identity: 20% PDB header:transcription Chain: B: PDB Molecule:transcriptional regulator, lysr family; PDBTitle: crystal structure of the full-length aphb n100e variant Phyre2 PDB 3isp chain A Region: 320 - 366 Aligned: 46 Modelled: 47 Confidence: 96.2% Identity: 20% PDB header:transcription Chain: A: PDB Molecule:hth-type transcriptional regulator PDBTitle: crystal structure of argp from mycobacterium tuberculosis Phyre2 1 c3onqB_ 2 c2gx5B_ 3 c2w1rA_ 4 c3ezuA_ 5 d1fipa_ 6 d1ntca_ 7 d1etob_ 8 d1umqa_ 9 c1umqA_ 10 d1etxa_ 11 c2w1tB_ 12 d1p0za_ 13 d1g2ha_ 14 c2esnC_ 15 c1iz1B_ 16 c3m1eA_ 17 d2esna1 18 c3e7lD_ 19 c3t1bB_ 20 c3ispA_ 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 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 239 240 241 242 243 244 245 246 247 248 249 250 251

Detailed template information

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

1 c3onqB_ 100.0 16 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 2 c2gx5B_ 98.8 16 PDB header:transcription Chain: B: PDB Molecule:gtp-sensing transcriptional pleiotropic repressor cody; PDBTitle: n-terminal gaf domain of transcriptional pleiotropic repressor cody 3 c2w1rA_ 97.8 14 PDB header:transcription Chain: A: PDB Molecule:stage v sporulation protein t; PDBTitle: crystal structure of the c-terminal domain of b. subtilis2 spovt 4 c3ezuA_ 97.3 14 PDB header:signaling protein Chain: A: PDB Molecule:ggdef domain protein; PDBTitle: crystal structure of multidomain protein of unknown function with2 ggdef-domain (np_951600.1) from geobacter sulfurreducens at 1.95 a3 resolution 5 d1fipa_ 97.3 16 Fold:DNA/RNA-binding 3-helical bundle Superfamily:Homeodomain-like Family:FIS-like 6 d1ntca_ 97.2 15 Fold:DNA/RNA-binding 3-helical bundle Superfamily:Homeodomain-like Family:FIS-like 7 d1etob_ 97.1 26 Fold:DNA/RNA-binding 3-helical bundle Superfamily:Homeodomain-like Family:FIS-like 8 d1umqa_ 97.1 19 Fold:DNA/RNA-binding 3-helical bundle Superfamily:Homeodomain-like Family:FIS-like 9 c1umqA_ 97.1 19 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 10 d1etxa_ 97.0 16 Fold:DNA/RNA-binding 3-helical bundle Superfamily:Homeodomain-like Family:FIS-like 11 c2w1tB_ 97.0 13 PDB header:transcription Chain: B: PDB Molecule:stage v sporulation protein t; PDBTitle: crystal structure of b. subtilis spovt 12 d1p0za_ 96.8 18 Fold:Profilin-like Superfamily:Sensory domain-like Family:Sensory domain of two-component sensor kinase 13 d1g2ha_ 96.7 9 Fold:DNA/RNA-binding 3-helical bundle Superfamily:Homeodomain-like Family:FIS-like 14 c2esnC_ 96.6 20 PDB header:structural genomics, unknown function Chain: C: PDB Molecule:probable transcriptional regulator; PDBTitle: the crystal structure of probable transcriptional regulator pa04772 from pseudomonas aeruginosa 15 c1iz1B_ 96.4 13 PDB header:dna binding protein Chain: B: PDB Molecule:lysr-type regulatory protein; PDBTitle: crystal structure of cbnr, a lysr family transcriptional2 regulator 16 c3m1eA_ 96.4 17 PDB header:transcription regulator Chain: A: PDB Molecule:hth-type transcriptional regulator benm; PDBTitle: crystal structure of benm_dbd 17 d2esna1 96.3 20 Fold:DNA/RNA-binding 3-helical bundle Superfamily:"Winged helix" DNA-binding domain Family:LysR-like transcriptional regulators 18 c3e7lD_ 96.2 10 PDB header:transcription regulator Chain: D: PDB Molecule:transcriptional regulator (ntrc family); PDBTitle: crystal structure of sigma54 activator ntrc4's dna binding2 domain 19 c3t1bB_ 96.2 20 PDB header:transcription Chain: B: PDB Molecule:transcriptional regulator, lysr family; PDBTitle: crystal structure of the full-length aphb n100e variant 20 c3ispA_ 96.2 20 PDB header:transcription Chain: A: PDB Molecule:hth-type transcriptional regulator PDBTitle: crystal structure of argp from mycobacterium tuberculosis 21 c3breA_ not modelled 96.1 13 PDB header:signaling protein Chain: A: PDB Molecule:probable two-component response regulator; PDBTitle: crystal structure of p.aeruginosa pa3702 22 c3fzjC_ not modelled 95.9 11 PDB header:transcription regulator Chain: C: PDB Molecule:lysr type regulator of tsambcd; PDBTitle: tsar low resolution crystal structure, tetragonal form 23 c3hhgF_ not modelled 95.8 13 PDB header:transcription regulator Chain: F: PDB Molecule:transcriptional regulator, lysr family; PDBTitle: structure of crga, a lysr-type transcriptional regulator from2 neisseria meningitidis. 24 c2vjwA_ not modelled 95.8 11 PDB header:hydrolase Chain: A: PDB Molecule:gaf family protein; PDBTitle: crystal structure of the second gaf domain of devs from2 mycobacterium smegmatis 25 d1b9ma1 not modelled 95.7 13 Fold:DNA/RNA-binding 3-helical bundle Superfamily:"Winged helix" DNA-binding domain Family:N-terminal domain of molybdate-dependent transcriptional regulator ModE 26 d1ixca1 not modelled 95.6 14 Fold:DNA/RNA-binding 3-helical bundle Superfamily:"Winged helix" DNA-binding domain Family:LysR-like transcriptional regulators 27 c3fzvC_ not modelled 95.6 14 PDB header:transcription regulator Chain: C: PDB Molecule:probable transcriptional regulator; PDBTitle: crystal structure of pa01 protein, putative lysr family2 transcriptional regulator from pseudomonas aeruginosa 28 c1w25B_ not modelled 95.6 12 PDB header:signaling protein Chain: B: PDB Molecule:stalked-cell differentiation controlling protein; PDBTitle: response regulator pled in complex with c-digmp 29 d3by8a1 not modelled 95.2 20 Fold:Profilin-like Superfamily:Sensory domain-like Family:Sensory domain of two-component sensor kinase 30 c1b9nA_ not modelled 94.7 14 PDB header:transcription Chain: A: PDB Molecule:protein (mode); PDBTitle: regulator from escherichia coli 31 c3fpvC_ not modelled 93.9 16 PDB header:heme binding protein Chain: C: PDB Molecule:extracellular haem-binding protein; PDBTitle: crystal structure of hbps 32 c1zljE_ not modelled 93.4 10 PDB header:transcription Chain: E: PDB Molecule:dormancy survival regulator; PDBTitle: crystal structure of the mycobacterium tuberculosis hypoxic2 response regulator dosr c-terminal domain 33 c3eeaB_ not modelled 93.3 12 PDB header:structural genomics, unknown function Chain: B: PDB Molecule:gaf domain/hd domain protein; PDBTitle: the crystal structure of the gaf domain/hd domain protein2 from geobacter sulfurreducens 34 c3mmhA_ not modelled 93.2 18 PDB header:oxidoreductase Chain: A: PDB Molecule:methionine-r-sulfoxide reductase; PDBTitle: x-ray structure of free methionine-r-sulfoxide reductase from2 neisseria meningitidis in complex with its substrate 35 d1a04a1 not modelled 92.3 11 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) 36 c2ijlB_ not modelled 92.3 4 PDB header:transcription Chain: B: PDB Molecule:molybdenum-binding transcriptional repressor; PDBTitle: the structure of a putative mode from agrobacterium tumefaciens. 37 d2veaa1 not modelled 92.2 16 Fold:Profilin-like Superfamily:GAF domain-like Family:GAF domain 38 c2rnjA_ not modelled 91.7 10 PDB header:transcription Chain: A: PDB Molecule:response regulator protein vrar; PDBTitle: nmr structure of the s. aureus vrar dna binding domain 39 d1rp3a2 not modelled 91.6 9 Fold:DNA/RNA-binding 3-helical bundle Superfamily:Sigma3 and sigma4 domains of RNA polymerase sigma factors Family:Sigma4 domain 40 c3hugA_ not modelled 91.3 17 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 41 d1p4wa_ not modelled 91.2 14 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) 42 c3e0yA_ not modelled 91.1 15 PDB header:structural genomics, unknown function Chain: A: PDB Molecule:conserved domain protein; PDBTitle: the crystal structure of a conserved domain from a protein of2 geobacter sulfurreducens pca 43 c3ibjB_ not modelled 91.0 15 PDB header:hydrolase Chain: B: PDB Molecule:cgmp-dependent 3',5'-cyclic phosphodiesterase; PDBTitle: x-ray structure of pde2a 44 d1l3la1 not modelled 91.0 8 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) 45 d1yioa1 not modelled 90.9 10 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) 46 c3qp5C_ not modelled 90.7 12 PDB header:transcription Chain: C: PDB Molecule:cvir transcriptional regulator; PDBTitle: crystal structure of cvir bound to antagonist chlorolactone (cl) 47 c3hcyB_ not modelled 90.1 10 PDB header:structural genomics, unknown function Chain: B: PDB Molecule:putative two-component sensor histidine kinase protein; PDBTitle: the crystal structure of the domain of putative two-component sensor2 histidine kinase protein from sinorhizobium meliloti 1021 48 d1fsea_ not modelled 90.0 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) 49 d1or7a1 not modelled 89.6 12 Fold:DNA/RNA-binding 3-helical bundle Superfamily:Sigma3 and sigma4 domains of RNA polymerase sigma factors Family:Sigma4 domain 50 c2krfB_ not modelled 89.5 17 PDB header:transcription Chain: B: PDB Molecule:transcriptional regulatory protein coma; PDBTitle: nmr solution structure of the dna binding domain of competence protein2 a 51 c3sztB_ not modelled 89.4 11 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 52 c3iclA_ not modelled 89.1 14 PDB header:structural genomics, unknown function Chain: A: PDB Molecule:eal/ggdef domain protein; PDBTitle: x-ray structure of protein (eal/ggdef domain protein) from2 m.capsulatus, northeast structural genomics consortium3 target mcr174c 53 c3mtkA_ not modelled 88.7 10 PDB header:transferase Chain: A: PDB Molecule:diguanylate cyclase/phosphodiesterase; PDBTitle: x-ray structure of diguanylate cyclase/phosphodiesterase from2 caldicellulosiruptor saccharolyticus, northeast structural genomics3 consortium target clr27c 54 d2coba1 not modelled 88.6 16 Fold:DNA/RNA-binding 3-helical bundle Superfamily:Homeodomain-like Family:Psq domain 55 c3c2wB_ not modelled 88.5 11 PDB header:signaling protein Chain: B: PDB Molecule:bacteriophytochrome; PDBTitle: crystal structure of the photosensory core domain of p.2 aeruginosa bacteriophytochrome pabphp in the pfr state 56 c3i5aA_ not modelled 88.2 12 PDB header:signaling protein Chain: A: PDB Molecule:response regulator/ggdef domain protein; PDBTitle: crystal structure of full-length wpsr from pseudomonas syringae 57 c3ksiA_ not modelled 88.1 13 PDB header:oxidoreductase Chain: A: PDB Molecule:putative uncharacterized protein; PDBTitle: structure of frmsr of staphylococcus aureus (complex with 2-propanol) 58 d2cg4a1 not modelled 88.1 12 Fold:DNA/RNA-binding 3-helical bundle Superfamily:"Winged helix" DNA-binding domain Family:Lrp/AsnC-like transcriptional regulator N-terminal domain 59 c1h0mD_ not modelled 87.5 8 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 60 c2q0oA_ not modelled 87.4 13 PDB header:transcription Chain: A: PDB Molecule:probable transcriptional activator protein trar; PDBTitle: crystal structure of an anti-activation complex in bacterial quorum2 sensing 61 c3p01C_ not modelled 87.4 15 PDB header:signaling protein Chain: C: PDB Molecule:two-component response regulator; PDBTitle: crystal structure of two-component response regulator from nostoc sp.2 pcc 7120 62 c3ignA_ not modelled 87.2 13 PDB header:transferase Chain: A: PDB Molecule:diguanylate cyclase; PDBTitle: crystal structure of the ggdef domain from marinobacter2 aquaeolei diguanylate cyclase complexed with c-di-gmp -3 northeast structural genomics consortium target mqr89a 63 c3o5yA_ not modelled 87.2 10 PDB header:transcription regulator Chain: A: PDB Molecule:sensor protein; PDBTitle: the crystal structure of the gaf domain of a two-component sensor2 histidine kinase from bacillus halodurans to 2.45a 64 c1x3uA_ not modelled 87.0 11 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 65 c3cloC_ not modelled 86.4 17 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 66 c2jpcA_ not modelled 85.9 14 PDB header:dna binding protein Chain: A: PDB Molecule:ssrb; PDBTitle: ssrb dna binding protein 67 d2cfxa1 not modelled 85.8 3 Fold:DNA/RNA-binding 3-helical bundle Superfamily:"Winged helix" DNA-binding domain Family:Lrp/AsnC-like transcriptional regulator N-terminal domain 68 d2a2la1 not modelled 85.6 18 Fold:Profilin-like Superfamily:GlcG-like Family:GlcG-like 69 c3fosA_ not modelled 85.2 14 PDB header:transferase Chain: A: PDB Molecule:sensor protein; PDBTitle: crystal structure of two-component sensor histidine kinase domain from2 bacillus subtilis subsp. subtilis str. 168 70 c2cfxD_ not modelled 85.1 3 PDB header:transcription Chain: D: PDB Molecule:hth-type transcriptional regulator lrpc; PDBTitle: structure of b.subtilis lrpc 71 c2vbzA_ not modelled 84.7 7 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 72 d1xsva_ not modelled 84.3 11 Fold:DNA/RNA-binding 3-helical bundle Superfamily:Sigma3 and sigma4 domains of RNA polymerase sigma factors Family:YlxM/p13-like 73 d1i1ga1 not modelled 84.0 17 Fold:DNA/RNA-binding 3-helical bundle Superfamily:"Winged helix" DNA-binding domain Family:Lrp/AsnC-like transcriptional regulator N-terminal domain 74 c2p6tH_ not modelled 83.9 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 75 d2cyya1 not modelled 83.5 17 Fold:DNA/RNA-binding 3-helical bundle Superfamily:"Winged helix" DNA-binding domain Family:Lrp/AsnC-like transcriptional regulator N-terminal domain 76 c2o8xA_ not modelled 83.3 12 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 77 c2cg4B_ not modelled 83.2 16 PDB header:transcription Chain: B: PDB Molecule:regulatory protein asnc; PDBTitle: structure of e.coli asnc 78 c2l4aA_ not modelled 83.2 14 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 79 d1s7oa_ not modelled 83.2 5 Fold:DNA/RNA-binding 3-helical bundle Superfamily:Sigma3 and sigma4 domains of RNA polymerase sigma factors Family:YlxM/p13-like 80 c3i5bA_ not modelled 83.2 13 PDB header:signaling protein Chain: A: PDB Molecule:wspr response regulator; PDBTitle: crystal structure of the isolated ggdef domain of wpsr from2 pseudomonas aeruginosa 81 c3trcA_ not modelled 82.5 16 PDB header:transferase Chain: A: PDB Molecule:phosphoenolpyruvate-protein phosphotransferase; PDBTitle: structure of the gaf domain from a phosphoenolpyruvate-protein2 phosphotransferase (ptsp) from coxiella burnetii 82 d1ulya_ not modelled 82.5 16 Fold:DNA/RNA-binding 3-helical bundle Superfamily:"Winged helix" DNA-binding domain Family:Hypothetical protein PH1932 83 c2e7xA_ not modelled 81.9 18 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 d1w25a3 not modelled 81.4 13 Fold:Ferredoxin-like Superfamily:Nucleotide cyclase Family:GGDEF domain 85 c3i4pA_ not modelled 81.3 9 PDB header:transcription regulator Chain: A: PDB Molecule:transcriptional regulator, asnc family; PDBTitle: crystal structure of asnc family transcriptional regulator from2 agrobacterium tumefaciens 86 c1bl0A_ not modelled 81.1 17 PDB header:transcription/dna Chain: A: PDB Molecule:protein (multiple antibiotic resistance protein); PDBTitle: multiple antibiotic resistance protein (mara)/dna complex 87 c3hyiA_ not modelled 79.9 18 PDB header:transcription regulator Chain: A: PDB Molecule:protein duf199/whia; PDBTitle: crystal structure of full-length duf199/whia from thermatoga maritima 88 d2jn6a1 not modelled 79.8 21 Fold:DNA/RNA-binding 3-helical bundle Superfamily:Homeodomain-like Family:Cgl2762-like 89 c2dbbA_ not modelled 78.6 10 PDB header:transcriptional regulator Chain: A: PDB Molecule:putative hth-type transcriptional regulator ph0061; PDBTitle: crystal structure of ph0061 90 d1i3ja_ not modelled 78.0 14 Fold:DNA-binding domain of intron-encoded endonucleases Superfamily:DNA-binding domain of intron-encoded endonucleases Family:DNA-binding domain of intron-encoded endonucleases 91 c3klnC_ not modelled 77.8 11 PDB header:transcription Chain: C: PDB Molecule:transcriptional regulator, luxr family; PDBTitle: vibrio cholerae vpst 92 c1rp3G_ not modelled 77.6 9 PDB header:transcription Chain: G: PDB Molecule:rna polymerase sigma factor sigma-28 (flia); PDBTitle: cocrystal structure of the flagellar sigma/anti-sigma2 complex, sigma-28/flgm 93 c2k9sA_ not modelled 77.4 9 PDB header:transcription Chain: A: PDB Molecule:arabinose operon regulatory protein; PDBTitle: solution structure of dna binding domain of e. coli arac 94 c3mzyA_ not modelled 76.6 7 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 95 c2e1cA_ not modelled 76.0 17 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 96 c1i1gA_ not modelled 75.9 17 PDB header:transcription Chain: A: PDB Molecule:transcriptional regulator lrpa; PDBTitle: crystal structure of the lrp-like transcriptional regulator from the2 archaeon pyrococcus furiosus 97 c3i5cA_ not modelled 75.5 15 PDB header:signaling protein Chain: A: PDB Molecule:fusion of general control protein gcn4 and wspr response PDBTitle: crystal structure of a fusion protein containing the leucine zipper of2 gcn4 and the ggdef domain of wspr from pseudomonas aeruginosa 98 c1or7A_ not modelled 75.1 12 PDB header:transcription Chain: A: PDB Molecule:rna polymerase sigma-e factor; PDBTitle: crystal structure of escherichia coli sigmae with the cytoplasmic2 domain of its anti-sigma rsea 99 d1mc0a1 not modelled 74.6 9 Fold:Profilin-like Superfamily:GAF domain-like Family:GAF domain 100 c3cuoB_ not modelled 73.9 8 PDB header:transcription regulator Chain: B: PDB Molecule:uncharacterized hth-type transcriptional regulator ygav; PDBTitle: crystal structure of the predicted dna-binding transcriptional2 regulator from e. coli 101 c2gqqB_ not modelled 73.8 12 PDB header:transcription Chain: B: PDB Molecule:leucine-responsive regulatory protein; PDBTitle: crystal structure of e. coli leucine-responsive regulatory protein2 (lrp) 102 c3ci6B_ not modelled 72.8 14 PDB header:transferase Chain: B: PDB Molecule:phosphoenolpyruvate-protein phosphotransferase; PDBTitle: crystal structure of the gaf domain from acinetobacter2 phosphoenolpyruvate-protein phosphotransferase 103 c2ia0A_ not modelled 72.7 17 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) 104 c1u78A_ not modelled 72.2 19 PDB header:dna binding protein/dna Chain: A: PDB Molecule:transposable element tc3 transposase; PDBTitle: structure of the bipartite dna-binding domain of tc32 transposase bound to transposon dna 105 c3pjwA_ not modelled 72.2 11 PDB header:lyase Chain: A: PDB Molecule:cyclic dimeric gmp binding protein; PDBTitle: structure of pseudomonas fluorescence lapd ggdef-eal dual domain, i23 106 c2q1zA_ not modelled 71.3 16 PDB header:transcription Chain: A: PDB Molecule:rpoe, ecf sige; PDBTitle: crystal structure of rhodobacter sphaeroides sige in complex with the2 anti-sigma chrr 107 d1jhfa1 not modelled 70.5 10 Fold:DNA/RNA-binding 3-helical bundle Superfamily:"Winged helix" DNA-binding domain Family:LexA repressor, N-terminal DNA-binding domain 108 d1vhma_ not modelled 70.5 16 Fold:Profilin-like Superfamily:GAF domain-like Family:GAF domain 109 c1vhmB_ not modelled 70.2 17 PDB header:structural genomics, unknown function Chain: B: PDB Molecule:protein yebr; PDBTitle: crystal structure of an hypothetical protein 110 d2p4wa1 not modelled 70.1 19 Fold:DNA/RNA-binding 3-helical bundle Superfamily:"Winged helix" DNA-binding domain Family:PF1790-like 111 c1rnlA_ not modelled 70.0 11 PDB header:signal transduction protein Chain: A: PDB Molecule:nitrate/nitrite response regulator protein narl; PDBTitle: the nitrate/nitrite response regulator protein narl from narl 112 c1zn2A_ not modelled 68.6 9 PDB header:transcription regulator Chain: A: PDB Molecule:response regulatory protein; PDBTitle: low resolution structure of response regulator styr 113 c3c3wB_ not modelled 68.2 16 PDB header:transcription Chain: B: PDB Molecule:two component transcriptional regulatory protein devr; PDBTitle: crystal structure of the mycobacterium tuberculosis hypoxic response2 regulator dosr 114 c3e98B_ not modelled 67.5 8 PDB header:unknown function Chain: B: PDB Molecule:gaf domain of unknown function; PDBTitle: crystal structure of a gaf domain containing protein that belongs to2 pfam duf484 family (pa5279) from pseudomonas aeruginosa at 2.43 a3 resolution 115 c2jscB_ not modelled 67.5 19 PDB header:transcription Chain: B: PDB Molecule:transcriptional regulator rv1994c/mt2050; PDBTitle: nmr structure of the cadmium metal-sensor cmtr from mycobacterium2 tuberculosis 116 d2oola1 not modelled 67.0 15 Fold:Profilin-like Superfamily:GAF domain-like Family:GAF domain 117 c2o9bA_ not modelled 66.4 18 PDB header:transferase Chain: A: PDB Molecule:bacteriophytochrome; PDBTitle: crystal structure of bacteriophytochrome chromophore binding domain 118 c3hvwA_ not modelled 66.1 10 PDB header:lyase Chain: A: PDB Molecule:diguanylate-cyclase (dgc); PDBTitle: crystal structure of the ggdef domain of the pa2567 protein2 from pseudomonas aeruginosa, northeast structural genomics3 consortium target par365c 119 d2o9ca1 not modelled 66.0 16 Fold:Profilin-like Superfamily:GAF domain-like Family:GAF domain 120 c3p01A_ not modelled 65.5 15 PDB header:signaling protein Chain: A: PDB Molecule:two-component response regulator; PDBTitle: crystal structure of two-component response regulator from nostoc sp.2 pcc 7120

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