| 2q72 |
| ID: | 1380611931 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 500 (471) | ||
| Sequences: | 2448 (1685.5) | ||
| Seq/Len: | 5.197 | ||
| Nf(neff/√len): | 77.7 |
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: 5.197).
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 |
| 228_N | 232_T | 3.279 | 1.00 |
| 225_D | 228_N | 3.276 | 1.00 |
| 199_M | 202_L | 3.221 | 1.00 |
| 237_K | 240_D | 3.219 | 1.00 |
| 336_G | 339_F | 2.901 | 1.00 |
| 234_D | 237_K | 2.853 | 1.00 |
| 180_V | 383_A | 2.846 | 1.00 |
| 200_P | 203_F | 2.750 | 1.00 |
| 214_F | 227_L | 2.696 | 1.00 |
| 199_M | 203_F | 2.602 | 1.00 |
| 173_L | 387_F | 2.504 | 1.00 |
| 212_R | 215_L | 2.438 | 1.00 |
| 323_G | 348_L | 2.438 | 1.00 |
| 119_A | 342_F | 2.358 | 1.00 |
| 5_R | 267_S | 2.314 | 1.00 |
| 212_R | 216_L | 2.224 | 1.00 |
| 69_G | 80_I | 2.148 | 1.00 |
| 59_M | 262_I | 2.129 | 1.00 |
| 271_K | 438_R | 2.111 | 1.00 |
| 389_S | 392_L | 2.098 | 1.00 |
| 21_N | 256_S | 2.089 | 1.00 |
| 212_R | 340_L | 2.063 | 1.00 |
| 170_I | 174_I | 2.052 | 1.00 |
| 19_A | 285_L | 2.049 | 1.00 |
| 65_M | 80_I | 2.048 | 1.00 |
| 30_R | 250_Q | 1.936 | 1.00 |
| 27_N | 286_N | 1.912 | 1.00 |
| 445_P | 448_Y | 1.910 | 1.00 |
| 404_D | 408_G | 1.898 | 1.00 |
| 286_N | 290_E | 1.868 | 1.00 |
| 21_N | 358_A | 1.867 | 1.00 |
| 307_G | 310_N | 1.866 | 1.00 |
| 55_G | 255_L | 1.854 | 1.00 |
| 361_Q | 375_R | 1.849 | 1.00 |
| 179_N | 356_S | 1.843 | 1.00 |
| 112_E | 352_G | 1.827 | 1.00 |
| 181_S | 185_R | 1.728 | 1.00 |
| 258_G | 416_G | 1.724 | 1.00 |
| 185_R | 193_R | 1.721 | 1.00 |
| 224_A | 228_N | 1.720 | 1.00 |
| 437_N | 443_K | 1.704 | 1.00 |
| 207_V | 211_I | 1.693 | 1.00 |
| 121_K | 147_F | 1.673 | 0.99 |
| 428_G | 431_K | 1.650 | 0.99 |
| 374_S | 377_H | 1.639 | 0.99 |
| 116_L | 349_F | 1.632 | 0.99 |
| 256_S | 261_A | 1.622 | 0.99 |
| 346_F | 350_F | 1.617 | 0.99 |
| 115_T | 349_F | 1.601 | 0.99 |
| 119_A | 346_F | 1.600 | 0.99 |
| 117_G | 151_Y | 1.591 | 0.99 |
| 264_T | 362_P | 1.563 | 0.99 |
| 190_G | 196_K | 1.560 | 0.99 |
| 60_W | 279_G | 1.550 | 0.99 |
| 236_E | 239_K | 1.547 | 0.99 |
| 231_W | 291_V | 1.539 | 0.99 |
| 230_L | 291_V | 1.530 | 0.99 |
| 216_L | 223_A | 1.524 | 0.99 |
| 56_I | 283_A | 1.511 | 0.99 |
| 119_A | 349_F | 1.506 | 0.99 |
| 224_A | 227_L | 1.501 | 0.99 |
| 82_Y | 91_K | 1.500 | 0.99 |
| 13_G | 192_E | 1.494 | 0.99 |
| 173_L | 177_F | 1.490 | 0.99 |
| 465_V | 469_R | 1.483 | 0.98 |
| 117_G | 121_K | 1.471 | 0.98 |
| 223_A | 226_G | 1.469 | 0.98 |
| 134_A | 146_E | 1.468 | 0.98 |
| 265_Y | 358_A | 1.453 | 0.98 |
| 44_M | 291_V | 1.453 | 0.98 |
| 304_A | 307_G | 1.451 | 0.98 |
| 5_R | 369_D | 1.433 | 0.98 |
| 122_F | 341_G | 1.426 | 0.98 |
| 192_E | 196_K | 1.422 | 0.98 |
| 145_K | 149_Y | 1.413 | 0.98 |
| 373_L | 381_W | 1.411 | 0.98 |
| 451_V | 455_I | 1.401 | 0.98 |
| 27_N | 47_Y | 1.399 | 0.98 |
| 365_A | 369_D | 1.396 | 0.98 |
| 50_A | 248_V | 1.395 | 0.98 |
| 390_A | 394_M | 1.394 | 0.97 |
| 390_A | 393_V | 1.393 | 0.97 |
| 189_K | 193_R | 1.379 | 0.97 |
| 450_Y | 455_I | 1.368 | 0.97 |
| 287_E | 290_E | 1.339 | 0.97 |
| 63_W | 279_G | 1.337 | 0.97 |
| 70_G | 271_K | 1.333 | 0.96 |
| 302_A | 326_T | 1.320 | 0.96 |
| 299_I | 304_A | 1.319 | 0.96 |
| 23_V | 27_N | 1.318 | 0.96 |
| 12_L | 16_L | 1.313 | 0.96 |
| 68_Y | 435_E | 1.313 | 0.96 |
| 200_P | 204_I | 1.310 | 0.96 |
| 204_I | 208_F | 1.308 | 0.96 |
| 435_E | 439_G | 1.306 | 0.96 |
| 19_A | 23_V | 1.303 | 0.96 |
| 303_V | 307_G | 1.303 | 0.96 |
| 434_E | 443_K | 1.298 | 0.96 |
| 123_L | 342_F | 1.292 | 0.96 |
| 449_Y | 453_R | 1.292 | 0.96 |
| 37_E | 242_G | 1.283 | 0.95 |
| 104_V | 259_F | 1.278 | 0.95 |
| 176_M | 180_V | 1.277 | 0.95 |
| 231_W | 296_S | 1.276 | 0.95 |
| 203_F | 289_A | 1.274 | 0.95 |
| 161_I | 164_P | 1.273 | 0.95 |
| 105_A | 356_S | 1.271 | 0.95 |
| 63_W | 262_I | 1.271 | 0.95 |
| 36_A | 229_F | 1.270 | 0.95 |
| 30_R | 34_Q | 1.266 | 0.95 |
| 76_T | 369_D | 1.258 | 0.95 |
| 261_A | 359_I | 1.246 | 0.94 |
| 417_L | 461_A | 1.238 | 0.94 |
| 210_V | 214_F | 1.232 | 0.94 |
| 90_A | 422_I | 1.231 | 0.94 |
| 63_W | 266_A | 1.230 | 0.94 |
| 309_A | 316_K | 1.218 | 0.93 |
| 21_N | 104_V | 1.216 | 0.93 |
| 421_I | 426_I | 1.216 | 0.93 |
| 63_W | 282_A | 1.215 | 0.93 |
| 433_W | 449_Y | 1.215 | 0.93 |
| 303_V | 310_N | 1.215 | 0.93 |
| 221_G | 226_G | 1.211 | 0.93 |
| 251_I | 287_E | 1.208 | 0.93 |
| 301_A | 304_A | 1.207 | 0.93 |
| 153_G | 164_P | 1.207 | 0.93 |
| 29_L | 33_V | 1.205 | 0.93 |
| 17_A | 265_Y | 1.205 | 0.93 |
| 193_R | 196_K | 1.203 | 0.93 |
| 171_V | 174_I | 1.202 | 0.93 |
| 216_L | 221_G | 1.200 | 0.93 |
| 400_L | 404_D | 1.197 | 0.93 |
| 302_A | 308_V | 1.195 | 0.93 |
| 185_R | 188_S | 1.194 | 0.92 |
| 417_L | 464_L | 1.191 | 0.92 |
| 157_G | 161_I | 1.190 | 0.92 |
| 158_D | 162_L | 1.184 | 0.92 |
| 20_G | 354_T | 1.184 | 0.92 |
| 53_L | 57_P | 1.183 | 0.92 |
| 79_A | 370_E | 1.177 | 0.92 |
| 77_T | 260_G | 1.175 | 0.92 |
| 377_H | 381_W | 1.170 | 0.91 |
| 38_N | 242_G | 1.169 | 0.91 |
| 383_A | 387_F | 1.161 | 0.91 |
| 60_W | 64_A | 1.160 | 0.91 |
| 427_F | 435_E | 1.156 | 0.91 |
| 153_G | 157_G | 1.152 | 0.91 |
| 357_I | 361_Q | 1.152 | 0.91 |
| 273_Q | 278_S | 1.151 | 0.91 |
| 430_D | 453_R | 1.150 | 0.91 |
| 46_P | 244_W | 1.145 | 0.90 |
| 450_Y | 454_Y | 1.142 | 0.90 |
| 28_F | 351_A | 1.140 | 0.90 |
| 112_E | 175_T | 1.138 | 0.90 |
| 131_P | 134_A | 1.138 | 0.90 |
| 180_V | 186_G | 1.136 | 0.90 |
| 320_F | 323_G | 1.129 | 0.89 |
| 10_T | 13_G | 1.128 | 0.89 |
| 198_A | 350_F | 1.127 | 0.89 |
| 46_P | 238_L | 1.126 | 0.89 |
| 207_V | 292_I | 1.124 | 0.89 |
| 17_A | 264_T | 1.124 | 0.89 |
| 77_T | 80_I | 1.124 | 0.89 |
| 192_E | 195_A | 1.120 | 0.89 |
| 42_A | 235_F | 1.115 | 0.89 |
| 185_R | 189_K | 1.114 | 0.89 |
| 302_A | 305_F | 1.113 | 0.89 |
| 216_L | 222_T | 1.112 | 0.88 |
| 58_L | 460_L | 1.112 | 0.88 |
| 177_F | 181_S | 1.111 | 0.88 |
| 157_G | 160_P | 1.110 | 0.88 |
| 266_A | 286_N | 1.110 | 0.88 |
| 323_G | 326_T | 1.108 | 0.88 |
| 212_R | 226_G | 1.105 | 0.88 |
| 160_P | 164_P | 1.099 | 0.88 |
| 104_V | 359_I | 1.098 | 0.88 |
| 324_F | 345_F | 1.094 | 0.87 |
| 274_D | 278_S | 1.092 | 0.87 |
| 154_V | 167_F | 1.092 | 0.87 |
| 67_R | 435_E | 1.090 | 0.87 |
| 164_P | 168_A | 1.089 | 0.87 |
| 167_F | 171_V | 1.088 | 0.87 |
| 9_A | 12_L | 1.082 | 0.87 |
| 298_S | 302_A | 1.077 | 0.86 |
| 32_P | 39_G | 1.076 | 0.86 |
| 212_R | 335_A | 1.072 | 0.86 |
| 244_W | 247_A | 1.071 | 0.86 |
| 378_A | 381_W | 1.069 | 0.86 |
| 64_A | 432_A | 1.068 | 0.86 |
| 17_A | 21_N | 1.067 | 0.86 |
| 8_W | 17_A | 1.062 | 0.85 |
| 14_L | 18_M | 1.061 | 0.85 |
| 138_D | 141_L | 1.057 | 0.85 |
| 153_G | 156_K | 1.057 | 0.85 |
| 339_F | 342_F | 1.056 | 0.85 |
| 172_F | 176_M | 1.052 | 0.84 |
| 11_R | 16_L | 1.046 | 0.84 |
| 255_L | 266_A | 1.045 | 0.84 |
| 213_V | 301_A | 1.045 | 0.84 |
| 344_W | 361_Q | 1.043 | 0.84 |
| 182_I | 353_L | 1.042 | 0.84 |
| 166_L | 173_L | 1.041 | 0.84 |
| 105_A | 359_I | 1.038 | 0.83 |
| 417_L | 421_I | 1.037 | 0.83 |
| 427_F | 431_K | 1.037 | 0.83 |
| 295_G | 300_P | 1.036 | 0.83 |
| 190_G | 195_A | 1.036 | 0.83 |
| 107_Y | 404_D | 1.035 | 0.83 |
| 329_A | 333_Q | 1.033 | 0.83 |
| 201_T | 204_I | 1.031 | 0.83 |
| 238_L | 243_V | 1.031 | 0.83 |
| 31_F | 39_G | 1.031 | 0.83 |
| 60_W | 275_I | 1.028 | 0.83 |
| 62_E | 66_G | 1.028 | 0.83 |
| 137_P | 141_L | 1.027 | 0.82 |
| 91_K | 95_V | 1.027 | 0.82 |
| 444_V | 447_I | 1.022 | 0.82 |
| 250_Q | 254_T | 1.022 | 0.82 |
| 116_L | 178_I | 1.017 | 0.82 |
| 208_F | 212_R | 1.016 | 0.81 |
| 334_T | 340_L | 1.011 | 0.81 |
| 402_E | 406_W | 1.010 | 0.81 |
| 153_G | 160_P | 1.010 | 0.81 |
| 414_F | 464_L | 1.008 | 0.81 |
| 8_W | 301_A | 1.008 | 0.81 |
| 342_F | 346_F | 1.005 | 0.81 |
| 52_L | 55_G | 1.003 | 0.80 |
| 88_R | 92_I | 1.001 | 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 | |
| 2a65A | 1 | 0.9807 | 100 | 0.018 | Contact Map |
| 4m48A | 1 | 0.9653 | 100 | 0.156 | Contact Map |
| 3giaA | 1 | 0.7996 | 98.6 | 0.926 | Contact Map |
| 4djkA | 2 | 0.8131 | 98.3 | 0.933 | Contact Map |
| 2jlnA | 1 | 0.8092 | 98.2 | 0.935 | Contact Map |
| 3l1lA | 1 | 0.7823 | 98.2 | 0.935 | Contact Map |
| 2xq2A | 1 | 0.7996 | 82.2 | 0.968 | Contact Map |
| 3dh4A | 4 | 0.7881 | 74 | 0.97 | Contact Map |
| 2wswA | 1 | 0.7264 | 54.8 | 0.973 | Contact Map |
| 3m73A | 1 | 0.2582 | 20.5 | 0.979 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)