| RodA |
| ID: | 1484171493 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 359 (353) | ||
| Sequences: | 6444 (4011.5) | ||
| Seq/Len: | 18.255 | ||
| Nf(neff/√len): | 213.5 |
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: 18.255).
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 |
| 12_D | 283_R | 4.232 | 1.00 |
| 284_I | 304_G | 4.204 | 1.00 |
| 284_I | 349_V | 3.397 | 1.00 |
| 300_L | 349_V | 3.312 | 1.00 |
| 62_R | 296_D | 3.211 | 1.00 |
| 262_A | 270_V | 3.109 | 1.00 |
| 165_A | 305_G | 3.086 | 1.00 |
| 228_I | 262_A | 2.837 | 1.00 |
| 23_L | 47_L | 2.599 | 1.00 |
| 54_A | 350_L | 2.516 | 1.00 |
| 76_S | 113_G | 2.399 | 1.00 |
| 50_G | 343_L | 2.381 | 1.00 |
| 19_V | 346_L | 2.342 | 1.00 |
| 57_V | 344_F | 2.300 | 1.00 |
| 331_L | 346_L | 2.297 | 1.00 |
| 331_L | 342_T | 2.292 | 1.00 |
| 36_D | 41_F | 2.282 | 1.00 |
| 169_V | 301_A | 2.252 | 1.00 |
| 76_S | 110_A | 2.246 | 1.00 |
| 18_L | 279_L | 2.201 | 1.00 |
| 258_F | 270_V | 2.171 | 1.00 |
| 18_L | 280_L | 2.170 | 1.00 |
| 303_V | 349_V | 2.126 | 1.00 |
| 261_W | 273_L | 2.107 | 1.00 |
| 317_V | 324_V | 2.094 | 1.00 |
| 107_L | 155_G | 2.066 | 1.00 |
| 296_D | 352_V | 2.038 | 1.00 |
| 238_Y | 265_W | 2.034 | 1.00 |
| 271_A | 275_A | 2.004 | 1.00 |
| 316_G | 322_V | 1.961 | 1.00 |
| 274_L | 315_L | 1.954 | 1.00 |
| 281_V | 308_G | 1.928 | 1.00 |
| 166_V | 302_G | 1.927 | 1.00 |
| 328_T | 338_S | 1.884 | 1.00 |
| 38_S | 42_R | 1.833 | 1.00 |
| 241_G | 260_V | 1.814 | 1.00 |
| 261_W | 332_F | 1.810 | 1.00 |
| 98_V | 101_P | 1.808 | 1.00 |
| 311_V | 315_L | 1.805 | 1.00 |
| 221_V | 324_V | 1.786 | 1.00 |
| 213_D | 216_G | 1.769 | 1.00 |
| 284_I | 300_L | 1.754 | 1.00 |
| 303_V | 345_S | 1.728 | 1.00 |
| 158_V | 327_L | 1.726 | 1.00 |
| 351_L | 355_D | 1.716 | 1.00 |
| 209_D | 212_R | 1.713 | 1.00 |
| 104_F | 109_L | 1.688 | 1.00 |
| 116_L | 299_F | 1.653 | 1.00 |
| 251_F | 254_T | 1.648 | 1.00 |
| 46_A | 336_G | 1.643 | 1.00 |
| 115_V | 302_G | 1.639 | 1.00 |
| 145_A | 149_L | 1.635 | 1.00 |
| 80_L | 110_A | 1.630 | 1.00 |
| 293_R | 296_D | 1.627 | 1.00 |
| 202_E | 217_Q | 1.617 | 1.00 |
| 161_F | 309_F | 1.614 | 1.00 |
| 281_V | 304_G | 1.610 | 1.00 |
| 258_F | 315_L | 1.609 | 1.00 |
| 310_Q | 338_S | 1.608 | 1.00 |
| 162_G | 306_M | 1.600 | 1.00 |
| 53_L | 344_F | 1.600 | 1.00 |
| 22_I | 332_F | 1.600 | 1.00 |
| 288_A | 300_L | 1.585 | 1.00 |
| 115_V | 162_G | 1.548 | 1.00 |
| 62_R | 293_R | 1.534 | 1.00 |
| 299_F | 352_V | 1.522 | 1.00 |
| 281_V | 311_V | 1.516 | 1.00 |
| 68_L | 71_P | 1.504 | 1.00 |
| 23_L | 343_L | 1.502 | 1.00 |
| 307_L | 342_T | 1.487 | 1.00 |
| 83_V | 97_F | 1.487 | 1.00 |
| 19_V | 343_L | 1.469 | 1.00 |
| 116_L | 295_A | 1.462 | 1.00 |
| 18_L | 276_L | 1.461 | 1.00 |
| 198_P | 201_R | 1.454 | 1.00 |
| 274_L | 311_V | 1.453 | 1.00 |
| 234_L | 268_V | 1.450 | 1.00 |
| 173_P | 176_H | 1.448 | 1.00 |
| 291_C | 352_V | 1.448 | 1.00 |
| 256_F | 324_V | 1.445 | 1.00 |
| 115_V | 306_M | 1.442 | 1.00 |
| 118_L | 163_V | 1.431 | 1.00 |
| 33_A | 260_V | 1.409 | 1.00 |
| 95_A | 107_L | 1.408 | 1.00 |
| 91_N | 251_F | 1.403 | 0.99 |
| 300_L | 352_V | 1.396 | 0.99 |
| 32_S | 264_E | 1.394 | 0.99 |
| 166_V | 298_L | 1.389 | 0.99 |
| 277_Y | 311_V | 1.386 | 0.99 |
| 25_L | 261_W | 1.383 | 0.99 |
| 114_L | 159_V | 1.383 | 0.99 |
| 122_L | 170_R | 1.379 | 0.99 |
| 241_G | 264_E | 1.356 | 0.99 |
| 109_L | 341_A | 1.355 | 0.99 |
| 221_V | 320_G | 1.355 | 0.99 |
| 233_L | 267_F | 1.352 | 0.99 |
| 98_V | 103_Q | 1.351 | 0.99 |
| 287_L | 300_L | 1.346 | 0.99 |
| 50_G | 347_G | 1.345 | 0.99 |
| 350_L | 353_H | 1.335 | 0.99 |
| 49_L | 340_M | 1.333 | 0.99 |
| 197_K | 200_Q | 1.320 | 0.99 |
| 286_A | 290_E | 1.319 | 0.99 |
| 54_A | 346_L | 1.314 | 0.99 |
| 287_L | 353_H | 1.313 | 0.99 |
| 273_L | 332_F | 1.299 | 0.99 |
| 108_E | 111_K | 1.293 | 0.99 |
| 218_G | 222_I | 1.284 | 0.99 |
| 48_F | 52_G | 1.282 | 0.99 |
| 62_R | 351_L | 1.276 | 0.99 |
| 54_A | 347_G | 1.264 | 0.99 |
| 66_F | 295_A | 1.263 | 0.99 |
| 119_A | 166_V | 1.261 | 0.99 |
| 25_L | 273_L | 1.261 | 0.99 |
| 153_L | 157_L | 1.260 | 0.99 |
| 201_R | 205_L | 1.258 | 0.99 |
| 39_L | 253_H | 1.246 | 0.98 |
| 47_L | 339_L | 1.245 | 0.98 |
| 27_L | 40_F | 1.242 | 0.98 |
| 223_Q | 226_I | 1.238 | 0.98 |
| 224_S | 318_A | 1.238 | 0.98 |
| 120_R | 124_D | 1.223 | 0.98 |
| 304_G | 349_V | 1.218 | 0.98 |
| 65_V | 348_L | 1.218 | 0.98 |
| 78_A | 82_L | 1.214 | 0.98 |
| 58_Q | 347_G | 1.209 | 0.98 |
| 41_F | 44_L | 1.208 | 0.98 |
| 225_T | 320_G | 1.185 | 0.98 |
| 267_F | 271_A | 1.180 | 0.98 |
| 25_L | 276_L | 1.179 | 0.98 |
| 154_G | 325_T | 1.170 | 0.97 |
| 168_L | 174_W | 1.165 | 0.97 |
| 43_Q | 46_A | 1.162 | 0.97 |
| 38_S | 41_F | 1.161 | 0.97 |
| 44_L | 48_F | 1.153 | 0.97 |
| 165_A | 309_F | 1.148 | 0.97 |
| 198_P | 202_E | 1.142 | 0.97 |
| 206_I | 217_Q | 1.141 | 0.97 |
| 306_M | 345_S | 1.139 | 0.97 |
| 233_L | 268_V | 1.127 | 0.97 |
| 288_A | 301_A | 1.126 | 0.97 |
| 119_A | 123_E | 1.123 | 0.97 |
| 62_R | 352_V | 1.117 | 0.96 |
| 224_S | 259_A | 1.116 | 0.96 |
| 41_F | 45_L | 1.107 | 0.96 |
| 214_P | 222_I | 1.102 | 0.96 |
| 310_Q | 328_T | 1.102 | 0.96 |
| 122_L | 166_V | 1.098 | 0.96 |
| 223_Q | 243_Q | 1.093 | 0.96 |
| 112_L | 344_F | 1.091 | 0.96 |
| 154_G | 317_V | 1.088 | 0.96 |
| 206_I | 218_G | 1.085 | 0.96 |
| 147_L | 159_V | 1.083 | 0.96 |
| 21_A | 276_L | 1.082 | 0.96 |
| 157_L | 161_F | 1.082 | 0.96 |
| 211_Y | 222_I | 1.079 | 0.95 |
| 155_G | 328_T | 1.076 | 0.95 |
| 42_R | 46_A | 1.076 | 0.95 |
| 115_V | 166_V | 1.073 | 0.95 |
| 73_Y | 143_V | 1.071 | 0.95 |
| 95_A | 154_G | 1.071 | 0.95 |
| 219_F | 223_Q | 1.070 | 0.95 |
| 31_R | 40_F | 1.063 | 0.95 |
| 29_N | 265_W | 1.062 | 0.95 |
| 202_E | 206_I | 1.060 | 0.95 |
| 162_G | 165_A | 1.054 | 0.95 |
| 51_L | 55_V | 1.050 | 0.94 |
| 349_V | 352_V | 1.050 | 0.94 |
| 261_W | 265_W | 1.049 | 0.94 |
| 152_D | 155_G | 1.048 | 0.94 |
| 93_A | 150_Q | 1.041 | 0.94 |
| 285_L | 304_G | 1.038 | 0.94 |
| 61_S | 64_L | 1.037 | 0.94 |
| 160_L | 164_F | 1.035 | 0.94 |
| 249_V | 259_A | 1.033 | 0.94 |
| 30_L | 33_A | 1.030 | 0.94 |
| 213_D | 217_Q | 1.027 | 0.94 |
| 230_S | 236_K | 1.019 | 0.93 |
| 39_L | 334_Y | 1.018 | 0.93 |
| 53_L | 340_M | 1.017 | 0.93 |
| 317_V | 325_T | 1.016 | 0.93 |
| 110_A | 113_G | 1.013 | 0.93 |
| 72_L | 113_G | 1.012 | 0.93 |
| 22_I | 273_L | 1.009 | 0.93 |
| 329_L | 332_F | 1.009 | 0.93 |
| 221_V | 224_S | 1.007 | 0.93 |
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 | |
| 3wu2Z | 2 | 0.1114 | 3.3 | 0.975 | Contact Map |
| 2k9jB | 1 | 0.1198 | 2.7 | 0.976 | Contact Map |
| 2l6wA | 2 | 0.0919 | 2.1 | 0.977 | Contact Map |
| 4qncA | 2 | 0.2284 | 2 | 0.977 | Contact Map |
| 4ogqE | 1 | 0.0864 | 1.8 | 0.978 | Contact Map |
| 4i0uA | 10 | 0.1811 | 1.6 | 0.979 | Contact Map |
| 1oedE | 1 | 0.2368 | 1.4 | 0.979 | Contact Map |
| 1pfiA | 2 | 0.1281 | 1.4 | 0.979 | Contact Map |
| 2k3cA | 1 | 0.0724 | 1.3 | 0.98 | Contact Map |
| 2h88D | 2 | 0.1393 | 1.3 | 0.98 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)