| dbpa2 |
| ID: | 1502211160 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 445 (416) | ||
| Sequences: | 8917 (4261.3) | ||
| Seq/Len: | 21.435 | ||
| Nf(neff/√len): | 208.9 |
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: 21.435).
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 |
| 55_T | 68_S | 4.732 | 1.00 |
| 274_R | 279_S | 4.552 | 1.00 |
| 371_A | 374_C | 4.184 | 1.00 |
| 257_L | 280_A | 3.751 | 1.00 |
| 52_W | 85_G | 3.740 | 1.00 |
| 255_S | 281_R | 3.375 | 1.00 |
| 105_A | 109_E | 3.319 | 1.00 |
| 242_C | 258_A | 2.857 | 1.00 |
| 270_Q | 274_R | 2.808 | 1.00 |
| 70_E | 85_G | 2.805 | 1.00 |
| 66_K | 137_Q | 2.781 | 1.00 |
| 107_V | 134_K | 2.593 | 1.00 |
| 106_L | 113_S | 2.544 | 1.00 |
| 59_V | 68_S | 2.506 | 1.00 |
| 106_L | 110_I | 2.447 | 1.00 |
| 40_N | 53_Y | 2.429 | 1.00 |
| 246_C | 258_A | 2.405 | 1.00 |
| 69_I | 119_T | 2.347 | 1.00 |
| 278_G | 281_R | 2.295 | 1.00 |
| 123_Q | 128_S | 2.295 | 1.00 |
| 82_S | 86_N | 2.286 | 1.00 |
| 35_I | 189_E | 2.280 | 1.00 |
| 271_T | 280_A | 2.270 | 1.00 |
| 297_S | 325_S | 2.259 | 1.00 |
| 232_H | 297_S | 2.244 | 1.00 |
| 118_M | 128_S | 2.205 | 1.00 |
| 198_A | 326_S | 2.194 | 1.00 |
| 71_E | 120_L | 2.169 | 1.00 |
| 231_D | 325_S | 2.154 | 1.00 |
| 273_V | 277_N | 2.098 | 1.00 |
| 43_Y | 164_R | 2.089 | 1.00 |
| 239_V | 262_D | 2.066 | 1.00 |
| 115_Q | 129_L | 2.062 | 1.00 |
| 387_D | 392_L | 2.031 | 1.00 |
| 257_L | 274_R | 2.017 | 1.00 |
| 115_Q | 120_L | 2.004 | 1.00 |
| 72_V | 81_I | 1.995 | 1.00 |
| 347_M | 367_A | 1.987 | 1.00 |
| 214_Q | 302_V | 1.987 | 1.00 |
| 306_L | 331_S | 1.969 | 1.00 |
| 85_G | 114_S | 1.966 | 1.00 |
| 254_Q | 282_I | 1.957 | 1.00 |
| 47_S | 183_L | 1.940 | 1.00 |
| 257_L | 271_T | 1.935 | 1.00 |
| 26_Q | 92_L | 1.931 | 1.00 |
| 59_V | 112_S | 1.923 | 1.00 |
| 69_I | 138_Q | 1.920 | 1.00 |
| 35_I | 38_T | 1.905 | 1.00 |
| 88_C | 294_D | 1.842 | 1.00 |
| 342_N | 346_E | 1.841 | 1.00 |
| 307_A | 313_H | 1.841 | 1.00 |
| 235_G | 289_A | 1.827 | 1.00 |
| 246_C | 250_N | 1.803 | 1.00 |
| 44_L | 57_Y | 1.797 | 1.00 |
| 84_F | 88_C | 1.797 | 1.00 |
| 84_F | 294_D | 1.785 | 1.00 |
| 65_V | 137_Q | 1.779 | 1.00 |
| 301_V | 320_T | 1.773 | 1.00 |
| 246_C | 284_V | 1.771 | 1.00 |
| 243_Q | 247_D | 1.771 | 1.00 |
| 170_A | 184_M | 1.710 | 1.00 |
| 343_I | 368_A | 1.704 | 1.00 |
| 113_S | 119_T | 1.682 | 1.00 |
| 300_L | 330_I | 1.677 | 1.00 |
| 38_T | 42_I | 1.657 | 1.00 |
| 32_D | 49_L | 1.644 | 1.00 |
| 110_I | 113_S | 1.642 | 1.00 |
| 69_I | 135_T | 1.638 | 1.00 |
| 17_C | 57_Y | 1.637 | 1.00 |
| 342_N | 345_S | 1.635 | 1.00 |
| 343_I | 371_A | 1.617 | 1.00 |
| 264_E | 267_D | 1.608 | 1.00 |
| 95_G | 111_R | 1.595 | 1.00 |
| 269_D | 273_V | 1.581 | 1.00 |
| 26_Q | 91_R | 1.573 | 1.00 |
| 42_I | 183_L | 1.557 | 1.00 |
| 79_I | 83_E | 1.551 | 1.00 |
| 121_S | 125_A | 1.541 | 1.00 |
| 52_W | 90_G | 1.530 | 1.00 |
| 95_G | 105_A | 1.519 | 1.00 |
| 195_T | 326_S | 1.514 | 1.00 |
| 22_V | 25_L | 1.503 | 1.00 |
| 423_Q | 427_K | 1.495 | 1.00 |
| 30_L | 37_I | 1.483 | 1.00 |
| 367_A | 371_A | 1.466 | 1.00 |
| 233_G | 282_I | 1.462 | 1.00 |
| 215_T | 219_A | 1.459 | 1.00 |
| 243_Q | 258_A | 1.450 | 1.00 |
| 221_N | 231_D | 1.450 | 1.00 |
| 34_P | 190_N | 1.429 | 1.00 |
| 68_S | 142_L | 1.429 | 1.00 |
| 276_A | 294_D | 1.427 | 1.00 |
| 249_L | 256_A | 1.425 | 1.00 |
| 287_D | 316_R | 1.418 | 1.00 |
| 231_D | 299_E | 1.416 | 1.00 |
| 103_I | 129_L | 1.411 | 1.00 |
| 103_I | 123_Q | 1.397 | 0.99 |
| 18_T | 22_V | 1.385 | 0.99 |
| 367_A | 370_M | 1.380 | 0.99 |
| 141_S | 159_N | 1.377 | 0.99 |
| 256_A | 284_V | 1.376 | 0.99 |
| 24_T | 53_Y | 1.371 | 0.99 |
| 259_L | 268_R | 1.365 | 0.99 |
| 421_V | 424_K | 1.348 | 0.99 |
| 102_N | 118_M | 1.335 | 0.99 |
| 246_C | 256_A | 1.332 | 0.99 |
| 40_N | 44_L | 1.330 | 0.99 |
| 215_T | 252_V | 1.323 | 0.99 |
| 147_A | 307_A | 1.322 | 0.99 |
| 236_F | 245_V | 1.319 | 0.99 |
| 135_T | 138_Q | 1.318 | 0.99 |
| 245_V | 248_A | 1.308 | 0.99 |
| 95_G | 109_E | 1.307 | 0.99 |
| 254_Q | 281_R | 1.301 | 0.99 |
| 377_G | 439_C | 1.297 | 0.99 |
| 199_S | 317_I | 1.294 | 0.99 |
| 55_T | 142_L | 1.292 | 0.99 |
| 424_K | 427_K | 1.273 | 0.99 |
| 241_D | 244_A | 1.270 | 0.99 |
| 247_D | 250_N | 1.269 | 0.99 |
| 418_R | 422_A | 1.258 | 0.99 |
| 41_I | 44_L | 1.255 | 0.99 |
| 252_V | 282_I | 1.254 | 0.99 |
| 83_E | 294_D | 1.254 | 0.99 |
| 68_S | 85_G | 1.250 | 0.99 |
| 20_L | 57_Y | 1.239 | 0.98 |
| 424_K | 428_Q | 1.237 | 0.98 |
| 198_A | 328_L | 1.235 | 0.98 |
| 41_I | 45_I | 1.232 | 0.98 |
| 418_R | 421_V | 1.231 | 0.98 |
| 103_I | 128_S | 1.230 | 0.98 |
| 247_D | 251_A | 1.230 | 0.98 |
| 245_V | 284_V | 1.218 | 0.98 |
| 55_T | 112_S | 1.218 | 0.98 |
| 62_I | 112_S | 1.215 | 0.98 |
| 85_G | 112_S | 1.207 | 0.98 |
| 54_M | 140_A | 1.207 | 0.98 |
| 72_V | 78_S | 1.205 | 0.98 |
| 417_V | 421_V | 1.200 | 0.98 |
| 48_L | 178_R | 1.199 | 0.98 |
| 173_A | 177_A | 1.198 | 0.98 |
| 25_L | 30_L | 1.191 | 0.98 |
| 317_I | 329_A | 1.191 | 0.98 |
| 99_L | 128_S | 1.181 | 0.98 |
| 23_D | 56_C | 1.174 | 0.98 |
| 52_W | 89_A | 1.171 | 0.98 |
| 42_I | 185_V | 1.168 | 0.97 |
| 242_C | 260_H | 1.164 | 0.97 |
| 70_E | 81_I | 1.161 | 0.97 |
| 105_A | 110_I | 1.161 | 0.97 |
| 67_K | 139_S | 1.159 | 0.97 |
| 196_D | 326_S | 1.159 | 0.97 |
| 56_C | 60_V | 1.155 | 0.97 |
| 199_S | 331_S | 1.155 | 0.97 |
| 235_G | 282_I | 1.155 | 0.97 |
| 233_G | 302_V | 1.152 | 0.97 |
| 373_L | 385_P | 1.149 | 0.97 |
| 263_L | 271_T | 1.146 | 0.97 |
| 58_L | 139_S | 1.133 | 0.97 |
| 34_P | 38_T | 1.131 | 0.97 |
| 129_L | 135_T | 1.129 | 0.97 |
| 259_L | 271_T | 1.129 | 0.97 |
| 67_K | 111_R | 1.127 | 0.97 |
| 37_I | 41_I | 1.113 | 0.96 |
| 32_D | 40_N | 1.113 | 0.96 |
| 301_V | 329_A | 1.112 | 0.96 |
| 42_I | 45_I | 1.112 | 0.96 |
| 24_T | 37_I | 1.111 | 0.96 |
| 40_N | 54_M | 1.104 | 0.96 |
| 219_A | 254_Q | 1.098 | 0.96 |
| 217_I | 330_I | 1.098 | 0.96 |
| 422_A | 426_W | 1.091 | 0.96 |
| 295_I | 298_L | 1.089 | 0.96 |
| 271_T | 274_R | 1.075 | 0.95 |
| 60_V | 111_R | 1.069 | 0.95 |
| 303_N | 317_I | 1.064 | 0.95 |
| 99_L | 103_I | 1.060 | 0.95 |
| 289_A | 293_L | 1.056 | 0.95 |
| 419_Q | 423_Q | 1.054 | 0.95 |
| 29_F | 49_L | 1.051 | 0.94 |
| 259_L | 285_A | 1.035 | 0.94 |
| 216_N | 220_L | 1.034 | 0.94 |
| 20_L | 53_Y | 1.025 | 0.93 |
| 235_G | 245_V | 1.023 | 0.93 |
| 122_E | 126_A | 1.022 | 0.93 |
| 370_M | 374_C | 1.014 | 0.93 |
| 425_A | 428_Q | 1.008 | 0.93 |
| 434_I | 439_C | 1.006 | 0.93 |
| 195_T | 324_G | 1.004 | 0.93 |
| 34_P | 37_I | 1.001 | 0.92 |
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 | |
| 4pxaA | 1 | 0.7888 | 100 | 0.455 | Contact Map |
| 3sqwA | 1 | 0.9506 | 100 | 0.457 | Contact Map |
| 3i5xA | 1 | 0.9528 | 100 | 0.463 | Contact Map |
| 2db3A | 4 | 0.7753 | 100 | 0.463 | Contact Map |
| 3fmpB | 2 | 0.4067 | 100 | 0.476 | Contact Map |
| 4nhoA | 1 | 0.7708 | 100 | 0.479 | Contact Map |
| 4w7sA | 2 | 0.8202 | 100 | 0.48 | Contact Map |
| 4d25A | 1 | 0.7753 | 100 | 0.481 | Contact Map |
| 4ljyA | 1 | 0.8315 | 100 | 0.485 | Contact Map |
| 4c9bA | 1 | 0.782 | 100 | 0.494 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)