| McoA with sp 44-527 |
| ID: | 1494587886 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 484 (453) | ||
| Sequences: | 4390 (2527.1) | ||
| Seq/Len: | 9.691 | ||
| Nf(neff/√len): | 118.7 |
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: 9.691).
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 |
| 53_F | 138_E | 5.660 | 1.00 |
| 204_I | 261_L | 4.472 | 1.00 |
| 61_S | 103_D | 4.281 | 1.00 |
| 256_E | 435_K | 4.234 | 1.00 |
| 59_T | 103_D | 3.497 | 1.00 |
| 438_V | 446_V | 3.482 | 1.00 |
| 19_R | 61_S | 3.466 | 1.00 |
| 51_V | 134_M | 3.456 | 1.00 |
| 23_T | 67_N | 3.257 | 1.00 |
| 63_D | 100_S | 3.210 | 1.00 |
| 235_G | 259_D | 3.184 | 1.00 |
| 209_I | 260_I | 3.170 | 1.00 |
| 21_S | 63_D | 3.065 | 1.00 |
| 21_S | 65_V | 3.042 | 1.00 |
| 19_R | 63_D | 2.993 | 1.00 |
| 209_I | 220_L | 2.849 | 1.00 |
| 252_V | 258_I | 2.823 | 1.00 |
| 421_E | 447_R | 2.820 | 1.00 |
| 64_F | 93_V | 2.760 | 1.00 |
| 231_F | 260_I | 2.620 | 1.00 |
| 65_V | 98_T | 2.617 | 1.00 |
| 399_E | 447_R | 2.616 | 1.00 |
| 222_L | 262_V | 2.615 | 1.00 |
| 134_M | 210_L | 2.595 | 1.00 |
| 400_Y | 410_M | 2.553 | 1.00 |
| 400_Y | 448_I | 2.507 | 1.00 |
| 204_I | 263_D | 2.507 | 1.00 |
| 213_S | 218_Y | 2.501 | 1.00 |
| 415_F | 482_V | 2.496 | 1.00 |
| 207_F | 260_I | 2.443 | 1.00 |
| 27_T | 41_V | 2.428 | 1.00 |
| 397_I | 420_L | 2.423 | 1.00 |
| 397_I | 449_A | 2.374 | 1.00 |
| 160_L | 209_I | 2.330 | 1.00 |
| 200_V | 264_F | 2.307 | 1.00 |
| 417_F | 448_I | 2.306 | 1.00 |
| 168_D | 172_Q | 2.272 | 1.00 |
| 42_Y | 115_Y | 2.259 | 1.00 |
| 29_L | 39_M | 2.232 | 1.00 |
| 162_I | 220_L | 2.203 | 1.00 |
| 94_K | 97_E | 2.191 | 1.00 |
| 26_W | 38_D | 2.182 | 1.00 |
| 206_R | 259_D | 2.165 | 1.00 |
| 412_I | 450_V | 2.137 | 1.00 |
| 56_K | 139_D | 2.106 | 1.00 |
| 85_S | 99_Y | 2.083 | 1.00 |
| 117_P | 126_Q | 2.032 | 1.00 |
| 23_T | 65_V | 2.022 | 1.00 |
| 134_M | 161_I | 2.011 | 1.00 |
| 206_R | 234_I | 2.005 | 1.00 |
| 465_H | 471_H | 1.981 | 1.00 |
| 223_L | 276_Y | 1.969 | 1.00 |
| 441_A | 444_E | 1.961 | 1.00 |
| 257_R | 436_D | 1.961 | 1.00 |
| 161_I | 212_G | 1.939 | 1.00 |
| 466_C | 471_H | 1.935 | 1.00 |
| 55_R | 138_E | 1.933 | 1.00 |
| 132_A | 163_Q | 1.931 | 1.00 |
| 113_Y | 238_G | 1.910 | 1.00 |
| 59_T | 105_T | 1.909 | 1.00 |
| 217_P | 439_I | 1.886 | 1.00 |
| 28_T | 38_D | 1.886 | 1.00 |
| 230_R | 246_E | 1.881 | 1.00 |
| 250_I | 258_I | 1.881 | 1.00 |
| 467_H | 471_H | 1.837 | 1.00 |
| 18_Q | 58_Q | 1.827 | 1.00 |
| 115_Y | 133_G | 1.770 | 1.00 |
| 233_V | 258_I | 1.759 | 1.00 |
| 230_R | 248_N | 1.747 | 1.00 |
| 461_I | 481_R | 1.715 | 1.00 |
| 219_R | 249_E | 1.701 | 1.00 |
| 41_V | 47_E | 1.699 | 1.00 |
| 156_I | 203_K | 1.670 | 1.00 |
| 354_R | 399_E | 1.653 | 1.00 |
| 25_K | 67_N | 1.634 | 1.00 |
| 391_N | 394_D | 1.630 | 1.00 |
| 232_W | 246_E | 1.605 | 1.00 |
| 197_Y | 324_R | 1.593 | 1.00 |
| 24_A | 42_Y | 1.583 | 1.00 |
| 156_I | 205_Y | 1.575 | 1.00 |
| 353_Q | 396_V | 1.572 | 1.00 |
| 233_V | 247_V | 1.567 | 1.00 |
| 24_A | 64_F | 1.536 | 1.00 |
| 418_Q | 434_W | 1.534 | 1.00 |
| 239_G | 416_Q | 1.499 | 1.00 |
| 250_I | 260_I | 1.498 | 1.00 |
| 253_A | 439_I | 1.497 | 1.00 |
| 238_G | 416_Q | 1.483 | 1.00 |
| 42_Y | 74_I | 1.466 | 1.00 |
| 264_F | 323_F | 1.455 | 1.00 |
| 472_H | 477_M | 1.453 | 1.00 |
| 412_I | 448_I | 1.453 | 1.00 |
| 128_Y | 214_N | 1.451 | 1.00 |
| 53_F | 157_D | 1.448 | 1.00 |
| 63_D | 98_T | 1.447 | 1.00 |
| 422_R | 444_E | 1.429 | 1.00 |
| 22_I | 52_I | 1.409 | 0.99 |
| 112_T | 208_R | 1.404 | 0.99 |
| 158_I | 198_M | 1.401 | 0.99 |
| 40_L | 129_Y | 1.384 | 0.99 |
| 17_G | 61_S | 1.383 | 0.99 |
| 158_I | 207_F | 1.382 | 0.99 |
| 220_L | 275_L | 1.369 | 0.99 |
| 222_L | 231_F | 1.358 | 0.99 |
| 222_L | 275_L | 1.357 | 0.99 |
| 200_V | 262_V | 1.351 | 0.99 |
| 127_V | 469_L | 1.340 | 0.99 |
| 76_W | 104_F | 1.338 | 0.99 |
| 72_S | 126_Q | 1.333 | 0.99 |
| 395_V | 451_D | 1.330 | 0.99 |
| 469_L | 472_H | 1.330 | 0.99 |
| 138_E | 157_D | 1.329 | 0.99 |
| 200_V | 297_E | 1.317 | 0.99 |
| 408_H | 413_H | 1.314 | 0.99 |
| 417_F | 438_V | 1.313 | 0.99 |
| 39_M | 165_K | 1.304 | 0.99 |
| 463_L | 477_M | 1.298 | 0.99 |
| 61_S | 100_S | 1.297 | 0.99 |
| 112_T | 134_M | 1.294 | 0.99 |
| 200_V | 205_Y | 1.292 | 0.99 |
| 421_E | 445_T | 1.292 | 0.99 |
| 236_V | 258_I | 1.274 | 0.99 |
| 399_E | 445_T | 1.267 | 0.99 |
| 209_I | 250_I | 1.263 | 0.99 |
| 54_L | 60_F | 1.262 | 0.99 |
| 93_V | 99_Y | 1.261 | 0.99 |
| 54_L | 135_I | 1.256 | 0.98 |
| 199_D | 324_R | 1.253 | 0.98 |
| 407_Y | 439_I | 1.252 | 0.98 |
| 60_F | 135_I | 1.245 | 0.98 |
| 64_F | 76_W | 1.245 | 0.98 |
| 209_I | 252_V | 1.244 | 0.98 |
| 234_I | 261_L | 1.239 | 0.98 |
| 54_L | 137_I | 1.235 | 0.98 |
| 213_S | 254_P | 1.224 | 0.98 |
| 409_P | 468_I | 1.221 | 0.98 |
| 214_N | 470_E | 1.218 | 0.98 |
| 28_T | 36_S | 1.216 | 0.98 |
| 188_I | 218_Y | 1.215 | 0.98 |
| 221_A | 276_Y | 1.206 | 0.98 |
| 208_R | 259_D | 1.206 | 0.98 |
| 275_L | 297_E | 1.202 | 0.98 |
| 51_V | 115_Y | 1.197 | 0.98 |
| 64_F | 74_I | 1.196 | 0.98 |
| 118_H | 467_H | 1.195 | 0.98 |
| 242_D | 340_S | 1.191 | 0.98 |
| 118_H | 466_C | 1.178 | 0.97 |
| 19_R | 103_D | 1.175 | 0.97 |
| 420_L | 449_A | 1.168 | 0.97 |
| 182_G | 406_M | 1.167 | 0.97 |
| 100_S | 103_D | 1.166 | 0.97 |
| 408_H | 471_H | 1.163 | 0.97 |
| 219_R | 251_L | 1.162 | 0.97 |
| 272_V | 322_E | 1.150 | 0.97 |
| 40_L | 68_S | 1.143 | 0.97 |
| 366_I | 410_M | 1.141 | 0.97 |
| 221_A | 249_E | 1.138 | 0.97 |
| 408_H | 466_C | 1.137 | 0.97 |
| 118_H | 471_H | 1.136 | 0.97 |
| 132_A | 212_G | 1.125 | 0.96 |
| 118_H | 465_H | 1.124 | 0.96 |
| 17_G | 59_T | 1.119 | 0.96 |
| 42_Y | 131_L | 1.119 | 0.96 |
| 408_H | 467_H | 1.118 | 0.96 |
| 414_G | 462_Y | 1.116 | 0.96 |
| 60_F | 104_F | 1.114 | 0.96 |
| 49_N | 192_L | 1.111 | 0.96 |
| 26_W | 69_G | 1.105 | 0.96 |
| 56_K | 140_E | 1.096 | 0.96 |
| 232_W | 263_D | 1.093 | 0.96 |
| 410_M | 464_L | 1.090 | 0.95 |
| 134_M | 159_P | 1.088 | 0.95 |
| 55_R | 58_Q | 1.086 | 0.95 |
| 193_T | 196_P | 1.080 | 0.95 |
| 471_H | 476_M | 1.078 | 0.95 |
| 43_E | 48_Y | 1.078 | 0.95 |
| 157_D | 259_D | 1.076 | 0.95 |
| 163_Q | 189_L | 1.068 | 0.95 |
| 163_Q | 212_G | 1.066 | 0.95 |
| 56_K | 108_D | 1.060 | 0.94 |
| 127_V | 132_A | 1.049 | 0.94 |
| 64_F | 101_Y | 1.046 | 0.94 |
| 75_H | 78_G | 1.041 | 0.94 |
| 162_I | 218_Y | 1.040 | 0.94 |
| 118_H | 413_H | 1.039 | 0.94 |
| 400_Y | 464_L | 1.029 | 0.93 |
| 357_L | 366_I | 1.028 | 0.93 |
| 40_L | 131_L | 1.027 | 0.93 |
| 412_I | 464_L | 1.025 | 0.93 |
| 167_F | 187_T | 1.024 | 0.93 |
| 55_R | 140_E | 1.022 | 0.93 |
| 229_M | 273_I | 1.022 | 0.93 |
| 30_E | 34_G | 1.022 | 0.93 |
| 49_N | 115_Y | 1.019 | 0.93 |
| 112_T | 235_G | 1.019 | 0.93 |
| 82_P | 85_S | 1.014 | 0.93 |
| 202_R | 264_F | 1.012 | 0.93 |
| 465_H | 476_M | 1.006 | 0.92 |
| 408_H | 465_H | 1.005 | 0.92 |
| 22_I | 60_F | 1.004 | 0.92 |
| 22_I | 42_Y | 1.003 | 0.92 |
| 396_V | 450_V | 1.002 | 0.92 |
| 219_R | 278_F | 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 | |
| 3abgA | 2 | 0.9132 | 100 | 0.177 | Contact Map |
| 2uxtA | 2 | 0.8574 | 100 | 0.18 | Contact Map |
| 4e9sA | 1 | 0.8884 | 100 | 0.196 | Contact Map |
| 2xu9A | 1 | 0.8946 | 100 | 0.197 | Contact Map |
| 3zx1A | 1 | 0.876 | 100 | 0.201 | Contact Map |
| 2wsdA | 1 | 0.8926 | 100 | 0.201 | Contact Map |
| 3gyrA | 12 | 0.9029 | 100 | 0.203 | Contact Map |
| 1zpuA | 6 | 0.8802 | 100 | 0.208 | Contact Map |
| 3aw5A | 1 | 0.8636 | 100 | 0.209 | Contact Map |
| 3sqrA | 1 | 0.9029 | 100 | 0.223 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)