| 1E6UA |
| ID: | 1411761311 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 315 (309) | ||
| Sequences: | 24680 (17657) | ||
| Seq/Len: | 79.871 | ||
| Nf(neff/√len): | 1004.5 |
HHblits Results: (2013_03)
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: 79.871).
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 |
| 219_A | 244_V | 3.045 | 1.00 |
| 299_S | 302_A | 2.996 | 1.00 |
| 261_K | 301_E | 2.984 | 1.00 |
| 21_Q | 218_A | 2.838 | 1.00 |
| 240_S | 288_R | 2.752 | 1.00 |
| 258_T | 301_E | 2.725 | 1.00 |
| 7_I | 19_R | 2.671 | 1.00 |
| 47_H | 95_Q | 2.572 | 1.00 |
| 166_Y | 303_G | 2.563 | 1.00 |
| 42_D | 45_A | 2.545 | 1.00 |
| 58_V | 93_A | 2.432 | 1.00 |
| 57_Q | 224_M | 2.417 | 1.00 |
| 8_A | 60_L | 2.371 | 1.00 |
| 218_A | 297_E | 2.252 | 1.00 |
| 80_Y | 84_M | 2.237 | 1.00 |
| 25_R | 225_E | 2.173 | 1.00 |
| 60_L | 103_F | 2.173 | 1.00 |
| 110_Y | 243_N | 2.138 | 1.00 |
| 104_L | 220_S | 2.126 | 1.00 |
| 38_L | 45_A | 2.101 | 1.00 |
| 59_Y | 224_M | 2.080 | 1.00 |
| 74_Y | 77_D | 2.021 | 1.00 |
| 6_F | 55_I | 2.001 | 1.00 |
| 100_K | 156_D | 1.993 | 1.00 |
| 4_R | 29_E | 1.990 | 1.00 |
| 21_Q | 25_R | 1.973 | 1.00 |
| 119_A | 122_E | 1.964 | 1.00 |
| 18_I | 59_Y | 1.959 | 1.00 |
| 254_E | 257_Q | 1.939 | 1.00 |
| 105_G | 109_I | 1.938 | 1.00 |
| 21_Q | 221_I | 1.913 | 1.00 |
| 14_V | 165_L | 1.906 | 1.00 |
| 251_T | 254_E | 1.903 | 1.00 |
| 253_R | 257_Q | 1.865 | 1.00 |
| 218_A | 222_H | 1.865 | 1.00 |
| 214_D | 306_S | 1.848 | 1.00 |
| 212_H | 306_S | 1.848 | 1.00 |
| 160_V | 223_V | 1.812 | 1.00 |
| 18_I | 217_A | 1.809 | 1.00 |
| 262_V | 305_A | 1.789 | 1.00 |
| 18_I | 61_A | 1.782 | 1.00 |
| 50_F | 58_V | 1.780 | 1.00 |
| 41_L | 80_Y | 1.777 | 1.00 |
| 290_H | 295_Y | 1.770 | 1.00 |
| 258_T | 261_K | 1.744 | 1.00 |
| 162_P | 220_S | 1.732 | 1.00 |
| 10_H | 32_L | 1.635 | 1.00 |
| 209_E | 247_G | 1.624 | 1.00 |
| 60_L | 86_E | 1.618 | 1.00 |
| 258_T | 262_V | 1.614 | 1.00 |
| 146_C | 157_Y | 1.606 | 1.00 |
| 197_D | 270_V | 1.605 | 1.00 |
| 160_V | 220_S | 1.603 | 1.00 |
| 212_H | 303_G | 1.567 | 1.00 |
| 89_I | 101_L | 1.515 | 1.00 |
| 59_Y | 220_S | 1.497 | 1.00 |
| 163_T | 284_L | 1.493 | 1.00 |
| 135_Y | 139_K | 1.489 | 1.00 |
| 162_P | 216_M | 1.482 | 1.00 |
| 48_D | 52_S | 1.477 | 1.00 |
| 298_I | 306_S | 1.477 | 1.00 |
| 247_G | 290_H | 1.470 | 1.00 |
| 213_V | 217_A | 1.468 | 1.00 |
| 212_H | 298_I | 1.468 | 1.00 |
| 56_D | 99_N | 1.464 | 1.00 |
| 305_A | 309_Q | 1.460 | 1.00 |
| 20_R | 169_H | 1.459 | 1.00 |
| 82_N | 138_A | 1.445 | 1.00 |
| 91_H | 94_H | 1.433 | 1.00 |
| 286_V | 296_H | 1.432 | 1.00 |
| 5_V | 27_D | 1.419 | 1.00 |
| 120_E | 288_R | 1.413 | 1.00 |
| 22_L | 221_I | 1.411 | 1.00 |
| 21_Q | 24_Q | 1.408 | 1.00 |
| 21_Q | 217_A | 1.404 | 0.99 |
| 289_L | 292_L | 1.394 | 0.99 |
| 211_L | 216_M | 1.390 | 0.99 |
| 302_A | 305_A | 1.381 | 0.99 |
| 218_A | 294_W | 1.375 | 0.99 |
| 87_S | 91_H | 1.374 | 0.99 |
| 287_T | 291_Q | 1.371 | 0.99 |
| 47_H | 92_A | 1.363 | 0.99 |
| 104_L | 162_P | 1.359 | 0.99 |
| 119_A | 285_D | 1.357 | 0.99 |
| 93_A | 101_L | 1.351 | 0.99 |
| 84_M | 87_S | 1.348 | 0.99 |
| 43_S | 91_H | 1.340 | 0.99 |
| 253_R | 271_F | 1.327 | 0.99 |
| 137_I | 141_A | 1.326 | 0.99 |
| 219_A | 289_L | 1.324 | 0.99 |
| 242_I | 291_Q | 1.322 | 0.99 |
| 262_V | 304_L | 1.321 | 0.99 |
| 68_I | 71_N | 1.316 | 0.99 |
| 100_K | 158_R | 1.311 | 0.99 |
| 81_Q | 85_I | 1.308 | 0.99 |
| 128_L | 140_I | 1.305 | 0.99 |
| 76_A | 80_Y | 1.301 | 0.99 |
| 223_V | 289_L | 1.297 | 0.99 |
| 40_L | 85_I | 1.293 | 0.99 |
| 86_E | 142_G | 1.286 | 0.99 |
| 16_S | 169_H | 1.278 | 0.99 |
| 10_H | 19_R | 1.274 | 0.99 |
| 221_I | 225_E | 1.272 | 0.99 |
| 13_M | 167_G | 1.264 | 0.99 |
| 8_A | 62_A | 1.238 | 0.98 |
| 118_M | 122_E | 1.227 | 0.98 |
| 87_S | 145_L | 1.221 | 0.98 |
| 4_R | 56_D | 1.221 | 0.98 |
| 27_D | 225_E | 1.204 | 0.98 |
| 250_C | 300_L | 1.204 | 0.98 |
| 144_K | 147_E | 1.201 | 0.98 |
| 61_A | 104_L | 1.200 | 0.98 |
| 91_H | 95_Q | 1.194 | 0.98 |
| 161_M | 243_N | 1.193 | 0.98 |
| 309_Q | 313_E | 1.192 | 0.98 |
| 13_M | 213_V | 1.185 | 0.98 |
| 207_M | 249_D | 1.185 | 0.98 |
| 5_V | 59_Y | 1.185 | 0.98 |
| 301_E | 305_A | 1.185 | 0.98 |
| 199_V | 270_V | 1.183 | 0.98 |
| 103_F | 142_G | 1.177 | 0.98 |
| 140_I | 144_K | 1.175 | 0.98 |
| 94_H | 153_Y | 1.171 | 0.98 |
| 212_H | 215_D | 1.169 | 0.97 |
| 93_A | 98_V | 1.163 | 0.97 |
| 147_E | 241_H | 1.158 | 0.97 |
| 302_A | 306_S | 1.158 | 0.97 |
| 286_V | 290_H | 1.138 | 0.97 |
| 79_I | 141_A | 1.135 | 0.97 |
| 90_I | 149_Y | 1.123 | 0.97 |
| 79_I | 138_A | 1.122 | 0.97 |
| 107_S | 163_T | 1.116 | 0.96 |
| 121_S | 288_R | 1.110 | 0.96 |
| 260_A | 266_K | 1.108 | 0.96 |
| 101_L | 146_C | 1.108 | 0.96 |
| 242_I | 288_R | 1.107 | 0.96 |
| 147_E | 157_Y | 1.105 | 0.96 |
| 21_Q | 214_D | 1.105 | 0.96 |
| 25_R | 221_I | 1.104 | 0.96 |
| 92_A | 96_N | 1.102 | 0.96 |
| 43_S | 88_N | 1.102 | 0.96 |
| 61_A | 220_S | 1.102 | 0.96 |
| 18_I | 22_L | 1.099 | 0.96 |
| 47_H | 96_N | 1.099 | 0.96 |
| 4_R | 55_I | 1.092 | 0.96 |
| 166_Y | 212_H | 1.082 | 0.96 |
| 244_V | 289_L | 1.074 | 0.95 |
| 250_C | 255_L | 1.072 | 0.95 |
| 109_I | 143_I | 1.070 | 0.95 |
| 5_V | 22_L | 1.069 | 0.95 |
| 161_M | 241_H | 1.067 | 0.95 |
| 5_V | 57_Q | 1.065 | 0.95 |
| 40_L | 62_A | 1.064 | 0.95 |
| 143_I | 161_M | 1.061 | 0.95 |
| 222_H | 226_L | 1.054 | 0.95 |
| 10_H | 30_L | 1.054 | 0.95 |
| 105_G | 143_I | 1.051 | 0.94 |
| 48_D | 51_A | 1.050 | 0.94 |
| 215_D | 246_T | 1.047 | 0.94 |
| 103_F | 159_S | 1.037 | 0.94 |
| 197_D | 268_R | 1.037 | 0.94 |
| 45_A | 49_F | 1.031 | 0.94 |
| 115_K | 122_E | 1.031 | 0.94 |
| 44_R | 48_D | 1.026 | 0.94 |
| 288_R | 291_Q | 1.022 | 0.93 |
| 17_A | 214_D | 1.020 | 0.93 |
| 205_T | 253_R | 1.020 | 0.93 |
| 45_A | 48_D | 1.015 | 0.93 |
| 115_K | 119_A | 1.014 | 0.93 |
| 20_R | 24_Q | 1.011 | 0.93 |
| 257_Q | 260_A | 1.004 | 0.93 |
| 179_V | 183_L | 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 | |
| 1e6uA | 1 | 1 | 100 | 0.164 | Contact Map |
| 3rufA | 4 | 0.9238 | 100 | 0.222 | Contact Map |
| 2hunA | 2 | 0.9175 | 100 | 0.229 | Contact Map |
| 2c20A | 6 | 0.9397 | 100 | 0.231 | Contact Map |
| 1sb8A | 1 | 0.9333 | 100 | 0.232 | Contact Map |
| 4e5yA | 4 | 0.9714 | 100 | 0.234 | Contact Map |
| 1gy8A | 4 | 0.9746 | 100 | 0.235 | Contact Map |
| 4egbA | 8 | 0.8825 | 100 | 0.238 | Contact Map |
| 3ko8A | 1 | 0.8794 | 100 | 0.239 | Contact Map |
| 1oc2A | 2 | 0.9143 | 100 | 0.239 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)