| 3C_5000 |
| ID: | 1496224478 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 50% gaps before running GREMLIN. |
| Length: | 183 (166) | ||
| Sequences: | 11281 (6750.1) | ||
| Seq/Len: | 67.958 | ||
| Nf(neff/√len): | 523.9 |
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: 67.958).
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 |
| 153_C | 156_K | 4.587 | 1.00 |
| 39_T | 66_A | 3.931 | 1.00 |
| 25_F | 41_A | 3.503 | 1.00 |
| 98_N | 116_V | 3.164 | 1.00 |
| 92_T | 175_K | 3.091 | 1.00 |
| 28_L | 157_V | 2.997 | 1.00 |
| 142_T | 161_H | 2.674 | 1.00 |
| 28_L | 160_M | 2.640 | 1.00 |
| 34_V | 76_T | 2.576 | 1.00 |
| 27_M | 35_A | 2.485 | 1.00 |
| 60_K | 78_K | 2.342 | 1.00 |
| 138_Y | 161_H | 2.296 | 1.00 |
| 40_H | 147_C | 2.155 | 1.00 |
| 33_N | 76_T | 2.098 | 1.00 |
| 151_I | 171_A | 2.072 | 1.00 |
| 28_L | 150_V | 2.068 | 1.00 |
| 59_A | 75_I | 2.031 | 1.00 |
| 98_N | 154_T | 1.986 | 1.00 |
| 150_V | 157_V | 1.948 | 1.00 |
| 40_H | 71_E | 1.935 | 1.00 |
| 92_T | 95_T | 1.931 | 1.00 |
| 67_G | 70_L | 1.930 | 1.00 |
| 72_I | 160_M | 1.853 | 1.00 |
| 94_I | 175_K | 1.834 | 1.00 |
| 90_I | 174_L | 1.740 | 1.00 |
| 28_L | 36_I | 1.681 | 1.00 |
| 39_T | 43_P | 1.659 | 1.00 |
| 138_Y | 151_I | 1.602 | 1.00 |
| 30_V | 36_I | 1.556 | 1.00 |
| 60_K | 76_T | 1.535 | 1.00 |
| 100_G | 154_T | 1.516 | 1.00 |
| 34_V | 74_I | 1.508 | 1.00 |
| 36_I | 177_S | 1.462 | 1.00 |
| 123_G | 134_R | 1.415 | 1.00 |
| 142_T | 169_G | 1.415 | 1.00 |
| 16_V | 27_M | 1.411 | 1.00 |
| 89_H | 157_V | 1.399 | 0.99 |
| 56_I | 75_I | 1.384 | 0.99 |
| 29_G | 35_A | 1.375 | 0.99 |
| 119_V | 136_L | 1.372 | 0.99 |
| 40_H | 145_G | 1.364 | 0.99 |
| 42_S | 73_T | 1.333 | 0.99 |
| 51_G | 54_V | 1.325 | 0.99 |
| 101_V | 151_I | 1.315 | 0.99 |
| 160_M | 177_S | 1.302 | 0.99 |
| 101_V | 161_H | 1.301 | 0.99 |
| 146_Q | 149_G | 1.284 | 0.99 |
| 47_I | 61_A | 1.282 | 0.99 |
| 38_P | 162_V | 1.279 | 0.99 |
| 138_Y | 142_T | 1.278 | 0.99 |
| 39_T | 68_T | 1.266 | 0.99 |
| 138_Y | 171_A | 1.252 | 0.99 |
| 159_G | 171_A | 1.248 | 0.99 |
| 71_E | 147_C | 1.246 | 0.98 |
| 48_V | 56_I | 1.245 | 0.98 |
| 99_D | 158_I | 1.239 | 0.98 |
| 11_A | 152_T | 1.228 | 0.98 |
| 16_V | 35_A | 1.205 | 0.98 |
| 30_V | 74_I | 1.201 | 0.98 |
| 151_I | 161_H | 1.195 | 0.98 |
| 46_S | 58_D | 1.194 | 0.98 |
| 38_P | 41_A | 1.184 | 0.98 |
| 116_V | 139_N | 1.179 | 0.98 |
| 39_T | 73_T | 1.162 | 0.97 |
| 19_T | 50_D | 1.161 | 0.97 |
| 99_D | 119_V | 1.158 | 0.97 |
| 99_D | 103_I | 1.133 | 0.97 |
| 135_T | 162_V | 1.104 | 0.96 |
| 88_P | 156_K | 1.103 | 0.96 |
| 26_T | 104_V | 1.097 | 0.96 |
| 35_A | 77_L | 1.094 | 0.96 |
| 54_V | 59_A | 1.093 | 0.96 |
| 51_G | 57_L | 1.082 | 0.96 |
| 103_I | 146_Q | 1.079 | 0.95 |
| 100_G | 113_Y | 1.078 | 0.95 |
| 34_V | 64_D | 1.058 | 0.95 |
| 54_V | 77_L | 1.049 | 0.94 |
| 38_P | 147_C | 1.047 | 0.94 |
| 38_P | 161_H | 1.047 | 0.94 |
| 143_R | 146_Q | 1.038 | 0.94 |
| 89_H | 152_T | 1.034 | 0.94 |
| 64_D | 76_T | 1.034 | 0.94 |
| 102_L | 152_T | 1.034 | 0.94 |
| 28_L | 89_H | 1.030 | 0.94 |
| 153_C | 158_I | 1.018 | 0.93 |
| 37_L | 73_T | 1.017 | 0.93 |
| 105_N | 146_Q | 1.013 | 0.93 |
| 57_L | 77_L | 1.011 | 0.93 |
| 145_G | 148_G | 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 | |
| 3zveA | 1 | 1 | 99.9 | 0.156 | Contact Map |
| 3q3yA | 2 | 0.9836 | 99.9 | 0.162 | Contact Map |
| 4dcdA | 1 | 0.9836 | 99.9 | 0.165 | Contact Map |
| 3qzrA | 2 | 0.9836 | 99.9 | 0.17 | Contact Map |
| 1cqqA | 1 | 0.9836 | 99.9 | 0.18 | Contact Map |
| 2b0fA | 1 | 0.9945 | 99.9 | 0.186 | Contact Map |
| 2ijd1 | 2 | 1 | 99.9 | 0.228 | Contact Map |
| 2bhgA | 2 | 0.9399 | 99.8 | 0.309 | Contact Map |
| 2halA | 1 | 0.9563 | 99.8 | 0.357 | Contact Map |
| 1lvmA | 2 | 0.9454 | 99.6 | 0.416 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)