| bcl6b_gremlin |
| ID: | 1449004312 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 131 (118) | ||
| Sequences: | 7113 (4864.2) | ||
| Seq/Len: | 60.280 | ||
| Nf(neff/√len): | 447.8 |
HHblits Results: (2015_06)
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: 60.280).
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 |
| 36_T | 43_P | 3.167 | 1.00 |
| 39_V | 84_F | 2.737 | 1.00 |
| 38_L | 72_V | 2.458 | 1.00 |
| 35_V | 46_A | 2.448 | 1.00 |
| 44_L | 81_A | 2.293 | 1.00 |
| 79_P | 109_A | 2.181 | 1.00 |
| 38_L | 43_P | 2.160 | 1.00 |
| 43_P | 72_V | 2.025 | 1.00 |
| 111_T | 119_V | 1.988 | 1.00 |
| 87_L | 115_M | 1.911 | 1.00 |
| 42_Q | 81_A | 1.888 | 1.00 |
| 80_E | 105_A | 1.872 | 1.00 |
| 36_T | 45_R | 1.810 | 1.00 |
| 38_L | 74_S | 1.748 | 1.00 |
| 42_Q | 85_A | 1.743 | 1.00 |
| 54_C | 91_M | 1.733 | 1.00 |
| 30_G | 45_R | 1.692 | 1.00 |
| 56_G | 114_Q | 1.675 | 1.00 |
| 91_M | 115_M | 1.630 | 1.00 |
| 24_N | 27_R | 1.616 | 1.00 |
| 47_H | 92_Y | 1.616 | 1.00 |
| 79_P | 84_F | 1.610 | 1.00 |
| 44_L | 88_L | 1.606 | 1.00 |
| 87_L | 109_A | 1.587 | 1.00 |
| 31_I | 59_Y | 1.585 | 1.00 |
| 37_L | 84_F | 1.539 | 1.00 |
| 87_L | 118_V | 1.501 | 1.00 |
| 26_L | 49_A | 1.500 | 1.00 |
| 57_F | 113_L | 1.460 | 1.00 |
| 85_A | 89_D | 1.446 | 1.00 |
| 44_L | 85_A | 1.441 | 1.00 |
| 107_L | 123_H | 1.419 | 1.00 |
| 37_L | 46_A | 1.349 | 0.99 |
| 58_F | 62_F | 1.336 | 0.99 |
| 78_G | 112_Y | 1.325 | 0.99 |
| 24_N | 28_L | 1.284 | 0.99 |
| 82_R | 102_T | 1.271 | 0.99 |
| 46_A | 88_L | 1.257 | 0.99 |
| 103_A | 125_F | 1.253 | 0.99 |
| 35_V | 62_F | 1.209 | 0.98 |
| 27_R | 89_D | 1.199 | 0.98 |
| 35_V | 73_L | 1.197 | 0.98 |
| 39_V | 44_L | 1.188 | 0.98 |
| 74_S | 77_G | 1.171 | 0.98 |
| 80_E | 83_G | 1.156 | 0.97 |
| 27_R | 30_G | 1.139 | 0.97 |
| 87_L | 113_L | 1.131 | 0.97 |
| 22_N | 54_C | 1.131 | 0.97 |
| 35_V | 51_L | 1.129 | 0.97 |
| 123_H | 127_Q | 1.128 | 0.97 |
| 40_G | 81_A | 1.118 | 0.96 |
| 36_T | 72_V | 1.116 | 0.96 |
| 52_I | 63_R | 1.100 | 0.96 |
| 86_P | 89_D | 1.091 | 0.96 |
| 83_G | 105_A | 1.082 | 0.96 |
| 48_K | 71_D | 1.075 | 0.95 |
| 33_T | 46_A | 1.064 | 0.95 |
| 31_I | 63_R | 1.061 | 0.95 |
| 59_Y | 63_R | 1.054 | 0.95 |
| 22_N | 25_E | 1.033 | 0.94 |
| 60_S | 114_Q | 1.022 | 0.93 |
| 28_L | 85_A | 1.013 | 0.93 |
| 67_G | 70_V | 1.009 | 0.93 |
| 21_G | 25_E | 1.007 | 0.93 |
| 83_G | 109_A | 1.004 | 0.93 |
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 | |
| 3i3nA | 2 | 0.9924 | 99.9 | 0.185 | Contact Map |
| 2z8hA | 1 | 0.9924 | 99.9 | 0.187 | Contact Map |
| 4hxiA | 1 | 0.8855 | 99.9 | 0.19 | Contact Map |
| 3hveA | 1 | 0.8321 | 99.9 | 0.193 | Contact Map |
| 4u2mA | 4 | 0.9618 | 99.9 | 0.203 | Contact Map |
| 3ohuA | 6 | 0.9466 | 99.9 | 0.204 | Contact Map |
| 3ga1A | 2 | 0.9313 | 99.9 | 0.206 | Contact Map |
| 4cxiA | 1 | 0.9466 | 99.9 | 0.207 | Contact Map |
| 1r29A | 1 | 0.9313 | 99.9 | 0.21 | Contact Map |
| 3b84A | 1 | 0.8626 | 99.9 | 0.213 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)