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OPENSEQ.org
YDCR - Uncharacterized HTH-type transcriptional regulator YdcR
UniProt: P77730 Sequence
 Download Alignment
We filter this alignment to remove sites that have > 75% gaps before running GREMLIN.
EcoGene: EG13761
Length: 468 (465)
Sequences: 6504
Seq/Len: 13.99
YDCR
Paralog alert: 0.71 [within 20: 0.08] - ratio of genomes with paralogs
Cluster includes: AAT ALAA ALAC ARNB AVTA CSDA HIS8 ISCS MALY RFFA SERC SUFS TYRB YBDL YDCR YJIR
GREMLIN Results:

Legend: The darker and larger the blue dots, the higher coevolution strength.

Residue pairs sorted by coevolution strength:
i j Scaled Score Prob
232_E 271_Q 4.209 1.00
221_D 261_K 3.7 1.00
421_H 462_K 3.486 1.00
373_E 450_G 3.02 1.00
372_A 376_Q 2.804 1.00
273_N 303_G 2.789 1.00
59_R 62_S 2.653 1.00
192_D 241_K 2.648 1.00
129_Q 353_D 2.608 1.00
455_Q 459_Q 2.598 1.00
259_P 263_A 2.528 1.00
181_N 185_Q 2.501 1.00
193_W 214_K 2.494 1.00
418_A 460_L 2.486 1.00
108_F 456_A 2.486 1.00
455_Q 458_K 2.458 1.00
173_T 179_A 2.454 1.00
269_L 276_L 2.448 1.00
21_Q 24_D 2.419 1.00
219_A 230_A 2.395 1.00
188_T 213_L 2.358 1.00
421_H 459_Q 2.274 1.00
147_N 349_L 2.235 1.00
391_K 404_E 2.19 1.00
155_A 167_P 2.143 1.00
270_N 301_H 2.142 1.00
377_R 454_E 2.139 1.00
229_Q 264_Q 2.113 1.00
127_L 350_A 2.074 1.00
128_A 132_K 2.057 1.00
384_R 454_E 2.044 1.00
230_A 233_L 2.03 1.00
149_E 356_S 2.005 1.00
12_R 53_Q 1.967 1.00
232_E 264_Q 1.956 1.00
153_A 356_S 1.931 1.00
310_F 351_L 1.924 1.00
417_A 420_T 1.905 1.00
183_S 277_I 1.905 1.00
117_L 370_Q 1.884 1.00
264_Q 267_A 1.868 1.00
176_A 307_C 1.85 1.00
226_I 243_C 1.834 1.00
294_P 297_A 1.812 1.00
232_E 272_Y 1.812 1.00
259_P 298_W 1.802 1.00
449_W 452_R 1.798 1.00
227_D 230_A 1.791 1.00
154_I 170_I 1.786 1.00
232_E 236_Q 1.781 1.00
263_A 267_A 1.774 1.00
242_A 277_I 1.769 1.00
155_A 170_I 1.764 1.00
336_Q 340_T 1.761 1.00
269_L 274_V 1.751 1.00
179_A 307_C 1.737 1.00
410_D 413_E 1.727 1.00
404_E 440_F 1.726 1.00
385_Y 458_K 1.717 1.00
235_L 274_V 1.716 1.00
154_I 172_I 1.714 1.00
183_S 305_L 1.71 1.00
224_E 261_K 1.697 1.00
146_G 151_R 1.688 1.00
26_L 56_I 1.67 1.00
245_L 265_L 1.656 1.00
313_C 360_Y 1.653 1.00
379_W 401_L 1.649 1.00
378_A 457_V 1.648 1.00
169_E 326_G 1.643 1.00
324_A 329_A 1.639 1.00
267_A 271_Q 1.627 1.00
344_S 347_M 1.626 1.00
204_A 244_W 1.618 1.00
377_R 381_A 1.614 1.00
228_L 268_L 1.608 1.00
194_V 208_L 1.601 1.00
235_L 268_L 1.595 1.00
163_I 296_K 1.595 1.00
381_A 457_V 1.589 1.00
127_L 131_S 1.574 1.00
221_D 227_D 1.567 1.00
305_L 324_A 1.566 1.00
379_W 394_H 1.561 1.00
152_Q 167_P 1.555 1.00
413_E 417_A 1.547 1.00
224_E 258_T 1.546 1.00
152_Q 156_R 1.542 1.00
378_A 401_L 1.54 1.00
380_Q 384_R 1.535 1.00
145_P 151_R 1.533 1.00
336_Q 343_T 1.53 1.00
415_S 425_I 1.526 1.00
268_L 272_Y 1.523 1.00
151_R 155_A 1.522 1.00
299_D 302_D 1.522 1.00
148_A 152_Q 1.519 1.00
381_A 458_K 1.518 1.00
178_E 340_T 1.518 1.00
266_V 298_W 1.511 1.00
411_A 429_K 1.51 1.00
281_V 309_S 1.508 1.00
260_Q 263_A 1.506 1.00
380_Q 454_E 1.505 1.00
153_A 352_V 1.501 1.00
184_L 208_L 1.5 1.00
198_N 219_A 1.498 1.00
193_W 216_L 1.488 1.00
145_P 333_Q 1.488 1.00
158_Y 323_V 1.484 1.00
121_Q 125_R 1.48 1.00
410_D 438_S 1.478 1.00
126_S 353_D 1.468 1.00
150_L 172_I 1.466 1.00
267_A 270_N 1.453 1.00
228_L 264_Q 1.451 1.00
402_W 428_G 1.448 1.00
381_A 454_E 1.442 1.00
376_Q 380_Q 1.428 1.00
277_I 307_C 1.427 1.00
171_V 332_I 1.424 1.00
228_L 261_K 1.423 1.00
7_L 38_M 1.421 1.00
221_D 224_E 1.417 1.00
195_I 240_V 1.414 1.00
204_A 208_L 1.404 0.99
379_W 383_L 1.391 0.99
186_A 335_L 1.39 0.99
227_D 261_K 1.389 0.99
113_P 371_L 1.388 0.99
126_S 130_V 1.388 0.99
29_L 40_F 1.371 0.99
266_V 304_V 1.371 0.99
178_E 336_Q 1.371 0.99
62_S 65_Y 1.366 0.99
133_T 353_D 1.363 0.99
130_V 350_A 1.358 0.99
259_P 293_L 1.352 0.99
258_T 261_K 1.352 0.99
266_V 295_A 1.347 0.99
198_N 217_S 1.346 0.99
108_F 453_E 1.346 0.99
159_A 164_T 1.344 0.99
377_R 450_G 1.343 0.99
353_D 356_S 1.338 0.99
153_A 156_R 1.331 0.99
225_G 261_K 1.329 0.99
353_D 357_T 1.327 0.99
417_A 463_L 1.326 0.99
458_K 462_K 1.321 0.99
293_L 298_W 1.319 0.99
153_A 355_L 1.314 0.99
375_K 379_W 1.297 0.99
149_E 352_V 1.297 0.99
13_E 17_S 1.297 0.99
243_C 274_V 1.287 0.99
425_I 441_F 1.28 0.99
3_K 6_Q 1.275 0.99
168_D 326_G 1.274 0.99
417_A 421_H 1.267 0.99
208_L 213_L 1.249 0.99
195_I 218_V 1.247 0.99
378_A 453_E 1.241 0.98
49_L 53_Q 1.236 0.98
186_A 332_I 1.236 0.98
197_E 250_Q 1.234 0.98
383_L 394_H 1.224 0.98
286_Y 292_P 1.223 0.98
320_I 351_L 1.222 0.98
125_R 129_Q 1.213 0.98
183_S 332_I 1.208 0.98
370_Q 374_R 1.207 0.98
280_D 283_S 1.207 0.98
454_E 458_K 1.203 0.98
233_L 237_E 1.201 0.98
452_R 455_Q 1.194 0.98
15_I 66_V 1.191 0.98
195_I 231_L 1.189 0.98
188_T 194_V 1.189 0.98
266_V 276_L 1.186 0.98
188_T 192_D 1.186 0.98
365_R 368_R 1.186 0.98
423_I 459_Q 1.182 0.98
56_I 64_Y 1.18 0.98
31_D 35_L 1.18 0.98
385_Y 454_E 1.178 0.98
268_L 274_V 1.174 0.98
185_Q 211_L 1.172 0.98
14_Q 19_I 1.172 0.98
158_Y 322_W 1.171 0.98
381_A 461_G 1.168 0.97
194_V 242_A 1.167 0.97
383_L 392_I 1.167 0.97
286_Y 289_R 1.165 0.97
288_G 396_D 1.162 0.97
148_A 151_R 1.162 0.97
461_G 465_Q 1.162 0.97
299_D 303_G 1.158 0.97
28_S 60_P 1.153 0.97
418_A 425_I 1.151 0.97
261_K 264_Q 1.148 0.97
260_Q 264_Q 1.145 0.97
25_R 65_Y 1.139 0.97
195_I 243_C 1.134 0.97
415_S 427_P 1.133 0.97
43_V 46_A 1.128 0.97
177_L 203_G 1.123 0.97
156_R 356_S 1.123 0.97
230_A 234_A 1.119 0.96
232_E 268_L 1.119 0.96
421_H 463_L 1.115 0.96
157_R 361_D 1.114 0.96
9_E 13_E 1.113 0.96
414_L 463_L 1.109 0.96
49_L 52_S 1.107 0.96
218_V 226_I 1.107 0.96
308_S 322_W 1.106 0.96
154_I 310_F 1.105 0.96
157_R 284_E 1.102 0.96
57_I 67_A 1.101 0.96
173_T 321_G 1.1 0.96
379_W 392_I 1.097 0.96
32_Q 36_S 1.096 0.96
381_A 385_Y 1.092 0.96
418_A 463_L 1.084 0.96
310_F 322_W 1.083 0.96
299_D 304_V 1.083 0.96
174_A 178_E 1.078 0.95
51_E 56_I 1.076 0.95
224_E 260_Q 1.075 0.95
288_G 375_K 1.071 0.95
375_K 445_T 1.071 0.95
8_A 49_L 1.066 0.95
249_S 397_S 1.059 0.95
130_V 353_D 1.058 0.95
149_E 349_L 1.056 0.95
266_V 299_D 1.049 0.94
189_E 192_D 1.049 0.94
236_Q 272_Y 1.047 0.94
114_D 374_R 1.044 0.94
385_Y 461_G 1.043 0.94
414_L 441_F 1.042 0.94
124_N 128_A 1.041 0.94
196_V 205_L 1.031 0.94
370_Q 373_E 1.031 0.94
369_R 372_A 1.025 0.93
270_N 300_R 1.024 0.93
352_V 356_S 1.023 0.93
275_T 303_G 1.023 0.93
423_I 456_A 1.019 0.93
324_A 332_I 1.009 0.93
390_V 403_L 1.008 0.93
329_A 333_Q 1.005 0.93
448_Q 452_R 1.002 0.92
Legend: The i and j are positions as given in the UniProt sequence. Only predictions with Scaled Score = (raw_score/average(raw_scores)) > 1 are listed. For all 3L/2 predictions, click on one of the links below.
HHsearch Results: GREMLIN results overlayed on top 10 PDB hits:
Legend: Blue filled circles are GREMLIN results (Scaled_score >1). The grey/red filled circles underneath are pdb residue contacts (min distance < 5 Angstroms). The shade of the circles is based on 10 HHsearch results which uses the overall probability and per-site alignment prob. Inter oligomeric contacts in the pdb are in shades of red.
PDB Chains Cov P(%) HHΔ   Acc
4mgrA40.96581000.311Contact Map0.808
3pplA20.83331000.408Contact Map0.588
3f6tA20.93381000.416Contact Map0.489
4je5A30.85681000.433Contact Map0.768
3qguA20.88681000.441Contact Map0.653
2x5fA20.85681000.444Contact Map0.606
3ez1A20.81621000.448Contact Map0.635
2r2nA40.83971000.456Contact Map0.777
1vp4A20.86751000.457Contact Map0.838
3aowA20.92521000.464Contact Map0.874
Sequence Conservation (Image Generated using WebLogo v3)
Legend: Color is used to show Hydrophobicity (Blue: Hydrophilic, Green: Neutral and Black: Hydrophobic). Amount of gaps is represented by width.
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