| vim |
| ID: | 1486043203 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 316 (315) | ||
| Sequences: | 2224 (1190.3) | ||
| Seq/Len: | 7.060 | ||
| Nf(neff/√len): | 67.1 |
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: 7.060).
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 |
| 114_Q | 118_N | 2.384 | 1.00 |
| 243_N | 247_E | 2.337 | 1.00 |
| 27_V | 30_L | 2.253 | 1.00 |
| 313_E | 316_R | 2.223 | 1.00 |
| 303_I | 306_Y | 2.186 | 1.00 |
| 31_E | 34_N | 2.130 | 1.00 |
| 73_D | 76_R | 2.083 | 1.00 |
| 109_L | 112_F | 1.922 | 1.00 |
| 224_E | 227_R | 1.845 | 1.00 |
| 244_E | 248_R | 1.842 | 1.00 |
| 299_L | 302_E | 1.819 | 1.00 |
| 123_R | 127_E | 1.809 | 1.00 |
| 252_E | 255_E | 1.786 | 1.00 |
| 20_F | 24_I | 1.780 | 1.00 |
| 302_E | 306_Y | 1.754 | 1.00 |
| 306_Y | 310_L | 1.752 | 1.00 |
| 281_E | 284_R | 1.733 | 1.00 |
| 237_D | 240_K | 1.725 | 1.00 |
| 299_L | 303_I | 1.704 | 1.00 |
| 125_D | 129_K | 1.681 | 1.00 |
| 102_R | 106_E | 1.667 | 1.00 |
| 196_W | 200_K | 1.655 | 1.00 |
| 29_F | 33_Q | 1.641 | 1.00 |
| 299_L | 306_Y | 1.608 | 1.00 |
| 151_L | 154_Q | 1.603 | 1.00 |
| 127_E | 131_E | 1.597 | 1.00 |
| 13_L | 20_F | 1.575 | 1.00 |
| 307_R | 311_E | 1.549 | 1.00 |
| 36_I | 40_E | 1.548 | 1.00 |
| 117_D | 120_S | 1.516 | 0.99 |
| 34_N | 37_L | 1.514 | 0.99 |
| 296_K | 306_Y | 1.506 | 0.99 |
| 30_L | 34_N | 1.500 | 0.99 |
| 243_N | 246_L | 1.495 | 0.99 |
| 30_L | 37_L | 1.485 | 0.99 |
| 253_M | 257_F | 1.463 | 0.99 |
| 17_N | 23_Y | 1.436 | 0.99 |
| 116_V | 120_S | 1.424 | 0.99 |
| 227_R | 230_Q | 1.417 | 0.99 |
| 302_E | 309_L | 1.404 | 0.99 |
| 300_D | 303_I | 1.401 | 0.99 |
| 90_R | 94_K | 1.385 | 0.99 |
| 142_K | 146_E | 1.372 | 0.99 |
| 308_K | 313_E | 1.370 | 0.99 |
| 57_E | 64_R | 1.370 | 0.99 |
| 197_Y | 201_F | 1.367 | 0.98 |
| 84_L | 87_D | 1.365 | 0.98 |
| 5_T | 12_E | 1.347 | 0.98 |
| 208_A | 211_N | 1.340 | 0.98 |
| 292_L | 302_E | 1.334 | 0.98 |
| 23_Y | 27_V | 1.332 | 0.98 |
| 60_M | 63_L | 1.326 | 0.98 |
| 302_E | 311_E | 1.321 | 0.98 |
| 191_Q | 195_E | 1.321 | 0.98 |
| 278_M | 281_E | 1.318 | 0.98 |
| 61_R | 65_R | 1.315 | 0.98 |
| 260_E | 264_Y | 1.310 | 0.98 |
| 85_A | 89_M | 1.308 | 0.98 |
| 27_V | 31_E | 1.303 | 0.98 |
| 100_L | 103_E | 1.302 | 0.98 |
| 166_V | 169_P | 1.302 | 0.98 |
| 215_L | 221_E | 1.299 | 0.98 |
| 18_D | 21_A | 1.296 | 0.98 |
| 19_R | 23_Y | 1.288 | 0.98 |
| 23_Y | 30_L | 1.288 | 0.98 |
| 303_I | 311_E | 1.287 | 0.98 |
| 260_E | 263_N | 1.277 | 0.97 |
| 164_V | 170_D | 1.271 | 0.97 |
| 179_R | 183_E | 1.268 | 0.97 |
| 60_M | 64_R | 1.266 | 0.97 |
| 136_E | 139_F | 1.266 | 0.97 |
| 31_E | 37_L | 1.263 | 0.97 |
| 116_V | 119_A | 1.261 | 0.97 |
| 132_S | 135_E | 1.248 | 0.97 |
| 76_R | 80_E | 1.246 | 0.97 |
| 116_V | 123_R | 1.229 | 0.96 |
| 117_D | 127_E | 1.229 | 0.96 |
| 296_K | 302_E | 1.227 | 0.96 |
| 303_I | 307_R | 1.226 | 0.96 |
| 17_N | 20_F | 1.221 | 0.96 |
| 182_Y | 185_V | 1.221 | 0.96 |
| 292_L | 296_K | 1.220 | 0.96 |
| 194_E | 198_K | 1.213 | 0.96 |
| 215_L | 218_A | 1.211 | 0.96 |
| 91_L | 94_K | 1.208 | 0.96 |
| 11_V | 14_Q | 1.207 | 0.96 |
| 39_A | 43_Q | 1.206 | 0.96 |
| 311_E | 314_E | 1.202 | 0.96 |
| 98_E | 102_R | 1.198 | 0.96 |
| 17_N | 34_N | 1.197 | 0.96 |
| 306_Y | 311_E | 1.196 | 0.96 |
| 296_K | 300_D | 1.194 | 0.96 |
| 108_T | 112_F | 1.192 | 0.96 |
| 292_L | 306_Y | 1.191 | 0.96 |
| 293_L | 296_K | 1.189 | 0.96 |
| 17_N | 27_V | 1.185 | 0.95 |
| 177_D | 182_Y | 1.183 | 0.95 |
| 135_E | 138_A | 1.179 | 0.95 |
| 85_A | 88_I | 1.178 | 0.95 |
| 165_D | 168_K | 1.178 | 0.95 |
| 20_F | 23_Y | 1.177 | 0.95 |
| 299_L | 310_L | 1.171 | 0.95 |
| 99_M | 103_E | 1.171 | 0.95 |
| 62_E | 66_Q | 1.170 | 0.95 |
| 13_L | 17_N | 1.166 | 0.95 |
| 187_A | 190_L | 1.164 | 0.95 |
| 120_S | 124_L | 1.163 | 0.95 |
| 259_V | 262_A | 1.162 | 0.95 |
| 117_D | 131_E | 1.160 | 0.95 |
| 38_L | 42_E | 1.160 | 0.95 |
| 177_D | 181_Q | 1.160 | 0.95 |
| 170_D | 175_L | 1.155 | 0.95 |
| 306_Y | 309_L | 1.145 | 0.94 |
| 27_V | 34_N | 1.144 | 0.94 |
| 126_L | 133_L | 1.144 | 0.94 |
| 296_K | 303_I | 1.140 | 0.94 |
| 170_D | 174_A | 1.137 | 0.94 |
| 97_E | 101_Q | 1.135 | 0.94 |
| 79_V | 86_E | 1.133 | 0.94 |
| 202_A | 205_S | 1.130 | 0.94 |
| 32_Q | 36_I | 1.129 | 0.94 |
| 287_R | 291_D | 1.125 | 0.93 |
| 187_A | 191_Q | 1.123 | 0.93 |
| 74_K | 80_E | 1.115 | 0.93 |
| 272_Q | 279_K | 1.113 | 0.93 |
| 9_E | 17_N | 1.112 | 0.93 |
| 151_L | 155_I | 1.109 | 0.93 |
| 172_T | 175_L | 1.106 | 0.93 |
| 255_E | 258_A | 1.094 | 0.92 |
| 171_L | 179_R | 1.091 | 0.92 |
| 9_E | 12_E | 1.090 | 0.92 |
| 114_Q | 117_D | 1.090 | 0.92 |
| 302_E | 310_L | 1.089 | 0.92 |
| 203_D | 207_A | 1.085 | 0.92 |
| 113_R | 133_L | 1.084 | 0.92 |
| 120_S | 123_R | 1.084 | 0.92 |
| 148_I | 155_I | 1.083 | 0.92 |
| 34_N | 41_L | 1.073 | 0.91 |
| 257_F | 261_A | 1.072 | 0.91 |
| 305_T | 311_E | 1.070 | 0.91 |
| 273_D | 277_N | 1.069 | 0.91 |
| 10_K | 14_Q | 1.066 | 0.91 |
| 20_F | 41_L | 1.065 | 0.91 |
| 310_L | 313_E | 1.065 | 0.91 |
| 234_C | 237_D | 1.065 | 0.91 |
| 95_L | 109_L | 1.064 | 0.91 |
| 166_V | 170_D | 1.062 | 0.91 |
| 27_V | 37_L | 1.060 | 0.91 |
| 40_E | 45_K | 1.060 | 0.91 |
| 173_A | 177_D | 1.055 | 0.90 |
| 201_F | 208_A | 1.052 | 0.90 |
| 214_A | 218_A | 1.049 | 0.90 |
| 294_N | 298_A | 1.049 | 0.90 |
| 164_V | 168_K | 1.045 | 0.90 |
| 98_E | 106_E | 1.042 | 0.90 |
| 74_K | 78_E | 1.034 | 0.89 |
| 21_A | 26_K | 1.034 | 0.89 |
| 292_L | 295_V | 1.028 | 0.89 |
| 210_R | 213_D | 1.026 | 0.89 |
| 83_N | 90_R | 1.024 | 0.88 |
| 185_V | 196_W | 1.018 | 0.88 |
| 282_M | 289_Y | 1.017 | 0.88 |
| 305_T | 309_L | 1.017 | 0.88 |
| 298_A | 308_K | 1.015 | 0.88 |
| 92_R | 96_Q | 1.013 | 0.88 |
| 84_L | 89_M | 1.013 | 0.88 |
| 43_Q | 46_G | 1.013 | 0.88 |
| 303_I | 310_L | 1.010 | 0.87 |
| 248_R | 255_E | 1.007 | 0.87 |
| 213_D | 216_R | 1.004 | 0.87 |
| 7_T | 11_V | 1.002 | 0.87 |
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 | |
| 1deqA | 4 | 0.4684 | 100 | 0.563 | Contact Map |
| 3tnuB | 1 | 0.3006 | 99.9 | 0.578 | Contact Map |
| 3tnuA | 1 | 0.2848 | 99.9 | 0.579 | Contact Map |
| 3ghgA | 4 | 0.5127 | 99.9 | 0.586 | Contact Map |
| 3s4rA | 2 | 0.288 | 99.9 | 0.652 | Contact Map |
| 3uf1A | 4 | 0.3576 | 99.8 | 0.684 | Contact Map |
| 1gk4A | 6 | 0.2532 | 99.7 | 0.699 | Contact Map |
| 3tyyA | 2 | 0.2373 | 99.7 | 0.717 | Contact Map |
| 1x8yA | 1 | 0.2342 | 99.7 | 0.717 | Contact Map |
| 3swkA | 2 | 0.2722 | 99.5 | 0.749 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)