| scEMC1 1-380 |
| ID: | 1505235215 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 380 (338) | ||
| Sequences: | 4152 (2975.9) | ||
| Seq/Len: | 12.284 | ||
| Nf(neff/√len): | 161.9 |
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: 12.284).
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 |
| 153_L | 189_L | 2.937 | 1.00 |
| 58_I | 72_F | 2.732 | 1.00 |
| 329_E | 349_F | 2.530 | 1.00 |
| 315_D | 319_K | 2.492 | 1.00 |
| 145_Q | 187_L | 2.473 | 1.00 |
| 304_V | 314_L | 2.459 | 1.00 |
| 189_L | 199_F | 2.355 | 1.00 |
| 251_A | 255_R | 2.320 | 1.00 |
| 112_W | 146_V | 2.311 | 1.00 |
| 116_D | 119_D | 2.308 | 1.00 |
| 188_V | 198_G | 2.286 | 1.00 |
| 73_N | 76_S | 2.232 | 1.00 |
| 303_I | 347_V | 2.152 | 1.00 |
| 60_S | 66_S | 2.132 | 1.00 |
| 57_L | 101_A | 2.120 | 1.00 |
| 134_T | 147_S | 2.103 | 1.00 |
| 57_L | 94_L | 2.050 | 1.00 |
| 86_P | 104_C | 2.037 | 1.00 |
| 91_E | 105_V | 2.017 | 1.00 |
| 284_L | 304_V | 1.996 | 1.00 |
| 129_N | 146_V | 1.967 | 1.00 |
| 336_M | 350_S | 1.952 | 1.00 |
| 27_S | 30_A | 1.920 | 1.00 |
| 94_L | 137_P | 1.901 | 1.00 |
| 66_S | 70_S | 1.886 | 1.00 |
| 102_M | 114_K | 1.842 | 1.00 |
| 69_V | 104_C | 1.822 | 1.00 |
| 303_I | 313_G | 1.822 | 1.00 |
| 148_I | 152_E | 1.821 | 1.00 |
| 57_L | 71_S | 1.783 | 1.00 |
| 354_H | 358_I | 1.775 | 1.00 |
| 102_M | 144_D | 1.765 | 1.00 |
| 215_W | 219_V | 1.761 | 1.00 |
| 157_D | 160_S | 1.739 | 1.00 |
| 271_Q | 274_P | 1.715 | 1.00 |
| 315_D | 318_N | 1.681 | 1.00 |
| 146_V | 156_L | 1.665 | 1.00 |
| 256_L | 304_V | 1.658 | 1.00 |
| 349_F | 360_V | 1.635 | 1.00 |
| 154_H | 166_K | 1.631 | 1.00 |
| 50_S | 94_L | 1.616 | 1.00 |
| 135_I | 146_V | 1.612 | 1.00 |
| 348_V | 359_E | 1.590 | 1.00 |
| 100_N | 114_K | 1.567 | 1.00 |
| 197_M | 211_Q | 1.546 | 1.00 |
| 129_N | 150_N | 1.535 | 1.00 |
| 102_M | 137_P | 1.508 | 1.00 |
| 145_Q | 155_I | 1.502 | 1.00 |
| 55_R | 80_L | 1.489 | 1.00 |
| 104_C | 115_Y | 1.480 | 1.00 |
| 204_T | 207_I | 1.478 | 1.00 |
| 293_D | 305_L | 1.462 | 1.00 |
| 200_S | 204_T | 1.454 | 1.00 |
| 329_E | 354_H | 1.453 | 1.00 |
| 116_D | 123_L | 1.423 | 1.00 |
| 40_L | 58_I | 1.407 | 0.99 |
| 24_A | 33_T | 1.405 | 0.99 |
| 102_M | 135_I | 1.404 | 0.99 |
| 221_D | 250_N | 1.393 | 0.99 |
| 188_V | 226_D | 1.391 | 0.99 |
| 48_P | 137_P | 1.384 | 0.99 |
| 137_P | 340_D | 1.381 | 0.99 |
| 55_R | 71_S | 1.379 | 0.99 |
| 109_S | 113_Q | 1.377 | 0.99 |
| 142_L | 345_E | 1.372 | 0.99 |
| 139_S | 184_P | 1.354 | 0.99 |
| 284_L | 308_D | 1.346 | 0.99 |
| 45_K | 59_L | 1.343 | 0.99 |
| 170_P | 189_L | 1.322 | 0.99 |
| 146_V | 150_N | 1.318 | 0.99 |
| 70_S | 82_R | 1.313 | 0.99 |
| 124_E | 165_W | 1.306 | 0.99 |
| 135_I | 144_D | 1.300 | 0.99 |
| 24_A | 36_Q | 1.299 | 0.99 |
| 57_L | 92_I | 1.281 | 0.99 |
| 196_Y | 249_W | 1.270 | 0.99 |
| 70_S | 79_I | 1.268 | 0.99 |
| 71_S | 83_N | 1.265 | 0.99 |
| 281_L | 314_L | 1.258 | 0.99 |
| 95_D | 98_D | 1.257 | 0.99 |
| 351_H | 354_H | 1.256 | 0.99 |
| 301_I | 346_L | 1.249 | 0.99 |
| 297_G | 344_D | 1.239 | 0.98 |
| 303_I | 340_D | 1.234 | 0.98 |
| 311_I | 349_F | 1.230 | 0.98 |
| 303_I | 337_F | 1.226 | 0.98 |
| 248_L | 302_L | 1.219 | 0.98 |
| 54_N | 300_K | 1.217 | 0.98 |
| 113_Q | 122_L | 1.217 | 0.98 |
| 23_Q | 58_I | 1.213 | 0.98 |
| 95_D | 100_N | 1.209 | 0.98 |
| 191_V | 195_Q | 1.208 | 0.98 |
| 122_L | 366_I | 1.204 | 0.98 |
| 122_L | 208_P | 1.201 | 0.98 |
| 113_Q | 125_E | 1.196 | 0.98 |
| 366_I | 369_S | 1.193 | 0.98 |
| 208_P | 366_I | 1.192 | 0.98 |
| 33_T | 79_I | 1.191 | 0.98 |
| 303_I | 311_I | 1.186 | 0.98 |
| 187_L | 201_A | 1.183 | 0.98 |
| 124_E | 161_K | 1.182 | 0.98 |
| 59_L | 89_I | 1.177 | 0.98 |
| 202_N | 318_N | 1.175 | 0.98 |
| 137_P | 180_H | 1.175 | 0.98 |
| 341_K | 344_D | 1.172 | 0.98 |
| 99_H | 345_E | 1.170 | 0.97 |
| 51_R | 98_D | 1.168 | 0.97 |
| 79_I | 163_A | 1.167 | 0.97 |
| 230_S | 245_S | 1.166 | 0.97 |
| 358_I | 366_I | 1.166 | 0.97 |
| 56_V | 101_A | 1.160 | 0.97 |
| 104_C | 107_S | 1.159 | 0.97 |
| 104_C | 113_Q | 1.155 | 0.97 |
| 124_E | 279_T | 1.150 | 0.97 |
| 79_I | 322_L | 1.146 | 0.97 |
| 215_W | 253_W | 1.146 | 0.97 |
| 60_S | 68_L | 1.142 | 0.97 |
| 56_V | 74_V | 1.137 | 0.97 |
| 33_T | 122_L | 1.137 | 0.97 |
| 277_V | 322_L | 1.135 | 0.97 |
| 121_F | 162_L | 1.133 | 0.97 |
| 301_I | 313_G | 1.122 | 0.97 |
| 255_R | 262_R | 1.117 | 0.96 |
| 245_S | 249_W | 1.115 | 0.96 |
| 188_V | 199_F | 1.114 | 0.96 |
| 58_I | 70_S | 1.108 | 0.96 |
| 249_W | 253_W | 1.108 | 0.96 |
| 35_W | 77_G | 1.107 | 0.96 |
| 54_N | 142_L | 1.107 | 0.96 |
| 163_A | 208_P | 1.099 | 0.96 |
| 83_N | 115_Y | 1.098 | 0.96 |
| 306_T | 310_F | 1.096 | 0.96 |
| 284_L | 306_T | 1.094 | 0.96 |
| 129_N | 148_I | 1.093 | 0.96 |
| 71_S | 114_K | 1.090 | 0.96 |
| 79_I | 208_P | 1.086 | 0.96 |
| 250_N | 254_L | 1.079 | 0.95 |
| 32_I | 162_L | 1.076 | 0.95 |
| 59_L | 92_I | 1.073 | 0.95 |
| 141_Y | 147_S | 1.070 | 0.95 |
| 54_N | 345_E | 1.068 | 0.95 |
| 210_W | 279_T | 1.059 | 0.95 |
| 33_T | 36_Q | 1.057 | 0.95 |
| 79_I | 277_V | 1.055 | 0.95 |
| 122_L | 322_L | 1.054 | 0.95 |
| 169_L | 172_G | 1.054 | 0.95 |
| 250_N | 291_V | 1.049 | 0.94 |
| 155_I | 198_G | 1.047 | 0.94 |
| 78_Q | 121_F | 1.046 | 0.94 |
| 94_L | 340_D | 1.045 | 0.94 |
| 306_T | 312_G | 1.040 | 0.94 |
| 334_V | 349_F | 1.034 | 0.94 |
| 262_R | 269_E | 1.031 | 0.94 |
| 26_F | 33_T | 1.029 | 0.94 |
| 312_G | 325_K | 1.028 | 0.94 |
| 215_W | 249_W | 1.026 | 0.94 |
| 181_R | 184_P | 1.026 | 0.94 |
| 118_H | 159_Q | 1.024 | 0.93 |
| 122_L | 125_E | 1.023 | 0.93 |
| 122_L | 163_A | 1.020 | 0.93 |
| 186_A | 346_L | 1.017 | 0.93 |
| 86_P | 107_S | 1.016 | 0.93 |
| 143_N | 346_L | 1.010 | 0.93 |
| 50_S | 57_L | 1.009 | 0.93 |
| 79_I | 366_I | 1.007 | 0.93 |
| 143_N | 301_I | 1.005 | 0.93 |
| 300_K | 315_D | 1.005 | 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 | |
| 4nsxA | 1 | 0.8816 | 100 | 0.378 | Contact Map |
| 1vyhC | 10 | 0.7921 | 100 | 0.38 | Contact Map |
| 3sfzA | 1 | 0.8737 | 100 | 0.383 | Contact Map |
| 4noxA | 1 | 0.85 | 100 | 0.391 | Contact Map |
| 4wjuA | 2 | 0.8342 | 100 | 0.396 | Contact Map |
| 4ci8A | 2 | 0.8474 | 100 | 0.401 | Contact Map |
| 1flgA | 2 | 0.8789 | 100 | 0.403 | Contact Map |
| 1yiqA | 1 | 0.8947 | 100 | 0.407 | Contact Map |
| 4wjsA | 1 | 0.8368 | 100 | 0.413 | Contact Map |
| 4u1eI | 1 | 0.7974 | 100 | 0.414 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)