Secondary structure and disorder prediction

		1	.	.	.	.	.	.	.	.	10	.	.	.	.	.	.	.	.	.	20	.	.	.	.	.	.	.	.	.	30	.	.	.	.	.	.	.	.	.	40	.	.	.	.	.	.	.	.	.	50	.	.	.	.	.	.	.	.	.	60
Sequence		M	A	S	V	S	I	S	C	P	S	C	S	A	T	D	G	V	V	R	N	G	K	S	T	A	G	H	Q	R	Y	L	C	S	H	C	R	K	T	W	Q	L	Q	F	T	Y	T	A	S	Q	P	G	T	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	T	A	R	I	M	G	V	G	L	N	T	I	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 2jn6 chain A domain 1 Region: 44 - 89 Aligned: 46 Modelled: 46 Confidence: 98.0% Identity: 13% Fold: DNA/RNA-binding 3-helical bundle Superfamily: Homeodomain-like Family: Cgl2762-like Phyre2 PDB 1k78 chain A domain 1 Region: 44 - 89 Aligned: 46 Modelled: 46 Confidence: 98.0% Identity: 17% Fold: DNA/RNA-binding 3-helical bundle Superfamily: Homeodomain-like Family: Paired domain Phyre2 PDB 6pax chain A domain 1 Region: 44 - 89 Aligned: 46 Modelled: 46 Confidence: 97.9% Identity: 20% Fold: DNA/RNA-binding 3-helical bundle Superfamily: Homeodomain-like Family: Paired domain Phyre2 PDB 1pdn chain C Region: 36 - 89 Aligned: 51 Modelled: 51 Confidence: 97.9% Identity: 16% 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: 97.8% Identity: 15% 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: 44 - 89 Aligned: 46 Modelled: 46 Confidence: 97.7% Identity: 20% 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 - 89 Aligned: 47 Modelled: 47 Confidence: 97.6% 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: 97.2% Identity: 16% 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 - 85 Aligned: 80 Modelled: 80 Confidence: 97.2% 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 2k27 chain A Region: 44 - 89 Aligned: 46 Modelled: 46 Confidence: 97.0% Identity: 20% PDB header:transcription regulator Chain: A: PDB Molecule:paired box protein pax-8; PDBTitle: solution structure of human pax8 paired box domain Phyre2 PDB 3hef chain B Region: 46 - 86 Aligned: 41 Modelled: 41 Confidence: 96.8% Identity: 17% PDB header:viral protein Chain: B: PDB Molecule:gene 1 protein; PDBTitle: crystal structure of the bacteriophage sf6 terminase small2 subunit Phyre2 PDB 2gm4 chain B Region: 47 - 86 Aligned: 40 Modelled: 40 Confidence: 96.5% Identity: 13% 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 3mzy chain A Region: 49 - 90 Aligned: 42 Modelled: 42 Confidence: 96.5% Identity: 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 Phyre2 PDB 1xsv chain A Region: 48 - 90 Aligned: 43 Modelled: 43 Confidence: 96.4% Identity: 7% Fold: DNA/RNA-binding 3-helical bundle Superfamily: Sigma3 and sigma4 domains of RNA polymerase sigma factors Family: YlxM/p13-like Phyre2 PDB 3hug chain A Region: 47 - 90 Aligned: 44 Modelled: 44 Confidence: 96.4% Identity: 16% 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 Phyre2 PDB 2elh chain A Region: 44 - 86 Aligned: 43 Modelled: 43 Confidence: 96.4% 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 1or7 chain A domain 1 Region: 47 - 90 Aligned: 44 Modelled: 44 Confidence: 96.3% Identity: 14% Fold: DNA/RNA-binding 3-helical bundle Superfamily: Sigma3 and sigma4 domains of RNA polymerase sigma factors Family: Sigma4 domain Phyre2 PDB 1zlj chain E Region: 54 - 90 Aligned: 37 Modelled: 37 Confidence: 96.3% Identity: 8% 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 - 90 Aligned: 37 Modelled: 37 Confidence: 96.2% Identity: 16% 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 - 90 Aligned: 37 Modelled: 37 Confidence: 96.1% 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 1 d2jn6a1 2 d1k78a1 3 d6paxa1 4 d1pdnc_ 5 c1u78A_ 6 c6paxA_ 7 c2rn7A_ 8 c2r0qF_ 9 c3gn5B_ 10 c2k27A_ 11 c3hefB_ 12 c2gm4B_ 13 c3mzyA_ 14 d1xsva_ 15 c3hugA_ 16 c2elhA_ 17 d1or7a1 18 c1zljE_ 19 c3sztB_ 20 c2q0oA_ 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 98.0 13 Fold:DNA/RNA-binding 3-helical bundle Superfamily:Homeodomain-like Family:Cgl2762-like 2 d1k78a1 98.0 17 Fold:DNA/RNA-binding 3-helical bundle Superfamily:Homeodomain-like Family:Paired domain 3 d6paxa1 97.9 20 Fold:DNA/RNA-binding 3-helical bundle Superfamily:Homeodomain-like Family:Paired domain 4 d1pdnc_ 97.9 16 Fold:DNA/RNA-binding 3-helical bundle Superfamily:Homeodomain-like Family:Paired domain 5 c1u78A_ 97.8 15 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_ 97.7 20 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_ 97.6 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_ 97.2 16 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_ 97.2 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 c2k27A_ 97.0 20 PDB header:transcription regulator Chain: A: PDB Molecule:paired box protein pax-8; PDBTitle: solution structure of human pax8 paired box domain 11 c3hefB_ 96.8 17 PDB header:viral protein Chain: B: PDB Molecule:gene 1 protein; PDBTitle: crystal structure of the bacteriophage sf6 terminase small2 subunit 12 c2gm4B_ 96.5 13 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 13 c3mzyA_ 96.5 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 14 d1xsva_ 96.4 7 Fold:DNA/RNA-binding 3-helical bundle Superfamily:Sigma3 and sigma4 domains of RNA polymerase sigma factors Family:YlxM/p13-like 15 c3hugA_ 96.4 16 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 16 c2elhA_ 96.4 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 17 d1or7a1 96.3 14 Fold:DNA/RNA-binding 3-helical bundle Superfamily:Sigma3 and sigma4 domains of RNA polymerase sigma factors Family:Sigma4 domain 18 c1zljE_ 96.3 8 PDB header:transcription Chain: E: PDB Molecule:dormancy survival regulator; PDBTitle: crystal structure of the mycobacterium tuberculosis hypoxic2 response regulator dosr c-terminal domain 19 c3sztB_ 96.2 16 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 20 c2q0oA_ 96.1 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 21 d1a04a1 not modelled 96.1 19 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 d1p4wa_ not modelled 96.0 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) 23 c2o8xA_ not modelled 96.0 11 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 24 c2vbzA_ not modelled 96.0 7 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 25 c2cg4B_ not modelled 96.0 17 PDB header:transcription Chain: B: PDB Molecule:regulatory protein asnc; PDBTitle: structure of e.coli asnc 26 c1x3uA_ not modelled 95.9 14 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 27 c2e7xA_ not modelled 95.9 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 d1rp3a2 not modelled 95.9 7 Fold:DNA/RNA-binding 3-helical bundle Superfamily:Sigma3 and sigma4 domains of RNA polymerase sigma factors Family:Sigma4 domain 29 d1fsea_ not modelled 95.9 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) 30 d1yioa1 not modelled 95.9 19 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) 31 c1or7A_ not modelled 95.8 14 PDB header:transcription Chain: A: PDB Molecule:rna polymerase sigma-e factor; PDBTitle: crystal structure of escherichia coli sigmae with the cytoplasmic2 domain of its anti-sigma rsea 32 c2jpcA_ not modelled 95.8 14 PDB header:dna binding protein Chain: A: PDB Molecule:ssrb; PDBTitle: ssrb dna binding protein 33 d2cg4a1 not modelled 95.8 17 Fold:DNA/RNA-binding 3-helical bundle Superfamily:"Winged helix" DNA-binding domain Family:Lrp/AsnC-like transcriptional regulator N-terminal domain 34 d1s7oa_ not modelled 95.8 12 Fold:DNA/RNA-binding 3-helical bundle Superfamily:Sigma3 and sigma4 domains of RNA polymerase sigma factors Family:YlxM/p13-like 35 d1l3la1 not modelled 95.8 16 Fold:DNA/RNA-binding 3-helical bundle Superfamily:C-terminal effector domain of the bipartite response regulators Family:GerE-like (LuxR/UhpA family of transcriptional regulators) 36 c2krfB_ not modelled 95.8 14 PDB header:transcription Chain: B: PDB Molecule:transcriptional regulatory protein coma; PDBTitle: nmr solution structure of the dna binding domain of competence protein2 a 37 c3qp5C_ not modelled 95.8 22 PDB header:transcription Chain: C: PDB Molecule:cvir transcriptional regulator; PDBTitle: crystal structure of cvir bound to antagonist chlorolactone (cl) 38 c1hlvA_ not modelled 95.7 20 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 39 c1h0mD_ not modelled 95.7 16 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 40 c3i4pA_ not modelled 95.7 12 PDB header:transcription regulator Chain: A: PDB Molecule:transcriptional regulator, asnc family; PDBTitle: crystal structure of asnc family transcriptional regulator from2 agrobacterium tumefaciens 41 c2ia0A_ not modelled 95.7 10 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) 42 c2cfxD_ not modelled 95.6 10 PDB header:transcription Chain: D: PDB Molecule:hth-type transcriptional regulator lrpc; PDBTitle: structure of b.subtilis lrpc 43 c2rnjA_ not modelled 95.6 16 PDB header:transcription Chain: A: PDB Molecule:response regulator protein vrar; PDBTitle: nmr structure of the s. aureus vrar dna binding domain 44 d1hlva1 not modelled 95.5 20 Fold:DNA/RNA-binding 3-helical bundle Superfamily:Homeodomain-like Family:Centromere-binding 45 c2p6tH_ not modelled 95.5 20 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 46 d2coba1 not modelled 95.4 19 Fold:DNA/RNA-binding 3-helical bundle Superfamily:Homeodomain-like Family:Psq domain 47 c1rnlA_ not modelled 95.3 19 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 48 c1rp3G_ not modelled 95.3 7 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 49 d2cfxa1 not modelled 95.2 10 Fold:DNA/RNA-binding 3-helical bundle Superfamily:"Winged helix" DNA-binding domain Family:Lrp/AsnC-like transcriptional regulator N-terminal domain 50 c2e1cA_ not modelled 95.2 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 51 c2dbbA_ not modelled 95.2 12 PDB header:transcriptional regulator Chain: A: PDB Molecule:putative hth-type transcriptional regulator ph0061; PDBTitle: crystal structure of ph0061 52 c3c3wB_ not modelled 95.1 11 PDB header:transcription Chain: B: PDB Molecule:two component transcriptional regulatory protein devr; PDBTitle: crystal structure of the mycobacterium tuberculosis hypoxic response2 regulator dosr 53 c1i1gA_ not modelled 95.1 10 PDB header:transcription Chain: A: PDB Molecule:transcriptional regulator lrpa; PDBTitle: crystal structure of the lrp-like transcriptional regulator from the2 archaeon pyrococcus furiosus 54 c3cloC_ not modelled 95.0 22 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 55 d1i1ga1 not modelled 95.0 10 Fold:DNA/RNA-binding 3-helical bundle Superfamily:"Winged helix" DNA-binding domain Family:Lrp/AsnC-like transcriptional regulator N-terminal domain 56 d2cyya1 not modelled 94.9 24 Fold:DNA/RNA-binding 3-helical bundle Superfamily:"Winged helix" DNA-binding domain Family:Lrp/AsnC-like transcriptional regulator N-terminal domain 57 d1bw6a_ not modelled 94.9 20 Fold:DNA/RNA-binding 3-helical bundle Superfamily:Homeodomain-like Family:Centromere-binding 58 d1biaa1 not modelled 94.9 14 Fold:DNA/RNA-binding 3-helical bundle Superfamily:"Winged helix" DNA-binding domain Family:Biotin repressor-like 59 c2w48D_ not modelled 94.8 21 PDB header:transcription Chain: D: PDB Molecule:sorbitol operon regulator; PDBTitle: crystal structure of the full-length sorbitol operon2 regulator sorc from klebsiella pneumoniae 60 c2gqqB_ not modelled 94.8 12 PDB header:transcription Chain: B: PDB Molecule:leucine-responsive regulatory protein; PDBTitle: crystal structure of e. coli leucine-responsive regulatory protein2 (lrp) 61 c3hosA_ not modelled 94.7 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 62 c2l4aA_ not modelled 94.7 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 d1twfi2 not modelled 94.7 13 Fold:Rubredoxin-like Superfamily:Zinc beta-ribbon Family:Transcriptional factor domain 64 c2ewnA_ not modelled 94.6 17 PDB header:ligase, transcription Chain: A: PDB Molecule:bira bifunctional protein; PDBTitle: ecoli biotin repressor with co-repressor analog 65 d1wiia_ not modelled 94.4 19 Fold:Rubredoxin-like Superfamily:Zinc beta-ribbon Family:Putative zinc binding domain 66 c2q1zA_ not modelled 94.2 16 PDB header:transcription Chain: A: PDB Molecule:rpoe, ecf sige; PDBTitle: crystal structure of rhodobacter sphaeroides sige in complex with the2 anti-sigma chrr 67 d1ijwc_ not modelled 94.2 23 Fold:DNA/RNA-binding 3-helical bundle Superfamily:Homeodomain-like Family:Recombinase DNA-binding domain 68 c3frwF_ not modelled 94.2 12 PDB header:structural genomics, unknown function Chain: F: PDB Molecule:putative trp repressor protein; PDBTitle: crystal structure of putative trpr protein from ruminococcus obeum 69 c3klnC_ not modelled 94.0 30 PDB header:transcription Chain: C: PDB Molecule:transcriptional regulator, luxr family; PDBTitle: vibrio cholerae vpst 70 d1hcra_ not modelled 94.0 23 Fold:DNA/RNA-binding 3-helical bundle Superfamily:Homeodomain-like Family:Recombinase DNA-binding domain 71 c3korD_ not modelled 93.8 15 PDB header:transcription Chain: D: PDB Molecule:possible trp repressor; PDBTitle: crystal structure of a putative trp repressor from staphylococcus2 aureus 72 c3iwfA_ not modelled 93.7 20 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 73 d1qypa_ not modelled 93.7 27 Fold:Rubredoxin-like Superfamily:Zinc beta-ribbon Family:Transcriptional factor domain 74 d1g2ha_ not modelled 93.7 25 Fold:DNA/RNA-binding 3-helical bundle Superfamily:Homeodomain-like Family:FIS-like 75 c1zn2A_ not modelled 93.6 19 PDB header:transcription regulator Chain: A: PDB Molecule:response regulatory protein; PDBTitle: low resolution structure of response regulator styr 76 c3h0gI_ not modelled 93.6 26 PDB header:transcription Chain: I: PDB Molecule:dna-directed rna polymerase ii subunit rpb9; PDBTitle: rna polymerase ii from schizosaccharomyces pombe 77 d1fipa_ not modelled 93.5 28 Fold:DNA/RNA-binding 3-helical bundle Superfamily:Homeodomain-like Family:FIS-like 78 d1ntca_ not modelled 93.4 22 Fold:DNA/RNA-binding 3-helical bundle Superfamily:Homeodomain-like Family:FIS-like 79 c1i3qI_ not modelled 93.3 14 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 80 d1ttya_ not modelled 93.1 9 Fold:DNA/RNA-binding 3-helical bundle Superfamily:Sigma3 and sigma4 domains of RNA polymerase sigma factors Family:Sigma4 domain 81 c3e7lD_ not modelled 93.1 19 PDB header:transcription regulator Chain: D: PDB Molecule:transcriptional regulator (ntrc family); PDBTitle: crystal structure of sigma54 activator ntrc4's dna binding2 domain 82 c2qa4Z_ not modelled 93.0 36 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 83 d1j5ya1 not modelled 92.9 14 Fold:DNA/RNA-binding 3-helical bundle Superfamily:"Winged helix" DNA-binding domain Family:Biotin repressor-like 84 d1etob_ not modelled 92.8 28 Fold:DNA/RNA-binding 3-helical bundle Superfamily:Homeodomain-like Family:FIS-like 85 d1etxa_ not modelled 92.7 28 Fold:DNA/RNA-binding 3-helical bundle Superfamily:Homeodomain-like Family:FIS-like 86 c3cc4Z_ not modelled 92.6 36 PDB header:ribosome Chain: Z: PDB Molecule:50s ribosomal protein l37ae; PDBTitle: co-crystal structure of anisomycin bound to the 50s ribosomal subunit 87 d2hsga1 not modelled 92.6 27 Fold:lambda repressor-like DNA-binding domains Superfamily:lambda repressor-like DNA-binding domains Family:GalR/LacI-like bacterial regulator 88 d1ffkw_ not modelled 92.4 30 Fold:Rubredoxin-like Superfamily:Zn-binding ribosomal proteins Family:Ribosomal protein L37ae 89 d1vqoz1 not modelled 92.4 36 Fold:Rubredoxin-like Superfamily:Zn-binding ribosomal proteins Family:Ribosomal protein L37ae 90 d2isya1 not modelled 92.4 15 Fold:DNA/RNA-binding 3-helical bundle Superfamily:"Winged helix" DNA-binding domain Family:Iron-dependent repressor protein 91 c2zkrz_ not modelled 92.4 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 92 d1umqa_ not modelled 92.3 18 Fold:DNA/RNA-binding 3-helical bundle Superfamily:Homeodomain-like Family:FIS-like 93 c1umqA_ not modelled 92.3 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 94 c4a17Y_ not modelled 92.3 30 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. 95 c1yshD_ not modelled 92.3 25 PDB header:structural protein/rna Chain: D: PDB Molecule:ribosomal protein l37a; PDBTitle: localization and dynamic behavior of ribosomal protein l30e 96 c1r71B_ not modelled 92.3 16 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 97 d1trra_ not modelled 92.3 30 Fold:DNA/RNA-binding 3-helical bundle Superfamily:TrpR-like Family:Trp repressor, TrpR 98 d1jhga_ not modelled 92.2 33 Fold:DNA/RNA-binding 3-helical bundle Superfamily:TrpR-like Family:Trp repressor, TrpR 99 d1mkma1 not modelled 92.2 12 Fold:DNA/RNA-binding 3-helical bundle Superfamily:"Winged helix" DNA-binding domain Family:Transcriptional regulator IclR, N-terminal domain 100 d1jj2y_ not modelled 92.1 31 Fold:Rubredoxin-like Superfamily:Zn-binding ribosomal proteins Family:Ribosomal protein L37ae 101 c2l0kA_ not modelled 92.0 18 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 102 c1rr7A_ not modelled 91.5 15 PDB header:transcription Chain: A: PDB Molecule:middle operon regulator; PDBTitle: crystal structure of the middle operon regulator protein of2 bacteriophage mu 103 d1rr7a_ not modelled 91.5 15 Fold:DNA/RNA-binding 3-helical bundle Superfamily:Homeodomain-like Family:Middle operon regulator, Mor 104 d1g3wa1 not modelled 91.5 12 Fold:DNA/RNA-binding 3-helical bundle Superfamily:"Winged helix" DNA-binding domain Family:Iron-dependent repressor protein 105 d1ku3a_ not modelled 91.5 9 Fold:DNA/RNA-binding 3-helical bundle Superfamily:Sigma3 and sigma4 domains of RNA polymerase sigma factors Family:Sigma4 domain 106 d1tfia_ not modelled 91.4 14 Fold:Rubredoxin-like Superfamily:Zinc beta-ribbon Family:Transcriptional factor domain 107 d1r71a_ not modelled 91.4 16 Fold:DNA/RNA-binding 3-helical bundle Superfamily:KorB DNA-binding domain-like Family:KorB DNA-binding domain-like 108 d1jhfa1 not modelled 91.4 20 Fold:DNA/RNA-binding 3-helical bundle Superfamily:"Winged helix" DNA-binding domain Family:LexA repressor, N-terminal DNA-binding domain 109 c2oqgA_ not modelled 91.3 16 PDB header:transcription Chain: A: PDB Molecule:possible transcriptional regulator, arsr family protein; PDBTitle: arsr-like transcriptional regulator from rhodococcus sp. rha1 110 d2bjca1 not modelled 91.3 26 Fold:lambda repressor-like DNA-binding domains Superfamily:lambda repressor-like DNA-binding domains Family:GalR/LacI-like bacterial regulator 111 c3cngC_ not modelled 91.2 19 PDB header:hydrolase Chain: C: PDB Molecule:nudix hydrolase; PDBTitle: crystal structure of nudix hydrolase from nitrosomonas europaea 112 d1uxca_ not modelled 91.2 24 Fold:lambda repressor-like DNA-binding domains Superfamily:lambda repressor-like DNA-binding domains Family:GalR/LacI-like bacterial regulator 113 d2ev0a1 not modelled 91.2 10 Fold:DNA/RNA-binding 3-helical bundle Superfamily:"Winged helix" DNA-binding domain Family:Iron-dependent repressor protein 114 d1lcda_ not modelled 91.0 26 Fold:lambda repressor-like DNA-binding domains Superfamily:lambda repressor-like DNA-binding domains Family:GalR/LacI-like bacterial regulator 115 d1uxda_ not modelled 90.9 24 Fold:lambda repressor-like DNA-binding domains Superfamily:lambda repressor-like DNA-binding domains Family:GalR/LacI-like bacterial regulator 116 d2ao9a1 not modelled 90.8 12 Fold:DNA/RNA-binding 3-helical bundle Superfamily:Homeodomain-like Family:Nanomeric phage protein-like 117 d1r1ua_ not modelled 90.8 7 Fold:DNA/RNA-binding 3-helical bundle Superfamily:"Winged helix" DNA-binding domain Family:ArsR-like transcriptional regulators 118 d1vz0a1 not modelled 90.6 16 Fold:DNA/RNA-binding 3-helical bundle Superfamily:KorB DNA-binding domain-like Family:KorB DNA-binding domain-like 119 c2kpjA_ not modelled 90.6 15 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 120 c3m1eA_ not modelled 90.4 7 PDB header:transcription regulator Chain: A: PDB Molecule:hth-type transcriptional regulator benm; PDBTitle: crystal structure of benm_dbd

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