Secondary structure and disorder prediction

		1	.	.	.	.	.	.	.	.	10	.	.	.	.	.	.	.	.	.	20	.	.	.	.	.	.	.	.	.	30	.	.	.	.	.	.	.	.	.	40	.	.	.	.	.	.	.	.	.	50	.	.	.	.	.	.	.	.	.	60
Sequence		M	R	L	F	G	Y	A	R	V	S	T	S	Q	Q	S	L	D	I	Q	V	R	A	L	K	D	A	G	V	K	A	N	R	I	F	T	D	K	A	S	G	S	S	S	D	R	K	G	L	D	L	L	R	M	K	V	E	E	G	D	V
Secondary structure
SS confidence
Disorder		?																																									?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	70	.	.	.	.	.	.	.	.	.	80	.	.	.	.	.	.	.	.	.	90	.	.	.	.	.	.	.	.	.	100	.	.	.	.	.	.	.	.	.	110	.	.	.	.	.	.	.	.	.	120
Sequence		I	L	V	K	K	L	D	R	L	G	R	D	T	A	D	M	I	Q	L	I	K	E	F	D	A	Q	G	V	S	I	R	F	I	D	D	G	I	S	T	D	G	E	M	G	K	M	V	V	T	I	L	S	A	V	A	Q	A	E	R	Q
Secondary structure
SS confidence
Disorder																																								?
Disorder confidence
		.	.	.	.	.	.	.	.	.	130	.	.	.	.	.	.	.	.	.	140	.	.	.	.	.	.	.	.	.	150	.	.	.	.	.	.	.	.	.	160	.	.	.	.	.	.	.	.	.	170	.	.	.	.	.	.	.	.	.	180
Sequence		R	I	L	E	R	T	N	E	G	R	Q	E	A	M	A	K	G	V	V	F	G	R	K	R	K	I	D	R	D	A	V	L	N	M	W	Q	Q	G	L	G	A	S	H	I	S	K	T	M	N	I	A	R	S	T	V	Y	K	V	I	N
Secondary structure
SS confidence
Disorder																		?	?	?	?		?	?
Disorder confidence
		.	.	.
Sequence		E	S	N
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 2gm4 chain B Region: 3 - 183 Aligned: 177 Modelled: 181 Confidence: 100.0% Identity: 94% 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 Phyre2 PDB 2r0q chain F Region: 1 - 182 Aligned: 173 Modelled: 181 Confidence: 100.0% Identity: 31% PDB header:recombination/dna Chain: F: PDB Molecule:putative transposon tn552 dna-invertase bin3; PDBTitle: crystal structure of a serine recombinase- dna regulatory2 complex Phyre2 PDB 1gdt chain A domain 2 Region: 1 - 140 Aligned: 140 Modelled: 140 Confidence: 100.0% Identity: 100% Fold: Resolvase-like Superfamily: Resolvase-like Family: gamma,delta resolvase, catalytic domain Phyre2 PDB 2gm4 chain A domain 2 Region: 1 - 140 Aligned: 136 Modelled: 140 Confidence: 100.0% Identity: 96% Fold: Resolvase-like Superfamily: Resolvase-like Family: gamma,delta resolvase, catalytic domain Phyre2 PDB 2rsl chain A Region: 1 - 122 Aligned: 115 Modelled: 122 Confidence: 99.9% Identity: 99% Fold: Resolvase-like Superfamily: Resolvase-like Family: gamma,delta resolvase, catalytic domain Phyre2 PDB 3plo chain X Region: 3 - 126 Aligned: 122 Modelled: 124 Confidence: 99.9% Identity: 42% PDB header:recombination Chain: X: PDB Molecule:dna-invertase; PDBTitle: crystal structure of the fis-independent mutant of gin Phyre2 PDB 1hx7 chain A Region: 1 - 105 Aligned: 105 Modelled: 105 Confidence: 99.9% Identity: 100% Fold: Resolvase-like Superfamily: Resolvase-like Family: gamma,delta resolvase, catalytic domain Phyre2 PDB 3g13 chain B Region: 1 - 121 Aligned: 121 Modelled: 121 Confidence: 99.9% Identity: 27% PDB header:recombination Chain: B: PDB Molecule:putative conjugative transposon recombinase; PDBTitle: crystal structure of putative conjugative transposon recombinase from2 clostridium difficile Phyre2 PDB 3guv chain A Region: 1 - 136 Aligned: 134 Modelled: 136 Confidence: 99.9% Identity: 31% PDB header:recombination Chain: A: PDB Molecule:site-specific recombinase, resolvase family protein; PDBTitle: crystal structure of a resolvase family site-specific recombinase from2 streptococcus pneumoniae Phyre2 PDB 3pkz chain K Region: 1 - 118 Aligned: 115 Modelled: 117 Confidence: 99.9% Identity: 34% PDB header:recombination Chain: K: PDB Molecule:recombinase sin; PDBTitle: structural basis for catalytic activation of a serine recombinase Phyre2 PDB 3lhf chain C Region: 2 - 135 Aligned: 128 Modelled: 130 Confidence: 99.9% Identity: 26% PDB header:recombination Chain: C: PDB Molecule:serine recombinase; PDBTitle: the crystal structure of a serine recombinase from2 sulfolobus solfataricus to 2.3a Phyre2 PDB 3bvp chain B Region: 2 - 122 Aligned: 120 Modelled: 121 Confidence: 99.8% Identity: 35% PDB header:recombination Chain: B: PDB Molecule:tp901-1 integrase; PDBTitle: crystal structure of the n-terminal catalytic domain of tp901-12 integrase Phyre2 PDB 3lhk chain A Region: 2 - 135 Aligned: 129 Modelled: 134 Confidence: 99.8% Identity: 22% PDB header:dna binding protein Chain: A: PDB Molecule:putative dna binding protein mj0014; PDBTitle: crystal structure of putative dna binding protein from2 methanocaldococcus jannaschii. Phyre2 PDB 1gdt chain A domain 1 Region: 141 - 183 Aligned: 43 Modelled: 43 Confidence: 97.5% Identity: 100% Fold: DNA/RNA-binding 3-helical bundle Superfamily: Homeodomain-like Family: Recombinase DNA-binding domain Phyre2 PDB 1u78 chain A Region: 138 - 181 Aligned: 44 Modelled: 44 Confidence: 97.3% Identity: 9% 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 1pdn chain C Region: 137 - 181 Aligned: 45 Modelled: 45 Confidence: 97.1% Identity: 22% Fold: DNA/RNA-binding 3-helical bundle Superfamily: Homeodomain-like Family: Paired domain Phyre2 PDB 6pax chain A Region: 137 - 181 Aligned: 45 Modelled: 45 Confidence: 97.1% Identity: 18% 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 1k78 chain A domain 1 Region: 140 - 181 Aligned: 42 Modelled: 42 Confidence: 97.0% Identity: 21% Fold: DNA/RNA-binding 3-helical bundle Superfamily: Homeodomain-like Family: Paired domain Phyre2 PDB 6pax chain A domain 1 Region: 140 - 181 Aligned: 42 Modelled: 42 Confidence: 96.7% Identity: 17% Fold: DNA/RNA-binding 3-helical bundle Superfamily: Homeodomain-like Family: Paired domain Phyre2 PDB 3szt chain B Region: 115 - 181 Aligned: 67 Modelled: 67 Confidence: 96.1% Identity: 15% 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 1 c2gm4B_ 2 c2r0qF_ 3 d1gdta2 4 d2gm4a2 5 d2rsla_ 6 c3ploX_ 7 d1hx7a_ 8 c3g13B_ 9 c3guvA_ 10 c3pkzK_ 11 c3lhfC_ 12 c3bvpB_ 13 c3lhkA_ 14 d1gdta1 15 c1u78A_ 16 d1pdnc_ 17 c6paxA_ 18 d1k78a1 19 d6paxa1 20 c3sztB_ 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 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 239 240 241 242 243 244 245 246 247 248 249 250 251 252 253 254 255 256 257 258 259 260 261 262 263 264 265 266 267 268 269 270 271 272 273 274 275 276 277 278 279 280 281 282 283 284 285 286 287 288 289 290 291 292 293 294 295 296 297 298 299 300 301 302 303 304 305 306 307 308 309 310 311 312 313 314 315 316 317 318 319 320 321 322 323 324 325 326 327 328 329 330 331 332 333 334 335 336 337 338 339 340 341 342 343 344 345 346 347 348 349 350 351 352 353 354 355 356 357 358 359 360 361 362 363 364 365 366 367 368 369 370 371 372 373 374 375 376 377 378 379 380 381 382 383 384 385 386 387 388 389 390 391 392 393 394 395 396 397 398 399 400 401 402 403 404 405 406 407 408 409 410 411 412 413 414 415 416 417 418 419 420 421 422 423

Detailed template information

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

1 c2gm4B_ 100.0 94 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 2 c2r0qF_ 100.0 31 PDB header:recombination/dna Chain: F: PDB Molecule:putative transposon tn552 dna-invertase bin3; PDBTitle: crystal structure of a serine recombinase- dna regulatory2 complex 3 d1gdta2 100.0 100 Fold:Resolvase-like Superfamily:Resolvase-like Family:gamma,delta resolvase, catalytic domain 4 d2gm4a2 100.0 96 Fold:Resolvase-like Superfamily:Resolvase-like Family:gamma,delta resolvase, catalytic domain 5 d2rsla_ 99.9 99 Fold:Resolvase-like Superfamily:Resolvase-like Family:gamma,delta resolvase, catalytic domain 6 c3ploX_ 99.9 42 PDB header:recombination Chain: X: PDB Molecule:dna-invertase; PDBTitle: crystal structure of the fis-independent mutant of gin 7 d1hx7a_ 99.9 100 Fold:Resolvase-like Superfamily:Resolvase-like Family:gamma,delta resolvase, catalytic domain 8 c3g13B_ 99.9 27 PDB header:recombination Chain: B: PDB Molecule:putative conjugative transposon recombinase; PDBTitle: crystal structure of putative conjugative transposon recombinase from2 clostridium difficile 9 c3guvA_ 99.9 31 PDB header:recombination Chain: A: PDB Molecule:site-specific recombinase, resolvase family protein; PDBTitle: crystal structure of a resolvase family site-specific recombinase from2 streptococcus pneumoniae 10 c3pkzK_ 99.9 34 PDB header:recombination Chain: K: PDB Molecule:recombinase sin; PDBTitle: structural basis for catalytic activation of a serine recombinase 11 c3lhfC_ 99.9 26 PDB header:recombination Chain: C: PDB Molecule:serine recombinase; PDBTitle: the crystal structure of a serine recombinase from2 sulfolobus solfataricus to 2.3a 12 c3bvpB_ 99.8 35 PDB header:recombination Chain: B: PDB Molecule:tp901-1 integrase; PDBTitle: crystal structure of the n-terminal catalytic domain of tp901-12 integrase 13 c3lhkA_ 99.8 22 PDB header:dna binding protein Chain: A: PDB Molecule:putative dna binding protein mj0014; PDBTitle: crystal structure of putative dna binding protein from2 methanocaldococcus jannaschii. 14 d1gdta1 97.5 100 Fold:DNA/RNA-binding 3-helical bundle Superfamily:Homeodomain-like Family:Recombinase DNA-binding domain 15 c1u78A_ 97.3 9 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 16 d1pdnc_ 97.1 22 Fold:DNA/RNA-binding 3-helical bundle Superfamily:Homeodomain-like Family:Paired domain 17 c6paxA_ 97.1 18 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 18 d1k78a1 97.0 21 Fold:DNA/RNA-binding 3-helical bundle Superfamily:Homeodomain-like Family:Paired domain 19 d6paxa1 96.7 17 Fold:DNA/RNA-binding 3-helical bundle Superfamily:Homeodomain-like Family:Paired domain 20 c3sztB_ 96.1 15 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 21 d2jn6a1 not modelled 96.0 18 Fold:DNA/RNA-binding 3-helical bundle Superfamily:Homeodomain-like Family:Cgl2762-like 22 c2elhA_ not modelled 95.8 9 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 23 c2k27A_ not modelled 95.4 18 PDB header:transcription regulator Chain: A: PDB Molecule:paired box protein pax-8; PDBTitle: solution structure of human pax8 paired box domain 24 c3mzyA_ not modelled 95.3 13 PDB header:rna binding protein Chain: A: PDB Molecule:rna polymerase sigma-h factor; PDBTitle: the crystal structure of the rna polymerase sigma-h factor from2 fusobacterium nucleatum to 2.5a 25 c3hefB_ not modelled 95.3 18 PDB header:viral protein Chain: B: PDB Molecule:gene 1 protein; PDBTitle: crystal structure of the bacteriophage sf6 terminase small2 subunit 26 c1zljE_ not modelled 95.2 22 PDB header:transcription Chain: E: PDB Molecule:dormancy survival regulator; PDBTitle: crystal structure of the mycobacterium tuberculosis hypoxic2 response regulator dosr c-terminal domain 27 d1a04a1 not modelled 95.1 28 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) 28 d1xsva_ not modelled 95.1 24 Fold:DNA/RNA-binding 3-helical bundle Superfamily:Sigma3 and sigma4 domains of RNA polymerase sigma factors Family:YlxM/p13-like 29 c3frwF_ not modelled 95.1 16 PDB header:structural genomics, unknown function Chain: F: PDB Molecule:putative trp repressor protein; PDBTitle: crystal structure of putative trpr protein from ruminococcus obeum 30 c2krfB_ not modelled 95.0 9 PDB header:transcription Chain: B: PDB Molecule:transcriptional regulatory protein coma; PDBTitle: nmr solution structure of the dna binding domain of competence protein2 a 31 c1x3uA_ not modelled 94.9 25 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 32 d1hlva1 not modelled 94.9 19 Fold:DNA/RNA-binding 3-helical bundle Superfamily:Homeodomain-like Family:Centromere-binding 33 c3hugA_ not modelled 94.9 22 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 34 c3korD_ not modelled 94.8 19 PDB header:transcription Chain: D: PDB Molecule:possible trp repressor; PDBTitle: crystal structure of a putative trp repressor from staphylococcus2 aureus 35 d1yioa1 not modelled 94.8 27 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 c2jpcA_ not modelled 94.7 25 PDB header:dna binding protein Chain: A: PDB Molecule:ssrb; PDBTitle: ssrb dna binding protein 37 d1p4wa_ not modelled 94.7 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) 38 d1l3la1 not modelled 94.6 16 Fold:DNA/RNA-binding 3-helical bundle Superfamily:C-terminal effector domain of the bipartite response regulators Family:GerE-like (LuxR/UhpA family of transcriptional regulators) 39 d1ijwc_ not modelled 94.6 23 Fold:DNA/RNA-binding 3-helical bundle Superfamily:Homeodomain-like Family:Recombinase DNA-binding domain 40 d1fsea_ not modelled 94.6 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) 41 c2q0oA_ not modelled 94.5 14 PDB header:transcription Chain: A: PDB Molecule:probable transcriptional activator protein trar; PDBTitle: crystal structure of an anti-activation complex in bacterial quorum2 sensing 42 c2rnjA_ not modelled 94.5 19 PDB header:transcription Chain: A: PDB Molecule:response regulator protein vrar; PDBTitle: nmr structure of the s. aureus vrar dna binding domain 43 d1hcra_ not modelled 94.4 23 Fold:DNA/RNA-binding 3-helical bundle Superfamily:Homeodomain-like Family:Recombinase DNA-binding domain 44 c1h0mD_ not modelled 94.3 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 45 c3qp5C_ not modelled 94.3 15 PDB header:transcription Chain: C: PDB Molecule:cvir transcriptional regulator; PDBTitle: crystal structure of cvir bound to antagonist chlorolactone (cl) 46 d1rp3a2 not modelled 94.2 16 Fold:DNA/RNA-binding 3-helical bundle Superfamily:Sigma3 and sigma4 domains of RNA polymerase sigma factors Family:Sigma4 domain 47 d1bw6a_ not modelled 94.1 19 Fold:DNA/RNA-binding 3-helical bundle Superfamily:Homeodomain-like Family:Centromere-binding 48 d1or7a1 not modelled 94.0 22 Fold:DNA/RNA-binding 3-helical bundle Superfamily:Sigma3 and sigma4 domains of RNA polymerase sigma factors Family:Sigma4 domain 49 c2o8xA_ not modelled 93.9 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 50 c1hlvA_ not modelled 93.8 19 PDB header:dna binding protein/dna Chain: A: PDB Molecule:major centromere autoantigen b; PDBTitle: crystal structure of cenp-b(1-129) complexed with the cenp-2 b box dna 51 c2rn7A_ not modelled 93.8 18 PDB header:unknown function Chain: A: PDB Molecule:is629 orfa; PDBTitle: nmr solution structure of tnpe protein from shigella2 flexneri. northeast structural genomics target sfr125 52 d1s7oa_ not modelled 93.6 13 Fold:DNA/RNA-binding 3-helical bundle Superfamily:Sigma3 and sigma4 domains of RNA polymerase sigma factors Family:YlxM/p13-like 53 d1qpza1 not modelled 93.6 29 Fold:lambda repressor-like DNA-binding domains Superfamily:lambda repressor-like DNA-binding domains Family:GalR/LacI-like bacterial regulator 54 d1umqa_ not modelled 93.5 12 Fold:DNA/RNA-binding 3-helical bundle Superfamily:Homeodomain-like Family:FIS-like 55 c1umqA_ not modelled 93.5 12 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 56 d1efaa1 not modelled 93.5 15 Fold:lambda repressor-like DNA-binding domains Superfamily:lambda repressor-like DNA-binding domains Family:GalR/LacI-like bacterial regulator 57 c1r71B_ not modelled 93.5 13 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 58 c1or7A_ not modelled 93.5 24 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 59 c3c3wB_ not modelled 93.5 15 PDB header:transcription Chain: B: PDB Molecule:two component transcriptional regulatory protein devr; PDBTitle: crystal structure of the mycobacterium tuberculosis hypoxic response2 regulator dosr 60 d1uxca_ not modelled 93.5 25 Fold:lambda repressor-like DNA-binding domains Superfamily:lambda repressor-like DNA-binding domains Family:GalR/LacI-like bacterial regulator 61 d2bjca1 not modelled 93.4 17 Fold:lambda repressor-like DNA-binding domains Superfamily:lambda repressor-like DNA-binding domains Family:GalR/LacI-like bacterial regulator 62 d1biaa1 not modelled 93.3 16 Fold:DNA/RNA-binding 3-helical bundle Superfamily:"Winged helix" DNA-binding domain Family:Biotin repressor-like 63 d2hsga1 not modelled 93.3 16 Fold:lambda repressor-like DNA-binding domains Superfamily:lambda repressor-like DNA-binding domains Family:GalR/LacI-like bacterial regulator 64 c3cloC_ not modelled 93.3 24 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 65 c1rp3G_ not modelled 93.3 16 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 66 d1nera_ not modelled 93.3 19 Fold:lambda repressor-like DNA-binding domains Superfamily:lambda repressor-like DNA-binding domains Family:Phage repressors 67 d1lcda_ not modelled 93.1 15 Fold:lambda repressor-like DNA-binding domains Superfamily:lambda repressor-like DNA-binding domains Family:GalR/LacI-like bacterial regulator 68 d1ttya_ not modelled 93.0 14 Fold:DNA/RNA-binding 3-helical bundle Superfamily:Sigma3 and sigma4 domains of RNA polymerase sigma factors Family:Sigma4 domain 69 d1r71a_ not modelled 93.0 13 Fold:DNA/RNA-binding 3-helical bundle Superfamily:KorB DNA-binding domain-like Family:KorB DNA-binding domain-like 70 d1g2ha_ not modelled 92.9 0 Fold:DNA/RNA-binding 3-helical bundle Superfamily:Homeodomain-like Family:FIS-like 71 d1jhga_ not modelled 92.9 4 Fold:DNA/RNA-binding 3-helical bundle Superfamily:TrpR-like Family:Trp repressor, TrpR 72 c2lcvA_ not modelled 92.9 8 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 73 d1uxda_ not modelled 92.8 27 Fold:lambda repressor-like DNA-binding domains Superfamily:lambda repressor-like DNA-binding domains Family:GalR/LacI-like bacterial regulator 74 d1vz0a1 not modelled 92.6 22 Fold:DNA/RNA-binding 3-helical bundle Superfamily:KorB DNA-binding domain-like Family:KorB DNA-binding domain-like 75 d1j5ya1 not modelled 92.5 6 Fold:DNA/RNA-binding 3-helical bundle Superfamily:"Winged helix" DNA-binding domain Family:Biotin repressor-like 76 d2cg4a1 not modelled 92.5 9 Fold:DNA/RNA-binding 3-helical bundle Superfamily:"Winged helix" DNA-binding domain Family:Lrp/AsnC-like transcriptional regulator N-terminal domain 77 c3hosA_ not modelled 92.3 4 PDB header:transferase, dna binding protein/dna Chain: A: PDB Molecule:transposable element mariner, complete cds; PDBTitle: crystal structure of the mariner mos1 paired end complex with mg 78 c3e7lD_ not modelled 92.3 15 PDB header:transcription regulator Chain: D: PDB Molecule:transcriptional regulator (ntrc family); PDBTitle: crystal structure of sigma54 activator ntrc4's dna binding2 domain 79 c2l8nA_ not modelled 92.2 9 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 80 d1mkma1 not modelled 92.2 19 Fold:DNA/RNA-binding 3-helical bundle Superfamily:"Winged helix" DNA-binding domain Family:Transcriptional regulator IclR, N-terminal domain 81 d1trra_ not modelled 92.1 6 Fold:DNA/RNA-binding 3-helical bundle Superfamily:TrpR-like Family:Trp repressor, TrpR 82 d2p7vb1 not modelled 92.1 14 Fold:DNA/RNA-binding 3-helical bundle Superfamily:Sigma3 and sigma4 domains of RNA polymerase sigma factors Family:Sigma4 domain 83 c1rnlA_ not modelled 92.0 27 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 84 c2l4aA_ not modelled 92.0 16 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 85 c2kpjA_ not modelled 92.0 9 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 86 d1fipa_ not modelled 91.9 20 Fold:DNA/RNA-binding 3-helical bundle Superfamily:Homeodomain-like Family:FIS-like 87 c3klnC_ not modelled 91.9 12 PDB header:transcription Chain: C: PDB Molecule:transcriptional regulator, luxr family; PDBTitle: vibrio cholerae vpst 88 d1ku3a_ not modelled 91.8 14 Fold:DNA/RNA-binding 3-helical bundle Superfamily:Sigma3 and sigma4 domains of RNA polymerase sigma factors Family:Sigma4 domain 89 d1smyf2 not modelled 91.5 11 Fold:DNA/RNA-binding 3-helical bundle Superfamily:Sigma3 and sigma4 domains of RNA polymerase sigma factors Family:Sigma4 domain 90 d2cfxa1 not modelled 91.5 6 Fold:DNA/RNA-binding 3-helical bundle Superfamily:"Winged helix" DNA-binding domain Family:Lrp/AsnC-like transcriptional regulator N-terminal domain 91 d1ku7a_ not modelled 91.4 14 Fold:DNA/RNA-binding 3-helical bundle Superfamily:Sigma3 and sigma4 domains of RNA polymerase sigma factors Family:Sigma4 domain 92 d1etxa_ not modelled 91.4 23 Fold:DNA/RNA-binding 3-helical bundle Superfamily:Homeodomain-like Family:FIS-like 93 d1i1ga1 not modelled 91.3 18 Fold:DNA/RNA-binding 3-helical bundle Superfamily:"Winged helix" DNA-binding domain Family:Lrp/AsnC-like transcriptional regulator N-terminal domain 94 d1etob_ not modelled 91.2 20 Fold:DNA/RNA-binding 3-helical bundle Superfamily:Homeodomain-like Family:FIS-like 95 c3t76A_ not modelled 91.1 13 PDB header:transcription regulator Chain: A: PDB Molecule:transcriptional regulator vanug; PDBTitle: crystal structure of transcriptional regulator vanug, form ii 96 d1rr7a_ not modelled 91.0 25 Fold:DNA/RNA-binding 3-helical bundle Superfamily:Homeodomain-like Family:Middle operon regulator, Mor 97 c1rr7A_ not modelled 91.0 25 PDB header:transcription Chain: A: PDB Molecule:middle operon regulator; PDBTitle: crystal structure of the middle operon regulator protein of2 bacteriophage mu 98 c3b7hA_ not modelled 91.0 17 PDB header:structural protein Chain: A: PDB Molecule:prophage lp1 protein 11; PDBTitle: crystal structure of the prophage lp1 protein 11 99 c2oqgA_ not modelled 90.9 19 PDB header:transcription Chain: A: PDB Molecule:possible transcriptional regulator, arsr family protein; PDBTitle: arsr-like transcriptional regulator from rhodococcus sp. rha1 100 c3fmyA_ not modelled 90.8 6 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) 101 d2cyya1 not modelled 90.7 26 Fold:DNA/RNA-binding 3-helical bundle Superfamily:"Winged helix" DNA-binding domain Family:Lrp/AsnC-like transcriptional regulator N-terminal domain 102 d2coba1 not modelled 90.7 17 Fold:DNA/RNA-binding 3-helical bundle Superfamily:Homeodomain-like Family:Psq domain 103 d2isya1 not modelled 90.3 12 Fold:DNA/RNA-binding 3-helical bundle Superfamily:"Winged helix" DNA-binding domain Family:Iron-dependent repressor protein 104 d1r69a_ not modelled 90.1 14 Fold:lambda repressor-like DNA-binding domains Superfamily:lambda repressor-like DNA-binding domains Family:Phage repressors 105 c3omtA_ not modelled 89.8 17 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. 106 d1r1ta_ not modelled 89.8 13 Fold:DNA/RNA-binding 3-helical bundle Superfamily:"Winged helix" DNA-binding domain Family:ArsR-like transcriptional regulators 107 c1r22B_ not modelled 89.7 13 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 108 d1ntca_ not modelled 89.6 7 Fold:DNA/RNA-binding 3-helical bundle Superfamily:Homeodomain-like Family:FIS-like 109 c2jscB_ not modelled 89.5 16 PDB header:transcription Chain: B: PDB Molecule:transcriptional regulator rv1994c/mt2050; PDBTitle: nmr structure of the cadmium metal-sensor cmtr from mycobacterium2 tuberculosis 110 d1z05a1 not modelled 89.3 20 Fold:DNA/RNA-binding 3-helical bundle Superfamily:"Winged helix" DNA-binding domain Family:ROK associated domain 111 c3op9A_ not modelled 89.3 17 PDB header:transcription regulator Chain: A: PDB Molecule:pli0006 protein; PDBTitle: crystal structure of transcriptional regulator from listeria innocua 112 d1adra_ not modelled 89.3 3 Fold:lambda repressor-like DNA-binding domains Superfamily:lambda repressor-like DNA-binding domains Family:Phage repressors 113 d1r1ua_ not modelled 89.1 19 Fold:DNA/RNA-binding 3-helical bundle Superfamily:"Winged helix" DNA-binding domain Family:ArsR-like transcriptional regulators 114 d1jt6a1 not modelled 89.0 13 Fold:DNA/RNA-binding 3-helical bundle Superfamily:Homeodomain-like Family:Tetracyclin repressor-like, N-terminal domain 115 c2l0kA_ not modelled 89.0 25 PDB header:transcription Chain: A: PDB Molecule:stage iii sporulation protein d; PDBTitle: nmr solution structure of a transcription factor spoiiid in complex2 with dna 116 d1g3wa1 not modelled 88.8 12 Fold:DNA/RNA-binding 3-helical bundle Superfamily:"Winged helix" DNA-binding domain Family:Iron-dependent repressor protein 117 c3bs3A_ not modelled 88.7 3 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 118 c2x48B_ not modelled 88.6 10 PDB header:viral protein Chain: B: PDB Molecule:cag38821; PDBTitle: orf 55 from sulfolobus islandicus rudivirus 1 119 c1f5tA_ not modelled 88.6 12 PDB header:transcription/dna Chain: A: PDB Molecule:diphtheria toxin repressor; PDBTitle: diphtheria tox repressor (c102d mutant) complexed with2 nickel and dtxr consensus binding sequence 120 c3pqkD_ not modelled 88.5 9 PDB header:transcription Chain: D: PDB Molecule:biofilm growth-associated repressor; PDBTitle: crystal structure of the transcriptional repressor bigr from xylella2 fastidiosa

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