| mcoa |
| ID: | 1491319949 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 485 (453) | ||
| Sequences: | 4364 (2504.8) | ||
| Seq/Len: | 9.634 | ||
| Nf(neff/√len): | 117.7 |
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: 9.634).
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 |
| 54_F | 139_E | 5.561 | 1.00 |
| 205_I | 262_L | 4.413 | 1.00 |
| 62_S | 104_D | 4.323 | 1.00 |
| 257_E | 436_K | 4.178 | 1.00 |
| 60_T | 104_D | 3.553 | 1.00 |
| 20_R | 62_S | 3.501 | 1.00 |
| 439_V | 447_V | 3.434 | 1.00 |
| 52_V | 135_M | 3.362 | 1.00 |
| 24_T | 68_N | 3.352 | 1.00 |
| 64_D | 101_S | 3.205 | 1.00 |
| 236_G | 260_D | 3.113 | 1.00 |
| 22_S | 64_D | 3.064 | 1.00 |
| 22_S | 66_V | 3.015 | 1.00 |
| 20_R | 64_D | 3.005 | 1.00 |
| 210_I | 261_I | 2.997 | 1.00 |
| 422_E | 448_R | 2.873 | 1.00 |
| 253_V | 259_I | 2.835 | 1.00 |
| 210_I | 221_L | 2.733 | 1.00 |
| 232_F | 261_I | 2.720 | 1.00 |
| 65_F | 94_V | 2.684 | 1.00 |
| 66_V | 99_T | 2.648 | 1.00 |
| 135_M | 211_L | 2.608 | 1.00 |
| 223_L | 263_V | 2.607 | 1.00 |
| 400_E | 448_R | 2.604 | 1.00 |
| 401_Y | 411_M | 2.556 | 1.00 |
| 205_I | 264_D | 2.540 | 1.00 |
| 401_Y | 449_I | 2.540 | 1.00 |
| 416_F | 483_V | 2.496 | 1.00 |
| 214_S | 219_Y | 2.470 | 1.00 |
| 208_F | 261_I | 2.450 | 1.00 |
| 398_I | 421_L | 2.447 | 1.00 |
| 28_T | 42_V | 2.400 | 1.00 |
| 398_I | 450_A | 2.361 | 1.00 |
| 161_L | 210_I | 2.301 | 1.00 |
| 201_V | 265_F | 2.288 | 1.00 |
| 30_L | 40_M | 2.266 | 1.00 |
| 169_D | 173_Q | 2.262 | 1.00 |
| 43_Y | 116_Y | 2.253 | 1.00 |
| 418_F | 449_I | 2.244 | 1.00 |
| 163_I | 221_L | 2.222 | 1.00 |
| 27_W | 39_D | 2.217 | 1.00 |
| 207_R | 260_D | 2.167 | 1.00 |
| 413_I | 451_V | 2.119 | 1.00 |
| 95_K | 98_E | 2.097 | 1.00 |
| 57_K | 140_D | 2.093 | 1.00 |
| 86_S | 100_Y | 2.053 | 1.00 |
| 118_P | 127_Q | 2.037 | 1.00 |
| 133_A | 164_Q | 1.976 | 1.00 |
| 135_M | 162_I | 1.969 | 1.00 |
| 231_R | 247_E | 1.968 | 1.00 |
| 24_T | 66_V | 1.960 | 1.00 |
| 466_H | 472_H | 1.953 | 1.00 |
| 442_A | 445_E | 1.950 | 1.00 |
| 56_R | 139_E | 1.946 | 1.00 |
| 224_L | 277_Y | 1.943 | 1.00 |
| 29_T | 39_D | 1.943 | 1.00 |
| 467_C | 472_H | 1.933 | 1.00 |
| 114_Y | 239_G | 1.923 | 1.00 |
| 251_I | 259_I | 1.908 | 1.00 |
| 162_I | 213_G | 1.905 | 1.00 |
| 60_T | 106_T | 1.895 | 1.00 |
| 207_R | 235_I | 1.891 | 1.00 |
| 218_P | 440_I | 1.881 | 1.00 |
| 258_R | 437_D | 1.870 | 1.00 |
| 468_H | 472_H | 1.859 | 1.00 |
| 19_Q | 59_Q | 1.851 | 1.00 |
| 234_V | 259_I | 1.755 | 1.00 |
| 231_R | 249_N | 1.749 | 1.00 |
| 116_Y | 134_G | 1.741 | 1.00 |
| 220_R | 250_E | 1.725 | 1.00 |
| 355_R | 400_E | 1.701 | 1.00 |
| 462_I | 482_R | 1.696 | 1.00 |
| 157_I | 204_K | 1.670 | 1.00 |
| 42_V | 48_E | 1.659 | 1.00 |
| 26_K | 68_N | 1.638 | 1.00 |
| 392_N | 395_D | 1.637 | 1.00 |
| 157_I | 206_Y | 1.612 | 1.00 |
| 198_Y | 325_R | 1.594 | 1.00 |
| 233_W | 247_E | 1.575 | 1.00 |
| 25_A | 43_Y | 1.571 | 1.00 |
| 25_A | 65_F | 1.544 | 1.00 |
| 234_V | 248_V | 1.541 | 1.00 |
| 354_Q | 397_V | 1.529 | 1.00 |
| 419_Q | 435_W | 1.524 | 1.00 |
| 254_A | 440_I | 1.512 | 1.00 |
| 239_G | 417_Q | 1.511 | 1.00 |
| 251_I | 261_I | 1.502 | 1.00 |
| 54_F | 158_D | 1.472 | 1.00 |
| 159_I | 199_M | 1.468 | 1.00 |
| 43_Y | 75_I | 1.453 | 1.00 |
| 240_G | 417_Q | 1.448 | 1.00 |
| 473_H | 478_M | 1.446 | 1.00 |
| 129_Y | 215_N | 1.443 | 1.00 |
| 64_D | 99_T | 1.436 | 1.00 |
| 159_I | 208_F | 1.434 | 1.00 |
| 423_R | 445_E | 1.429 | 1.00 |
| 413_I | 449_I | 1.426 | 1.00 |
| 265_F | 324_F | 1.423 | 1.00 |
| 113_T | 209_R | 1.388 | 0.99 |
| 223_L | 232_F | 1.387 | 0.99 |
| 201_V | 263_V | 1.379 | 0.99 |
| 41_L | 130_Y | 1.369 | 0.99 |
| 396_V | 452_D | 1.356 | 0.99 |
| 223_L | 276_L | 1.355 | 0.99 |
| 470_L | 473_H | 1.350 | 0.99 |
| 139_E | 158_D | 1.349 | 0.99 |
| 409_H | 414_H | 1.347 | 0.99 |
| 18_G | 62_S | 1.341 | 0.99 |
| 77_W | 105_F | 1.341 | 0.99 |
| 23_I | 53_I | 1.341 | 0.99 |
| 55_L | 138_I | 1.335 | 0.99 |
| 464_L | 478_M | 1.322 | 0.99 |
| 62_S | 101_S | 1.321 | 0.99 |
| 128_V | 470_L | 1.318 | 0.99 |
| 221_L | 276_L | 1.307 | 0.99 |
| 200_D | 325_R | 1.300 | 0.99 |
| 113_T | 135_M | 1.297 | 0.99 |
| 61_F | 136_I | 1.296 | 0.99 |
| 94_V | 100_Y | 1.293 | 0.99 |
| 55_L | 61_F | 1.285 | 0.99 |
| 201_V | 298_E | 1.285 | 0.99 |
| 201_V | 206_Y | 1.278 | 0.99 |
| 418_F | 439_V | 1.278 | 0.99 |
| 73_S | 127_Q | 1.271 | 0.99 |
| 40_M | 166_K | 1.271 | 0.99 |
| 65_F | 77_W | 1.269 | 0.99 |
| 55_L | 136_I | 1.269 | 0.99 |
| 400_E | 446_T | 1.263 | 0.99 |
| 422_E | 446_T | 1.259 | 0.99 |
| 237_V | 259_I | 1.256 | 0.98 |
| 210_I | 251_I | 1.255 | 0.98 |
| 210_I | 253_V | 1.255 | 0.98 |
| 29_T | 37_S | 1.249 | 0.98 |
| 410_P | 469_I | 1.249 | 0.98 |
| 222_A | 277_Y | 1.228 | 0.98 |
| 408_Y | 440_I | 1.227 | 0.98 |
| 209_R | 260_D | 1.226 | 0.98 |
| 215_N | 471_E | 1.224 | 0.98 |
| 243_D | 341_S | 1.203 | 0.98 |
| 101_S | 104_D | 1.192 | 0.98 |
| 119_H | 468_H | 1.187 | 0.98 |
| 189_I | 219_Y | 1.181 | 0.97 |
| 276_L | 298_E | 1.175 | 0.97 |
| 220_R | 252_L | 1.175 | 0.97 |
| 52_V | 116_Y | 1.172 | 0.97 |
| 421_L | 450_A | 1.172 | 0.97 |
| 214_S | 255_P | 1.170 | 0.97 |
| 409_H | 472_H | 1.167 | 0.97 |
| 119_H | 472_H | 1.160 | 0.97 |
| 235_I | 262_L | 1.157 | 0.97 |
| 367_I | 411_M | 1.156 | 0.97 |
| 409_H | 467_C | 1.155 | 0.97 |
| 50_N | 193_L | 1.154 | 0.97 |
| 41_L | 69_S | 1.153 | 0.97 |
| 273_V | 323_E | 1.151 | 0.97 |
| 65_F | 75_I | 1.149 | 0.97 |
| 358_L | 367_I | 1.148 | 0.97 |
| 119_H | 467_C | 1.137 | 0.97 |
| 20_R | 104_D | 1.135 | 0.97 |
| 61_F | 105_F | 1.135 | 0.97 |
| 183_G | 407_M | 1.134 | 0.97 |
| 415_G | 463_Y | 1.127 | 0.96 |
| 27_W | 70_G | 1.123 | 0.96 |
| 133_A | 213_G | 1.110 | 0.96 |
| 119_H | 466_H | 1.108 | 0.96 |
| 222_A | 250_E | 1.106 | 0.96 |
| 194_T | 197_P | 1.105 | 0.96 |
| 76_H | 79_G | 1.104 | 0.96 |
| 409_H | 468_H | 1.103 | 0.96 |
| 43_Y | 132_L | 1.100 | 0.96 |
| 233_W | 264_D | 1.092 | 0.95 |
| 164_Q | 190_L | 1.090 | 0.95 |
| 56_R | 59_Q | 1.085 | 0.95 |
| 44_E | 49_Y | 1.084 | 0.95 |
| 164_Q | 213_G | 1.083 | 0.95 |
| 18_G | 60_T | 1.083 | 0.95 |
| 454_S | 460_H | 1.082 | 0.95 |
| 57_K | 141_E | 1.077 | 0.95 |
| 220_R | 279_F | 1.074 | 0.95 |
| 158_D | 207_R | 1.074 | 0.95 |
| 41_L | 132_L | 1.069 | 0.95 |
| 135_M | 160_P | 1.063 | 0.95 |
| 411_M | 465_L | 1.061 | 0.94 |
| 472_H | 477_M | 1.057 | 0.94 |
| 168_F | 188_T | 1.055 | 0.94 |
| 128_V | 133_A | 1.053 | 0.94 |
| 57_K | 109_D | 1.046 | 0.94 |
| 119_H | 414_H | 1.043 | 0.94 |
| 230_M | 274_I | 1.041 | 0.94 |
| 401_Y | 465_L | 1.040 | 0.94 |
| 31_E | 35_G | 1.037 | 0.94 |
| 83_P | 86_S | 1.035 | 0.93 |
| 236_G | 241_L | 1.030 | 0.93 |
| 56_R | 141_E | 1.029 | 0.93 |
| 163_I | 219_Y | 1.021 | 0.93 |
| 50_N | 116_Y | 1.011 | 0.92 |
| 409_H | 466_H | 1.006 | 0.92 |
| 466_H | 477_M | 1.005 | 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
- See coupling matrix (for protein design or mutagenesis)
- 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 | |
| 3abgA | 2 | 0.9134 | 100 | 0.187 | Contact Map |
| 2uxtA | 2 | 0.8557 | 100 | 0.189 | Contact Map |
| 2xu9A | 1 | 0.8928 | 100 | 0.205 | Contact Map |
| 4e9sA | 1 | 0.8866 | 100 | 0.205 | Contact Map |
| 3zx1A | 1 | 0.8763 | 100 | 0.207 | Contact Map |
| 2wsdA | 1 | 0.8928 | 100 | 0.21 | Contact Map |
| 3gyrA | 12 | 0.9031 | 100 | 0.212 | Contact Map |
| 3aw5A | 1 | 0.8619 | 100 | 0.217 | Contact Map |
| 1zpuA | 6 | 0.8784 | 100 | 0.217 | Contact Map |
| 3sqrA | 1 | 0.899 | 100 | 0.228 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)