| TEST |
| ID: | 1504611876 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 480 (443) | ||
| Sequences: | 2361 (1820.4) | ||
| Seq/Len: | 5.330 | ||
| Nf(neff/√len): | 86.5 |
Jackhmmer Results: (2016_04)
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: 5.330).
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 |
| 247_E | 373_G | 3.400 | 1.00 |
| 378_S | 405_H | 3.065 | 1.00 |
| 262_D | 403_M | 2.726 | 1.00 |
| 256_E | 287_H | 2.693 | 1.00 |
| 167_V | 178_M | 2.594 | 1.00 |
| 260_A | 290_I | 2.573 | 1.00 |
| 378_S | 382_G | 2.253 | 1.00 |
| 339_M | 379_L | 2.216 | 1.00 |
| 343_M | 376_A | 2.136 | 1.00 |
| 254_G | 339_M | 2.057 | 1.00 |
| 228_E | 289_K | 2.016 | 1.00 |
| 213_L | 225_F | 2.003 | 1.00 |
| 167_V | 176_Y | 1.990 | 1.00 |
| 332_W | 383_L | 1.959 | 1.00 |
| 412_V | 415_H | 1.954 | 1.00 |
| 247_E | 407_F | 1.875 | 1.00 |
| 387_D | 390_Q | 1.803 | 1.00 |
| 236_F | 278_E | 1.751 | 1.00 |
| 106_V | 110_L | 1.710 | 1.00 |
| 281_M | 291_T | 1.696 | 1.00 |
| 415_H | 420_K | 1.677 | 1.00 |
| 48_R | 51_P | 1.675 | 1.00 |
| 251_R | 410_G | 1.672 | 1.00 |
| 151_E | 168_K | 1.667 | 1.00 |
| 178_M | 226_V | 1.565 | 0.99 |
| 42_P | 46_D | 1.564 | 0.99 |
| 105_T | 109_G | 1.563 | 0.99 |
| 275_L | 338_V | 1.532 | 0.99 |
| 44_D | 48_R | 1.519 | 0.99 |
| 32_D | 35_F | 1.508 | 0.99 |
| 69_R | 73_F | 1.487 | 0.99 |
| 43_Q | 47_Q | 1.471 | 0.98 |
| 64_K | 67_R | 1.465 | 0.98 |
| 103_I | 107_A | 1.447 | 0.98 |
| 73_F | 76_R | 1.440 | 0.98 |
| 379_L | 402_I | 1.434 | 0.98 |
| 207_H | 263_Y | 1.432 | 0.98 |
| 150_F | 215_Y | 1.430 | 0.98 |
| 72_T | 76_R | 1.403 | 0.98 |
| 262_D | 266_S | 1.403 | 0.98 |
| 68_P | 72_T | 1.387 | 0.98 |
| 82_T | 86_R | 1.387 | 0.98 |
| 276_K | 312_T | 1.386 | 0.98 |
| 60_C | 65_T | 1.380 | 0.97 |
| 38_Y | 41_R | 1.375 | 0.97 |
| 258_V | 402_I | 1.373 | 0.97 |
| 385_K | 390_Q | 1.363 | 0.97 |
| 100_T | 104_Q | 1.355 | 0.97 |
| 94_E | 98_E | 1.352 | 0.97 |
| 234_E | 278_E | 1.348 | 0.97 |
| 107_A | 111_K | 1.346 | 0.97 |
| 60_C | 68_P | 1.342 | 0.97 |
| 151_E | 170_K | 1.334 | 0.97 |
| 272_Y | 338_V | 1.331 | 0.97 |
| 66_E | 69_R | 1.323 | 0.96 |
| 122_S | 125_P | 1.322 | 0.96 |
| 250_A | 339_M | 1.319 | 0.96 |
| 112_K | 115_E | 1.318 | 0.96 |
| 67_R | 72_T | 1.316 | 0.96 |
| 81_T | 85_E | 1.313 | 0.96 |
| 155_L | 158_K | 1.309 | 0.96 |
| 35_F | 38_Y | 1.302 | 0.96 |
| 36_I | 39_K | 1.297 | 0.96 |
| 83_V | 86_R | 1.292 | 0.96 |
| 41_R | 44_D | 1.291 | 0.96 |
| 111_K | 114_E | 1.286 | 0.96 |
| 155_L | 165_I | 1.285 | 0.96 |
| 63_M | 66_E | 1.278 | 0.95 |
| 42_P | 47_Q | 1.276 | 0.95 |
| 82_T | 85_E | 1.276 | 0.95 |
| 254_G | 335_L | 1.271 | 0.95 |
| 34_T | 38_Y | 1.264 | 0.95 |
| 68_P | 71_N | 1.260 | 0.95 |
| 85_E | 88_F | 1.260 | 0.95 |
| 65_T | 68_P | 1.259 | 0.95 |
| 108_D | 112_K | 1.257 | 0.95 |
| 41_R | 45_V | 1.255 | 0.95 |
| 311_G | 348_P | 1.253 | 0.95 |
| 102_A | 106_V | 1.251 | 0.95 |
| 60_C | 63_M | 1.247 | 0.95 |
| 84_I | 87_T | 1.247 | 0.95 |
| 183_K | 218_Q | 1.245 | 0.95 |
| 108_D | 111_K | 1.245 | 0.95 |
| 70_P | 73_F | 1.244 | 0.95 |
| 326_Y | 330_V | 1.242 | 0.94 |
| 105_T | 110_L | 1.240 | 0.94 |
| 344_C | 372_L | 1.239 | 0.94 |
| 64_K | 68_P | 1.237 | 0.94 |
| 54_N | 57_V | 1.235 | 0.94 |
| 92_T | 98_E | 1.228 | 0.94 |
| 117_E | 121_R | 1.222 | 0.94 |
| 42_P | 45_V | 1.221 | 0.94 |
| 351_N | 356_K | 1.221 | 0.94 |
| 47_Q | 51_P | 1.217 | 0.94 |
| 86_R | 90_V | 1.209 | 0.93 |
| 81_T | 84_I | 1.204 | 0.93 |
| 297_K | 306_M | 1.203 | 0.93 |
| 108_D | 113_Q | 1.203 | 0.93 |
| 39_K | 42_P | 1.202 | 0.93 |
| 34_T | 37_G | 1.201 | 0.93 |
| 56_S | 59_Q | 1.200 | 0.93 |
| 85_E | 89_H | 1.198 | 0.93 |
| 104_Q | 108_D | 1.197 | 0.93 |
| 30_K | 33_G | 1.194 | 0.93 |
| 71_N | 75_I | 1.194 | 0.93 |
| 400_K | 404_Q | 1.189 | 0.93 |
| 45_V | 49_E | 1.187 | 0.93 |
| 110_L | 113_Q | 1.183 | 0.92 |
| 62_L | 65_T | 1.183 | 0.92 |
| 94_E | 97_E | 1.181 | 0.92 |
| 50_A | 53_N | 1.177 | 0.92 |
| 68_P | 73_F | 1.176 | 0.92 |
| 48_R | 52_L | 1.175 | 0.92 |
| 86_R | 89_H | 1.173 | 0.92 |
| 69_R | 72_T | 1.170 | 0.92 |
| 87_T | 91_E | 1.168 | 0.92 |
| 66_E | 70_P | 1.168 | 0.92 |
| 92_T | 95_E | 1.168 | 0.92 |
| 206_R | 212_A | 1.163 | 0.91 |
| 35_F | 39_K | 1.161 | 0.91 |
| 166_L | 175_Y | 1.161 | 0.91 |
| 261_L | 335_L | 1.158 | 0.91 |
| 109_G | 113_Q | 1.155 | 0.91 |
| 337_V | 347_L | 1.154 | 0.91 |
| 51_P | 54_N | 1.150 | 0.91 |
| 392_L | 402_I | 1.149 | 0.91 |
| 88_F | 92_T | 1.146 | 0.91 |
| 40_E | 44_D | 1.144 | 0.91 |
| 87_T | 90_V | 1.144 | 0.91 |
| 67_R | 71_N | 1.138 | 0.90 |
| 108_D | 114_E | 1.137 | 0.90 |
| 80_W | 85_E | 1.135 | 0.90 |
| 101_T | 107_A | 1.132 | 0.90 |
| 253_Y | 288_I | 1.130 | 0.90 |
| 104_Q | 107_A | 1.130 | 0.90 |
| 84_I | 88_F | 1.129 | 0.90 |
| 382_G | 392_L | 1.129 | 0.90 |
| 65_T | 70_P | 1.125 | 0.90 |
| 97_E | 100_T | 1.122 | 0.89 |
| 277_L | 315_Y | 1.120 | 0.89 |
| 364_E | 386_K | 1.115 | 0.89 |
| 55_F | 58_A | 1.115 | 0.89 |
| 37_G | 41_R | 1.114 | 0.89 |
| 80_W | 83_V | 1.111 | 0.89 |
| 273_R | 326_Y | 1.111 | 0.89 |
| 40_E | 43_Q | 1.111 | 0.89 |
| 111_K | 115_E | 1.111 | 0.89 |
| 106_V | 112_K | 1.108 | 0.89 |
| 332_W | 399_A | 1.105 | 0.88 |
| 47_Q | 50_A | 1.103 | 0.88 |
| 36_I | 40_E | 1.103 | 0.88 |
| 49_E | 53_N | 1.101 | 0.88 |
| 37_G | 40_E | 1.098 | 0.88 |
| 61_Q | 64_K | 1.097 | 0.88 |
| 165_I | 180_I | 1.094 | 0.88 |
| 44_D | 49_E | 1.094 | 0.88 |
| 96_R | 99_W | 1.089 | 0.88 |
| 33_G | 36_I | 1.089 | 0.88 |
| 110_L | 114_E | 1.084 | 0.87 |
| 57_V | 62_L | 1.084 | 0.87 |
| 35_F | 40_E | 1.082 | 0.87 |
| 62_L | 66_E | 1.080 | 0.87 |
| 434_D | 438_F | 1.078 | 0.87 |
| 155_L | 163_K | 1.078 | 0.87 |
| 99_W | 103_I | 1.074 | 0.87 |
| 74_I | 77_C | 1.071 | 0.86 |
| 113_Q | 117_E | 1.070 | 0.86 |
| 52_L | 56_S | 1.069 | 0.86 |
| 46_D | 50_A | 1.068 | 0.86 |
| 56_S | 60_C | 1.064 | 0.86 |
| 102_A | 107_A | 1.064 | 0.86 |
| 53_N | 61_Q | 1.064 | 0.86 |
| 99_W | 105_T | 1.063 | 0.86 |
| 39_K | 53_N | 1.063 | 0.86 |
| 166_L | 229_Y | 1.062 | 0.86 |
| 69_R | 75_I | 1.062 | 0.86 |
| 93_P | 98_E | 1.061 | 0.86 |
| 61_Q | 67_R | 1.060 | 0.86 |
| 93_P | 96_R | 1.059 | 0.85 |
| 125_P | 128_N | 1.057 | 0.85 |
| 54_N | 58_A | 1.054 | 0.85 |
| 44_D | 47_Q | 1.049 | 0.85 |
| 105_T | 111_K | 1.047 | 0.85 |
| 379_L | 392_L | 1.045 | 0.84 |
| 43_Q | 46_D | 1.045 | 0.84 |
| 101_T | 108_D | 1.043 | 0.84 |
| 122_S | 126_S | 1.042 | 0.84 |
| 36_I | 43_Q | 1.040 | 0.84 |
| 447_I | 450_T | 1.038 | 0.84 |
| 49_E | 52_L | 1.036 | 0.84 |
| 333_W | 349_F | 1.036 | 0.84 |
| 98_E | 109_G | 1.035 | 0.84 |
| 57_V | 60_C | 1.034 | 0.84 |
| 98_E | 103_I | 1.034 | 0.84 |
| 103_I | 106_V | 1.032 | 0.83 |
| 79_Q | 87_T | 1.031 | 0.83 |
| 39_K | 44_D | 1.031 | 0.83 |
| 97_E | 105_T | 1.027 | 0.83 |
| 123_G | 127_D | 1.025 | 0.83 |
| 66_E | 74_I | 1.025 | 0.83 |
| 67_R | 70_P | 1.022 | 0.83 |
| 101_T | 104_Q | 1.021 | 0.83 |
| 169_E | 172_T | 1.020 | 0.82 |
| 79_Q | 83_V | 1.020 | 0.82 |
| 31_N | 39_K | 1.019 | 0.82 |
| 94_E | 102_A | 1.019 | 0.82 |
| 118_M | 122_S | 1.019 | 0.82 |
| 191_E | 194_H | 1.018 | 0.82 |
| 232_G | 286_G | 1.017 | 0.82 |
| 99_W | 102_A | 1.017 | 0.82 |
| 379_L | 405_H | 1.016 | 0.82 |
| 276_K | 279_N | 1.016 | 0.82 |
| 107_A | 113_Q | 1.016 | 0.82 |
| 70_P | 74_I | 1.015 | 0.82 |
| 51_P | 55_F | 1.015 | 0.82 |
| 383_L | 392_L | 1.014 | 0.82 |
| 61_Q | 65_T | 1.013 | 0.82 |
| 258_V | 335_L | 1.013 | 0.82 |
| 72_T | 75_I | 1.009 | 0.81 |
| 219_T | 224_C | 1.008 | 0.81 |
| 44_D | 52_L | 1.007 | 0.81 |
| 39_K | 45_V | 1.004 | 0.81 |
| 102_A | 105_T | 1.004 | 0.81 |
| 79_Q | 82_T | 1.003 | 0.81 |
| 128_N | 131_A | 1.003 | 0.81 |
| 70_P | 75_I | 1.000 | 0.81 |
| 101_T | 106_V | 1.000 | 0.81 |
| 100_T | 103_I | 1.000 | 0.81 |
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 | |
| 4gv1A | 1 | 0.6854 | 100 | 0.31 | Contact Map |
| 4ejnA | 1 | 0.7833 | 100 | 0.329 | Contact Map |
| 4lqsA | 1 | 0.7312 | 100 | 0.335 | Contact Map |
| 4dc2A | 1 | 0.6729 | 100 | 0.338 | Contact Map |
| 2i0eA | 2 | 0.6729 | 100 | 0.342 | Contact Map |
| 3pfqA | 1 | 0.7375 | 100 | 0.342 | Contact Map |
| 4aw2A | 1 | 0.7854 | 100 | 0.344 | Contact Map |
| 2r5tA | 1 | 0.5896 | 100 | 0.346 | Contact Map |
| 3txoA | 1 | 0.6562 | 100 | 0.347 | Contact Map |
| 1xjdA | 1 | 0.5792 | 100 | 0.35 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)