| RNF -force run |
| ID: | 1504816623 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 442 (379) | ||
| Sequences: | 82 (49.4) | ||
| Seq/Len: | 0.216 | ||
| Nf(neff/√len): | 2.5 |
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: 0.216).
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_S | 93_T | 1.937 | 0.60 |
| 4_A | 12_L | 1.785 | 0.51 |
| 153_E | 159_E | 1.706 | 0.46 |
| 151_R | 345_Y | 1.656 | 0.43 |
| 34_Q | 52_H | 1.611 | 0.40 |
| 91_L | 108_F | 1.601 | 0.39 |
| 249_L | 254_Q | 1.577 | 0.38 |
| 289_E | 359_R | 1.536 | 0.36 |
| 124_L | 127_R | 1.523 | 0.35 |
| 88_L | 128_L | 1.522 | 0.35 |
| 318_Y | 349_I | 1.518 | 0.35 |
| 108_F | 117_F | 1.516 | 0.35 |
| 127_R | 131_I | 1.488 | 0.33 |
| 337_T | 349_I | 1.487 | 0.33 |
| 8_G | 19_V | 1.485 | 0.33 |
| 114_K | 344_P | 1.462 | 0.32 |
| 249_L | 260_L | 1.460 | 0.32 |
| 371_L | 376_D | 1.454 | 0.31 |
| 127_R | 140_P | 1.451 | 0.31 |
| 62_L | 240_R | 1.449 | 0.31 |
| 321_Q | 324_D | 1.449 | 0.31 |
| 12_L | 51_I | 1.442 | 0.31 |
| 156_R | 162_L | 1.437 | 0.30 |
| 240_R | 270_E | 1.423 | 0.30 |
| 305_E | 324_D | 1.422 | 0.30 |
| 152_A | 193_C | 1.419 | 0.29 |
| 22_L | 30_I | 1.418 | 0.29 |
| 368_S | 372_Q | 1.414 | 0.29 |
| 104_I | 107_S | 1.413 | 0.29 |
| 110_S | 118_L | 1.412 | 0.29 |
| 91_L | 94_L | 1.412 | 0.29 |
| 13_E | 120_L | 1.397 | 0.28 |
| 286_I | 342_I | 1.397 | 0.28 |
| 19_V | 22_L | 1.382 | 0.28 |
| 91_L | 117_F | 1.375 | 0.27 |
| 123_E | 133_T | 1.366 | 0.27 |
| 371_L | 374_T | 1.358 | 0.26 |
| 14_Q | 50_A | 1.356 | 0.26 |
| 126_E | 139_R | 1.350 | 0.26 |
| 1_L | 180_A | 1.347 | 0.26 |
| 96_P | 108_F | 1.343 | 0.26 |
| 99_Q | 300_F | 1.341 | 0.26 |
| 101_H | 105_C | 1.299 | 0.24 |
| 13_E | 104_I | 1.294 | 0.23 |
| 23_Q | 39_E | 1.288 | 0.23 |
| 365_D | 369_E | 1.287 | 0.23 |
| 186_K | 189_T | 1.286 | 0.23 |
| 205_V | 240_R | 1.286 | 0.23 |
| 128_L | 144_S | 1.278 | 0.23 |
| 369_E | 375_H | 1.271 | 0.22 |
| 370_S | 378_S | 1.269 | 0.22 |
| 19_V | 35_A | 1.264 | 0.22 |
| 304_W | 310_R | 1.263 | 0.22 |
| 213_S | 234_H | 1.261 | 0.22 |
| 367_Q | 371_L | 1.258 | 0.22 |
| 23_Q | 28_E | 1.257 | 0.22 |
| 3_S | 104_I | 1.254 | 0.22 |
| 127_R | 158_L | 1.250 | 0.22 |
| 373_N | 377_D | 1.244 | 0.21 |
| 146_I | 331_E | 1.243 | 0.21 |
| 367_Q | 375_H | 1.237 | 0.21 |
| 160_P | 228_F | 1.235 | 0.21 |
| 232_C | 314_E | 1.233 | 0.21 |
| 369_E | 377_D | 1.229 | 0.21 |
| 78_E | 317_I | 1.228 | 0.21 |
| 228_F | 306_E | 1.227 | 0.21 |
| 87_Q | 91_L | 1.225 | 0.21 |
| 37_V | 48_E | 1.220 | 0.20 |
| 349_I | 358_P | 1.217 | 0.20 |
| 140_P | 158_L | 1.216 | 0.20 |
| 19_V | 106_S | 1.216 | 0.20 |
| 185_P | 197_V | 1.213 | 0.20 |
| 195_S | 198_G | 1.212 | 0.20 |
| 106_S | 350_A | 1.212 | 0.20 |
| 366_E | 371_L | 1.206 | 0.20 |
| 20_K | 48_E | 1.203 | 0.20 |
| 270_E | 339_T | 1.203 | 0.20 |
| 12_L | 117_F | 1.199 | 0.19 |
| 305_E | 348_S | 1.198 | 0.19 |
| 153_E | 161_L | 1.193 | 0.19 |
| 4_A | 117_F | 1.185 | 0.19 |
| 29_A | 48_E | 1.172 | 0.18 |
| 193_C | 346_V | 1.169 | 0.18 |
| 20_K | 36_M | 1.163 | 0.18 |
| 254_Q | 261_T | 1.162 | 0.18 |
| 316_E | 348_S | 1.159 | 0.18 |
| 263_H | 272_M | 1.157 | 0.18 |
| 315_Q | 349_I | 1.157 | 0.18 |
| 125_M | 128_L | 1.154 | 0.18 |
| 366_E | 376_D | 1.152 | 0.18 |
| 194_P | 199_K | 1.150 | 0.18 |
| 309_Q | 318_Y | 1.147 | 0.18 |
| 34_Q | 166_P | 1.143 | 0.17 |
| 8_G | 350_A | 1.142 | 0.17 |
| 223_G | 263_H | 1.142 | 0.17 |
| 275_V | 335_L | 1.140 | 0.17 |
| 363_P | 373_N | 1.138 | 0.17 |
| 236_E | 311_V | 1.134 | 0.17 |
| 4_A | 8_G | 1.134 | 0.17 |
| 80_K | 128_L | 1.134 | 0.17 |
| 337_T | 358_P | 1.129 | 0.17 |
| 72_A | 293_L | 1.129 | 0.17 |
| 223_G | 265_S | 1.127 | 0.17 |
| 34_Q | 60_D | 1.127 | 0.17 |
| 125_M | 142_Q | 1.126 | 0.17 |
| 70_L | 94_L | 1.122 | 0.17 |
| 127_R | 162_L | 1.121 | 0.17 |
| 33_L | 50_A | 1.121 | 0.17 |
| 370_S | 375_H | 1.118 | 0.17 |
| 125_M | 144_S | 1.117 | 0.17 |
| 123_E | 134_R | 1.117 | 0.17 |
| 306_E | 310_R | 1.116 | 0.16 |
| 180_A | 195_S | 1.116 | 0.16 |
| 108_F | 114_K | 1.116 | 0.16 |
| 186_K | 192_H | 1.114 | 0.16 |
| 304_W | 315_Q | 1.112 | 0.16 |
| 93_T | 337_T | 1.112 | 0.16 |
| 32_L | 84_F | 1.111 | 0.16 |
| 2_E | 76_Q | 1.111 | 0.16 |
| 25_A | 113_N | 1.109 | 0.16 |
| 297_R | 357_E | 1.106 | 0.16 |
| 48_E | 55_F | 1.102 | 0.16 |
| 371_L | 378_S | 1.100 | 0.16 |
| 20_K | 55_F | 1.100 | 0.16 |
| 2_E | 302_E | 1.099 | 0.16 |
| 336_T | 342_I | 1.099 | 0.16 |
| 155_A | 158_L | 1.099 | 0.16 |
| 240_R | 252_Q | 1.098 | 0.16 |
| 70_L | 91_L | 1.097 | 0.16 |
| 253_V | 260_L | 1.097 | 0.16 |
| 265_S | 297_R | 1.091 | 0.16 |
| 131_I | 140_P | 1.089 | 0.16 |
| 14_Q | 162_L | 1.085 | 0.15 |
| 69_L | 162_L | 1.083 | 0.15 |
| 186_K | 193_C | 1.078 | 0.15 |
| 233_R | 300_F | 1.072 | 0.15 |
| 81_D | 225_N | 1.069 | 0.15 |
| 15_A | 114_K | 1.068 | 0.15 |
| 372_Q | 375_H | 1.068 | 0.15 |
| 134_R | 269_A | 1.066 | 0.15 |
| 15_A | 140_P | 1.065 | 0.15 |
| 40_V | 282_L | 1.064 | 0.15 |
| 245_E | 311_V | 1.063 | 0.15 |
| 316_E | 338_I | 1.061 | 0.15 |
| 91_L | 96_P | 1.060 | 0.15 |
| 13_E | 25_A | 1.060 | 0.15 |
| 212_R | 345_Y | 1.059 | 0.15 |
| 108_F | 118_L | 1.059 | 0.15 |
| 4_A | 96_P | 1.058 | 0.15 |
| 154_F | 256_L | 1.058 | 0.15 |
| 237_D | 244_A | 1.056 | 0.15 |
| 189_T | 192_H | 1.055 | 0.15 |
| 293_L | 307_A | 1.055 | 0.15 |
| 338_I | 358_P | 1.054 | 0.14 |
| 318_Y | 358_P | 1.053 | 0.14 |
| 367_Q | 372_Q | 1.053 | 0.14 |
| 84_F | 215_S | 1.053 | 0.14 |
| 366_E | 372_Q | 1.051 | 0.14 |
| 8_G | 106_S | 1.050 | 0.14 |
| 88_L | 91_L | 1.049 | 0.14 |
| 341_Q | 345_Y | 1.049 | 0.14 |
| 79_E | 85_K | 1.047 | 0.14 |
| 124_L | 311_V | 1.046 | 0.14 |
| 308_Y | 351_K | 1.046 | 0.14 |
| 249_L | 253_V | 1.041 | 0.14 |
| 339_T | 344_P | 1.039 | 0.14 |
| 5_Y | 12_L | 1.038 | 0.14 |
| 131_I | 138_L | 1.037 | 0.14 |
| 305_E | 312_A | 1.034 | 0.14 |
| 62_L | 72_A | 1.032 | 0.14 |
| 81_D | 291_A | 1.032 | 0.14 |
| 50_A | 69_L | 1.031 | 0.14 |
| 304_W | 311_V | 1.030 | 0.14 |
| 87_Q | 108_F | 1.027 | 0.14 |
| 101_H | 122_Y | 1.027 | 0.14 |
| 128_L | 314_E | 1.025 | 0.14 |
| 80_K | 88_L | 1.024 | 0.14 |
| 22_L | 47_E | 1.022 | 0.14 |
| 305_E | 309_Q | 1.021 | 0.13 |
| 255_E | 261_T | 1.020 | 0.13 |
| 351_K | 356_L | 1.020 | 0.13 |
| 4_A | 47_E | 1.019 | 0.13 |
| 220_L | 236_E | 1.019 | 0.13 |
| 54_L | 349_I | 1.017 | 0.13 |
| 314_E | 319_E | 1.016 | 0.13 |
| 62_L | 108_F | 1.015 | 0.13 |
| 25_A | 30_I | 1.015 | 0.13 |
| 296_M | 306_E | 1.010 | 0.13 |
| 107_S | 111_L | 1.010 | 0.13 |
| 371_L | 375_H | 1.010 | 0.13 |
| 153_E | 160_P | 1.009 | 0.13 |
| 316_E | 331_E | 1.008 | 0.13 |
| 322_L | 352_V | 1.008 | 0.13 |
| 13_E | 184_G | 1.008 | 0.13 |
| 375_H | 378_S | 1.006 | 0.13 |
| 58_M | 205_V | 1.006 | 0.13 |
| 62_L | 293_L | 1.006 | 0.13 |
| 217_K | 223_G | 1.006 | 0.13 |
| 91_L | 114_K | 1.004 | 0.13 |
| 22_L | 60_D | 1.003 | 0.13 |
| 56_G | 307_A | 1.002 | 0.13 |
| 25_A | 33_L | 1.001 | 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 | |
| 4nqjA | 3 | 0.3801 | 96.9 | 0.958 | Contact Map |
| 3okqA | 1 | 0.2805 | 96.4 | 0.961 | Contact Map |
| 4ltbA | 2 | 0.3756 | 95.9 | 0.963 | Contact Map |
| 4tn3A | 2 | 0.681 | 92.1 | 0.969 | Contact Map |
| 4kblA | 2 | 0.2896 | 73.5 | 0.975 | Contact Map |
| 4m3lA | 4 | 0.1357 | 43.6 | 0.98 | Contact Map |
| 4rsiB | 1 | 0.7172 | 43.6 | 0.98 | Contact Map |
| 1t3jA | 1 | 0.1403 | 35 | 0.981 | Contact Map |
| 2dfsA | 2 | 0.1765 | 31.7 | 0.981 | Contact Map |
| 4iffA | 4 | 0.1855 | 29.9 | 0.981 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)