| IYD |
| ID: | 1510273979 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 222 (198) | ||
| Sequences: | 15967 (10346.4) | ||
| Seq/Len: | 80.641 | ||
| Nf(neff/√len): | 735.3 |
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: 80.641).
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 |
| 46_P | 49_V | 4.091 | 1.00 |
| 52_N | 165_A | 3.606 | 1.00 |
| 47_L | 75_S | 3.238 | 1.00 |
| 47_L | 51_E | 2.852 | 1.00 |
| 43_R | 200_Y | 2.702 | 1.00 |
| 53_I | 162_I | 2.606 | 1.00 |
| 71_F | 154_A | 2.469 | 1.00 |
| 168_V | 201_P | 2.431 | 1.00 |
| 33_H | 163_H | 2.405 | 1.00 |
| 72_V | 129_F | 2.367 | 1.00 |
| 49_V | 165_A | 2.349 | 1.00 |
| 129_F | 190_E | 2.253 | 1.00 |
| 167_L | 200_Y | 2.175 | 1.00 |
| 82_K | 183_I | 2.142 | 1.00 |
| 29_Q | 33_H | 2.105 | 1.00 |
| 159_L | 169_A | 2.079 | 1.00 |
| 70_T | 220_V | 2.040 | 1.00 |
| 77_P | 81_A | 2.040 | 1.00 |
| 155_C | 194_L | 2.000 | 1.00 |
| 55_M | 58_S | 1.971 | 1.00 |
| 49_V | 167_L | 1.961 | 1.00 |
| 71_F | 126_I | 1.942 | 1.00 |
| 56_T | 161_A | 1.925 | 1.00 |
| 41_S | 202_A | 1.897 | 1.00 |
| 39_E | 202_A | 1.876 | 1.00 |
| 49_V | 200_Y | 1.790 | 1.00 |
| 181_Q | 192_P | 1.767 | 1.00 |
| 26_E | 29_Q | 1.740 | 1.00 |
| 57_A | 158_L | 1.728 | 1.00 |
| 153_I | 156_G | 1.724 | 1.00 |
| 155_C | 196_V | 1.714 | 1.00 |
| 159_L | 196_V | 1.690 | 1.00 |
| 162_I | 198_V | 1.631 | 1.00 |
| 149_E | 152_G | 1.619 | 1.00 |
| 27_Y | 31_M | 1.610 | 1.00 |
| 81_A | 120_E | 1.605 | 1.00 |
| 128_V | 155_C | 1.587 | 1.00 |
| 53_I | 158_L | 1.550 | 1.00 |
| 70_T | 190_E | 1.543 | 1.00 |
| 79_I | 82_K | 1.531 | 1.00 |
| 75_S | 124_Y | 1.527 | 1.00 |
| 49_V | 52_N | 1.494 | 1.00 |
| 163_H | 168_V | 1.489 | 1.00 |
| 28_Y | 52_N | 1.479 | 1.00 |
| 179_F | 182_K | 1.468 | 1.00 |
| 126_I | 158_L | 1.464 | 1.00 |
| 29_Q | 32_D | 1.430 | 1.00 |
| 176_P | 179_F | 1.424 | 1.00 |
| 76_D | 79_I | 1.412 | 1.00 |
| 44_A | 75_S | 1.411 | 1.00 |
| 132_A | 191_R | 1.408 | 1.00 |
| 27_Y | 30_F | 1.401 | 0.99 |
| 41_S | 200_Y | 1.394 | 0.99 |
| 28_Y | 32_D | 1.394 | 0.99 |
| 77_P | 80_K | 1.384 | 0.99 |
| 127_V | 192_P | 1.368 | 0.99 |
| 125_L | 195_L | 1.363 | 0.99 |
| 32_D | 59_T | 1.358 | 0.99 |
| 53_I | 198_V | 1.338 | 0.99 |
| 86_A | 183_I | 1.337 | 0.99 |
| 159_L | 171_T | 1.334 | 0.99 |
| 167_L | 198_V | 1.331 | 0.99 |
| 25_A | 29_Q | 1.313 | 0.99 |
| 161_A | 164_Q | 1.294 | 0.99 |
| 74_V | 127_V | 1.279 | 0.99 |
| 40_F | 197_P | 1.279 | 0.99 |
| 32_D | 55_M | 1.275 | 0.99 |
| 84_R | 120_E | 1.272 | 0.99 |
| 60_A | 157_F | 1.261 | 0.99 |
| 161_A | 165_A | 1.249 | 0.99 |
| 130_R | 147_V | 1.248 | 0.99 |
| 129_F | 186_R | 1.245 | 0.98 |
| 215_K | 219_M | 1.237 | 0.98 |
| 73_V | 124_Y | 1.229 | 0.98 |
| 48_E | 51_E | 1.225 | 0.98 |
| 131_K | 189_N | 1.216 | 0.98 |
| 151_V | 193_F | 1.213 | 0.98 |
| 72_V | 190_E | 1.209 | 0.98 |
| 128_V | 151_V | 1.205 | 0.98 |
| 156_G | 160_A | 1.193 | 0.98 |
| 124_Y | 198_V | 1.184 | 0.98 |
| 62_S | 67_Q | 1.176 | 0.98 |
| 36_T | 170_L | 1.176 | 0.98 |
| 78_Q | 82_K | 1.151 | 0.97 |
| 83_I | 180_L | 1.149 | 0.97 |
| 128_V | 196_V | 1.129 | 0.97 |
| 81_A | 85_Q | 1.121 | 0.97 |
| 27_Y | 160_A | 1.114 | 0.96 |
| 126_I | 198_V | 1.111 | 0.96 |
| 169_A | 196_V | 1.106 | 0.96 |
| 51_E | 55_M | 1.105 | 0.96 |
| 46_P | 200_Y | 1.103 | 0.96 |
| 148_Q | 193_F | 1.096 | 0.96 |
| 54_V | 219_M | 1.092 | 0.96 |
| 127_V | 195_L | 1.091 | 0.96 |
| 50_I | 124_Y | 1.089 | 0.96 |
| 71_F | 128_V | 1.089 | 0.96 |
| 171_T | 194_L | 1.088 | 0.96 |
| 51_E | 216_A | 1.080 | 0.95 |
| 53_I | 167_L | 1.078 | 0.95 |
| 30_F | 164_Q | 1.076 | 0.95 |
| 31_M | 160_A | 1.071 | 0.95 |
| 54_V | 57_A | 1.055 | 0.95 |
| 28_Y | 56_T | 1.047 | 0.94 |
| 54_V | 73_V | 1.044 | 0.94 |
| 73_V | 126_I | 1.044 | 0.94 |
| 56_T | 165_A | 1.020 | 0.93 |
| 178_N | 182_K | 1.019 | 0.93 |
| 39_E | 203_E | 1.018 | 0.93 |
| 170_L | 197_P | 1.014 | 0.93 |
| 128_V | 158_L | 1.011 | 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 | |
| 3gb5A | 1 | 0.8198 | 100 | 0.199 | Contact Map |
| 1noxA | 1 | 0.7748 | 100 | 0.255 | Contact Map |
| 4qlxA | 2 | 0.8198 | 100 | 0.259 | Contact Map |
| 3ge6A | 2 | 0.7928 | 100 | 0.26 | Contact Map |
| 3of4A | 3 | 0.7748 | 100 | 0.261 | Contact Map |
| 3bemA | 2 | 0.7973 | 100 | 0.263 | Contact Map |
| 1icrA | 2 | 0.7928 | 100 | 0.266 | Contact Map |
| 3eo8A | 6 | 0.8829 | 100 | 0.266 | Contact Map |
| 3n2sA | 4 | 0.7658 | 100 | 0.267 | Contact Map |
| 3qdlA | 4 | 0.7523 | 100 | 0.267 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)