| gtusc_one |
| ID: | 1440012501 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 446 (431) | ||
| Sequences: | 1496 (824.1) | ||
| Seq/Len: | 3.471 | ||
| Nf(neff/√len): | 39.7 |
HHblits Results: (2015_06)
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: 3.471).
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 |
| 12_Q | 16_H | 3.253 | 1.00 |
| 72_E | 75_V | 2.897 | 1.00 |
| 395_D | 427_R | 2.840 | 1.00 |
| 6_I | 127_I | 2.835 | 1.00 |
| 9_Q | 15_N | 2.682 | 1.00 |
| 20_F | 23_S | 2.422 | 1.00 |
| 239_T | 243_R | 2.388 | 1.00 |
| 188_I | 430_V | 2.360 | 1.00 |
| 11_G | 14_G | 2.131 | 1.00 |
| 295_M | 322_I | 2.092 | 1.00 |
| 9_Q | 18_G | 2.079 | 1.00 |
| 345_P | 349_S | 2.034 | 1.00 |
| 413_F | 421_D | 1.996 | 1.00 |
| 344_F | 347_W | 1.976 | 1.00 |
| 346_S | 349_S | 1.973 | 1.00 |
| 124_D | 161_R | 1.966 | 1.00 |
| 4_E | 11_G | 1.963 | 1.00 |
| 67_I | 122_K | 1.863 | 0.99 |
| 394_F | 398_F | 1.809 | 0.99 |
| 119_I | 150_L | 1.794 | 0.99 |
| 398_F | 424_A | 1.781 | 0.99 |
| 127_I | 133_F | 1.774 | 0.99 |
| 428_E | 432_S | 1.768 | 0.99 |
| 169_T | 198_S | 1.737 | 0.99 |
| 91_N | 126_E | 1.728 | 0.99 |
| 345_P | 351_A | 1.698 | 0.99 |
| 211_N | 215_K | 1.698 | 0.99 |
| 344_F | 349_S | 1.692 | 0.99 |
| 189_L | 426_S | 1.662 | 0.99 |
| 347_W | 351_A | 1.622 | 0.98 |
| 427_R | 431_Q | 1.605 | 0.98 |
| 435_E | 438_V | 1.603 | 0.98 |
| 26_A | 31_I | 1.602 | 0.98 |
| 29_H | 35_G | 1.598 | 0.98 |
| 6_I | 11_G | 1.565 | 0.98 |
| 217_F | 222_I | 1.553 | 0.97 |
| 18_G | 22_W | 1.545 | 0.97 |
| 13_C | 172_V | 1.540 | 0.97 |
| 345_P | 348_S | 1.530 | 0.97 |
| 252_M | 354_V | 1.528 | 0.97 |
| 144_G | 147_G | 1.526 | 0.97 |
| 344_F | 351_A | 1.503 | 0.97 |
| 209_L | 231_I | 1.495 | 0.97 |
| 136_F | 158_L | 1.494 | 0.97 |
| 136_F | 162_Y | 1.485 | 0.96 |
| 289_H | 293_D | 1.468 | 0.96 |
| 406_N | 409_V | 1.452 | 0.96 |
| 194_L | 387_F | 1.446 | 0.96 |
| 47_D | 50_T | 1.445 | 0.96 |
| 206_N | 228_N | 1.440 | 0.96 |
| 335_M | 354_V | 1.432 | 0.95 |
| 103_N | 108_G | 1.432 | 0.95 |
| 331_I | 338_L | 1.422 | 0.95 |
| 26_A | 54_F | 1.419 | 0.95 |
| 398_F | 401_G | 1.415 | 0.95 |
| 401_G | 408_N | 1.412 | 0.95 |
| 431_Q | 435_E | 1.410 | 0.95 |
| 140_H | 169_T | 1.410 | 0.95 |
| 249_Y | 258_T | 1.405 | 0.95 |
| 78_D | 82_T | 1.397 | 0.95 |
| 4_E | 9_Q | 1.390 | 0.94 |
| 93_W | 122_K | 1.377 | 0.94 |
| 142_V | 190_A | 1.375 | 0.94 |
| 242_I | 252_M | 1.366 | 0.94 |
| 404_L | 408_N | 1.364 | 0.94 |
| 348_S | 351_A | 1.364 | 0.94 |
| 64_P | 71_S | 1.357 | 0.93 |
| 37_S | 41_D | 1.353 | 0.93 |
| 420_Q | 423_F | 1.352 | 0.93 |
| 194_L | 200_A | 1.350 | 0.93 |
| 8_L | 11_G | 1.350 | 0.93 |
| 105_W | 108_G | 1.349 | 0.93 |
| 124_D | 128_D | 1.342 | 0.93 |
| 140_H | 171_S | 1.339 | 0.93 |
| 31_I | 35_G | 1.337 | 0.93 |
| 185_Y | 206_N | 1.320 | 0.92 |
| 345_P | 350_S | 1.318 | 0.92 |
| 187_T | 390_A | 1.313 | 0.92 |
| 104_S | 108_G | 1.311 | 0.92 |
| 155_L | 169_T | 1.309 | 0.92 |
| 159_C | 199_D | 1.309 | 0.92 |
| 142_V | 187_T | 1.302 | 0.91 |
| 76_I | 94_V | 1.298 | 0.91 |
| 173_F | 191_L | 1.286 | 0.91 |
| 88_D | 91_N | 1.283 | 0.91 |
| 159_C | 167_L | 1.280 | 0.90 |
| 133_F | 136_F | 1.278 | 0.90 |
| 346_S | 351_A | 1.278 | 0.90 |
| 41_D | 44_T | 1.273 | 0.90 |
| 194_L | 268_L | 1.273 | 0.90 |
| 124_D | 162_Y | 1.270 | 0.90 |
| 152_S | 156_E | 1.267 | 0.90 |
| 411_D | 420_Q | 1.265 | 0.90 |
| 138_L | 155_L | 1.261 | 0.90 |
| 347_W | 350_S | 1.256 | 0.89 |
| 406_N | 410_G | 1.255 | 0.89 |
| 14_G | 144_G | 1.247 | 0.89 |
| 144_G | 228_N | 1.238 | 0.88 |
| 401_G | 420_Q | 1.234 | 0.88 |
| 395_D | 431_Q | 1.231 | 0.88 |
| 14_G | 17_V | 1.230 | 0.88 |
| 128_D | 131_D | 1.229 | 0.88 |
| 142_V | 169_T | 1.228 | 0.88 |
| 436_D | 439_A | 1.226 | 0.88 |
| 28_E | 31_I | 1.222 | 0.88 |
| 142_V | 194_L | 1.216 | 0.87 |
| 33_T | 83_F | 1.206 | 0.87 |
| 13_C | 16_H | 1.205 | 0.87 |
| 344_F | 348_S | 1.200 | 0.86 |
| 388_E | 392_N | 1.190 | 0.86 |
| 11_G | 18_G | 1.190 | 0.86 |
| 433_L | 437_Y | 1.189 | 0.86 |
| 127_I | 162_Y | 1.189 | 0.86 |
| 241_S | 355_N | 1.187 | 0.85 |
| 102_G | 105_W | 1.187 | 0.85 |
| 121_N | 124_D | 1.187 | 0.85 |
| 407_Y | 423_F | 1.185 | 0.85 |
| 139_L | 235_I | 1.184 | 0.85 |
| 322_I | 335_M | 1.181 | 0.85 |
| 214_G | 275_F | 1.175 | 0.85 |
| 306_V | 354_V | 1.172 | 0.84 |
| 11_G | 15_N | 1.172 | 0.84 |
| 148_S | 172_V | 1.171 | 0.84 |
| 9_Q | 22_W | 1.164 | 0.84 |
| 408_N | 420_Q | 1.163 | 0.84 |
| 186_N | 206_N | 1.163 | 0.84 |
| 138_L | 169_T | 1.162 | 0.84 |
| 5_I | 9_Q | 1.161 | 0.84 |
| 237_S | 375_M | 1.161 | 0.84 |
| 11_G | 22_W | 1.159 | 0.84 |
| 361_P | 373_S | 1.157 | 0.83 |
| 321_T | 354_V | 1.150 | 0.83 |
| 263_P | 266_H | 1.143 | 0.82 |
| 50_T | 56_E | 1.143 | 0.82 |
| 173_F | 203_V | 1.140 | 0.82 |
| 38_Q | 42_S | 1.139 | 0.82 |
| 77_A | 80_E | 1.139 | 0.82 |
| 412_L | 422_E | 1.138 | 0.82 |
| 62_F | 361_P | 1.137 | 0.82 |
| 76_I | 79_V | 1.135 | 0.82 |
| 194_L | 204_F | 1.134 | 0.82 |
| 142_V | 171_S | 1.130 | 0.81 |
| 342_I | 346_S | 1.127 | 0.81 |
| 144_G | 206_N | 1.127 | 0.81 |
| 15_N | 21_L | 1.125 | 0.81 |
| 428_E | 431_Q | 1.120 | 0.81 |
| 270_P | 377_L | 1.119 | 0.80 |
| 15_N | 18_G | 1.118 | 0.80 |
| 72_E | 108_G | 1.117 | 0.80 |
| 13_C | 68_M | 1.111 | 0.80 |
| 21_L | 235_I | 1.111 | 0.80 |
| 225_Q | 229_Q | 1.109 | 0.80 |
| 212_I | 305_L | 1.109 | 0.80 |
| 151_G | 194_L | 1.109 | 0.80 |
| 391_C | 395_D | 1.103 | 0.79 |
| 141_S | 144_G | 1.100 | 0.79 |
| 32_G | 215_K | 1.098 | 0.79 |
| 28_E | 35_G | 1.098 | 0.79 |
| 123_I | 158_L | 1.096 | 0.79 |
| 258_T | 262_S | 1.095 | 0.78 |
| 384_V | 438_V | 1.094 | 0.78 |
| 68_M | 76_I | 1.094 | 0.78 |
| 152_S | 193_R | 1.089 | 0.78 |
| 304_S | 387_F | 1.086 | 0.78 |
| 172_V | 198_S | 1.082 | 0.77 |
| 279_Y | 285_A | 1.081 | 0.77 |
| 146_T | 149_G | 1.080 | 0.77 |
| 38_Q | 41_D | 1.078 | 0.77 |
| 157_A | 160_D | 1.078 | 0.77 |
| 9_Q | 68_M | 1.076 | 0.77 |
| 420_Q | 424_A | 1.075 | 0.77 |
| 193_R | 204_F | 1.072 | 0.76 |
| 91_N | 317_N | 1.070 | 0.76 |
| 239_T | 244_F | 1.068 | 0.76 |
| 181_V | 184_S | 1.068 | 0.76 |
| 26_A | 29_H | 1.067 | 0.76 |
| 22_W | 28_E | 1.066 | 0.76 |
| 219_N | 222_I | 1.065 | 0.76 |
| 268_L | 387_F | 1.060 | 0.75 |
| 66_A | 91_N | 1.059 | 0.75 |
| 50_T | 128_D | 1.059 | 0.75 |
| 401_G | 405_N | 1.059 | 0.75 |
| 170_Y | 235_I | 1.058 | 0.75 |
| 413_F | 425_E | 1.052 | 0.74 |
| 6_I | 67_I | 1.050 | 0.74 |
| 428_E | 436_D | 1.049 | 0.74 |
| 113_T | 157_A | 1.049 | 0.74 |
| 100_S | 105_W | 1.048 | 0.74 |
| 13_C | 20_F | 1.047 | 0.74 |
| 401_G | 404_L | 1.046 | 0.74 |
| 116_Q | 153_N | 1.045 | 0.74 |
| 81_N | 84_R | 1.042 | 0.73 |
| 298_L | 374_G | 1.041 | 0.73 |
| 258_T | 263_P | 1.040 | 0.73 |
| 405_N | 411_D | 1.037 | 0.73 |
| 192_R | 429_V | 1.036 | 0.73 |
| 5_I | 11_G | 1.035 | 0.73 |
| 105_W | 204_F | 1.034 | 0.73 |
| 427_R | 434_M | 1.031 | 0.72 |
| 207_A | 210_L | 1.030 | 0.72 |
| 200_A | 268_L | 1.029 | 0.72 |
| 186_N | 189_L | 1.028 | 0.72 |
| 159_C | 197_D | 1.023 | 0.72 |
| 213_S | 217_F | 1.022 | 0.71 |
| 425_E | 437_Y | 1.022 | 0.71 |
| 100_S | 151_G | 1.019 | 0.71 |
| 51_K | 62_F | 1.018 | 0.71 |
| 402_A | 405_N | 1.018 | 0.71 |
| 244_F | 249_Y | 1.017 | 0.71 |
| 407_Y | 411_D | 1.016 | 0.71 |
| 428_E | 434_M | 1.014 | 0.71 |
| 4_E | 134_E | 1.014 | 0.71 |
| 147_G | 369_E | 1.011 | 0.70 |
| 185_Y | 228_N | 1.010 | 0.70 |
| 42_S | 45_E | 1.006 | 0.70 |
| 321_T | 386_V | 1.006 | 0.70 |
| 19_K | 23_S | 1.003 | 0.69 |
| 77_A | 82_T | 1.003 | 0.69 |
| 440_A | 443_D | 1.001 | 0.69 |
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 | |
| 4i4tA | 2 | 0.9686 | 100 | 0.099 | Contact Map |
| 4i4tB | 2 | 0.9552 | 100 | 0.099 | Contact Map |
| 3cb2A | 2 | 0.9462 | 100 | 0.099 | Contact Map |
| 2btoA | 2 | 0.9462 | 100 | 0.118 | Contact Map |
| 2btqB | 1 | 0.8677 | 100 | 0.121 | Contact Map |
| 3zidA | 2 | 0.796 | 100 | 0.416 | Contact Map |
| 3v3tA | 1 | 0.657 | 100 | 0.545 | Contact Map |
| 4b46A | 1 | 0.722 | 100 | 0.571 | Contact Map |
| 4b45A | 1 | 0.7332 | 100 | 0.58 | Contact Map |
| 3j4sA | 1 | 0.796 | 100 | 0.595 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)