| 1B5QA |
| ID: | 1411598316 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 459 (447) | ||
| Sequences: | 3648 (2732.4) | ||
| Seq/Len: | 8.161 | ||
| Nf(neff/√len): | 129.2 |
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: 8.161).
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 |
| 2_R | 256_D | 4.974 | 1.00 |
| 8_A | 36_I | 4.916 | 1.00 |
| 15_A | 259_M | 4.869 | 1.00 |
| 443_G | 447_A | 4.732 | 1.00 |
| 4_I | 245_V | 3.818 | 1.00 |
| 235_E | 246_K | 3.616 | 1.00 |
| 4_I | 253_Y | 3.605 | 1.00 |
| 36_I | 229_L | 3.587 | 1.00 |
| 2_R | 26_D | 3.486 | 1.00 |
| 212_Y | 225_P | 3.351 | 1.00 |
| 36_I | 209_A | 3.340 | 1.00 |
| 4_I | 255_A | 3.186 | 1.00 |
| 28_L | 228_Q | 3.033 | 1.00 |
| 10_M | 436_V | 2.980 | 1.00 |
| 6_V | 260_V | 2.967 | 1.00 |
| 34_D | 230_N | 2.873 | 1.00 |
| 30_L | 253_Y | 2.852 | 1.00 |
| 32_A | 232_V | 2.850 | 1.00 |
| 228_Q | 251_S | 2.722 | 1.00 |
| 4_I | 30_L | 2.684 | 1.00 |
| 16_A | 29_I | 2.600 | 1.00 |
| 260_V | 267_L | 2.479 | 1.00 |
| 30_L | 228_Q | 2.449 | 1.00 |
| 237_K | 244_T | 2.394 | 1.00 |
| 2_R | 28_L | 2.375 | 1.00 |
| 202_E | 206_Y | 2.348 | 1.00 |
| 30_L | 233_V | 2.334 | 1.00 |
| 357_S | 360_Q | 2.318 | 1.00 |
| 247_T | 253_Y | 2.301 | 1.00 |
| 42_K | 49_N | 2.290 | 1.00 |
| 428_T | 445_D | 2.285 | 1.00 |
| 261_S | 424_T | 2.268 | 1.00 |
| 418_V | 421_V | 2.229 | 1.00 |
| 30_L | 255_A | 2.219 | 1.00 |
| 246_K | 252_V | 2.193 | 1.00 |
| 231_K | 247_T | 2.146 | 1.00 |
| 4_I | 28_L | 2.140 | 1.00 |
| 259_M | 450_L | 2.132 | 1.00 |
| 26_D | 226_R | 2.094 | 1.00 |
| 209_A | 227_L | 2.067 | 1.00 |
| 5_V | 27_L | 2.064 | 1.00 |
| 234_R | 248_E | 2.060 | 1.00 |
| 28_L | 256_D | 2.051 | 1.00 |
| 11_S | 442_S | 2.047 | 1.00 |
| 228_Q | 253_Y | 2.041 | 1.00 |
| 231_K | 249_D | 2.020 | 1.00 |
| 44_N | 49_N | 2.007 | 1.00 |
| 207_Y | 210_G | 1.927 | 1.00 |
| 228_Q | 231_K | 1.917 | 1.00 |
| 209_A | 213_L | 1.897 | 1.00 |
| 35_H | 41_H | 1.890 | 1.00 |
| 18_R | 448_E | 1.889 | 1.00 |
| 17_K | 21_E | 1.889 | 1.00 |
| 8_A | 29_I | 1.881 | 1.00 |
| 424_T | 446_S | 1.844 | 1.00 |
| 33_T | 395_Y | 1.834 | 1.00 |
| 20_S | 27_L | 1.821 | 1.00 |
| 232_V | 394_F | 1.819 | 1.00 |
| 22_A | 451_I | 1.813 | 1.00 |
| 11_S | 424_T | 1.804 | 1.00 |
| 247_T | 250_N | 1.783 | 1.00 |
| 6_V | 262_A | 1.781 | 1.00 |
| 3_V | 24_I | 1.770 | 1.00 |
| 18_R | 21_E | 1.763 | 1.00 |
| 237_K | 246_K | 1.757 | 1.00 |
| 14_S | 440_Y | 1.744 | 1.00 |
| 260_V | 421_V | 1.737 | 1.00 |
| 446_S | 449_I | 1.723 | 1.00 |
| 301_F | 366_M | 1.710 | 1.00 |
| 262_A | 272_I | 1.703 | 1.00 |
| 18_R | 444_I | 1.689 | 1.00 |
| 232_V | 248_E | 1.684 | 1.00 |
| 24_I | 451_I | 1.663 | 1.00 |
| 257_Y | 422_Y | 1.639 | 1.00 |
| 2_R | 24_I | 1.639 | 1.00 |
| 234_R | 246_K | 1.633 | 1.00 |
| 5_V | 29_I | 1.624 | 1.00 |
| 29_I | 36_I | 1.624 | 1.00 |
| 262_A | 267_L | 1.614 | 1.00 |
| 370_R | 375_G | 1.582 | 1.00 |
| 11_S | 261_S | 1.582 | 1.00 |
| 33_T | 392_D | 1.561 | 1.00 |
| 233_V | 245_V | 1.557 | 1.00 |
| 425_G | 442_S | 1.545 | 1.00 |
| 235_E | 275_K | 1.526 | 1.00 |
| 201_Y | 436_V | 1.524 | 1.00 |
| 67_P | 441_L | 1.518 | 1.00 |
| 3_V | 19_L | 1.518 | 1.00 |
| 428_T | 442_S | 1.517 | 1.00 |
| 363_A | 367_Q | 1.507 | 1.00 |
| 24_I | 27_L | 1.488 | 1.00 |
| 358_D | 388_R | 1.479 | 0.99 |
| 3_V | 257_Y | 1.471 | 0.99 |
| 422_Y | 453_C | 1.471 | 0.99 |
| 30_L | 245_V | 1.464 | 0.99 |
| 279_P | 418_V | 1.455 | 0.99 |
| 212_Y | 227_L | 1.452 | 0.99 |
| 40_M | 205_V | 1.438 | 0.99 |
| 15_A | 443_G | 1.427 | 0.99 |
| 67_P | 444_I | 1.413 | 0.99 |
| 245_V | 258_V | 1.406 | 0.99 |
| 203_A | 206_Y | 1.403 | 0.99 |
| 29_I | 227_L | 1.401 | 0.99 |
| 5_V | 259_M | 1.397 | 0.99 |
| 39_R | 53_G | 1.385 | 0.99 |
| 283_V | 287_Y | 1.382 | 0.99 |
| 28_L | 255_A | 1.366 | 0.99 |
| 445_D | 449_I | 1.360 | 0.99 |
| 36_I | 205_V | 1.356 | 0.99 |
| 135_S | 138_A | 1.354 | 0.99 |
| 79_R | 198_Q | 1.349 | 0.99 |
| 33_T | 41_H | 1.347 | 0.99 |
| 211_Q | 215_T | 1.338 | 0.99 |
| 29_I | 212_Y | 1.322 | 0.99 |
| 231_K | 253_Y | 1.320 | 0.99 |
| 257_Y | 420_R | 1.314 | 0.98 |
| 244_T | 254_S | 1.301 | 0.98 |
| 255_A | 258_V | 1.294 | 0.98 |
| 422_Y | 446_S | 1.290 | 0.98 |
| 20_S | 212_Y | 1.289 | 0.98 |
| 299_L | 366_M | 1.284 | 0.98 |
| 263_S | 266_V | 1.271 | 0.98 |
| 424_T | 443_G | 1.267 | 0.98 |
| 361_T | 386_V | 1.266 | 0.98 |
| 444_I | 448_E | 1.262 | 0.98 |
| 24_I | 256_D | 1.257 | 0.98 |
| 48_I | 300_K | 1.249 | 0.98 |
| 68_I | 440_Y | 1.246 | 0.98 |
| 5_V | 16_A | 1.245 | 0.98 |
| 32_A | 394_F | 1.242 | 0.98 |
| 9_G | 12_G | 1.232 | 0.97 |
| 5_V | 12_G | 1.230 | 0.97 |
| 400_S | 426_E | 1.221 | 0.97 |
| 44_N | 47_G | 1.209 | 0.97 |
| 429_S | 438_G | 1.205 | 0.97 |
| 370_R | 379_P | 1.205 | 0.97 |
| 5_V | 9_G | 1.199 | 0.97 |
| 8_A | 229_L | 1.198 | 0.97 |
| 284_R | 287_Y | 1.192 | 0.97 |
| 21_E | 74_S | 1.183 | 0.97 |
| 10_M | 40_M | 1.170 | 0.96 |
| 13_I | 29_I | 1.166 | 0.96 |
| 231_K | 251_S | 1.164 | 0.96 |
| 439_A | 443_G | 1.163 | 0.96 |
| 422_Y | 450_L | 1.163 | 0.96 |
| 28_L | 226_R | 1.161 | 0.96 |
| 284_R | 288_Q | 1.157 | 0.96 |
| 415_R | 449_I | 1.151 | 0.96 |
| 443_G | 446_S | 1.148 | 0.96 |
| 210_G | 213_L | 1.139 | 0.95 |
| 8_A | 13_I | 1.139 | 0.95 |
| 235_E | 273_Q | 1.132 | 0.95 |
| 18_R | 22_A | 1.125 | 0.95 |
| 359_E | 363_A | 1.122 | 0.95 |
| 238_Y | 418_V | 1.120 | 0.95 |
| 239_S | 242_G | 1.118 | 0.95 |
| 15_A | 446_S | 1.117 | 0.95 |
| 362_K | 366_M | 1.115 | 0.95 |
| 264_L | 427_H | 1.112 | 0.95 |
| 26_D | 256_D | 1.103 | 0.94 |
| 107_K | 110_E | 1.101 | 0.94 |
| 203_A | 207_Y | 1.101 | 0.94 |
| 238_Y | 420_R | 1.099 | 0.94 |
| 17_K | 208_L | 1.093 | 0.94 |
| 30_L | 247_T | 1.093 | 0.94 |
| 34_D | 229_L | 1.091 | 0.94 |
| 17_K | 212_Y | 1.090 | 0.94 |
| 17_K | 211_Q | 1.090 | 0.94 |
| 236_I | 260_V | 1.087 | 0.94 |
| 36_I | 227_L | 1.081 | 0.93 |
| 301_F | 381_A | 1.080 | 0.93 |
| 33_T | 263_S | 1.076 | 0.93 |
| 72_V | 78_L | 1.076 | 0.93 |
| 334_Q | 337_D | 1.075 | 0.93 |
| 243_V | 258_V | 1.067 | 0.93 |
| 10_M | 14_S | 1.067 | 0.93 |
| 28_L | 253_Y | 1.066 | 0.93 |
| 434_G | 438_G | 1.066 | 0.93 |
| 392_D | 395_Y | 1.059 | 0.93 |
| 19_L | 447_A | 1.057 | 0.92 |
| 244_T | 252_V | 1.056 | 0.92 |
| 446_S | 450_L | 1.053 | 0.92 |
| 16_A | 212_Y | 1.052 | 0.92 |
| 280_T | 284_R | 1.048 | 0.92 |
| 54_A | 437_H | 1.038 | 0.92 |
| 264_L | 268_Q | 1.036 | 0.91 |
| 213_L | 226_R | 1.036 | 0.91 |
| 282_K | 286_I | 1.029 | 0.91 |
| 6_V | 233_V | 1.029 | 0.91 |
| 73_N | 79_R | 1.027 | 0.91 |
| 11_S | 439_A | 1.026 | 0.91 |
| 257_Y | 450_L | 1.023 | 0.91 |
| 69_W | 73_N | 1.022 | 0.91 |
| 8_A | 12_G | 1.021 | 0.91 |
| 259_M | 422_Y | 1.018 | 0.90 |
| 9_G | 13_I | 1.018 | 0.90 |
| 360_Q | 363_A | 1.014 | 0.90 |
| 14_S | 18_R | 1.010 | 0.90 |
| 7_G | 12_G | 1.004 | 0.90 |
| 23_G | 27_L | 1.003 | 0.90 |
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 | |
| 1b37A | 3 | 1 | 100 | 0.224 | Contact Map |
| 4i59A | 4 | 0.9107 | 100 | 0.334 | Contact Map |
| 1s3eA | 2 | 0.9281 | 100 | 0.352 | Contact Map |
| 2yg5A | 1 | 0.9129 | 100 | 0.357 | Contact Map |
| 1rsgA | 2 | 0.9085 | 100 | 0.362 | Contact Map |
| 3zn0A | 1 | 0.9368 | 100 | 0.363 | Contact Map |
| 2iidA | 4 | 0.915 | 100 | 0.372 | Contact Map |
| 2vvmA | 2 | 0.9085 | 100 | 0.38 | Contact Map |
| 2z3yA | 1 | 0.9237 | 100 | 0.381 | Contact Map |
| 3i6dA | 2 | 0.8649 | 100 | 0.393 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)