| Bacterial E2 |
| ID: | 1461607372 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 580 (545) | ||
| Sequences: | 813 (463.3) | ||
| Seq/Len: | 1.492 | ||
| Nf(neff/√len): | 19.8 |
HHblits Results: (2016_02)
Sequences per length for each position, BEFORE the coverage/gap filter was applied
Legend: Dots above the red line, indicates positions where there is > 5 sequences per length (if visible, green bar = 20 seq/len). Point of this graphic is to give you an idea if resubmitting a sub-portion of your sequence might help increase the overall Seq/Len (which after applying the coverage filter is at: 1.492).
Sequences per length for each position, AFTER the coverage/gap filter was applied
Residue pairs sorted by coevolution strength:
Legend: The darker and larger the blue dots, the higher strength in covariance. Below we provide the list of the top [1.5 x length] covarying residues with sequence seperation > 3. The i and j are positions as given in the input sequence.
| i | j | Scaled score | Prob |
| 26_A | 156_G | 4.477 | 1.00 |
| 49_I | 179_I | 4.418 | 1.00 |
| 36_S | 166_S | 4.108 | 1.00 |
| 24_L | 154_L | 4.073 | 1.00 |
| 40_L | 170_L | 4.068 | 1.00 |
| 74_L | 204_I | 3.941 | 1.00 |
| 12_I | 142_I | 3.768 | 1.00 |
| 68_I | 198_L | 3.723 | 1.00 |
| 35_Q | 165_Q | 3.694 | 1.00 |
| 48_E | 178_E | 3.583 | 1.00 |
| 46_T | 176_T | 3.526 | 1.00 |
| 19_E | 149_P | 3.479 | 1.00 |
| 32_E | 162_E | 3.397 | 1.00 |
| 47_M | 177_M | 3.357 | 1.00 |
| 34_E | 164_D | 3.354 | 1.00 |
| 20_I | 150_I | 3.343 | 1.00 |
| 39_T | 169_T | 3.280 | 1.00 |
| 16_T | 146_G | 3.255 | 1.00 |
| 67_R | 197_T | 3.234 | 1.00 |
| 38_L | 168_L | 3.182 | 1.00 |
| 33_P | 163_P | 3.180 | 1.00 |
| 42_S | 172_S | 3.155 | 1.00 |
| 475_A | 479_K | 3.081 | 1.00 |
| 14_D | 144_D | 2.999 | 1.00 |
| 22_E | 152_E | 2.975 | 1.00 |
| 64_V | 194_V | 2.967 | 1.00 |
| 15_F | 145_F | 2.945 | 1.00 |
| 37_L | 167_I | 2.882 | 1.00 |
| 75_M | 205_L | 2.861 | 1.00 |
| 60_V | 190_I | 2.839 | 1.00 |
| 17_D | 147_E | 2.826 | 1.00 |
| 11_D | 141_D | 2.807 | 1.00 |
| 62_V | 192_V | 2.758 | 1.00 |
| 63_A | 193_K | 2.757 | 1.00 |
| 21_I | 151_I | 2.695 | 1.00 |
| 70_K | 200_R | 2.588 | 1.00 |
| 9_L | 139_L | 2.583 | 1.00 |
| 52_P | 182_P | 2.564 | 1.00 |
| 66_E | 196_D | 2.543 | 1.00 |
| 69_G | 199_N | 2.536 | 1.00 |
| 464_K | 472_E | 2.532 | 1.00 |
| 27_P | 157_V | 2.496 | 1.00 |
| 45_A | 175_A | 2.483 | 1.00 |
| 72_A | 202_D | 2.464 | 1.00 |
| 30_R | 160_R | 2.462 | 1.00 |
| 57_V | 187_V | 2.416 | 1.00 |
| 51_S | 181_S | 2.386 | 1.00 |
| 80_D | 210_S | 2.338 | 0.99 |
| 54_A | 184_A | 2.266 | 0.99 |
| 411_L | 469_L | 2.208 | 0.99 |
| 419_A | 462_D | 2.136 | 0.99 |
| 374_H | 547_S | 2.123 | 0.99 |
| 77_V | 207_L | 2.112 | 0.99 |
| 31_I | 161_V | 2.112 | 0.99 |
| 157_V | 189_S | 2.099 | 0.99 |
| 18_V | 148_V | 2.036 | 0.98 |
| 188_E | 208_R | 2.017 | 0.98 |
| 442_H | 459_R | 1.985 | 0.98 |
| 380_A | 528_K | 1.980 | 0.98 |
| 41_E | 171_E | 1.971 | 0.98 |
| 23_I | 153_V | 1.944 | 0.97 |
| 61_K | 191_A | 1.942 | 0.97 |
| 460_D | 463_K | 1.937 | 0.97 |
| 59_E | 189_S | 1.922 | 0.97 |
| 27_P | 59_E | 1.917 | 0.97 |
| 478_A | 482_D | 1.894 | 0.97 |
| 73_L | 203_L | 1.857 | 0.96 |
| 444_G | 455_V | 1.854 | 0.96 |
| 58_Q | 78_E | 1.824 | 0.96 |
| 411_L | 443_L | 1.813 | 0.96 |
| 71_E | 201_G | 1.785 | 0.95 |
| 31_I | 57_V | 1.761 | 0.95 |
| 53_I | 183_A | 1.753 | 0.95 |
| 27_P | 60_V | 1.698 | 0.93 |
| 24_L | 36_S | 1.693 | 0.93 |
| 427_S | 438_K | 1.676 | 0.93 |
| 193_K | 196_D | 1.675 | 0.93 |
| 58_Q | 188_E | 1.662 | 0.92 |
| 480_A | 485_L | 1.649 | 0.92 |
| 421_M | 564_L | 1.647 | 0.92 |
| 415_A | 441_T | 1.613 | 0.91 |
| 8_L | 138_R | 1.612 | 0.91 |
| 13_G | 143_G | 1.610 | 0.91 |
| 411_L | 473_L | 1.609 | 0.91 |
| 445_V | 473_L | 1.605 | 0.91 |
| 451_N | 483_G | 1.605 | 0.91 |
| 493_G | 516_E | 1.593 | 0.90 |
| 6_N | 76_T | 1.580 | 0.90 |
| 12_I | 141_D | 1.547 | 0.88 |
| 25_V | 155_V | 1.544 | 0.88 |
| 377_Q | 548_Y | 1.538 | 0.88 |
| 187_V | 205_L | 1.537 | 0.88 |
| 57_V | 75_M | 1.535 | 0.88 |
| 350_E | 439_H | 1.526 | 0.87 |
| 377_Q | 505_G | 1.522 | 0.87 |
| 160_R | 186_E | 1.510 | 0.87 |
| 510_P | 521_G | 1.490 | 0.86 |
| 135_I | 183_A | 1.487 | 0.85 |
| 65_G | 195_G | 1.482 | 0.85 |
| 50_P | 180_P | 1.482 | 0.85 |
| 56_T | 186_E | 1.471 | 0.85 |
| 59_E | 76_T | 1.427 | 0.82 |
| 155_V | 187_V | 1.405 | 0.81 |
| 359_K | 433_E | 1.399 | 0.80 |
| 88_A | 125_A | 1.390 | 0.80 |
| 23_I | 60_V | 1.386 | 0.79 |
| 183_A | 207_L | 1.382 | 0.79 |
| 30_R | 56_T | 1.371 | 0.78 |
| 154_L | 166_S | 1.371 | 0.78 |
| 352_Q | 437_M | 1.345 | 0.77 |
| 136_D | 203_L | 1.337 | 0.76 |
| 473_L | 477_S | 1.335 | 0.76 |
| 37_L | 181_S | 1.330 | 0.75 |
| 286_F | 311_V | 1.324 | 0.75 |
| 364_H | 367_R | 1.317 | 0.74 |
| 361_S | 365_L | 1.311 | 0.74 |
| 168_L | 204_I | 1.308 | 0.74 |
| 292_V | 297_V | 1.296 | 0.73 |
| 37_L | 51_S | 1.294 | 0.73 |
| 360_I | 364_H | 1.293 | 0.72 |
| 384_T | 539_R | 1.279 | 0.71 |
| 520_L | 565_L | 1.277 | 0.71 |
| 32_E | 54_A | 1.274 | 0.71 |
| 411_L | 461_V | 1.269 | 0.70 |
| 136_D | 206_R | 1.263 | 0.70 |
| 455_V | 519_I | 1.262 | 0.70 |
| 550_H | 555_G | 1.256 | 0.69 |
| 290_L | 312_Q | 1.247 | 0.68 |
| 532_N | 537_S | 1.245 | 0.68 |
| 426_A | 552_V | 1.237 | 0.68 |
| 162_E | 184_A | 1.236 | 0.67 |
| 354_L | 428_L | 1.235 | 0.67 |
| 157_V | 190_I | 1.235 | 0.67 |
| 351_T | 434_G | 1.235 | 0.67 |
| 153_V | 190_I | 1.227 | 0.67 |
| 7_V | 137_V | 1.227 | 0.67 |
| 25_V | 57_V | 1.227 | 0.67 |
| 335_L | 371_S | 1.222 | 0.66 |
| 11_D | 142_I | 1.220 | 0.66 |
| 479_K | 489_D | 1.219 | 0.66 |
| 532_N | 535_E | 1.218 | 0.66 |
| 296_Q | 314_Y | 1.201 | 0.64 |
| 134_L | 206_R | 1.200 | 0.64 |
| 117_T | 121_E | 1.197 | 0.64 |
| 440_Y | 460_D | 1.197 | 0.64 |
| 513_N | 519_I | 1.194 | 0.64 |
| 53_I | 77_V | 1.193 | 0.63 |
| 376_T | 547_S | 1.193 | 0.63 |
| 33_P | 54_A | 1.193 | 0.63 |
| 61_K | 76_T | 1.184 | 0.63 |
| 454_V | 490_M | 1.180 | 0.62 |
| 63_A | 66_E | 1.175 | 0.62 |
| 348_Q | 439_H | 1.167 | 0.61 |
| 404_L | 408_P | 1.164 | 0.61 |
| 395_A | 398_E | 1.160 | 0.60 |
| 320_S | 323_A | 1.149 | 0.59 |
| 372_V | 512_V | 1.149 | 0.59 |
| 426_A | 437_M | 1.144 | 0.59 |
| 443_L | 469_L | 1.129 | 0.57 |
| 127_A | 130_A | 1.128 | 0.57 |
| 426_A | 429_S | 1.123 | 0.57 |
| 365_L | 455_V | 1.116 | 0.56 |
| 424_L | 517_V | 1.115 | 0.56 |
| 187_V | 190_I | 1.105 | 0.55 |
| 10_P | 140_P | 1.097 | 0.54 |
| 435_L | 552_V | 1.096 | 0.54 |
| 32_E | 35_Q | 1.083 | 0.52 |
| 377_Q | 523_S | 1.078 | 0.52 |
| 360_I | 367_R | 1.077 | 0.52 |
| 486_L | 489_D | 1.067 | 0.51 |
| 405_T | 545_S | 1.064 | 0.50 |
| 448_D | 560_R | 1.062 | 0.50 |
| 286_F | 290_L | 1.058 | 0.50 |
| 458_L | 473_L | 1.052 | 0.49 |
| 429_S | 434_G | 1.051 | 0.49 |
| 362_G | 466_V | 1.047 | 0.49 |
| 461_V | 469_L | 1.041 | 0.48 |
| 286_F | 312_Q | 1.039 | 0.48 |
| 382_D | 539_R | 1.039 | 0.48 |
| 529_P | 539_R | 1.038 | 0.48 |
| 442_H | 489_D | 1.037 | 0.48 |
| 520_L | 546_L | 1.035 | 0.47 |
| 531_W | 536_F | 1.033 | 0.47 |
| 31_I | 77_V | 1.033 | 0.47 |
| 137_V | 205_L | 1.032 | 0.47 |
| 76_T | 206_R | 1.025 | 0.46 |
| 414_V | 495_F | 1.021 | 0.46 |
| 505_G | 548_Y | 1.018 | 0.46 |
| 455_V | 513_N | 1.018 | 0.46 |
| 163_P | 181_S | 1.017 | 0.46 |
| 358_K | 368_C | 1.013 | 0.45 |
| 151_I | 170_L | 1.009 | 0.45 |
| 459_R | 519_I | 1.006 | 0.45 |
| 527_M | 540_L | 1.001 | 0.44 |
Prob = P(contact | scaled_score, seq/len).
Scaled Score = (raw_score/average(raw_scores)).
- Text file of contact predictions (all 3L/2 predictions)
- Generate restraints for ROSETTA Structure Modeling
- Import to GREMLIN BETA - features includes ability to upload PDB and latest P(contact) calculation based on eLife 2015 fitting to PDB data.
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-position alignment confidence. Inter oligomeric contacts in the pdb are in shades of red.
| PDB | M | Cov | P(%) | HHΔ | |
| 3dvaI | 2 | 0.0724 | 100 | 0.41 | Contact Map |
| 4n72A | 3 | 0.4224 | 100 | 0.601 | Contact Map |
| 1dpbA | 1 | 0.419 | 100 | 0.601 | Contact Map |
| 2ii3A | 8 | 0.4017 | 100 | 0.606 | Contact Map |
| 1sczA | 1 | 0.4 | 100 | 0.616 | Contact Map |
| 3maeA | 3 | 0.4086 | 100 | 0.617 | Contact Map |
| 3b8kA | 1 | 0.4086 | 100 | 0.62 | Contact Map |
| 3l60A | 1 | 0.3914 | 100 | 0.627 | Contact Map |
| 3rqcA | 7 | 0.3793 | 100 | 0.634 | Contact Map |
| 2xt6A | 2 | 0.331 | 100 | 0.654 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)