| 4V1J |
| ID: | 1513368391 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 142 (136) | ||
| Sequences: | 718 (447.9) | ||
| Seq/Len: | 5.279 | ||
| Nf(neff/√len): | 38.4 |
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: 5.279).
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 |
| 99_C | 135_C | 3.114 | 1.00 |
| 15_A | 70_M | 2.649 | 1.00 |
| 7_T | 10_A | 1.979 | 1.00 |
| 3_M | 6_Y | 1.949 | 1.00 |
| 99_C | 132_P | 1.765 | 1.00 |
| 133_S | 136_R | 1.586 | 0.99 |
| 16_I | 86_L | 1.580 | 0.99 |
| 132_P | 135_C | 1.555 | 0.99 |
| 101_Q | 131_L | 1.551 | 0.99 |
| 77_N | 80_K | 1.524 | 0.99 |
| 87_W | 100_G | 1.505 | 0.99 |
| 29_Y | 35_E | 1.493 | 0.99 |
| 8_A | 130_H | 1.478 | 0.98 |
| 121_A | 124_K | 1.465 | 0.98 |
| 20_E | 23_K | 1.452 | 0.98 |
| 65_V | 87_W | 1.421 | 0.98 |
| 14_E | 18_L | 1.368 | 0.97 |
| 29_Y | 33_H | 1.367 | 0.97 |
| 18_L | 53_G | 1.356 | 0.97 |
| 126_I | 131_L | 1.349 | 0.97 |
| 5_D | 129_K | 1.342 | 0.97 |
| 19_A | 68_A | 1.317 | 0.96 |
| 116_T | 121_A | 1.309 | 0.96 |
| 18_L | 70_M | 1.307 | 0.96 |
| 110_A | 122_N | 1.306 | 0.96 |
| 118_A | 122_N | 1.304 | 0.96 |
| 12_V | 126_I | 1.304 | 0.96 |
| 115_V | 118_A | 1.301 | 0.96 |
| 14_E | 55_Y | 1.286 | 0.96 |
| 5_D | 9_R | 1.283 | 0.95 |
| 79_I | 82_K | 1.268 | 0.95 |
| 118_A | 121_A | 1.249 | 0.95 |
| 117_A | 120_A | 1.244 | 0.94 |
| 26_V | 47_T | 1.238 | 0.94 |
| 21_G | 24_S | 1.234 | 0.94 |
| 15_A | 56_V | 1.233 | 0.94 |
| 13_S | 17_L | 1.214 | 0.93 |
| 107_K | 121_A | 1.204 | 0.93 |
| 17_L | 20_E | 1.202 | 0.93 |
| 2_P | 9_R | 1.191 | 0.93 |
| 64_G | 97_W | 1.190 | 0.93 |
| 3_M | 10_A | 1.186 | 0.92 |
| 109_K | 121_A | 1.176 | 0.92 |
| 114_D | 118_A | 1.168 | 0.92 |
| 22_Q | 45_V | 1.167 | 0.92 |
| 29_Y | 39_N | 1.167 | 0.92 |
| 61_V | 64_G | 1.162 | 0.91 |
| 116_T | 119_A | 1.157 | 0.91 |
| 40_N | 43_A | 1.143 | 0.90 |
| 57_K | 71_A | 1.141 | 0.90 |
| 66_V | 88_A | 1.133 | 0.90 |
| 108_A | 121_A | 1.118 | 0.89 |
| 36_W | 66_V | 1.116 | 0.89 |
| 71_A | 74_N | 1.110 | 0.89 |
| 17_L | 22_Q | 1.104 | 0.88 |
| 14_E | 17_L | 1.103 | 0.88 |
| 110_A | 118_A | 1.096 | 0.88 |
| 55_Y | 93_G | 1.095 | 0.88 |
| 115_V | 120_A | 1.093 | 0.88 |
| 11_Q | 53_G | 1.070 | 0.86 |
| 82_K | 127_D | 1.070 | 0.86 |
| 64_G | 88_A | 1.066 | 0.86 |
| 117_A | 121_A | 1.063 | 0.86 |
| 54_K | 75_V | 1.058 | 0.85 |
| 114_D | 117_A | 1.049 | 0.85 |
| 60_E | 69_Q | 1.047 | 0.84 |
| 7_T | 129_K | 1.036 | 0.84 |
| 84_L | 125_K | 1.032 | 0.83 |
| 35_E | 80_K | 1.029 | 0.83 |
| 106_D | 121_A | 1.019 | 0.82 |
| 110_A | 116_T | 1.013 | 0.82 |
| 109_K | 123_G | 1.013 | 0.82 |
| 29_Y | 37_P | 1.012 | 0.82 |
| 28_E | 32_N | 1.010 | 0.81 |
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 | |
| 3jyzA | 1 | 0.9014 | 99.9 | 0.239 | Contact Map |
| 1qveA | 2 | 0.8169 | 99.9 | 0.28 | Contact Map |
| 1x6zA | 1 | 0.7465 | 99.8 | 0.339 | Contact Map |
| 3sojA | 2 | 0.7324 | 99.8 | 0.388 | Contact Map |
| 2hi2A | 1 | 0.9577 | 99.7 | 0.428 | Contact Map |
| 3sokA | 2 | 0.8028 | 99.6 | 0.483 | Contact Map |
| 1oqwA | 2 | 0.7746 | 99.5 | 0.53 | Contact Map |
| 4noaA | 1 | 0.7465 | 98.2 | 0.706 | Contact Map |
| 2m3kA | 1 | 0.7676 | 94.4 | 0.814 | Contact Map |
| 3g20A | 2 | 0.6901 | 81.7 | 0.856 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)