| HD ACT low coverage |
| ID: | 1425311656 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 50% gaps before running GREMLIN. |
| Length: | 268 (264) | ||
| Sequences: | 1338 (781.9) | ||
| Seq/Len: | 5.068 | ||
| Nf(neff/√len): | 48.1 |
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: 5.068).
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 |
| 39_L | 112_L | 4.541 | 1.00 |
| 129_K | 132_A | 4.248 | 1.00 |
| 64_A | 69_D | 4.208 | 1.00 |
| 53_I | 60_K | 4.127 | 1.00 |
| 125_L | 168_H | 3.532 | 1.00 |
| 123_R | 160_E | 2.683 | 1.00 |
| 42_A | 70_E | 2.565 | 1.00 |
| 60_K | 76_E | 2.555 | 1.00 |
| 139_R | 143_D | 2.544 | 1.00 |
| 203_A | 209_Q | 2.523 | 1.00 |
| 7_Y | 58_V | 2.410 | 1.00 |
| 170_N | 173_A | 2.354 | 1.00 |
| 3_R | 66_L | 2.313 | 1.00 |
| 2_N | 6_V | 2.269 | 1.00 |
| 252_S | 264_V | 2.136 | 1.00 |
| 74_L | 113_V | 2.072 | 1.00 |
| 53_I | 63_I | 2.069 | 1.00 |
| 176_A | 180_R | 2.044 | 1.00 |
| 131_Q | 134_R | 2.038 | 1.00 |
| 73_E | 106_K | 1.976 | 1.00 |
| 122_M | 164_L | 1.968 | 1.00 |
| 1_M | 44_I | 1.930 | 1.00 |
| 166_F | 170_N | 1.925 | 1.00 |
| 8_A | 24_Y | 1.888 | 1.00 |
| 175_N | 178_I | 1.882 | 1.00 |
| 104_I | 108_V | 1.866 | 1.00 |
| 18_A | 128_I | 1.849 | 1.00 |
| 10_R | 13_G | 1.824 | 1.00 |
| 46_T | 74_L | 1.821 | 1.00 |
| 219_G | 247_H | 1.787 | 1.00 |
| 31_A | 44_I | 1.760 | 1.00 |
| 134_R | 168_H | 1.733 | 1.00 |
| 34_L | 47_A | 1.721 | 1.00 |
| 131_Q | 135_E | 1.720 | 1.00 |
| 53_I | 76_E | 1.706 | 1.00 |
| 203_A | 206_V | 1.688 | 0.99 |
| 53_I | 72_G | 1.679 | 0.99 |
| 46_T | 113_V | 1.666 | 0.99 |
| 166_F | 173_A | 1.661 | 0.99 |
| 62_E | 65_K | 1.641 | 0.99 |
| 196_L | 252_S | 1.603 | 0.99 |
| 33_I | 123_R | 1.586 | 0.99 |
| 128_I | 137_I | 1.583 | 0.99 |
| 159_T | 185_R | 1.563 | 0.99 |
| 198_A | 255_L | 1.540 | 0.99 |
| 60_K | 72_G | 1.516 | 0.99 |
| 200_I | 206_V | 1.506 | 0.99 |
| 34_L | 43_T | 1.498 | 0.99 |
| 7_Y | 66_L | 1.478 | 0.98 |
| 5_Y | 9_M | 1.442 | 0.98 |
| 6_V | 9_M | 1.440 | 0.98 |
| 60_K | 64_A | 1.424 | 0.98 |
| 41_T | 45_V | 1.409 | 0.98 |
| 39_L | 43_T | 1.403 | 0.97 |
| 214_I | 240_V | 1.393 | 0.97 |
| 224_L | 238_I | 1.381 | 0.97 |
| 13_G | 16_T | 1.371 | 0.97 |
| 113_V | 150_R | 1.350 | 0.97 |
| 195_R | 239_D | 1.339 | 0.96 |
| 207_L | 220_N | 1.329 | 0.96 |
| 112_L | 166_F | 1.307 | 0.96 |
| 125_L | 138_A | 1.298 | 0.96 |
| 157_I | 196_L | 1.297 | 0.95 |
| 61_E | 64_A | 1.289 | 0.95 |
| 7_Y | 11_M | 1.271 | 0.95 |
| 11_M | 57_P | 1.236 | 0.94 |
| 244_D | 247_H | 1.230 | 0.94 |
| 53_I | 79_T | 1.225 | 0.93 |
| 211_C | 260_T | 1.223 | 0.93 |
| 122_M | 125_L | 1.221 | 0.93 |
| 61_E | 65_K | 1.216 | 0.93 |
| 64_A | 72_G | 1.210 | 0.93 |
| 211_C | 221_I | 1.201 | 0.92 |
| 29_E | 32_G | 1.191 | 0.92 |
| 31_A | 47_A | 1.177 | 0.91 |
| 240_V | 251_I | 1.164 | 0.91 |
| 56_T | 59_T | 1.159 | 0.91 |
| 60_K | 73_E | 1.158 | 0.91 |
| 174_R | 178_I | 1.155 | 0.90 |
| 209_Q | 258_C | 1.155 | 0.90 |
| 58_V | 66_L | 1.146 | 0.90 |
| 226_M | 236_V | 1.145 | 0.90 |
| 99_K | 110_V | 1.144 | 0.90 |
| 120_H | 124_T | 1.134 | 0.89 |
| 11_M | 62_E | 1.132 | 0.89 |
| 55_D | 80_K | 1.125 | 0.89 |
| 212_T | 216_E | 1.121 | 0.89 |
| 102_L | 205_G | 1.110 | 0.88 |
| 55_D | 121_N | 1.103 | 0.87 |
| 45_V | 71_I | 1.098 | 0.87 |
| 94_A | 97_L | 1.092 | 0.87 |
| 197_H | 265_D | 1.091 | 0.87 |
| 203_A | 260_T | 1.089 | 0.87 |
| 173_A | 176_A | 1.074 | 0.86 |
| 206_V | 209_Q | 1.072 | 0.85 |
| 176_A | 244_D | 1.072 | 0.85 |
| 125_L | 137_I | 1.071 | 0.85 |
| 139_R | 196_L | 1.068 | 0.85 |
| 54_E | 121_N | 1.065 | 0.85 |
| 167_E | 175_N | 1.063 | 0.85 |
| 118_R | 141_T | 1.063 | 0.85 |
| 58_V | 62_E | 1.063 | 0.85 |
| 78_V | 81_L | 1.055 | 0.84 |
| 187_E | 191_A | 1.054 | 0.84 |
| 261_V | 264_V | 1.052 | 0.84 |
| 9_M | 13_G | 1.044 | 0.83 |
| 184_L | 189_G | 1.040 | 0.83 |
| 214_I | 238_I | 1.039 | 0.83 |
| 111_L | 148_L | 1.018 | 0.81 |
| 197_H | 237_D | 1.016 | 0.81 |
| 35_T | 52_V | 1.011 | 0.80 |
| 46_T | 75_V | 1.011 | 0.80 |
| 184_L | 187_E | 1.007 | 0.80 |
| 97_L | 180_R | 1.005 | 0.80 |
| 213_I | 251_I | 1.001 | 0.80 |
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 | |
| 1vj7A | 2 | 0.8993 | 100 | 0.324 | Contact Map |
| 3nr1A | 2 | 0.6269 | 100 | 0.588 | Contact Map |
| 3nqwA | 2 | 0.6119 | 100 | 0.598 | Contact Map |
| 3l9dA | 2 | 0.3619 | 99.6 | 0.856 | Contact Map |
| 1y7pA | 3 | 0.291 | 99.1 | 0.888 | Contact Map |
| 2ko1A | 2 | 0.2948 | 99 | 0.892 | Contact Map |
| 2lvwA | 2 | 0.3097 | 98.8 | 0.898 | Contact Map |
| 2pc6A | 4 | 0.2873 | 98.7 | 0.905 | Contact Map |
| 2f1fA | 2 | 0.2836 | 98.6 | 0.905 | Contact Map |
| 1zpvA | 3 | 0.291 | 98.5 | 0.908 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)