| 3SEI_A |
| ID: | 1415933227 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 143 (137) | ||
| Sequences: | 462 (299.5) | ||
| Seq/Len: | 3.372 | ||
| Nf(neff/√len): | 25.6 |
Jackhmmer Results: (2014_04_16)
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: 3.372).
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 |
| 25_Y | 57_H | 2.370 | 1.00 |
| 114_W | 128_Q | 2.110 | 1.00 |
| 29_F | 34_Y | 1.885 | 1.00 |
| 112_I | 115_E | 1.751 | 0.99 |
| 98_L | 102_G | 1.691 | 0.99 |
| 43_T | 50_I | 1.648 | 0.98 |
| 36_L | 39_I | 1.620 | 0.98 |
| 117_L | 131_L | 1.568 | 0.98 |
| 94_Y | 127_H | 1.556 | 0.97 |
| 35_D | 68_L | 1.516 | 0.97 |
| 39_I | 46_D | 1.510 | 0.97 |
| 128_Q | 131_L | 1.482 | 0.96 |
| 26_A | 51_G | 1.473 | 0.96 |
| 136_R | 140_E | 1.442 | 0.95 |
| 85_W | 93_Q | 1.438 | 0.95 |
| 25_Y | 29_F | 1.431 | 0.95 |
| 47_L | 94_Y | 1.416 | 0.95 |
| 60_K | 122_I | 1.410 | 0.95 |
| 13_V | 73_W | 1.406 | 0.95 |
| 126_G | 129_K | 1.397 | 0.94 |
| 61_I | 72_D | 1.385 | 0.94 |
| 103_Y | 113_T | 1.368 | 0.93 |
| 68_L | 74_L | 1.367 | 0.93 |
| 8_K | 40_S | 1.334 | 0.92 |
| 44_P | 58_R | 1.329 | 0.92 |
| 17_L | 29_F | 1.326 | 0.92 |
| 52_V | 61_I | 1.306 | 0.91 |
| 93_Q | 104_E | 1.305 | 0.91 |
| 29_F | 35_D | 1.298 | 0.91 |
| 22_L | 60_K | 1.297 | 0.91 |
| 51_G | 121_G | 1.287 | 0.90 |
| 98_L | 112_I | 1.284 | 0.90 |
| 67_G | 109_I | 1.284 | 0.90 |
| 36_L | 40_S | 1.266 | 0.89 |
| 8_K | 36_L | 1.262 | 0.89 |
| 47_L | 58_R | 1.239 | 0.88 |
| 16_W | 68_L | 1.228 | 0.87 |
| 78_K | 93_Q | 1.214 | 0.87 |
| 42_M | 50_I | 1.189 | 0.85 |
| 9_S | 12_A | 1.154 | 0.83 |
| 89_I | 135_V | 1.149 | 0.82 |
| 8_K | 33_G | 1.143 | 0.82 |
| 93_Q | 127_H | 1.143 | 0.82 |
| 25_Y | 58_R | 1.142 | 0.82 |
| 136_R | 139_A | 1.132 | 0.81 |
| 64_E | 102_G | 1.125 | 0.80 |
| 22_L | 25_Y | 1.122 | 0.80 |
| 133_L | 136_R | 1.110 | 0.79 |
| 38_T | 47_L | 1.107 | 0.79 |
| 87_S | 92_A | 1.103 | 0.78 |
| 97_V | 101_N | 1.103 | 0.78 |
| 21_Q | 103_Y | 1.102 | 0.78 |
| 26_A | 30_I | 1.097 | 0.78 |
| 68_L | 94_Y | 1.095 | 0.78 |
| 134_A | 139_A | 1.088 | 0.77 |
| 32_A | 117_L | 1.070 | 0.75 |
| 25_Y | 46_D | 1.064 | 0.75 |
| 54_K | 59_K | 1.063 | 0.75 |
| 118_Q | 131_L | 1.057 | 0.74 |
| 83_A | 99_V | 1.057 | 0.74 |
| 59_K | 84_V | 1.047 | 0.73 |
| 9_S | 13_V | 1.043 | 0.73 |
| 31_S | 50_I | 1.037 | 0.72 |
| 35_D | 38_T | 1.037 | 0.72 |
| 34_Y | 103_Y | 1.032 | 0.72 |
| 31_S | 113_T | 1.029 | 0.71 |
| 85_W | 116_D | 1.014 | 0.70 |
| 63_A | 66_S | 1.013 | 0.70 |
| 44_P | 51_G | 1.001 | 0.68 |
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 | |
| 4is7A | 1 | 0.958 | 100 | 0.205 | Contact Map |
| 3seiA | 2 | 0.979 | 100 | 0.21 | Contact Map |
| 3tacB | 1 | 0.965 | 100 | 0.224 | Contact Map |
| 3tadC | 2 | 0.979 | 100 | 0.234 | Contact Map |
| 2kivA | 1 | 0.9021 | 100 | 0.276 | Contact Map |
| 2ke7A | 1 | 0.4196 | 99.6 | 0.567 | Contact Map |
| 2lmrA | 1 | 0.5105 | 99.5 | 0.612 | Contact Map |
| 4nl9A | 2 | 0.4685 | 99.5 | 0.612 | Contact Map |
| 2y9tA | 1 | 0.4825 | 99.4 | 0.621 | Contact Map |
| 2k4pA | 1 | 0.4476 | 99.4 | 0.622 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)