Secondary structure and disorder prediction

		1	.	.	.	.	.	.	.	.	10	.	.	.	.	.	.	.	.	.	20	.	.	.	.	.	.	.	.	.	30	.	.	.	.	.	.	.	.	.	40	.	.	.	.	.	.	.	.	.	50	.	.	.	.	.	.	.	.	.	60
Sequence		M	E	S	N	F	I	D	W	H	P	A	D	I	I	A	G	L	R	K	K	G	T	S	M	A	A	E	S	R	R	N	G	L	S	S	S	T	L	A	N	A	L	S	R	P	W	P	K	G	E	M	I	I	A	K	A	L	G	T	D
Secondary structure
SS confidence
Disorder		?	?	?	?	?	?	?													?											?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	70	.	.	.	.	.	.	.	.	.	80	.	.	.	.	.	.	.	.	.	90	.	.
Sequence		P	W	V	I	W	P	S	R	Y	H	D	P	Q	T	H	E	F	I	D	R	T	Q	L	M	R	S	Y	T	K	P	K	K
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 1ner chain A Region: 2 - 73 Aligned: 72 Modelled: 72 Confidence: 100.0% Identity: 57% Fold: lambda repressor-like DNA-binding domains Superfamily: lambda repressor-like DNA-binding domains Family: Phage repressors Phyre2 PDB 3b7h chain A Region: 10 - 65 Aligned: 56 Modelled: 56 Confidence: 97.8% Identity: 14% PDB header:structural protein Chain: A: PDB Molecule:prophage lp1 protein 11; PDBTitle: crystal structure of the prophage lp1 protein 11 Phyre2 PDB 1lmb chain 3 Region: 10 - 67 Aligned: 58 Modelled: 58 Confidence: 97.6% Identity: 17% Fold: lambda repressor-like DNA-binding domains Superfamily: lambda repressor-like DNA-binding domains Family: Phage repressors Phyre2 PDB 3t76 chain A Region: 1 - 65 Aligned: 63 Modelled: 65 Confidence: 97.6% Identity: 16% PDB header:transcription regulator Chain: A: PDB Molecule:transcriptional regulator vanug; PDBTitle: crystal structure of transcriptional regulator vanug, form ii Phyre2 PDB 1rio chain A Region: 11 - 67 Aligned: 57 Modelled: 57 Confidence: 97.5% Identity: 18% Fold: lambda repressor-like DNA-binding domains Superfamily: lambda repressor-like DNA-binding domains Family: Phage repressors Phyre2 PDB 1lli chain B Region: 10 - 67 Aligned: 58 Modelled: 58 Confidence: 97.5% Identity: 17% Fold: lambda repressor-like DNA-binding domains Superfamily: lambda repressor-like DNA-binding domains Family: Phage repressors Phyre2 PDB 2bno chain A Region: 11 - 67 Aligned: 57 Modelled: 57 Confidence: 97.4% Identity: 19% PDB header:oxidoreductase Chain: A: PDB Molecule:epoxidase; PDBTitle: the structure of hydroxypropylphosphonic acid epoxidase2 from s. wedmorenis. Phyre2 PDB 1b0n chain A domain 2 Region: 11 - 67 Aligned: 57 Modelled: 57 Confidence: 97.4% Identity: 16% Fold: lambda repressor-like DNA-binding domains Superfamily: lambda repressor-like DNA-binding domains Family: SinR domain-like Phyre2 PDB 1sq8 chain A Region: 11 - 65 Aligned: 55 Modelled: 55 Confidence: 97.4% Identity: 16% Fold: lambda repressor-like DNA-binding domains Superfamily: lambda repressor-like DNA-binding domains Family: Phage repressors Phyre2 PDB 1r69 chain A Region: 11 - 64 Aligned: 54 Modelled: 54 Confidence: 97.4% Identity: 13% Fold: lambda repressor-like DNA-binding domains Superfamily: lambda repressor-like DNA-binding domains Family: Phage repressors Phyre2 PDB 2eby chain A Region: 9 - 64 Aligned: 56 Modelled: 56 Confidence: 97.4% Identity: 11% PDB header:transcription Chain: A: PDB Molecule:putative hth-type transcriptional regulator ybaq; PDBTitle: crystal structure of a hypothetical protein from e. coli Phyre2 PDB 1y7y chain A domain 1 Region: 11 - 65 Aligned: 55 Modelled: 55 Confidence: 97.3% Identity: 18% Fold: lambda repressor-like DNA-binding domains Superfamily: lambda repressor-like DNA-binding domains Family: SinR domain-like Phyre2 PDB 1y9q chain A domain 1 Region: 11 - 67 Aligned: 57 Modelled: 57 Confidence: 97.2% Identity: 19% Fold: lambda repressor-like DNA-binding domains Superfamily: lambda repressor-like DNA-binding domains Family: Probable transcriptional regulator VC1968, N-terminal domain Phyre2 PDB 2ewt chain A Region: 11 - 66 Aligned: 56 Modelled: 56 Confidence: 97.1% Identity: 14% PDB header:dna binding protein Chain: A: PDB Molecule:putative dna-binding protein; PDBTitle: crystal structure of the dna-binding domain of bldd Phyre2 PDB 2b5a chain A domain 1 Region: 11 - 65 Aligned: 55 Modelled: 55 Confidence: 97.1% Identity: 15% Fold: lambda repressor-like DNA-binding domains Superfamily: lambda repressor-like DNA-binding domains Family: SinR domain-like Phyre2 PDB 3trb chain A Region: 9 - 64 Aligned: 56 Modelled: 56 Confidence: 97.1% Identity: 21% PDB header:dna binding protein Chain: A: PDB Molecule:virulence-associated protein i; PDBTitle: structure of an addiction module antidote protein of a higa (higa)2 family from coxiella burnetii Phyre2 PDB 1y9q chain A Region: 11 - 65 Aligned: 55 Modelled: 55 Confidence: 97.1% Identity: 20% 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 Phyre2 PDB 1adr chain A Region: 11 - 65 Aligned: 55 Modelled: 55 Confidence: 97.1% Identity: 24% Fold: lambda repressor-like DNA-binding domains Superfamily: lambda repressor-like DNA-binding domains Family: Phage repressors Phyre2 PDB 1b0n chain A Region: 11 - 65 Aligned: 55 Modelled: 55 Confidence: 97.1% Identity: 18% PDB header:transcription regulator Chain: A: PDB Molecule:protein (sinr protein); PDBTitle: sinr protein/sini protein complex Phyre2 PDB 3bs3 chain A Region: 13 - 65 Aligned: 53 Modelled: 53 Confidence: 97.1% Identity: 25% 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 Phyre2 1 d1nera_ 2 c3b7hA_ 3 d1lmb3_ 4 c3t76A_ 5 d1rioa_ 6 d1llib_ 7 c2bnoA_ 8 d1b0na2 9 d1sq8a_ 10 d1r69a_ 11 c2ebyA_ 12 d1y7ya1 13 d1y9qa1 14 c2ewtA_ 15 d2b5aa1 16 c3trbA_ 17 c1y9qA_ 18 d1adra_ 19 c1b0nA_ 20 c3bs3A_ 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 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 239 240 241 242 243 244 245 246 247 248 249 250 251 252 253 254 255 256 257 258 259 260 261 262 263 264 265 266 267 268 269 270 271 272 273 274 275 276 277 278 279 280 281 282 283 284 285 286 287 288 289 290 291 292 293 294 295 296 297 298 299 300 301 302 303 304 305 306 307 308 309 310 311 312 313 314 315 316 317 318 319 320 321 322 323 324 325 326 327 328 329 330 331 332 333 334 335 336 337 338 339 340 341 342 343 344 345 346 347 348 349 350 351 352 353 354 355 356 357 358 359 360 361 362 363 364 365 366 367 368 369 370 371 372 373 374 375 376 377 378 379 380 381 382 383 384 385 386 387 388 389 390 391 392 393 394 395 396 397 398 399 400 401 402 403 404 405 406 407 408 409 410 411 412 413 414 415 416 417 418 419 420 421 422 423 424 425 426 427 428 429 430 431 432 433 434 435 436 437 438 439 440 441 442 443 444 445 446 447 448 449 450 451 452 453 454 455 456 457 458 459 460 461 462 463 464 465 466 467 468 469 470 471 472 473 474 475 476 477 478 479 480 481 482 483 484

Detailed template information

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

1 d1nera_ 100.0 57 Fold:lambda repressor-like DNA-binding domains Superfamily:lambda repressor-like DNA-binding domains Family:Phage repressors 2 c3b7hA_ 97.8 14 PDB header:structural protein Chain: A: PDB Molecule:prophage lp1 protein 11; PDBTitle: crystal structure of the prophage lp1 protein 11 3 d1lmb3_ 97.6 17 Fold:lambda repressor-like DNA-binding domains Superfamily:lambda repressor-like DNA-binding domains Family:Phage repressors 4 c3t76A_ 97.6 16 PDB header:transcription regulator Chain: A: PDB Molecule:transcriptional regulator vanug; PDBTitle: crystal structure of transcriptional regulator vanug, form ii 5 d1rioa_ 97.5 18 Fold:lambda repressor-like DNA-binding domains Superfamily:lambda repressor-like DNA-binding domains Family:Phage repressors 6 d1llib_ 97.5 17 Fold:lambda repressor-like DNA-binding domains Superfamily:lambda repressor-like DNA-binding domains Family:Phage repressors 7 c2bnoA_ 97.4 19 PDB header:oxidoreductase Chain: A: PDB Molecule:epoxidase; PDBTitle: the structure of hydroxypropylphosphonic acid epoxidase2 from s. wedmorenis. 8 d1b0na2 97.4 16 Fold:lambda repressor-like DNA-binding domains Superfamily:lambda repressor-like DNA-binding domains Family:SinR domain-like 9 d1sq8a_ 97.4 16 Fold:lambda repressor-like DNA-binding domains Superfamily:lambda repressor-like DNA-binding domains Family:Phage repressors 10 d1r69a_ 97.4 13 Fold:lambda repressor-like DNA-binding domains Superfamily:lambda repressor-like DNA-binding domains Family:Phage repressors 11 c2ebyA_ 97.4 11 PDB header:transcription Chain: A: PDB Molecule:putative hth-type transcriptional regulator ybaq; PDBTitle: crystal structure of a hypothetical protein from e. coli 12 d1y7ya1 97.3 18 Fold:lambda repressor-like DNA-binding domains Superfamily:lambda repressor-like DNA-binding domains Family:SinR domain-like 13 d1y9qa1 97.2 19 Fold:lambda repressor-like DNA-binding domains Superfamily:lambda repressor-like DNA-binding domains Family:Probable transcriptional regulator VC1968, N-terminal domain 14 c2ewtA_ 97.1 14 PDB header:dna binding protein Chain: A: PDB Molecule:putative dna-binding protein; PDBTitle: crystal structure of the dna-binding domain of bldd 15 d2b5aa1 97.1 15 Fold:lambda repressor-like DNA-binding domains Superfamily:lambda repressor-like DNA-binding domains Family:SinR domain-like 16 c3trbA_ 97.1 21 PDB header:dna binding protein Chain: A: PDB Molecule:virulence-associated protein i; PDBTitle: structure of an addiction module antidote protein of a higa (higa)2 family from coxiella burnetii 17 c1y9qA_ 97.1 20 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 18 d1adra_ 97.1 24 Fold:lambda repressor-like DNA-binding domains Superfamily:lambda repressor-like DNA-binding domains Family:Phage repressors 19 c1b0nA_ 97.1 18 PDB header:transcription regulator Chain: A: PDB Molecule:protein (sinr protein); PDBTitle: sinr protein/sini protein complex 20 c3bs3A_ 97.1 25 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 21 c3omtA_ not modelled 97.1 20 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. 22 d1utxa_ not modelled 97.1 21 Fold:lambda repressor-like DNA-binding domains Superfamily:lambda repressor-like DNA-binding domains Family:SinR domain-like 23 d2croa_ not modelled 97.0 12 Fold:lambda repressor-like DNA-binding domains Superfamily:lambda repressor-like DNA-binding domains Family:Phage repressors 24 c3clcC_ not modelled 97.0 18 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 25 d2icta1 not modelled 97.0 19 Fold:lambda repressor-like DNA-binding domains Superfamily:lambda repressor-like DNA-binding domains Family:SinR domain-like 26 d2ofya1 not modelled 96.9 21 Fold:lambda repressor-like DNA-binding domains Superfamily:lambda repressor-like DNA-binding domains Family:SinR domain-like 27 c2kpjA_ not modelled 96.9 11 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 28 c3op9A_ not modelled 96.9 11 PDB header:transcription regulator Chain: A: PDB Molecule:pli0006 protein; PDBTitle: crystal structure of transcriptional regulator from listeria innocua 29 c3f52A_ not modelled 96.9 15 PDB header:transcription activator Chain: A: PDB Molecule:clp gene regulator (clgr); PDBTitle: crystal structure of the clp gene regulator clgr from c. glutamicum 30 c3ivpD_ not modelled 96.9 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. 31 c3f6wE_ not modelled 96.8 16 PDB header:dna binding protein Chain: E: PDB Molecule:xre-family like protein; PDBTitle: xre-family like protein from pseudomonas syringae pv. tomato str.2 dc3000 32 c3cecA_ not modelled 96.8 20 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 33 d2r1jl1 not modelled 96.7 24 Fold:lambda repressor-like DNA-binding domains Superfamily:lambda repressor-like DNA-binding domains Family:Phage repressors 34 c3bdnB_ not modelled 96.6 16 PDB header:transcription/dna Chain: B: PDB Molecule:lambda repressor; PDBTitle: crystal structure of the lambda repressor 35 c3kxaD_ not modelled 96.6 25 PDB header:structural genomics, unknown function Chain: D: PDB Molecule:putative uncharacterized protein; PDBTitle: crystal structure of ngo0477 from neisseria gonorrhoeae 36 c2o38A_ not modelled 96.3 18 PDB header:structural genomics, unknown function Chain: A: PDB Molecule:hypothetical protein; PDBTitle: putative xre family transcriptional regulator 37 d2o38a1 not modelled 96.3 18 Fold:lambda repressor-like DNA-binding domains Superfamily:lambda repressor-like DNA-binding domains Family:NE1354 38 d2a6ca1 not modelled 96.3 12 Fold:lambda repressor-like DNA-binding domains Superfamily:lambda repressor-like DNA-binding domains Family:NE1354 39 c3bd1B_ not modelled 96.2 25 PDB header:transcription Chain: B: PDB Molecule:cro protein; PDBTitle: structure of the cro protein from putative prophage element xfaso 1 in2 xylella fastidiosa strain ann-1 40 c3mlfC_ not modelled 96.0 15 PDB header:transcription regulator Chain: C: PDB Molecule:transcriptional regulator; PDBTitle: putative transcriptional regulator from staphylococcus aureus. 41 c3lisB_ not modelled 95.9 13 PDB header:transcription Chain: B: PDB Molecule:csp231i c protein; PDBTitle: crystal structure of the restriction-modification controller protein2 c.csp231i (monoclinic form) 42 c2wusR_ not modelled 95.9 9 PDB header:structural protein Chain: R: PDB Molecule:putative uncharacterized protein; PDBTitle: bacterial actin mreb assembles in complex with cell shape2 protein rodz 43 c3eusB_ not modelled 95.8 14 PDB header:dna binding protein Chain: B: PDB Molecule:dna-binding protein; PDBTitle: the crystal structure of the dna binding protein from silicibacter2 pomeroyi 44 d2hsga1 not modelled 95.6 17 Fold:lambda repressor-like DNA-binding domains Superfamily:lambda repressor-like DNA-binding domains Family:GalR/LacI-like bacterial regulator 45 c2fjrB_ not modelled 95.6 15 PDB header:transcription regulator Chain: B: PDB Molecule:repressor protein ci; PDBTitle: crystal structure of bacteriophage 186 46 c3h5tA_ not modelled 95.6 26 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 47 c2xcjB_ not modelled 95.5 20 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 48 d1lcda_ not modelled 95.4 16 Fold:lambda repressor-like DNA-binding domains Superfamily:lambda repressor-like DNA-binding domains Family:GalR/LacI-like bacterial regulator 49 d2bjca1 not modelled 95.2 16 Fold:lambda repressor-like DNA-binding domains Superfamily:lambda repressor-like DNA-binding domains Family:GalR/LacI-like bacterial regulator 50 c3fymA_ not modelled 95.0 11 PDB header:dna binding protein Chain: A: PDB Molecule:putative uncharacterized protein; PDBTitle: the 1a structure of ymfm, a putative dna-binding membrane2 protein from staphylococcus aureus 51 d1x57a1 not modelled 94.9 20 Fold:lambda repressor-like DNA-binding domains Superfamily:lambda repressor-like DNA-binding domains Family:EDF1-like 52 d1efaa1 not modelled 94.9 17 Fold:lambda repressor-like DNA-binding domains Superfamily:lambda repressor-like DNA-binding domains Family:GalR/LacI-like bacterial regulator 53 c2l8nA_ not modelled 94.8 23 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 54 c2lcvA_ not modelled 94.7 23 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 55 d1uxca_ not modelled 94.7 18 Fold:lambda repressor-like DNA-binding domains Superfamily:lambda repressor-like DNA-binding domains Family:GalR/LacI-like bacterial regulator 56 c2jvlA_ not modelled 94.6 17 PDB header:transcription Chain: A: PDB Molecule:trmbf1; PDBTitle: nmr structure of the c-terminal domain of mbf1 of trichoderma reesei 57 c3dnvB_ not modelled 94.3 12 PDB header:transcription/dna Chain: B: PDB Molecule:hth-type transcriptional regulator hipb; PDBTitle: mdt protein 58 c1bdhA_ not modelled 94.2 15 PDB header:transcription/dna Chain: A: PDB Molecule:protein (purine repressor); PDBTitle: purine repressor mutant-hypoxanthine-palindromic operator2 complex 59 c3kjxD_ not modelled 94.1 28 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 60 c3fmyA_ not modelled 94.0 13 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) 61 d1uxda_ not modelled 93.9 18 Fold:lambda repressor-like DNA-binding domains Superfamily:lambda repressor-like DNA-binding domains Family:GalR/LacI-like bacterial regulator 62 d2ppxa1 not modelled 93.9 21 Fold:lambda repressor-like DNA-binding domains Superfamily:lambda repressor-like DNA-binding domains Family:SinR domain-like 63 c2ppxA_ not modelled 93.9 21 PDB header:structural genomics, unknown function Chain: A: PDB Molecule:uncharacterized protein atu1735; PDBTitle: crystal structure of a hth xre-family like protein from agrobacterium2 tumefaciens 64 d1dwka1 not modelled 93.9 22 Fold:lambda repressor-like DNA-binding domains Superfamily:lambda repressor-like DNA-binding domains Family:Cyanase N-terminal domain 65 c3pxpA_ not modelled 93.8 17 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 66 c1zvvA_ not modelled 93.6 20 PDB header:transcription/dna Chain: A: PDB Molecule:glucose-resistance amylase regulator; PDBTitle: crystal structure of a ccpa-crh-dna complex 67 d1qpza1 not modelled 93.4 15 Fold:lambda repressor-like DNA-binding domains Superfamily:lambda repressor-like DNA-binding domains Family:GalR/LacI-like bacterial regulator 68 c2ef8A_ not modelled 93.3 18 PDB header:transcription regulator Chain: A: PDB Molecule:putative transcription factor; PDBTitle: crystal structure of c.ecot38is 69 d1k78a1 not modelled 92.9 24 Fold:DNA/RNA-binding 3-helical bundle Superfamily:Homeodomain-like Family:Paired domain 70 c2iv1J_ not modelled 92.3 22 PDB header:lyase Chain: J: PDB Molecule:cyanate hydratase; PDBTitle: site directed mutagenesis of key residues involved in the2 catalytic mechanism of cyanase 71 c1u78A_ not modelled 92.1 18 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 72 d1pdnc_ not modelled 90.2 21 Fold:DNA/RNA-binding 3-helical bundle Superfamily:Homeodomain-like Family:Paired domain 73 c2gm4B_ not modelled 90.1 12 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 74 c2elhA_ not modelled 89.8 28 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 75 d6paxa1 not modelled 89.4 24 Fold:DNA/RNA-binding 3-helical bundle Superfamily:Homeodomain-like Family:Paired domain 76 c6paxA_ not modelled 88.4 24 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 77 d2coba1 not modelled 88.0 15 Fold:DNA/RNA-binding 3-helical bundle Superfamily:Homeodomain-like Family:Psq domain 78 d2cg4a1 not modelled 86.5 21 Fold:DNA/RNA-binding 3-helical bundle Superfamily:"Winged helix" DNA-binding domain Family:Lrp/AsnC-like transcriptional regulator N-terminal domain 79 d1bw6a_ not modelled 86.4 26 Fold:DNA/RNA-binding 3-helical bundle Superfamily:Homeodomain-like Family:Centromere-binding 80 c3gn5B_ not modelled 86.0 15 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) 81 c2k27A_ not modelled 84.8 24 PDB header:transcription regulator Chain: A: PDB Molecule:paired box protein pax-8; PDBTitle: solution structure of human pax8 paired box domain 82 c3mzyA_ not modelled 84.5 14 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 83 d1hlva1 not modelled 83.8 24 Fold:DNA/RNA-binding 3-helical bundle Superfamily:Homeodomain-like Family:Centromere-binding 84 c2cg4B_ not modelled 82.2 21 PDB header:transcription Chain: B: PDB Molecule:regulatory protein asnc; PDBTitle: structure of e.coli asnc 85 c2r0qF_ not modelled 82.1 7 PDB header:recombination/dna Chain: F: PDB Molecule:putative transposon tn552 dna-invertase bin3; PDBTitle: crystal structure of a serine recombinase- dna regulatory2 complex 86 c2vbzA_ not modelled 82.1 24 PDB header:dna-binding protein Chain: A: PDB Molecule:transcriptional regulatory protein; PDBTitle: feast or famine regulatory protein (rv3291c)from m.2 tuberculosis complexed with l-tryptophan 87 c2dbbA_ not modelled 81.5 6 PDB header:transcriptional regulator Chain: A: PDB Molecule:putative hth-type transcriptional regulator ph0061; PDBTitle: crystal structure of ph0061 88 d1i1ga1 not modelled 80.5 21 Fold:DNA/RNA-binding 3-helical bundle Superfamily:"Winged helix" DNA-binding domain Family:Lrp/AsnC-like transcriptional regulator N-terminal domain 89 c2e1cA_ not modelled 79.9 27 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 90 c2l4aA_ not modelled 79.8 33 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 91 c2p6tH_ not modelled 79.5 27 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 92 d2obpa1 not modelled 79.4 26 Fold:DNA/RNA-binding 3-helical bundle Superfamily:"Winged helix" DNA-binding domain Family:ReutB4095-like 93 d1r71a_ not modelled 79.4 19 Fold:DNA/RNA-binding 3-helical bundle Superfamily:KorB DNA-binding domain-like Family:KorB DNA-binding domain-like 94 d1umqa_ not modelled 79.2 18 Fold:DNA/RNA-binding 3-helical bundle Superfamily:Homeodomain-like Family:FIS-like 95 c1umqA_ not modelled 79.2 18 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 96 d2jn6a1 not modelled 79.0 21 Fold:DNA/RNA-binding 3-helical bundle Superfamily:Homeodomain-like Family:Cgl2762-like 97 d1vz0a1 not modelled 78.8 35 Fold:DNA/RNA-binding 3-helical bundle Superfamily:KorB DNA-binding domain-like Family:KorB DNA-binding domain-like 98 c3e7lD_ not modelled 78.3 17 PDB header:transcription regulator Chain: D: PDB Molecule:transcriptional regulator (ntrc family); PDBTitle: crystal structure of sigma54 activator ntrc4's dna binding2 domain 99 c2cfxD_ not modelled 78.2 25 PDB header:transcription Chain: D: PDB Molecule:hth-type transcriptional regulator lrpc; PDBTitle: structure of b.subtilis lrpc 100 c2ia0A_ not modelled 78.1 18 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) 101 c3i4pA_ not modelled 78.0 18 PDB header:transcription regulator Chain: A: PDB Molecule:transcriptional regulator, asnc family; PDBTitle: crystal structure of asnc family transcriptional regulator from2 agrobacterium tumefaciens 102 c2e7xA_ not modelled 77.6 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 103 c3m1eA_ not modelled 77.5 9 PDB header:transcription regulator Chain: A: PDB Molecule:hth-type transcriptional regulator benm; PDBTitle: crystal structure of benm_dbd 104 c1r71B_ not modelled 76.8 19 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 105 c1i1gA_ not modelled 76.3 18 PDB header:transcription Chain: A: PDB Molecule:transcriptional regulator lrpa; PDBTitle: crystal structure of the lrp-like transcriptional regulator from the2 archaeon pyrococcus furiosus 106 d1ntca_ not modelled 76.2 20 Fold:DNA/RNA-binding 3-helical bundle Superfamily:Homeodomain-like Family:FIS-like 107 c2oerA_ not modelled 75.7 21 PDB header:transcription Chain: A: PDB Molecule:probable transcriptional regulator; PDBTitle: probable transcriptional regulator from pseudomonas2 aeruginosa 108 d2cyya1 not modelled 75.7 27 Fold:DNA/RNA-binding 3-helical bundle Superfamily:"Winged helix" DNA-binding domain Family:Lrp/AsnC-like transcriptional regulator N-terminal domain 109 c1or7A_ not modelled 75.2 15 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 110 d1fipa_ not modelled 74.9 14 Fold:DNA/RNA-binding 3-helical bundle Superfamily:Homeodomain-like Family:FIS-like 111 d1xsva_ not modelled 74.8 13 Fold:DNA/RNA-binding 3-helical bundle Superfamily:Sigma3 and sigma4 domains of RNA polymerase sigma factors Family:YlxM/p13-like 112 c1rr7A_ not modelled 74.5 22 PDB header:transcription Chain: A: PDB Molecule:middle operon regulator; PDBTitle: crystal structure of the middle operon regulator protein of2 bacteriophage mu 113 d1rr7a_ not modelled 74.5 22 Fold:DNA/RNA-binding 3-helical bundle Superfamily:Homeodomain-like Family:Middle operon regulator, Mor 114 c1s7eA_ not modelled 74.2 27 PDB header:transcription Chain: A: PDB Molecule:hepatocyte nuclear factor 6; PDBTitle: solution structure of hnf-6 115 d1mkma1 not modelled 74.0 13 Fold:DNA/RNA-binding 3-helical bundle Superfamily:"Winged helix" DNA-binding domain Family:Transcriptional regulator IclR, N-terminal domain 116 c3tgnA_ not modelled 71.8 18 PDB header:transcription Chain: A: PDB Molecule:adc operon repressor adcr; PDBTitle: crystal structure of the zinc-dependent marr family transcriptional2 regulator adcr in the zn(ii)-bound state 117 c3hugA_ not modelled 71.4 19 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 118 d2cfxa1 not modelled 71.4 26 Fold:DNA/RNA-binding 3-helical bundle Superfamily:"Winged helix" DNA-binding domain Family:Lrp/AsnC-like transcriptional regulator N-terminal domain 119 c2i10A_ not modelled 71.3 13 PDB header:transcription Chain: A: PDB Molecule:putative tetr transcriptional regulator; PDBTitle: putative tetr transcriptional regulator from rhodococcus sp. rha1 120 c3k2zA_ not modelled 71.1 21 PDB header:hydrolase Chain: A: PDB Molecule:lexa repressor; PDBTitle: crystal structure of a lexa protein from thermotoga maritima

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