| gremlin_chainA |
| ID: | 1517403186 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 354 (299) | ||
| Sequences: | 2030 (1289.2) | ||
| Seq/Len: | 6.789 | ||
| Nf(neff/√len): | 74.6 |
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: 6.789).
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 |
| 289_N | 331_N | 2.711 | 1.00 |
| 67_H | 71_E | 2.459 | 1.00 |
| 301_L | 306_A | 2.454 | 1.00 |
| 122_L | 128_C | 2.359 | 1.00 |
| 287_L | 328_A | 2.352 | 1.00 |
| 268_L | 286_T | 2.312 | 1.00 |
| 199_S | 209_I | 2.139 | 1.00 |
| 166_L | 171_S | 2.077 | 1.00 |
| 244_N | 289_N | 2.033 | 1.00 |
| 108_L | 150_V | 2.024 | 1.00 |
| 209_I | 215_A | 2.021 | 1.00 |
| 284_C | 328_A | 2.015 | 1.00 |
| 153_N | 197_N | 1.945 | 1.00 |
| 56_L | 107_A | 1.878 | 1.00 |
| 57_M | 60_S | 1.819 | 1.00 |
| 69_M | 74_G | 1.817 | 1.00 |
| 239_G | 286_T | 1.802 | 1.00 |
| 165_T | 168_E | 1.744 | 1.00 |
| 246_S | 259_L | 1.744 | 1.00 |
| 53_V | 107_A | 1.719 | 1.00 |
| 284_C | 325_S | 1.682 | 1.00 |
| 306_A | 310_L | 1.679 | 1.00 |
| 207_A | 211_A | 1.668 | 1.00 |
| 105_G | 150_V | 1.648 | 1.00 |
| 257_Q | 261_E | 1.615 | 1.00 |
| 60_S | 69_M | 1.611 | 1.00 |
| 208_D | 211_A | 1.590 | 1.00 |
| 199_S | 244_N | 1.589 | 1.00 |
| 53_V | 57_M | 1.551 | 0.99 |
| 112_T | 122_L | 1.547 | 0.99 |
| 310_L | 328_A | 1.545 | 0.99 |
| 259_L | 264_C | 1.535 | 0.99 |
| 120_A | 125_M | 1.530 | 0.99 |
| 79_A | 128_C | 1.484 | 0.99 |
| 55_V | 58_K | 1.476 | 0.99 |
| 60_S | 110_N | 1.435 | 0.99 |
| 285_G | 288_W | 1.433 | 0.99 |
| 192_L | 241_I | 1.419 | 0.99 |
| 57_M | 103_Y | 1.411 | 0.99 |
| 58_K | 61_F | 1.390 | 0.99 |
| 269_L | 306_A | 1.386 | 0.99 |
| 299_E | 303_D | 1.372 | 0.98 |
| 313_L | 321_I | 1.363 | 0.98 |
| 146_V | 156_W | 1.359 | 0.98 |
| 54_C | 58_K | 1.339 | 0.98 |
| 119_K | 206_K | 1.328 | 0.98 |
| 242_L | 286_T | 1.316 | 0.98 |
| 155_S | 166_L | 1.288 | 0.97 |
| 155_S | 197_N | 1.279 | 0.97 |
| 103_Y | 109_T | 1.267 | 0.97 |
| 106_M | 149_S | 1.252 | 0.97 |
| 53_V | 78_I | 1.249 | 0.97 |
| 68_A | 72_L | 1.248 | 0.97 |
| 88_M | 93_N | 1.247 | 0.97 |
| 151_L | 194_A | 1.245 | 0.97 |
| 78_I | 107_A | 1.239 | 0.96 |
| 291_S | 301_L | 1.238 | 0.96 |
| 164_K | 168_E | 1.235 | 0.96 |
| 240_G | 243_R | 1.235 | 0.96 |
| 282_N | 285_G | 1.233 | 0.96 |
| 132_L | 147_I | 1.227 | 0.96 |
| 145_Q | 187_T | 1.217 | 0.96 |
| 188_L | 191_V | 1.210 | 0.96 |
| 280_V | 321_I | 1.208 | 0.96 |
| 193_S | 237_S | 1.202 | 0.96 |
| 112_T | 153_N | 1.202 | 0.96 |
| 149_S | 190_S | 1.193 | 0.95 |
| 322_A | 329_L | 1.190 | 0.95 |
| 223_L | 238_G | 1.190 | 0.95 |
| 240_G | 282_N | 1.175 | 0.95 |
| 51_P | 54_C | 1.175 | 0.95 |
| 185_E | 231_T | 1.174 | 0.95 |
| 143_L | 150_V | 1.168 | 0.95 |
| 175_L | 194_A | 1.166 | 0.95 |
| 196_W | 240_G | 1.161 | 0.94 |
| 124_S | 162_S | 1.160 | 0.94 |
| 109_T | 149_S | 1.159 | 0.94 |
| 60_S | 107_A | 1.156 | 0.94 |
| 113_F | 153_N | 1.153 | 0.94 |
| 284_C | 313_L | 1.149 | 0.94 |
| 189_K | 239_G | 1.147 | 0.94 |
| 88_M | 91_L | 1.138 | 0.94 |
| 246_S | 289_N | 1.135 | 0.93 |
| 231_T | 276_S | 1.132 | 0.93 |
| 106_M | 109_T | 1.131 | 0.93 |
| 133_V | 169_V | 1.130 | 0.93 |
| 89_Y | 93_N | 1.125 | 0.93 |
| 280_V | 316_S | 1.124 | 0.93 |
| 152_R | 163_K | 1.123 | 0.93 |
| 90_G | 93_N | 1.119 | 0.93 |
| 167_R | 174_A | 1.117 | 0.93 |
| 263_N | 286_T | 1.114 | 0.93 |
| 294_N | 297_D | 1.113 | 0.93 |
| 59_L | 276_S | 1.106 | 0.92 |
| 298_Q | 335_N | 1.106 | 0.92 |
| 89_Y | 94_D | 1.104 | 0.92 |
| 192_L | 234_I | 1.103 | 0.92 |
| 128_C | 135_Q | 1.101 | 0.92 |
| 56_L | 78_I | 1.099 | 0.92 |
| 87_E | 90_G | 1.098 | 0.92 |
| 165_T | 169_V | 1.095 | 0.92 |
| 88_M | 94_D | 1.094 | 0.92 |
| 256_R | 293_R | 1.094 | 0.92 |
| 105_G | 147_I | 1.091 | 0.92 |
| 109_T | 119_K | 1.083 | 0.91 |
| 216_L | 242_L | 1.081 | 0.91 |
| 196_W | 237_S | 1.075 | 0.91 |
| 184_K | 187_T | 1.074 | 0.91 |
| 89_Y | 92_T | 1.073 | 0.91 |
| 291_S | 331_N | 1.069 | 0.90 |
| 258_I | 262_N | 1.064 | 0.90 |
| 65_H | 260_R | 1.063 | 0.90 |
| 245_V | 255_H | 1.063 | 0.90 |
| 79_A | 126_K | 1.062 | 0.90 |
| 50_C | 99_T | 1.059 | 0.90 |
| 136_L | 148_A | 1.058 | 0.90 |
| 143_L | 146_V | 1.057 | 0.90 |
| 288_W | 327_A | 1.057 | 0.90 |
| 133_V | 171_S | 1.054 | 0.90 |
| 148_A | 175_L | 1.054 | 0.90 |
| 197_N | 244_N | 1.054 | 0.90 |
| 154_L | 175_L | 1.052 | 0.89 |
| 110_N | 244_N | 1.046 | 0.89 |
| 187_T | 191_V | 1.043 | 0.89 |
| 87_E | 92_T | 1.042 | 0.89 |
| 265_L | 332_L | 1.042 | 0.89 |
| 271_H | 279_I | 1.039 | 0.89 |
| 77_A | 81_L | 1.038 | 0.89 |
| 242_L | 259_L | 1.037 | 0.89 |
| 132_L | 154_L | 1.036 | 0.88 |
| 273_K | 309_M | 1.035 | 0.88 |
| 51_P | 66_R | 1.032 | 0.88 |
| 68_A | 71_E | 1.030 | 0.88 |
| 259_L | 295_P | 1.027 | 0.88 |
| 64_E | 259_L | 1.026 | 0.88 |
| 271_H | 274_S | 1.025 | 0.88 |
| 243_R | 285_G | 1.022 | 0.88 |
| 168_E | 329_L | 1.022 | 0.88 |
| 87_E | 91_L | 1.020 | 0.87 |
| 59_L | 75_L | 1.020 | 0.87 |
| 204_E | 207_A | 1.020 | 0.87 |
| 49_I | 187_T | 1.016 | 0.87 |
| 76_Q | 79_A | 1.012 | 0.87 |
| 310_L | 322_A | 1.011 | 0.87 |
| 54_C | 106_M | 1.004 | 0.86 |
| 152_R | 282_N | 1.001 | 0.86 |
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 | |
| 3nmwA | 2 | 0.9237 | 100 | 0.277 | Contact Map |
| 3nmzA | 2 | 0.9407 | 100 | 0.388 | Contact Map |
| 4plqA | 1 | 0.7994 | 100 | 0.43 | Contact Map |
| 4rxhB | 1 | 0 | 100 | 0.431 | Contact Map |
| 3opbA | 2 | 0.935 | 100 | 0.436 | Contact Map |
| 4uadA | 1 | 0.9237 | 100 | 0.436 | Contact Map |
| 4uaeA | 1 | 0.8418 | 100 | 0.438 | Contact Map |
| 4uafB | 1 | 0.9322 | 100 | 0.443 | Contact Map |
| 2jdqA | 2 | 0.9266 | 100 | 0.447 | Contact Map |
| 4b8jA | 1 | 0.9209 | 100 | 0.456 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)