Secondary structure and disorder prediction

		1	.	.	.	.	.	.	.	.	10	.	.	.	.	.	.	.	.	.	20	.	.	.	.	.	.	.	.	.	30	.	.	.	.	.	.	.	.	.	40	.	.	.	.	.	.	.	.	.	50	.	.	.	.	.	.	.	.	.	60
Sequence		M	A	Q	Q	S	P	Y	S	A	A	M	A	E	Q	R	H	Q	E	W	L	R	F	V	D	L	L	K	N	A	Y	Q	N	D	L	H	L	P	L	L	N	L	M	L	T	P	D	E	R	E	A	L	G	T	R	V	R	I	V	E	E
Secondary structure
SS confidence
Disorder		?	?	?	?	?	?	?	?				?	?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	70	.	.	.	.	.	.	.	.	.	80	.	.	.	.	.	.	.	.	.	90	.	.	.	.	.	.	.	.	.	100	.	.	.	.	.	.	.	.
Sequence		L	L	R	G	E	M	S	Q	R	E	L	K	N	E	L	G	A	G	I	A	T	I	T	R	G	S	N	S	L	K	A	A	P	V	E	L	R	Q	W	L	E	E	V	L	L	K	S	D
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 1trr chain A Region: 2 - 105 Aligned: 104 Modelled: 104 Confidence: 100.0% Identity: 99% Fold: DNA/RNA-binding 3-helical bundle Superfamily: TrpR-like Family: Trp repressor, TrpR Phyre2 PDB 1jhg chain A Region: 8 - 108 Aligned: 101 Modelled: 101 Confidence: 100.0% Identity: 99% Fold: DNA/RNA-binding 3-helical bundle Superfamily: TrpR-like Family: Trp repressor, TrpR Phyre2 PDB 3kor chain D Region: 8 - 108 Aligned: 100 Modelled: 101 Confidence: 100.0% Identity: 17% PDB header:transcription Chain: D: PDB Molecule:possible trp repressor; PDBTitle: crystal structure of a putative trp repressor from staphylococcus2 aureus Phyre2 PDB 3frw chain F Region: 13 - 106 Aligned: 93 Modelled: 94 Confidence: 100.0% Identity: 17% PDB header:structural genomics, unknown function Chain: F: PDB Molecule:putative trp repressor protein; PDBTitle: crystal structure of putative trpr protein from ruminococcus obeum Phyre2 PDB 1rio chain A Region: 43 - 104 Aligned: 60 Modelled: 62 Confidence: 95.3% Identity: 23% Fold: lambda repressor-like DNA-binding domains Superfamily: lambda repressor-like DNA-binding domains Family: Phage repressors Phyre2 PDB 1u78 chain A Region: 53 - 84 Aligned: 31 Modelled: 32 Confidence: 95.2% Identity: 13% 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 Phyre2 PDB 3szt chain B Region: 43 - 82 Aligned: 32 Modelled: 40 Confidence: 95.1% Identity: 22% 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 Phyre2 PDB 1r71 chain A Region: 43 - 101 Aligned: 52 Modelled: 59 Confidence: 95.0% Identity: 25% Fold: DNA/RNA-binding 3-helical bundle Superfamily: KorB DNA-binding domain-like Family: KorB DNA-binding domain-like Phyre2 PDB 2bjc chain A domain 1 Region: 64 - 108 Aligned: 45 Modelled: 45 Confidence: 94.7% Identity: 16% Fold: lambda repressor-like DNA-binding domains Superfamily: lambda repressor-like DNA-binding domains Family: GalR/LacI-like bacterial regulator Phyre2 PDB 1lcd chain A Region: 64 - 108 Aligned: 45 Modelled: 45 Confidence: 94.7% Identity: 13% Fold: lambda repressor-like DNA-binding domains Superfamily: lambda repressor-like DNA-binding domains Family: GalR/LacI-like bacterial regulator Phyre2 PDB 1s7o chain A Region: 33 - 91 Aligned: 52 Modelled: 59 Confidence: 94.6% Identity: 13% Fold: DNA/RNA-binding 3-helical bundle Superfamily: Sigma3 and sigma4 domains of RNA polymerase sigma factors Family: YlxM/p13-like Phyre2 PDB 1qpz chain A domain 1 Region: 67 - 108 Aligned: 42 Modelled: 42 Confidence: 94.5% Identity: 10% Fold: lambda repressor-like DNA-binding domains Superfamily: lambda repressor-like DNA-binding domains Family: GalR/LacI-like bacterial regulator Phyre2 PDB 1bdh chain A Region: 67 - 106 Aligned: 40 Modelled: 40 Confidence: 94.4% Identity: 10% PDB header:transcription/dna Chain: A: PDB Molecule:protein (purine repressor); PDBTitle: purine repressor mutant-hypoxanthine-palindromic operator2 complex Phyre2 PDB 1efa chain A domain 1 Region: 64 - 108 Aligned: 45 Modelled: 45 Confidence: 94.4% Identity: 13% Fold: lambda repressor-like DNA-binding domains Superfamily: lambda repressor-like DNA-binding domains Family: GalR/LacI-like bacterial regulator Phyre2 PDB 3iwf chain A Region: 43 - 92 Aligned: 48 Modelled: 50 Confidence: 94.4% Identity: 17% 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 Phyre2 PDB 1r22 chain B Region: 33 - 93 Aligned: 54 Modelled: 61 Confidence: 94.3% Identity: 20% PDB header:transcription repressor Chain: B: PDB Molecule:transcriptional repressor smtb; PDBTitle: crystal structure of the cyanobacterial metallothionein2 repressor smtb (c14s/c61s/c121s mutant) in the zn2alpha5-3 form Phyre2 PDB 2ofy chain A domain 1 Region: 43 - 84 Aligned: 41 Modelled: 42 Confidence: 94.2% Identity: 27% Fold: lambda repressor-like DNA-binding domains Superfamily: lambda repressor-like DNA-binding domains Family: SinR domain-like Phyre2 PDB 6pax chain A Region: 51 - 91 Aligned: 40 Modelled: 41 Confidence: 94.2% Identity: 25% PDB header:gene regulation/dna Chain: A: PDB Molecule:homeobox protein pax-6; PDBTitle: crystal structure of the human pax-6 paired domain-dna2 complex reveals a general model for pax protein-dna3 interactions Phyre2 PDB 2q0o chain A Region: 43 - 82 Aligned: 32 Modelled: 40 Confidence: 94.1% Identity: 22% PDB header:transcription Chain: A: PDB Molecule:probable transcriptional activator protein trar; PDBTitle: crystal structure of an anti-activation complex in bacterial quorum2 sensing Phyre2 PDB 2oqg chain A Region: 33 - 92 Aligned: 53 Modelled: 60 Confidence: 94.1% Identity: 25% PDB header:transcription Chain: A: PDB Molecule:possible transcriptional regulator, arsr family protein; PDBTitle: arsr-like transcriptional regulator from rhodococcus sp. rha1 Phyre2 1 d1trra_ 2 d1jhga_ 3 c3korD_ 4 c3frwF_ 5 d1rioa_ 6 c1u78A_ 7 c3sztB_ 8 d1r71a_ 9 d2bjca1 10 d1lcda_ 11 d1s7oa_ 12 d1qpza1 13 c1bdhA_ 14 d1efaa1 15 c3iwfA_ 16 c1r22B_ 17 d2ofya1 18 c6paxA_ 19 c2q0oA_ 20 c2oqgA_ 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 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 239 240 241 242 243 244 245 246 247 248 249 250 251 252 253 254 255 256 257 258 259 260 261 262 263 264 265 266 267 268 269 270 271 272 273 274 275 276 277 278 279 280 281 282 283 284 285 286 287 288 289 290 291 292 293 294 295 296 297 298 299 300 301 302 303 304 305 306 307 308 309 310 311 312 313 314 315 316 317 318 319 320 321 322 323 324 325 326

Detailed template information

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

1 d1trra_ 100.0 99 Fold:DNA/RNA-binding 3-helical bundle Superfamily:TrpR-like Family:Trp repressor, TrpR 2 d1jhga_ 100.0 99 Fold:DNA/RNA-binding 3-helical bundle Superfamily:TrpR-like Family:Trp repressor, TrpR 3 c3korD_ 100.0 17 PDB header:transcription Chain: D: PDB Molecule:possible trp repressor; PDBTitle: crystal structure of a putative trp repressor from staphylococcus2 aureus 4 c3frwF_ 100.0 17 PDB header:structural genomics, unknown function Chain: F: PDB Molecule:putative trp repressor protein; PDBTitle: crystal structure of putative trpr protein from ruminococcus obeum 5 d1rioa_ 95.3 23 Fold:lambda repressor-like DNA-binding domains Superfamily:lambda repressor-like DNA-binding domains Family:Phage repressors 6 c1u78A_ 95.2 13 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 7 c3sztB_ 95.1 22 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 8 d1r71a_ 95.0 25 Fold:DNA/RNA-binding 3-helical bundle Superfamily:KorB DNA-binding domain-like Family:KorB DNA-binding domain-like 9 d2bjca1 94.7 16 Fold:lambda repressor-like DNA-binding domains Superfamily:lambda repressor-like DNA-binding domains Family:GalR/LacI-like bacterial regulator 10 d1lcda_ 94.7 13 Fold:lambda repressor-like DNA-binding domains Superfamily:lambda repressor-like DNA-binding domains Family:GalR/LacI-like bacterial regulator 11 d1s7oa_ 94.6 13 Fold:DNA/RNA-binding 3-helical bundle Superfamily:Sigma3 and sigma4 domains of RNA polymerase sigma factors Family:YlxM/p13-like 12 d1qpza1 94.5 10 Fold:lambda repressor-like DNA-binding domains Superfamily:lambda repressor-like DNA-binding domains Family:GalR/LacI-like bacterial regulator 13 c1bdhA_ 94.4 10 PDB header:transcription/dna Chain: A: PDB Molecule:protein (purine repressor); PDBTitle: purine repressor mutant-hypoxanthine-palindromic operator2 complex 14 d1efaa1 94.4 13 Fold:lambda repressor-like DNA-binding domains Superfamily:lambda repressor-like DNA-binding domains Family:GalR/LacI-like bacterial regulator 15 c3iwfA_ 94.4 17 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 16 c1r22B_ 94.3 20 PDB header:transcription repressor Chain: B: PDB Molecule:transcriptional repressor smtb; PDBTitle: crystal structure of the cyanobacterial metallothionein2 repressor smtb (c14s/c61s/c121s mutant) in the zn2alpha5-3 form 17 d2ofya1 94.2 27 Fold:lambda repressor-like DNA-binding domains Superfamily:lambda repressor-like DNA-binding domains Family:SinR domain-like 18 c6paxA_ 94.2 25 PDB header:gene regulation/dna Chain: A: PDB Molecule:homeobox protein pax-6; PDBTitle: crystal structure of the human pax-6 paired domain-dna2 complex reveals a general model for pax protein-dna3 interactions 19 c2q0oA_ 94.1 22 PDB header:transcription Chain: A: PDB Molecule:probable transcriptional activator protein trar; PDBTitle: crystal structure of an anti-activation complex in bacterial quorum2 sensing 20 c2oqgA_ 94.1 25 PDB header:transcription Chain: A: PDB Molecule:possible transcriptional regulator, arsr family protein; PDBTitle: arsr-like transcriptional regulator from rhodococcus sp. rha1 21 c1r71B_ not modelled 94.1 17 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 22 c3h5tA_ not modelled 94.0 18 PDB header:transcription regulator Chain: A: PDB Molecule:transcriptional regulator, laci family; PDBTitle: crystal structure of a transcriptional regulator, lacl2 family protein from corynebacterium glutamicum 23 d2hsga1 not modelled 94.0 16 Fold:lambda repressor-like DNA-binding domains Superfamily:lambda repressor-like DNA-binding domains Family:GalR/LacI-like bacterial regulator 24 d1xsva_ not modelled 94.0 13 Fold:DNA/RNA-binding 3-helical bundle Superfamily:Sigma3 and sigma4 domains of RNA polymerase sigma factors Family:YlxM/p13-like 25 c2krfB_ not modelled 93.9 26 PDB header:transcription Chain: B: PDB Molecule:transcriptional regulatory protein coma; PDBTitle: nmr solution structure of the dna binding domain of competence protein2 a 26 c2w48D_ not modelled 93.9 28 PDB header:transcription Chain: D: PDB Molecule:sorbitol operon regulator; PDBTitle: crystal structure of the full-length sorbitol operon2 regulator sorc from klebsiella pneumoniae 27 d1pdnc_ not modelled 93.8 15 Fold:DNA/RNA-binding 3-helical bundle Superfamily:Homeodomain-like Family:Paired domain 28 d1vz0a1 not modelled 93.7 24 Fold:DNA/RNA-binding 3-helical bundle Superfamily:KorB DNA-binding domain-like Family:KorB DNA-binding domain-like 29 c1zvvA_ not modelled 93.6 17 PDB header:transcription/dna Chain: A: PDB Molecule:glucose-resistance amylase regulator; PDBTitle: crystal structure of a ccpa-crh-dna complex 30 d1uxca_ not modelled 93.6 14 Fold:lambda repressor-like DNA-binding domains Superfamily:lambda repressor-like DNA-binding domains Family:GalR/LacI-like bacterial regulator 31 d1k78a1 not modelled 93.5 21 Fold:DNA/RNA-binding 3-helical bundle Superfamily:Homeodomain-like Family:Paired domain 32 c3f6oB_ not modelled 93.5 17 PDB header:transcription regulator Chain: B: PDB Molecule:probable transcriptional regulator, arsr family PDBTitle: crystal structure of arsr family transcriptional regulator,2 rha00566 33 d1l3la1 not modelled 93.5 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) 34 c2jvlA_ not modelled 93.4 21 PDB header:transcription Chain: A: PDB Molecule:trmbf1; PDBTitle: nmr structure of the c-terminal domain of mbf1 of trichoderma reesei 35 d1fsea_ not modelled 93.4 29 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 c1zx4B_ not modelled 93.4 21 PDB header:translation Chain: B: PDB Molecule:plasmid partition par b protein; PDBTitle: structure of parb bound to dna 37 c1y9qA_ not modelled 93.4 10 PDB header:transcription regulator Chain: A: PDB Molecule:transcriptional regulator, hth_3 family; PDBTitle: crystal structure of hth_3 family transcriptional regulator2 from vibrio cholerae 38 c3f6vA_ not modelled 93.3 29 PDB header:transcription regulator Chain: A: PDB Molecule:possible transcriptional regulator, arsr family PDBTitle: crystal structure of possible transcriptional regulator for2 arsenical resistance 39 c3eusB_ not modelled 93.2 16 PDB header:dna binding protein Chain: B: PDB Molecule:dna-binding protein; PDBTitle: the crystal structure of the dna binding protein from silicibacter2 pomeroyi 40 c1x3uA_ not modelled 93.1 13 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 41 c2bnoA_ not modelled 93.0 15 PDB header:oxidoreductase Chain: A: PDB Molecule:epoxidase; PDBTitle: the structure of hydroxypropylphosphonic acid epoxidase2 from s. wedmorenis. 42 d1uxda_ not modelled 93.0 14 Fold:lambda repressor-like DNA-binding domains Superfamily:lambda repressor-like DNA-binding domains Family:GalR/LacI-like bacterial regulator 43 c2lcvA_ not modelled 93.0 12 PDB header:transcription regulator Chain: A: PDB Molecule:hth-type transcriptional repressor cytr; PDBTitle: structure of the cytidine repressor dna-binding domain; an alternate2 calculation 44 c2kkoB_ not modelled 92.9 24 PDB header:dna binding protein Chain: B: PDB Molecule:possible transcriptional regulatory protein PDBTitle: solution nmr structure of the homodimeric winged helix-turn-2 helix dna-binding domain (fragment 1-100) mb0332 from3 mycobacterium bovis, a possible arsr-family transcriptional4 regulator. northeast structural genomics consortium target5 mbr242e. 45 d1ku7a_ not modelled 92.9 19 Fold:DNA/RNA-binding 3-helical bundle Superfamily:Sigma3 and sigma4 domains of RNA polymerase sigma factors Family:Sigma4 domain 46 d1y9qa1 not modelled 92.9 7 Fold:lambda repressor-like DNA-binding domains Superfamily:lambda repressor-like DNA-binding domains Family:Probable transcriptional regulator VC1968, N-terminal domain 47 c2l8nA_ not modelled 92.8 12 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 48 d1y7ya1 not modelled 92.7 16 Fold:lambda repressor-like DNA-binding domains Superfamily:lambda repressor-like DNA-binding domains Family:SinR domain-like 49 d1r1ua_ not modelled 92.6 24 Fold:DNA/RNA-binding 3-helical bundle Superfamily:"Winged helix" DNA-binding domain Family:ArsR-like transcriptional regulators 50 c3kjxD_ not modelled 92.4 11 PDB header:transcription regulator Chain: D: PDB Molecule:transcriptional regulator, laci family; PDBTitle: crystal structure of a transcriptional regulator, lacl2 family protein from silicibacter pomeroyi 51 d1ttya_ not modelled 92.4 18 Fold:DNA/RNA-binding 3-helical bundle Superfamily:Sigma3 and sigma4 domains of RNA polymerase sigma factors Family:Sigma4 domain 52 c3qp5C_ not modelled 92.3 16 PDB header:transcription Chain: C: PDB Molecule:cvir transcriptional regulator; PDBTitle: crystal structure of cvir bound to antagonist chlorolactone (cl) 53 c3cloC_ not modelled 92.3 25 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 54 c2jscB_ not modelled 92.2 28 PDB header:transcription Chain: B: PDB Molecule:transcriptional regulator rv1994c/mt2050; PDBTitle: nmr structure of the cadmium metal-sensor cmtr from mycobacterium2 tuberculosis 55 d6paxa1 not modelled 92.1 24 Fold:DNA/RNA-binding 3-helical bundle Superfamily:Homeodomain-like Family:Paired domain 56 c3pqkD_ not modelled 92.1 21 PDB header:transcription Chain: D: PDB Molecule:biofilm growth-associated repressor; PDBTitle: crystal structure of the transcriptional repressor bigr from xylella2 fastidiosa 57 c3mzyA_ not modelled 92.0 15 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 58 c2gm4B_ not modelled 92.0 6 PDB header:recombination, dna Chain: B: PDB Molecule:transposon gamma-delta resolvase; PDBTitle: an activated, tetrameric gamma-delta resolvase: hin chimaera bound to2 cleaved dna 59 c2kpjA_ not modelled 92.0 12 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 60 c1h0mD_ not modelled 92.0 18 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 61 c2rnjA_ not modelled 91.8 26 PDB header:transcription Chain: A: PDB Molecule:response regulator protein vrar; PDBTitle: nmr structure of the s. aureus vrar dna binding domain 62 d1r1ta_ not modelled 91.7 23 Fold:DNA/RNA-binding 3-helical bundle Superfamily:"Winged helix" DNA-binding domain Family:ArsR-like transcriptional regulators 63 c3f52A_ not modelled 91.7 24 PDB header:transcription activator Chain: A: PDB Molecule:clp gene regulator (clgr); PDBTitle: crystal structure of the clp gene regulator clgr from c. glutamicum 64 c3cuoB_ not modelled 91.7 20 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 65 c1or7A_ not modelled 91.6 14 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 66 d1ku9a_ not modelled 91.6 11 Fold:DNA/RNA-binding 3-helical bundle Superfamily:"Winged helix" DNA-binding domain Family:DNA-binding protein Mj223 67 c3op9A_ not modelled 91.3 11 PDB header:transcription regulator Chain: A: PDB Molecule:pli0006 protein; PDBTitle: crystal structure of transcriptional regulator from listeria innocua 68 d1ku3a_ not modelled 91.2 21 Fold:DNA/RNA-binding 3-helical bundle Superfamily:Sigma3 and sigma4 domains of RNA polymerase sigma factors Family:Sigma4 domain 69 d1a04a1 not modelled 91.1 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) 70 c3ivpD_ not modelled 91.0 13 PDB header:dna binding protein Chain: D: PDB Molecule:putative transposon-related dna-binding protein; PDBTitle: the structure of a possible transposon-related dna-binding protein2 from clostridium difficile 630. 71 d1llib_ not modelled 90.8 25 Fold:lambda repressor-like DNA-binding domains Superfamily:lambda repressor-like DNA-binding domains Family:Phage repressors 72 d2p4wa1 not modelled 90.8 28 Fold:DNA/RNA-binding 3-helical bundle Superfamily:"Winged helix" DNA-binding domain Family:PF1790-like 73 c3hugA_ not modelled 90.8 25 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 74 d2b5aa1 not modelled 90.7 15 Fold:lambda repressor-like DNA-binding domains Superfamily:lambda repressor-like DNA-binding domains Family:SinR domain-like 75 d2jn6a1 not modelled 90.7 19 Fold:DNA/RNA-binding 3-helical bundle Superfamily:Homeodomain-like Family:Cgl2762-like 76 d2p7vb1 not modelled 90.5 21 Fold:DNA/RNA-binding 3-helical bundle Superfamily:Sigma3 and sigma4 domains of RNA polymerase sigma factors Family:Sigma4 domain 77 c1b0nA_ not modelled 90.4 19 PDB header:transcription regulator Chain: A: PDB Molecule:protein (sinr protein); PDBTitle: sinr protein/sini protein complex 78 c3fmyA_ not modelled 90.3 20 PDB header:dna binding protein Chain: A: PDB Molecule:hth-type transcriptional regulator mqsa PDBTitle: structure of the c-terminal domain of the e. coli protein2 mqsa (ygit/b3021) 79 c3clcC_ not modelled 90.3 11 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 80 c1vz0B_ not modelled 90.3 24 PDB header:nuclear protein Chain: B: PDB Molecule:chromosome partitioning protein parb; PDBTitle: chromosome segregation protein spo0j from thermus2 thermophilus 81 c3jthA_ not modelled 90.3 21 PDB header:transcription Chain: A: PDB Molecule:transcription activator hlyu; PDBTitle: crystal structure of a transcriptional regulator hlyu from2 vibrio vulnificus cmcp6 82 c3t76A_ not modelled 90.2 15 PDB header:transcription regulator Chain: A: PDB Molecule:transcriptional regulator vanug; PDBTitle: crystal structure of transcriptional regulator vanug, form ii 83 c2zkzC_ not modelled 90.2 23 PDB header:transcription Chain: C: PDB Molecule:transcriptional repressor pagr; PDBTitle: crystal structure of the transcriptional repressor pagr of bacillus2 anthracis 84 d1yioa1 not modelled 90.1 21 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) 85 c2ewtA_ not modelled 89.7 13 PDB header:dna binding protein Chain: A: PDB Molecule:putative dna-binding protein; PDBTitle: crystal structure of the dna-binding domain of bldd 86 c2wusR_ not modelled 89.6 11 PDB header:structural protein Chain: R: PDB Molecule:putative uncharacterized protein; PDBTitle: bacterial actin mreb assembles in complex with cell shape2 protein rodz 87 d1p4wa_ not modelled 89.5 31 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) 88 c3b7hA_ not modelled 89.5 8 PDB header:structural protein Chain: A: PDB Molecule:prophage lp1 protein 11; PDBTitle: crystal structure of the prophage lp1 protein 11 89 c3kxaD_ not modelled 89.5 22 PDB header:structural genomics, unknown function Chain: D: PDB Molecule:putative uncharacterized protein; PDBTitle: crystal structure of ngo0477 from neisseria gonorrhoeae 90 d1adra_ not modelled 89.4 21 Fold:lambda repressor-like DNA-binding domains Superfamily:lambda repressor-like DNA-binding domains Family:Phage repressors 91 d2a6ca1 not modelled 89.1 15 Fold:lambda repressor-like DNA-binding domains Superfamily:lambda repressor-like DNA-binding domains Family:NE1354 92 d1r69a_ not modelled 89.1 21 Fold:lambda repressor-like DNA-binding domains Superfamily:lambda repressor-like DNA-binding domains Family:Phage repressors 93 c3dnvB_ not modelled 89.1 20 PDB header:transcription/dna Chain: B: PDB Molecule:hth-type transcriptional regulator hipb; PDBTitle: mdt protein 94 c3d1nK_ not modelled 88.8 21 PDB header:transcription regulator/dna Chain: K: PDB Molecule:pou domain, class 6, transcription factor 1; PDBTitle: structure of human brn-5 transcription factor in complex2 with corticotrophin-releasing hormone gene promoter 95 c1zljE_ not modelled 88.7 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 96 c2ia0A_ not modelled 88.6 22 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) 97 d1b0na2 not modelled 88.1 19 Fold:lambda repressor-like DNA-binding domains Superfamily:lambda repressor-like DNA-binding domains Family:SinR domain-like 98 d2o38a1 not modelled 88.0 20 Fold:lambda repressor-like DNA-binding domains Superfamily:lambda repressor-like DNA-binding domains Family:NE1354 99 c2o38A_ not modelled 88.0 20 PDB header:structural genomics, unknown function Chain: A: PDB Molecule:hypothetical protein; PDBTitle: putative xre family transcriptional regulator 100 c2cg4B_ not modelled 87.8 24 PDB header:transcription Chain: B: PDB Molecule:regulatory protein asnc; PDBTitle: structure of e.coli asnc 101 c3pxpA_ not modelled 87.7 34 PDB header:transcription regulator Chain: A: PDB Molecule:helix-turn-helix domain protein; PDBTitle: crystal structure of a pas and dna binding domain containing protein2 (caur_2278) from chloroflexus aurantiacus j-10-fl at 2.30 a3 resolution 102 d1hlva1 not modelled 87.7 14 Fold:DNA/RNA-binding 3-helical bundle Superfamily:Homeodomain-like Family:Centromere-binding 103 c2o8xA_ not modelled 87.5 14 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 104 d1or7a1 not modelled 87.4 29 Fold:DNA/RNA-binding 3-helical bundle Superfamily:Sigma3 and sigma4 domains of RNA polymerase sigma factors Family:Sigma4 domain 105 c3bs3A_ not modelled 87.1 22 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 106 c2e7xA_ not modelled 87.1 21 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 107 d1rp3a2 not modelled 87.0 9 Fold:DNA/RNA-binding 3-helical bundle Superfamily:Sigma3 and sigma4 domains of RNA polymerase sigma factors Family:Sigma4 domain 108 d1x57a1 not modelled 86.8 9 Fold:lambda repressor-like DNA-binding domains Superfamily:lambda repressor-like DNA-binding domains Family:EDF1-like 109 d1sq8a_ not modelled 86.7 25 Fold:lambda repressor-like DNA-binding domains Superfamily:lambda repressor-like DNA-binding domains Family:Phage repressors 110 c2elhA_ not modelled 86.7 8 PDB header:dna binding protein Chain: A: PDB Molecule:cg11849-pa; PDBTitle: solution structure of the cenp-b n-terminal dna-binding2 domain of fruit fly distal antenna cg11849-pa 111 c2xcjB_ not modelled 86.7 13 PDB header:viral protein Chain: B: PDB Molecule:c protein; PDBTitle: crystal structure of p2 c, the immunity repressor of2 temperate e. coli phage p2 112 c2r0qF_ not modelled 86.6 15 PDB header:recombination/dna Chain: F: PDB Molecule:putative transposon tn552 dna-invertase bin3; PDBTitle: crystal structure of a serine recombinase- dna regulatory2 complex 113 c3gn5B_ not modelled 86.6 23 PDB header:dna binding protein Chain: B: PDB Molecule:hth-type transcriptional regulator mqsa (ygit/b3021); PDBTitle: structure of the e. coli protein mqsa (ygit/b3021) 114 d2croa_ not modelled 86.4 25 Fold:lambda repressor-like DNA-binding domains Superfamily:lambda repressor-like DNA-binding domains Family:Phage repressors 115 c3cecA_ not modelled 86.2 19 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 116 c2p6tH_ not modelled 86.1 19 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 117 d2r1jl1 not modelled 85.7 22 Fold:lambda repressor-like DNA-binding domains Superfamily:lambda repressor-like DNA-binding domains Family:Phage repressors 118 c2dbbA_ not modelled 85.6 27 PDB header:transcriptional regulator Chain: A: PDB Molecule:putative hth-type transcriptional regulator ph0061; PDBTitle: crystal structure of ph0061 119 c3c3wB_ not modelled 85.4 21 PDB header:transcription Chain: B: PDB Molecule:two component transcriptional regulatory protein devr; PDBTitle: crystal structure of the mycobacterium tuberculosis hypoxic response2 regulator dosr 120 c1z05A_ not modelled 85.2 21 PDB header:transcription Chain: A: PDB Molecule:transcriptional regulator, rok family; PDBTitle: crystal structure of the rok family transcriptional regulator, homolog2 of e.coli mlc protein.

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