| prlr -force run |
| ID: | 1480502399 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 363 (363) | ||
| Sequences: | 88 (56.5) | ||
| Seq/Len: | 0.242 | ||
| Nf(neff/√len): | 3.0 |
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: 0.242).
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 |
| 17_I | 21_D | 1.825 | 0.57 |
| 107_E | 153_K | 1.746 | 0.52 |
| 17_I | 24_L | 1.745 | 0.52 |
| 19_G | 24_L | 1.745 | 0.52 |
| 21_D | 24_L | 1.745 | 0.52 |
| 10_P | 17_I | 1.706 | 0.49 |
| 10_P | 19_G | 1.706 | 0.49 |
| 10_P | 21_D | 1.706 | 0.49 |
| 12_V | 17_I | 1.677 | 0.47 |
| 12_V | 19_G | 1.677 | 0.47 |
| 12_V | 21_D | 1.677 | 0.47 |
| 17_I | 25_L | 1.672 | 0.47 |
| 19_G | 25_L | 1.672 | 0.47 |
| 21_D | 25_L | 1.672 | 0.47 |
| 11_P | 17_I | 1.635 | 0.45 |
| 11_P | 19_G | 1.635 | 0.45 |
| 11_P | 21_D | 1.635 | 0.45 |
| 10_P | 24_L | 1.626 | 0.44 |
| 41_D | 334_A | 1.612 | 0.43 |
| 12_V | 24_L | 1.594 | 0.42 |
| 16_K | 19_G | 1.563 | 0.40 |
| 16_K | 21_D | 1.563 | 0.40 |
| 14_G | 17_I | 1.554 | 0.40 |
| 14_G | 19_G | 1.554 | 0.40 |
| 14_G | 21_D | 1.554 | 0.40 |
| 10_P | 25_L | 1.552 | 0.39 |
| 11_P | 24_L | 1.552 | 0.39 |
| 76_S | 274_K | 1.534 | 0.38 |
| 12_V | 25_L | 1.516 | 0.37 |
| 170_S | 173_N | 1.506 | 0.37 |
| 16_K | 24_L | 1.477 | 0.35 |
| 88_T | 198_D | 1.474 | 0.35 |
| 11_P | 25_L | 1.472 | 0.35 |
| 14_G | 24_L | 1.470 | 0.35 |
| 37_L | 150_G | 1.467 | 0.34 |
| 274_K | 303_P | 1.457 | 0.34 |
| 10_P | 16_K | 1.440 | 0.33 |
| 10_P | 14_G | 1.427 | 0.32 |
| 32_E | 289_K | 1.422 | 0.32 |
| 53_V | 257_N | 1.415 | 0.31 |
| 224_H | 294_M | 1.405 | 0.31 |
| 12_V | 16_K | 1.403 | 0.31 |
| 16_K | 25_L | 1.402 | 0.31 |
| 14_G | 25_L | 1.394 | 0.30 |
| 40_Q | 50_D | 1.389 | 0.30 |
| 81_P | 153_K | 1.375 | 0.29 |
| 11_P | 16_K | 1.365 | 0.29 |
| 11_P | 14_G | 1.353 | 0.28 |
| 186_G | 196_G | 1.351 | 0.28 |
| 105_C | 297_N | 1.349 | 0.28 |
| 174_I | 181_A | 1.340 | 0.28 |
| 274_K | 332_A | 1.338 | 0.27 |
| 1_G | 48_Y | 1.331 | 0.27 |
| 4_M | 8_I | 1.323 | 0.27 |
| 102_S | 286_E | 1.322 | 0.27 |
| 18_K | 26_E | 1.319 | 0.26 |
| 1_G | 4_M | 1.317 | 0.26 |
| 54_E | 64_Q | 1.310 | 0.26 |
| 137_C | 185_A | 1.305 | 0.26 |
| 93_G | 97_S | 1.300 | 0.26 |
| 183_G | 240_T | 1.299 | 0.25 |
| 168_R | 345_L | 1.282 | 0.25 |
| 25_L | 256_V | 1.271 | 0.24 |
| 136_Q | 217_Q | 1.254 | 0.23 |
| 62_E | 100_L | 1.254 | 0.23 |
| 43_P | 293_V | 1.253 | 0.23 |
| 176_D | 271_N | 1.247 | 0.23 |
| 89_D | 97_S | 1.242 | 0.23 |
| 89_D | 93_G | 1.239 | 0.23 |
| 170_S | 183_G | 1.229 | 0.22 |
| 34_L | 192_L | 1.222 | 0.22 |
| 76_S | 332_A | 1.215 | 0.22 |
| 120_V | 363_H | 1.215 | 0.22 |
| 106_E | 249_D | 1.211 | 0.21 |
| 88_T | 228_D | 1.209 | 0.21 |
| 119_E | 123_K | 1.207 | 0.21 |
| 35_S | 56_L | 1.207 | 0.21 |
| 46_S | 266_P | 1.202 | 0.21 |
| 255_K | 286_E | 1.201 | 0.21 |
| 93_G | 157_W | 1.198 | 0.21 |
| 97_S | 157_W | 1.197 | 0.21 |
| 217_Q | 224_H | 1.182 | 0.20 |
| 80_K | 354_D | 1.173 | 0.20 |
| 55_Y | 59_D | 1.171 | 0.20 |
| 87_D | 97_S | 1.164 | 0.20 |
| 133_W | 218_R | 1.163 | 0.19 |
| 87_D | 93_G | 1.163 | 0.19 |
| 9_F | 316_S | 1.161 | 0.19 |
| 87_D | 92_R | 1.160 | 0.19 |
| 23_H | 26_E | 1.157 | 0.19 |
| 20_F | 24_L | 1.157 | 0.19 |
| 70_H | 153_K | 1.156 | 0.19 |
| 8_I | 71_S | 1.154 | 0.19 |
| 86_P | 322_P | 1.153 | 0.19 |
| 133_W | 230_D | 1.147 | 0.19 |
| 55_Y | 137_C | 1.146 | 0.19 |
| 95_C | 329_A | 1.145 | 0.19 |
| 89_D | 157_W | 1.136 | 0.18 |
| 169_S | 264_L | 1.129 | 0.18 |
| 52_L | 91_G | 1.128 | 0.18 |
| 28_G | 43_P | 1.123 | 0.18 |
| 319_E | 329_A | 1.123 | 0.18 |
| 284_N | 295_D | 1.123 | 0.18 |
| 243_G | 341_S | 1.122 | 0.18 |
| 7_C | 20_F | 1.119 | 0.18 |
| 93_G | 354_D | 1.119 | 0.18 |
| 8_I | 331_K | 1.113 | 0.18 |
| 94_S | 97_S | 1.113 | 0.18 |
| 170_S | 363_H | 1.113 | 0.18 |
| 4_M | 99_S | 1.113 | 0.18 |
| 40_Q | 262_L | 1.104 | 0.17 |
| 9_F | 41_D | 1.101 | 0.17 |
| 143_K | 219_E | 1.098 | 0.17 |
| 156_T | 259_D | 1.096 | 0.17 |
| 41_D | 49_E | 1.094 | 0.17 |
| 29_K | 157_W | 1.093 | 0.17 |
| 66_L | 172_H | 1.091 | 0.17 |
| 164_Q | 202_S | 1.090 | 0.17 |
| 216_Q | 334_A | 1.087 | 0.17 |
| 45_T | 153_K | 1.084 | 0.17 |
| 7_C | 10_P | 1.082 | 0.16 |
| 253_I | 353_L | 1.081 | 0.16 |
| 8_I | 16_K | 1.078 | 0.16 |
| 29_K | 57_E | 1.076 | 0.16 |
| 36_A | 289_K | 1.073 | 0.16 |
| 274_K | 336_F | 1.067 | 0.16 |
| 311_A | 336_F | 1.067 | 0.16 |
| 58_V | 295_D | 1.066 | 0.16 |
| 150_G | 215_T | 1.062 | 0.16 |
| 79_M | 188_P | 1.062 | 0.16 |
| 200_L | 363_H | 1.058 | 0.16 |
| 35_S | 100_L | 1.058 | 0.16 |
| 249_D | 269_R | 1.056 | 0.16 |
| 265_L | 291_S | 1.055 | 0.16 |
| 66_L | 252_E | 1.055 | 0.16 |
| 184_P | 331_K | 1.054 | 0.15 |
| 200_L | 274_K | 1.053 | 0.15 |
| 89_D | 94_S | 1.053 | 0.15 |
| 54_E | 94_S | 1.052 | 0.15 |
| 59_D | 92_R | 1.045 | 0.15 |
| 253_I | 260_G | 1.045 | 0.15 |
| 128_E | 209_R | 1.045 | 0.15 |
| 3_S | 7_C | 1.039 | 0.15 |
| 167_P | 263_S | 1.038 | 0.15 |
| 120_V | 138_I | 1.038 | 0.15 |
| 9_F | 288_A | 1.036 | 0.15 |
| 8_I | 11_P | 1.036 | 0.15 |
| 173_N | 220_V | 1.034 | 0.15 |
| 9_F | 17_I | 1.034 | 0.15 |
| 9_F | 19_G | 1.034 | 0.15 |
| 9_F | 21_D | 1.034 | 0.15 |
| 242_F | 265_L | 1.032 | 0.15 |
| 274_K | 363_H | 1.030 | 0.15 |
| 41_D | 288_A | 1.029 | 0.15 |
| 138_I | 363_H | 1.029 | 0.15 |
| 18_K | 256_V | 1.028 | 0.15 |
| 208_S | 276_K | 1.026 | 0.15 |
| 9_F | 198_D | 1.024 | 0.15 |
| 50_D | 122_E | 1.024 | 0.15 |
| 244_S | 288_A | 1.023 | 0.14 |
| 257_N | 328_Q | 1.022 | 0.14 |
| 87_D | 157_W | 1.018 | 0.14 |
| 56_L | 303_P | 1.017 | 0.14 |
| 143_K | 221_E | 1.016 | 0.14 |
| 17_I | 20_F | 1.016 | 0.14 |
| 37_L | 137_C | 1.016 | 0.14 |
| 133_W | 289_K | 1.013 | 0.14 |
| 301_L | 304_D | 1.012 | 0.14 |
| 28_G | 97_S | 1.010 | 0.14 |
| 50_D | 181_A | 1.008 | 0.14 |
| 180_L | 264_L | 1.007 | 0.14 |
| 51_L | 252_E | 1.006 | 0.14 |
| 101_L | 340_S | 1.006 | 0.14 |
| 68_S | 259_D | 1.005 | 0.14 |
| 97_S | 354_D | 1.005 | 0.14 |
| 57_E | 96_D | 1.003 | 0.14 |
| 51_L | 57_E | 1.001 | 0.14 |
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 | |
| 3luiA | 3 | 0.1708 | 75.7 | 0.973 | Contact Map |
| 2i4kA | 1 | 0.157 | 64 | 0.975 | Contact Map |
| 2l73A | 1 | 0.1928 | 59.1 | 0.976 | Contact Map |
| 1h6hA | 1 | 0.1763 | 50.7 | 0.977 | Contact Map |
| 4az9A | 2 | 0.157 | 50.5 | 0.977 | Contact Map |
| 1kmdA | 1 | 0.1708 | 48.8 | 0.977 | Contact Map |
| 1ocsA | 1 | 0.1653 | 43.9 | 0.978 | Contact Map |
| 4p2iA | 2 | 0.1212 | 39 | 0.978 | Contact Map |
| 4oxwA | 1 | 0.1515 | 36.5 | 0.979 | Contact Map |
| 4bgjA | 1 | 0.1625 | 36.2 | 0.979 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)