| F r3 -end -force run |
| ID: | 1516357929 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 404 (402) | ||
| Sequences: | 398 (248.7) | ||
| Seq/Len: | 0.990 | ||
| Nf(neff/√len): | 12.4 |
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: 0.990).
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 |
| 228_V | 263_W | 3.149 | 1.00 |
| 116_R | 146_D | 2.884 | 1.00 |
| 291_E | 308_K | 2.724 | 1.00 |
| 265_I | 290_L | 2.320 | 0.99 |
| 269_L | 284_V | 2.150 | 0.97 |
| 106_F | 154_G | 2.149 | 0.97 |
| 225_S | 268_G | 2.130 | 0.97 |
| 165_D | 207_G | 1.978 | 0.95 |
| 212_F | 224_V | 1.978 | 0.95 |
| 12_L | 16_Q | 1.846 | 0.92 |
| 31_R | 36_E | 1.843 | 0.92 |
| 111_G | 151_D | 1.769 | 0.90 |
| 76_Y | 80_L | 1.767 | 0.90 |
| 381_P | 398_L | 1.690 | 0.87 |
| 14_L | 28_L | 1.676 | 0.86 |
| 321_V | 331_M | 1.596 | 0.82 |
| 280_L | 369_M | 1.561 | 0.80 |
| 383_L | 396_F | 1.552 | 0.80 |
| 365_F | 385_I | 1.529 | 0.78 |
| 335_V | 394_F | 1.510 | 0.77 |
| 112_I | 148_W | 1.499 | 0.76 |
| 220_P | 324_A | 1.487 | 0.76 |
| 166_V | 204_V | 1.478 | 0.75 |
| 39_P | 44_P | 1.472 | 0.75 |
| 335_V | 363_G | 1.467 | 0.74 |
| 77_G | 80_L | 1.466 | 0.74 |
| 213_L | 222_A | 1.464 | 0.74 |
| 355_I | 358_S | 1.446 | 0.73 |
| 334_S | 366_N | 1.434 | 0.72 |
| 337_D | 361_N | 1.416 | 0.70 |
| 229_K | 260_N | 1.412 | 0.70 |
| 24_A | 29_E | 1.391 | 0.68 |
| 11_L | 32_V | 1.391 | 0.68 |
| 389_D | 393_D | 1.369 | 0.67 |
| 61_V | 66_G | 1.369 | 0.67 |
| 318_G | 324_A | 1.363 | 0.66 |
| 116_R | 124_L | 1.360 | 0.66 |
| 13_E | 16_Q | 1.344 | 0.65 |
| 5_E | 24_A | 1.329 | 0.63 |
| 158_L | 208_I | 1.328 | 0.63 |
| 216_S | 219_M | 1.322 | 0.63 |
| 22_Q | 26_A | 1.317 | 0.62 |
| 235_E | 238_G | 1.316 | 0.62 |
| 29_E | 38_Q | 1.315 | 0.62 |
| 108_F | 154_G | 1.313 | 0.62 |
| 285_S | 316_Q | 1.313 | 0.62 |
| 124_L | 128_L | 1.308 | 0.61 |
| 283_S | 318_G | 1.307 | 0.61 |
| 264_S | 287_T | 1.306 | 0.61 |
| 175_S | 283_S | 1.302 | 0.61 |
| 367_V | 383_L | 1.293 | 0.60 |
| 54_F | 57_S | 1.288 | 0.60 |
| 217_A | 220_P | 1.279 | 0.59 |
| 168_V | 350_G | 1.277 | 0.59 |
| 120_R | 142_R | 1.277 | 0.59 |
| 230_A | 263_W | 1.277 | 0.59 |
| 9_Q | 13_E | 1.270 | 0.58 |
| 93_L | 268_G | 1.265 | 0.58 |
| 128_L | 131_D | 1.265 | 0.58 |
| 129_A | 134_F | 1.255 | 0.57 |
| 387_M | 394_F | 1.252 | 0.56 |
| 93_L | 207_G | 1.251 | 0.56 |
| 115_A | 299_S | 1.243 | 0.56 |
| 29_E | 33_R | 1.242 | 0.56 |
| 67_T | 70_A | 1.236 | 0.55 |
| 6_T | 25_L | 1.234 | 0.55 |
| 124_L | 253_P | 1.223 | 0.54 |
| 99_G | 107_S | 1.222 | 0.54 |
| 53_D | 56_Q | 1.221 | 0.54 |
| 45_K | 50_S | 1.220 | 0.54 |
| 4_I | 12_L | 1.218 | 0.53 |
| 131_D | 322_A | 1.216 | 0.53 |
| 280_L | 329_M | 1.214 | 0.53 |
| 108_F | 201_I | 1.210 | 0.53 |
| 28_L | 31_R | 1.205 | 0.52 |
| 158_L | 206_F | 1.205 | 0.52 |
| 231_P | 235_E | 1.202 | 0.52 |
| 46_R | 65_S | 1.200 | 0.52 |
| 231_P | 263_W | 1.199 | 0.52 |
| 158_L | 164_F | 1.194 | 0.51 |
| 286_Y | 313_D | 1.194 | 0.51 |
| 41_T | 45_K | 1.193 | 0.51 |
| 41_T | 58_G | 1.192 | 0.51 |
| 379_I | 400_F | 1.185 | 0.50 |
| 110_T | 170_V | 1.184 | 0.50 |
| 363_G | 387_M | 1.176 | 0.49 |
| 142_R | 174_E | 1.173 | 0.49 |
| 146_D | 201_I | 1.171 | 0.49 |
| 300_D | 387_M | 1.164 | 0.48 |
| 45_K | 49_K | 1.164 | 0.48 |
| 19_E | 33_R | 1.163 | 0.48 |
| 201_I | 204_V | 1.163 | 0.48 |
| 83_D | 86_P | 1.161 | 0.48 |
| 79_S | 90_V | 1.159 | 0.48 |
| 162_W | 210_Y | 1.157 | 0.48 |
| 373_A | 379_I | 1.151 | 0.47 |
| 49_K | 61_V | 1.146 | 0.47 |
| 95_N | 394_F | 1.142 | 0.46 |
| 49_K | 53_D | 1.140 | 0.46 |
| 273_K | 387_M | 1.139 | 0.46 |
| 241_L | 247_N | 1.135 | 0.46 |
| 275_F | 280_L | 1.130 | 0.45 |
| 208_I | 264_S | 1.128 | 0.45 |
| 127_F | 209_A | 1.127 | 0.45 |
| 45_K | 52_A | 1.127 | 0.45 |
| 55_K | 59_S | 1.126 | 0.45 |
| 10_E | 15_K | 1.126 | 0.45 |
| 161_R | 258_T | 1.124 | 0.45 |
| 53_D | 63_A | 1.124 | 0.45 |
| 124_L | 358_S | 1.123 | 0.45 |
| 102_G | 262_V | 1.120 | 0.44 |
| 22_Q | 27_V | 1.117 | 0.44 |
| 24_A | 27_V | 1.116 | 0.44 |
| 370_T | 373_A | 1.116 | 0.44 |
| 163_Q | 272_V | 1.114 | 0.44 |
| 107_S | 270_S | 1.113 | 0.44 |
| 43_A | 46_R | 1.111 | 0.43 |
| 5_E | 278_A | 1.110 | 0.43 |
| 160_N | 221_D | 1.100 | 0.42 |
| 253_P | 358_S | 1.098 | 0.42 |
| 63_A | 67_T | 1.096 | 0.42 |
| 278_A | 338_L | 1.095 | 0.42 |
| 25_L | 30_Q | 1.095 | 0.42 |
| 311_L | 319_V | 1.094 | 0.42 |
| 30_Q | 34_Q | 1.093 | 0.42 |
| 228_V | 265_I | 1.091 | 0.42 |
| 215_E | 274_T | 1.089 | 0.41 |
| 74_S | 201_I | 1.088 | 0.41 |
| 16_Q | 28_L | 1.086 | 0.41 |
| 128_L | 134_F | 1.086 | 0.41 |
| 223_V | 228_V | 1.084 | 0.41 |
| 6_T | 19_E | 1.083 | 0.41 |
| 48_A | 56_Q | 1.080 | 0.41 |
| 224_V | 267_P | 1.077 | 0.40 |
| 61_V | 69_G | 1.075 | 0.40 |
| 364_Y | 384_A | 1.070 | 0.40 |
| 11_L | 162_W | 1.068 | 0.40 |
| 47_L | 51_P | 1.067 | 0.40 |
| 234_K | 345_L | 1.067 | 0.40 |
| 50_S | 54_F | 1.065 | 0.39 |
| 365_F | 383_L | 1.065 | 0.39 |
| 64_S | 201_I | 1.064 | 0.39 |
| 20_A | 23_K | 1.063 | 0.39 |
| 115_A | 321_V | 1.063 | 0.39 |
| 95_N | 175_S | 1.061 | 0.39 |
| 284_V | 315_F | 1.061 | 0.39 |
| 329_M | 391_A | 1.060 | 0.39 |
| 27_V | 162_W | 1.059 | 0.39 |
| 58_G | 62_A | 1.058 | 0.39 |
| 204_V | 290_L | 1.055 | 0.38 |
| 47_L | 52_A | 1.054 | 0.38 |
| 132_S | 379_I | 1.053 | 0.38 |
| 45_K | 48_A | 1.049 | 0.38 |
| 237_F | 282_G | 1.049 | 0.38 |
| 48_A | 61_V | 1.049 | 0.38 |
| 4_I | 8_K | 1.049 | 0.38 |
| 363_G | 400_F | 1.047 | 0.38 |
| 165_D | 227_R | 1.043 | 0.37 |
| 101_F | 274_T | 1.042 | 0.37 |
| 38_Q | 212_F | 1.042 | 0.37 |
| 26_A | 30_Q | 1.042 | 0.37 |
| 237_F | 323_F | 1.041 | 0.37 |
| 31_R | 35_V | 1.039 | 0.37 |
| 377_L | 400_F | 1.039 | 0.37 |
| 235_E | 370_T | 1.038 | 0.37 |
| 46_R | 50_S | 1.038 | 0.37 |
| 168_V | 204_V | 1.038 | 0.37 |
| 51_P | 64_S | 1.037 | 0.37 |
| 104_G | 264_S | 1.035 | 0.37 |
| 319_V | 369_M | 1.035 | 0.37 |
| 163_Q | 340_Q | 1.032 | 0.36 |
| 8_K | 19_E | 1.031 | 0.36 |
| 52_A | 56_Q | 1.029 | 0.36 |
| 10_E | 34_Q | 1.027 | 0.36 |
| 76_Y | 79_S | 1.026 | 0.36 |
| 130_L | 372_A | 1.026 | 0.36 |
| 52_A | 68_G | 1.025 | 0.36 |
| 48_A | 54_F | 1.024 | 0.36 |
| 8_K | 13_E | 1.024 | 0.36 |
| 9_Q | 43_A | 1.024 | 0.36 |
| 89_S | 237_F | 1.024 | 0.36 |
| 150_L | 283_S | 1.020 | 0.35 |
| 207_G | 268_G | 1.019 | 0.35 |
| 220_P | 286_Y | 1.019 | 0.35 |
| 27_V | 33_R | 1.017 | 0.35 |
| 109_E | 136_G | 1.015 | 0.35 |
| 120_R | 173_R | 1.012 | 0.35 |
| 182_A | 192_E | 1.012 | 0.35 |
| 10_E | 28_L | 1.012 | 0.35 |
| 91_S | 282_G | 1.010 | 0.35 |
| 388_T | 393_D | 1.009 | 0.35 |
| 145_A | 175_S | 1.008 | 0.34 |
| 313_D | 375_E | 1.008 | 0.34 |
| 127_F | 134_F | 1.006 | 0.34 |
| 148_W | 158_L | 1.005 | 0.34 |
| 40_A | 64_S | 1.005 | 0.34 |
| 131_D | 135_L | 1.004 | 0.34 |
| 59_S | 62_A | 1.004 | 0.34 |
| 71_T | 162_W | 1.003 | 0.34 |
| 93_L | 97_A | 1.000 | 0.34 |
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 | |
| 4rl8A | 4 | 0 | 99.9 | 0.796 | Contact Map |
| 3pguA | 1 | 0.8218 | 93.1 | 0.956 | Contact Map |
| 2x27X | 1 | 0.4851 | 90.7 | 0.959 | Contact Map |
| 2yy0A | 4 | 0.0891 | 89.8 | 0.96 | Contact Map |
| 1ormA | 1 | 0.3564 | 89.3 | 0.96 | Contact Map |
| 3iynQ | 4 | 0.1188 | 88.6 | 0.961 | Contact Map |
| 1qjpA | 1 | 0.3391 | 88.4 | 0.961 | Contact Map |
| 3kvnX | 2 | 0.7599 | 88.3 | 0.961 | Contact Map |
| 3qraA | 1 | 0.3465 | 87.4 | 0.961 | Contact Map |
| 2f1vA | 6 | 0.4455 | 86.9 | 0.962 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)