| AdhSeq |
| ID: | 1433329373 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 373 (351) | ||
| Sequences: | 21293 (14769.4) | ||
| Seq/Len: | 60.664 | ||
| Nf(neff/√len): | 788.3 |
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: 60.664).
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 |
| 41_V | 166_L | 3.525 | 1.00 |
| 353_K | 356_E | 3.512 | 1.00 |
| 39_K | 74_E | 3.477 | 1.00 |
| 41_V | 72_I | 3.237 | 1.00 |
| 37_R | 74_E | 3.063 | 1.00 |
| 36_V | 157_V | 2.961 | 1.00 |
| 87_D | 159_K | 2.863 | 1.00 |
| 212_K | 238_T | 2.839 | 1.00 |
| 165_P | 168_K | 2.832 | 1.00 |
| 349_L | 360_L | 2.705 | 1.00 |
| 84_R | 87_D | 2.691 | 1.00 |
| 167_E | 348_V | 2.679 | 1.00 |
| 194_T | 218_R | 2.656 | 1.00 |
| 230_A | 234_E | 2.617 | 1.00 |
| 39_K | 72_I | 2.609 | 1.00 |
| 33_A | 78_E | 2.576 | 1.00 |
| 229_F | 233_K | 2.562 | 1.00 |
| 253_V | 256_E | 2.532 | 1.00 |
| 39_K | 149_Y | 2.531 | 1.00 |
| 88_K | 160_I | 2.471 | 1.00 |
| 34_H | 79_G | 2.451 | 1.00 |
| 195_C | 211_C | 2.412 | 1.00 |
| 82_T | 154_E | 2.410 | 1.00 |
| 218_R | 239_E | 2.396 | 1.00 |
| 33_A | 79_G | 2.382 | 1.00 |
| 28_V | 149_Y | 2.298 | 1.00 |
| 350_P | 353_K | 2.295 | 1.00 |
| 347_H | 360_L | 2.288 | 1.00 |
| 15_W | 24_E | 2.279 | 1.00 |
| 190_T | 193_S | 2.251 | 1.00 |
| 208_I | 237_A | 2.214 | 1.00 |
| 69_A | 145_T | 2.206 | 1.00 |
| 37_R | 151_V | 2.195 | 1.00 |
| 88_K | 166_L | 2.185 | 1.00 |
| 196_A | 262_V | 2.177 | 1.00 |
| 32_K | 35_E | 2.173 | 1.00 |
| 226_K | 230_A | 2.086 | 1.00 |
| 196_A | 222_V | 2.063 | 1.00 |
| 74_E | 149_Y | 2.059 | 1.00 |
| 349_L | 357_G | 1.989 | 1.00 |
| 70_A | 166_L | 1.982 | 1.00 |
| 359_D | 363_S | 1.978 | 1.00 |
| 176_F | 206_S | 1.972 | 1.00 |
| 230_A | 233_K | 1.954 | 1.00 |
| 69_A | 91_P | 1.927 | 1.00 |
| 54_S | 362_R | 1.923 | 1.00 |
| 332_A | 336_A | 1.922 | 1.00 |
| 30_P | 75_S | 1.913 | 1.00 |
| 226_K | 242_N | 1.902 | 1.00 |
| 356_E | 359_D | 1.892 | 1.00 |
| 168_K | 342_D | 1.886 | 1.00 |
| 229_F | 240_C | 1.885 | 1.00 |
| 360_L | 365_E | 1.875 | 1.00 |
| 160_I | 169_V | 1.867 | 1.00 |
| 282_C | 289_S | 1.865 | 1.00 |
| 223_D | 229_F | 1.839 | 1.00 |
| 163_A | 335_M | 1.829 | 1.00 |
| 193_S | 288_V | 1.811 | 1.00 |
| 76_I | 85_P | 1.805 | 1.00 |
| 75_S | 85_P | 1.803 | 1.00 |
| 77_G | 80_V | 1.788 | 1.00 |
| 88_K | 162_A | 1.777 | 1.00 |
| 184_V | 214_A | 1.763 | 1.00 |
| 263_D | 283_Q | 1.748 | 1.00 |
| 200_L | 221_G | 1.744 | 1.00 |
| 35_E | 153_D | 1.739 | 1.00 |
| 37_R | 149_Y | 1.738 | 1.00 |
| 231_K | 234_E | 1.731 | 1.00 |
| 83_V | 159_K | 1.729 | 1.00 |
| 288_V | 312_T | 1.718 | 1.00 |
| 72_I | 88_K | 1.701 | 1.00 |
| 160_I | 166_L | 1.689 | 1.00 |
| 15_W | 22_S | 1.687 | 1.00 |
| 220_I | 262_V | 1.671 | 1.00 |
| 83_V | 87_D | 1.654 | 1.00 |
| 35_E | 151_V | 1.651 | 1.00 |
| 356_E | 360_L | 1.637 | 1.00 |
| 239_E | 257_M | 1.635 | 1.00 |
| 265_S | 278_A | 1.627 | 1.00 |
| 348_V | 372_T | 1.618 | 1.00 |
| 208_I | 221_G | 1.613 | 1.00 |
| 288_V | 314_K | 1.610 | 1.00 |
| 31_P | 151_V | 1.605 | 1.00 |
| 34_H | 153_D | 1.601 | 1.00 |
| 40_M | 69_A | 1.596 | 1.00 |
| 100_C | 103_C | 1.583 | 1.00 |
| 37_R | 75_S | 1.576 | 1.00 |
| 36_V | 83_V | 1.572 | 1.00 |
| 13_V | 24_E | 1.565 | 1.00 |
| 198_F | 278_A | 1.561 | 1.00 |
| 42_A | 167_E | 1.524 | 1.00 |
| 226_K | 245_D | 1.520 | 1.00 |
| 187_A | 264_F | 1.510 | 1.00 |
| 73_V | 83_V | 1.501 | 1.00 |
| 31_P | 37_R | 1.498 | 1.00 |
| 72_I | 166_L | 1.494 | 1.00 |
| 355_N | 359_D | 1.494 | 1.00 |
| 242_N | 245_D | 1.493 | 1.00 |
| 146_F | 358_F | 1.473 | 1.00 |
| 207_V | 266_F | 1.471 | 1.00 |
| 282_C | 287_G | 1.470 | 1.00 |
| 218_R | 238_T | 1.440 | 1.00 |
| 346_T | 360_L | 1.438 | 1.00 |
| 10_K | 25_E | 1.417 | 1.00 |
| 83_V | 157_V | 1.411 | 1.00 |
| 194_T | 220_I | 1.405 | 0.99 |
| 38_I | 71_G | 1.392 | 0.99 |
| 41_V | 88_K | 1.391 | 0.99 |
| 198_F | 222_V | 1.384 | 0.99 |
| 249_P | 252_E | 1.370 | 0.99 |
| 265_S | 282_C | 1.368 | 0.99 |
| 226_K | 229_F | 1.358 | 0.99 |
| 97_C | 100_C | 1.352 | 0.99 |
| 31_P | 35_E | 1.347 | 0.99 |
| 42_A | 166_L | 1.337 | 0.99 |
| 332_A | 335_M | 1.312 | 0.99 |
| 40_M | 150_T | 1.309 | 0.99 |
| 53_V | 358_F | 1.304 | 0.99 |
| 221_G | 237_A | 1.297 | 0.99 |
| 189_V | 216_A | 1.294 | 0.99 |
| 97_C | 103_C | 1.273 | 0.99 |
| 224_I | 243_P | 1.269 | 0.99 |
| 233_K | 240_C | 1.266 | 0.99 |
| 34_H | 154_E | 1.262 | 0.99 |
| 213_A | 338_K | 1.261 | 0.99 |
| 282_C | 311_R | 1.247 | 0.99 |
| 152_V | 157_V | 1.241 | 0.98 |
| 164_S | 169_V | 1.238 | 0.98 |
| 10_K | 148_Q | 1.237 | 0.98 |
| 253_V | 257_M | 1.237 | 0.98 |
| 234_E | 343_P | 1.221 | 0.98 |
| 100_C | 111_C | 1.199 | 0.98 |
| 103_C | 111_C | 1.194 | 0.98 |
| 45_I | 357_G | 1.194 | 0.98 |
| 248_K | 253_V | 1.191 | 0.98 |
| 28_V | 37_R | 1.190 | 0.98 |
| 194_T | 263_D | 1.182 | 0.98 |
| 12_A | 354_I | 1.176 | 0.98 |
| 16_E | 19_K | 1.170 | 0.97 |
| 23_I | 352_E | 1.164 | 0.97 |
| 340_A | 343_P | 1.160 | 0.97 |
| 252_E | 256_E | 1.146 | 0.97 |
| 11_A | 26_V | 1.144 | 0.97 |
| 187_A | 290_V | 1.137 | 0.97 |
| 211_C | 216_A | 1.136 | 0.97 |
| 194_T | 217_A | 1.135 | 0.97 |
| 229_F | 242_N | 1.131 | 0.97 |
| 329_K | 332_A | 1.126 | 0.97 |
| 42_A | 372_T | 1.116 | 0.96 |
| 267_E | 270_G | 1.114 | 0.96 |
| 43_T | 145_T | 1.104 | 0.96 |
| 193_S | 263_D | 1.102 | 0.96 |
| 38_I | 89_V | 1.098 | 0.96 |
| 76_I | 80_V | 1.096 | 0.96 |
| 359_D | 362_R | 1.080 | 0.95 |
| 197_V | 211_C | 1.078 | 0.95 |
| 224_I | 244_Q | 1.077 | 0.95 |
| 197_V | 207_V | 1.075 | 0.95 |
| 233_K | 239_E | 1.075 | 0.95 |
| 220_I | 239_E | 1.069 | 0.95 |
| 44_G | 68_E | 1.068 | 0.95 |
| 328_P | 332_A | 1.067 | 0.95 |
| 39_K | 148_Q | 1.061 | 0.95 |
| 53_V | 362_R | 1.056 | 0.95 |
| 213_A | 333_D | 1.048 | 0.94 |
| 80_V | 154_E | 1.040 | 0.94 |
| 43_T | 146_F | 1.030 | 0.94 |
| 185_K | 326_S | 1.029 | 0.94 |
| 41_V | 70_A | 1.026 | 0.94 |
| 74_E | 85_P | 1.024 | 0.93 |
| 189_V | 193_S | 1.021 | 0.93 |
| 179_G | 210_G | 1.016 | 0.93 |
| 196_A | 281_C | 1.014 | 0.93 |
| 198_F | 265_S | 1.012 | 0.93 |
| 227_D | 230_A | 1.009 | 0.93 |
| 146_F | 354_I | 1.008 | 0.93 |
| 10_K | 352_E | 1.004 | 0.93 |
| 269_I | 274_T | 1.003 | 0.93 |
| 232_A | 237_A | 1.001 | 0.92 |
| 12_A | 23_I | 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 | |
| 1cdoA | 2 | 1 | 100 | 0.111 | Contact Map |
| 1e3iA | 2 | 0.9973 | 100 | 0.118 | Contact Map |
| 2jhfA | 2 | 1 | 100 | 0.119 | Contact Map |
| 1p0fA | 2 | 0.9946 | 100 | 0.126 | Contact Map |
| 3ukoA | 2 | 0.9973 | 100 | 0.135 | Contact Map |
| 2fzwA | 2 | 0.9946 | 100 | 0.137 | Contact Map |
| 4rqtA | 1 | 0.992 | 100 | 0.156 | Contact Map |
| 1f8fA | 1 | 0.9598 | 100 | 0.173 | Contact Map |
| 4ej6A | 1 | 0.9035 | 100 | 0.209 | Contact Map |
| 1vj0A | 4 | 0.9357 | 100 | 0.215 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)