| ORF1995 -force run |
| ID: | 1488526878 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 425 (386) | ||
| Sequences: | 59 (54) | ||
| Seq/Len: | 0.153 | ||
| Nf(neff/√len): | 2.7 |
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: 0.153).
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 |
| 95_E | 124_L | 1.806 | 0.42 |
| 122_L | 265_I | 1.768 | 0.40 |
| 163_I | 183_L | 1.674 | 0.35 |
| 18_E | 336_P | 1.667 | 0.35 |
| 116_I | 171_V | 1.657 | 0.34 |
| 18_E | 188_L | 1.652 | 0.34 |
| 132_I | 226_C | 1.634 | 0.33 |
| 349_K | 411_T | 1.560 | 0.30 |
| 212_I | 222_T | 1.560 | 0.30 |
| 113_V | 321_I | 1.550 | 0.29 |
| 145_G | 222_T | 1.545 | 0.29 |
| 186_F | 363_A | 1.533 | 0.28 |
| 171_V | 314_Y | 1.517 | 0.28 |
| 25_E | 420_D | 1.495 | 0.27 |
| 20_T | 139_M | 1.483 | 0.26 |
| 398_D | 415_L | 1.480 | 0.26 |
| 203_A | 322_A | 1.468 | 0.25 |
| 9_L | 324_I | 1.448 | 0.25 |
| 231_I | 334_T | 1.436 | 0.24 |
| 91_F | 235_S | 1.425 | 0.24 |
| 407_Y | 415_L | 1.423 | 0.24 |
| 180_F | 193_I | 1.419 | 0.23 |
| 182_Y | 323_S | 1.398 | 0.23 |
| 183_L | 262_L | 1.393 | 0.22 |
| 211_K | 328_G | 1.391 | 0.22 |
| 265_I | 324_I | 1.386 | 0.22 |
| 414_D | 424_L | 1.380 | 0.22 |
| 336_P | 341_P | 1.369 | 0.21 |
| 21_H | 232_S | 1.368 | 0.21 |
| 95_E | 155_G | 1.351 | 0.21 |
| 157_F | 262_L | 1.338 | 0.20 |
| 11_T | 160_L | 1.336 | 0.20 |
| 129_S | 150_L | 1.334 | 0.20 |
| 240_A | 267_F | 1.328 | 0.20 |
| 71_D | 97_S | 1.319 | 0.20 |
| 46_I | 340_V | 1.318 | 0.20 |
| 128_T | 364_F | 1.310 | 0.19 |
| 302_S | 416_N | 1.306 | 0.19 |
| 10_V | 405_G | 1.291 | 0.19 |
| 163_I | 177_L | 1.289 | 0.19 |
| 117_I | 153_L | 1.283 | 0.18 |
| 341_P | 404_Q | 1.273 | 0.18 |
| 91_F | 172_I | 1.272 | 0.18 |
| 146_Y | 320_A | 1.268 | 0.18 |
| 289_L | 341_P | 1.267 | 0.18 |
| 209_K | 232_S | 1.265 | 0.18 |
| 287_I | 322_A | 1.262 | 0.18 |
| 129_S | 239_D | 1.260 | 0.18 |
| 226_C | 329_L | 1.259 | 0.18 |
| 18_E | 341_P | 1.258 | 0.18 |
| 94_L | 97_S | 1.257 | 0.18 |
| 47_G | 64_S | 1.252 | 0.17 |
| 51_K | 186_F | 1.252 | 0.17 |
| 65_I | 182_Y | 1.250 | 0.17 |
| 112_F | 122_L | 1.247 | 0.17 |
| 21_H | 61_N | 1.246 | 0.17 |
| 193_I | 316_T | 1.240 | 0.17 |
| 164_I | 318_L | 1.237 | 0.17 |
| 66_P | 264_G | 1.234 | 0.17 |
| 14_K | 222_T | 1.229 | 0.17 |
| 60_N | 140_Q | 1.228 | 0.17 |
| 114_I | 122_L | 1.224 | 0.16 |
| 79_E | 111_K | 1.222 | 0.16 |
| 390_R | 396_A | 1.219 | 0.16 |
| 190_V | 314_Y | 1.216 | 0.16 |
| 148_A | 180_F | 1.208 | 0.16 |
| 66_P | 125_P | 1.208 | 0.16 |
| 159_W | 230_F | 1.207 | 0.16 |
| 42_F | 376_I | 1.203 | 0.16 |
| 185_G | 233_N | 1.203 | 0.16 |
| 131_L | 210_W | 1.201 | 0.16 |
| 111_K | 140_Q | 1.197 | 0.16 |
| 148_A | 333_I | 1.194 | 0.16 |
| 241_S | 321_I | 1.186 | 0.15 |
| 114_I | 222_T | 1.184 | 0.15 |
| 236_F | 369_P | 1.180 | 0.15 |
| 211_K | 330_D | 1.178 | 0.15 |
| 39_F | 241_S | 1.178 | 0.15 |
| 93_F | 333_I | 1.174 | 0.15 |
| 170_F | 259_G | 1.169 | 0.15 |
| 43_I | 145_G | 1.169 | 0.15 |
| 55_S | 185_G | 1.167 | 0.15 |
| 46_I | 236_F | 1.167 | 0.15 |
| 162_S | 313_L | 1.167 | 0.15 |
| 24_I | 232_S | 1.164 | 0.15 |
| 128_T | 162_S | 1.159 | 0.15 |
| 21_H | 420_D | 1.152 | 0.14 |
| 135_R | 261_Y | 1.150 | 0.14 |
| 135_R | 268_G | 1.150 | 0.14 |
| 261_Y | 268_G | 1.150 | 0.14 |
| 196_S | 420_D | 1.149 | 0.14 |
| 52_N | 420_D | 1.140 | 0.14 |
| 168_R | 398_D | 1.131 | 0.14 |
| 53_F | 368_N | 1.129 | 0.14 |
| 333_I | 340_V | 1.128 | 0.14 |
| 47_G | 97_S | 1.127 | 0.14 |
| 14_K | 181_R | 1.127 | 0.14 |
| 152_T | 237_G | 1.124 | 0.14 |
| 114_I | 314_Y | 1.124 | 0.14 |
| 72_I | 270_F | 1.124 | 0.14 |
| 195_D | 212_I | 1.123 | 0.14 |
| 147_M | 176_S | 1.123 | 0.14 |
| 231_I | 396_A | 1.123 | 0.14 |
| 9_L | 99_N | 1.122 | 0.14 |
| 164_I | 308_L | 1.118 | 0.13 |
| 125_P | 141_G | 1.118 | 0.13 |
| 167_W | 273_L | 1.116 | 0.13 |
| 94_L | 246_F | 1.115 | 0.13 |
| 43_I | 177_L | 1.114 | 0.13 |
| 188_L | 237_G | 1.114 | 0.13 |
| 126_T | 259_G | 1.113 | 0.13 |
| 142_L | 260_A | 1.112 | 0.13 |
| 14_K | 229_P | 1.112 | 0.13 |
| 149_G | 346_L | 1.112 | 0.13 |
| 194_W | 230_F | 1.110 | 0.13 |
| 124_L | 272_L | 1.109 | 0.13 |
| 17_V | 319_C | 1.108 | 0.13 |
| 145_G | 149_G | 1.108 | 0.13 |
| 9_L | 275_F | 1.108 | 0.13 |
| 83_L | 342_Q | 1.106 | 0.13 |
| 9_L | 326_Y | 1.105 | 0.13 |
| 164_I | 263_L | 1.103 | 0.13 |
| 81_S | 139_M | 1.103 | 0.13 |
| 168_R | 244_E | 1.102 | 0.13 |
| 120_L | 420_D | 1.101 | 0.13 |
| 12_S | 250_N | 1.100 | 0.13 |
| 153_L | 160_L | 1.100 | 0.13 |
| 302_S | 309_N | 1.097 | 0.13 |
| 39_F | 117_I | 1.097 | 0.13 |
| 237_G | 340_V | 1.097 | 0.13 |
| 14_K | 262_L | 1.096 | 0.13 |
| 231_I | 329_L | 1.095 | 0.13 |
| 184_L | 333_I | 1.094 | 0.13 |
| 23_L | 74_S | 1.092 | 0.13 |
| 136_R | 309_N | 1.092 | 0.13 |
| 15_D | 173_P | 1.091 | 0.13 |
| 149_G | 287_I | 1.088 | 0.13 |
| 300_S | 324_I | 1.086 | 0.13 |
| 19_I | 291_I | 1.086 | 0.13 |
| 224_Q | 264_G | 1.085 | 0.13 |
| 153_L | 165_L | 1.085 | 0.13 |
| 24_I | 364_F | 1.083 | 0.13 |
| 66_P | 217_F | 1.083 | 0.13 |
| 112_F | 184_L | 1.082 | 0.13 |
| 8_S | 309_N | 1.080 | 0.12 |
| 398_D | 416_N | 1.078 | 0.12 |
| 10_V | 244_E | 1.076 | 0.12 |
| 225_S | 315_A | 1.075 | 0.12 |
| 242_I | 265_I | 1.071 | 0.12 |
| 216_N | 333_I | 1.070 | 0.12 |
| 183_L | 319_C | 1.067 | 0.12 |
| 178_D | 185_G | 1.065 | 0.12 |
| 390_R | 397_F | 1.064 | 0.12 |
| 212_I | 304_Y | 1.064 | 0.12 |
| 241_S | 244_E | 1.064 | 0.12 |
| 97_S | 258_H | 1.062 | 0.12 |
| 138_V | 266_L | 1.062 | 0.12 |
| 216_N | 316_T | 1.062 | 0.12 |
| 156_N | 277_C | 1.062 | 0.12 |
| 301_T | 316_T | 1.059 | 0.12 |
| 216_N | 310_F | 1.056 | 0.12 |
| 13_V | 411_T | 1.053 | 0.12 |
| 69_I | 257_I | 1.052 | 0.12 |
| 20_T | 402_Y | 1.050 | 0.12 |
| 39_F | 346_L | 1.050 | 0.12 |
| 407_Y | 417_Y | 1.050 | 0.12 |
| 275_F | 307_I | 1.050 | 0.12 |
| 309_N | 416_N | 1.046 | 0.12 |
| 77_I | 198_K | 1.044 | 0.12 |
| 113_V | 175_L | 1.044 | 0.12 |
| 211_K | 215_L | 1.042 | 0.12 |
| 199_E | 241_S | 1.041 | 0.12 |
| 52_N | 412_I | 1.037 | 0.11 |
| 148_A | 335_N | 1.036 | 0.11 |
| 94_L | 319_C | 1.033 | 0.11 |
| 123_I | 237_G | 1.033 | 0.11 |
| 168_R | 416_N | 1.032 | 0.11 |
| 46_I | 238_P | 1.032 | 0.11 |
| 286_S | 364_F | 1.032 | 0.11 |
| 170_F | 308_L | 1.031 | 0.11 |
| 246_F | 270_F | 1.031 | 0.11 |
| 15_D | 118_N | 1.031 | 0.11 |
| 398_D | 417_Y | 1.028 | 0.11 |
| 120_L | 332_T | 1.027 | 0.11 |
| 84_D | 258_H | 1.027 | 0.11 |
| 159_W | 327_Y | 1.026 | 0.11 |
| 17_V | 189_L | 1.025 | 0.11 |
| 146_Y | 158_L | 1.024 | 0.11 |
| 226_C | 320_A | 1.024 | 0.11 |
| 49_F | 128_T | 1.023 | 0.11 |
| 125_P | 264_G | 1.021 | 0.11 |
| 53_F | 67_I | 1.020 | 0.11 |
| 128_T | 229_P | 1.019 | 0.11 |
| 142_L | 270_F | 1.017 | 0.11 |
| 132_I | 329_L | 1.016 | 0.11 |
| 276_T | 304_Y | 1.016 | 0.11 |
| 148_A | 369_P | 1.016 | 0.11 |
| 62_I | 92_T | 1.015 | 0.11 |
| 66_P | 135_R | 1.014 | 0.11 |
| 66_P | 261_Y | 1.014 | 0.11 |
| 66_P | 268_G | 1.014 | 0.11 |
| 398_D | 407_Y | 1.014 | 0.11 |
| 9_L | 232_S | 1.013 | 0.11 |
| 287_I | 308_L | 1.013 | 0.11 |
| 91_F | 180_F | 1.010 | 0.11 |
| 140_Q | 241_S | 1.010 | 0.11 |
| 113_V | 116_I | 1.009 | 0.11 |
| 276_T | 313_L | 1.009 | 0.11 |
| 140_Q | 199_E | 1.008 | 0.11 |
| 240_A | 422_F | 1.007 | 0.11 |
| 206_D | 399_A | 1.007 | 0.11 |
| 167_W | 321_I | 1.006 | 0.11 |
| 205_E | 253_Q | 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 | |
| 4d3tA | 1 | 0.1435 | 29.1 | 0.981 | Contact Map |
| 2ortA | 1 | 0.1718 | 29 | 0.981 | Contact Map |
| 4fvyA | 2 | 0.24 | 26.5 | 0.981 | Contact Map |
| 2flqA | 2 | 0.1459 | 25.9 | 0.981 | Contact Map |
| 1ifpA | 1 | 0.1035 | 8.9 | 0.985 | Contact Map |
| 2c7hA | 1 | 0.1694 | 5.9 | 0.986 | Contact Map |
| 1qfqB | 1 | 0.0824 | 4.5 | 0.987 | Contact Map |
| 3v6zE | 2 | 0.1718 | 3.5 | 0.987 | Contact Map |
| 4c8hA | 3 | 0.1412 | 2.9 | 0.988 | Contact Map |
| 3fajA | 1 | 0.0894 | 2.7 | 0.988 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)