| Above-300 synthetase |
| ID: | 1485737414 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 640 (611) | ||
| Sequences: | 3193 (2276.7) | ||
| Seq/Len: | 5.226 | ||
| Nf(neff/√len): | 92.1 |
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: 5.226).
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 |
| 35_G | 59_P | 4.264 | 1.00 |
| 170_R | 193_A | 4.166 | 1.00 |
| 282_K | 310_D | 3.977 | 1.00 |
| 103_A | 107_W | 3.918 | 1.00 |
| 25_L | 47_G | 3.843 | 1.00 |
| 237_L | 522_F | 3.835 | 1.00 |
| 264_S | 545_M | 3.528 | 1.00 |
| 254_A | 266_A | 3.518 | 1.00 |
| 89_I | 106_R | 3.494 | 1.00 |
| 86_W | 114_Y | 3.316 | 1.00 |
| 21_I | 45_A | 3.256 | 1.00 |
| 133_C | 143_F | 3.227 | 1.00 |
| 301_D | 313_L | 3.144 | 1.00 |
| 172_S | 189_S | 3.113 | 1.00 |
| 543_R | 546_E | 3.092 | 1.00 |
| 239_S | 271_R | 3.049 | 1.00 |
| 138_F | 520_V | 2.993 | 1.00 |
| 107_W | 114_Y | 2.923 | 1.00 |
| 64_M | 105_L | 2.905 | 1.00 |
| 63_T | 70_A | 2.865 | 1.00 |
| 238_F | 268_V | 2.849 | 1.00 |
| 103_A | 111_C | 2.828 | 1.00 |
| 71_V | 97_A | 2.817 | 1.00 |
| 140_V | 512_Y | 2.797 | 1.00 |
| 122_A | 133_C | 2.622 | 1.00 |
| 137_H | 517_K | 2.541 | 1.00 |
| 111_C | 115_L | 2.519 | 1.00 |
| 58_G | 95_A | 2.517 | 1.00 |
| 64_M | 68_K | 2.515 | 1.00 |
| 36_S | 49_A | 2.492 | 1.00 |
| 235_R | 547_G | 2.477 | 1.00 |
| 159_G | 333_E | 2.461 | 1.00 |
| 153_A | 164_L | 2.444 | 1.00 |
| 330_E | 632_Q | 2.390 | 1.00 |
| 244_N | 518_P | 2.354 | 1.00 |
| 302_A | 552_A | 2.343 | 1.00 |
| 6_G | 154_F | 2.341 | 1.00 |
| 253_G | 356_V | 2.338 | 1.00 |
| 282_K | 312_T | 2.337 | 1.00 |
| 369_V | 523_C | 2.304 | 1.00 |
| 133_C | 204_L | 2.266 | 1.00 |
| 199_P | 213_L | 2.230 | 1.00 |
| 503_A | 510_P | 2.224 | 1.00 |
| 89_I | 102_H | 2.194 | 1.00 |
| 203_T | 214_R | 2.183 | 1.00 |
| 233_E | 236_H | 2.180 | 1.00 |
| 240_Q | 518_P | 2.173 | 1.00 |
| 235_R | 548_V | 2.171 | 1.00 |
| 140_V | 245_R | 2.163 | 1.00 |
| 301_D | 305_T | 2.149 | 1.00 |
| 350_T | 353_A | 2.135 | 1.00 |
| 352_G | 357_K | 2.127 | 1.00 |
| 69_L | 101_M | 2.127 | 1.00 |
| 517_K | 521_E | 2.040 | 1.00 |
| 198_L | 204_L | 2.028 | 1.00 |
| 365_G | 514_F | 2.028 | 1.00 |
| 518_P | 521_E | 2.019 | 1.00 |
| 230_A | 526_L | 2.017 | 1.00 |
| 172_S | 193_A | 2.005 | 1.00 |
| 547_G | 551_P | 1.991 | 1.00 |
| 237_L | 519_L | 1.987 | 1.00 |
| 116_Q | 518_P | 1.987 | 1.00 |
| 64_M | 102_H | 1.977 | 1.00 |
| 100_V | 111_C | 1.971 | 1.00 |
| 234_F | 522_F | 1.954 | 1.00 |
| 233_E | 237_L | 1.946 | 1.00 |
| 172_S | 196_F | 1.935 | 1.00 |
| 54_T | 80_R | 1.934 | 1.00 |
| 103_A | 115_L | 1.915 | 1.00 |
| 546_E | 555_W | 1.911 | 1.00 |
| 533_R | 539_H | 1.907 | 1.00 |
| 235_R | 544_A | 1.899 | 1.00 |
| 110_A | 113_T | 1.891 | 1.00 |
| 233_E | 522_F | 1.890 | 1.00 |
| 227_R | 543_R | 1.879 | 1.00 |
| 199_P | 202_H | 1.872 | 1.00 |
| 240_Q | 244_N | 1.865 | 1.00 |
| 104_Y | 132_F | 1.854 | 1.00 |
| 263_S | 303_V | 1.851 | 1.00 |
| 285_S | 300_I | 1.851 | 1.00 |
| 197_R | 334_G | 1.842 | 1.00 |
| 100_V | 115_L | 1.838 | 1.00 |
| 124_W | 131_L | 1.834 | 1.00 |
| 116_Q | 517_K | 1.832 | 1.00 |
| 73_A | 77_L | 1.830 | 1.00 |
| 234_F | 369_V | 1.819 | 1.00 |
| 68_K | 127_E | 1.813 | 1.00 |
| 153_A | 161_L | 1.804 | 1.00 |
| 477_A | 528_A | 1.794 | 1.00 |
| 155_A | 160_P | 1.786 | 1.00 |
| 104_Y | 123_I | 1.780 | 1.00 |
| 112_A | 203_T | 1.778 | 1.00 |
| 71_V | 123_I | 1.762 | 1.00 |
| 217_W | 521_E | 1.762 | 1.00 |
| 283_T | 309_F | 1.754 | 1.00 |
| 70_A | 126_A | 1.752 | 1.00 |
| 41_D | 126_A | 1.746 | 1.00 |
| 266_A | 309_F | 1.735 | 1.00 |
| 5_A | 47_G | 1.730 | 1.00 |
| 264_S | 544_A | 1.708 | 1.00 |
| 627_S | 631_R | 1.707 | 1.00 |
| 539_H | 543_R | 1.705 | 1.00 |
| 116_Q | 516_D | 1.693 | 1.00 |
| 111_C | 132_F | 1.692 | 1.00 |
| 231_A | 544_A | 1.689 | 1.00 |
| 116_Q | 240_Q | 1.683 | 1.00 |
| 30_H | 157_E | 1.683 | 1.00 |
| 121_F | 134_A | 1.680 | 1.00 |
| 227_R | 539_H | 1.676 | 1.00 |
| 351_A | 359_L | 1.674 | 0.99 |
| 77_L | 100_V | 1.667 | 0.99 |
| 202_H | 213_L | 1.661 | 0.99 |
| 102_H | 105_L | 1.648 | 0.99 |
| 283_T | 311_S | 1.638 | 0.99 |
| 245_R | 512_Y | 1.633 | 0.99 |
| 202_H | 215_P | 1.628 | 0.99 |
| 241_S | 245_R | 1.618 | 0.99 |
| 29_R | 49_A | 1.618 | 0.99 |
| 522_F | 526_L | 1.616 | 0.99 |
| 132_F | 203_T | 1.614 | 0.99 |
| 551_P | 555_W | 1.613 | 0.99 |
| 145_Y | 196_F | 1.605 | 0.99 |
| 192_Y | 633_V | 1.597 | 0.99 |
| 21_I | 47_G | 1.593 | 0.99 |
| 477_A | 480_A | 1.591 | 0.99 |
| 119_F | 134_A | 1.590 | 0.99 |
| 546_E | 551_P | 1.590 | 0.99 |
| 109_E | 214_R | 1.588 | 0.99 |
| 81_D | 247_R | 1.586 | 0.99 |
| 112_A | 134_A | 1.581 | 0.99 |
| 25_L | 49_A | 1.537 | 0.99 |
| 8_L | 131_L | 1.526 | 0.99 |
| 239_S | 268_V | 1.514 | 0.99 |
| 347_I | 351_A | 1.514 | 0.99 |
| 332_Q | 502_A | 1.512 | 0.99 |
| 130_A | 207_T | 1.512 | 0.99 |
| 134_A | 203_T | 1.510 | 0.99 |
| 121_F | 132_F | 1.505 | 0.99 |
| 230_A | 530_E | 1.498 | 0.99 |
| 68_K | 128_R | 1.496 | 0.99 |
| 86_W | 107_W | 1.496 | 0.99 |
| 231_A | 543_R | 1.491 | 0.99 |
| 514_F | 541_L | 1.489 | 0.99 |
| 111_C | 121_F | 1.488 | 0.99 |
| 227_R | 530_E | 1.479 | 0.98 |
| 130_A | 205_T | 1.479 | 0.98 |
| 348_Y | 503_A | 1.478 | 0.98 |
| 254_A | 269_A | 1.474 | 0.98 |
| 266_A | 283_T | 1.472 | 0.98 |
| 5_A | 24_M | 1.462 | 0.98 |
| 266_A | 307_H | 1.461 | 0.98 |
| 80_R | 99_L | 1.451 | 0.98 |
| 132_F | 205_T | 1.450 | 0.98 |
| 370_S | 532_L | 1.425 | 0.98 |
| 104_Y | 111_C | 1.417 | 0.98 |
| 234_F | 519_L | 1.410 | 0.98 |
| 103_A | 114_Y | 1.406 | 0.98 |
| 123_I | 132_F | 1.403 | 0.98 |
| 519_L | 523_C | 1.395 | 0.98 |
| 284_F | 355_S | 1.394 | 0.98 |
| 234_F | 238_F | 1.393 | 0.98 |
| 218_Q | 488_S | 1.392 | 0.97 |
| 28_M | 49_A | 1.389 | 0.97 |
| 112_A | 132_F | 1.383 | 0.97 |
| 363_H | 498_V | 1.381 | 0.97 |
| 300_I | 304_L | 1.380 | 0.97 |
| 147_P | 196_F | 1.379 | 0.97 |
| 5_A | 25_L | 1.378 | 0.97 |
| 263_S | 549_L | 1.378 | 0.97 |
| 180_L | 626_L | 1.376 | 0.97 |
| 26_S | 49_A | 1.372 | 0.97 |
| 80_R | 94_V | 1.367 | 0.97 |
| 46_L | 154_F | 1.366 | 0.97 |
| 22_Q | 26_S | 1.360 | 0.97 |
| 118_D | 245_R | 1.356 | 0.97 |
| 68_K | 105_L | 1.352 | 0.97 |
| 237_L | 518_P | 1.346 | 0.97 |
| 73_A | 97_A | 1.343 | 0.97 |
| 71_V | 101_M | 1.343 | 0.97 |
| 88_G | 91_D | 1.341 | 0.97 |
| 22_Q | 36_S | 1.340 | 0.97 |
| 6_G | 122_A | 1.338 | 0.97 |
| 64_M | 69_L | 1.323 | 0.96 |
| 235_R | 239_S | 1.323 | 0.96 |
| 69_L | 105_L | 1.321 | 0.96 |
| 319_Y | 323_A | 1.316 | 0.96 |
| 327_R | 349_R | 1.316 | 0.96 |
| 254_A | 283_T | 1.314 | 0.96 |
| 116_Q | 244_N | 1.313 | 0.96 |
| 590_A | 627_S | 1.309 | 0.96 |
| 227_R | 533_R | 1.304 | 0.96 |
| 89_I | 105_L | 1.302 | 0.96 |
| 64_M | 89_I | 1.297 | 0.96 |
| 331_E | 505_N | 1.289 | 0.96 |
| 269_A | 281_L | 1.287 | 0.96 |
| 100_V | 121_F | 1.282 | 0.95 |
| 238_F | 514_F | 1.280 | 0.95 |
| 161_L | 195_I | 1.278 | 0.95 |
| 178_G | 189_S | 1.271 | 0.95 |
| 320_A | 323_A | 1.271 | 0.95 |
| 109_E | 205_T | 1.268 | 0.95 |
| 284_F | 354_K | 1.266 | 0.95 |
| 226_L | 229_D | 1.261 | 0.95 |
| 122_A | 154_F | 1.261 | 0.95 |
| 46_L | 72_T | 1.259 | 0.95 |
| 297_K | 313_L | 1.259 | 0.95 |
| 269_A | 360_L | 1.258 | 0.95 |
| 54_T | 248_G | 1.258 | 0.95 |
| 237_L | 240_Q | 1.255 | 0.95 |
| 109_E | 132_F | 1.253 | 0.95 |
| 68_K | 126_A | 1.247 | 0.94 |
| 268_V | 548_V | 1.242 | 0.94 |
| 232_E | 547_G | 1.231 | 0.94 |
| 263_S | 299_F | 1.228 | 0.94 |
| 102_H | 106_R | 1.228 | 0.94 |
| 40_T | 45_A | 1.227 | 0.94 |
| 289_E | 317_G | 1.224 | 0.94 |
| 112_A | 121_F | 1.219 | 0.93 |
| 35_G | 48_H | 1.219 | 0.93 |
| 25_L | 38_W | 1.218 | 0.93 |
| 118_D | 140_V | 1.214 | 0.93 |
| 231_A | 235_R | 1.210 | 0.93 |
| 317_G | 320_A | 1.203 | 0.93 |
| 349_R | 353_A | 1.199 | 0.93 |
| 64_M | 67_A | 1.197 | 0.93 |
| 187_P | 493_P | 1.182 | 0.92 |
| 201_R | 217_W | 1.178 | 0.92 |
| 35_G | 52_D | 1.172 | 0.92 |
| 499_L | 510_P | 1.160 | 0.91 |
| 227_R | 231_A | 1.155 | 0.91 |
| 138_F | 487_L | 1.151 | 0.91 |
| 215_P | 218_Q | 1.146 | 0.90 |
| 265_V | 514_F | 1.145 | 0.90 |
| 231_A | 547_G | 1.138 | 0.90 |
| 8_L | 44_T | 1.138 | 0.90 |
| 297_K | 315_G | 1.136 | 0.90 |
| 71_V | 121_F | 1.131 | 0.90 |
| 302_A | 305_T | 1.130 | 0.90 |
| 116_Q | 245_R | 1.128 | 0.89 |
| 162_L | 169_T | 1.127 | 0.89 |
| 28_M | 155_A | 1.125 | 0.89 |
| 125_D | 128_R | 1.119 | 0.89 |
| 54_T | 95_A | 1.119 | 0.89 |
| 6_G | 133_C | 1.116 | 0.89 |
| 69_L | 104_Y | 1.111 | 0.88 |
| 124_W | 129_Q | 1.111 | 0.88 |
| 2_S | 74_D | 1.099 | 0.88 |
| 28_M | 160_P | 1.097 | 0.88 |
| 62_L | 101_M | 1.095 | 0.88 |
| 57_D | 93_P | 1.092 | 0.87 |
| 176_I | 626_L | 1.088 | 0.87 |
| 63_T | 67_A | 1.088 | 0.87 |
| 81_D | 94_V | 1.087 | 0.87 |
| 69_L | 127_E | 1.086 | 0.87 |
| 340_G | 498_V | 1.079 | 0.86 |
| 587_D | 591_P | 1.078 | 0.86 |
| 280_R | 310_D | 1.078 | 0.86 |
| 22_Q | 38_W | 1.074 | 0.86 |
| 551_P | 554_Q | 1.071 | 0.86 |
| 144_Y | 501_K | 1.068 | 0.86 |
| 69_L | 128_R | 1.066 | 0.86 |
| 198_L | 213_L | 1.065 | 0.85 |
| 363_H | 499_L | 1.060 | 0.85 |
| 25_L | 36_S | 1.057 | 0.85 |
| 295_D | 315_G | 1.054 | 0.85 |
| 118_D | 141_K | 1.054 | 0.85 |
| 287_V | 297_K | 1.051 | 0.84 |
| 145_Y | 152_F | 1.045 | 0.84 |
| 345_R | 506_F | 1.045 | 0.84 |
| 198_L | 202_H | 1.044 | 0.84 |
| 544_A | 547_G | 1.044 | 0.84 |
| 375_L | 486_V | 1.044 | 0.84 |
| 4_I | 72_T | 1.036 | 0.83 |
| 370_S | 483_H | 1.035 | 0.83 |
| 27_R | 163_A | 1.034 | 0.83 |
| 133_C | 152_F | 1.029 | 0.83 |
| 100_V | 112_A | 1.029 | 0.83 |
| 69_L | 102_H | 1.026 | 0.82 |
| 238_F | 264_S | 1.019 | 0.82 |
| 79_N | 82_E | 1.019 | 0.82 |
| 121_F | 133_C | 1.014 | 0.81 |
| 34_D | 357_K | 1.014 | 0.81 |
| 329_L | 625_S | 1.011 | 0.81 |
| 289_E | 315_G | 1.011 | 0.81 |
| 4_I | 122_A | 1.010 | 0.81 |
| 333_E | 501_K | 1.010 | 0.81 |
| 27_R | 330_E | 1.008 | 0.81 |
| 58_G | 93_P | 1.002 | 0.80 |
| 62_L | 93_P | 1.001 | 0.80 |
| 230_A | 522_F | 1.001 | 0.80 |
| 20_D | 164_L | 1.001 | 0.80 |
| 3_G | 31_R | 1.000 | 0.80 |
| 9_L | 12_G | 1.000 | 0.80 |
| 100_V | 123_I | 1.000 | 0.80 |
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 | |
| 1q15A | 4 | 0.7422 | 100 | 0.358 | Contact Map |
| 1ct9A | 4 | 0.7484 | 100 | 0.364 | Contact Map |
| 1jgtA | 2 | 0.7359 | 100 | 0.376 | Contact Map |
| 1ao0A | 4 | 0.5312 | 100 | 0.723 | Contact Map |
| 1xffA | 2 | 0.3031 | 100 | 0.744 | Contact Map |
| 1te5A | 2 | 0.2875 | 100 | 0.747 | Contact Map |
| 1ecfA | 2 | 0.5641 | 100 | 0.766 | Contact Map |
| 4amvA | 3 | 0.7937 | 100 | 0.779 | Contact Map |
| 3mdnA | 4 | 0.2547 | 100 | 0.787 | Contact Map |
| 4zflA | 12 | 0 | 99.9 | 0.805 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)