| T0807 |
| ID: | 1401990655 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 284 (272) | ||
| Sequences: | 14207 (10450.8) | ||
| Seq/Len: | 52.232 | ||
| Nf(neff/√len): | 633.7 |
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: 52.232).
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 |
| 96_E | 135_K | 3.152 | 1.00 |
| 40_A | 250_V | 2.815 | 1.00 |
| 79_S | 107_L | 2.744 | 1.00 |
| 95_C | 130_L | 2.694 | 1.00 |
| 69_R | 103_Q | 2.528 | 1.00 |
| 77_L | 104_T | 2.524 | 1.00 |
| 219_R | 264_E | 2.514 | 1.00 |
| 31_R | 66_Q | 2.414 | 1.00 |
| 92_H | 133_E | 2.314 | 1.00 |
| 218_A | 267_Q | 2.306 | 1.00 |
| 40_A | 44_H | 2.302 | 1.00 |
| 7_R | 13_A | 2.256 | 1.00 |
| 218_A | 264_E | 2.223 | 1.00 |
| 261_S | 264_E | 2.217 | 1.00 |
| 79_S | 98_S | 2.214 | 1.00 |
| 229_A | 258_I | 2.070 | 1.00 |
| 92_H | 129_K | 1.975 | 1.00 |
| 107_L | 136_I | 1.962 | 1.00 |
| 111_L | 163_T | 1.862 | 1.00 |
| 95_C | 110_Y | 1.851 | 1.00 |
| 49_I | 64_V | 1.800 | 1.00 |
| 97_N | 101_R | 1.794 | 1.00 |
| 111_L | 191_M | 1.758 | 1.00 |
| 129_K | 133_E | 1.723 | 1.00 |
| 35_V | 67_A | 1.721 | 1.00 |
| 213_I | 217_N | 1.710 | 1.00 |
| 182_W | 186_H | 1.706 | 1.00 |
| 221_I | 258_I | 1.696 | 1.00 |
| 189_P | 238_L | 1.689 | 1.00 |
| 262_G | 266_A | 1.685 | 1.00 |
| 41_G | 46_L | 1.684 | 1.00 |
| 129_K | 132_A | 1.675 | 1.00 |
| 215_M | 226_L | 1.673 | 1.00 |
| 6_V | 16_A | 1.669 | 1.00 |
| 78_V | 111_L | 1.667 | 1.00 |
| 222_T | 251_Q | 1.666 | 1.00 |
| 44_H | 253_A | 1.661 | 1.00 |
| 18_G | 48_V | 1.644 | 1.00 |
| 183_C | 190_V | 1.638 | 1.00 |
| 214_N | 267_Q | 1.632 | 1.00 |
| 35_V | 66_Q | 1.630 | 1.00 |
| 71_L | 74_R | 1.625 | 1.00 |
| 62_E | 101_R | 1.623 | 1.00 |
| 95_C | 107_L | 1.576 | 1.00 |
| 150_Q | 154_R | 1.561 | 1.00 |
| 53_E | 94_A | 1.551 | 1.00 |
| 44_H | 250_V | 1.546 | 1.00 |
| 128_E | 132_A | 1.538 | 1.00 |
| 92_H | 126_A | 1.537 | 1.00 |
| 59_G | 62_E | 1.537 | 1.00 |
| 246_I | 250_V | 1.533 | 1.00 |
| 38_L | 67_A | 1.530 | 1.00 |
| 88_K | 92_H | 1.529 | 1.00 |
| 106_Y | 137_R | 1.523 | 1.00 |
| 5_T | 13_A | 1.487 | 1.00 |
| 81_V | 91_M | 1.486 | 1.00 |
| 35_V | 70_G | 1.472 | 1.00 |
| 130_L | 136_I | 1.457 | 1.00 |
| 12_A | 138_R | 1.444 | 1.00 |
| 37_A | 249_V | 1.441 | 1.00 |
| 61_E | 98_S | 1.410 | 1.00 |
| 150_Q | 182_W | 1.407 | 0.99 |
| 243_A | 248_H | 1.394 | 0.99 |
| 136_I | 139_W | 1.391 | 0.99 |
| 88_K | 129_K | 1.386 | 0.99 |
| 166_V | 190_V | 1.377 | 0.99 |
| 150_Q | 185_Q | 1.369 | 0.99 |
| 221_I | 225_Q | 1.365 | 0.99 |
| 222_T | 225_Q | 1.363 | 0.99 |
| 243_A | 249_V | 1.361 | 0.99 |
| 249_V | 253_A | 1.361 | 0.99 |
| 42_I | 75_V | 1.354 | 0.99 |
| 233_R | 265_L | 1.347 | 0.99 |
| 40_A | 43_D | 1.342 | 0.99 |
| 39_R | 67_A | 1.320 | 0.99 |
| 72_R | 104_T | 1.313 | 0.99 |
| 21_T | 49_I | 1.305 | 0.99 |
| 96_E | 100_R | 1.295 | 0.99 |
| 35_V | 39_R | 1.293 | 0.99 |
| 181_P | 185_Q | 1.292 | 0.99 |
| 266_A | 270_R | 1.289 | 0.99 |
| 250_V | 254_A | 1.284 | 0.99 |
| 92_H | 96_E | 1.283 | 0.99 |
| 72_R | 106_Y | 1.267 | 0.99 |
| 12_A | 76_V | 1.265 | 0.99 |
| 127_M | 139_W | 1.251 | 0.99 |
| 126_A | 129_K | 1.249 | 0.99 |
| 170_L | 268_L | 1.249 | 0.99 |
| 88_K | 126_A | 1.242 | 0.98 |
| 39_R | 43_D | 1.240 | 0.98 |
| 40_A | 246_I | 1.239 | 0.98 |
| 33_Q | 36_A | 1.235 | 0.98 |
| 234_H | 265_L | 1.234 | 0.98 |
| 30_Q | 33_Q | 1.217 | 0.98 |
| 212_I | 223_V | 1.208 | 0.98 |
| 62_E | 100_R | 1.201 | 0.98 |
| 76_V | 109_M | 1.195 | 0.98 |
| 247_E | 250_V | 1.195 | 0.98 |
| 214_N | 217_N | 1.185 | 0.98 |
| 254_A | 257_D | 1.185 | 0.98 |
| 178_D | 181_P | 1.180 | 0.98 |
| 88_K | 122_E | 1.177 | 0.98 |
| 97_N | 100_R | 1.170 | 0.97 |
| 211_D | 214_N | 1.164 | 0.97 |
| 212_I | 268_L | 1.161 | 0.97 |
| 221_I | 226_L | 1.157 | 0.97 |
| 93_R | 97_N | 1.155 | 0.97 |
| 10_E | 138_R | 1.154 | 0.97 |
| 173_R | 176_E | 1.154 | 0.97 |
| 81_V | 110_Y | 1.144 | 0.97 |
| 145_D | 148_D | 1.129 | 0.97 |
| 218_A | 261_S | 1.129 | 0.97 |
| 228_L | 255_A | 1.127 | 0.97 |
| 9_G | 162_A | 1.123 | 0.97 |
| 62_E | 66_Q | 1.122 | 0.97 |
| 267_Q | 270_R | 1.120 | 0.96 |
| 138_R | 162_A | 1.111 | 0.96 |
| 88_K | 125_E | 1.108 | 0.96 |
| 102_L | 107_L | 1.101 | 0.96 |
| 215_M | 219_R | 1.093 | 0.96 |
| 143_N | 193_Y | 1.093 | 0.96 |
| 66_Q | 103_Q | 1.093 | 0.96 |
| 96_E | 133_E | 1.092 | 0.96 |
| 229_A | 255_A | 1.081 | 0.95 |
| 78_V | 191_M | 1.078 | 0.95 |
| 219_R | 261_S | 1.077 | 0.95 |
| 226_L | 258_I | 1.062 | 0.95 |
| 79_S | 110_Y | 1.059 | 0.95 |
| 48_V | 191_M | 1.056 | 0.95 |
| 153_W | 186_H | 1.053 | 0.95 |
| 123_T | 126_A | 1.051 | 0.94 |
| 38_L | 49_I | 1.051 | 0.94 |
| 48_V | 78_V | 1.049 | 0.94 |
| 99_L | 135_K | 1.047 | 0.94 |
| 109_M | 163_T | 1.045 | 0.94 |
| 53_E | 90_A | 1.038 | 0.94 |
| 87_G | 90_A | 1.036 | 0.94 |
| 171_A | 209_H | 1.034 | 0.94 |
| 89_A | 93_R | 1.027 | 0.94 |
| 15_P | 46_L | 1.026 | 0.94 |
| 225_Q | 251_Q | 1.021 | 0.93 |
| 65_G | 103_Q | 1.019 | 0.93 |
| 221_I | 229_A | 1.018 | 0.93 |
| 130_L | 133_E | 1.015 | 0.93 |
| 15_P | 47_T | 1.008 | 0.93 |
| 94_A | 110_Y | 1.005 | 0.93 |
| 130_L | 135_K | 1.005 | 0.93 |
| 234_H | 269_D | 1.001 | 0.92 |
| 266_A | 269_D | 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 | |
| 1pyfA | 1 | 0.9437 | 100 | 0.152 | Contact Map |
| 3n2tA | 1 | 0.9859 | 100 | 0.157 | Contact Map |
| 1ur3M | 1 | 0.9683 | 100 | 0.158 | Contact Map |
| 3eauA | 1 | 0.9718 | 100 | 0.162 | Contact Map |
| 1pz1A | 2 | 0.9754 | 100 | 0.164 | Contact Map |
| 1lqaA | 2 | 0.9718 | 100 | 0.171 | Contact Map |
| 1ynpA | 2 | 0.9542 | 100 | 0.173 | Contact Map |
| 3lutA | 1 | 0.9683 | 100 | 0.176 | Contact Map |
| 3erpA | 2 | 0.9648 | 100 | 0.178 | Contact Map |
| 3o0kA | 4 | 0.8979 | 100 | 0.18 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)