| Rstspo 20-158 |
| ID: | 1394162526 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 139 (131) | ||
| Sequences: | 847 (701.4) | ||
| Seq/Len: | 6.466 | ||
| Nf(neff/√len): | 61.3 |
HHblits Results: (2013_03)
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: 6.466).
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 |
| 89_W | 118_T | 3.750 | 1.00 |
| 44_R | 103_D | 3.566 | 1.00 |
| 71_V | 84_V | 3.538 | 1.00 |
| 20_W | 122_G | 3.197 | 1.00 |
| 92_V | 117_A | 2.945 | 1.00 |
| 25_W | 29_L | 2.497 | 1.00 |
| 79_A | 128_M | 2.158 | 1.00 |
| 82_L | 124_N | 2.078 | 1.00 |
| 89_W | 117_A | 1.767 | 1.00 |
| 126_E | 129_R | 1.766 | 1.00 |
| 57_F | 98_A | 1.724 | 1.00 |
| 96_M | 107_G | 1.719 | 1.00 |
| 11_W | 78_M | 1.713 | 1.00 |
| 95_T | 110_F | 1.710 | 1.00 |
| 42_A | 58_Y | 1.650 | 1.00 |
| 100_F | 107_G | 1.647 | 1.00 |
| 42_A | 55_L | 1.606 | 1.00 |
| 88_M | 113_Y | 1.603 | 1.00 |
| 38_M | 42_A | 1.580 | 0.99 |
| 11_W | 76_K | 1.580 | 0.99 |
| 64_F | 91_F | 1.579 | 0.99 |
| 82_L | 125_F | 1.539 | 0.99 |
| 95_T | 99_F | 1.535 | 0.99 |
| 17_K | 21_N | 1.507 | 0.99 |
| 57_F | 94_A | 1.470 | 0.99 |
| 125_F | 129_R | 1.466 | 0.99 |
| 81_A | 84_V | 1.424 | 0.99 |
| 65_N | 113_Y | 1.414 | 0.99 |
| 35_Y | 65_N | 1.405 | 0.99 |
| 27_F | 68_W | 1.254 | 0.96 |
| 68_W | 72_F | 1.247 | 0.96 |
| 68_W | 124_N | 1.245 | 0.96 |
| 2_T | 6_L | 1.240 | 0.96 |
| 41_A | 110_F | 1.231 | 0.96 |
| 121_T | 124_N | 1.228 | 0.96 |
| 126_E | 130_L | 1.221 | 0.96 |
| 64_F | 84_V | 1.217 | 0.96 |
| 89_W | 121_T | 1.212 | 0.95 |
| 20_W | 126_E | 1.130 | 0.93 |
| 45_V | 99_F | 1.127 | 0.93 |
| 122_G | 126_E | 1.120 | 0.92 |
| 11_W | 21_N | 1.117 | 0.92 |
| 8_P | 11_W | 1.103 | 0.91 |
| 77_R | 81_A | 1.100 | 0.91 |
| 61_Q | 95_T | 1.089 | 0.91 |
| 19_W | 122_G | 1.079 | 0.90 |
| 11_W | 17_K | 1.056 | 0.89 |
| 61_Q | 65_N | 1.046 | 0.88 |
| 21_N | 119_A | 1.040 | 0.88 |
| 58_Y | 99_F | 1.036 | 0.88 |
| 108_V | 111_V | 1.036 | 0.88 |
| 39_S | 43_M | 1.029 | 0.87 |
| 77_R | 80_T | 1.023 | 0.87 |
| 17_K | 127_A | 1.015 | 0.86 |
| 28_P | 120_A | 1.015 | 0.86 |
| 94_A | 98_A | 1.013 | 0.86 |
| 71_V | 81_A | 1.012 | 0.86 |
| 40_L | 43_M | 1.011 | 0.86 |
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 | |
| 3zuxA | 1 | 0.8921 | 2.1 | 0.956 | Contact Map |
| 4n7wA | 2 | 0.9209 | 1.1 | 0.963 | Contact Map |
| 3rlfF | 1 | 0.6691 | 1 | 0.963 | Contact Map |
| 3effK | 4 | 0.6691 | 0.9 | 0.965 | Contact Map |
| 1vsy3 | 2 | 0.3885 | 0.8 | 0.966 | Contact Map |
| 2f3yB | 1 | 0.1295 | 0.8 | 0.966 | Contact Map |
| 2lk9A | 1 | 0.1583 | 0.8 | 0.966 | Contact Map |
| 2wtbA | 1 | 0.295 | 0.8 | 0.966 | Contact Map |
| 4nv5A | 2 | 0.7698 | 0.8 | 0.966 | Contact Map |
| 2k1eA | 4 | 0.6547 | 0.8 | 0.966 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)