| L5 |
| ID: | 1494604844 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 360 (334) | ||
| Sequences: | 8516 (6172.1) | ||
| Seq/Len: | 25.497 | ||
| Nf(neff/√len): | 337.7 |
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: 25.497).
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 |
| 263_R | 266_A | 4.034 | 1.00 |
| 179_H | 240_T | 3.776 | 1.00 |
| 12_Y | 44_E | 3.651 | 1.00 |
| 164_E | 203_K | 3.631 | 1.00 |
| 179_H | 269_S | 3.053 | 1.00 |
| 40_A | 44_E | 3.048 | 1.00 |
| 170_G | 271_V | 2.999 | 1.00 |
| 275_D | 290_K | 2.851 | 1.00 |
| 82_A | 297_G | 2.821 | 1.00 |
| 257_I | 268_I | 2.820 | 1.00 |
| 121_G | 304_L | 2.813 | 1.00 |
| 168_R | 207_R | 2.735 | 1.00 |
| 157_N | 307_L | 2.707 | 1.00 |
| 36_E | 40_A | 2.679 | 1.00 |
| 32_A | 36_E | 2.483 | 1.00 |
| 167_T | 171_V | 2.436 | 1.00 |
| 23_V | 38_V | 2.410 | 1.00 |
| 198_L | 202_H | 2.401 | 1.00 |
| 226_F | 259_E | 2.317 | 1.00 |
| 86_R | 302_D | 2.208 | 1.00 |
| 35_R | 39_E | 2.153 | 1.00 |
| 263_R | 267_D | 2.150 | 1.00 |
| 262_L | 267_D | 2.134 | 1.00 |
| 172_E | 176_A | 2.099 | 1.00 |
| 65_G | 119_V | 2.092 | 1.00 |
| 299_T | 302_D | 2.086 | 1.00 |
| 87_A | 301_V | 2.065 | 1.00 |
| 85_S | 294_R | 2.061 | 1.00 |
| 86_R | 89_Q | 2.018 | 1.00 |
| 230_M | 260_S | 1.995 | 1.00 |
| 167_T | 243_L | 1.980 | 1.00 |
| 225_G | 252_G | 1.869 | 1.00 |
| 168_R | 204_Y | 1.850 | 1.00 |
| 9_V | 41_A | 1.850 | 1.00 |
| 165_D | 169_L | 1.833 | 1.00 |
| 185_L | 253_A | 1.816 | 1.00 |
| 290_K | 322_S | 1.793 | 1.00 |
| 173_H | 329_T | 1.781 | 1.00 |
| 13_A | 41_A | 1.770 | 1.00 |
| 175_V | 208_N | 1.765 | 1.00 |
| 172_E | 208_N | 1.751 | 1.00 |
| 184_L | 245_A | 1.730 | 1.00 |
| 177_L | 329_T | 1.727 | 1.00 |
| 171_V | 175_V | 1.724 | 1.00 |
| 166_G | 273_Y | 1.720 | 1.00 |
| 229_T | 253_A | 1.713 | 1.00 |
| 168_R | 203_K | 1.709 | 1.00 |
| 164_E | 199_A | 1.693 | 1.00 |
| 24_V | 42_M | 1.682 | 1.00 |
| 172_E | 204_Y | 1.670 | 1.00 |
| 8_D | 11_E | 1.670 | 1.00 |
| 9_V | 13_A | 1.661 | 1.00 |
| 168_R | 172_E | 1.637 | 1.00 |
| 292_D | 295_L | 1.634 | 1.00 |
| 171_V | 204_Y | 1.612 | 1.00 |
| 200_G | 204_Y | 1.601 | 1.00 |
| 86_R | 298_Q | 1.589 | 1.00 |
| 257_I | 262_L | 1.578 | 1.00 |
| 275_D | 326_R | 1.568 | 1.00 |
| 174_L | 241_A | 1.550 | 1.00 |
| 226_F | 256_A | 1.549 | 1.00 |
| 242_M | 253_A | 1.540 | 1.00 |
| 171_V | 201_W | 1.532 | 1.00 |
| 7_Y | 11_E | 1.523 | 1.00 |
| 173_H | 177_L | 1.521 | 1.00 |
| 285_P | 327_K | 1.515 | 1.00 |
| 254_M | 264_V | 1.510 | 1.00 |
| 244_V | 253_A | 1.499 | 1.00 |
| 82_A | 294_R | 1.495 | 1.00 |
| 230_M | 256_A | 1.491 | 1.00 |
| 306_Q | 311_Q | 1.475 | 1.00 |
| 230_M | 259_E | 1.469 | 1.00 |
| 173_H | 325_K | 1.465 | 1.00 |
| 7_Y | 17_Y | 1.465 | 1.00 |
| 172_E | 207_R | 1.463 | 1.00 |
| 256_A | 259_E | 1.461 | 1.00 |
| 162_S | 165_D | 1.458 | 1.00 |
| 66_V | 83_I | 1.447 | 1.00 |
| 171_V | 200_G | 1.445 | 1.00 |
| 6_L | 20_V | 1.437 | 1.00 |
| 12_Y | 41_A | 1.437 | 1.00 |
| 53_A | 56_L | 1.431 | 1.00 |
| 254_M | 270_V | 1.427 | 1.00 |
| 229_T | 242_M | 1.409 | 1.00 |
| 4_V | 45_L | 1.408 | 1.00 |
| 148_L | 300_S | 1.405 | 0.99 |
| 64_I | 87_A | 1.403 | 0.99 |
| 258_T | 283_I | 1.401 | 0.99 |
| 182_I | 241_A | 1.399 | 0.99 |
| 179_H | 241_A | 1.396 | 0.99 |
| 254_M | 282_Y | 1.389 | 0.99 |
| 167_T | 200_G | 1.387 | 0.99 |
| 181_Q | 238_V | 1.387 | 0.99 |
| 50_N | 53_A | 1.383 | 0.99 |
| 176_A | 208_N | 1.370 | 0.99 |
| 201_W | 205_L | 1.364 | 0.99 |
| 170_G | 243_L | 1.354 | 0.99 |
| 180_Q | 240_T | 1.345 | 0.99 |
| 50_N | 56_L | 1.323 | 0.99 |
| 41_A | 45_L | 1.322 | 0.99 |
| 295_L | 299_T | 1.319 | 0.99 |
| 252_G | 256_A | 1.317 | 0.99 |
| 295_L | 298_Q | 1.310 | 0.99 |
| 86_R | 301_V | 1.308 | 0.99 |
| 6_L | 17_Y | 1.299 | 0.99 |
| 269_S | 329_T | 1.296 | 0.99 |
| 181_Q | 213_I | 1.295 | 0.99 |
| 205_L | 210_I | 1.287 | 0.99 |
| 173_H | 176_A | 1.286 | 0.99 |
| 247_D | 250_A | 1.285 | 0.99 |
| 9_V | 45_L | 1.282 | 0.99 |
| 226_F | 255_R | 1.277 | 0.99 |
| 247_D | 288_T | 1.277 | 0.99 |
| 31_S | 34_T | 1.276 | 0.99 |
| 183_A | 232_M | 1.276 | 0.99 |
| 299_T | 317_Q | 1.274 | 0.99 |
| 86_R | 90_L | 1.274 | 0.99 |
| 41_A | 44_E | 1.268 | 0.99 |
| 272_G | 288_T | 1.261 | 0.99 |
| 123_I | 300_S | 1.258 | 0.99 |
| 90_L | 305_L | 1.256 | 0.99 |
| 202_H | 206_T | 1.249 | 0.99 |
| 297_G | 301_V | 1.248 | 0.99 |
| 65_G | 114_L | 1.246 | 0.98 |
| 292_D | 319_L | 1.246 | 0.98 |
| 23_V | 42_M | 1.233 | 0.98 |
| 242_M | 268_I | 1.233 | 0.98 |
| 87_A | 94_V | 1.230 | 0.98 |
| 39_E | 43_A | 1.217 | 0.98 |
| 175_V | 210_I | 1.215 | 0.98 |
| 123_I | 304_L | 1.214 | 0.98 |
| 39_E | 42_M | 1.214 | 0.98 |
| 256_A | 260_S | 1.197 | 0.98 |
| 23_V | 30_V | 1.196 | 0.98 |
| 227_Q | 231_Q | 1.192 | 0.98 |
| 199_A | 203_K | 1.188 | 0.98 |
| 164_E | 200_G | 1.186 | 0.98 |
| 78_Q | 294_R | 1.179 | 0.98 |
| 166_G | 321_V | 1.176 | 0.98 |
| 240_T | 269_S | 1.175 | 0.98 |
| 175_V | 204_Y | 1.166 | 0.97 |
| 183_A | 239_P | 1.166 | 0.97 |
| 65_G | 122_L | 1.161 | 0.97 |
| 204_Y | 207_R | 1.159 | 0.97 |
| 305_L | 309_Q | 1.158 | 0.97 |
| 159_I | 303_R | 1.154 | 0.97 |
| 271_V | 287_T | 1.153 | 0.97 |
| 181_Q | 240_T | 1.149 | 0.97 |
| 224_S | 227_Q | 1.146 | 0.97 |
| 182_I | 205_L | 1.143 | 0.97 |
| 62_L | 92_A | 1.142 | 0.97 |
| 12_Y | 45_L | 1.134 | 0.97 |
| 162_S | 318_L | 1.130 | 0.97 |
| 234_N | 260_S | 1.127 | 0.97 |
| 63_L | 93_S | 1.127 | 0.97 |
| 83_I | 297_G | 1.115 | 0.96 |
| 174_L | 271_V | 1.114 | 0.96 |
| 90_L | 302_D | 1.113 | 0.96 |
| 164_E | 168_R | 1.111 | 0.96 |
| 304_L | 308_S | 1.097 | 0.96 |
| 164_E | 196_L | 1.091 | 0.96 |
| 226_F | 230_M | 1.090 | 0.96 |
| 66_V | 80_V | 1.084 | 0.96 |
| 204_Y | 208_N | 1.083 | 0.96 |
| 247_D | 272_G | 1.082 | 0.96 |
| 34_T | 37_K | 1.081 | 0.95 |
| 32_A | 35_R | 1.081 | 0.95 |
| 203_K | 207_R | 1.074 | 0.95 |
| 62_L | 120_S | 1.064 | 0.95 |
| 63_L | 95_V | 1.061 | 0.95 |
| 229_T | 257_I | 1.061 | 0.95 |
| 169_L | 321_V | 1.054 | 0.95 |
| 165_D | 168_R | 1.049 | 0.94 |
| 302_D | 306_Q | 1.049 | 0.94 |
| 22_R | 27_A | 1.035 | 0.94 |
| 37_K | 41_A | 1.035 | 0.94 |
| 163_H | 196_L | 1.022 | 0.93 |
| 26_Q | 35_R | 1.021 | 0.93 |
| 163_H | 197_R | 1.013 | 0.93 |
| 66_V | 94_V | 1.012 | 0.93 |
| 169_L | 289_I | 1.001 | 0.92 |
| 33_K | 36_E | 1.001 | 0.92 |
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 | |
| 1jyeA | 1 | 0.75 | 100 | 0.111 | Contact Map |
| 3dbiA | 3 | 0.7611 | 100 | 0.13 | Contact Map |
| 4o5aA | 1 | 0.7444 | 100 | 0.146 | Contact Map |
| 3ctpA | 2 | 0.7333 | 100 | 0.153 | Contact Map |
| 3bilA | 2 | 0.7083 | 100 | 0.154 | Contact Map |
| 3kjxA | 4 | 0.9139 | 100 | 0.156 | Contact Map |
| 2hsgA | 1 | 0.8972 | 100 | 0.156 | Contact Map |
| 3e3mA | 4 | 0.7361 | 100 | 0.157 | Contact Map |
| 1qpzA | 1 | 0.9278 | 100 | 0.157 | Contact Map |
| 2o20A | 8 | 0.7528 | 100 | 0.16 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)