| PopZH2H3H4_104-177 |
| ID: | 1440143618 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 75 (70) | ||
| Sequences: | 359 (245.7) | ||
| Seq/Len: | 5.129 | ||
| Nf(neff/√len): | 29.4 |
Jackhmmer Results: (2015_08)
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: 5.129).
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 |
| 33_T | 37_V | 1.891 | 1.00 |
| 42_L | 46_L | 1.820 | 1.00 |
| 3_E | 6_V | 1.791 | 1.00 |
| 61_K | 66_V | 1.707 | 1.00 |
| 55_P | 59_E | 1.623 | 0.99 |
| 18_F | 70_S | 1.598 | 0.99 |
| 57_I | 61_K | 1.575 | 0.99 |
| 15_A | 67_Q | 1.573 | 0.99 |
| 13_A | 20_S | 1.469 | 0.98 |
| 41_L | 45_L | 1.455 | 0.98 |
| 54_L | 62_V | 1.444 | 0.98 |
| 68_R | 71_R | 1.443 | 0.98 |
| 24_A | 30_D | 1.425 | 0.98 |
| 59_E | 65_E | 1.405 | 0.98 |
| 7_G | 10_A | 1.359 | 0.97 |
| 51_D | 62_V | 1.353 | 0.97 |
| 51_D | 54_L | 1.351 | 0.97 |
| 33_T | 38_V | 1.298 | 0.96 |
| 36_D | 39_R | 1.256 | 0.94 |
| 10_A | 13_A | 1.252 | 0.94 |
| 24_A | 31_G | 1.212 | 0.93 |
| 14_A | 29_K | 1.201 | 0.93 |
| 53_N | 56_R | 1.186 | 0.92 |
| 37_V | 41_L | 1.181 | 0.92 |
| 41_L | 53_N | 1.132 | 0.89 |
| 19_G | 29_K | 1.128 | 0.89 |
| 58_V | 62_V | 1.120 | 0.89 |
| 32_R | 36_D | 1.117 | 0.89 |
| 35_E | 43_R | 1.107 | 0.88 |
| 11_A | 14_A | 1.107 | 0.88 |
| 37_V | 45_L | 1.103 | 0.88 |
| 15_A | 64_E | 1.095 | 0.87 |
| 26_L | 33_T | 1.045 | 0.84 |
| 8_V | 57_I | 1.042 | 0.83 |
| 9_S | 57_I | 1.038 | 0.83 |
| 47_K | 51_D | 1.037 | 0.83 |
| 26_L | 29_K | 1.032 | 0.83 |
| 20_S | 24_A | 1.026 | 0.82 |
| 5_L | 30_D | 1.012 | 0.81 |
| 11_A | 52_Q | 1.008 | 0.80 |
| 48_E | 52_Q | 1.008 | 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 | |
| 1kijA | 2 | 0.9467 | 54.3 | 0.856 | Contact Map |
| 4wubA | 1 | 0.9467 | 43.9 | 0.865 | Contact Map |
| 3zkbA | 16 | 0.9467 | 40.1 | 0.868 | Contact Map |
| 4hy1A | 2 | 0.8933 | 39.9 | 0.868 | Contact Map |
| 4urlA | 2 | 0.9467 | 31.9 | 0.875 | Contact Map |
| 3lnuA | 1 | 0.9333 | 30.6 | 0.876 | Contact Map |
| 1s16A | 2 | 0.9467 | 29.5 | 0.877 | Contact Map |
| 3ewtE | 1 | 0.1867 | 26.7 | 0.88 | Contact Map |
| 3t38A | 2 | 0.88 | 26.3 | 0.88 | Contact Map |
| 3cwvA | 2 | 0.8133 | 22.2 | 0.884 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)