| vim 95-410 |
| ID: | 1486042639 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 316 (315) | ||
| Sequences: | 3133 (1735.4) | ||
| Seq/Len: | 9.946 | ||
| Nf(neff/√len): | 97.8 |
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: 9.946).
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 |
| 109_L | 112_F | 2.575 | 1.00 |
| 27_V | 30_L | 2.289 | 1.00 |
| 81_R | 84_L | 2.288 | 1.00 |
| 303_I | 306_Y | 2.251 | 1.00 |
| 60_M | 63_L | 2.211 | 1.00 |
| 281_E | 284_R | 2.076 | 1.00 |
| 229_V | 232_L | 2.034 | 1.00 |
| 237_D | 240_K | 2.020 | 1.00 |
| 313_E | 316_R | 1.992 | 1.00 |
| 123_R | 127_E | 1.927 | 1.00 |
| 170_D | 174_A | 1.902 | 1.00 |
| 275_I | 278_M | 1.818 | 1.00 |
| 73_D | 76_R | 1.806 | 1.00 |
| 36_I | 40_E | 1.799 | 1.00 |
| 243_N | 246_L | 1.789 | 1.00 |
| 243_N | 247_E | 1.764 | 1.00 |
| 76_R | 80_E | 1.732 | 1.00 |
| 114_Q | 118_N | 1.731 | 1.00 |
| 88_I | 91_L | 1.717 | 1.00 |
| 34_N | 37_L | 1.656 | 1.00 |
| 61_R | 65_R | 1.650 | 1.00 |
| 307_R | 311_E | 1.646 | 1.00 |
| 200_K | 203_D | 1.620 | 1.00 |
| 299_L | 306_Y | 1.598 | 1.00 |
| 270_R | 274_E | 1.588 | 1.00 |
| 306_Y | 309_L | 1.586 | 1.00 |
| 179_R | 183_E | 1.577 | 1.00 |
| 20_F | 24_I | 1.576 | 1.00 |
| 130_V | 133_L | 1.563 | 1.00 |
| 296_K | 300_D | 1.560 | 1.00 |
| 102_R | 106_E | 1.542 | 1.00 |
| 30_L | 34_N | 1.533 | 1.00 |
| 224_E | 227_R | 1.499 | 1.00 |
| 125_D | 129_K | 1.474 | 1.00 |
| 20_F | 23_Y | 1.456 | 1.00 |
| 136_E | 139_F | 1.456 | 1.00 |
| 67_V | 70_L | 1.440 | 1.00 |
| 277_N | 281_E | 1.434 | 1.00 |
| 99_M | 103_E | 1.429 | 1.00 |
| 196_W | 200_K | 1.409 | 0.99 |
| 29_F | 33_Q | 1.408 | 0.99 |
| 250_M | 253_M | 1.403 | 0.99 |
| 191_Q | 195_E | 1.401 | 0.99 |
| 284_R | 288_E | 1.384 | 0.99 |
| 208_A | 211_N | 1.384 | 0.99 |
| 222_S | 225_Y | 1.378 | 0.99 |
| 18_D | 21_A | 1.371 | 0.99 |
| 16_L | 19_R | 1.363 | 0.99 |
| 136_E | 140_L | 1.358 | 0.99 |
| 38_L | 42_E | 1.354 | 0.99 |
| 17_N | 20_F | 1.350 | 0.99 |
| 302_E | 306_Y | 1.341 | 0.99 |
| 306_Y | 310_L | 1.337 | 0.99 |
| 260_E | 263_N | 1.337 | 0.99 |
| 23_Y | 27_V | 1.335 | 0.99 |
| 252_E | 255_E | 1.326 | 0.99 |
| 120_S | 124_L | 1.323 | 0.99 |
| 116_V | 120_S | 1.320 | 0.99 |
| 62_E | 66_Q | 1.319 | 0.99 |
| 305_T | 308_K | 1.306 | 0.99 |
| 98_E | 102_R | 1.295 | 0.99 |
| 302_E | 305_T | 1.292 | 0.99 |
| 244_E | 248_R | 1.291 | 0.99 |
| 299_L | 303_I | 1.290 | 0.99 |
| 147_E | 151_L | 1.278 | 0.99 |
| 151_L | 154_Q | 1.275 | 0.99 |
| 148_I | 151_L | 1.275 | 0.99 |
| 287_R | 291_D | 1.270 | 0.99 |
| 17_N | 27_V | 1.258 | 0.99 |
| 173_A | 177_D | 1.256 | 0.99 |
| 202_A | 206_E | 1.250 | 0.99 |
| 90_R | 93_E | 1.248 | 0.98 |
| 5_T | 12_E | 1.247 | 0.98 |
| 187_A | 191_Q | 1.244 | 0.98 |
| 98_E | 112_F | 1.241 | 0.98 |
| 293_L | 296_K | 1.239 | 0.98 |
| 84_L | 87_D | 1.234 | 0.98 |
| 227_R | 230_Q | 1.225 | 0.98 |
| 155_I | 158_Q | 1.219 | 0.98 |
| 283_A | 301_I | 1.217 | 0.98 |
| 173_A | 176_R | 1.214 | 0.98 |
| 39_A | 43_Q | 1.213 | 0.98 |
| 19_R | 23_Y | 1.212 | 0.98 |
| 135_E | 138_A | 1.211 | 0.98 |
| 235_E | 240_K | 1.208 | 0.98 |
| 117_D | 131_E | 1.205 | 0.98 |
| 302_E | 309_L | 1.203 | 0.98 |
| 63_L | 66_Q | 1.201 | 0.98 |
| 97_E | 101_Q | 1.198 | 0.98 |
| 74_K | 78_E | 1.196 | 0.98 |
| 272_Q | 279_K | 1.192 | 0.98 |
| 292_L | 296_K | 1.191 | 0.98 |
| 247_E | 251_R | 1.190 | 0.98 |
| 100_L | 103_E | 1.188 | 0.98 |
| 17_N | 23_Y | 1.177 | 0.98 |
| 177_D | 181_Q | 1.176 | 0.98 |
| 117_D | 120_S | 1.174 | 0.98 |
| 25_D | 28_R | 1.173 | 0.98 |
| 91_L | 94_K | 1.172 | 0.97 |
| 253_M | 257_F | 1.169 | 0.97 |
| 57_E | 60_M | 1.166 | 0.97 |
| 116_V | 119_A | 1.165 | 0.97 |
| 234_C | 237_D | 1.164 | 0.97 |
| 7_T | 11_V | 1.164 | 0.97 |
| 194_E | 197_Y | 1.154 | 0.97 |
| 308_K | 313_E | 1.154 | 0.97 |
| 107_N | 111_S | 1.153 | 0.97 |
| 126_L | 133_L | 1.143 | 0.97 |
| 71_T | 78_E | 1.141 | 0.97 |
| 252_E | 256_N | 1.137 | 0.97 |
| 294_N | 298_A | 1.134 | 0.97 |
| 132_S | 135_E | 1.132 | 0.97 |
| 85_A | 88_I | 1.131 | 0.97 |
| 40_E | 45_K | 1.130 | 0.97 |
| 278_M | 281_E | 1.129 | 0.97 |
| 176_R | 180_Q | 1.128 | 0.97 |
| 273_D | 277_N | 1.125 | 0.97 |
| 193_A | 197_Y | 1.124 | 0.97 |
| 255_E | 258_A | 1.124 | 0.97 |
| 85_A | 89_M | 1.120 | 0.96 |
| 60_M | 64_R | 1.116 | 0.96 |
| 300_D | 303_I | 1.116 | 0.96 |
| 311_E | 314_E | 1.108 | 0.96 |
| 11_V | 14_Q | 1.104 | 0.96 |
| 13_L | 17_N | 1.101 | 0.96 |
| 260_E | 264_Y | 1.099 | 0.96 |
| 10_K | 14_Q | 1.093 | 0.96 |
| 298_A | 308_K | 1.091 | 0.96 |
| 108_T | 111_S | 1.089 | 0.96 |
| 119_A | 131_E | 1.086 | 0.96 |
| 55_L | 59_E | 1.085 | 0.96 |
| 296_K | 306_Y | 1.085 | 0.96 |
| 236_V | 239_L | 1.083 | 0.95 |
| 292_L | 306_Y | 1.083 | 0.95 |
| 164_V | 170_D | 1.079 | 0.95 |
| 259_V | 262_A | 1.076 | 0.95 |
| 292_L | 302_E | 1.069 | 0.95 |
| 83_N | 87_D | 1.068 | 0.95 |
| 215_L | 218_A | 1.066 | 0.95 |
| 257_F | 261_A | 1.062 | 0.95 |
| 148_I | 155_I | 1.060 | 0.95 |
| 286_L | 290_Q | 1.055 | 0.95 |
| 98_E | 101_Q | 1.055 | 0.95 |
| 302_E | 307_R | 1.054 | 0.95 |
| 203_D | 207_A | 1.054 | 0.95 |
| 186_A | 193_A | 1.050 | 0.94 |
| 41_L | 44_L | 1.049 | 0.94 |
| 27_V | 34_N | 1.047 | 0.94 |
| 127_E | 131_E | 1.043 | 0.94 |
| 135_E | 139_F | 1.039 | 0.94 |
| 27_V | 31_E | 1.038 | 0.94 |
| 267_T | 272_Q | 1.033 | 0.94 |
| 294_N | 297_M | 1.033 | 0.94 |
| 303_I | 310_L | 1.029 | 0.94 |
| 79_V | 83_N | 1.026 | 0.93 |
| 308_K | 312_G | 1.026 | 0.93 |
| 172_T | 176_R | 1.019 | 0.93 |
| 282_M | 286_L | 1.019 | 0.93 |
| 288_E | 313_E | 1.014 | 0.93 |
| 197_Y | 201_F | 1.011 | 0.93 |
| 82_D | 85_A | 1.010 | 0.93 |
| 165_D | 168_K | 1.010 | 0.93 |
| 43_Q | 46_G | 1.008 | 0.93 |
| 53_G | 57_E | 1.006 | 0.93 |
| 166_V | 169_P | 1.004 | 0.92 |
| 299_L | 305_T | 1.002 | 0.92 |
| 296_K | 303_I | 1.000 | 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 | |
| 3tnuA | 1 | 0.2848 | 99.7 | 0.549 | Contact Map |
| 3tnuB | 1 | 0.3006 | 99.7 | 0.551 | Contact Map |
| 1deqA | 4 | 0.4684 | 99.7 | 0.551 | Contact Map |
| 3ghgA | 4 | 0.5127 | 99.7 | 0.569 | Contact Map |
| 3s4rA | 2 | 0.288 | 99.4 | 0.632 | Contact Map |
| 3uf1A | 4 | 0.3576 | 99.2 | 0.674 | Contact Map |
| 1i84S | 2 | 0.2816 | 99.2 | 0.675 | Contact Map |
| 1gk4A | 6 | 0.2532 | 99.1 | 0.681 | Contact Map |
| 1x8yA | 1 | 0.2342 | 99.1 | 0.689 | Contact Map |
| 3tyyA | 2 | 0.2373 | 99.1 | 0.692 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)