| CC_31100 |
| ID: | 1433252616 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 50% gaps before running GREMLIN. |
| Length: | 269 (123) | ||
| Sequences: | 79584 (63131.9) | ||
| Seq/Len: | 647.024 | ||
| Nf(neff/√len): | 5692.4 |
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: 647.024).
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 |
| 31_A | 48_P | 2.995 | 1.00 |
| 31_A | 50_P | 2.640 | 1.00 |
| 35_T | 48_P | 2.590 | 1.00 |
| 24_V | 55_G | 2.236 | 1.00 |
| 47_F | 64_P | 2.139 | 1.00 |
| 53_E | 75_G | 2.051 | 1.00 |
| 72_G | 103_E | 2.039 | 1.00 |
| 56_Y | 84_K | 1.960 | 1.00 |
| 89_D | 93_R | 1.885 | 1.00 |
| 41_L | 131_E | 1.876 | 1.00 |
| 76_V | 84_K | 1.869 | 1.00 |
| 69_V | 81_F | 1.868 | 1.00 |
| 49_A | 58_L | 1.866 | 1.00 |
| 60_R | 88_S | 1.827 | 1.00 |
| 52_A | 76_V | 1.815 | 1.00 |
| 51_T | 75_G | 1.799 | 1.00 |
| 119_E | 133_R | 1.773 | 1.00 |
| 47_F | 58_L | 1.750 | 1.00 |
| 20_R | 47_F | 1.722 | 1.00 |
| 50_P | 54_K | 1.712 | 1.00 |
| 99_M | 117_V | 1.688 | 1.00 |
| 47_F | 62_A | 1.667 | 1.00 |
| 37_H | 127_L | 1.664 | 1.00 |
| 82_T | 97_V | 1.617 | 1.00 |
| 22_M | 49_A | 1.507 | 1.00 |
| 86_R | 118_H | 1.504 | 1.00 |
| 20_R | 45_Q | 1.446 | 1.00 |
| 35_T | 39_R | 1.443 | 1.00 |
| 51_T | 54_K | 1.391 | 0.99 |
| 76_V | 80_A | 1.363 | 0.99 |
| 84_K | 88_S | 1.336 | 0.99 |
| 83_R | 115_A | 1.332 | 0.99 |
| 71_H | 79_L | 1.327 | 0.99 |
| 58_L | 62_A | 1.305 | 0.99 |
| 67_I | 95_A | 1.305 | 0.99 |
| 77_D | 80_A | 1.297 | 0.99 |
| 53_E | 76_V | 1.239 | 0.98 |
| 103_E | 108_A | 1.236 | 0.98 |
| 59_A | 85_L | 1.236 | 0.98 |
| 58_L | 61_A | 1.213 | 0.98 |
| 52_A | 81_F | 1.206 | 0.98 |
| 84_K | 87_R | 1.189 | 0.98 |
| 106_A | 110_F | 1.186 | 0.98 |
| 58_L | 64_P | 1.177 | 0.98 |
| 56_Y | 81_F | 1.170 | 0.97 |
| 110_F | 114_D | 1.155 | 0.97 |
| 20_R | 62_A | 1.131 | 0.97 |
| 100_C | 125_F | 1.126 | 0.97 |
| 129_D | 133_R | 1.121 | 0.97 |
| 20_R | 65_Q | 1.103 | 0.96 |
| 82_T | 99_M | 1.063 | 0.95 |
| 105_T | 108_A | 1.062 | 0.95 |
| 133_R | 136_A | 1.053 | 0.95 |
| 99_M | 112_A | 1.050 | 0.94 |
| 111_G | 115_A | 1.048 | 0.94 |
| 20_R | 44_V | 1.037 | 0.94 |
| 79_L | 112_A | 1.028 | 0.94 |
| 119_E | 136_A | 1.020 | 0.93 |
| 71_H | 99_M | 1.010 | 0.93 |
| 79_L | 111_G | 1.007 | 0.93 |
| 53_E | 57_A | 1.002 | 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 | |
| 3c3wA | 2 | 0.7732 | 99.9 | 0.458 | Contact Map |
| 4ldzA | 2 | 0.7175 | 99.9 | 0.497 | Contact Map |
| 1a04A | 2 | 0.7509 | 99.9 | 0.502 | Contact Map |
| 4gvpA | 4 | 0.7621 | 99.9 | 0.505 | Contact Map |
| 1ys7A | 2 | 0.7807 | 99.9 | 0.509 | Contact Map |
| 1yioA | 1 | 0.7286 | 99.9 | 0.511 | Contact Map |
| 4hyeA | 2 | 0.7323 | 99.9 | 0.512 | Contact Map |
| 3q9sA | 1 | 0.7398 | 99.8 | 0.522 | Contact Map |
| 1kgsA | 1 | 0.7918 | 99.8 | 0.523 | Contact Map |
| 3kloA | 4 | 0.7807 | 99.8 | 0.527 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)