| TetraDIX 20-103 |
| ID: | 1511997460 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 84 (82) | ||
| Sequences: | 389 (219) | ||
| Seq/Len: | 4.744 | ||
| Nf(neff/√len): | 24.2 |
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: 4.744).
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 |
| 50_F | 71_P | 2.350 | 1.00 |
| 37_K | 66_N | 2.054 | 1.00 |
| 60_W | 80_K | 1.937 | 1.00 |
| 42_L | 62_D | 1.573 | 0.99 |
| 20_N | 49_R | 1.542 | 0.99 |
| 31_I | 77_I | 1.472 | 0.98 |
| 14_D | 40_F | 1.409 | 0.97 |
| 6_F | 21_V | 1.391 | 0.97 |
| 49_R | 60_W | 1.372 | 0.97 |
| 18_I | 54_Y | 1.348 | 0.96 |
| 64_P | 74_E | 1.324 | 0.96 |
| 46_Y | 82_T | 1.324 | 0.96 |
| 62_D | 80_K | 1.256 | 0.94 |
| 47_I | 62_D | 1.239 | 0.93 |
| 41_P | 49_R | 1.215 | 0.92 |
| 46_Y | 57_Q | 1.212 | 0.92 |
| 50_F | 77_I | 1.209 | 0.92 |
| 20_N | 62_D | 1.185 | 0.91 |
| 58_V | 61_M | 1.178 | 0.90 |
| 32_R | 68_K | 1.169 | 0.90 |
| 36_I | 39_Y | 1.158 | 0.89 |
| 49_R | 62_D | 1.144 | 0.89 |
| 43_N | 74_E | 1.140 | 0.88 |
| 63_I | 71_P | 1.136 | 0.88 |
| 52_Y | 55_N | 1.135 | 0.88 |
| 34_A | 66_N | 1.133 | 0.88 |
| 4_N | 32_R | 1.131 | 0.88 |
| 32_R | 37_K | 1.104 | 0.86 |
| 4_N | 75_G | 1.100 | 0.86 |
| 25_P | 38_S | 1.093 | 0.86 |
| 36_I | 70_L | 1.092 | 0.85 |
| 15_D | 24_V | 1.085 | 0.85 |
| 71_P | 78_F | 1.074 | 0.84 |
| 16_P | 20_N | 1.073 | 0.84 |
| 24_V | 74_E | 1.066 | 0.84 |
| 30_E | 68_K | 1.057 | 0.83 |
| 54_Y | 57_Q | 1.057 | 0.83 |
| 38_S | 46_Y | 1.043 | 0.82 |
| 9_I | 63_I | 1.034 | 0.81 |
| 65_E | 68_K | 1.033 | 0.81 |
| 24_V | 72_I | 1.028 | 0.80 |
| 58_V | 70_L | 1.019 | 0.80 |
| 23_C | 52_Y | 1.018 | 0.79 |
| 20_N | 42_L | 1.016 | 0.79 |
| 6_F | 9_I | 1.009 | 0.79 |
| 25_P | 53_R | 1.007 | 0.78 |
| 32_R | 45_Q | 1.003 | 0.78 |
| 8_H | 65_E | 1.001 | 0.78 |
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 | |
| 3pz7A | 1 | 0.9524 | 99.9 | 0.153 | Contact Map |
| 4wipA | 3 | 0 | 99.9 | 0.165 | Contact Map |
| 3pz8A | 8 | 0.9524 | 99.9 | 0.169 | Contact Map |
| 1wspA | 3 | 0.9286 | 99.9 | 0.188 | Contact Map |
| 2c7hA | 1 | 0.9048 | 25.5 | 0.882 | Contact Map |
| 1ncgA | 1 | 0.75 | 12.2 | 0.898 | Contact Map |
| 2yqgA | 1 | 0.8929 | 11.9 | 0.899 | Contact Map |
| 2kr0A | 1 | 0.881 | 6.6 | 0.91 | Contact Map |
| 3q2vA | 2 | 0.9643 | 5.3 | 0.914 | Contact Map |
| 3k6dA | 1 | 0.7619 | 5.1 | 0.914 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)