| T0808 19-418 -force run |
| ID: | 1406008802 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 400 (395) | ||
| Sequences: | 82 (71.7) | ||
| Seq/Len: | 0.208 | ||
| Nf(neff/√len): | 3.6 |
Jackhmmer Results: (2014_04_16)
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: 0.208).
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 |
| 43_F | 99_I | 2.302 | 0.78 |
| 156_W | 272_Y | 2.080 | 0.67 |
| 197_L | 240_Q | 1.987 | 0.62 |
| 333_R | 383_C | 1.970 | 0.61 |
| 335_T | 383_C | 1.929 | 0.58 |
| 172_S | 227_V | 1.925 | 0.58 |
| 202_S | 237_S | 1.823 | 0.52 |
| 208_N | 211_E | 1.789 | 0.50 |
| 156_W | 298_R | 1.789 | 0.50 |
| 345_A | 353_Y | 1.759 | 0.48 |
| 259_I | 296_Y | 1.753 | 0.47 |
| 221_L | 287_F | 1.683 | 0.43 |
| 145_L | 317_V | 1.678 | 0.43 |
| 257_M | 271_A | 1.666 | 0.42 |
| 155_E | 258_Q | 1.661 | 0.42 |
| 157_F | 299_P | 1.601 | 0.38 |
| 234_N | 283_L | 1.587 | 0.38 |
| 243_L | 284_I | 1.579 | 0.37 |
| 230_G | 234_N | 1.546 | 0.35 |
| 202_S | 209_P | 1.542 | 0.35 |
| 287_F | 349_V | 1.517 | 0.34 |
| 16_T | 265_G | 1.515 | 0.34 |
| 251_N | 275_A | 1.494 | 0.32 |
| 76_L | 364_Y | 1.462 | 0.31 |
| 156_W | 334_L | 1.440 | 0.30 |
| 202_S | 212_I | 1.439 | 0.30 |
| 101_L | 282_K | 1.435 | 0.29 |
| 265_G | 365_L | 1.434 | 0.29 |
| 344_T | 381_F | 1.416 | 0.28 |
| 310_Q | 368_G | 1.399 | 0.28 |
| 171_H | 367_M | 1.397 | 0.28 |
| 272_Y | 334_L | 1.392 | 0.27 |
| 168_E | 367_M | 1.391 | 0.27 |
| 16_T | 40_S | 1.387 | 0.27 |
| 49_T | 121_N | 1.383 | 0.27 |
| 341_H | 377_M | 1.376 | 0.27 |
| 136_W | 218_I | 1.365 | 0.26 |
| 291_K | 368_G | 1.333 | 0.25 |
| 272_Y | 299_P | 1.331 | 0.24 |
| 147_Y | 159_N | 1.318 | 0.24 |
| 202_S | 206_T | 1.318 | 0.24 |
| 209_P | 237_S | 1.302 | 0.23 |
| 44_Y | 114_I | 1.285 | 0.22 |
| 140_G | 289_R | 1.281 | 0.22 |
| 220_L | 276_T | 1.274 | 0.22 |
| 335_T | 387_G | 1.263 | 0.21 |
| 131_D | 375_V | 1.262 | 0.21 |
| 136_W | 354_Q | 1.260 | 0.21 |
| 181_E | 294_T | 1.256 | 0.21 |
| 139_R | 289_R | 1.250 | 0.21 |
| 186_M | 319_F | 1.246 | 0.21 |
| 212_I | 237_S | 1.242 | 0.21 |
| 25_T | 63_I | 1.237 | 0.20 |
| 169_T | 368_G | 1.237 | 0.20 |
| 128_Y | 300_H | 1.232 | 0.20 |
| 140_G | 355_G | 1.232 | 0.20 |
| 40_S | 100_D | 1.232 | 0.20 |
| 186_M | 196_I | 1.230 | 0.20 |
| 188_Y | 296_Y | 1.224 | 0.20 |
| 7_V | 155_E | 1.220 | 0.20 |
| 29_V | 300_H | 1.219 | 0.20 |
| 296_Y | 299_P | 1.212 | 0.19 |
| 59_G | 379_T | 1.210 | 0.19 |
| 7_V | 39_V | 1.207 | 0.19 |
| 324_A | 388_K | 1.205 | 0.19 |
| 168_E | 188_Y | 1.199 | 0.19 |
| 103_G | 111_F | 1.199 | 0.19 |
| 259_I | 266_N | 1.199 | 0.19 |
| 270_T | 287_F | 1.196 | 0.19 |
| 29_V | 375_V | 1.195 | 0.19 |
| 168_E | 171_H | 1.195 | 0.19 |
| 171_H | 207_Q | 1.194 | 0.19 |
| 206_T | 237_S | 1.184 | 0.18 |
| 231_E | 269_Y | 1.181 | 0.18 |
| 139_R | 371_F | 1.178 | 0.18 |
| 15_V | 196_I | 1.177 | 0.18 |
| 91_I | 186_M | 1.177 | 0.18 |
| 140_G | 203_P | 1.175 | 0.18 |
| 7_V | 29_V | 1.170 | 0.18 |
| 129_V | 137_G | 1.170 | 0.18 |
| 137_G | 287_F | 1.167 | 0.18 |
| 221_L | 270_T | 1.167 | 0.18 |
| 48_P | 319_F | 1.167 | 0.18 |
| 157_F | 272_Y | 1.164 | 0.18 |
| 76_L | 167_G | 1.164 | 0.18 |
| 140_G | 371_F | 1.161 | 0.18 |
| 257_M | 296_Y | 1.159 | 0.18 |
| 137_G | 202_S | 1.156 | 0.17 |
| 190_S | 370_F | 1.154 | 0.17 |
| 14_Y | 257_M | 1.154 | 0.17 |
| 319_F | 365_L | 1.147 | 0.17 |
| 162_T | 252_T | 1.146 | 0.17 |
| 139_R | 355_G | 1.141 | 0.17 |
| 34_N | 42_Y | 1.140 | 0.17 |
| 229_I | 297_K | 1.139 | 0.17 |
| 176_A | 255_F | 1.139 | 0.17 |
| 24_I | 103_G | 1.139 | 0.17 |
| 131_D | 134_D | 1.137 | 0.17 |
| 26_Q | 274_Y | 1.136 | 0.17 |
| 195_R | 286_S | 1.135 | 0.17 |
| 91_I | 326_S | 1.134 | 0.17 |
| 221_L | 298_R | 1.127 | 0.16 |
| 272_Y | 298_R | 1.125 | 0.16 |
| 240_Q | 397_L | 1.125 | 0.16 |
| 237_S | 283_L | 1.123 | 0.16 |
| 45_L | 99_I | 1.122 | 0.16 |
| 213_P | 234_N | 1.120 | 0.16 |
| 289_R | 355_G | 1.119 | 0.16 |
| 48_P | 128_Y | 1.116 | 0.16 |
| 101_L | 204_F | 1.116 | 0.16 |
| 385_P | 388_K | 1.115 | 0.16 |
| 186_M | 214_D | 1.109 | 0.16 |
| 141_P | 240_Q | 1.107 | 0.16 |
| 209_P | 234_N | 1.106 | 0.16 |
| 341_H | 354_Q | 1.103 | 0.16 |
| 14_Y | 263_G | 1.103 | 0.16 |
| 87_G | 285_A | 1.103 | 0.16 |
| 197_L | 397_L | 1.102 | 0.16 |
| 51_A | 128_Y | 1.102 | 0.16 |
| 265_G | 394_W | 1.102 | 0.16 |
| 295_W | 344_T | 1.098 | 0.15 |
| 135_Y | 292_T | 1.097 | 0.15 |
| 156_W | 299_P | 1.096 | 0.15 |
| 149_L | 365_L | 1.095 | 0.15 |
| 193_E | 290_P | 1.094 | 0.15 |
| 253_Y | 292_T | 1.086 | 0.15 |
| 202_S | 283_L | 1.083 | 0.15 |
| 12_N | 371_F | 1.082 | 0.15 |
| 197_L | 242_Y | 1.082 | 0.15 |
| 300_H | 394_W | 1.081 | 0.15 |
| 136_W | 150_P | 1.080 | 0.15 |
| 243_L | 308_P | 1.079 | 0.15 |
| 158_Y | 254_K | 1.079 | 0.15 |
| 308_P | 365_L | 1.078 | 0.15 |
| 231_E | 234_N | 1.075 | 0.15 |
| 43_F | 119_A | 1.075 | 0.15 |
| 61_S | 103_G | 1.074 | 0.15 |
| 253_Y | 355_G | 1.073 | 0.15 |
| 40_S | 98_R | 1.073 | 0.15 |
| 141_P | 164_P | 1.073 | 0.15 |
| 30_T | 76_L | 1.072 | 0.15 |
| 323_W | 390_P | 1.072 | 0.15 |
| 114_I | 217_K | 1.071 | 0.15 |
| 319_F | 326_S | 1.069 | 0.15 |
| 7_V | 84_V | 1.068 | 0.15 |
| 203_P | 289_R | 1.068 | 0.15 |
| 66_S | 125_K | 1.067 | 0.15 |
| 171_H | 174_Y | 1.067 | 0.15 |
| 289_R | 371_F | 1.066 | 0.14 |
| 234_N | 237_S | 1.064 | 0.14 |
| 213_P | 237_S | 1.063 | 0.14 |
| 64_K | 71_G | 1.063 | 0.14 |
| 10_S | 272_Y | 1.063 | 0.14 |
| 274_Y | 348_Q | 1.061 | 0.14 |
| 200_V | 284_I | 1.061 | 0.14 |
| 365_L | 381_F | 1.058 | 0.14 |
| 49_T | 220_L | 1.055 | 0.14 |
| 108_G | 113_E | 1.055 | 0.14 |
| 16_T | 266_N | 1.054 | 0.14 |
| 34_N | 364_Y | 1.050 | 0.14 |
| 172_S | 390_P | 1.050 | 0.14 |
| 218_I | 230_G | 1.048 | 0.14 |
| 139_R | 203_P | 1.046 | 0.14 |
| 155_E | 260_R | 1.045 | 0.14 |
| 94_A | 312_Y | 1.042 | 0.14 |
| 145_L | 184_F | 1.042 | 0.14 |
| 190_S | 194_R | 1.042 | 0.14 |
| 172_S | 218_I | 1.041 | 0.14 |
| 145_L | 176_A | 1.040 | 0.14 |
| 49_T | 192_T | 1.038 | 0.14 |
| 280_E | 295_W | 1.038 | 0.14 |
| 145_L | 234_N | 1.038 | 0.14 |
| 57_A | 76_L | 1.037 | 0.14 |
| 12_N | 202_S | 1.037 | 0.14 |
| 243_L | 360_D | 1.037 | 0.14 |
| 319_F | 374_S | 1.036 | 0.14 |
| 91_I | 389_E | 1.035 | 0.14 |
| 192_T | 248_K | 1.035 | 0.14 |
| 259_I | 295_W | 1.034 | 0.14 |
| 188_Y | 367_M | 1.033 | 0.14 |
| 14_Y | 310_Q | 1.032 | 0.13 |
| 206_T | 213_P | 1.031 | 0.13 |
| 99_I | 134_D | 1.028 | 0.13 |
| 181_E | 204_F | 1.028 | 0.13 |
| 175_M | 290_P | 1.028 | 0.13 |
| 344_T | 370_F | 1.028 | 0.13 |
| 218_I | 234_N | 1.027 | 0.13 |
| 45_L | 196_I | 1.026 | 0.13 |
| 44_Y | 374_S | 1.025 | 0.13 |
| 190_S | 322_Q | 1.024 | 0.13 |
| 213_P | 397_L | 1.023 | 0.13 |
| 13_G | 41_I | 1.023 | 0.13 |
| 89_I | 134_D | 1.022 | 0.13 |
| 29_V | 357_N | 1.021 | 0.13 |
| 35_P | 191_P | 1.021 | 0.13 |
| 203_P | 239_G | 1.020 | 0.13 |
| 241_S | 337_A | 1.020 | 0.13 |
| 14_Y | 368_G | 1.018 | 0.13 |
| 175_M | 240_Q | 1.018 | 0.13 |
| 132_F | 349_V | 1.015 | 0.13 |
| 60_H | 161_I | 1.015 | 0.13 |
| 319_F | 338_T | 1.014 | 0.13 |
| 177_A | 397_L | 1.014 | 0.13 |
| 188_Y | 223_Q | 1.014 | 0.13 |
| 104_V | 170_M | 1.013 | 0.13 |
| 40_S | 43_F | 1.013 | 0.13 |
| 193_E | 305_N | 1.013 | 0.13 |
| 355_G | 371_F | 1.012 | 0.13 |
| 14_Y | 121_N | 1.010 | 0.13 |
| 367_M | 371_F | 1.010 | 0.13 |
| 137_G | 212_I | 1.009 | 0.13 |
| 218_I | 231_E | 1.008 | 0.13 |
| 209_P | 212_I | 1.008 | 0.13 |
| 137_G | 345_A | 1.007 | 0.13 |
| 76_L | 191_P | 1.005 | 0.13 |
| 164_P | 261_P | 1.005 | 0.13 |
| 13_G | 268_T | 1.004 | 0.13 |
| 205_D | 361_N | 1.004 | 0.13 |
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 | |
| 2bgoA | 1 | 0.27 | 91.3 | 0.969 | Contact Map |
| 2vzsA | 2 | 0.0225 | 87.6 | 0.971 | Contact Map |
| 4kmqA | 1 | 0.28 | 84.2 | 0.972 | Contact Map |
| 2vzpA | 2 | 0.275 | 78.7 | 0.974 | Contact Map |
| 2w87A | 2 | 0.3075 | 73.8 | 0.975 | Contact Map |
| 2y8kA | 1 | 0.29 | 65.1 | 0.976 | Contact Map |
| 2w47A | 1 | 0.295 | 56.7 | 0.978 | Contact Map |
| 2xwxA | 2 | 0.2975 | 49.6 | 0.979 | Contact Map |
| 2wz8A | 1 | 0.2875 | 46.8 | 0.979 | Contact Map |
| 2w3jA | 1 | 0.305 | 38.4 | 0.98 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)