Secondary structure and disorder prediction

		1	.	.	.	.	.	.	.	.	10	.	.	.	.	.	.	.	.	.	20	.	.	.	.	.	.	.	.	.	30	.	.	.	.	.	.	.	.	.	40	.	.	.	.	.	.	.	.	.	50	.	.	.	.	.	.	.	.	.	60
Sequence		M	S	G	K	R	Y	P	E	E	F	K	T	E	A	V	K	Q	V	V	D	L	G	Y	S	V	A	S	V	A	T	R	L	D	I	T	T	H	S	L	Y	A	W	I	K	K	Y	G	P	D	S	S	T	N	K	E	Q	S	D	A	Q
Secondary structure
SS confidence
Disorder		?	?	?	?	?	?	?																																								?	?	?	?	?	?	?	?	?	?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	70	.	.	.	.	.	.	.	.	.	80	.	.	.	.	.	.	.	.	.	90	.	.	.	.	.	.	.	.	.	100	.	.	.	.	.	.	.	.	.	110	.	.
Sequence		A	E	I	R	R	L	Q	K	E	L	K	R	V	T	D	E	R	D	I	L	K	K	A	A	V	D	S	I	C	Q	C	N	T	P	F	N	Y	L	F	R	C	F	E	L	Q	C	L	S	R	S	V	V
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 2jn6 chain A domain 1 Region: 1 - 91 Aligned: 88 Modelled: 91 Confidence: 99.8% Identity: 27% Fold: DNA/RNA-binding 3-helical bundle Superfamily: Homeodomain-like Family: Cgl2762-like Phyre2 PDB 2rn7 chain A Region: 1 - 89 Aligned: 89 Modelled: 89 Confidence: 99.8% Identity: 20% 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 Phyre2 PDB 1hlv chain A Region: 2 - 94 Aligned: 93 Modelled: 93 Confidence: 98.1% Identity: 16% 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 Phyre2 PDB 6pax chain A Region: 3 - 72 Aligned: 69 Modelled: 70 Confidence: 98.0% Identity: 12% 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 1pdn chain C Region: 3 - 56 Aligned: 53 Modelled: 54 Confidence: 97.9% Identity: 13% Fold: DNA/RNA-binding 3-helical bundle Superfamily: Homeodomain-like Family: Paired domain Phyre2 PDB 2elh chain A Region: 2 - 45 Aligned: 43 Modelled: 44 Confidence: 97.9% Identity: 26% 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 Phyre2 PDB 6pax chain A domain 1 Region: 3 - 55 Aligned: 52 Modelled: 53 Confidence: 97.8% Identity: 13% Fold: DNA/RNA-binding 3-helical bundle Superfamily: Homeodomain-like Family: Paired domain Phyre2 PDB 1u78 chain A Region: 2 - 58 Aligned: 56 Modelled: 57 Confidence: 97.7% 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 1k78 chain A domain 1 Region: 4 - 55 Aligned: 51 Modelled: 52 Confidence: 97.7% Identity: 12% Fold: DNA/RNA-binding 3-helical bundle Superfamily: Homeodomain-like Family: Paired domain Phyre2 PDB 1bw6 chain A Region: 2 - 44 Aligned: 43 Modelled: 43 Confidence: 97.5% Identity: 16% Fold: DNA/RNA-binding 3-helical bundle Superfamily: Homeodomain-like Family: Centromere-binding Phyre2 PDB 2cob chain A domain 1 Region: 2 - 57 Aligned: 56 Modelled: 56 Confidence: 97.5% Identity: 18% Fold: DNA/RNA-binding 3-helical bundle Superfamily: Homeodomain-like Family: Psq domain Phyre2 PDB 1hlv chain A domain 1 Region: 2 - 45 Aligned: 44 Modelled: 44 Confidence: 97.4% Identity: 16% Fold: DNA/RNA-binding 3-helical bundle Superfamily: Homeodomain-like Family: Centromere-binding Phyre2 PDB 2w48 chain D Region: 8 - 72 Aligned: 65 Modelled: 65 Confidence: 96.9% Identity: 14% PDB header:transcription Chain: D: PDB Molecule:sorbitol operon regulator; PDBTitle: crystal structure of the full-length sorbitol operon2 regulator sorc from klebsiella pneumoniae Phyre2 PDB 3hef chain B Region: 5 - 83 Aligned: 67 Modelled: 79 Confidence: 96.8% Identity: 16% PDB header:viral protein Chain: B: PDB Molecule:gene 1 protein; PDBTitle: crystal structure of the bacteriophage sf6 terminase small2 subunit Phyre2 PDB 2glo chain A Region: 2 - 45 Aligned: 44 Modelled: 44 Confidence: 96.8% Identity: 16% PDB header:transcription/dna Chain: A: PDB Molecule:brinker cg9653-pa; PDBTitle: solution structure of the brinker dna binding domain in2 complex with the omb enhancer Phyre2 PDB 2k27 chain A Region: 3 - 70 Aligned: 67 Modelled: 68 Confidence: 96.6% Identity: 13% PDB header:transcription regulator Chain: A: PDB Molecule:paired box protein pax-8; PDBTitle: solution structure of human pax8 paired box domain Phyre2 PDB 2ao9 chain A domain 1 Region: 7 - 45 Aligned: 39 Modelled: 39 Confidence: 95.1% Identity: 21% Fold: DNA/RNA-binding 3-helical bundle Superfamily: Homeodomain-like Family: Nanomeric phage protein-like Phyre2 PDB 1ntc chain A Region: 10 - 49 Aligned: 40 Modelled: 40 Confidence: 94.6% Identity: 18% Fold: DNA/RNA-binding 3-helical bundle Superfamily: Homeodomain-like Family: FIS-like Phyre2 PDB 1iuf chain A Region: 1 - 45 Aligned: 45 Modelled: 45 Confidence: 94.6% Identity: 13% PDB header:dna binding protein Chain: A: PDB Molecule:centromere abp1 protein; PDBTitle: low resolution solution structure of the two dna-binding2 domains in schizosaccharomyces pombe abp1 protein Phyre2 PDB 3e7l chain D Region: 10 - 53 Aligned: 44 Modelled: 44 Confidence: 94.4% Identity: 18% PDB header:transcription regulator Chain: D: PDB Molecule:transcriptional regulator (ntrc family); PDBTitle: crystal structure of sigma54 activator ntrc4's dna binding2 domain Phyre2 1 d2jn6a1 2 c2rn7A_ 3 c1hlvA_ 4 c6paxA_ 5 d1pdnc_ 6 c2elhA_ 7 d6paxa1 8 c1u78A_ 9 d1k78a1 10 d1bw6a_ 11 d2coba1 12 d1hlva1 13 c2w48D_ 14 c3hefB_ 15 c2gloA_ 16 c2k27A_ 17 d2ao9a1 18 d1ntca_ 19 c1iufA_ 20 c3e7lD_ 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 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 239 240 241 242 243 244 245 246 247 248 249 250 251 252 253 254 255 256 257 258 259 260 261 262 263 264 265 266 267 268 269 270 271 272 273 274 275 276 277 278 279 280 281 282 283 284 285 286 287 288 289 290 291 292 293 294 295 296 297 298 299 300 301 302 303 304 305 306 307 308 309 310 311 312 313 314 315 316 317 318 319 320 321 322 323 324 325 326 327 328 329 330 331 332 333 334 335 336 337 338 339 340 341 342 343 344 345 346 347 348 349 350 351 352 353 354 355 356 357 358 359 360 361 362 363 364 365 366 367 368 369 370 371 372 373 374 375 376 377 378 379 380 381 382 383 384 385 386 387 388 389 390 391 392 393 394 395 396 397 398 399 400 401 402 403 404 405 406 407 408 409 410 411 412 413 414 415 416 417 418 419 420 421 422 423 424 425 426 427 428 429 430 431 432 433 434 435 436 437 438 439 440 441 442 443 444 445 446 447 448 449 450 451 452 453 454 455 456 457 458 459 460 461 462 463 464 465 466 467 468 469 470 471 472 473 474 475 476 477 478 479 480 481 482 483 484 485 486 487 488 489 490 491 492 493 494 495 496 497 498 499

Detailed template information

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

1 d2jn6a1 99.8 27 Fold:DNA/RNA-binding 3-helical bundle Superfamily:Homeodomain-like Family:Cgl2762-like 2 c2rn7A_ 99.8 20 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 3 c1hlvA_ 98.1 16 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 4 c6paxA_ 98.0 12 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 5 d1pdnc_ 97.9 13 Fold:DNA/RNA-binding 3-helical bundle Superfamily:Homeodomain-like Family:Paired domain 6 c2elhA_ 97.9 26 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 7 d6paxa1 97.8 13 Fold:DNA/RNA-binding 3-helical bundle Superfamily:Homeodomain-like Family:Paired domain 8 c1u78A_ 97.7 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 9 d1k78a1 97.7 12 Fold:DNA/RNA-binding 3-helical bundle Superfamily:Homeodomain-like Family:Paired domain 10 d1bw6a_ 97.5 16 Fold:DNA/RNA-binding 3-helical bundle Superfamily:Homeodomain-like Family:Centromere-binding 11 d2coba1 97.5 18 Fold:DNA/RNA-binding 3-helical bundle Superfamily:Homeodomain-like Family:Psq domain 12 d1hlva1 97.4 16 Fold:DNA/RNA-binding 3-helical bundle Superfamily:Homeodomain-like Family:Centromere-binding 13 c2w48D_ 96.9 14 PDB header:transcription Chain: D: PDB Molecule:sorbitol operon regulator; PDBTitle: crystal structure of the full-length sorbitol operon2 regulator sorc from klebsiella pneumoniae 14 c3hefB_ 96.8 16 PDB header:viral protein Chain: B: PDB Molecule:gene 1 protein; PDBTitle: crystal structure of the bacteriophage sf6 terminase small2 subunit 15 c2gloA_ 96.8 16 PDB header:transcription/dna Chain: A: PDB Molecule:brinker cg9653-pa; PDBTitle: solution structure of the brinker dna binding domain in2 complex with the omb enhancer 16 c2k27A_ 96.6 13 PDB header:transcription regulator Chain: A: PDB Molecule:paired box protein pax-8; PDBTitle: solution structure of human pax8 paired box domain 17 d2ao9a1 95.1 21 Fold:DNA/RNA-binding 3-helical bundle Superfamily:Homeodomain-like Family:Nanomeric phage protein-like 18 d1ntca_ 94.6 18 Fold:DNA/RNA-binding 3-helical bundle Superfamily:Homeodomain-like Family:FIS-like 19 c1iufA_ 94.6 13 PDB header:dna binding protein Chain: A: PDB Molecule:centromere abp1 protein; PDBTitle: low resolution solution structure of the two dna-binding2 domains in schizosaccharomyces pombe abp1 protein 20 c3e7lD_ 94.4 18 PDB header:transcription regulator Chain: D: PDB Molecule:transcriptional regulator (ntrc family); PDBTitle: crystal structure of sigma54 activator ntrc4's dna binding2 domain 21 c2r0qF_ not modelled 94.4 18 PDB header:recombination/dna Chain: F: PDB Molecule:putative transposon tn552 dna-invertase bin3; PDBTitle: crystal structure of a serine recombinase- dna regulatory2 complex 22 c3hosA_ not modelled 94.2 15 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 23 c2kpjA_ not modelled 93.9 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 24 d1umqa_ not modelled 93.9 16 Fold:DNA/RNA-binding 3-helical bundle Superfamily:Homeodomain-like Family:FIS-like 25 c1umqA_ not modelled 93.9 16 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 26 d1ijwc_ not modelled 93.8 13 Fold:DNA/RNA-binding 3-helical bundle Superfamily:Homeodomain-like Family:Recombinase DNA-binding domain 27 c2o8xA_ not modelled 93.8 17 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 28 d1rp3a2 not modelled 93.6 12 Fold:DNA/RNA-binding 3-helical bundle Superfamily:Sigma3 and sigma4 domains of RNA polymerase sigma factors Family:Sigma4 domain 29 d1fipa_ not modelled 93.5 18 Fold:DNA/RNA-binding 3-helical bundle Superfamily:Homeodomain-like Family:FIS-like 30 c1or7A_ not modelled 93.5 16 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 31 d1etxa_ not modelled 93.4 23 Fold:DNA/RNA-binding 3-helical bundle Superfamily:Homeodomain-like Family:FIS-like 32 c2cg4B_ not modelled 93.4 7 PDB header:transcription Chain: B: PDB Molecule:regulatory protein asnc; PDBTitle: structure of e.coli asnc 33 d1hcra_ not modelled 93.4 13 Fold:DNA/RNA-binding 3-helical bundle Superfamily:Homeodomain-like Family:Recombinase DNA-binding domain 34 c2l0kA_ not modelled 93.3 16 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 35 c3mzyA_ not modelled 93.3 24 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 36 c2gm4B_ not modelled 93.2 18 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 37 d1or7a1 not modelled 93.2 17 Fold:DNA/RNA-binding 3-helical bundle Superfamily:Sigma3 and sigma4 domains of RNA polymerase sigma factors Family:Sigma4 domain 38 c2zhhA_ not modelled 93.0 13 PDB header:transcription Chain: A: PDB Molecule:redox-sensitive transcriptional activator soxr; PDBTitle: crystal structure of soxr 39 c3hugA_ not modelled 93.0 17 PDB header:transcription/membrane protein Chain: A: PDB Molecule:rna polymerase sigma factor; PDBTitle: crystal structure of mycobacterium tuberculosis anti-sigma factor rsla2 in complex with -35 promoter binding domain of sigl 40 d1xsva_ not modelled 92.4 15 Fold:DNA/RNA-binding 3-helical bundle Superfamily:Sigma3 and sigma4 domains of RNA polymerase sigma factors Family:YlxM/p13-like 41 c2vz4A_ not modelled 92.3 16 PDB header:transcription Chain: A: PDB Molecule:hth-type transcriptional activator tipa; PDBTitle: the n-terminal domain of merr-like protein tipal bound to2 promoter dna 42 d1jhga_ not modelled 92.2 6 Fold:DNA/RNA-binding 3-helical bundle Superfamily:TrpR-like Family:Trp repressor, TrpR 43 d2ezla_ not modelled 92.2 24 Fold:DNA/RNA-binding 3-helical bundle Superfamily:Homeodomain-like Family:Recombinase DNA-binding domain 44 d1trra_ not modelled 92.1 10 Fold:DNA/RNA-binding 3-helical bundle Superfamily:TrpR-like Family:Trp repressor, TrpR 45 c2e7xA_ not modelled 92.1 26 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 46 d1r1ua_ not modelled 91.9 9 Fold:DNA/RNA-binding 3-helical bundle Superfamily:"Winged helix" DNA-binding domain Family:ArsR-like transcriptional regulators 47 c3i4pA_ not modelled 91.8 16 PDB header:transcription regulator Chain: A: PDB Molecule:transcriptional regulator, asnc family; PDBTitle: crystal structure of asnc family transcriptional regulator from2 agrobacterium tumefaciens 48 c2ia0A_ not modelled 91.8 9 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) 49 d1q06a_ not modelled 91.8 18 Fold:Putative DNA-binding domain Superfamily:Putative DNA-binding domain Family:DNA-binding N-terminal domain of transcription activators 50 c2cfxD_ not modelled 91.6 5 PDB header:transcription Chain: D: PDB Molecule:hth-type transcriptional regulator lrpc; PDBTitle: structure of b.subtilis lrpc 51 c3gp4B_ not modelled 91.5 6 PDB header:transcription regulator Chain: B: PDB Molecule:transcriptional regulator, merr family; PDBTitle: crystal structure of putative merr family transcriptional regulator2 from listeria monocytogenes 52 c1rp3G_ not modelled 91.4 12 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 53 c2oqgA_ not modelled 91.2 18 PDB header:transcription Chain: A: PDB Molecule:possible transcriptional regulator, arsr family protein; PDBTitle: arsr-like transcriptional regulator from rhodococcus sp. rha1 54 c3frwF_ not modelled 91.2 7 PDB header:structural genomics, unknown function Chain: F: PDB Molecule:putative trp repressor protein; PDBTitle: crystal structure of putative trpr protein from ruminococcus obeum 55 d1ulya_ not modelled 91.1 16 Fold:DNA/RNA-binding 3-helical bundle Superfamily:"Winged helix" DNA-binding domain Family:Hypothetical protein PH1932 56 c1r71B_ not modelled 91.1 5 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 57 c1r22B_ not modelled 91.0 7 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 58 c3op9A_ not modelled 91.0 14 PDB header:transcription regulator Chain: A: PDB Molecule:pli0006 protein; PDBTitle: crystal structure of transcriptional regulator from listeria innocua 59 d1g2ha_ not modelled 90.9 19 Fold:DNA/RNA-binding 3-helical bundle Superfamily:Homeodomain-like Family:FIS-like 60 d1r71a_ not modelled 90.9 5 Fold:DNA/RNA-binding 3-helical bundle Superfamily:KorB DNA-binding domain-like Family:KorB DNA-binding domain-like 61 d1r8da_ not modelled 90.7 19 Fold:Putative DNA-binding domain Superfamily:Putative DNA-binding domain Family:DNA-binding N-terminal domain of transcription activators 62 d1s7oa_ not modelled 90.7 14 Fold:DNA/RNA-binding 3-helical bundle Superfamily:Sigma3 and sigma4 domains of RNA polymerase sigma factors Family:YlxM/p13-like 63 d1r1ta_ not modelled 90.6 5 Fold:DNA/RNA-binding 3-helical bundle Superfamily:"Winged helix" DNA-binding domain Family:ArsR-like transcriptional regulators 64 c2vbzA_ not modelled 90.5 12 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 65 c3b7hA_ not modelled 90.5 12 PDB header:structural protein Chain: A: PDB Molecule:prophage lp1 protein 11; PDBTitle: crystal structure of the prophage lp1 protein 11 66 c2p6tH_ not modelled 90.3 5 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 67 c3gpvA_ not modelled 90.3 13 PDB header:transcription regulator Chain: A: PDB Molecule:transcriptional regulator, merr family; PDBTitle: crystal structure of a transcriptional regulator, merr2 family from bacillus thuringiensis 68 d1rzsa_ not modelled 90.3 25 Fold:lambda repressor-like DNA-binding domains Superfamily:lambda repressor-like DNA-binding domains Family:Phage repressors 69 c3korD_ not modelled 90.2 12 PDB header:transcription Chain: D: PDB Molecule:possible trp repressor; PDBTitle: crystal structure of a putative trp repressor from staphylococcus2 aureus 70 d2b5aa1 not modelled 90.1 14 Fold:lambda repressor-like DNA-binding domains Superfamily:lambda repressor-like DNA-binding domains Family:SinR domain-like 71 c3t76A_ not modelled 90.0 9 PDB header:transcription regulator Chain: A: PDB Molecule:transcriptional regulator vanug; PDBTitle: crystal structure of transcriptional regulator vanug, form ii 72 c3f6oB_ not modelled 89.8 11 PDB header:transcription regulator Chain: B: PDB Molecule:probable transcriptional regulator, arsr family PDBTitle: crystal structure of arsr family transcriptional regulator,2 rha00566 73 d1y9qa1 not modelled 89.8 11 Fold:lambda repressor-like DNA-binding domains Superfamily:lambda repressor-like DNA-binding domains Family:Probable transcriptional regulator VC1968, N-terminal domain 74 d1x57a1 not modelled 89.8 13 Fold:lambda repressor-like DNA-binding domains Superfamily:lambda repressor-like DNA-binding domains Family:EDF1-like 75 c3sztB_ not modelled 89.7 17 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 76 d1etob_ not modelled 89.7 18 Fold:DNA/RNA-binding 3-helical bundle Superfamily:Homeodomain-like Family:FIS-like 77 d2cg4a1 not modelled 89.7 7 Fold:DNA/RNA-binding 3-helical bundle Superfamily:"Winged helix" DNA-binding domain Family:Lrp/AsnC-like transcriptional regulator N-terminal domain 78 d1y7ya1 not modelled 89.2 12 Fold:lambda repressor-like DNA-binding domains Superfamily:lambda repressor-like DNA-binding domains Family:SinR domain-like 79 d1vz0a1 not modelled 89.2 11 Fold:DNA/RNA-binding 3-helical bundle Superfamily:KorB DNA-binding domain-like Family:KorB DNA-binding domain-like 80 d1ku7a_ not modelled 89.1 23 Fold:DNA/RNA-binding 3-helical bundle Superfamily:Sigma3 and sigma4 domains of RNA polymerase sigma factors Family:Sigma4 domain 81 c2dbbA_ not modelled 88.6 16 PDB header:transcriptional regulator Chain: A: PDB Molecule:putative hth-type transcriptional regulator ph0061; PDBTitle: crystal structure of ph0061 82 c2jmlA_ not modelled 88.6 16 PDB header:transcription Chain: A: PDB Molecule:dna binding domain/transcriptional regulator; PDBTitle: solution structure of the n-terminal domain of cara repressor 83 c3jthA_ not modelled 88.4 14 PDB header:transcription Chain: A: PDB Molecule:transcription activator hlyu; PDBTitle: crystal structure of a transcriptional regulator hlyu from2 vibrio vulnificus cmcp6 84 c2pbxB_ not modelled 88.2 10 PDB header:transcription Chain: B: PDB Molecule:hemagglutinin/protease regulatory protein; PDBTitle: vibrio cholerae hapr 85 c2jscB_ not modelled 88.2 9 PDB header:transcription Chain: B: PDB Molecule:transcriptional regulator rv1994c/mt2050; PDBTitle: nmr structure of the cadmium metal-sensor cmtr from mycobacterium2 tuberculosis 86 c1zljE_ not modelled 88.1 9 PDB header:transcription Chain: E: PDB Molecule:dormancy survival regulator; PDBTitle: crystal structure of the mycobacterium tuberculosis hypoxic2 response regulator dosr c-terminal domain 87 c3f6vA_ not modelled 88.1 9 PDB header:transcription regulator Chain: A: PDB Molecule:possible transcriptional regulator, arsr family PDBTitle: crystal structure of possible transcriptional regulator for2 arsenical resistance 88 d1l3la1 not modelled 88.0 11 Fold:DNA/RNA-binding 3-helical bundle Superfamily:C-terminal effector domain of the bipartite response regulators Family:GerE-like (LuxR/UhpA family of transcriptional regulators) 89 d1a04a1 not modelled 87.9 23 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) 90 c3pqkD_ not modelled 87.8 14 PDB header:transcription Chain: D: PDB Molecule:biofilm growth-associated repressor; PDBTitle: crystal structure of the transcriptional repressor bigr from xylella2 fastidiosa 91 c3bs3A_ not modelled 87.8 7 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 92 d1adra_ not modelled 87.8 9 Fold:lambda repressor-like DNA-binding domains Superfamily:lambda repressor-like DNA-binding domains Family:Phage repressors 93 c3gziA_ not modelled 87.8 5 PDB header:transcription Chain: A: PDB Molecule:transcriptional regulator, tetr family; PDBTitle: crystal structure of a transcriptional regulator of the tetr family2 (shew_3567) from shewanella loihica pv-4 at 2.05 a resolution 94 d1biaa1 not modelled 87.8 7 Fold:DNA/RNA-binding 3-helical bundle Superfamily:"Winged helix" DNA-binding domain Family:Biotin repressor-like 95 d1sq8a_ not modelled 87.8 11 Fold:lambda repressor-like DNA-binding domains Superfamily:lambda repressor-like DNA-binding domains Family:Phage repressors 96 c2kkoB_ not modelled 87.7 9 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. 97 c1i1gA_ not modelled 87.6 12 PDB header:transcription Chain: A: PDB Molecule:transcriptional regulator lrpa; PDBTitle: crystal structure of the lrp-like transcriptional regulator from the2 archaeon pyrococcus furiosus 98 d1r69a_ not modelled 87.5 18 Fold:lambda repressor-like DNA-binding domains Superfamily:lambda repressor-like DNA-binding domains Family:Phage repressors 99 d1r8ea1 not modelled 87.4 21 Fold:Putative DNA-binding domain Superfamily:Putative DNA-binding domain Family:DNA-binding N-terminal domain of transcription activators 100 c2krfB_ not modelled 87.4 17 PDB header:transcription Chain: B: PDB Molecule:transcriptional regulatory protein coma; PDBTitle: nmr solution structure of the dna binding domain of competence protein2 a 101 c1rnlA_ not modelled 87.3 22 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 102 d1b0na2 not modelled 87.3 15 Fold:lambda repressor-like DNA-binding domains Superfamily:lambda repressor-like DNA-binding domains Family:SinR domain-like 103 d1yioa1 not modelled 87.2 17 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) 104 c3omtA_ not modelled 87.1 15 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. 105 c2q0oA_ not modelled 87.0 12 PDB header:transcription Chain: A: PDB Molecule:probable transcriptional activator protein trar; PDBTitle: crystal structure of an anti-activation complex in bacterial quorum2 sensing 106 d1utxa_ not modelled 87.0 10 Fold:lambda repressor-like DNA-binding domains Superfamily:lambda repressor-like DNA-binding domains Family:SinR domain-like 107 d1p4wa_ not modelled 86.9 18 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) 108 c2jpcA_ not modelled 86.8 17 PDB header:dna binding protein Chain: A: PDB Molecule:ssrb; PDBTitle: ssrb dna binding protein 109 c3qaoA_ not modelled 86.8 14 PDB header:transcription regulator Chain: A: PDB Molecule:merr-like transcriptional regulator; PDBTitle: the crystal structure of the n-terminal domain of a merr-like2 transcriptional regulator from listeria monocytogenes egd-e 110 c2l4aA_ not modelled 86.8 7 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 111 c2e1cA_ not modelled 86.8 12 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 112 c2w7nA_ not modelled 86.8 22 PDB header:transcription/dna Chain: A: PDB Molecule:trfb transcriptional repressor protein; PDBTitle: crystal structure of kora bound to operator dna: insight2 into repressor cooperation in rp4 gene regulation 113 d1wh5a_ not modelled 86.8 9 Fold:DNA/RNA-binding 3-helical bundle Superfamily:Homeodomain-like Family:Homeodomain 114 d1fsea_ not modelled 86.7 14 Fold:DNA/RNA-binding 3-helical bundle Superfamily:C-terminal effector domain of the bipartite response regulators Family:GerE-like (LuxR/UhpA family of transcriptional regulators) 115 c2ao9H_ not modelled 86.6 24 PDB header:structural genomics, unknown function Chain: H: PDB Molecule:phage protein; PDBTitle: structural genomics, the crystal structure of a phage protein2 (phbc6a51) from bacillus cereus atcc 14579 116 d2cyya1 not modelled 86.5 12 Fold:DNA/RNA-binding 3-helical bundle Superfamily:"Winged helix" DNA-binding domain Family:Lrp/AsnC-like transcriptional regulator N-terminal domain 117 d1ttya_ not modelled 86.5 9 Fold:DNA/RNA-binding 3-helical bundle Superfamily:Sigma3 and sigma4 domains of RNA polymerase sigma factors Family:Sigma4 domain 118 c2ewtA_ not modelled 86.3 10 PDB header:dna binding protein Chain: A: PDB Molecule:putative dna-binding protein; PDBTitle: crystal structure of the dna-binding domain of bldd 119 c3cuoB_ not modelled 86.2 5 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 120 c2xcjB_ not modelled 85.9 11 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

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