| Mi -force run |
| ID: | 1488468514 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 381 (370) | ||
| Sequences: | 60 (37.2) | ||
| Seq/Len: | 0.162 | ||
| Nf(neff/√len): | 1.9 |
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: 0.162).
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 |
| 351_N | 362_V | 1.845 | 0.46 |
| 329_V | 334_F | 1.762 | 0.41 |
| 57_K | 62_Q | 1.695 | 0.38 |
| 354_Y | 360_S | 1.686 | 0.37 |
| 346_V | 352_R | 1.614 | 0.33 |
| 347_G | 352_R | 1.614 | 0.33 |
| 157_V | 171_E | 1.610 | 0.33 |
| 351_N | 354_Y | 1.604 | 0.33 |
| 138_E | 144_G | 1.598 | 0.33 |
| 351_N | 360_S | 1.560 | 0.31 |
| 352_R | 360_S | 1.542 | 0.30 |
| 23_K | 27_L | 1.526 | 0.29 |
| 23_K | 31_I | 1.526 | 0.29 |
| 27_L | 31_I | 1.526 | 0.29 |
| 327_S | 331_H | 1.507 | 0.28 |
| 327_S | 333_A | 1.472 | 0.27 |
| 327_S | 334_F | 1.471 | 0.27 |
| 110_H | 135_P | 1.442 | 0.25 |
| 339_R | 342_G | 1.435 | 0.25 |
| 346_V | 354_Y | 1.410 | 0.24 |
| 347_G | 354_Y | 1.410 | 0.24 |
| 374_P | 379_W | 1.398 | 0.23 |
| 376_F | 379_W | 1.398 | 0.23 |
| 338_K | 341_Y | 1.381 | 0.23 |
| 345_V | 357_S | 1.379 | 0.23 |
| 346_V | 360_S | 1.377 | 0.23 |
| 347_G | 360_S | 1.377 | 0.23 |
| 24_P | 27_L | 1.357 | 0.22 |
| 24_P | 31_I | 1.357 | 0.22 |
| 352_R | 362_V | 1.352 | 0.22 |
| 123_R | 249_E | 1.348 | 0.21 |
| 327_S | 332_F | 1.343 | 0.21 |
| 352_R | 365_Q | 1.340 | 0.21 |
| 359_S | 366_L | 1.338 | 0.21 |
| 52_N | 59_V | 1.337 | 0.21 |
| 354_Y | 362_V | 1.327 | 0.21 |
| 346_V | 351_N | 1.320 | 0.20 |
| 347_G | 351_N | 1.320 | 0.20 |
| 268_E | 355_R | 1.316 | 0.20 |
| 130_R | 134_L | 1.314 | 0.20 |
| 373_R | 379_W | 1.311 | 0.20 |
| 233_Q | 249_E | 1.296 | 0.20 |
| 34_P | 353_S | 1.295 | 0.19 |
| 134_L | 141_S | 1.295 | 0.19 |
| 22_R | 187_L | 1.293 | 0.19 |
| 352_R | 355_R | 1.288 | 0.19 |
| 357_S | 366_L | 1.287 | 0.19 |
| 201_H | 348_N | 1.283 | 0.19 |
| 122_G | 125_K | 1.277 | 0.19 |
| 236_R | 262_S | 1.268 | 0.19 |
| 240_R | 355_R | 1.264 | 0.18 |
| 339_R | 365_Q | 1.260 | 0.18 |
| 57_K | 60_S | 1.259 | 0.18 |
| 137_Q | 141_S | 1.259 | 0.18 |
| 345_V | 359_S | 1.255 | 0.18 |
| 134_L | 137_Q | 1.253 | 0.18 |
| 114_L | 380_L | 1.253 | 0.18 |
| 345_V | 349_W | 1.244 | 0.18 |
| 345_V | 350_L | 1.237 | 0.17 |
| 321_R | 342_G | 1.234 | 0.17 |
| 130_R | 135_P | 1.229 | 0.17 |
| 175_P | 327_S | 1.228 | 0.17 |
| 137_Q | 146_E | 1.214 | 0.17 |
| 141_S | 146_E | 1.213 | 0.17 |
| 378_Y | 381_T | 1.211 | 0.17 |
| 301_G | 307_K | 1.208 | 0.17 |
| 83_S | 88_I | 1.208 | 0.17 |
| 339_R | 344_G | 1.207 | 0.17 |
| 174_R | 327_S | 1.207 | 0.17 |
| 20_Q | 24_P | 1.197 | 0.16 |
| 373_R | 377_T | 1.189 | 0.16 |
| 99_S | 145_T | 1.188 | 0.16 |
| 188_S | 191_S | 1.186 | 0.16 |
| 141_S | 145_T | 1.183 | 0.16 |
| 156_I | 159_P | 1.180 | 0.16 |
| 163_G | 167_R | 1.173 | 0.15 |
| 18_R | 29_I | 1.170 | 0.15 |
| 351_N | 358_I | 1.168 | 0.15 |
| 14_V | 20_Q | 1.168 | 0.15 |
| 339_R | 346_V | 1.165 | 0.15 |
| 339_R | 347_G | 1.165 | 0.15 |
| 130_R | 146_E | 1.163 | 0.15 |
| 153_M | 257_D | 1.162 | 0.15 |
| 252_A | 292_H | 1.159 | 0.15 |
| 300_D | 348_N | 1.158 | 0.15 |
| 138_E | 239_K | 1.158 | 0.15 |
| 166_F | 183_T | 1.157 | 0.15 |
| 350_L | 356_R | 1.154 | 0.15 |
| 360_S | 365_Q | 1.149 | 0.15 |
| 21_S | 29_I | 1.147 | 0.15 |
| 350_L | 359_S | 1.147 | 0.15 |
| 76_P | 150_P | 1.144 | 0.15 |
| 135_P | 146_E | 1.143 | 0.15 |
| 246_S | 260_D | 1.134 | 0.14 |
| 279_S | 284_A | 1.134 | 0.14 |
| 324_R | 339_R | 1.132 | 0.14 |
| 241_S | 264_F | 1.130 | 0.14 |
| 242_F | 264_F | 1.130 | 0.14 |
| 346_V | 365_Q | 1.129 | 0.14 |
| 347_G | 365_Q | 1.129 | 0.14 |
| 130_R | 137_Q | 1.125 | 0.14 |
| 330_K | 334_F | 1.124 | 0.14 |
| 335_D | 366_L | 1.118 | 0.14 |
| 161_A | 167_R | 1.116 | 0.14 |
| 115_H | 336_R | 1.116 | 0.14 |
| 324_R | 365_Q | 1.113 | 0.14 |
| 329_V | 333_A | 1.112 | 0.14 |
| 156_I | 181_P | 1.112 | 0.14 |
| 339_R | 352_R | 1.110 | 0.14 |
| 354_Y | 365_Q | 1.109 | 0.14 |
| 167_R | 181_P | 1.107 | 0.14 |
| 266_K | 327_S | 1.107 | 0.14 |
| 362_V | 365_Q | 1.104 | 0.14 |
| 80_R | 83_S | 1.104 | 0.14 |
| 82_A | 112_R | 1.103 | 0.14 |
| 158_D | 188_S | 1.098 | 0.13 |
| 159_P | 188_S | 1.098 | 0.13 |
| 345_V | 356_R | 1.098 | 0.13 |
| 346_V | 355_R | 1.097 | 0.13 |
| 347_G | 355_R | 1.097 | 0.13 |
| 123_R | 216_Q | 1.094 | 0.13 |
| 373_R | 376_F | 1.093 | 0.13 |
| 73_E | 153_M | 1.092 | 0.13 |
| 374_P | 377_T | 1.092 | 0.13 |
| 116_H | 121_Y | 1.091 | 0.13 |
| 137_Q | 150_P | 1.085 | 0.13 |
| 156_I | 188_S | 1.085 | 0.13 |
| 112_R | 208_I | 1.085 | 0.13 |
| 85_S | 157_V | 1.079 | 0.13 |
| 184_P | 188_S | 1.077 | 0.13 |
| 250_E | 264_F | 1.075 | 0.13 |
| 113_S | 117_C | 1.074 | 0.13 |
| 164_R | 183_T | 1.072 | 0.13 |
| 331_H | 334_F | 1.071 | 0.13 |
| 99_S | 106_R | 1.071 | 0.13 |
| 115_H | 127_S | 1.070 | 0.13 |
| 349_W | 357_S | 1.070 | 0.13 |
| 175_P | 202_L | 1.068 | 0.13 |
| 299_P | 304_I | 1.068 | 0.13 |
| 22_R | 27_L | 1.064 | 0.12 |
| 22_R | 31_I | 1.064 | 0.12 |
| 121_Y | 125_K | 1.063 | 0.12 |
| 136_S | 141_S | 1.062 | 0.12 |
| 137_Q | 145_T | 1.059 | 0.12 |
| 346_V | 362_V | 1.056 | 0.12 |
| 347_G | 362_V | 1.056 | 0.12 |
| 215_F | 219_A | 1.054 | 0.12 |
| 342_G | 365_Q | 1.054 | 0.12 |
| 128_C | 154_P | 1.054 | 0.12 |
| 299_P | 307_K | 1.053 | 0.12 |
| 356_R | 363_Q | 1.052 | 0.12 |
| 350_L | 363_Q | 1.052 | 0.12 |
| 354_Y | 358_I | 1.049 | 0.12 |
| 180_P | 260_D | 1.049 | 0.12 |
| 112_R | 127_S | 1.047 | 0.12 |
| 291_P | 380_L | 1.047 | 0.12 |
| 321_R | 339_R | 1.047 | 0.12 |
| 143_Q | 147_S | 1.046 | 0.12 |
| 143_Q | 338_K | 1.046 | 0.12 |
| 185_G | 188_S | 1.042 | 0.12 |
| 182_L | 187_L | 1.041 | 0.12 |
| 208_I | 216_Q | 1.041 | 0.12 |
| 342_G | 346_V | 1.040 | 0.12 |
| 342_G | 347_G | 1.040 | 0.12 |
| 276_V | 279_S | 1.040 | 0.12 |
| 251_D | 264_F | 1.038 | 0.12 |
| 350_L | 357_S | 1.037 | 0.12 |
| 240_R | 246_S | 1.036 | 0.12 |
| 359_S | 363_Q | 1.035 | 0.12 |
| 335_D | 357_S | 1.034 | 0.12 |
| 93_A | 98_V | 1.032 | 0.12 |
| 154_P | 245_P | 1.024 | 0.12 |
| 355_R | 360_S | 1.023 | 0.12 |
| 93_A | 109_W | 1.022 | 0.11 |
| 245_P | 275_D | 1.022 | 0.11 |
| 82_A | 201_H | 1.022 | 0.11 |
| 191_S | 194_S | 1.021 | 0.11 |
| 184_P | 211_A | 1.021 | 0.11 |
| 60_S | 88_I | 1.020 | 0.11 |
| 181_P | 188_S | 1.019 | 0.11 |
| 285_S | 293_S | 1.018 | 0.11 |
| 25_P | 31_I | 1.018 | 0.11 |
| 99_S | 220_A | 1.018 | 0.11 |
| 220_A | 236_R | 1.016 | 0.11 |
| 182_L | 255_G | 1.015 | 0.11 |
| 324_R | 372_H | 1.014 | 0.11 |
| 222_L | 257_D | 1.014 | 0.11 |
| 254_D | 264_F | 1.014 | 0.11 |
| 13_S | 320_Q | 1.013 | 0.11 |
| 338_K | 342_G | 1.012 | 0.11 |
| 324_R | 346_V | 1.012 | 0.11 |
| 324_R | 347_G | 1.012 | 0.11 |
| 100_G | 180_P | 1.012 | 0.11 |
| 359_S | 371_S | 1.012 | 0.11 |
| 158_D | 181_P | 1.011 | 0.11 |
| 159_P | 181_P | 1.011 | 0.11 |
| 240_R | 268_E | 1.009 | 0.11 |
| 41_E | 46_L | 1.009 | 0.11 |
| 259_F | 353_S | 1.008 | 0.11 |
| 219_A | 236_R | 1.008 | 0.11 |
| 110_H | 130_R | 1.007 | 0.11 |
| 163_G | 181_P | 1.006 | 0.11 |
| 239_K | 252_A | 1.003 | 0.11 |
| 353_S | 370_D | 1.002 | 0.11 |
| 339_R | 360_S | 1.001 | 0.11 |
| 241_S | 250_E | 1.001 | 0.11 |
| 242_F | 250_E | 1.001 | 0.11 |
| 113_S | 116_H | 1.000 | 0.11 |
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 | |
| 3q7aB | 1 | 0.2441 | 4.6 | 0.988 | Contact Map |
| 2psbA | 1 | 0.1942 | 3.1 | 0.989 | Contact Map |
| 1oqeK | 8 | 0.0709 | 2.7 | 0.989 | Contact Map |
| 3l70I | 2 | 0.0761 | 2.6 | 0.989 | Contact Map |
| 2b9iC | 1 | 0.0367 | 2.5 | 0.989 | Contact Map |
| 3cwbI | 2 | 0.0761 | 2.4 | 0.989 | Contact Map |
| 3bbnE | 1 | 0.0709 | 2.3 | 0.989 | Contact Map |
| 1oigA | 1 | 0.063 | 2.2 | 0.989 | Contact Map |
| 4bjtA | 3 | 0.21 | 2 | 0.99 | Contact Map |
| 2h6fB | 1 | 0.2231 | 1.9 | 0.99 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)