| T0793 -force run |
| ID: | 1401130541 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 595 (547) | ||
| Sequences: | 193 (161.9) | ||
| Seq/Len: | 0.353 | ||
| Nf(neff/√len): | 6.9 |
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: 0.353).
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 |
| 212_S | 321_D | 3.419 | 0.99 |
| 241_W | 307_S | 3.086 | 0.99 |
| 213_S | 395_R | 2.864 | 0.98 |
| 227_A | 356_L | 2.783 | 0.97 |
| 224_V | 261_V | 2.248 | 0.87 |
| 207_S | 264_E | 2.239 | 0.87 |
| 246_N | 289_S | 2.143 | 0.84 |
| 179_L | 403_I | 2.072 | 0.81 |
| 162_N | 351_N | 2.050 | 0.80 |
| 247_A | 287_Q | 2.014 | 0.78 |
| 246_N | 250_G | 1.925 | 0.74 |
| 171_V | 181_V | 1.924 | 0.74 |
| 217_S | 308_T | 1.883 | 0.71 |
| 212_S | 264_E | 1.875 | 0.71 |
| 321_D | 392_T | 1.863 | 0.70 |
| 180_A | 208_F | 1.799 | 0.66 |
| 206_F | 403_I | 1.761 | 0.64 |
| 249_E | 285_G | 1.761 | 0.64 |
| 119_L | 122_P | 1.758 | 0.64 |
| 220_A | 306_I | 1.753 | 0.63 |
| 257_G | 302_G | 1.727 | 0.62 |
| 250_G | 289_S | 1.687 | 0.59 |
| 160_F | 358_L | 1.679 | 0.58 |
| 212_S | 341_A | 1.666 | 0.58 |
| 249_E | 288_R | 1.651 | 0.57 |
| 174_H | 207_S | 1.636 | 0.56 |
| 184_G | 226_V | 1.628 | 0.55 |
| 203_G | 267_S | 1.620 | 0.54 |
| 252_L | 260_I | 1.618 | 0.54 |
| 207_S | 309_S | 1.614 | 0.54 |
| 246_N | 288_R | 1.613 | 0.54 |
| 252_L | 280_I | 1.609 | 0.54 |
| 185_I | 355_V | 1.607 | 0.54 |
| 113_Y | 116_V | 1.598 | 0.53 |
| 402_V | 408_K | 1.588 | 0.52 |
| 167_Y | 330_I | 1.584 | 0.52 |
| 541_F | 544_L | 1.570 | 0.51 |
| 160_F | 354_H | 1.566 | 0.51 |
| 261_V | 308_T | 1.565 | 0.51 |
| 351_N | 354_H | 1.539 | 0.49 |
| 120_E | 127_I | 1.530 | 0.48 |
| 207_S | 212_S | 1.498 | 0.46 |
| 207_S | 400_Y | 1.485 | 0.45 |
| 213_S | 341_A | 1.473 | 0.44 |
| 392_T | 406_S | 1.466 | 0.44 |
| 70_S | 83_K | 1.458 | 0.43 |
| 25_K | 31_E | 1.431 | 0.41 |
| 218_T | 262_F | 1.414 | 0.40 |
| 220_A | 243_A | 1.406 | 0.40 |
| 250_G | 296_K | 1.405 | 0.39 |
| 119_L | 294_E | 1.404 | 0.39 |
| 182_I | 419_D | 1.401 | 0.39 |
| 252_L | 305_V | 1.388 | 0.38 |
| 301_W | 306_I | 1.380 | 0.38 |
| 189_V | 359_V | 1.379 | 0.38 |
| 204_I | 304_S | 1.376 | 0.38 |
| 268_T | 334_F | 1.368 | 0.37 |
| 291_V | 295_V | 1.359 | 0.36 |
| 280_I | 305_V | 1.359 | 0.36 |
| 11_F | 336_T | 1.359 | 0.36 |
| 257_G | 264_E | 1.353 | 0.36 |
| 358_L | 361_K | 1.351 | 0.36 |
| 222_L | 344_I | 1.338 | 0.35 |
| 44_A | 78_L | 1.337 | 0.35 |
| 68_F | 293_G | 1.324 | 0.34 |
| 174_H | 282_E | 1.322 | 0.34 |
| 220_A | 288_R | 1.313 | 0.33 |
| 330_I | 382_E | 1.313 | 0.33 |
| 220_A | 224_V | 1.309 | 0.33 |
| 81_L | 124_G | 1.304 | 0.33 |
| 342_D | 345_K | 1.301 | 0.33 |
| 289_S | 293_G | 1.299 | 0.33 |
| 159_T | 374_F | 1.299 | 0.33 |
| 257_G | 293_G | 1.297 | 0.33 |
| 207_S | 265_L | 1.295 | 0.32 |
| 217_S | 506_V | 1.291 | 0.32 |
| 118_I | 121_T | 1.286 | 0.32 |
| 249_E | 407_A | 1.286 | 0.32 |
| 212_S | 224_V | 1.285 | 0.32 |
| 241_W | 244_T | 1.282 | 0.32 |
| 213_S | 320_N | 1.278 | 0.31 |
| 256_Y | 283_G | 1.278 | 0.31 |
| 165_N | 169_D | 1.264 | 0.31 |
| 167_Y | 507_V | 1.262 | 0.30 |
| 156_P | 354_H | 1.255 | 0.30 |
| 304_S | 328_I | 1.252 | 0.30 |
| 286_R | 309_S | 1.251 | 0.30 |
| 36_M | 136_I | 1.245 | 0.29 |
| 182_I | 407_A | 1.239 | 0.29 |
| 74_T | 289_S | 1.235 | 0.29 |
| 313_I | 350_L | 1.227 | 0.28 |
| 240_S | 344_I | 1.225 | 0.28 |
| 217_S | 438_R | 1.220 | 0.28 |
| 171_V | 308_T | 1.219 | 0.28 |
| 220_A | 261_V | 1.214 | 0.28 |
| 203_G | 213_S | 1.212 | 0.27 |
| 185_I | 439_S | 1.210 | 0.27 |
| 162_N | 354_H | 1.209 | 0.27 |
| 174_H | 323_L | 1.209 | 0.27 |
| 241_W | 395_R | 1.208 | 0.27 |
| 207_S | 282_E | 1.204 | 0.27 |
| 11_F | 19_K | 1.202 | 0.27 |
| 218_T | 308_T | 1.201 | 0.27 |
| 286_R | 404_T | 1.197 | 0.27 |
| 206_F | 328_I | 1.195 | 0.27 |
| 357_P | 405_T | 1.193 | 0.26 |
| 204_I | 289_S | 1.190 | 0.26 |
| 208_F | 252_L | 1.189 | 0.26 |
| 212_S | 218_T | 1.189 | 0.26 |
| 210_G | 226_V | 1.187 | 0.26 |
| 85_G | 406_S | 1.186 | 0.26 |
| 36_M | 312_S | 1.182 | 0.26 |
| 205_L | 426_Y | 1.181 | 0.26 |
| 192_F | 217_S | 1.181 | 0.26 |
| 549_E | 554_L | 1.180 | 0.26 |
| 206_F | 330_I | 1.177 | 0.26 |
| 118_I | 122_P | 1.177 | 0.26 |
| 184_G | 227_A | 1.175 | 0.25 |
| 179_L | 330_I | 1.175 | 0.25 |
| 167_Y | 393_G | 1.171 | 0.25 |
| 161_D | 164_F | 1.171 | 0.25 |
| 28_G | 161_D | 1.167 | 0.25 |
| 221_A | 345_K | 1.167 | 0.25 |
| 205_L | 458_K | 1.167 | 0.25 |
| 204_I | 399_R | 1.165 | 0.25 |
| 337_N | 341_A | 1.164 | 0.25 |
| 410_L | 426_Y | 1.162 | 0.25 |
| 224_V | 237_L | 1.160 | 0.25 |
| 217_S | 285_G | 1.157 | 0.25 |
| 174_H | 177_L | 1.150 | 0.24 |
| 226_V | 243_A | 1.148 | 0.24 |
| 242_N | 286_R | 1.148 | 0.24 |
| 46_F | 78_L | 1.147 | 0.24 |
| 240_S | 526_K | 1.144 | 0.24 |
| 185_I | 359_V | 1.144 | 0.24 |
| 124_G | 127_I | 1.143 | 0.24 |
| 86_Y | 516_I | 1.140 | 0.24 |
| 354_H | 358_L | 1.136 | 0.23 |
| 305_V | 328_I | 1.136 | 0.23 |
| 208_F | 393_G | 1.133 | 0.23 |
| 170_E | 308_T | 1.131 | 0.23 |
| 108_P | 230_P | 1.128 | 0.23 |
| 173_G | 177_L | 1.123 | 0.23 |
| 203_G | 283_G | 1.123 | 0.23 |
| 247_A | 286_R | 1.123 | 0.23 |
| 456_R | 471_N | 1.121 | 0.23 |
| 14_D | 19_K | 1.120 | 0.23 |
| 246_N | 249_E | 1.119 | 0.23 |
| 230_P | 544_L | 1.119 | 0.23 |
| 242_N | 246_N | 1.117 | 0.23 |
| 369_E | 452_V | 1.115 | 0.22 |
| 241_W | 262_F | 1.115 | 0.22 |
| 258_I | 415_S | 1.115 | 0.22 |
| 359_V | 362_Y | 1.115 | 0.22 |
| 317_S | 323_L | 1.114 | 0.22 |
| 219_A | 224_V | 1.108 | 0.22 |
| 348_V | 391_N | 1.107 | 0.22 |
| 40_I | 344_I | 1.107 | 0.22 |
| 266_S | 438_R | 1.104 | 0.22 |
| 350_L | 362_Y | 1.103 | 0.22 |
| 177_L | 264_E | 1.101 | 0.22 |
| 258_I | 414_L | 1.099 | 0.22 |
| 136_I | 294_E | 1.099 | 0.22 |
| 25_K | 29_D | 1.099 | 0.22 |
| 42_V | 186_S | 1.099 | 0.22 |
| 28_G | 224_V | 1.099 | 0.22 |
| 300_N | 513_K | 1.098 | 0.22 |
| 446_D | 515_F | 1.096 | 0.21 |
| 205_L | 456_R | 1.096 | 0.21 |
| 40_I | 230_P | 1.095 | 0.21 |
| 58_I | 126_L | 1.094 | 0.21 |
| 115_G | 118_I | 1.094 | 0.21 |
| 166_M | 170_E | 1.090 | 0.21 |
| 248_L | 280_I | 1.088 | 0.21 |
| 128_S | 134_K | 1.087 | 0.21 |
| 512_D | 524_T | 1.086 | 0.21 |
| 176_L | 422_N | 1.086 | 0.21 |
| 116_V | 332_E | 1.085 | 0.21 |
| 29_D | 32_K | 1.081 | 0.21 |
| 73_L | 288_R | 1.080 | 0.21 |
| 208_F | 246_N | 1.078 | 0.21 |
| 321_D | 436_S | 1.077 | 0.21 |
| 73_L | 78_L | 1.075 | 0.21 |
| 39_P | 359_V | 1.073 | 0.20 |
| 213_S | 329_E | 1.071 | 0.20 |
| 410_L | 442_D | 1.069 | 0.20 |
| 184_G | 392_T | 1.069 | 0.20 |
| 383_A | 526_K | 1.068 | 0.20 |
| 111_E | 116_V | 1.067 | 0.20 |
| 247_A | 257_G | 1.066 | 0.20 |
| 78_L | 288_R | 1.065 | 0.20 |
| 245_R | 396_M | 1.065 | 0.20 |
| 252_L | 392_T | 1.063 | 0.20 |
| 209_T | 330_I | 1.063 | 0.20 |
| 183_F | 206_F | 1.062 | 0.20 |
| 267_S | 282_E | 1.059 | 0.20 |
| 160_F | 164_F | 1.059 | 0.20 |
| 15_S | 20_E | 1.059 | 0.20 |
| 171_V | 218_T | 1.059 | 0.20 |
| 394_I | 475_I | 1.057 | 0.20 |
| 243_A | 248_L | 1.057 | 0.20 |
| 190_T | 340_N | 1.055 | 0.20 |
| 135_S | 306_I | 1.055 | 0.20 |
| 330_I | 480_D | 1.055 | 0.20 |
| 163_W | 355_V | 1.053 | 0.20 |
| 214_T | 275_G | 1.053 | 0.20 |
| 127_I | 220_A | 1.053 | 0.20 |
| 352_Y | 419_D | 1.053 | 0.20 |
| 383_A | 480_D | 1.052 | 0.19 |
| 96_L | 325_V | 1.051 | 0.19 |
| 101_Q | 293_G | 1.049 | 0.19 |
| 436_S | 498_H | 1.049 | 0.19 |
| 381_F | 404_T | 1.049 | 0.19 |
| 185_I | 377_E | 1.049 | 0.19 |
| 321_D | 406_S | 1.047 | 0.19 |
| 70_S | 284_Q | 1.047 | 0.19 |
| 295_V | 298_P | 1.046 | 0.19 |
| 19_K | 361_K | 1.045 | 0.19 |
| 176_L | 305_V | 1.045 | 0.19 |
| 262_F | 406_S | 1.041 | 0.19 |
| 409_I | 513_K | 1.041 | 0.19 |
| 267_S | 447_V | 1.041 | 0.19 |
| 268_T | 289_S | 1.041 | 0.19 |
| 167_Y | 409_I | 1.040 | 0.19 |
| 157_K | 260_I | 1.038 | 0.19 |
| 471_N | 489_N | 1.038 | 0.19 |
| 219_A | 265_L | 1.037 | 0.19 |
| 262_F | 307_S | 1.036 | 0.19 |
| 346_K | 403_I | 1.034 | 0.19 |
| 50_I | 493_Q | 1.032 | 0.19 |
| 76_R | 426_Y | 1.030 | 0.19 |
| 404_T | 408_K | 1.030 | 0.19 |
| 285_G | 479_D | 1.030 | 0.19 |
| 437_E | 448_I | 1.027 | 0.18 |
| 40_I | 409_I | 1.027 | 0.18 |
| 292_H | 312_S | 1.026 | 0.18 |
| 237_L | 363_L | 1.026 | 0.18 |
| 117_G | 363_L | 1.026 | 0.18 |
| 240_S | 460_S | 1.024 | 0.18 |
| 328_I | 357_P | 1.022 | 0.18 |
| 134_K | 352_Y | 1.022 | 0.18 |
| 165_N | 219_A | 1.021 | 0.18 |
| 213_S | 325_V | 1.020 | 0.18 |
| 83_K | 279_S | 1.020 | 0.18 |
| 18_W | 58_I | 1.019 | 0.18 |
| 243_A | 247_A | 1.018 | 0.18 |
| 16_F | 29_D | 1.018 | 0.18 |
| 13_L | 20_E | 1.016 | 0.18 |
| 82_I | 288_R | 1.015 | 0.18 |
| 228_G | 242_N | 1.014 | 0.18 |
| 42_V | 79_P | 1.010 | 0.18 |
| 286_R | 458_K | 1.010 | 0.18 |
| 306_I | 402_V | 1.009 | 0.18 |
| 184_G | 208_F | 1.008 | 0.18 |
| 72_I | 224_V | 1.007 | 0.18 |
| 451_F | 472_Y | 1.007 | 0.18 |
| 206_F | 438_R | 1.006 | 0.18 |
| 248_L | 287_Q | 1.005 | 0.17 |
| 266_S | 395_R | 1.005 | 0.17 |
| 207_S | 307_S | 1.003 | 0.17 |
| 307_S | 325_V | 1.003 | 0.17 |
| 48_D | 58_I | 1.003 | 0.17 |
| 250_G | 288_R | 1.001 | 0.17 |
| 46_F | 246_N | 1.001 | 0.17 |
| 177_L | 325_V | 1.001 | 0.17 |
| 45_R | 352_Y | 1.001 | 0.17 |
| 189_V | 323_L | 1.001 | 0.17 |
| 355_V | 413_V | 1.000 | 0.17 |
| 86_Y | 155_T | 1.000 | 0.17 |
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 | |
| 1ofhA | 3 | 0.4639 | 96.9 | 0.956 | Contact Map |
| 3b9pA | 1 | 0.4202 | 96.6 | 0.958 | Contact Map |
| 3hwsA | 6 | 0.4672 | 96.5 | 0.958 | Contact Map |
| 1um8A | 1 | 0.4504 | 96 | 0.96 | Contact Map |
| 2bjvA | 1 | 0.3479 | 95.8 | 0.961 | Contact Map |
| 3n70A | 8 | 0.2303 | 95.8 | 0.961 | Contact Map |
| 3sylA | 2 | 0.4437 | 95.4 | 0.962 | Contact Map |
| 2qbyB | 1 | 0.5261 | 95.1 | 0.963 | Contact Map |
| 1l8qA | 1 | 0.4857 | 95.1 | 0.963 | Contact Map |
| 1g8pA | 1 | 0.4487 | 95 | 0.963 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)