| dbpa4 |
| ID: | 1502231822 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 457 (451) | ||
| Sequences: | 5781 (3812.8) | ||
| Seq/Len: | 12.818 | ||
| Nf(neff/√len): | 179.5 |
Jackhmmer Results: (2016_04)
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: 12.818).
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 |
| 58_G | 91_L | 4.643 | 1.00 |
| 61_L | 74_A | 3.976 | 1.00 |
| 128_A | 133_L | 3.969 | 1.00 |
| 29_V | 45_V | 3.796 | 1.00 |
| 11_P | 63_Q | 3.728 | 1.00 |
| 136_H | 141_T | 3.632 | 1.00 |
| 78_C | 87_V | 3.412 | 1.00 |
| 37_I | 181_L | 3.251 | 1.00 |
| 41_K | 203_L | 3.237 | 1.00 |
| 20_E | 97_F | 3.234 | 1.00 |
| 318_L | 343_S | 2.964 | 1.00 |
| 138_Q | 169_D | 2.706 | 1.00 |
| 248_C | 254_C | 2.658 | 1.00 |
| 91_L | 103_I | 2.608 | 1.00 |
| 61_L | 151_V | 2.486 | 1.00 |
| 251_K | 274_D | 2.482 | 1.00 |
| 36_A | 203_L | 2.456 | 1.00 |
| 309_S | 337_N | 2.454 | 1.00 |
| 134_L | 169_D | 2.421 | 1.00 |
| 90_E | 93_R | 2.390 | 1.00 |
| 192_A | 204_A | 2.382 | 1.00 |
| 77_L | 133_L | 2.379 | 1.00 |
| 150_L | 171_I | 2.301 | 1.00 |
| 266_Q | 294_V | 2.270 | 1.00 |
| 20_E | 96_R | 2.262 | 1.00 |
| 128_A | 142_V | 2.223 | 1.00 |
| 248_C | 257_V | 2.204 | 1.00 |
| 233_Q | 264_V | 2.158 | 1.00 |
| 5_S | 19_N | 2.142 | 1.00 |
| 217_E | 365_N | 2.129 | 1.00 |
| 36_A | 205_I | 2.128 | 1.00 |
| 134_L | 138_Q | 2.090 | 1.00 |
| 329_I | 341_A | 2.072 | 1.00 |
| 14_Q | 63_Q | 2.025 | 1.00 |
| 217_E | 340_L | 1.949 | 1.00 |
| 75_L | 147_L | 1.940 | 1.00 |
| 319_A | 325_H | 1.939 | 1.00 |
| 253_D | 317_E | 1.931 | 1.00 |
| 23_Y | 55_A | 1.906 | 1.00 |
| 215_P | 338_S | 1.903 | 1.00 |
| 61_L | 149_T | 1.891 | 1.00 |
| 315_N | 343_S | 1.886 | 1.00 |
| 71_Q | 146_A | 1.856 | 1.00 |
| 269_L | 292_A | 1.855 | 1.00 |
| 104_L | 123_P | 1.854 | 1.00 |
| 285_V | 289_N | 1.832 | 1.00 |
| 12_P | 16_T | 1.828 | 1.00 |
| 218_Q | 325_H | 1.808 | 1.00 |
| 16_T | 97_F | 1.807 | 1.00 |
| 254_C | 272_H | 1.765 | 1.00 |
| 255_Q | 270_S | 1.763 | 1.00 |
| 286_R | 291_S | 1.749 | 1.00 |
| 218_Q | 329_I | 1.733 | 1.00 |
| 216_I | 333_A | 1.733 | 1.00 |
| 64_Q | 148_N | 1.721 | 1.00 |
| 37_I | 43_V | 1.714 | 1.00 |
| 17_N | 97_F | 1.697 | 1.00 |
| 258_C | 268_A | 1.689 | 1.00 |
| 88_A | 103_I | 1.688 | 1.00 |
| 40_G | 179_Q | 1.683 | 1.00 |
| 135_D | 139_K | 1.660 | 1.00 |
| 228_K | 317_E | 1.653 | 1.00 |
| 244_C | 314_V | 1.633 | 1.00 |
| 88_A | 105_T | 1.619 | 1.00 |
| 257_V | 296_V | 1.618 | 1.00 |
| 73_Q | 148_N | 1.604 | 1.00 |
| 42_D | 202_P | 1.600 | 1.00 |
| 38_L | 63_Q | 1.597 | 1.00 |
| 246_V | 294_V | 1.595 | 1.00 |
| 258_C | 270_S | 1.579 | 1.00 |
| 14_Q | 59_L | 1.575 | 1.00 |
| 91_L | 125_I | 1.574 | 1.00 |
| 157_R | 160_D | 1.573 | 1.00 |
| 62_L | 98_L | 1.570 | 1.00 |
| 199_Q | 202_P | 1.553 | 1.00 |
| 116_R | 141_T | 1.546 | 1.00 |
| 261_L | 296_V | 1.545 | 1.00 |
| 269_L | 283_T | 1.539 | 1.00 |
| 168_D | 197_R | 1.528 | 1.00 |
| 66_D | 69_L | 1.519 | 1.00 |
| 36_A | 39_A | 1.510 | 1.00 |
| 297_A | 301_A | 1.498 | 1.00 |
| 229_I | 260_A | 1.471 | 1.00 |
| 46_Q | 206_E | 1.469 | 1.00 |
| 76_V | 91_L | 1.465 | 1.00 |
| 73_Q | 124_H | 1.457 | 1.00 |
| 10_L | 59_L | 1.456 | 1.00 |
| 113_G | 117_D | 1.438 | 1.00 |
| 74_A | 149_T | 1.438 | 1.00 |
| 406_G | 409_G | 1.433 | 1.00 |
| 57_F | 87_V | 1.429 | 1.00 |
| 315_N | 329_I | 1.419 | 1.00 |
| 232_L | 316_F | 1.409 | 1.00 |
| 91_L | 127_V | 1.404 | 0.99 |
| 387_I | 400_V | 1.394 | 0.99 |
| 235_L | 342_I | 1.392 | 0.99 |
| 255_Q | 272_H | 1.390 | 0.99 |
| 312_L | 342_I | 1.387 | 0.99 |
| 85_D | 281_D | 1.374 | 0.99 |
| 64_Q | 149_T | 1.361 | 0.99 |
| 42_D | 200_R | 1.356 | 0.99 |
| 164_S | 168_D | 1.349 | 0.99 |
| 400_V | 425_V | 1.346 | 0.99 |
| 18_L | 23_Y | 1.341 | 0.99 |
| 7_L | 10_L | 1.339 | 0.99 |
| 411_D | 414_D | 1.332 | 0.99 |
| 401_L | 415_I | 1.332 | 0.99 |
| 220_F | 345_C | 1.331 | 0.99 |
| 219_Q | 367_Q | 1.327 | 0.99 |
| 77_L | 128_A | 1.321 | 0.99 |
| 41_K | 201_D | 1.316 | 0.99 |
| 213_L | 216_I | 1.316 | 0.99 |
| 219_Q | 340_L | 1.312 | 0.99 |
| 45_V | 183_F | 1.308 | 0.99 |
| 19_N | 24_L | 1.305 | 0.99 |
| 21_L | 93_R | 1.305 | 0.99 |
| 66_D | 124_H | 1.294 | 0.99 |
| 88_A | 92_R | 1.287 | 0.99 |
| 14_Q | 94_L | 1.287 | 0.99 |
| 396_R | 399_D | 1.286 | 0.99 |
| 126_I | 142_V | 1.281 | 0.99 |
| 169_D | 173_F | 1.279 | 0.99 |
| 32_A | 203_L | 1.274 | 0.99 |
| 40_G | 64_Q | 1.263 | 0.99 |
| 137_L | 173_F | 1.263 | 0.99 |
| 254_C | 270_S | 1.249 | 0.99 |
| 112_F | 116_R | 1.235 | 0.98 |
| 237_S | 266_Q | 1.229 | 0.98 |
| 244_C | 294_V | 1.221 | 0.98 |
| 241_P | 244_C | 1.220 | 0.98 |
| 242_S | 311_E | 1.216 | 0.98 |
| 62_L | 95_A | 1.215 | 0.98 |
| 232_L | 314_V | 1.214 | 0.98 |
| 42_D | 180_T | 1.208 | 0.98 |
| 301_A | 305_L | 1.203 | 0.98 |
| 248_C | 296_V | 1.199 | 0.98 |
| 175_P | 178_R | 1.196 | 0.98 |
| 322_P | 359_M | 1.194 | 0.98 |
| 224_S | 227_G | 1.190 | 0.98 |
| 42_D | 178_R | 1.190 | 0.98 |
| 229_I | 264_V | 1.183 | 0.98 |
| 229_I | 257_V | 1.180 | 0.98 |
| 134_L | 166_A | 1.180 | 0.98 |
| 37_I | 60_G | 1.178 | 0.98 |
| 357_S | 363_K | 1.177 | 0.98 |
| 318_L | 356_I | 1.168 | 0.97 |
| 436_K | 439_K | 1.166 | 0.97 |
| 166_A | 169_D | 1.157 | 0.97 |
| 269_L | 286_R | 1.153 | 0.97 |
| 28_P | 32_A | 1.152 | 0.97 |
| 3_A | 6_T | 1.152 | 0.97 |
| 315_N | 341_A | 1.148 | 0.97 |
| 104_L | 118_S | 1.146 | 0.97 |
| 11_P | 14_Q | 1.141 | 0.97 |
| 192_A | 196_G | 1.141 | 0.97 |
| 23_Y | 94_L | 1.139 | 0.97 |
| 425_V | 428_A | 1.136 | 0.97 |
| 229_I | 316_F | 1.128 | 0.97 |
| 112_F | 141_T | 1.127 | 0.97 |
| 72_T | 126_I | 1.117 | 0.96 |
| 16_T | 19_N | 1.111 | 0.96 |
| 446_I | 451_C | 1.105 | 0.96 |
| 102_K | 121_H | 1.103 | 0.96 |
| 440_Q | 444_G | 1.102 | 0.96 |
| 410_L | 414_D | 1.098 | 0.96 |
| 36_A | 43_V | 1.093 | 0.96 |
| 95_A | 101_T | 1.088 | 0.96 |
| 412_G | 416_G | 1.088 | 0.96 |
| 233_Q | 260_A | 1.086 | 0.96 |
| 147_L | 174_A | 1.082 | 0.96 |
| 244_C | 312_L | 1.082 | 0.96 |
| 217_E | 338_S | 1.080 | 0.95 |
| 389_G | 393_A | 1.073 | 0.95 |
| 54_T | 87_V | 1.071 | 0.95 |
| 33_A | 37_I | 1.070 | 0.95 |
| 55_A | 94_L | 1.068 | 0.95 |
| 245_V | 310_L | 1.064 | 0.95 |
| 410_L | 415_I | 1.064 | 0.95 |
| 232_L | 246_V | 1.064 | 0.95 |
| 65_I | 101_T | 1.063 | 0.95 |
| 287_F | 295_L | 1.060 | 0.95 |
| 415_I | 418_I | 1.048 | 0.94 |
| 33_A | 43_V | 1.045 | 0.94 |
| 222_E | 347_P | 1.036 | 0.94 |
| 75_L | 174_A | 1.032 | 0.94 |
| 189_E | 193_A | 1.031 | 0.94 |
| 65_I | 74_A | 1.026 | 0.94 |
| 57_F | 78_C | 1.024 | 0.93 |
| 67_A | 124_H | 1.023 | 0.93 |
| 236_L | 294_V | 1.021 | 0.93 |
| 169_D | 172_R | 1.018 | 0.93 |
| 402_G | 406_G | 1.017 | 0.93 |
| 18_L | 22_G | 1.014 | 0.93 |
| 36_A | 41_K | 1.011 | 0.93 |
| 42_D | 199_Q | 1.009 | 0.93 |
| 399_D | 402_G | 1.009 | 0.93 |
| 246_V | 316_F | 1.007 | 0.93 |
| 230_P | 264_V | 1.003 | 0.93 |
| 416_G | 420_V | 1.002 | 0.92 |
| 400_V | 405_T | 1.002 | 0.92 |
| 322_P | 326_V | 1.001 | 0.92 |
| 16_T | 20_E | 1.000 | 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 | 0.8184 | 100 | 0.322 | Contact Map |
| 2db3A | 4 | 0.8074 | 100 | 0.33 | Contact Map |
| 4nhoA | 1 | 0.8031 | 100 | 0.339 | Contact Map |
| 4ljyA | 1 | 0.8468 | 100 | 0.342 | Contact Map |
| 3sqwA | 1 | 0.9759 | 100 | 0.346 | Contact Map |
| 3fmpB | 2 | 0.4464 | 100 | 0.347 | Contact Map |
| 4d25A | 1 | 0.8096 | 100 | 0.347 | Contact Map |
| 3i5xA | 1 | 0.9562 | 100 | 0.35 | Contact Map |
| 4w7sA | 2 | 0.8512 | 100 | 0.353 | Contact Map |
| 4c9bA | 1 | 0.8118 | 100 | 0.357 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)