| 1kea |
| ID: | 1452700027 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 221 (213) | ||
| Sequences: | 6853 (4252.8) | ||
| Seq/Len: | 32.174 | ||
| Nf(neff/√len): | 291.4 |
HHblits Results: (2015_06)
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: 32.174).
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 |
| 113_N | 116_A | 3.939 | 1.00 |
| 66_C | 69_D | 3.245 | 1.00 |
| 101_V | 105_D | 2.892 | 1.00 |
| 63_K | 77_E | 2.756 | 1.00 |
| 101_V | 121_P | 2.733 | 1.00 |
| 112_R | 138_K | 2.698 | 1.00 |
| 198_A | 203_K | 2.503 | 1.00 |
| 79_A | 89_N | 2.422 | 1.00 |
| 203_K | 206_K | 2.421 | 1.00 |
| 106_Y | 119_D | 2.336 | 1.00 |
| 78_I | 96_K | 2.286 | 1.00 |
| 96_K | 100_R | 2.272 | 1.00 |
| 63_K | 81_D | 2.163 | 1.00 |
| 80_K | 83_K | 2.134 | 1.00 |
| 74_P | 77_E | 2.049 | 1.00 |
| 114_R | 118_L | 2.019 | 1.00 |
| 43_I | 98_L | 1.985 | 1.00 |
| 34_D | 37_V | 1.947 | 1.00 |
| 26_D | 31_H | 1.896 | 1.00 |
| 15_T | 212_L | 1.851 | 1.00 |
| 94_Q | 97_E | 1.849 | 1.00 |
| 68_E | 103_I | 1.835 | 1.00 |
| 163_N | 167_K | 1.822 | 1.00 |
| 210_S | 216_Y | 1.798 | 1.00 |
| 40_I | 95_L | 1.795 | 1.00 |
| 105_D | 119_D | 1.790 | 1.00 |
| 100_R | 104_N | 1.778 | 1.00 |
| 68_E | 72_K | 1.737 | 1.00 |
| 36_Y | 67_F | 1.735 | 1.00 |
| 97_E | 121_P | 1.726 | 1.00 |
| 65_K | 69_D | 1.707 | 1.00 |
| 75_K | 96_K | 1.690 | 1.00 |
| 75_K | 79_A | 1.660 | 1.00 |
| 148_V | 165_N | 1.651 | 1.00 |
| 116_A | 119_D | 1.613 | 1.00 |
| 17_L | 184_D | 1.607 | 1.00 |
| 197_C | 207_C | 1.603 | 1.00 |
| 36_Y | 99_A | 1.597 | 1.00 |
| 64_Y | 73_T | 1.591 | 1.00 |
| 157_G | 168_A | 1.565 | 1.00 |
| 58_D | 62_V | 1.551 | 1.00 |
| 12_F | 209_M | 1.523 | 1.00 |
| 97_E | 100_R | 1.507 | 1.00 |
| 33_R | 37_V | 1.493 | 1.00 |
| 73_T | 78_I | 1.487 | 1.00 |
| 103_I | 108_G | 1.470 | 1.00 |
| 114_R | 132_M | 1.467 | 1.00 |
| 204_C | 207_C | 1.438 | 1.00 |
| 15_T | 211_K | 1.436 | 1.00 |
| 48_T | 52_H | 1.434 | 1.00 |
| 109_R | 112_R | 1.426 | 1.00 |
| 90_Q | 94_Q | 1.416 | 1.00 |
| 191_D | 195_I | 1.410 | 1.00 |
| 114_R | 140_A | 1.401 | 0.99 |
| 197_C | 204_C | 1.400 | 0.99 |
| 59_K | 62_V | 1.392 | 0.99 |
| 132_M | 138_K | 1.392 | 0.99 |
| 64_Y | 81_D | 1.355 | 0.99 |
| 52_H | 55_K | 1.350 | 0.99 |
| 37_V | 61_F | 1.348 | 0.99 |
| 11_V | 15_T | 1.347 | 0.99 |
| 156_G | 214_S | 1.346 | 0.99 |
| 45_L | 50_A | 1.341 | 0.99 |
| 204_C | 213_C | 1.321 | 0.99 |
| 154_Y | 209_M | 1.302 | 0.99 |
| 90_Q | 93_E | 1.297 | 0.99 |
| 59_K | 81_D | 1.261 | 0.99 |
| 79_A | 88_S | 1.254 | 0.99 |
| 177_V | 185_F | 1.238 | 0.98 |
| 112_R | 136_F | 1.237 | 0.98 |
| 48_T | 85_I | 1.236 | 0.98 |
| 74_P | 96_K | 1.220 | 0.98 |
| 35_P | 135_A | 1.217 | 0.98 |
| 101_V | 119_D | 1.203 | 0.98 |
| 101_V | 106_Y | 1.192 | 0.98 |
| 20_W | 192_F | 1.188 | 0.98 |
| 76_S | 79_A | 1.165 | 0.97 |
| 17_L | 181_K | 1.165 | 0.97 |
| 55_K | 58_D | 1.164 | 0.97 |
| 98_L | 120_L | 1.161 | 0.97 |
| 118_L | 125_K | 1.161 | 0.97 |
| 21_N | 184_D | 1.150 | 0.97 |
| 215_Y | 218_K | 1.143 | 0.97 |
| 102_V | 110_V | 1.130 | 0.97 |
| 21_N | 181_K | 1.129 | 0.97 |
| 141_A | 174_E | 1.125 | 0.97 |
| 184_D | 188_G | 1.124 | 0.97 |
| 40_I | 61_F | 1.107 | 0.96 |
| 12_F | 154_Y | 1.105 | 0.96 |
| 196_I | 208_G | 1.100 | 0.96 |
| 19_F | 208_G | 1.097 | 0.96 |
| 57_Y | 61_F | 1.088 | 0.96 |
| 97_E | 101_V | 1.083 | 0.96 |
| 49_T | 52_H | 1.083 | 0.96 |
| 106_Y | 116_A | 1.082 | 0.96 |
| 28_P | 58_D | 1.078 | 0.95 |
| 54_K | 58_D | 1.052 | 0.95 |
| 39_L | 43_I | 1.051 | 0.94 |
| 105_D | 116_A | 1.044 | 0.94 |
| 181_K | 184_D | 1.042 | 0.94 |
| 70_I | 78_I | 1.040 | 0.94 |
| 125_K | 166_H | 1.036 | 0.94 |
| 137_G | 183_R | 1.020 | 0.93 |
| 154_Y | 212_L | 1.012 | 0.93 |
| 11_V | 14_S | 1.011 | 0.93 |
| 117_I | 132_M | 1.007 | 0.93 |
| 75_K | 93_E | 1.001 | 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 | |
| 3n5nX | 2 | 0.9955 | 100 | 0.163 | Contact Map |
| 1keaA | 1 | 0.9819 | 100 | 0.164 | Contact Map |
| 3fspA | 1 | 0.9683 | 100 | 0.172 | Contact Map |
| 1ornA | 1 | 0.9593 | 100 | 0.178 | Contact Map |
| 1kg2A | 1 | 0.9683 | 100 | 0.18 | Contact Map |
| 4uobA | 1 | 0 | 100 | 0.196 | Contact Map |
| 4unfA | 1 | 0 | 100 | 0.2 | Contact Map |
| 2abkA | 1 | 0.9548 | 100 | 0.201 | Contact Map |
| 1pu6A | 2 | 0.8462 | 100 | 0.342 | Contact Map |
| 3n0uA | 3 | 0.8778 | 100 | 0.439 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)