| 1G2E_A |
| ID: | 1515161491 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 83 (81) | ||
| Sequences: | 32930 (19099.3) | ||
| Seq/Len: | 406.543 | ||
| Nf(neff/√len): | 2122.1 |
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: 406.543).
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 |
| 53_D | 56_D | 2.274 | 1.00 |
| 28_E | 52_I | 2.267 | 1.00 |
| 18_E | 70_Q | 2.224 | 1.00 |
| 30_E | 52_I | 2.216 | 1.00 |
| 15_T | 18_E | 2.213 | 1.00 |
| 26_I | 63_T | 2.164 | 1.00 |
| 4_N | 50_N | 1.791 | 1.00 |
| 59_K | 63_T | 1.724 | 1.00 |
| 58_E | 78_Y | 1.690 | 1.00 |
| 54_P | 78_Y | 1.689 | 1.00 |
| 54_P | 58_E | 1.631 | 1.00 |
| 8_N | 75_K | 1.621 | 1.00 |
| 35_V | 46_Y | 1.615 | 1.00 |
| 68_R | 73_T | 1.557 | 1.00 |
| 22_L | 67_L | 1.556 | 1.00 |
| 37_D | 40_T | 1.516 | 1.00 |
| 28_E | 56_D | 1.515 | 1.00 |
| 12_Q | 72_K | 1.509 | 1.00 |
| 26_I | 64_L | 1.500 | 1.00 |
| 16_Q | 20_R | 1.488 | 1.00 |
| 20_R | 24_G | 1.370 | 0.99 |
| 3_T | 57_A | 1.364 | 0.99 |
| 69_L | 74_I | 1.323 | 0.99 |
| 66_G | 73_T | 1.322 | 0.99 |
| 12_Q | 42_Q | 1.296 | 0.99 |
| 11_P | 14_M | 1.288 | 0.99 |
| 30_E | 50_N | 1.281 | 0.99 |
| 31_S | 50_N | 1.263 | 0.99 |
| 57_A | 78_Y | 1.236 | 0.98 |
| 52_I | 56_D | 1.236 | 0.98 |
| 64_L | 67_L | 1.231 | 0.98 |
| 5_L | 61_I | 1.231 | 0.98 |
| 5_L | 57_A | 1.201 | 0.98 |
| 21_S | 24_G | 1.188 | 0.98 |
| 13_N | 70_Q | 1.183 | 0.98 |
| 34_L | 43_S | 1.161 | 0.97 |
| 7_V | 23_F | 1.136 | 0.97 |
| 22_L | 64_L | 1.118 | 0.96 |
| 8_N | 77_S | 1.118 | 0.96 |
| 51_Y | 60_A | 1.115 | 0.96 |
| 58_E | 62_N | 1.105 | 0.96 |
| 35_V | 48_F | 1.105 | 0.96 |
| 23_F | 49_V | 1.104 | 0.96 |
| 34_L | 47_G | 1.100 | 0.96 |
| 61_I | 78_Y | 1.093 | 0.96 |
| 4_N | 31_S | 1.053 | 0.95 |
| 68_R | 71_T | 1.048 | 0.94 |
| 55_K | 59_K | 1.046 | 0.94 |
| 12_Q | 45_G | 1.027 | 0.94 |
| 3_T | 30_E | 1.024 | 0.93 |
| 22_L | 69_L | 1.019 | 0.93 |
| 17_E | 21_S | 1.015 | 0.93 |
| 59_K | 62_N | 1.003 | 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 | |
| 3pgwS | 2 | 1 | 99.1 | -0.193 | Contact Map |
| 3q2sC | 2 | 0.9759 | 99 | -0.158 | Contact Map |
| 3n9uC | 2 | 0.9759 | 99 | -0.154 | Contact Map |
| 1rk8A | 1 | 0.988 | 99 | -0.146 | Contact Map |
| 1u6fA | 1 | 1 | 99 | -0.134 | Contact Map |
| 2jrsA | 1 | 1 | 99 | -0.131 | Contact Map |
| 4wikA | 2 | 0.9759 | 99 | -0.13 | Contact Map |
| 2kxnB | 1 | 1 | 98.9 | -0.125 | Contact Map |
| 2mtgA | 1 | 1 | 98.9 | -0.123 | Contact Map |
| 1oo0B | 1 | 1 | 98.9 | -0.122 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)