| beps |
| ID: | 1507305840 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 123 (114) | ||
| Sequences: | 5370 (3595.9) | ||
| Seq/Len: | 47.105 | ||
| Nf(neff/√len): | 336.8 |
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: 47.105).
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 |
| 81_N | 94_Q | 3.988 | 1.00 |
| 11_L | 48_L | 3.719 | 1.00 |
| 39_A | 47_G | 3.155 | 1.00 |
| 12_R | 16_F | 2.430 | 1.00 |
| 51_L | 76_L | 2.277 | 1.00 |
| 115_T | 118_R | 2.204 | 1.00 |
| 44_I | 83_L | 2.176 | 1.00 |
| 15_P | 41_G | 2.026 | 1.00 |
| 76_L | 101_L | 1.986 | 1.00 |
| 118_R | 122_A | 1.962 | 1.00 |
| 47_G | 50_R | 1.909 | 1.00 |
| 43_E | 46_E | 1.890 | 1.00 |
| 55_L | 101_L | 1.842 | 1.00 |
| 58_K | 72_E | 1.816 | 1.00 |
| 49_Q | 53_Q | 1.793 | 1.00 |
| 54_T | 75_E | 1.779 | 1.00 |
| 55_L | 76_L | 1.767 | 1.00 |
| 14_I | 87_R | 1.758 | 1.00 |
| 91_G | 95_R | 1.754 | 1.00 |
| 88_E | 92_R | 1.699 | 1.00 |
| 12_R | 44_I | 1.660 | 1.00 |
| 75_E | 79_S | 1.656 | 1.00 |
| 15_P | 40_I | 1.642 | 1.00 |
| 84_H | 91_G | 1.639 | 1.00 |
| 73_A | 98_F | 1.544 | 1.00 |
| 10_Y | 13_H | 1.515 | 1.00 |
| 43_E | 47_G | 1.497 | 1.00 |
| 118_R | 121_V | 1.459 | 1.00 |
| 77_F | 94_Q | 1.424 | 1.00 |
| 84_H | 92_R | 1.404 | 0.99 |
| 80_L | 94_Q | 1.381 | 0.99 |
| 72_E | 105_A | 1.378 | 0.99 |
| 7_W | 87_R | 1.354 | 0.99 |
| 53_Q | 57_E | 1.331 | 0.99 |
| 80_L | 97_F | 1.326 | 0.99 |
| 7_W | 13_H | 1.289 | 0.99 |
| 89_G | 92_R | 1.255 | 0.99 |
| 84_H | 88_E | 1.243 | 0.98 |
| 77_F | 119_M | 1.233 | 0.98 |
| 117_E | 121_V | 1.229 | 0.98 |
| 72_E | 101_L | 1.210 | 0.98 |
| 116_K | 120_M | 1.208 | 0.98 |
| 77_F | 81_N | 1.192 | 0.98 |
| 45_Q | 49_Q | 1.174 | 0.98 |
| 50_R | 53_Q | 1.170 | 0.97 |
| 94_Q | 98_F | 1.164 | 0.97 |
| 48_L | 52_D | 1.157 | 0.97 |
| 73_A | 101_L | 1.144 | 0.97 |
| 100_N | 104_A | 1.136 | 0.97 |
| 79_S | 82_Q | 1.131 | 0.97 |
| 18_F | 38_F | 1.121 | 0.97 |
| 101_L | 105_A | 1.116 | 0.96 |
| 73_A | 102_A | 1.110 | 0.96 |
| 16_F | 38_F | 1.097 | 0.96 |
| 112_S | 115_T | 1.072 | 0.95 |
| 36_N | 82_Q | 1.069 | 0.95 |
| 80_L | 93_T | 1.061 | 0.95 |
| 7_W | 10_Y | 1.049 | 0.94 |
| 101_L | 104_A | 1.037 | 0.94 |
| 81_N | 91_G | 1.030 | 0.94 |
| 111_F | 114_I | 1.019 | 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 | |
| 4npsA | 1 | 0.9187 | 99.9 | 0.092 | Contact Map |
| 4n67A | 1 | 1 | 99.9 | 0.093 | Contact Map |
| 4m16A | 1 | 1 | 99.9 | 0.099 | Contact Map |
| 4py3A | 10 | 0 | 99.9 | 0.104 | Contact Map |
| 2jk8A | 2 | 1 | 99.9 | 0.114 | Contact Map |
| 3zc7A | 1 | 0.878 | 99.9 | 0.118 | Contact Map |
| 3shgA | 1 | 0.878 | 99.9 | 0.119 | Contact Map |
| 4u04A | 2 | 0.8455 | 99.9 | 0.155 | Contact Map |
| 4rglA | 1 | 0.8618 | 99.9 | 0.167 | Contact Map |
| 3cucA | 2 | 0.8943 | 99.9 | 0.175 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)