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OPENSEQ.org
RP54 - RNA polymerase sigma-54 factor
UniProt: P24255 Sequence
 Download Alignment
We filter this alignment to remove sites that have > 75% gaps before running GREMLIN.
EcoGene: EG10898
Length: 477 (476)
Sequences: 1070
Seq/Len: 2.25
RP54
Paralog alert: 0.05 [within 20: 0.00] - ratio of genomes with paralogs
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
424_V 442_L 3.085 1.00
423_L 449_Q 3.051 1.00
193_K 197_D 3.044 1.00
276_V 344_S 2.986 1.00
141_A 182_I 2.927 1.00
346_C 370_I 2.756 1.00
179_L 193_K 2.753 1.00
342_R 374_V 2.697 1.00
219_I 249_A 2.687 1.00
188_V 205_Q 2.606 1.00
145_V 185_F 2.574 1.00
366_V 369_D 2.494 1.00
136_T 174_E 2.481 1.00
159_E 172_I 2.42 1.00
148_V 191_A 2.34 1.00
144_I 182_I 2.315 1.00
137_D 178_V 2.283 1.00
428_I 465_L 2.262 1.00
236_M 243_E 2.256 1.00
158_L 179_L 2.225 1.00
148_V 182_I 2.221 1.00
257_D 263_S 2.198 1.00
124_L 145_V 2.154 1.00
376_M 381_I 2.13 1.00
280_K 356_E 2.101 1.00
192_A 201_I 2.091 0.99
182_I 191_A 2.081 0.99
285_W 356_E 2.072 0.99
278_V 390_L 2.069 0.99
236_M 246_L 2.038 0.99
215_E 241_L 2.037 0.99
40_A 325_D 2.017 0.99
134_S 137_D 2.017 0.99
140_I 178_V 1.997 0.99
141_A 178_V 1.967 0.99
397_F 401_Y 1.955 0.99
179_L 183_Q 1.935 0.99
149_D 155_T 1.931 0.99
137_D 177_A 1.914 0.99
128_V 141_A 1.878 0.99
176_E 193_K 1.854 0.98
374_V 381_I 1.854 0.98
128_V 145_V 1.85 0.98
183_Q 193_K 1.848 0.98
257_D 262_Q 1.842 0.98
128_V 185_F 1.833 0.98
287_V 348_V 1.828 0.98
354_F 397_F 1.819 0.98
354_F 402_F 1.802 0.98
346_C 373_A 1.801 0.98
15_M 22_A 1.797 0.98
216_A 249_A 1.742 0.97
140_I 175_V 1.738 0.97
367_L 400_K 1.737 0.97
153_Y 198_C 1.728 0.97
141_A 185_F 1.711 0.97
297_L 330_I 1.707 0.97
153_Y 195_L 1.688 0.97
13_L 23_I 1.656 0.96
200_L 217_R 1.649 0.96
367_L 385_T 1.629 0.96
223_H 239_T 1.614 0.96
397_F 402_F 1.605 0.95
220_I 224_L 1.604 0.95
342_R 376_M 1.603 0.95
272_V 389_Y 1.587 0.95
350_Q 370_I 1.58 0.95
195_L 259_R 1.579 0.95
140_I 170_I 1.576 0.95
226_L 235_L 1.575 0.95
199_L 256_L 1.57 0.95
131_T 185_F 1.536 0.94
345_R 349_E 1.532 0.94
344_S 390_L 1.53 0.94
350_Q 365_M 1.528 0.94
198_C 261_G 1.52 0.93
123_Y 264_I 1.512 0.93
427_L 445_L 1.503 0.93
424_V 446_L 1.502 0.93
398_E 401_Y 1.491 0.92
48_E 300_N 1.489 0.92
137_D 181_R 1.485 0.92
346_C 349_E 1.476 0.92
196_R 224_L 1.468 0.92
447_S 452_M 1.468 0.92
172_I 176_E 1.462 0.91
354_F 401_Y 1.447 0.91
235_L 246_L 1.425 0.90
124_L 190_V 1.421 0.90
426_K 430_A 1.42 0.90
151_T 155_T 1.417 0.90
445_L 448_E 1.414 0.90
206_F 252_L 1.412 0.89
224_L 228_A 1.403 0.89
215_E 249_A 1.402 0.89
328_W 335_S 1.386 0.88
355_F 392_S 1.38 0.88
218_L 222_D 1.376 0.88
232_F 246_L 1.372 0.88
241_L 249_A 1.37 0.87
179_L 192_A 1.356 0.87
201_I 204_S 1.351 0.86
162_L 175_V 1.35 0.86
123_Y 186_D 1.349 0.86
242_K 245_V 1.347 0.86
440_S 444_S 1.344 0.86
281_H 284_H 1.341 0.86
226_L 231_D 1.34 0.86
182_I 185_F 1.337 0.86
157_P 160_D 1.337 0.86
427_L 442_L 1.335 0.86
153_Y 303_Y 1.324 0.85
41_L 47_L 1.324 0.85
137_D 174_E 1.322 0.85
158_L 175_V 1.314 0.84
153_Y 259_R 1.309 0.84
125_M 142_T 1.308 0.84
193_K 198_C 1.302 0.84
195_L 198_C 1.294 0.83
18_Q 25_L 1.293 0.83
47_L 297_L 1.29 0.83
201_I 205_Q 1.282 0.82
188_V 201_I 1.28 0.82
183_Q 201_I 1.28 0.82
144_I 175_V 1.278 0.82
23_I 328_W 1.265 0.81
223_H 226_L 1.263 0.81
16_T 19_L 1.259 0.81
196_R 221_S 1.259 0.81
441_K 444_S 1.254 0.80
352_Q 356_E 1.253 0.80
355_F 393_P 1.244 0.80
179_L 201_I 1.242 0.79
204_S 217_R 1.239 0.79
392_S 395_G 1.238 0.79
36_E 40_A 1.237 0.79
223_H 235_L 1.236 0.79
141_A 144_I 1.231 0.79
342_R 442_L 1.224 0.78
431_E 436_P 1.215 0.77
278_V 348_V 1.212 0.77
349_E 373_A 1.212 0.77
289_L 341_L 1.21 0.77
16_T 23_I 1.195 0.76
28_L 400_K 1.186 0.75
213_L 217_R 1.186 0.75
257_D 329_L 1.172 0.74
280_K 285_W 1.167 0.73
405_S 417_S 1.163 0.73
357_Q 361_Y 1.159 0.72
178_V 181_R 1.158 0.72
360_E 426_K 1.152 0.72
192_A 198_C 1.149 0.72
340_L 404_S 1.147 0.71
20_Q 24_R 1.147 0.71
158_L 172_I 1.146 0.71
261_G 402_F 1.144 0.71
47_L 326_A 1.142 0.71
13_L 16_T 1.141 0.71
378_E 459_A 1.14 0.71
15_M 23_I 1.138 0.70
158_L 193_K 1.138 0.70
299_I 326_A 1.137 0.70
354_F 398_E 1.136 0.70
203_L 256_L 1.132 0.70
21_Q 328_W 1.124 0.69
404_S 416_S 1.123 0.69
350_Q 373_A 1.121 0.69
15_M 470_S 1.111 0.68
426_K 449_Q 1.109 0.68
252_L 255_S 1.109 0.68
46_L 319_I 1.108 0.68
5_L 416_S 1.108 0.68
25_L 384_V 1.108 0.68
37_L 329_L 1.107 0.67
432_N 436_P 1.105 0.67
127_Q 187_P 1.105 0.67
144_I 191_A 1.102 0.67
184_R 201_I 1.1 0.67
347_I 365_M 1.1 0.67
118_Q 123_Y 1.095 0.66
355_F 394_R 1.092 0.66
20_Q 331_K 1.085 0.65
198_C 259_R 1.084 0.65
43_S 322_N 1.082 0.65
241_L 246_L 1.081 0.65
280_K 283_G 1.08 0.65
454_A 457_T 1.076 0.64
223_H 238_V 1.073 0.64
419_A 451_I 1.067 0.63
425_K 429_A 1.063 0.63
140_I 174_E 1.061 0.63
153_Y 193_K 1.06 0.63
347_I 402_F 1.059 0.62
141_A 145_V 1.058 0.62
224_L 227_L 1.055 0.62
192_A 370_I 1.047 0.61
144_I 158_L 1.04 0.60
13_L 19_L 1.035 0.60
290_N 295_P 1.033 0.60
389_Y 398_E 1.033 0.60
123_Y 126_W 1.027 0.59
277_L 391_H 1.024 0.59
335_S 340_L 1.02 0.58
244_D 247_K 1.018 0.58
421_R 468_P 1.018 0.58
41_L 297_L 1.017 0.58
363_K 425_K 1.015 0.58
217_R 221_S 1.015 0.58
457_T 460_K 1.014 0.57
175_V 178_V 1.011 0.57
18_Q 23_I 1.008 0.57
354_F 358_G 1.003 0.56
227_L 394_R 1.002 0.56
19_L 28_L 1.001 0.56
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
2k9mA10.27251000.746Contact Map0.427
2ahqA10.15931000.8Contact Map0.422
2k9lA10.159399.60.878Contact Map0.479
1jyeA10.182496.70.947Contact Map0.653
1qpzA10.176196.50.948Contact Map0.491
1k78A30.301996.40.949Contact Map0.754
3dbiA30.222296.20.95Contact Map0.429
1zs4A40.17496.20.95Contact Map0.636
1uxcA10.134296.10.95Contact Map0.763
3ctpA20.2159960.951Contact Map0.328
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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