| 3C_nsah_aligh |
| ID: | 1496309641 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 50% gaps before running GREMLIN. |
| Length: | 183 (164) | ||
| Sequences: | 13586 (8391.9) | ||
| Seq/Len: | 82.841 | ||
| Nf(neff/√len): | 655.3 |
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: 82.841).
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_T | 156_K | 5.199 | 1.00 |
| 25_F | 41_A | 4.011 | 1.00 |
| 39_T | 66_T | 3.898 | 1.00 |
| 28_L | 157_V | 3.336 | 1.00 |
| 34_V | 76_K | 3.108 | 1.00 |
| 92_K | 175_L | 2.880 | 1.00 |
| 28_L | 160_I | 2.789 | 1.00 |
| 27_M | 35_A | 2.733 | 1.00 |
| 138_Y | 161_H | 2.677 | 1.00 |
| 142_T | 161_H | 2.579 | 1.00 |
| 33_R | 76_K | 2.556 | 1.00 |
| 57_L | 78_D | 2.427 | 1.00 |
| 56_V | 75_V | 2.354 | 1.00 |
| 40_H | 147_C | 2.348 | 1.00 |
| 151_V | 171_A | 2.299 | 1.00 |
| 28_L | 150_V | 2.282 | 1.00 |
| 48_Y | 53_E | 2.104 | 1.00 |
| 40_H | 71_E | 2.023 | 1.00 |
| 94_E | 175_L | 2.017 | 1.00 |
| 150_V | 157_V | 2.009 | 1.00 |
| 90_L | 174_L | 1.975 | 1.00 |
| 34_V | 74_I | 1.861 | 1.00 |
| 67_D | 70_L | 1.856 | 1.00 |
| 72_I | 160_I | 1.855 | 1.00 |
| 39_T | 43_V | 1.783 | 1.00 |
| 16_V | 35_A | 1.782 | 1.00 |
| 28_L | 36_V | 1.764 | 1.00 |
| 99_D | 116_V | 1.744 | 1.00 |
| 99_D | 154_T | 1.647 | 1.00 |
| 30_V | 36_V | 1.645 | 1.00 |
| 138_Y | 151_V | 1.638 | 1.00 |
| 31_Y | 34_V | 1.634 | 1.00 |
| 46_T | 55_K | 1.633 | 1.00 |
| 54_T | 77_L | 1.614 | 1.00 |
| 92_K | 95_D | 1.607 | 1.00 |
| 97_Y | 100_A | 1.570 | 1.00 |
| 29_G | 35_A | 1.540 | 1.00 |
| 11_M | 152_T | 1.537 | 1.00 |
| 16_V | 27_M | 1.455 | 1.00 |
| 38_P | 41_A | 1.396 | 0.99 |
| 42_S | 73_T | 1.385 | 0.99 |
| 88_H | 156_K | 1.378 | 0.99 |
| 123_G | 134_R | 1.355 | 0.99 |
| 114_I | 117_G | 1.352 | 0.99 |
| 38_P | 162_V | 1.340 | 0.99 |
| 71_E | 147_C | 1.297 | 0.99 |
| 151_V | 161_H | 1.287 | 0.99 |
| 153_T | 158_I | 1.279 | 0.99 |
| 142_T | 169_G | 1.270 | 0.99 |
| 143_R | 146_Q | 1.259 | 0.99 |
| 35_A | 77_L | 1.235 | 0.98 |
| 30_V | 74_I | 1.218 | 0.98 |
| 39_T | 73_T | 1.213 | 0.98 |
| 34_V | 64_D | 1.205 | 0.98 |
| 57_L | 76_K | 1.204 | 0.98 |
| 29_G | 77_L | 1.198 | 0.98 |
| 39_T | 68_T | 1.195 | 0.98 |
| 146_Q | 149_G | 1.187 | 0.98 |
| 138_Y | 171_A | 1.177 | 0.98 |
| 48_Y | 55_K | 1.175 | 0.98 |
| 64_D | 76_K | 1.173 | 0.98 |
| 26_T | 149_G | 1.150 | 0.97 |
| 159_G | 171_A | 1.137 | 0.97 |
| 119_V | 136_L | 1.113 | 0.96 |
| 101_V | 154_T | 1.111 | 0.96 |
| 138_Y | 142_T | 1.106 | 0.96 |
| 38_P | 161_H | 1.105 | 0.96 |
| 19_R | 48_Y | 1.099 | 0.96 |
| 93_Y | 175_L | 1.088 | 0.96 |
| 135_I | 162_V | 1.079 | 0.95 |
| 37_I | 42_S | 1.078 | 0.95 |
| 145_G | 148_G | 1.076 | 0.95 |
| 40_H | 145_G | 1.057 | 0.95 |
| 102_L | 151_V | 1.033 | 0.94 |
| 35_A | 75_V | 1.009 | 0.93 |
| 104_V | 146_Q | 1.001 | 0.92 |
| 54_T | 79_R | 1.000 | 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 | |
| 3q3yA | 2 | 0.9836 | 99.9 | 0.155 | Contact Map |
| 3qzrA | 2 | 0.9836 | 99.9 | 0.159 | Contact Map |
| 3zveA | 1 | 1 | 99.9 | 0.163 | Contact Map |
| 1cqqA | 1 | 0.9836 | 99.9 | 0.173 | Contact Map |
| 4dcdA | 1 | 0.9836 | 99.9 | 0.176 | Contact Map |
| 2b0fA | 1 | 0.9945 | 99.9 | 0.178 | Contact Map |
| 2ijd1 | 2 | 1 | 99.9 | 0.23 | Contact Map |
| 2bhgA | 2 | 0.9454 | 99.8 | 0.31 | Contact Map |
| 2halA | 1 | 0.9617 | 99.8 | 0.351 | Contact Map |
| 1lvmA | 2 | 0.9399 | 99.6 | 0.437 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)