| 3qe7 |
| ID: | 1408399684 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 407 (404) | ||
| Sequences: | 2125 (1259.5) | ||
| Seq/Len: | 5.260 | ||
| Nf(neff/√len): | 62.7 |
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: 5.260).
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 |
| 165_V | 188_V | 4.532 | 1.00 |
| 92_I | 275_G | 4.091 | 1.00 |
| 161_T | 192_L | 4.077 | 1.00 |
| 128_V | 392_A | 3.721 | 1.00 |
| 209_W | 318_K | 3.224 | 1.00 |
| 166_T | 185_G | 3.142 | 1.00 |
| 45_L | 314_S | 3.074 | 1.00 |
| 169_G | 184_I | 2.682 | 1.00 |
| 202_T | 206_N | 2.618 | 1.00 |
| 201_T | 204_I | 2.523 | 1.00 |
| 191_A | 195_A | 2.463 | 1.00 |
| 97_L | 229_L | 2.407 | 1.00 |
| 141_A | 159_S | 2.403 | 1.00 |
| 22_L | 309_F | 2.395 | 1.00 |
| 89_G | 220_F | 2.322 | 1.00 |
| 161_T | 165_V | 2.318 | 1.00 |
| 207_A | 318_K | 2.303 | 1.00 |
| 243_L | 263_S | 2.287 | 1.00 |
| 48_G | 311_I | 2.285 | 1.00 |
| 163_L | 337_L | 2.273 | 1.00 |
| 158_I | 193_S | 2.237 | 1.00 |
| 18_S | 305_G | 2.233 | 1.00 |
| 158_I | 198_I | 2.192 | 1.00 |
| 165_V | 169_G | 2.163 | 1.00 |
| 204_I | 322_A | 2.113 | 1.00 |
| 96_V | 272_V | 2.100 | 1.00 |
| 187_L | 191_A | 2.033 | 1.00 |
| 102_S | 265_F | 2.030 | 1.00 |
| 372_I | 395_V | 2.028 | 1.00 |
| 46_F | 277_F | 1.995 | 1.00 |
| 369_I | 396_G | 1.977 | 1.00 |
| 166_T | 334_V | 1.933 | 1.00 |
| 96_V | 100_L | 1.915 | 1.00 |
| 93_M | 225_I | 1.914 | 1.00 |
| 50_G | 270_S | 1.891 | 1.00 |
| 161_T | 188_V | 1.873 | 1.00 |
| 99_C | 272_V | 1.844 | 1.00 |
| 157_I | 161_T | 1.844 | 1.00 |
| 83_G | 86_V | 1.818 | 1.00 |
| 85_E | 219_R | 1.818 | 1.00 |
| 189_G | 330_V | 1.804 | 1.00 |
| 99_C | 265_F | 1.779 | 1.00 |
| 116_L | 401_L | 1.751 | 1.00 |
| 308_I | 312_L | 1.749 | 1.00 |
| 203_P | 325_M | 1.746 | 1.00 |
| 372_I | 391_L | 1.716 | 1.00 |
| 207_A | 321_A | 1.713 | 1.00 |
| 86_V | 219_R | 1.704 | 1.00 |
| 52_L | 307_A | 1.703 | 1.00 |
| 22_L | 306_A | 1.700 | 1.00 |
| 61_K | 257_D | 1.689 | 1.00 |
| 15_I | 309_F | 1.687 | 1.00 |
| 158_I | 196_M | 1.662 | 0.99 |
| 190_Y | 199_V | 1.647 | 0.99 |
| 297_V | 302_V | 1.632 | 0.99 |
| 259_G | 262_R | 1.623 | 0.99 |
| 14_T | 305_G | 1.618 | 0.99 |
| 101_V | 236_I | 1.617 | 0.99 |
| 131_L | 343_G | 1.608 | 0.99 |
| 253_D | 256_R | 1.596 | 0.99 |
| 77_L | 80_L | 1.511 | 0.99 |
| 21_H | 288_N | 1.506 | 0.99 |
| 191_A | 194_F | 1.505 | 0.99 |
| 95_G | 271_T | 1.502 | 0.99 |
| 361_Q | 404_K | 1.488 | 0.99 |
| 365_L | 399_L | 1.482 | 0.99 |
| 173_F | 177_L | 1.467 | 0.98 |
| 76_V | 87_A | 1.455 | 0.98 |
| 173_F | 178_A | 1.447 | 0.98 |
| 195_A | 198_I | 1.435 | 0.98 |
| 4_G | 7_E | 1.434 | 0.98 |
| 118_P | 400_S | 1.432 | 0.98 |
| 398_G | 402_I | 1.412 | 0.98 |
| 239_H | 263_S | 1.411 | 0.98 |
| 204_I | 207_A | 1.409 | 0.98 |
| 52_L | 304_G | 1.401 | 0.98 |
| 176_F | 180_I | 1.394 | 0.98 |
| 169_G | 173_F | 1.361 | 0.97 |
| 165_V | 185_G | 1.353 | 0.97 |
| 3_I | 9_P | 1.352 | 0.97 |
| 47_N | 65_Y | 1.350 | 0.97 |
| 25_M | 29_T | 1.343 | 0.97 |
| 190_Y | 325_M | 1.341 | 0.97 |
| 52_L | 311_I | 1.335 | 0.97 |
| 205_I | 208_H | 1.334 | 0.97 |
| 92_I | 218_P | 1.332 | 0.97 |
| 154_K | 198_I | 1.325 | 0.96 |
| 163_L | 368_V | 1.324 | 0.96 |
| 99_C | 268_G | 1.324 | 0.96 |
| 3_I | 7_E | 1.320 | 0.96 |
| 142_G | 150_T | 1.320 | 0.96 |
| 66_L | 284_T | 1.296 | 0.96 |
| 292_M | 298_Y | 1.295 | 0.96 |
| 36_F | 76_V | 1.289 | 0.96 |
| 221_E | 224_A | 1.279 | 0.95 |
| 361_Q | 365_L | 1.272 | 0.95 |
| 357_Y | 366_T | 1.266 | 0.95 |
| 65_Y | 306_A | 1.262 | 0.95 |
| 161_T | 196_M | 1.261 | 0.95 |
| 319_L | 322_A | 1.261 | 0.95 |
| 126_V | 242_H | 1.256 | 0.95 |
| 67_G | 285_Y | 1.252 | 0.95 |
| 91_F | 275_G | 1.249 | 0.95 |
| 157_I | 196_M | 1.248 | 0.94 |
| 247_A | 255_L | 1.237 | 0.94 |
| 211_A | 317_G | 1.234 | 0.94 |
| 95_G | 268_G | 1.231 | 0.94 |
| 140_M | 159_S | 1.228 | 0.94 |
| 202_T | 205_I | 1.222 | 0.94 |
| 63_P | 90_G | 1.219 | 0.94 |
| 242_H | 286_G | 1.210 | 0.93 |
| 11_L | 15_I | 1.209 | 0.93 |
| 203_P | 206_N | 1.203 | 0.93 |
| 168_L | 398_G | 1.197 | 0.93 |
| 184_I | 188_V | 1.197 | 0.93 |
| 194_F | 199_V | 1.187 | 0.92 |
| 45_L | 277_F | 1.186 | 0.92 |
| 21_H | 25_M | 1.185 | 0.92 |
| 127_A | 370_L | 1.185 | 0.92 |
| 239_H | 243_L | 1.184 | 0.92 |
| 168_L | 172_L | 1.179 | 0.92 |
| 8_R | 301_W | 1.178 | 0.92 |
| 144_L | 380_N | 1.175 | 0.92 |
| 92_I | 272_V | 1.172 | 0.92 |
| 177_L | 184_I | 1.150 | 0.91 |
| 243_L | 267_N | 1.150 | 0.91 |
| 165_V | 192_L | 1.147 | 0.91 |
| 394_I | 398_G | 1.144 | 0.90 |
| 318_K | 321_A | 1.143 | 0.90 |
| 101_V | 162_T | 1.141 | 0.90 |
| 69_S | 235_V | 1.139 | 0.90 |
| 5_V | 9_P | 1.136 | 0.90 |
| 194_F | 201_T | 1.135 | 0.90 |
| 55_L | 303_I | 1.134 | 0.90 |
| 137_A | 159_S | 1.134 | 0.90 |
| 242_H | 289_I | 1.132 | 0.90 |
| 24_A | 291_V | 1.123 | 0.89 |
| 55_L | 304_G | 1.118 | 0.89 |
| 9_P | 299_S | 1.113 | 0.89 |
| 340_G | 363_L | 1.111 | 0.89 |
| 222_W | 225_I | 1.109 | 0.88 |
| 15_I | 205_I | 1.104 | 0.88 |
| 140_M | 339_Y | 1.100 | 0.88 |
| 380_N | 385_E | 1.093 | 0.88 |
| 101_V | 104_I | 1.091 | 0.87 |
| 274_S | 282_N | 1.089 | 0.87 |
| 98_F | 235_V | 1.085 | 0.87 |
| 193_S | 197_G | 1.085 | 0.87 |
| 45_L | 311_I | 1.084 | 0.87 |
| 3_I | 10_P | 1.080 | 0.87 |
| 246_T | 292_M | 1.079 | 0.87 |
| 6_S | 10_P | 1.077 | 0.86 |
| 238_E | 283_T | 1.074 | 0.86 |
| 120_A | 124_A | 1.074 | 0.86 |
| 21_H | 24_A | 1.073 | 0.86 |
| 144_L | 151_P | 1.070 | 0.86 |
| 43_V | 280_T | 1.069 | 0.86 |
| 187_L | 322_A | 1.066 | 0.86 |
| 163_L | 167_V | 1.062 | 0.85 |
| 369_I | 395_V | 1.056 | 0.85 |
| 126_V | 129_I | 1.055 | 0.85 |
| 164_A | 167_V | 1.055 | 0.85 |
| 160_I | 164_A | 1.055 | 0.85 |
| 137_A | 162_T | 1.046 | 0.84 |
| 5_V | 299_S | 1.043 | 0.84 |
| 25_M | 288_N | 1.040 | 0.84 |
| 86_V | 221_E | 1.039 | 0.84 |
| 28_A | 287_E | 1.036 | 0.83 |
| 370_L | 374_V | 1.034 | 0.83 |
| 340_G | 344_A | 1.034 | 0.83 |
| 239_H | 267_N | 1.030 | 0.83 |
| 186_V | 237_A | 1.026 | 0.83 |
| 162_T | 278_G | 1.025 | 0.83 |
| 65_Y | 303_I | 1.024 | 0.82 |
| 92_I | 96_V | 1.021 | 0.82 |
| 79_L | 224_A | 1.020 | 0.82 |
| 138_A | 375_S | 1.020 | 0.82 |
| 6_S | 252_K | 1.018 | 0.82 |
| 120_A | 366_T | 1.016 | 0.82 |
| 89_G | 93_M | 1.014 | 0.82 |
| 299_S | 302_V | 1.012 | 0.81 |
| 143_L | 151_P | 1.004 | 0.81 |
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 | |
| 3qe7A | 1 | 1 | 100 | 0.337 | Contact Map |
| 2jlnA | 1 | 0.8747 | 12.8 | 0.975 | Contact Map |
| 2nwlA | 3 | 0.5012 | 2.6 | 0.982 | Contact Map |
| 1cmxA | 2 | 0.1229 | 2.4 | 0.982 | Contact Map |
| 3wo6A | 1 | 0.1032 | 1.6 | 0.984 | Contact Map |
| 1pw4A | 1 | 0.4693 | 1.4 | 0.984 | Contact Map |
| 4m48A | 1 | 0.1351 | 1.3 | 0.985 | Contact Map |
| 3mbdA | 1 | 0.1278 | 1 | 0.986 | Contact Map |
| 3arcZ | 2 | 0.1523 | 1 | 0.986 | Contact Map |
| 2ksfA | 1 | 0.2629 | 0.9 | 0.986 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)