| T0814 -force run |
| ID: | 1402513489 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 424 (398) | ||
| Sequences: | 140 (127.3) | ||
| Seq/Len: | 0.352 | ||
| Nf(neff/√len): | 6.4 |
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: 0.352).
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 |
| 348_N | 355_E | 5.421 | 1.00 |
| 82_N | 86_T | 2.768 | 0.97 |
| 277_D | 369_Y | 2.758 | 0.97 |
| 186_F | 397_I | 2.708 | 0.96 |
| 160_E | 410_R | 2.488 | 0.93 |
| 402_R | 409_D | 2.406 | 0.92 |
| 167_A | 397_I | 2.335 | 0.90 |
| 195_I | 202_L | 2.215 | 0.86 |
| 134_S | 160_E | 1.791 | 0.66 |
| 141_V | 152_F | 1.779 | 0.65 |
| 141_V | 224_I | 1.766 | 0.64 |
| 188_I | 399_V | 1.763 | 0.64 |
| 280_R | 385_E | 1.734 | 0.62 |
| 82_N | 408_Y | 1.670 | 0.58 |
| 40_V | 62_I | 1.651 | 0.56 |
| 327_S | 344_K | 1.634 | 0.55 |
| 360_L | 365_Y | 1.618 | 0.54 |
| 74_Y | 151_I | 1.599 | 0.53 |
| 244_E | 290_D | 1.591 | 0.52 |
| 131_F | 252_S | 1.569 | 0.51 |
| 252_S | 310_D | 1.566 | 0.51 |
| 157_S | 411_L | 1.564 | 0.50 |
| 87_Q | 398_Y | 1.506 | 0.46 |
| 84_D | 88_S | 1.483 | 0.45 |
| 329_Y | 343_S | 1.472 | 0.44 |
| 257_G | 375_G | 1.467 | 0.44 |
| 40_V | 154_A | 1.449 | 0.42 |
| 92_P | 100_Q | 1.447 | 0.42 |
| 66_G | 74_Y | 1.426 | 0.41 |
| 141_V | 401_Y | 1.418 | 0.40 |
| 38_L | 251_L | 1.408 | 0.40 |
| 345_M | 356_K | 1.400 | 0.39 |
| 76_Y | 98_G | 1.395 | 0.39 |
| 181_H | 387_N | 1.387 | 0.38 |
| 37_T | 70_G | 1.386 | 0.38 |
| 130_Q | 345_M | 1.380 | 0.38 |
| 78_V | 86_T | 1.380 | 0.38 |
| 167_A | 186_F | 1.376 | 0.37 |
| 396_S | 414_V | 1.376 | 0.37 |
| 206_V | 237_L | 1.349 | 0.36 |
| 290_D | 392_Q | 1.343 | 0.35 |
| 244_E | 392_Q | 1.341 | 0.35 |
| 151_I | 165_I | 1.323 | 0.34 |
| 315_H | 365_Y | 1.319 | 0.34 |
| 94_E | 407_R | 1.316 | 0.34 |
| 40_V | 60_I | 1.304 | 0.33 |
| 62_I | 154_A | 1.302 | 0.33 |
| 122_L | 139_I | 1.299 | 0.33 |
| 90_L | 260_V | 1.297 | 0.32 |
| 141_V | 411_L | 1.295 | 0.32 |
| 23_Q | 398_Y | 1.292 | 0.32 |
| 88_S | 198_P | 1.292 | 0.32 |
| 328_V | 358_V | 1.291 | 0.32 |
| 28_T | 251_L | 1.289 | 0.32 |
| 141_V | 153_T | 1.275 | 0.31 |
| 219_L | 237_L | 1.273 | 0.31 |
| 207_Y | 212_R | 1.264 | 0.30 |
| 40_V | 249_E | 1.254 | 0.30 |
| 66_G | 212_R | 1.252 | 0.30 |
| 119_N | 354_Y | 1.243 | 0.29 |
| 97_N | 130_Q | 1.240 | 0.29 |
| 335_F | 343_S | 1.240 | 0.29 |
| 330_L | 358_V | 1.240 | 0.29 |
| 211_R | 214_N | 1.236 | 0.29 |
| 54_L | 367_Y | 1.236 | 0.29 |
| 95_Y | 158_V | 1.231 | 0.29 |
| 171_G | 251_L | 1.230 | 0.28 |
| 134_S | 345_M | 1.224 | 0.28 |
| 88_S | 156_F | 1.209 | 0.27 |
| 287_Y | 315_H | 1.208 | 0.27 |
| 246_R | 385_E | 1.206 | 0.27 |
| 280_R | 369_Y | 1.204 | 0.27 |
| 166_S | 411_L | 1.202 | 0.27 |
| 193_F | 401_Y | 1.200 | 0.27 |
| 36_K | 74_Y | 1.200 | 0.27 |
| 80_H | 88_S | 1.194 | 0.26 |
| 169_V | 342_K | 1.193 | 0.26 |
| 94_E | 343_S | 1.193 | 0.26 |
| 37_T | 187_N | 1.191 | 0.26 |
| 160_E | 354_Y | 1.179 | 0.26 |
| 158_V | 280_R | 1.175 | 0.25 |
| 241_A | 358_V | 1.168 | 0.25 |
| 195_I | 201_D | 1.167 | 0.25 |
| 326_G | 375_G | 1.167 | 0.25 |
| 82_N | 409_D | 1.164 | 0.25 |
| 208_Q | 241_A | 1.157 | 0.24 |
| 58_E | 274_L | 1.152 | 0.24 |
| 55_G | 166_S | 1.151 | 0.24 |
| 203_K | 402_R | 1.151 | 0.24 |
| 76_Y | 126_N | 1.150 | 0.24 |
| 38_L | 245_Y | 1.143 | 0.24 |
| 249_E | 370_L | 1.141 | 0.24 |
| 348_N | 351_T | 1.139 | 0.24 |
| 115_T | 197_Y | 1.136 | 0.23 |
| 119_N | 193_F | 1.135 | 0.23 |
| 69_S | 201_D | 1.135 | 0.23 |
| 157_S | 407_R | 1.133 | 0.23 |
| 82_N | 94_E | 1.132 | 0.23 |
| 119_N | 407_R | 1.131 | 0.23 |
| 124_L | 191_K | 1.128 | 0.23 |
| 51_Y | 56_G | 1.128 | 0.23 |
| 133_V | 310_D | 1.128 | 0.23 |
| 81_C | 329_Y | 1.127 | 0.23 |
| 365_Y | 405_G | 1.127 | 0.23 |
| 263_I | 304_D | 1.123 | 0.23 |
| 112_G | 345_M | 1.121 | 0.23 |
| 183_Q | 238_I | 1.120 | 0.23 |
| 157_S | 212_R | 1.117 | 0.22 |
| 229_I | 242_G | 1.117 | 0.22 |
| 107_F | 203_K | 1.115 | 0.22 |
| 318_L | 384_I | 1.111 | 0.22 |
| 398_Y | 406_A | 1.110 | 0.22 |
| 206_V | 378_V | 1.108 | 0.22 |
| 119_N | 341_E | 1.106 | 0.22 |
| 62_I | 249_E | 1.103 | 0.22 |
| 143_N | 149_Q | 1.102 | 0.22 |
| 310_D | 403_P | 1.102 | 0.22 |
| 35_I | 344_K | 1.095 | 0.21 |
| 260_V | 274_L | 1.095 | 0.21 |
| 38_L | 62_I | 1.094 | 0.21 |
| 98_G | 126_N | 1.092 | 0.21 |
| 169_V | 388_Y | 1.084 | 0.21 |
| 31_N | 310_D | 1.082 | 0.21 |
| 212_R | 215_A | 1.082 | 0.21 |
| 285_Y | 365_Y | 1.080 | 0.21 |
| 96_M | 202_L | 1.080 | 0.21 |
| 215_A | 401_Y | 1.076 | 0.21 |
| 41_K | 249_E | 1.076 | 0.21 |
| 119_N | 160_E | 1.075 | 0.20 |
| 102_T | 163_V | 1.074 | 0.20 |
| 34_Q | 359_L | 1.072 | 0.20 |
| 329_Y | 358_V | 1.072 | 0.20 |
| 155_C | 249_E | 1.072 | 0.20 |
| 227_N | 366_N | 1.070 | 0.20 |
| 35_I | 104_I | 1.069 | 0.20 |
| 143_N | 257_G | 1.067 | 0.20 |
| 171_G | 178_N | 1.067 | 0.20 |
| 136_N | 395_Y | 1.061 | 0.20 |
| 127_D | 380_Q | 1.060 | 0.20 |
| 100_Q | 246_R | 1.059 | 0.20 |
| 115_T | 359_L | 1.057 | 0.20 |
| 132_K | 409_D | 1.056 | 0.20 |
| 79_V | 257_G | 1.053 | 0.19 |
| 104_I | 295_F | 1.053 | 0.19 |
| 104_I | 118_S | 1.052 | 0.19 |
| 21_N | 77_N | 1.051 | 0.19 |
| 90_L | 116_Q | 1.051 | 0.19 |
| 206_V | 348_N | 1.051 | 0.19 |
| 116_Q | 204_I | 1.048 | 0.19 |
| 168_S | 185_S | 1.047 | 0.19 |
| 100_Q | 131_F | 1.045 | 0.19 |
| 101_G | 133_V | 1.045 | 0.19 |
| 80_H | 113_T | 1.040 | 0.19 |
| 63_N | 118_S | 1.040 | 0.19 |
| 163_V | 193_F | 1.040 | 0.19 |
| 35_I | 115_T | 1.037 | 0.19 |
| 121_R | 387_N | 1.037 | 0.19 |
| 141_V | 148_D | 1.036 | 0.19 |
| 244_E | 413_G | 1.035 | 0.19 |
| 213_D | 375_G | 1.030 | 0.18 |
| 115_T | 415_T | 1.028 | 0.18 |
| 157_S | 398_Y | 1.028 | 0.18 |
| 250_F | 312_Y | 1.026 | 0.18 |
| 78_V | 314_V | 1.025 | 0.18 |
| 118_S | 396_S | 1.023 | 0.18 |
| 360_L | 405_G | 1.021 | 0.18 |
| 82_N | 97_N | 1.017 | 0.18 |
| 117_Y | 213_D | 1.017 | 0.18 |
| 403_P | 410_R | 1.015 | 0.18 |
| 229_I | 273_E | 1.014 | 0.18 |
| 82_N | 401_Y | 1.014 | 0.18 |
| 196_T | 245_Y | 1.013 | 0.18 |
| 118_S | 339_L | 1.011 | 0.18 |
| 54_L | 84_D | 1.010 | 0.18 |
| 38_L | 93_I | 1.009 | 0.18 |
| 78_V | 230_S | 1.008 | 0.18 |
| 74_Y | 388_Y | 1.007 | 0.18 |
| 126_N | 231_Y | 1.006 | 0.17 |
| 52_I | 340_D | 1.004 | 0.17 |
| 213_D | 399_V | 1.004 | 0.17 |
| 37_T | 54_L | 1.002 | 0.17 |
| 198_P | 260_V | 1.002 | 0.17 |
| 165_I | 224_I | 1.001 | 0.17 |
| 304_D | 380_Q | 1.001 | 0.17 |
| 176_D | 181_H | 1.000 | 0.17 |
| 251_L | 364_S | 1.000 | 0.17 |
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 | |
| 4r7fA | 1 | 0.934 | 100 | 0.078 | Contact Map |
| 4aeeA | 2 | 0.2925 | 96.4 | 0.959 | Contact Map |
| 1z0nA | 3 | 0.2028 | 95.6 | 0.961 | Contact Map |
| 2qlvB | 2 | 0.2005 | 95.4 | 0.962 | Contact Map |
| 2lu3A | 1 | 0.2406 | 95.1 | 0.963 | Contact Map |
| 4aefA | 2 | 0.2807 | 94.1 | 0.965 | Contact Map |
| 1ac0A | 1 | 0.2382 | 92.6 | 0.967 | Contact Map |
| 4cfeB | 2 | 0.2193 | 90.8 | 0.968 | Contact Map |
| 2z0bA | 6 | 0.2618 | 78.4 | 0.973 | Contact Map |
| 4rkkA | 2 | 0.2665 | 63.4 | 0.976 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)