| DegQ |
| ID: | 1378862361 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 395 (388) | ||
| Sequences: | 1908 (1422.9) | ||
| Seq/Len: | 4.918 | ||
| Nf(neff/√len): | 72.2 |
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: 4.918).
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 |
| 160_N | 164_E | 5.947 | 1.00 |
| 285_L | 294_V | 4.621 | 1.00 |
| 256_S | 284_G | 4.174 | 1.00 |
| 314_A | 317_G | 4.003 | 1.00 |
| 57_I | 71_L | 3.810 | 1.00 |
| 98_D | 101_K | 3.383 | 1.00 |
| 149_I | 183_G | 3.135 | 1.00 |
| 95_A | 164_E | 3.124 | 1.00 |
| 334_I | 348_L | 3.122 | 1.00 |
| 82_L | 199_I | 3.020 | 1.00 |
| 67_F | 85_I | 2.951 | 1.00 |
| 364_S | 367_E | 2.942 | 1.00 |
| 102_L | 166_I | 2.864 | 1.00 |
| 48_N | 74_S | 2.844 | 1.00 |
| 126_V | 143_I | 2.779 | 1.00 |
| 284_G | 291_P | 2.768 | 1.00 |
| 317_G | 323_G | 2.757 | 1.00 |
| 352_D | 385_R | 2.720 | 1.00 |
| 282_K | 293_E | 2.669 | 1.00 |
| 70_K | 86_Q | 2.603 | 1.00 |
| 100_D | 189_N | 2.579 | 1.00 |
| 240_G | 244_A | 2.564 | 1.00 |
| 36_I | 61_L | 2.526 | 1.00 |
| 258_N | 275_T | 2.487 | 1.00 |
| 43_Y | 72_I | 2.410 | 1.00 |
| 234_V | 248_V | 2.395 | 1.00 |
| 98_D | 189_N | 2.349 | 1.00 |
| 357_V | 368_M | 2.255 | 1.00 |
| 234_V | 254_I | 2.215 | 1.00 |
| 35_V | 165_L | 2.204 | 1.00 |
| 280_K | 295_E | 2.203 | 1.00 |
| 45_L | 191_A | 2.171 | 1.00 |
| 248_V | 285_L | 2.151 | 1.00 |
| 313_P | 317_G | 2.147 | 1.00 |
| 285_L | 292_L | 2.130 | 1.00 |
| 45_L | 195_A | 2.092 | 1.00 |
| 255_T | 286_L | 2.061 | 1.00 |
| 157_A | 165_L | 2.056 | 1.00 |
| 257_L | 275_T | 2.036 | 1.00 |
| 43_Y | 82_L | 2.005 | 1.00 |
| 282_K | 295_E | 1.966 | 1.00 |
| 248_V | 283_L | 1.963 | 1.00 |
| 284_G | 293_E | 1.956 | 1.00 |
| 35_V | 157_A | 1.955 | 1.00 |
| 44_V | 85_I | 1.929 | 1.00 |
| 257_L | 272_I | 1.925 | 1.00 |
| 37_I | 195_A | 1.918 | 1.00 |
| 69_A | 83_L | 1.912 | 1.00 |
| 363_N | 367_E | 1.899 | 1.00 |
| 94_I | 159_L | 1.898 | 1.00 |
| 102_L | 126_V | 1.862 | 1.00 |
| 56_K | 68_D | 1.833 | 1.00 |
| 317_G | 321_S | 1.791 | 1.00 |
| 280_K | 297_T | 1.783 | 1.00 |
| 196_Q | 200_D | 1.752 | 1.00 |
| 384_V | 387_N | 1.702 | 1.00 |
| 209_L | 296_V | 1.678 | 0.99 |
| 385_R | 390_I | 1.640 | 0.99 |
| 248_V | 294_V | 1.631 | 0.99 |
| 58_S | 66_E | 1.605 | 0.99 |
| 314_A | 323_G | 1.600 | 0.99 |
| 70_K | 84_Q | 1.589 | 0.99 |
| 255_T | 291_P | 1.575 | 0.99 |
| 256_S | 261_P | 1.573 | 0.99 |
| 107_F | 123_S | 1.518 | 0.99 |
| 14_K | 18_D | 1.499 | 0.98 |
| 36_I | 91_L | 1.492 | 0.98 |
| 11_E | 16_F | 1.489 | 0.98 |
| 209_L | 241_S | 1.476 | 0.98 |
| 367_E | 370_K | 1.448 | 0.98 |
| 96_I | 188_S | 1.430 | 0.98 |
| 256_S | 259_G | 1.428 | 0.98 |
| 314_A | 319_T | 1.425 | 0.98 |
| 94_I | 165_L | 1.404 | 0.97 |
| 318_A | 323_G | 1.404 | 0.97 |
| 151_R | 175_P | 1.403 | 0.97 |
| 239_P | 244_A | 1.396 | 0.97 |
| 11_E | 19_D | 1.385 | 0.97 |
| 80_I | 168_I | 1.380 | 0.97 |
| 147_A | 183_G | 1.368 | 0.97 |
| 168_I | 191_A | 1.360 | 0.97 |
| 10_E | 13_K | 1.356 | 0.97 |
| 252_D | 287_R | 1.355 | 0.97 |
| 43_Y | 199_I | 1.355 | 0.97 |
| 13_K | 17_G | 1.353 | 0.96 |
| 145_T | 158_L | 1.344 | 0.96 |
| 255_T | 284_G | 1.344 | 0.96 |
| 215_E | 265_F | 1.340 | 0.96 |
| 49_H | 79_D | 1.339 | 0.96 |
| 126_V | 166_I | 1.322 | 0.96 |
| 174_A | 177_G | 1.315 | 0.96 |
| 314_A | 318_A | 1.308 | 0.96 |
| 332_I | 362_V | 1.296 | 0.95 |
| 360_D | 371_V | 1.293 | 0.95 |
| 362_V | 367_E | 1.290 | 0.95 |
| 34_G | 44_V | 1.279 | 0.95 |
| 52_N | 76_D | 1.275 | 0.95 |
| 230_R | 261_P | 1.272 | 0.95 |
| 96_I | 192_R | 1.266 | 0.94 |
| 246_A | 296_V | 1.265 | 0.94 |
| 220_I | 224_F | 1.263 | 0.94 |
| 257_L | 283_L | 1.257 | 0.94 |
| 245_K | 299_D | 1.254 | 0.94 |
| 367_E | 371_V | 1.254 | 0.94 |
| 357_V | 362_V | 1.248 | 0.94 |
| 241_S | 244_A | 1.248 | 0.94 |
| 314_A | 321_S | 1.248 | 0.94 |
| 212_K | 236_E | 1.238 | 0.93 |
| 11_E | 14_K | 1.237 | 0.93 |
| 275_T | 298_L | 1.230 | 0.93 |
| 201_F | 205_K | 1.227 | 0.93 |
| 205_K | 300_T | 1.225 | 0.93 |
| 319_T | 336_E | 1.219 | 0.93 |
| 10_E | 14_K | 1.205 | 0.92 |
| 207_G | 298_L | 1.203 | 0.92 |
| 35_V | 159_L | 1.200 | 0.92 |
| 192_R | 196_Q | 1.199 | 0.92 |
| 43_Y | 84_Q | 1.197 | 0.92 |
| 99_S | 189_N | 1.194 | 0.92 |
| 320_L | 323_G | 1.194 | 0.92 |
| 276_E | 279_T | 1.185 | 0.91 |
| 117_L | 120_T | 1.175 | 0.91 |
| 52_N | 71_L | 1.172 | 0.91 |
| 317_G | 320_L | 1.172 | 0.91 |
| 216_M | 226_L | 1.159 | 0.90 |
| 175_P | 180_V | 1.157 | 0.90 |
| 249_K | 292_L | 1.156 | 0.90 |
| 45_L | 188_S | 1.153 | 0.90 |
| 249_K | 288_N | 1.151 | 0.90 |
| 32_G | 50_V | 1.151 | 0.90 |
| 36_I | 85_I | 1.149 | 0.90 |
| 44_V | 83_L | 1.144 | 0.89 |
| 362_V | 371_V | 1.139 | 0.89 |
| 11_E | 18_D | 1.133 | 0.89 |
| 366_A | 370_K | 1.130 | 0.89 |
| 319_T | 323_G | 1.126 | 0.88 |
| 48_N | 52_N | 1.124 | 0.88 |
| 49_H | 154_S | 1.123 | 0.88 |
| 10_E | 17_G | 1.121 | 0.88 |
| 211_I | 232_A | 1.118 | 0.88 |
| 136_L | 171_A | 1.116 | 0.88 |
| 14_K | 17_G | 1.113 | 0.88 |
| 13_K | 18_D | 1.112 | 0.87 |
| 216_M | 229_Q | 1.112 | 0.87 |
| 63_D | 67_F | 1.109 | 0.87 |
| 366_A | 369_R | 1.100 | 0.87 |
| 313_P | 318_A | 1.098 | 0.87 |
| 79_D | 154_S | 1.097 | 0.86 |
| 14_K | 19_D | 1.093 | 0.86 |
| 322_D | 332_I | 1.092 | 0.86 |
| 88_P | 91_L | 1.091 | 0.86 |
| 80_I | 188_S | 1.090 | 0.86 |
| 10_E | 15_F | 1.085 | 0.86 |
| 35_V | 168_I | 1.081 | 0.85 |
| 13_K | 19_D | 1.071 | 0.85 |
| 8_I | 11_E | 1.071 | 0.85 |
| 113_N | 171_A | 1.070 | 0.85 |
| 355_I | 384_V | 1.067 | 0.84 |
| 61_L | 85_I | 1.062 | 0.84 |
| 137_E | 140_E | 1.059 | 0.84 |
| 237_V | 250_A | 1.059 | 0.84 |
| 343_A | 347_G | 1.059 | 0.84 |
| 82_L | 195_A | 1.052 | 0.83 |
| 78_S | 194_L | 1.051 | 0.83 |
| 42_G | 84_Q | 1.049 | 0.83 |
| 360_D | 370_K | 1.048 | 0.83 |
| 35_V | 94_I | 1.044 | 0.83 |
| 60_Q | 66_E | 1.026 | 0.81 |
| 140_E | 171_A | 1.026 | 0.81 |
| 108_A | 166_I | 1.023 | 0.81 |
| 214_T | 220_I | 1.022 | 0.81 |
| 11_E | 17_G | 1.021 | 0.81 |
| 46_T | 49_H | 1.018 | 0.80 |
| 48_N | 76_D | 1.017 | 0.80 |
| 258_N | 279_T | 1.015 | 0.80 |
| 332_I | 365_I | 1.014 | 0.80 |
| 121_A | 125_I | 1.010 | 0.80 |
| 80_I | 186_I | 1.008 | 0.79 |
| 275_T | 281_V | 1.006 | 0.79 |
| 203_E | 300_T | 1.003 | 0.79 |
| 36_I | 44_V | 1.001 | 0.79 |
| 102_L | 143_I | 1.000 | 0.79 |
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 | |
| 4a8cA | 12 | 0.9443 | 100 | 0.309 | Contact Map |
| 1ky9A | 2 | 0.9468 | 100 | 0.325 | Contact Map |
| 3pv2A | 4 | 0.9114 | 100 | 0.331 | Contact Map |
| 4flnA | 3 | 0.9544 | 100 | 0.422 | Contact Map |
| 3stjA | 12 | 0.7114 | 100 | 0.451 | Contact Map |
| 1te0A | 2 | 0.7671 | 100 | 0.523 | Contact Map |
| 4ic6A | 3 | 0.7342 | 100 | 0.527 | Contact Map |
| 3qo6A | 3 | 0.7443 | 100 | 0.551 | Contact Map |
| 3numA | 1 | 0.4127 | 100 | 0.563 | Contact Map |
| 1y8tA | 3 | 0.6987 | 100 | 0.568 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)