| 4mfuoj 30-370 |
| ID: | 1495077732 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 341 (285) | ||
| Sequences: | 29517 (17115.7) | ||
| Seq/Len: | 103.568 | ||
| Nf(neff/√len): | 1013.8 |
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: 103.568).
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 |
| 148_K | 186_V | 2.165 | 1.00 |
| 86_L | 91_V | 2.148 | 1.00 |
| 178_L | 183_G | 2.083 | 1.00 |
| 192_S | 236_L | 1.979 | 1.00 |
| 165_A | 213_D | 1.944 | 1.00 |
| 168_L | 178_L | 1.942 | 1.00 |
| 56_S | 101_R | 1.933 | 1.00 |
| 49_G | 94_L | 1.876 | 1.00 |
| 176_E | 180_E | 1.853 | 1.00 |
| 168_L | 217_S | 1.852 | 1.00 |
| 271_F | 276_G | 1.850 | 1.00 |
| 157_K | 202_A | 1.843 | 1.00 |
| 259_M | 271_F | 1.818 | 1.00 |
| 269_H | 273_D | 1.818 | 1.00 |
| 35_L | 40_A | 1.817 | 1.00 |
| 216_C | 253_K | 1.806 | 1.00 |
| 179_G | 224_N | 1.794 | 1.00 |
| 237_M | 254_V | 1.753 | 1.00 |
| 213_D | 250_S | 1.746 | 1.00 |
| 242_R | 279_T | 1.740 | 1.00 |
| 148_K | 189_Q | 1.735 | 1.00 |
| 100_E | 142_W | 1.724 | 1.00 |
| 226_E | 230_K | 1.722 | 1.00 |
| 133_E | 139_L | 1.719 | 1.00 |
| 228_F | 233_G | 1.700 | 1.00 |
| 124_A | 166_I | 1.699 | 1.00 |
| 162_E | 210_N | 1.674 | 1.00 |
| 219_L | 228_F | 1.644 | 1.00 |
| 84_D | 88_D | 1.607 | 1.00 |
| 113_V | 151_M | 1.602 | 1.00 |
| 270_K | 273_D | 1.599 | 1.00 |
| 219_L | 257_H | 1.599 | 1.00 |
| 227_R | 230_K | 1.593 | 1.00 |
| 187_L | 214_S | 1.585 | 1.00 |
| 229_L | 267_N | 1.557 | 1.00 |
| 95_L | 119_I | 1.554 | 1.00 |
| 67_T | 86_L | 1.554 | 1.00 |
| 96_V | 139_L | 1.542 | 1.00 |
| 238_N | 276_G | 1.540 | 1.00 |
| 144_L | 183_G | 1.539 | 1.00 |
| 118_A | 159_Y | 1.521 | 1.00 |
| 45_L | 91_V | 1.516 | 1.00 |
| 134_G | 174_N | 1.516 | 1.00 |
| 33_H | 37_E | 1.495 | 1.00 |
| 242_R | 282_P | 1.494 | 1.00 |
| 61_D | 115_N | 1.489 | 1.00 |
| 208_M | 243_E | 1.489 | 1.00 |
| 212_F | 254_V | 1.487 | 1.00 |
| 142_W | 145_K | 1.482 | 1.00 |
| 94_L | 97_Q | 1.479 | 1.00 |
| 67_T | 122_N | 1.456 | 1.00 |
| 100_E | 145_K | 1.446 | 1.00 |
| 188_L | 233_G | 1.441 | 1.00 |
| 210_N | 213_D | 1.436 | 1.00 |
| 248_R | 286_K | 1.433 | 1.00 |
| 250_S | 253_K | 1.416 | 1.00 |
| 209_E | 246_I | 1.414 | 1.00 |
| 236_L | 239_L | 1.407 | 0.99 |
| 63_L | 119_I | 1.402 | 0.99 |
| 26_A | 35_L | 1.402 | 0.99 |
| 26_A | 65_E | 1.380 | 0.99 |
| 143_L | 163_V | 1.379 | 0.99 |
| 216_C | 254_V | 1.368 | 0.99 |
| 132_T | 135_A | 1.368 | 0.99 |
| 121_E | 162_E | 1.365 | 0.99 |
| 15_L | 18_I | 1.358 | 0.99 |
| 161_S | 214_S | 1.350 | 0.99 |
| 124_A | 133_E | 1.334 | 0.99 |
| 279_T | 282_P | 1.323 | 0.99 |
| 44_L | 62_L | 1.317 | 0.99 |
| 177_L | 180_E | 1.316 | 0.99 |
| 158_L | 204_E | 1.312 | 0.99 |
| 117_L | 163_V | 1.303 | 0.99 |
| 61_D | 65_E | 1.294 | 0.99 |
| 186_V | 189_Q | 1.292 | 0.99 |
| 216_C | 219_L | 1.289 | 0.99 |
| 205_Q | 208_M | 1.286 | 0.99 |
| 187_L | 211_L | 1.285 | 0.99 |
| 47_L | 55_V | 1.285 | 0.99 |
| 113_V | 116_T | 1.284 | 0.99 |
| 143_L | 160_C | 1.276 | 0.99 |
| 121_E | 163_V | 1.254 | 0.99 |
| 15_L | 50_H | 1.251 | 0.99 |
| 96_V | 142_W | 1.245 | 0.98 |
| 159_Y | 162_E | 1.244 | 0.98 |
| 304_H | 307_S | 1.242 | 0.98 |
| 157_K | 160_C | 1.241 | 0.98 |
| 53_T | 109_E | 1.234 | 0.98 |
| 34_L | 37_E | 1.233 | 0.98 |
| 237_M | 251_A | 1.233 | 0.98 |
| 16_N | 20_Q | 1.220 | 0.98 |
| 43_S | 46_G | 1.206 | 0.98 |
| 307_S | 311_S | 1.190 | 0.98 |
| 208_M | 211_L | 1.190 | 0.98 |
| 117_L | 160_C | 1.189 | 0.98 |
| 120_V | 163_V | 1.185 | 0.98 |
| 93_A | 136_Q | 1.180 | 0.98 |
| 64_Q | 115_N | 1.177 | 0.98 |
| 64_Q | 118_A | 1.176 | 0.98 |
| 270_K | 274_I | 1.175 | 0.98 |
| 60_V | 98_N | 1.171 | 0.98 |
| 58_A | 61_D | 1.169 | 0.97 |
| 21_E | 24_V | 1.165 | 0.97 |
| 20_Q | 58_A | 1.163 | 0.97 |
| 23_H | 58_A | 1.162 | 0.97 |
| 56_S | 59_V | 1.161 | 0.97 |
| 165_A | 168_L | 1.154 | 0.97 |
| 252_L | 308_I | 1.150 | 0.97 |
| 153_F | 156_N | 1.146 | 0.97 |
| 44_L | 59_V | 1.132 | 0.97 |
| 57_I | 115_N | 1.131 | 0.97 |
| 175_R | 221_L | 1.129 | 0.97 |
| 57_I | 61_D | 1.126 | 0.97 |
| 302_E | 305_V | 1.113 | 0.96 |
| 157_K | 207_M | 1.111 | 0.96 |
| 303_E | 307_S | 1.110 | 0.96 |
| 225_R | 261_G | 1.110 | 0.96 |
| 121_E | 124_A | 1.109 | 0.96 |
| 98_N | 112_G | 1.109 | 0.96 |
| 60_V | 116_T | 1.104 | 0.96 |
| 144_L | 186_V | 1.099 | 0.96 |
| 22_M | 62_L | 1.092 | 0.96 |
| 19_I | 62_L | 1.084 | 0.96 |
| 51_D | 55_V | 1.075 | 0.95 |
| 50_H | 55_V | 1.075 | 0.95 |
| 115_N | 118_A | 1.073 | 0.95 |
| 311_S | 314_R | 1.068 | 0.95 |
| 256_D | 259_M | 1.061 | 0.95 |
| 158_L | 206_E | 1.061 | 0.95 |
| 255_L | 308_I | 1.061 | 0.95 |
| 151_M | 156_N | 1.060 | 0.95 |
| 113_V | 156_N | 1.057 | 0.95 |
| 95_L | 116_T | 1.056 | 0.95 |
| 162_E | 166_I | 1.047 | 0.94 |
| 208_M | 247_S | 1.047 | 0.94 |
| 49_G | 97_Q | 1.043 | 0.94 |
| 164_L | 214_S | 1.041 | 0.94 |
| 27_T | 65_E | 1.040 | 0.94 |
| 20_Q | 24_V | 1.030 | 0.94 |
| 249_S | 300_E | 1.030 | 0.94 |
| 227_R | 231_G | 1.029 | 0.94 |
| 184_I | 188_L | 1.028 | 0.94 |
| 216_C | 250_S | 1.028 | 0.94 |
| 138_G | 141_Q | 1.028 | 0.94 |
| 192_S | 239_L | 1.023 | 0.93 |
| 97_Q | 100_E | 1.021 | 0.93 |
| 154_D | 158_L | 1.019 | 0.93 |
| 87_V | 130_M | 1.015 | 0.93 |
| 240_M | 251_A | 1.014 | 0.93 |
| 213_D | 217_S | 1.012 | 0.93 |
| 19_I | 47_L | 1.012 | 0.93 |
| 161_S | 190_Q | 1.011 | 0.93 |
| 110_A | 153_F | 1.010 | 0.93 |
| 280_I | 308_I | 1.010 | 0.93 |
| 257_H | 260_I | 1.005 | 0.93 |
| 215_L | 254_V | 1.004 | 0.93 |
| 217_S | 220_M | 1.003 | 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 | |
| 4cb9A | 1 | 0.9853 | 100 | 0.15 | Contact Map |
| 4mfuA | 1 | 1 | 100 | 0.152 | Contact Map |
| 4rxhB | 1 | 0 | 99.9 | 0.304 | Contact Map |
| 4uadA | 1 | 0.8798 | 99.9 | 0.307 | Contact Map |
| 3nmzA | 2 | 0.827 | 99.9 | 0.309 | Contact Map |
| 3nmwA | 2 | 0.827 | 99.9 | 0.311 | Contact Map |
| 4uaeA | 1 | 0.8827 | 99.9 | 0.311 | Contact Map |
| 4uafB | 1 | 0.8944 | 99.9 | 0.318 | Contact Map |
| 2jdqA | 2 | 0.8768 | 99.9 | 0.322 | Contact Map |
| 4b8jA | 1 | 0.8798 | 99.9 | 0.322 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)