| 5_blade 3K1U_A |
| ID: | 1483622340 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 314 (304) | ||
| Sequences: | 6214 (3505.4) | ||
| Seq/Len: | 20.441 | ||
| Nf(neff/√len): | 201.0 |
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: 20.441).
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 |
| 139_K | 161_E | 7.053 | 1.00 |
| 41_T | 44_G | 5.677 | 1.00 |
| 21_Y | 38_K | 5.320 | 1.00 |
| 201_K | 223_E | 5.137 | 1.00 |
| 77_A | 103_Q | 4.164 | 1.00 |
| 266_H | 295_I | 4.090 | 1.00 |
| 201_K | 221_T | 3.692 | 1.00 |
| 21_Y | 40_K | 3.656 | 1.00 |
| 299_R | 303_T | 3.411 | 1.00 |
| 25_T | 114_W | 3.236 | 1.00 |
| 161_E | 169_K | 3.052 | 1.00 |
| 261_S | 266_H | 2.829 | 1.00 |
| 143_V | 159_I | 2.806 | 1.00 |
| 135_E | 140_L | 2.727 | 1.00 |
| 260_V | 267_D | 2.455 | 1.00 |
| 263_D | 266_H | 2.423 | 1.00 |
| 73_F | 76_G | 2.403 | 1.00 |
| 77_A | 105_E | 2.328 | 1.00 |
| 159_I | 229_L | 2.320 | 1.00 |
| 38_K | 48_A | 2.316 | 1.00 |
| 228_L | 234_W | 2.262 | 1.00 |
| 104_N | 113_N | 2.248 | 1.00 |
| 258_F | 296_I | 2.238 | 1.00 |
| 77_A | 107_E | 2.217 | 1.00 |
| 164_N | 167_T | 2.216 | 1.00 |
| 160_A | 168_L | 2.182 | 1.00 |
| 299_R | 305_D | 2.141 | 1.00 |
| 71_I | 80_I | 2.124 | 1.00 |
| 173_V | 229_L | 2.118 | 1.00 |
| 221_T | 303_T | 2.098 | 1.00 |
| 17_H | 78_W | 1.986 | 1.00 |
| 25_T | 71_I | 1.863 | 1.00 |
| 163_E | 167_T | 1.799 | 1.00 |
| 198_K | 298_W | 1.746 | 1.00 |
| 51_V | 80_I | 1.741 | 1.00 |
| 17_H | 73_F | 1.737 | 1.00 |
| 137_N | 197_K | 1.724 | 1.00 |
| 103_Q | 117_K | 1.709 | 1.00 |
| 271_Y | 294_Q | 1.691 | 1.00 |
| 298_W | 304_P | 1.689 | 1.00 |
| 22_Y | 39_A | 1.684 | 1.00 |
| 144_W | 160_A | 1.681 | 1.00 |
| 222_A | 234_W | 1.679 | 1.00 |
| 38_K | 46_R | 1.668 | 1.00 |
| 16_K | 262_E | 1.664 | 1.00 |
| 143_V | 234_W | 1.657 | 1.00 |
| 205_T | 219_M | 1.657 | 1.00 |
| 143_V | 228_L | 1.652 | 1.00 |
| 197_K | 202_I | 1.640 | 1.00 |
| 134_F | 202_I | 1.639 | 1.00 |
| 79_Y | 101_V | 1.637 | 1.00 |
| 273_A | 292_R | 1.630 | 1.00 |
| 103_Q | 115_V | 1.629 | 1.00 |
| 38_K | 110_F | 1.629 | 1.00 |
| 34_I | 80_I | 1.577 | 1.00 |
| 223_E | 235_T | 1.574 | 1.00 |
| 297_N | 305_D | 1.565 | 1.00 |
| 196_L | 258_F | 1.564 | 1.00 |
| 267_D | 298_W | 1.564 | 1.00 |
| 221_T | 235_T | 1.550 | 1.00 |
| 195_V | 234_W | 1.535 | 1.00 |
| 136_H | 197_K | 1.534 | 1.00 |
| 14_I | 270_V | 1.502 | 1.00 |
| 25_T | 109_P | 1.501 | 1.00 |
| 159_I | 234_W | 1.491 | 1.00 |
| 9_R | 37_R | 1.473 | 1.00 |
| 270_V | 293_A | 1.468 | 1.00 |
| 73_F | 78_W | 1.436 | 1.00 |
| 158_Y | 174_M | 1.433 | 1.00 |
| 196_L | 298_W | 1.424 | 1.00 |
| 217_I | 269_I | 1.424 | 1.00 |
| 39_A | 45_L | 1.411 | 1.00 |
| 108_N | 113_N | 1.392 | 0.99 |
| 269_I | 306_F | 1.387 | 0.99 |
| 16_K | 20_G | 1.371 | 0.99 |
| 131_A | 142_Y | 1.364 | 0.99 |
| 15_Y | 78_W | 1.364 | 0.99 |
| 141_Y | 229_L | 1.355 | 0.99 |
| 53_V | 80_I | 1.348 | 0.99 |
| 81_Y | 133_I | 1.342 | 0.99 |
| 34_I | 66_I | 1.338 | 0.99 |
| 241_V | 306_F | 1.336 | 0.99 |
| 174_M | 177_K | 1.318 | 0.99 |
| 268_V | 295_I | 1.315 | 0.99 |
| 143_V | 195_V | 1.310 | 0.99 |
| 9_R | 26_A | 1.308 | 0.99 |
| 35_E | 47_N | 1.298 | 0.99 |
| 205_T | 217_I | 1.282 | 0.99 |
| 208_A | 218_G | 1.278 | 0.99 |
| 196_L | 205_T | 1.276 | 0.99 |
| 256_N | 269_I | 1.264 | 0.99 |
| 259_T | 270_V | 1.260 | 0.99 |
| 205_T | 258_F | 1.251 | 0.99 |
| 200_G | 223_E | 1.247 | 0.99 |
| 261_S | 268_V | 1.233 | 0.98 |
| 81_Y | 142_Y | 1.231 | 0.98 |
| 268_V | 293_A | 1.228 | 0.98 |
| 81_Y | 165_P | 1.217 | 0.98 |
| 260_V | 264_G | 1.214 | 0.98 |
| 159_I | 228_L | 1.206 | 0.98 |
| 39_A | 42_I | 1.198 | 0.98 |
| 134_F | 228_L | 1.193 | 0.98 |
| 201_K | 222_A | 1.184 | 0.98 |
| 108_N | 114_W | 1.177 | 0.98 |
| 70_E | 132_T | 1.170 | 0.97 |
| 42_I | 293_A | 1.159 | 0.97 |
| 198_K | 267_D | 1.147 | 0.97 |
| 250_Q | 292_R | 1.113 | 0.96 |
| 253_P | 273_A | 1.110 | 0.96 |
| 136_H | 202_I | 1.109 | 0.96 |
| 222_A | 233_S | 1.108 | 0.96 |
| 26_A | 37_R | 1.100 | 0.96 |
| 37_R | 47_N | 1.100 | 0.96 |
| 36_V | 71_I | 1.099 | 0.96 |
| 100_F | 116_E | 1.096 | 0.96 |
| 143_V | 204_I | 1.092 | 0.96 |
| 190_N | 206_Y | 1.091 | 0.96 |
| 198_K | 260_V | 1.082 | 0.96 |
| 80_I | 102_I | 1.070 | 0.95 |
| 104_N | 112_G | 1.069 | 0.95 |
| 252_G | 274_R | 1.069 | 0.95 |
| 35_E | 50_P | 1.067 | 0.95 |
| 257_S | 270_V | 1.064 | 0.95 |
| 197_K | 200_G | 1.063 | 0.95 |
| 24_F | 291_T | 1.060 | 0.95 |
| 267_D | 296_I | 1.056 | 0.95 |
| 61_E | 100_F | 1.056 | 0.95 |
| 217_I | 256_N | 1.056 | 0.95 |
| 176_T | 220_L | 1.054 | 0.95 |
| 105_E | 115_V | 1.053 | 0.95 |
| 205_T | 256_N | 1.052 | 0.95 |
| 163_E | 169_K | 1.043 | 0.94 |
| 66_I | 82_F | 1.043 | 0.94 |
| 160_A | 170_T | 1.041 | 0.94 |
| 157_I | 206_Y | 1.038 | 0.94 |
| 133_I | 142_Y | 1.036 | 0.94 |
| 25_T | 36_V | 1.033 | 0.94 |
| 99_M | 142_Y | 1.027 | 0.94 |
| 25_T | 34_I | 1.025 | 0.93 |
| 222_A | 228_L | 1.024 | 0.93 |
| 133_I | 140_L | 1.022 | 0.93 |
| 39_A | 43_E | 1.016 | 0.93 |
| 230_D | 233_S | 1.016 | 0.93 |
| 271_Y | 292_R | 1.015 | 0.93 |
| 82_F | 100_F | 1.014 | 0.93 |
| 230_D | 234_W | 1.011 | 0.93 |
| 99_M | 131_A | 1.009 | 0.93 |
| 109_P | 114_W | 1.003 | 0.93 |
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 | |
| 3akhA | 1 | 0.9841 | 100 | 0.146 | Contact Map |
| 3k1uA | 1 | 0.9904 | 100 | 0.176 | Contact Map |
| 3c2uA | 4 | 0.9268 | 100 | 0.251 | Contact Map |
| 1yrzA | 2 | 0.9204 | 100 | 0.257 | Contact Map |
| 4kc7A | 3 | 0.8726 | 100 | 0.26 | Contact Map |
| 4qqsA | 2 | 0.9299 | 100 | 0.261 | Contact Map |
| 2exhA | 4 | 0.9268 | 100 | 0.263 | Contact Map |
| 1yifA | 4 | 0.9268 | 100 | 0.269 | Contact Map |
| 2x8sA | 2 | 0.8662 | 100 | 0.274 | Contact Map |
| 4kcaA | 2 | 0.8949 | 100 | 0.283 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)