| sss xav |
| ID: | 1417536927 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 539 (539) | ||
| Sequences: | 5075 (4123.8) | ||
| Seq/Len: | 9.416 | ||
| Nf(neff/√len): | 177.6 |
HHblits Results: (2013_03)
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: 9.416).
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 |
| 138_D | 141_A | 4.338 | 1.00 |
| 239_R | 244_N | 4.294 | 1.00 |
| 225_L | 230_D | 3.599 | 1.00 |
| 5_T | 8_Q | 2.894 | 1.00 |
| 101_R | 117_E | 2.646 | 1.00 |
| 219_I | 247_E | 2.498 | 1.00 |
| 418_T | 422_T | 2.426 | 1.00 |
| 381_D | 392_I | 2.421 | 1.00 |
| 215_P | 242_E | 2.318 | 1.00 |
| 413_R | 416_D | 2.251 | 1.00 |
| 25_V | 194_L | 2.184 | 1.00 |
| 91_R | 95_E | 2.182 | 1.00 |
| 251_N | 254_V | 2.145 | 1.00 |
| 212_I | 215_P | 2.056 | 1.00 |
| 385_L | 392_I | 2.038 | 1.00 |
| 70_A | 134_T | 1.922 | 1.00 |
| 166_A | 170_K | 1.906 | 1.00 |
| 6_L | 216_M | 1.886 | 1.00 |
| 148_N | 152_P | 1.871 | 1.00 |
| 7_R | 11_L | 1.858 | 1.00 |
| 188_V | 192_V | 1.858 | 1.00 |
| 159_D | 163_T | 1.832 | 1.00 |
| 219_I | 250_F | 1.831 | 1.00 |
| 224_E | 245_A | 1.820 | 1.00 |
| 348_V | 453_G | 1.804 | 1.00 |
| 9_R | 211_A | 1.795 | 1.00 |
| 173_D | 177_T | 1.779 | 1.00 |
| 226_T | 253_M | 1.755 | 1.00 |
| 108_D | 111_S | 1.722 | 1.00 |
| 75_N | 78_E | 1.712 | 1.00 |
| 312_E | 315_R | 1.707 | 1.00 |
| 334_G | 467_I | 1.703 | 1.00 |
| 210_R | 214_N | 1.689 | 1.00 |
| 111_S | 115_E | 1.682 | 1.00 |
| 223_L | 246_I | 1.681 | 1.00 |
| 133_T | 138_D | 1.660 | 1.00 |
| 223_L | 249_G | 1.659 | 1.00 |
| 170_K | 174_E | 1.657 | 1.00 |
| 9_R | 241_D | 1.653 | 1.00 |
| 191_L | 195_G | 1.646 | 1.00 |
| 129_D | 132_A | 1.643 | 1.00 |
| 392_I | 422_T | 1.637 | 1.00 |
| 336_V | 340_R | 1.634 | 1.00 |
| 95_E | 99_F | 1.631 | 1.00 |
| 26_V | 30_R | 1.624 | 1.00 |
| 342_E | 461_G | 1.622 | 1.00 |
| 455_A | 459_Q | 1.617 | 1.00 |
| 133_T | 141_A | 1.614 | 1.00 |
| 242_E | 245_A | 1.606 | 1.00 |
| 114_V | 118_K | 1.585 | 1.00 |
| 319_E | 322_S | 1.577 | 1.00 |
| 347_N | 449_E | 1.576 | 1.00 |
| 225_L | 233_R | 1.569 | 1.00 |
| 224_E | 252_G | 1.565 | 1.00 |
| 39_V | 42_I | 1.564 | 1.00 |
| 36_E | 183_V | 1.561 | 1.00 |
| 277_E | 515_Q | 1.552 | 1.00 |
| 45_D | 49_G | 1.542 | 1.00 |
| 7_R | 209_L | 1.541 | 1.00 |
| 220_V | 249_G | 1.538 | 1.00 |
| 98_D | 102_R | 1.530 | 1.00 |
| 80_R | 84_E | 1.524 | 1.00 |
| 119_D | 160_I | 1.521 | 1.00 |
| 94_E | 98_D | 1.520 | 1.00 |
| 412_R | 417_Q | 1.498 | 1.00 |
| 177_T | 181_K | 1.492 | 1.00 |
| 64_F | 68_Q | 1.491 | 1.00 |
| 381_D | 385_L | 1.475 | 1.00 |
| 313_L | 485_M | 1.475 | 1.00 |
| 14_F | 17_I | 1.460 | 1.00 |
| 132_A | 136_A | 1.455 | 1.00 |
| 116_F | 157_G | 1.454 | 1.00 |
| 241_D | 244_N | 1.452 | 1.00 |
| 110_R | 114_V | 1.448 | 1.00 |
| 90_D | 128_A | 1.441 | 1.00 |
| 391_A | 412_R | 1.438 | 1.00 |
| 49_G | 100_Y | 1.437 | 1.00 |
| 209_L | 213_A | 1.433 | 1.00 |
| 24_M | 28_D | 1.428 | 0.99 |
| 84_E | 88_K | 1.427 | 0.99 |
| 234_R | 258_K | 1.420 | 0.99 |
| 345_M | 348_V | 1.418 | 0.99 |
| 40_V | 44_T | 1.415 | 0.99 |
| 501_Q | 504_D | 1.413 | 0.99 |
| 417_Q | 424_D | 1.412 | 0.99 |
| 117_E | 121_Q | 1.409 | 0.99 |
| 364_E | 367_G | 1.408 | 0.99 |
| 374_T | 378_K | 1.403 | 0.99 |
| 499_L | 502_L | 1.402 | 0.99 |
| 128_A | 132_A | 1.400 | 0.99 |
| 187_E | 191_L | 1.397 | 0.99 |
| 21_M | 24_M | 1.397 | 0.99 |
| 56_I | 93_L | 1.396 | 0.99 |
| 107_D | 110_R | 1.383 | 0.99 |
| 98_D | 101_R | 1.381 | 0.99 |
| 115_E | 119_D | 1.373 | 0.99 |
| 162_A | 166_A | 1.372 | 0.99 |
| 368_N | 424_D | 1.369 | 0.99 |
| 340_R | 459_Q | 1.368 | 0.99 |
| 106_R | 109_D | 1.364 | 0.99 |
| 13_S | 17_I | 1.358 | 0.99 |
| 462_D | 465_S | 1.357 | 0.99 |
| 473_T | 476_P | 1.355 | 0.99 |
| 87_P | 91_R | 1.355 | 0.99 |
| 391_A | 409_T | 1.355 | 0.99 |
| 160_I | 163_T | 1.347 | 0.99 |
| 18_L | 201_A | 1.344 | 0.99 |
| 217_R | 242_E | 1.338 | 0.99 |
| 341_M | 457_M | 1.335 | 0.99 |
| 43_N | 48_P | 1.334 | 0.99 |
| 277_E | 280_A | 1.332 | 0.99 |
| 514_R | 518_L | 1.328 | 0.99 |
| 130_I | 142_A | 1.321 | 0.99 |
| 70_A | 83_L | 1.315 | 0.99 |
| 183_V | 187_E | 1.308 | 0.99 |
| 223_L | 253_M | 1.307 | 0.99 |
| 49_G | 168_N | 1.303 | 0.99 |
| 335_Q | 468_I | 1.302 | 0.99 |
| 115_E | 160_I | 1.300 | 0.99 |
| 450_V | 453_G | 1.300 | 0.99 |
| 253_M | 257_L | 1.298 | 0.99 |
| 58_A | 61_F | 1.291 | 0.99 |
| 326_Q | 329_S | 1.287 | 0.99 |
| 129_D | 149_E | 1.280 | 0.99 |
| 215_P | 244_N | 1.277 | 0.99 |
| 149_E | 152_P | 1.276 | 0.99 |
| 329_S | 333_S | 1.276 | 0.99 |
| 515_Q | 518_L | 1.276 | 0.99 |
| 28_D | 190_M | 1.276 | 0.99 |
| 129_D | 133_T | 1.273 | 0.99 |
| 368_N | 371_Q | 1.273 | 0.99 |
| 223_L | 250_F | 1.272 | 0.99 |
| 263_K | 529_D | 1.272 | 0.99 |
| 245_A | 248_T | 1.270 | 0.99 |
| 288_T | 505_A | 1.268 | 0.99 |
| 372_V | 418_T | 1.268 | 0.99 |
| 192_V | 196_M | 1.264 | 0.98 |
| 11_L | 209_L | 1.261 | 0.98 |
| 331_A | 468_I | 1.259 | 0.98 |
| 232_T | 539_V | 1.255 | 0.98 |
| 234_R | 251_N | 1.251 | 0.98 |
| 484_G | 488_Q | 1.250 | 0.98 |
| 107_D | 111_S | 1.248 | 0.98 |
| 23_L | 27_V | 1.247 | 0.98 |
| 211_A | 215_P | 1.243 | 0.98 |
| 118_K | 122_E | 1.243 | 0.98 |
| 121_Q | 125_R | 1.236 | 0.98 |
| 201_A | 205_G | 1.233 | 0.98 |
| 451_R | 455_A | 1.233 | 0.98 |
| 46_A | 171_Q | 1.232 | 0.98 |
| 234_R | 255_D | 1.230 | 0.98 |
| 112_M | 167_E | 1.225 | 0.98 |
| 14_F | 20_I | 1.223 | 0.98 |
| 47_V | 50_I | 1.217 | 0.98 |
| 144_T | 148_N | 1.216 | 0.98 |
| 69_D | 72_N | 1.210 | 0.98 |
| 47_V | 172_A | 1.206 | 0.98 |
| 226_T | 254_V | 1.203 | 0.98 |
| 486_Q | 490_T | 1.201 | 0.98 |
| 43_N | 172_A | 1.200 | 0.98 |
| 464_L | 467_I | 1.195 | 0.98 |
| 39_V | 179_I | 1.194 | 0.98 |
| 120_L | 157_G | 1.194 | 0.98 |
| 151_R | 155_Y | 1.193 | 0.98 |
| 493_E | 496_N | 1.192 | 0.98 |
| 189_G | 192_V | 1.192 | 0.98 |
| 494_Q | 497_Q | 1.190 | 0.98 |
| 68_Q | 72_N | 1.188 | 0.97 |
| 528_N | 532_S | 1.183 | 0.97 |
| 272_A | 276_T | 1.182 | 0.97 |
| 224_E | 228_G | 1.182 | 0.97 |
| 31_R | 186_A | 1.181 | 0.97 |
| 365_K | 435_S | 1.179 | 0.97 |
| 235_L | 251_N | 1.178 | 0.97 |
| 10_I | 14_F | 1.178 | 0.97 |
| 409_T | 412_R | 1.177 | 0.97 |
| 229_G | 246_I | 1.173 | 0.97 |
| 436_V | 440_V | 1.172 | 0.97 |
| 185_S | 189_G | 1.164 | 0.97 |
| 259_G | 263_K | 1.162 | 0.97 |
| 197_A | 201_A | 1.159 | 0.97 |
| 202_L | 206_F | 1.159 | 0.97 |
| 375_T | 421_A | 1.158 | 0.97 |
| 385_L | 464_L | 1.157 | 0.97 |
| 6_L | 212_I | 1.157 | 0.97 |
| 376_I | 392_I | 1.155 | 0.97 |
| 188_V | 191_L | 1.154 | 0.97 |
| 43_N | 49_G | 1.153 | 0.97 |
| 195_G | 199_A | 1.153 | 0.97 |
| 174_E | 178_S | 1.149 | 0.97 |
| 92_Q | 95_E | 1.146 | 0.97 |
| 234_R | 254_V | 1.145 | 0.97 |
| 219_I | 246_I | 1.137 | 0.96 |
| 472_Q | 476_P | 1.136 | 0.96 |
| 125_R | 129_D | 1.135 | 0.96 |
| 462_D | 466_Q | 1.133 | 0.96 |
| 88_K | 92_Q | 1.131 | 0.96 |
| 362_L | 432_I | 1.128 | 0.96 |
| 52_Y | 99_F | 1.127 | 0.96 |
| 32_L | 35_I | 1.126 | 0.96 |
| 301_A | 305_E | 1.126 | 0.96 |
| 99_F | 102_R | 1.124 | 0.96 |
| 304_R | 308_A | 1.123 | 0.96 |
| 359_L | 439_G | 1.123 | 0.96 |
| 216_M | 246_I | 1.117 | 0.96 |
| 283_K | 287_A | 1.115 | 0.96 |
| 305_E | 308_A | 1.111 | 0.96 |
| 516_S | 519_A | 1.111 | 0.96 |
| 330_L | 466_Q | 1.110 | 0.96 |
| 418_T | 428_M | 1.106 | 0.96 |
| 511_E | 515_Q | 1.104 | 0.96 |
| 13_S | 20_I | 1.100 | 0.96 |
| 312_E | 480_M | 1.096 | 0.95 |
| 18_L | 21_M | 1.095 | 0.95 |
| 247_E | 251_N | 1.092 | 0.95 |
| 14_F | 205_G | 1.089 | 0.95 |
| 220_V | 246_I | 1.088 | 0.95 |
| 17_I | 201_A | 1.088 | 0.95 |
| 392_I | 503_S | 1.087 | 0.95 |
| 83_L | 135_G | 1.087 | 0.95 |
| 239_R | 242_E | 1.084 | 0.95 |
| 432_I | 436_V | 1.078 | 0.95 |
| 155_Y | 159_D | 1.075 | 0.95 |
| 95_E | 98_D | 1.075 | 0.95 |
| 315_R | 319_E | 1.072 | 0.95 |
| 370_T | 433_Q | 1.071 | 0.95 |
| 281_T | 512_S | 1.070 | 0.95 |
| 224_E | 249_G | 1.069 | 0.95 |
| 476_P | 483_E | 1.069 | 0.95 |
| 278_I | 282_S | 1.069 | 0.95 |
| 243_F | 247_E | 1.068 | 0.94 |
| 94_E | 124_K | 1.068 | 0.94 |
| 70_A | 79_R | 1.066 | 0.94 |
| 21_M | 197_A | 1.064 | 0.94 |
| 221_K | 224_E | 1.062 | 0.94 |
| 433_Q | 436_V | 1.061 | 0.94 |
| 100_Y | 109_D | 1.061 | 0.94 |
| 296_T | 299_I | 1.060 | 0.94 |
| 494_Q | 498_A | 1.057 | 0.94 |
| 61_F | 65_V | 1.056 | 0.94 |
| 337_G | 456_D | 1.052 | 0.94 |
| 88_K | 91_R | 1.051 | 0.94 |
| 273_T | 280_A | 1.051 | 0.94 |
| 260_L | 264_T | 1.050 | 0.94 |
| 27_V | 31_R | 1.050 | 0.94 |
| 294_A | 298_E | 1.048 | 0.94 |
| 84_E | 87_P | 1.047 | 0.94 |
| 522_E | 525_L | 1.043 | 0.94 |
| 179_I | 183_V | 1.041 | 0.93 |
| 73_S | 78_E | 1.040 | 0.93 |
| 261_V | 264_T | 1.039 | 0.93 |
| 318_T | 486_Q | 1.037 | 0.93 |
| 108_D | 167_E | 1.036 | 0.93 |
| 392_I | 418_T | 1.035 | 0.93 |
| 385_L | 413_R | 1.034 | 0.93 |
| 301_A | 304_R | 1.034 | 0.93 |
| 504_D | 508_Q | 1.032 | 0.93 |
| 100_Y | 168_N | 1.032 | 0.93 |
| 46_A | 168_N | 1.032 | 0.93 |
| 246_I | 253_M | 1.032 | 0.93 |
| 67_M | 127_R | 1.031 | 0.93 |
| 474_L | 478_V | 1.030 | 0.93 |
| 333_S | 336_V | 1.029 | 0.93 |
| 251_N | 255_D | 1.029 | 0.93 |
| 28_D | 197_A | 1.028 | 0.93 |
| 115_E | 163_T | 1.027 | 0.93 |
| 381_D | 422_T | 1.026 | 0.93 |
| 272_A | 277_E | 1.025 | 0.93 |
| 346_R | 458_Q | 1.024 | 0.93 |
| 70_A | 135_G | 1.024 | 0.93 |
| 35_I | 39_V | 1.024 | 0.93 |
| 49_G | 109_D | 1.022 | 0.93 |
| 32_L | 183_V | 1.022 | 0.93 |
| 69_D | 82_T | 1.021 | 0.93 |
| 226_T | 250_F | 1.020 | 0.93 |
| 114_V | 117_E | 1.017 | 0.92 |
| 333_S | 459_Q | 1.015 | 0.92 |
| 83_L | 87_P | 1.014 | 0.92 |
| 230_D | 538_K | 1.014 | 0.92 |
| 221_K | 225_L | 1.011 | 0.92 |
| 359_L | 362_L | 1.011 | 0.92 |
| 376_I | 418_T | 1.011 | 0.92 |
| 307_S | 492_A | 1.010 | 0.92 |
| 133_T | 145_R | 1.010 | 0.92 |
| 339_A | 343_D | 1.009 | 0.92 |
| 311_R | 493_E | 1.007 | 0.92 |
| 501_Q | 505_A | 1.005 | 0.92 |
| 377_T | 381_D | 1.003 | 0.92 |
| 78_E | 81_A | 1.002 | 0.92 |
| 333_S | 466_Q | 1.002 | 0.92 |
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 | |
| 3zx6A | 2 | 0.5603 | 100 | 0.426 | Contact Map |
| 1qu7A | 2 | 0.4156 | 100 | 0.559 | Contact Map |
| 3g67A | 2 | 0.3952 | 100 | 0.6 | Contact Map |
| 2ch7A | 1 | 0.5473 | 100 | 0.613 | Contact Map |
| 4i3mA | 1 | 0.2727 | 99.9 | 0.765 | Contact Map |
| 2d4uA | 2 | 0.2931 | 99.2 | 0.88 | Contact Map |
| 4cq4A | 4 | 0.18 | 99.2 | 0.881 | Contact Map |
| 3zccA | 2 | 0.2022 | 99.2 | 0.882 | Contact Map |
| 2f95B | 1 | 0.0983 | 99.1 | 0.886 | Contact Map |
| 4gycB | 1 | 0.1132 | 98.8 | 0.899 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)