| T0899 65-423 -force run |
| ID: | 1464736338 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 359 (339) | ||
| Sequences: | 59 (46) | ||
| Seq/Len: | 0.174 | ||
| Nf(neff/√len): | 2.5 |
HHblits Results: (2016_02)
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: 0.174).
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 |
| 13_D | 17_S | 1.924 | 0.53 |
| 217_P | 277_L | 1.795 | 0.45 |
| 48_V | 325_Y | 1.782 | 0.44 |
| 14_N | 351_D | 1.737 | 0.42 |
| 342_Y | 350_V | 1.613 | 0.35 |
| 25_L | 141_A | 1.591 | 0.34 |
| 50_S | 91_E | 1.589 | 0.34 |
| 13_D | 114_E | 1.588 | 0.34 |
| 9_L | 143_L | 1.566 | 0.32 |
| 29_L | 69_G | 1.553 | 0.32 |
| 18_M | 150_D | 1.525 | 0.30 |
| 47_G | 85_R | 1.490 | 0.29 |
| 36_I | 49_I | 1.488 | 0.29 |
| 124_L | 257_V | 1.467 | 0.28 |
| 45_Q | 146_V | 1.427 | 0.26 |
| 271_D | 342_Y | 1.424 | 0.26 |
| 301_Y | 334_L | 1.418 | 0.25 |
| 155_K | 255_G | 1.406 | 0.25 |
| 145_V | 299_V | 1.398 | 0.25 |
| 151_A | 334_L | 1.397 | 0.25 |
| 12_T | 117_F | 1.390 | 0.24 |
| 57_R | 189_S | 1.389 | 0.24 |
| 22_Q | 153_E | 1.386 | 0.24 |
| 10_F | 287_P | 1.371 | 0.23 |
| 141_A | 323_W | 1.366 | 0.23 |
| 137_F | 224_T | 1.360 | 0.23 |
| 15_S | 114_E | 1.356 | 0.23 |
| 17_S | 114_E | 1.356 | 0.23 |
| 12_T | 165_A | 1.351 | 0.23 |
| 22_Q | 325_Y | 1.349 | 0.22 |
| 139_E | 337_D | 1.348 | 0.22 |
| 140_D | 278_A | 1.338 | 0.22 |
| 47_G | 325_Y | 1.331 | 0.22 |
| 58_F | 191_S | 1.323 | 0.21 |
| 265_L | 325_Y | 1.321 | 0.21 |
| 110_G | 336_G | 1.317 | 0.21 |
| 12_T | 256_I | 1.313 | 0.21 |
| 28_N | 32_F | 1.310 | 0.21 |
| 41_M | 237_R | 1.305 | 0.21 |
| 49_I | 144_V | 1.304 | 0.21 |
| 63_K | 336_G | 1.295 | 0.20 |
| 107_A | 257_V | 1.290 | 0.20 |
| 23_E | 298_R | 1.284 | 0.20 |
| 117_F | 242_K | 1.279 | 0.20 |
| 60_A | 207_E | 1.275 | 0.20 |
| 171_F | 268_I | 1.272 | 0.20 |
| 268_I | 347_R | 1.270 | 0.19 |
| 119_P | 185_L | 1.266 | 0.19 |
| 51_T | 265_L | 1.265 | 0.19 |
| 79_S | 111_P | 1.263 | 0.19 |
| 234_L | 237_R | 1.262 | 0.19 |
| 199_L | 202_H | 1.260 | 0.19 |
| 11_V | 31_R | 1.248 | 0.19 |
| 114_E | 255_G | 1.247 | 0.19 |
| 33_T | 327_P | 1.246 | 0.19 |
| 6_V | 140_D | 1.243 | 0.18 |
| 32_F | 265_L | 1.243 | 0.18 |
| 131_G | 240_E | 1.231 | 0.18 |
| 44_Y | 314_V | 1.220 | 0.18 |
| 117_F | 256_I | 1.218 | 0.18 |
| 243_G | 281_I | 1.214 | 0.17 |
| 27_R | 328_E | 1.210 | 0.17 |
| 47_G | 136_F | 1.201 | 0.17 |
| 29_L | 95_L | 1.193 | 0.17 |
| 51_T | 116_F | 1.193 | 0.17 |
| 199_L | 204_K | 1.189 | 0.17 |
| 140_D | 332_V | 1.175 | 0.16 |
| 146_V | 284_T | 1.174 | 0.16 |
| 6_V | 44_Y | 1.173 | 0.16 |
| 163_Q | 221_G | 1.170 | 0.16 |
| 304_P | 307_L | 1.170 | 0.16 |
| 45_Q | 346_A | 1.167 | 0.16 |
| 19_K | 79_S | 1.164 | 0.16 |
| 46_I | 321_G | 1.164 | 0.16 |
| 16_E | 185_L | 1.163 | 0.16 |
| 24_N | 332_V | 1.158 | 0.16 |
| 61_T | 90_K | 1.158 | 0.16 |
| 25_L | 283_L | 1.157 | 0.16 |
| 69_G | 74_I | 1.155 | 0.16 |
| 343_Q | 351_D | 1.153 | 0.16 |
| 47_G | 327_P | 1.148 | 0.15 |
| 119_P | 276_T | 1.148 | 0.15 |
| 90_K | 256_I | 1.142 | 0.15 |
| 44_Y | 188_A | 1.142 | 0.15 |
| 183_G | 237_R | 1.138 | 0.15 |
| 41_M | 205_Y | 1.138 | 0.15 |
| 36_I | 119_P | 1.136 | 0.15 |
| 15_S | 32_F | 1.135 | 0.15 |
| 17_S | 32_F | 1.135 | 0.15 |
| 48_V | 265_L | 1.133 | 0.15 |
| 95_L | 99_L | 1.132 | 0.15 |
| 16_E | 112_E | 1.130 | 0.15 |
| 23_E | 328_E | 1.129 | 0.15 |
| 15_S | 119_P | 1.125 | 0.15 |
| 17_S | 119_P | 1.125 | 0.15 |
| 123_A | 332_V | 1.122 | 0.15 |
| 72_R | 323_W | 1.122 | 0.15 |
| 117_F | 153_E | 1.120 | 0.15 |
| 232_E | 262_G | 1.117 | 0.14 |
| 11_V | 119_P | 1.117 | 0.14 |
| 48_V | 323_W | 1.117 | 0.14 |
| 48_V | 136_F | 1.110 | 0.14 |
| 57_R | 208_Q | 1.108 | 0.14 |
| 145_V | 298_R | 1.104 | 0.14 |
| 123_A | 316_P | 1.104 | 0.14 |
| 5_Q | 143_L | 1.100 | 0.14 |
| 243_G | 251_K | 1.098 | 0.14 |
| 15_S | 322_G | 1.094 | 0.14 |
| 17_S | 322_G | 1.094 | 0.14 |
| 69_G | 143_L | 1.092 | 0.14 |
| 90_K | 169_L | 1.092 | 0.14 |
| 62_K | 236_V | 1.089 | 0.14 |
| 14_N | 77_G | 1.088 | 0.14 |
| 117_F | 233_E | 1.088 | 0.14 |
| 253_I | 334_L | 1.088 | 0.14 |
| 41_M | 203_P | 1.088 | 0.14 |
| 141_A | 334_L | 1.083 | 0.14 |
| 6_V | 15_S | 1.082 | 0.13 |
| 6_V | 17_S | 1.082 | 0.13 |
| 198_A | 202_H | 1.082 | 0.13 |
| 260_N | 332_V | 1.078 | 0.13 |
| 67_G | 148_L | 1.077 | 0.13 |
| 66_Y | 76_D | 1.073 | 0.13 |
| 236_V | 262_G | 1.073 | 0.13 |
| 16_E | 31_R | 1.073 | 0.13 |
| 51_T | 118_A | 1.072 | 0.13 |
| 14_N | 132_V | 1.070 | 0.13 |
| 66_Y | 74_I | 1.066 | 0.13 |
| 13_D | 119_P | 1.065 | 0.13 |
| 148_L | 188_A | 1.064 | 0.13 |
| 86_F | 94_L | 1.062 | 0.13 |
| 161_A | 273_T | 1.059 | 0.13 |
| 190_D | 209_C | 1.059 | 0.13 |
| 64_D | 71_L | 1.053 | 0.13 |
| 44_Y | 91_E | 1.053 | 0.13 |
| 15_S | 140_D | 1.051 | 0.13 |
| 17_S | 140_D | 1.051 | 0.13 |
| 37_N | 297_I | 1.050 | 0.13 |
| 52_W | 277_L | 1.050 | 0.13 |
| 11_V | 265_L | 1.047 | 0.13 |
| 260_N | 291_A | 1.046 | 0.13 |
| 11_V | 142_Q | 1.046 | 0.13 |
| 133_N | 265_L | 1.045 | 0.13 |
| 14_N | 49_I | 1.044 | 0.12 |
| 146_V | 161_A | 1.044 | 0.12 |
| 334_L | 344_D | 1.043 | 0.12 |
| 46_I | 132_V | 1.042 | 0.12 |
| 4_P | 119_P | 1.041 | 0.12 |
| 136_F | 325_Y | 1.039 | 0.12 |
| 147_F | 322_G | 1.038 | 0.12 |
| 288_R | 331_S | 1.036 | 0.12 |
| 151_A | 325_Y | 1.035 | 0.12 |
| 261_F | 289_A | 1.035 | 0.12 |
| 145_V | 316_P | 1.033 | 0.12 |
| 50_S | 161_A | 1.032 | 0.12 |
| 51_T | 155_K | 1.032 | 0.12 |
| 148_L | 153_E | 1.030 | 0.12 |
| 62_K | 70_E | 1.030 | 0.12 |
| 40_A | 90_K | 1.030 | 0.12 |
| 28_N | 187_K | 1.029 | 0.12 |
| 198_A | 205_Y | 1.029 | 0.12 |
| 46_I | 284_T | 1.028 | 0.12 |
| 121_T | 146_V | 1.028 | 0.12 |
| 165_A | 281_I | 1.028 | 0.12 |
| 119_P | 162_E | 1.027 | 0.12 |
| 10_F | 146_V | 1.026 | 0.12 |
| 118_A | 151_A | 1.026 | 0.12 |
| 79_S | 87_V | 1.025 | 0.12 |
| 123_A | 240_E | 1.024 | 0.12 |
| 107_A | 255_G | 1.024 | 0.12 |
| 143_L | 171_F | 1.023 | 0.12 |
| 25_L | 124_L | 1.021 | 0.12 |
| 120_L | 347_R | 1.018 | 0.12 |
| 24_N | 89_K | 1.015 | 0.12 |
| 146_V | 244_A | 1.015 | 0.12 |
| 79_S | 208_Q | 1.015 | 0.12 |
| 28_N | 183_G | 1.014 | 0.12 |
| 151_A | 303_T | 1.013 | 0.12 |
| 13_D | 149_T | 1.010 | 0.12 |
| 347_R | 350_V | 1.009 | 0.12 |
| 41_M | 198_A | 1.008 | 0.12 |
| 296_Q | 317_N | 1.008 | 0.12 |
| 18_M | 22_Q | 1.004 | 0.12 |
| 130_G | 270_S | 1.003 | 0.11 |
| 50_S | 296_Q | 1.003 | 0.11 |
| 128_G | 147_F | 1.001 | 0.11 |
| 202_H | 251_K | 1.001 | 0.11 |
| 98_T | 186_V | 1.000 | 0.11 |
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 | |
| 4nehB | 1 | 0.7911 | 99.2 | 0.889 | Contact Map |
| 3fcsB | 2 | 0.7688 | 99.2 | 0.892 | Contact Map |
| 3t3pB | 2 | 0.7604 | 99.1 | 0.893 | Contact Map |
| 4wk0B | 1 | 0.7883 | 99.1 | 0.894 | Contact Map |
| 3v4vB | 2 | 0.8273 | 99.1 | 0.896 | Contact Map |
| 4um9B | 1 | 0.7549 | 99 | 0.899 | Contact Map |
| 1ijbA | 1 | 0.532 | 98.6 | 0.911 | Contact Map |
| 2b2xA | 2 | 0.5209 | 98.6 | 0.911 | Contact Map |
| 4igiA | 1 | 0.5292 | 98.6 | 0.913 | Contact Map |
| 4bj3A | 2 | 0.507 | 98.6 | 0.913 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)