| EccE1 -force run |
| ID: | 1409160855 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 462 (460) | ||
| Sequences: | 55 (42.9) | ||
| Seq/Len: | 0.120 | ||
| Nf(neff/√len): | 2.0 |
HHblits Results: (2013_03)
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: 0.120).
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 |
| 104_A | 216_A | 3.196 | 0.91 |
| 315_L | 319_Q | 1.854 | 0.38 |
| 150_V | 339_G | 1.846 | 0.38 |
| 172_I | 286_V | 1.721 | 0.32 |
| 142_C | 340_S | 1.710 | 0.32 |
| 150_V | 278_R | 1.683 | 0.30 |
| 376_F | 389_V | 1.656 | 0.29 |
| 172_I | 216_A | 1.631 | 0.28 |
| 216_A | 286_V | 1.615 | 0.27 |
| 160_A | 189_A | 1.596 | 0.27 |
| 368_G | 372_T | 1.575 | 0.26 |
| 239_Y | 357_P | 1.560 | 0.25 |
| 214_A | 360_D | 1.545 | 0.25 |
| 51_T | 185_I | 1.539 | 0.24 |
| 311_G | 368_G | 1.497 | 0.23 |
| 57_I | 115_P | 1.480 | 0.22 |
| 393_F | 396_F | 1.473 | 0.22 |
| 290_P | 344_L | 1.462 | 0.21 |
| 156_V | 194_T | 1.429 | 0.20 |
| 183_T | 340_S | 1.415 | 0.20 |
| 118_I | 298_V | 1.412 | 0.20 |
| 40_L | 302_T | 1.396 | 0.19 |
| 103_V | 185_I | 1.378 | 0.19 |
| 201_R | 282_T | 1.377 | 0.19 |
| 33_Y | 330_A | 1.376 | 0.19 |
| 111_R | 356_M | 1.375 | 0.19 |
| 207_G | 210_R | 1.374 | 0.18 |
| 106_I | 230_A | 1.370 | 0.18 |
| 156_V | 214_A | 1.370 | 0.18 |
| 48_A | 354_V | 1.369 | 0.18 |
| 343_V | 355_Y | 1.367 | 0.18 |
| 34_W | 380_A | 1.352 | 0.18 |
| 204_G | 344_L | 1.346 | 0.18 |
| 106_I | 367_L | 1.345 | 0.18 |
| 102_L | 270_G | 1.344 | 0.18 |
| 43_L | 80_E | 1.337 | 0.17 |
| 104_A | 286_V | 1.334 | 0.17 |
| 203_E | 340_S | 1.333 | 0.17 |
| 106_I | 123_A | 1.328 | 0.17 |
| 156_V | 187_L | 1.327 | 0.17 |
| 211_Y | 376_F | 1.319 | 0.17 |
| 207_G | 311_G | 1.300 | 0.16 |
| 47_V | 99_G | 1.297 | 0.16 |
| 198_A | 210_R | 1.294 | 0.16 |
| 167_L | 312_F | 1.290 | 0.16 |
| 74_P | 225_S | 1.285 | 0.16 |
| 96_R | 319_Q | 1.285 | 0.16 |
| 138_L | 176_P | 1.281 | 0.16 |
| 118_I | 286_V | 1.273 | 0.15 |
| 41_A | 86_T | 1.272 | 0.15 |
| 131_T | 227_G | 1.269 | 0.15 |
| 187_L | 290_P | 1.267 | 0.15 |
| 42_S | 76_D | 1.264 | 0.15 |
| 150_V | 375_Q | 1.259 | 0.15 |
| 334_C | 367_L | 1.253 | 0.15 |
| 426_D | 447_R | 1.251 | 0.15 |
| 54_G | 387_V | 1.246 | 0.15 |
| 148_D | 177_A | 1.244 | 0.15 |
| 223_L | 387_V | 1.238 | 0.15 |
| 183_T | 339_G | 1.233 | 0.14 |
| 145_L | 290_P | 1.232 | 0.14 |
| 86_T | 108_L | 1.222 | 0.14 |
| 147_A | 183_T | 1.220 | 0.14 |
| 161_A | 287_R | 1.219 | 0.14 |
| 86_T | 103_V | 1.212 | 0.14 |
| 112_P | 309_P | 1.210 | 0.14 |
| 96_R | 188_R | 1.207 | 0.14 |
| 149_I | 241_H | 1.201 | 0.14 |
| 98_Q | 288_V | 1.196 | 0.13 |
| 146_E | 157_G | 1.195 | 0.13 |
| 57_I | 295_Q | 1.195 | 0.13 |
| 179_A | 341_A | 1.192 | 0.13 |
| 177_A | 289_A | 1.191 | 0.13 |
| 42_S | 99_G | 1.188 | 0.13 |
| 61_V | 132_G | 1.175 | 0.13 |
| 168_Y | 188_R | 1.175 | 0.13 |
| 319_Q | 322_A | 1.174 | 0.13 |
| 36_A | 57_I | 1.171 | 0.13 |
| 137_L | 340_S | 1.169 | 0.13 |
| 108_L | 376_F | 1.161 | 0.13 |
| 190_D | 325_G | 1.161 | 0.13 |
| 46_I | 284_T | 1.159 | 0.13 |
| 175_D | 183_T | 1.158 | 0.13 |
| 25_I | 28_F | 1.158 | 0.13 |
| 117_V | 135_E | 1.157 | 0.13 |
| 243_T | 339_G | 1.156 | 0.13 |
| 164_V | 368_G | 1.154 | 0.12 |
| 249_R | 322_A | 1.154 | 0.12 |
| 142_C | 361_V | 1.153 | 0.12 |
| 128_M | 269_G | 1.152 | 0.12 |
| 149_I | 291_G | 1.151 | 0.12 |
| 207_G | 238_D | 1.151 | 0.12 |
| 45_V | 286_V | 1.150 | 0.12 |
| 167_L | 219_I | 1.149 | 0.12 |
| 202_D | 355_Y | 1.145 | 0.12 |
| 189_A | 210_R | 1.145 | 0.12 |
| 97_W | 396_F | 1.144 | 0.12 |
| 276_S | 389_V | 1.144 | 0.12 |
| 70_R | 138_L | 1.140 | 0.12 |
| 187_L | 287_R | 1.139 | 0.12 |
| 120_D | 339_G | 1.136 | 0.12 |
| 152_A | 156_V | 1.135 | 0.12 |
| 126_D | 290_P | 1.135 | 0.12 |
| 337_P | 382_A | 1.133 | 0.12 |
| 187_L | 302_T | 1.132 | 0.12 |
| 179_A | 207_G | 1.132 | 0.12 |
| 297_T | 319_Q | 1.130 | 0.12 |
| 106_I | 286_V | 1.130 | 0.12 |
| 282_T | 323_L | 1.130 | 0.12 |
| 90_G | 172_I | 1.129 | 0.12 |
| 52_F | 55_R | 1.125 | 0.12 |
| 108_L | 212_L | 1.124 | 0.12 |
| 150_V | 345_V | 1.124 | 0.12 |
| 250_E | 385_A | 1.123 | 0.12 |
| 48_A | 368_G | 1.120 | 0.12 |
| 110_P | 207_G | 1.120 | 0.12 |
| 174_T | 396_F | 1.119 | 0.12 |
| 185_I | 230_A | 1.119 | 0.12 |
| 311_G | 323_L | 1.117 | 0.12 |
| 143_P | 296_S | 1.117 | 0.12 |
| 60_W | 286_V | 1.117 | 0.12 |
| 51_T | 67_W | 1.116 | 0.12 |
| 104_A | 172_I | 1.114 | 0.12 |
| 42_S | 194_T | 1.112 | 0.12 |
| 143_P | 278_R | 1.109 | 0.11 |
| 280_D | 381_A | 1.108 | 0.11 |
| 90_G | 148_D | 1.106 | 0.11 |
| 134_V | 186_V | 1.104 | 0.11 |
| 327_H | 378_V | 1.104 | 0.11 |
| 238_D | 388_T | 1.102 | 0.11 |
| 129_L | 146_E | 1.100 | 0.11 |
| 47_V | 149_I | 1.098 | 0.11 |
| 54_G | 250_E | 1.098 | 0.11 |
| 392_Q | 397_A | 1.098 | 0.11 |
| 354_V | 368_G | 1.097 | 0.11 |
| 34_W | 352_C | 1.097 | 0.11 |
| 254_M | 291_G | 1.094 | 0.11 |
| 184_W | 301_T | 1.093 | 0.11 |
| 35_W | 54_G | 1.092 | 0.11 |
| 340_S | 360_D | 1.091 | 0.11 |
| 286_V | 366_N | 1.090 | 0.11 |
| 142_C | 203_E | 1.087 | 0.11 |
| 57_I | 62_A | 1.087 | 0.11 |
| 118_I | 274_W | 1.086 | 0.11 |
| 142_C | 198_A | 1.083 | 0.11 |
| 187_L | 361_V | 1.082 | 0.11 |
| 39_A | 128_M | 1.082 | 0.11 |
| 184_W | 357_P | 1.081 | 0.11 |
| 202_D | 288_V | 1.081 | 0.11 |
| 99_G | 149_I | 1.081 | 0.11 |
| 44_G | 51_T | 1.078 | 0.11 |
| 75_P | 255_I | 1.077 | 0.11 |
| 209_A | 389_V | 1.077 | 0.11 |
| 299_L | 382_A | 1.076 | 0.11 |
| 281_H | 337_P | 1.074 | 0.11 |
| 220_A | 357_P | 1.074 | 0.11 |
| 63_A | 345_V | 1.074 | 0.11 |
| 175_D | 341_A | 1.073 | 0.11 |
| 134_V | 149_I | 1.072 | 0.11 |
| 46_I | 91_D | 1.068 | 0.11 |
| 57_I | 356_M | 1.065 | 0.11 |
| 66_A | 324_Q | 1.065 | 0.11 |
| 45_V | 135_E | 1.063 | 0.11 |
| 154_Y | 227_G | 1.063 | 0.11 |
| 219_I | 385_A | 1.062 | 0.11 |
| 60_W | 107_E | 1.061 | 0.11 |
| 173_G | 235_S | 1.060 | 0.10 |
| 4_P | 15_L | 1.059 | 0.10 |
| 156_V | 339_G | 1.058 | 0.10 |
| 106_I | 191_P | 1.057 | 0.10 |
| 353_P | 389_V | 1.056 | 0.10 |
| 39_A | 70_R | 1.055 | 0.10 |
| 108_L | 356_M | 1.055 | 0.10 |
| 38_I | 256_K | 1.053 | 0.10 |
| 35_W | 48_A | 1.052 | 0.10 |
| 275_W | 357_P | 1.052 | 0.10 |
| 240_D | 265_Y | 1.052 | 0.10 |
| 102_L | 387_V | 1.051 | 0.10 |
| 185_I | 358_F | 1.050 | 0.10 |
| 186_V | 323_L | 1.050 | 0.10 |
| 407_E | 430_L | 1.049 | 0.10 |
| 225_S | 356_M | 1.049 | 0.10 |
| 246_G | 389_V | 1.049 | 0.10 |
| 86_T | 339_G | 1.048 | 0.10 |
| 40_L | 53_Y | 1.046 | 0.10 |
| 129_L | 330_A | 1.046 | 0.10 |
| 298_V | 358_F | 1.046 | 0.10 |
| 49_T | 106_I | 1.045 | 0.10 |
| 275_W | 319_Q | 1.044 | 0.10 |
| 179_A | 396_F | 1.043 | 0.10 |
| 412_W | 439_R | 1.043 | 0.10 |
| 164_V | 336_L | 1.042 | 0.10 |
| 108_L | 209_A | 1.040 | 0.10 |
| 156_V | 361_V | 1.040 | 0.10 |
| 357_P | 360_D | 1.039 | 0.10 |
| 297_T | 397_A | 1.039 | 0.10 |
| 41_A | 302_T | 1.038 | 0.10 |
| 262_T | 306_P | 1.038 | 0.10 |
| 219_I | 277_A | 1.037 | 0.10 |
| 214_A | 225_S | 1.036 | 0.10 |
| 230_A | 265_Y | 1.034 | 0.10 |
| 140_V | 215_S | 1.033 | 0.10 |
| 38_I | 46_I | 1.032 | 0.10 |
| 145_L | 153_G | 1.032 | 0.10 |
| 40_L | 138_L | 1.031 | 0.10 |
| 77_S | 115_P | 1.030 | 0.10 |
| 190_D | 323_L | 1.030 | 0.10 |
| 107_E | 231_V | 1.029 | 0.10 |
| 288_V | 327_H | 1.028 | 0.10 |
| 3_N | 26_I | 1.027 | 0.10 |
| 172_I | 209_A | 1.025 | 0.10 |
| 63_A | 133_L | 1.023 | 0.10 |
| 183_T | 360_D | 1.023 | 0.10 |
| 105_V | 375_Q | 1.021 | 0.10 |
| 143_P | 178_P | 1.021 | 0.10 |
| 409_K | 427_R | 1.020 | 0.10 |
| 183_T | 341_A | 1.020 | 0.10 |
| 238_D | 339_G | 1.019 | 0.10 |
| 288_V | 343_V | 1.018 | 0.10 |
| 129_L | 244_D | 1.018 | 0.10 |
| 149_I | 245_I | 1.018 | 0.10 |
| 224_A | 334_C | 1.017 | 0.10 |
| 52_F | 268_P | 1.015 | 0.10 |
| 37_G | 70_R | 1.015 | 0.10 |
| 70_R | 230_A | 1.014 | 0.10 |
| 118_I | 320_R | 1.014 | 0.10 |
| 131_T | 287_R | 1.014 | 0.10 |
| 37_G | 146_E | 1.013 | 0.10 |
| 55_R | 366_N | 1.013 | 0.10 |
| 111_R | 129_L | 1.013 | 0.10 |
| 112_P | 311_G | 1.012 | 0.10 |
| 115_P | 253_S | 1.012 | 0.10 |
| 219_I | 285_R | 1.011 | 0.10 |
| 107_E | 160_A | 1.011 | 0.10 |
| 112_P | 277_A | 1.011 | 0.10 |
| 198_A | 230_A | 1.007 | 0.09 |
| 111_R | 149_I | 1.005 | 0.09 |
| 358_F | 362_D | 1.004 | 0.09 |
| 183_T | 343_V | 1.003 | 0.09 |
| 252_W | 334_C | 1.003 | 0.09 |
| 33_Y | 219_I | 1.002 | 0.09 |
| 104_A | 193_R | 1.002 | 0.09 |
| 147_A | 387_V | 1.001 | 0.09 |
| 183_T | 212_L | 1.000 | 0.09 |
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 | |
| 4l67B | 1 | 0.0433 | 18.2 | 0.981 | Contact Map |
| 4p02B | 1 | 0.1255 | 8.7 | 0.984 | Contact Map |
| 3ixzA | 1 | 0.145 | 7 | 0.985 | Contact Map |
| 2zxeA | 1 | 0.1429 | 6.6 | 0.985 | Contact Map |
| 2kluA | 1 | 0.1494 | 5.2 | 0.986 | Contact Map |
| 2l2tA | 2 | 0.0952 | 4 | 0.986 | Contact Map |
| 2lcnA | 1 | 0.0411 | 3.9 | 0.986 | Contact Map |
| 2lcoA | 1 | 0.0411 | 3.5 | 0.987 | Contact Map |
| 4ag6A | 4 | 0.2641 | 2.7 | 0.987 | Contact Map |
| 3j08A | 2 | 0.1364 | 2.6 | 0.988 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)