| 1CQXA |
| ID: | 1411604242 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 403 (401) | ||
| Sequences: | 764 (546.7) | ||
| Seq/Len: | 1.905 | ||
| Nf(neff/√len): | 27.3 |
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: 1.905).
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 |
| 159_I | 244_V | 5.219 | 1.00 |
| 308_H | 330_Y | 3.112 | 1.00 |
| 18_A | 66_E | 2.946 | 1.00 |
| 3_T | 124_Q | 2.935 | 1.00 |
| 6_T | 124_Q | 2.846 | 1.00 |
| 286_K | 313_R | 2.797 | 1.00 |
| 103_L | 123_A | 2.754 | 1.00 |
| 162_K | 170_T | 2.588 | 1.00 |
| 174_L | 221_I | 2.559 | 1.00 |
| 32_M | 97_I | 2.526 | 1.00 |
| 211_S | 222_S | 2.477 | 1.00 |
| 64_Y | 129_L | 2.445 | 1.00 |
| 3_T | 6_T | 2.348 | 1.00 |
| 194_A | 251_K | 2.313 | 1.00 |
| 86_A | 256_Y | 2.311 | 1.00 |
| 79_K | 136_M | 2.230 | 1.00 |
| 161_E | 173_I | 2.177 | 0.99 |
| 70_D | 73_S | 2.163 | 0.99 |
| 273_S | 281_M | 2.159 | 0.99 |
| 270_V | 363_A | 2.148 | 0.99 |
| 171_S | 220_R | 2.115 | 0.99 |
| 261_I | 284_M | 2.041 | 0.99 |
| 160_R | 175_E | 2.036 | 0.99 |
| 114_A | 119_I | 1.966 | 0.99 |
| 91_K | 94_Q | 1.945 | 0.99 |
| 228_G | 233_P | 1.898 | 0.98 |
| 87_S | 207_Q | 1.876 | 0.98 |
| 225_R | 242_D | 1.815 | 0.97 |
| 31_R | 104_A | 1.793 | 0.97 |
| 156_T | 251_K | 1.786 | 0.97 |
| 245_N | 248_D | 1.774 | 0.97 |
| 131_D | 135_G | 1.764 | 0.97 |
| 82_A | 136_M | 1.747 | 0.97 |
| 4_Q | 8_D | 1.740 | 0.96 |
| 24_I | 105_A | 1.728 | 0.96 |
| 169_I | 276_V | 1.708 | 0.96 |
| 193_V | 250_V | 1.700 | 0.96 |
| 299_V | 349_V | 1.686 | 0.96 |
| 305_S | 333_P | 1.661 | 0.95 |
| 212_D | 286_K | 1.659 | 0.95 |
| 35_A | 101_H | 1.656 | 0.95 |
| 158_V | 249_Q | 1.648 | 0.95 |
| 270_V | 365_Y | 1.647 | 0.95 |
| 159_I | 174_L | 1.646 | 0.95 |
| 27_C | 31_R | 1.609 | 0.94 |
| 382_K | 388_E | 1.606 | 0.94 |
| 16_V | 113_A | 1.601 | 0.94 |
| 156_T | 249_Q | 1.600 | 0.94 |
| 318_A | 324_L | 1.575 | 0.93 |
| 301_G | 349_V | 1.564 | 0.93 |
| 161_E | 246_V | 1.561 | 0.92 |
| 31_R | 101_H | 1.557 | 0.92 |
| 138_S | 152_K | 1.556 | 0.92 |
| 158_V | 175_E | 1.551 | 0.92 |
| 175_E | 217_R | 1.538 | 0.92 |
| 158_V | 177_A | 1.531 | 0.91 |
| 138_S | 142_E | 1.520 | 0.91 |
| 165_E | 171_S | 1.519 | 0.91 |
| 120_S | 124_Q | 1.515 | 0.91 |
| 16_V | 19_E | 1.513 | 0.91 |
| 14_A | 18_A | 1.503 | 0.90 |
| 17_L | 21_G | 1.461 | 0.89 |
| 107_K | 116_D | 1.434 | 0.88 |
| 100_E | 104_A | 1.427 | 0.87 |
| 124_Q | 128_N | 1.424 | 0.87 |
| 107_K | 119_I | 1.415 | 0.87 |
| 24_I | 27_C | 1.412 | 0.86 |
| 26_K | 30_Q | 1.409 | 0.86 |
| 172_F | 240_L | 1.403 | 0.86 |
| 223_V | 240_L | 1.401 | 0.86 |
| 39_L | 207_Q | 1.399 | 0.86 |
| 13_T | 118_I | 1.398 | 0.86 |
| 381_L | 386_I | 1.393 | 0.85 |
| 91_K | 96_P | 1.386 | 0.85 |
| 111_G | 115_T | 1.385 | 0.85 |
| 244_V | 250_V | 1.385 | 0.85 |
| 333_P | 337_D | 1.385 | 0.85 |
| 93_E | 96_P | 1.383 | 0.85 |
| 6_T | 128_N | 1.379 | 0.85 |
| 192_S | 205_I | 1.378 | 0.85 |
| 14_A | 62_Y | 1.372 | 0.84 |
| 273_S | 300_H | 1.359 | 0.83 |
| 163_R | 173_I | 1.359 | 0.83 |
| 42_V | 94_Q | 1.352 | 0.83 |
| 165_E | 211_S | 1.342 | 0.82 |
| 155_R | 180_G | 1.342 | 0.82 |
| 195_I | 236_V | 1.335 | 0.82 |
| 63_A | 77_V | 1.332 | 0.82 |
| 11_K | 69_E | 1.325 | 0.81 |
| 314_L | 326_L | 1.324 | 0.81 |
| 165_E | 222_S | 1.318 | 0.81 |
| 16_V | 110_L | 1.314 | 0.81 |
| 367_I | 391_I | 1.297 | 0.79 |
| 27_C | 105_A | 1.288 | 0.79 |
| 395_V | 399_D | 1.274 | 0.78 |
| 119_I | 123_A | 1.264 | 0.77 |
| 61_V | 106_I | 1.258 | 0.76 |
| 305_S | 337_D | 1.253 | 0.76 |
| 302_A | 307_V | 1.252 | 0.76 |
| 24_I | 113_A | 1.251 | 0.76 |
| 183_V | 219_Y | 1.250 | 0.76 |
| 139_E | 142_E | 1.249 | 0.76 |
| 64_Y | 74_L | 1.248 | 0.76 |
| 171_S | 222_S | 1.245 | 0.75 |
| 27_C | 108_E | 1.239 | 0.75 |
| 370_P | 374_M | 1.239 | 0.75 |
| 74_L | 125_A | 1.239 | 0.75 |
| 14_A | 17_L | 1.233 | 0.74 |
| 301_G | 331_D | 1.232 | 0.74 |
| 315_R | 328_V | 1.228 | 0.74 |
| 39_L | 101_H | 1.220 | 0.73 |
| 173_I | 218_T | 1.218 | 0.73 |
| 182_V | 185_F | 1.217 | 0.73 |
| 6_T | 120_S | 1.217 | 0.73 |
| 31_R | 108_E | 1.217 | 0.73 |
| 331_D | 376_M | 1.210 | 0.72 |
| 74_L | 129_L | 1.210 | 0.72 |
| 164_P | 170_T | 1.206 | 0.72 |
| 87_S | 192_S | 1.204 | 0.72 |
| 75_M | 78_L | 1.200 | 0.71 |
| 17_L | 68_I | 1.193 | 0.71 |
| 124_Q | 393_Y | 1.192 | 0.71 |
| 4_Q | 7_K | 1.188 | 0.70 |
| 44_N | 47_H | 1.187 | 0.70 |
| 191_T | 252_L | 1.186 | 0.70 |
| 278_L | 298_F | 1.182 | 0.70 |
| 101_H | 104_A | 1.178 | 0.69 |
| 268_P | 295_Q | 1.177 | 0.69 |
| 340_G | 343_Y | 1.176 | 0.69 |
| 5_K | 8_D | 1.173 | 0.69 |
| 113_A | 116_D | 1.172 | 0.69 |
| 28_F | 99_G | 1.172 | 0.69 |
| 115_T | 118_I | 1.167 | 0.68 |
| 7_K | 77_V | 1.152 | 0.67 |
| 71_P | 132_V | 1.145 | 0.66 |
| 57_L | 98_V | 1.144 | 0.66 |
| 9_I | 118_I | 1.143 | 0.66 |
| 62_Y | 66_E | 1.143 | 0.66 |
| 273_S | 298_F | 1.142 | 0.66 |
| 35_A | 100_E | 1.128 | 0.65 |
| 68_I | 125_A | 1.123 | 0.64 |
| 274_G | 376_M | 1.120 | 0.64 |
| 32_M | 90_V | 1.120 | 0.64 |
| 185_F | 210_L | 1.117 | 0.63 |
| 136_M | 140_L | 1.116 | 0.63 |
| 99_G | 103_L | 1.114 | 0.63 |
| 337_D | 343_Y | 1.111 | 0.63 |
| 157_F | 176_P | 1.105 | 0.62 |
| 64_Y | 128_N | 1.102 | 0.62 |
| 27_C | 30_Q | 1.102 | 0.62 |
| 204_Q | 207_Q | 1.099 | 0.62 |
| 126_Y | 130_A | 1.094 | 0.61 |
| 33_F | 101_H | 1.084 | 0.60 |
| 156_T | 177_A | 1.078 | 0.59 |
| 151_W | 209_S | 1.077 | 0.59 |
| 68_I | 74_L | 1.077 | 0.59 |
| 61_V | 69_E | 1.076 | 0.59 |
| 299_V | 329_F | 1.073 | 0.59 |
| 32_M | 38_E | 1.068 | 0.58 |
| 269_I | 288_A | 1.061 | 0.58 |
| 36_H | 100_E | 1.061 | 0.58 |
| 285_L | 314_L | 1.060 | 0.57 |
| 78_L | 133_L | 1.059 | 0.57 |
| 58_A | 110_L | 1.058 | 0.57 |
| 47_H | 50_Q | 1.048 | 0.56 |
| 173_I | 220_R | 1.046 | 0.56 |
| 39_L | 42_V | 1.045 | 0.56 |
| 82_A | 133_L | 1.045 | 0.56 |
| 172_F | 284_M | 1.044 | 0.56 |
| 271_L | 294_R | 1.044 | 0.56 |
| 40_K | 45_M | 1.041 | 0.55 |
| 311_R | 342_D | 1.041 | 0.55 |
| 17_L | 62_Y | 1.038 | 0.55 |
| 46_A | 50_Q | 1.035 | 0.55 |
| 318_A | 326_L | 1.026 | 0.54 |
| 304_N | 332_Q | 1.024 | 0.53 |
| 71_P | 78_L | 1.021 | 0.53 |
| 22_Y | 55_Q | 1.020 | 0.53 |
| 225_R | 238_N | 1.016 | 0.53 |
| 22_Y | 26_K | 1.015 | 0.53 |
| 159_I | 250_V | 1.014 | 0.52 |
| 10_V | 19_E | 1.012 | 0.52 |
| 268_P | 271_L | 1.009 | 0.52 |
| 85_H | 95_Y | 1.009 | 0.52 |
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 | |
| 1cqxA | 2 | 1 | 100 | 0.339 | Contact Map |
| 1gvhA | 1 | 0.9777 | 100 | 0.376 | Contact Map |
| 4g1vA | 1 | 0.9529 | 100 | 0.38 | Contact Map |
| 4eh1A | 2 | 0.5906 | 100 | 0.672 | Contact Map |
| 2piaA | 1 | 0.5707 | 100 | 0.7 | Contact Map |
| 1tvcA | 1 | 0.6055 | 100 | 0.7 | Contact Map |
| 1krhA | 2 | 0.7916 | 100 | 0.701 | Contact Map |
| 1qfjA | 4 | 0.5533 | 100 | 0.701 | Contact Map |
| 2r6hA | 4 | 0.5955 | 100 | 0.703 | Contact Map |
| 2eixA | 2 | 0.5906 | 100 | 0.708 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)