Secondary structure and disorder prediction

		1	.	.	.	.	.	.	.	.	10	.	.	.	.	.	.	.	.	.	20	.	.	.	.	.	.	.	.	.	30	.	.	.	.	.	.	.	.	.	40	.	.	.	.	.	.	.	.	.	50	.	.	.	.	.	.	.	.	.	60
Sequence		M	A	S	I	S	I	R	C	P	S	C	S	A	T	E	G	V	V	R	N	G	K	S	T	A	G	H	Q	R	Y	L	C	S	P	C	R	K	T	W	Q	L	Q	F	T	Y	T	A	S	Q	P	G	K	H	Q	K	I	I	D	M	A
Secondary structure
SS confidence
Disorder		?	?	?	?	?	?																		?	?	?																	?	?	?	?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	70	.	.	.	.	.	.	.	.	.	80	.	.	.	.	.	.	.	.	.	90	.
Sequence		M	N	G	V	G	C	R	A	S	A	R	I	M	G	V	G	L	N	T	V	L	R	H	L	K	N	S	G	R	S	R
Secondary structure
SS confidence
Disorder																													?	?	?	?
Disorder confidence

Confidence Key
High(9)											Low (0)

?	Disordered
	Alpha helix
	Beta strand

Domain analysis

Hover over an aligned region to see model and summary info

Please note, only up to the top 20 hits are modelled to reduce computer load

Rank Aligned region

PDB 1k78 chain A domain 1 Region: 44 - 90 Aligned: 47 Modelled: 47 Confidence: 97.8% Identity: 19% Fold: DNA/RNA-binding 3-helical bundle Superfamily: Homeodomain-like Family: Paired domain Phyre2 PDB 6pax chain A domain 1 Region: 36 - 90 Aligned: 52 Modelled: 55 Confidence: 97.8% Identity: 17% Fold: DNA/RNA-binding 3-helical bundle Superfamily: Homeodomain-like Family: Paired domain Phyre2 PDB 2jn6 chain A domain 1 Region: 44 - 89 Aligned: 46 Modelled: 46 Confidence: 97.8% Identity: 13% Fold: DNA/RNA-binding 3-helical bundle Superfamily: Homeodomain-like Family: Cgl2762-like Phyre2 PDB 1pdn chain C Region: 36 - 89 Aligned: 51 Modelled: 54 Confidence: 97.7% Identity: 18% Fold: DNA/RNA-binding 3-helical bundle Superfamily: Homeodomain-like Family: Paired domain Phyre2 PDB 1u78 chain A Region: 43 - 89 Aligned: 47 Modelled: 47 Confidence: 97.7% Identity: 13% PDB header:dna binding protein/dna Chain: A: PDB Molecule:transposable element tc3 transposase; PDBTitle: structure of the bipartite dna-binding domain of tc32 transposase bound to transposon dna Phyre2 PDB 6pax chain A Region: 36 - 89 Aligned: 51 Modelled: 54 Confidence: 97.6% 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 2rn7 chain A Region: 43 - 90 Aligned: 48 Modelled: 48 Confidence: 97.4% Identity: 17% 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 2r0q chain F Region: 51 - 88 Aligned: 38 Modelled: 38 Confidence: 97.3% Identity: 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 Phyre2 PDB 3gn5 chain B Region: 6 - 83 Aligned: 78 Modelled: 78 Confidence: 97.3% Identity: 21% 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) Phyre2 PDB 2gm4 chain B Region: 45 - 87 Aligned: 43 Modelled: 43 Confidence: 96.9% Identity: 16% 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 2k27 chain A Region: 45 - 89 Aligned: 45 Modelled: 45 Confidence: 96.6% Identity: 22% PDB header:transcription regulator Chain: A: PDB Molecule:paired box protein pax-8; PDBTitle: solution structure of human pax8 paired box domain Phyre2 PDB 2elh chain A Region: 44 - 86 Aligned: 43 Modelled: 43 Confidence: 96.5% Identity: 23% 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 3hef chain B Region: 45 - 86 Aligned: 42 Modelled: 42 Confidence: 96.5% Identity: 19% PDB header:viral protein Chain: B: PDB Molecule:gene 1 protein; PDBTitle: crystal structure of the bacteriophage sf6 terminase small2 subunit Phyre2 PDB 1zlj chain E Region: 50 - 89 Aligned: 40 Modelled: 40 Confidence: 96.0% Identity: 10% PDB header:transcription Chain: E: PDB Molecule:dormancy survival regulator; PDBTitle: crystal structure of the mycobacterium tuberculosis hypoxic2 response regulator dosr c-terminal domain Phyre2 PDB 3szt chain B Region: 54 - 89 Aligned: 36 Modelled: 36 Confidence: 95.9% Identity: 19% PDB header:transcription Chain: B: PDB Molecule:quorum-sensing control repressor; PDBTitle: quorum sensing control repressor, qscr, bound to n-3-oxo-dodecanoyl-l-2 homoserine lactone Phyre2 PDB 2q0o chain A Region: 54 - 89 Aligned: 36 Modelled: 36 Confidence: 95.9% Identity: 19% PDB header:transcription Chain: A: PDB Molecule:probable transcriptional activator protein trar; PDBTitle: crystal structure of an anti-activation complex in bacterial quorum2 sensing Phyre2 PDB 2vbz chain A Region: 50 - 91 Aligned: 42 Modelled: 42 Confidence: 95.9% Identity: 10% 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 Phyre2 PDB 2w48 chain D Region: 52 - 89 Aligned: 38 Modelled: 38 Confidence: 95.9% Identity: 18% 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 2cg4 chain A domain 1 Region: 50 - 90 Aligned: 41 Modelled: 41 Confidence: 95.8% Identity: 15% Fold: DNA/RNA-binding 3-helical bundle Superfamily: "Winged helix" DNA-binding domain Family: Lrp/AsnC-like transcriptional regulator N-terminal domain Phyre2 PDB 1p4w chain A Region: 51 - 89 Aligned: 39 Modelled: 39 Confidence: 95.8% Identity: 13% Fold: DNA/RNA-binding 3-helical bundle Superfamily: C-terminal effector domain of the bipartite response regulators Family: GerE-like (LuxR/UhpA family of transcriptional regulators) Phyre2 1 d1k78a1 2 d6paxa1 3 d2jn6a1 4 d1pdnc_ 5 c1u78A_ 6 c6paxA_ 7 c2rn7A_ 8 c2r0qF_ 9 c3gn5B_ 10 c2gm4B_ 11 c2k27A_ 12 c2elhA_ 13 c3hefB_ 14 c1zljE_ 15 c3sztB_ 16 c2q0oA_ 17 c2vbzA_ 18 c2w48D_ 19 d2cg4a1 20 d1p4wa_ 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 d1k78a1 97.8 19 Fold:DNA/RNA-binding 3-helical bundle Superfamily:Homeodomain-like Family:Paired domain 2 d6paxa1 97.8 17 Fold:DNA/RNA-binding 3-helical bundle Superfamily:Homeodomain-like Family:Paired domain 3 d2jn6a1 97.8 13 Fold:DNA/RNA-binding 3-helical bundle Superfamily:Homeodomain-like Family:Cgl2762-like 4 d1pdnc_ 97.7 18 Fold:DNA/RNA-binding 3-helical bundle Superfamily:Homeodomain-like Family:Paired domain 5 c1u78A_ 97.7 13 PDB header:dna binding protein/dna Chain: A: PDB Molecule:transposable element tc3 transposase; PDBTitle: structure of the bipartite dna-binding domain of tc32 transposase bound to transposon dna 6 c6paxA_ 97.6 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 7 c2rn7A_ 97.4 17 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 8 c2r0qF_ 97.3 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 9 c3gn5B_ 97.3 21 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) 10 c2gm4B_ 96.9 16 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 11 c2k27A_ 96.6 22 PDB header:transcription regulator Chain: A: PDB Molecule:paired box protein pax-8; PDBTitle: solution structure of human pax8 paired box domain 12 c2elhA_ 96.5 23 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 13 c3hefB_ 96.5 19 PDB header:viral protein Chain: B: PDB Molecule:gene 1 protein; PDBTitle: crystal structure of the bacteriophage sf6 terminase small2 subunit 14 c1zljE_ 96.0 10 PDB header:transcription Chain: E: PDB Molecule:dormancy survival regulator; PDBTitle: crystal structure of the mycobacterium tuberculosis hypoxic2 response regulator dosr c-terminal domain 15 c3sztB_ 95.9 19 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 16 c2q0oA_ 95.9 19 PDB header:transcription Chain: A: PDB Molecule:probable transcriptional activator protein trar; PDBTitle: crystal structure of an anti-activation complex in bacterial quorum2 sensing 17 c2vbzA_ 95.9 10 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 18 c2w48D_ 95.9 18 PDB header:transcription Chain: D: PDB Molecule:sorbitol operon regulator; PDBTitle: crystal structure of the full-length sorbitol operon2 regulator sorc from klebsiella pneumoniae 19 d2cg4a1 95.8 15 Fold:DNA/RNA-binding 3-helical bundle Superfamily:"Winged helix" DNA-binding domain Family:Lrp/AsnC-like transcriptional regulator N-terminal domain 20 d1p4wa_ 95.8 13 Fold:DNA/RNA-binding 3-helical bundle Superfamily:C-terminal effector domain of the bipartite response regulators Family:GerE-like (LuxR/UhpA family of transcriptional regulators) 21 d1a04a1 not modelled 95.8 20 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) 22 d1xsva_ not modelled 95.8 10 Fold:DNA/RNA-binding 3-helical bundle Superfamily:Sigma3 and sigma4 domains of RNA polymerase sigma factors Family:YlxM/p13-like 23 d1hlva1 not modelled 95.8 20 Fold:DNA/RNA-binding 3-helical bundle Superfamily:Homeodomain-like Family:Centromere-binding 24 c2cg4B_ not modelled 95.8 14 PDB header:transcription Chain: B: PDB Molecule:regulatory protein asnc; PDBTitle: structure of e.coli asnc 25 c3mzyA_ not modelled 95.8 12 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 26 c1hlvA_ not modelled 95.7 18 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 27 c2e7xA_ not modelled 95.7 12 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 28 c1x3uA_ not modelled 95.6 15 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 29 d1bw6a_ not modelled 95.6 20 Fold:DNA/RNA-binding 3-helical bundle Superfamily:Homeodomain-like Family:Centromere-binding 30 c3i4pA_ not modelled 95.6 12 PDB header:transcription regulator Chain: A: PDB Molecule:transcriptional regulator, asnc family; PDBTitle: crystal structure of asnc family transcriptional regulator from2 agrobacterium tumefaciens 31 d1fsea_ not modelled 95.6 13 Fold:DNA/RNA-binding 3-helical bundle Superfamily:C-terminal effector domain of the bipartite response regulators Family:GerE-like (LuxR/UhpA family of transcriptional regulators) 32 c3qp5C_ not modelled 95.6 25 PDB header:transcription Chain: C: PDB Molecule:cvir transcriptional regulator; PDBTitle: crystal structure of cvir bound to antagonist chlorolactone (cl) 33 c2cfxD_ not modelled 95.6 12 PDB header:transcription Chain: D: PDB Molecule:hth-type transcriptional regulator lrpc; PDBTitle: structure of b.subtilis lrpc 34 c2krfB_ not modelled 95.5 10 PDB header:transcription Chain: B: PDB Molecule:transcriptional regulatory protein coma; PDBTitle: nmr solution structure of the dna binding domain of competence protein2 a 35 d1yioa1 not modelled 95.5 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) 36 c3hugA_ not modelled 95.5 20 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 37 c1h0mD_ not modelled 95.5 19 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 38 d1l3la1 not modelled 95.5 20 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 d1or7a1 not modelled 95.5 17 Fold:DNA/RNA-binding 3-helical bundle Superfamily:Sigma3 and sigma4 domains of RNA polymerase sigma factors Family:Sigma4 domain 40 c2ia0A_ not modelled 95.5 7 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) 41 c2jpcA_ not modelled 95.4 17 PDB header:dna binding protein Chain: A: PDB Molecule:ssrb; PDBTitle: ssrb dna binding protein 42 d2coba1 not modelled 95.4 19 Fold:DNA/RNA-binding 3-helical bundle Superfamily:Homeodomain-like Family:Psq domain 43 c2dbbA_ not modelled 95.2 10 PDB header:transcriptional regulator Chain: A: PDB Molecule:putative hth-type transcriptional regulator ph0061; PDBTitle: crystal structure of ph0061 44 c2p6tH_ not modelled 95.2 17 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 45 c2e1cA_ not modelled 95.2 24 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 46 c2rnjA_ not modelled 95.2 19 PDB header:transcription Chain: A: PDB Molecule:response regulator protein vrar; PDBTitle: nmr structure of the s. aureus vrar dna binding domain 47 c1or7A_ not modelled 95.2 17 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 48 d1rp3a2 not modelled 95.1 10 Fold:DNA/RNA-binding 3-helical bundle Superfamily:Sigma3 and sigma4 domains of RNA polymerase sigma factors Family:Sigma4 domain 49 d2cyya1 not modelled 95.1 24 Fold:DNA/RNA-binding 3-helical bundle Superfamily:"Winged helix" DNA-binding domain Family:Lrp/AsnC-like transcriptional regulator N-terminal domain 50 d2cfxa1 not modelled 95.0 12 Fold:DNA/RNA-binding 3-helical bundle Superfamily:"Winged helix" DNA-binding domain Family:Lrp/AsnC-like transcriptional regulator N-terminal domain 51 c1i1gA_ not modelled 95.0 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 52 d1s7oa_ not modelled 94.9 14 Fold:DNA/RNA-binding 3-helical bundle Superfamily:Sigma3 and sigma4 domains of RNA polymerase sigma factors Family:YlxM/p13-like 53 c2o8xA_ not modelled 94.9 10 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 54 c3frwF_ not modelled 94.9 9 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 d1i1ga1 not modelled 94.9 12 Fold:DNA/RNA-binding 3-helical bundle Superfamily:"Winged helix" DNA-binding domain Family:Lrp/AsnC-like transcriptional regulator N-terminal domain 56 c3c3wB_ not modelled 94.7 13 PDB header:transcription Chain: B: PDB Molecule:two component transcriptional regulatory protein devr; PDBTitle: crystal structure of the mycobacterium tuberculosis hypoxic response2 regulator dosr 57 c3korD_ not modelled 94.7 12 PDB header:transcription Chain: D: PDB Molecule:possible trp repressor; PDBTitle: crystal structure of a putative trp repressor from staphylococcus2 aureus 58 d1twfi2 not modelled 94.7 15 Fold:Rubredoxin-like Superfamily:Zinc beta-ribbon Family:Transcriptional factor domain 59 c1rnlA_ not modelled 94.7 20 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 60 c2gqqB_ not modelled 94.7 12 PDB header:transcription Chain: B: PDB Molecule:leucine-responsive regulatory protein; PDBTitle: crystal structure of e. coli leucine-responsive regulatory protein2 (lrp) 61 d1biaa1 not modelled 94.6 14 Fold:DNA/RNA-binding 3-helical bundle Superfamily:"Winged helix" DNA-binding domain Family:Biotin repressor-like 62 c2l4aA_ not modelled 94.6 10 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 63 c3cloC_ not modelled 94.5 25 PDB header:transcription regulator Chain: C: PDB Molecule:transcriptional regulator; PDBTitle: crystal structure of putative transcriptional regulator containing a2 luxr dna binding domain (np_811094.1) from bacteroides3 thetaiotaomicron vpi-5482 at 2.04 a resolution 64 c1rp3G_ not modelled 94.4 10 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 65 d1wiia_ not modelled 94.4 19 Fold:Rubredoxin-like Superfamily:Zinc beta-ribbon Family:Putative zinc binding domain 66 d1g2ha_ not modelled 94.3 22 Fold:DNA/RNA-binding 3-helical bundle Superfamily:Homeodomain-like Family:FIS-like 67 d2hsga1 not modelled 94.2 32 Fold:lambda repressor-like DNA-binding domains Superfamily:lambda repressor-like DNA-binding domains Family:GalR/LacI-like bacterial regulator 68 c2qa4Z_ not modelled 94.1 32 PDB header:ribosome Chain: Z: PDB Molecule:50s ribosomal protein l37ae; PDBTitle: a more complete structure of the the l7/l12 stalk of the2 haloarcula marismortui 50s large ribosomal subunit 69 d1ijwc_ not modelled 94.0 23 Fold:DNA/RNA-binding 3-helical bundle Superfamily:Homeodomain-like Family:Recombinase DNA-binding domain 70 c3iwfA_ not modelled 93.9 11 PDB header:transcription regulator Chain: A: PDB Molecule:transcription regulator rpir family; PDBTitle: the crystal structure of the n-terminal domain of a rpir2 transcriptional regulator from staphylococcus epidermidis to 1.4a 71 c3cc4Z_ not modelled 93.8 32 PDB header:ribosome Chain: Z: PDB Molecule:50s ribosomal protein l37ae; PDBTitle: co-crystal structure of anisomycin bound to the 50s ribosomal subunit 72 d1hcra_ not modelled 93.8 23 Fold:DNA/RNA-binding 3-helical bundle Superfamily:Homeodomain-like Family:Recombinase DNA-binding domain 73 d1vqoz1 not modelled 93.7 32 Fold:Rubredoxin-like Superfamily:Zn-binding ribosomal proteins Family:Ribosomal protein L37ae 74 d1ffkw_ not modelled 93.7 25 Fold:Rubredoxin-like Superfamily:Zn-binding ribosomal proteins Family:Ribosomal protein L37ae 75 d1jhga_ not modelled 93.6 26 Fold:DNA/RNA-binding 3-helical bundle Superfamily:TrpR-like Family:Trp repressor, TrpR 76 c4a17Y_ not modelled 93.6 32 PDB header:ribosome Chain: Y: PDB Molecule:rpl37a; PDBTitle: t.thermophila 60s ribosomal subunit in complex with2 initiation factor 6. this file contains 5s rrna,3 5.8s rrna and proteins of molecule 2. 77 c2zkrz_ not modelled 93.6 25 PDB header:ribosomal protein/rna Chain: Z: PDB Molecule:e site t-rna; PDBTitle: structure of a mammalian ribosomal 60s subunit within an2 80s complex obtained by docking homology models of the rna3 and proteins into an 8.7 a cryo-em map 78 c1yshD_ not modelled 93.6 25 PDB header:structural protein/rna Chain: D: PDB Molecule:ribosomal protein l37a; PDBTitle: localization and dynamic behavior of ribosomal protein l30e 79 d1lcda_ not modelled 93.5 33 Fold:lambda repressor-like DNA-binding domains Superfamily:lambda repressor-like DNA-binding domains Family:GalR/LacI-like bacterial regulator 80 d1qypa_ not modelled 93.5 27 Fold:Rubredoxin-like Superfamily:Zinc beta-ribbon Family:Transcriptional factor domain 81 d2bjca1 not modelled 93.5 33 Fold:lambda repressor-like DNA-binding domains Superfamily:lambda repressor-like DNA-binding domains Family:GalR/LacI-like bacterial regulator 82 c2ewnA_ not modelled 93.5 15 PDB header:ligase, transcription Chain: A: PDB Molecule:bira bifunctional protein; PDBTitle: ecoli biotin repressor with co-repressor analog 83 d1uxca_ not modelled 93.5 24 Fold:lambda repressor-like DNA-binding domains Superfamily:lambda repressor-like DNA-binding domains Family:GalR/LacI-like bacterial regulator 84 d1jj2y_ not modelled 93.4 25 Fold:Rubredoxin-like Superfamily:Zn-binding ribosomal proteins Family:Ribosomal protein L37ae 85 c3hosA_ not modelled 93.2 12 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 86 c3klnC_ not modelled 93.2 33 PDB header:transcription Chain: C: PDB Molecule:transcriptional regulator, luxr family; PDBTitle: vibrio cholerae vpst 87 c3h5tA_ not modelled 93.2 14 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 88 d1ntca_ not modelled 93.1 28 Fold:DNA/RNA-binding 3-helical bundle Superfamily:Homeodomain-like Family:FIS-like 89 d1trra_ not modelled 93.1 19 Fold:DNA/RNA-binding 3-helical bundle Superfamily:TrpR-like Family:Trp repressor, TrpR 90 d1efaa1 not modelled 92.9 32 Fold:lambda repressor-like DNA-binding domains Superfamily:lambda repressor-like DNA-binding domains Family:GalR/LacI-like bacterial regulator 91 d1r1ua_ not modelled 92.9 10 Fold:DNA/RNA-binding 3-helical bundle Superfamily:"Winged helix" DNA-binding domain Family:ArsR-like transcriptional regulators 92 d2isya1 not modelled 92.9 18 Fold:DNA/RNA-binding 3-helical bundle Superfamily:"Winged helix" DNA-binding domain Family:Iron-dependent repressor protein 93 d1fipa_ not modelled 92.9 26 Fold:DNA/RNA-binding 3-helical bundle Superfamily:Homeodomain-like Family:FIS-like 94 c2oqgA_ not modelled 92.8 12 PDB header:transcription Chain: A: PDB Molecule:possible transcriptional regulator, arsr family protein; PDBTitle: arsr-like transcriptional regulator from rhodococcus sp. rha1 95 c1r71B_ not modelled 92.8 14 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 96 d1r1ta_ not modelled 92.8 12 Fold:DNA/RNA-binding 3-helical bundle Superfamily:"Winged helix" DNA-binding domain Family:ArsR-like transcriptional regulators 97 d1uxda_ not modelled 92.7 24 Fold:lambda repressor-like DNA-binding domains Superfamily:lambda repressor-like DNA-binding domains Family:GalR/LacI-like bacterial regulator 98 c3h0gI_ not modelled 92.7 26 PDB header:transcription Chain: I: PDB Molecule:dna-directed rna polymerase ii subunit rpb9; PDBTitle: rna polymerase ii from schizosaccharomyces pombe 99 c1i3qI_ not modelled 92.7 15 PDB header:transcription Chain: I: PDB Molecule:dna-directed rna polymerase ii 14.2kd PDBTitle: rna polymerase ii crystal form i at 3.1 a resolution 100 d1ttya_ not modelled 92.7 8 Fold:DNA/RNA-binding 3-helical bundle Superfamily:Sigma3 and sigma4 domains of RNA polymerase sigma factors Family:Sigma4 domain 101 d1etob_ not modelled 92.7 28 Fold:DNA/RNA-binding 3-helical bundle Superfamily:Homeodomain-like Family:FIS-like 102 d1qpza1 not modelled 92.7 20 Fold:lambda repressor-like DNA-binding domains Superfamily:lambda repressor-like DNA-binding domains Family:GalR/LacI-like bacterial regulator 103 c3kjxD_ not modelled 92.5 30 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 104 c1s1i9_ not modelled 92.5 32 PDB header:ribosome Chain: 9: PDB Molecule:60s ribosomal protein l43; PDBTitle: structure of the ribosomal 80s-eef2-sordarin complex from2 yeast obtained by docking atomic models for rna and protein3 components into a 11.7 a cryo-em map. this file, 1s1i,4 contains 60s subunit. the 40s ribosomal subunit is in file5 1s1h. 105 c3jyw9_ not modelled 92.4 35 PDB header:ribosome Chain: 9: PDB Molecule:60s ribosomal protein l43; PDBTitle: structure of the 60s proteins for eukaryotic ribosome based on cryo-em2 map of thermomyces lanuginosus ribosome at 8.9a resolution 106 d1umqa_ not modelled 92.4 15 Fold:DNA/RNA-binding 3-helical bundle Superfamily:Homeodomain-like Family:FIS-like 107 c1umqA_ not modelled 92.4 15 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 108 d1g3wa1 not modelled 92.3 15 Fold:DNA/RNA-binding 3-helical bundle Superfamily:"Winged helix" DNA-binding domain Family:Iron-dependent repressor protein 109 d1etxa_ not modelled 92.2 28 Fold:DNA/RNA-binding 3-helical bundle Superfamily:Homeodomain-like Family:FIS-like 110 c2l8nA_ not modelled 92.0 29 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 111 d1j5ya1 not modelled 92.0 11 Fold:DNA/RNA-binding 3-helical bundle Superfamily:"Winged helix" DNA-binding domain Family:Biotin repressor-like 112 c1zn2A_ not modelled 92.0 22 PDB header:transcription regulator Chain: A: PDB Molecule:response regulatory protein; PDBTitle: low resolution structure of response regulator styr 113 d1r71a_ not modelled 92.0 14 Fold:DNA/RNA-binding 3-helical bundle Superfamily:KorB DNA-binding domain-like Family:KorB DNA-binding domain-like 114 c1r22B_ not modelled 91.9 12 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 115 c3e7lD_ not modelled 91.8 16 PDB header:transcription regulator Chain: D: PDB Molecule:transcriptional regulator (ntrc family); PDBTitle: crystal structure of sigma54 activator ntrc4's dna binding2 domain 116 c2lcvA_ not modelled 91.8 29 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 117 c2kkoB_ not modelled 91.8 24 PDB header:dna binding protein Chain: B: PDB Molecule:possible transcriptional regulatory protein PDBTitle: solution nmr structure of the homodimeric winged helix-turn-2 helix dna-binding domain (fragment 1-100) mb0332 from3 mycobacterium bovis, a possible arsr-family transcriptional4 regulator. northeast structural genomics consortium target5 mbr242e. 118 c3cuoB_ not modelled 91.7 21 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 119 d1pfta_ not modelled 91.6 23 Fold:Rubredoxin-like Superfamily:Zinc beta-ribbon Family:Transcriptional factor domain 120 d2p4wa1 not modelled 91.5 22 Fold:DNA/RNA-binding 3-helical bundle Superfamily:"Winged helix" DNA-binding domain Family:PF1790-like

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