| examplemyo |
| ID: | 1518572404 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 153 (147) | ||
| Sequences: | 3834 (2063.1) | ||
| Seq/Len: | 26.082 | ||
| Nf(neff/√len): | 170.2 |
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: 26.082).
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 |
| 6_E | 133_K | 4.035 | 1.00 |
| 11_L | 80_G | 2.765 | 1.00 |
| 116_H | 128_Q | 2.754 | 1.00 |
| 100_P | 103_Y | 2.574 | 1.00 |
| 18_E | 77_K | 2.478 | 1.00 |
| 27_D | 117_S | 2.452 | 1.00 |
| 31_R | 113_H | 2.110 | 1.00 |
| 3_S | 6_E | 2.035 | 1.00 |
| 13_V | 131_M | 2.029 | 1.00 |
| 32_L | 106_F | 2.028 | 1.00 |
| 35_S | 113_H | 2.012 | 1.00 |
| 4_E | 8_Q | 1.959 | 1.00 |
| 35_S | 110_A | 1.931 | 1.00 |
| 123_F | 128_Q | 1.805 | 1.00 |
| 75_I | 138_F | 1.765 | 1.00 |
| 14_W | 73_G | 1.764 | 1.00 |
| 140_K | 144_A | 1.728 | 1.00 |
| 108_S | 135_L | 1.721 | 1.00 |
| 6_E | 129_G | 1.701 | 1.00 |
| 22_A | 66_V | 1.700 | 1.00 |
| 20_D | 23_G | 1.699 | 1.00 |
| 5_G | 8_Q | 1.685 | 1.00 |
| 129_G | 133_K | 1.664 | 1.00 |
| 13_V | 127_A | 1.656 | 1.00 |
| 124_G | 127_A | 1.648 | 1.00 |
| 25_G | 69_L | 1.635 | 1.00 |
| 108_S | 136_E | 1.634 | 1.00 |
| 90_A | 145_K | 1.618 | 1.00 |
| 128_Q | 132_N | 1.603 | 1.00 |
| 29_L | 64_H | 1.600 | 1.00 |
| 10_V | 134_A | 1.571 | 1.00 |
| 9_L | 130_A | 1.567 | 1.00 |
| 31_R | 110_A | 1.553 | 1.00 |
| 90_A | 142_I | 1.530 | 1.00 |
| 9_L | 127_A | 1.515 | 1.00 |
| 16_K | 122_D | 1.510 | 1.00 |
| 5_G | 126_D | 1.477 | 1.00 |
| 27_D | 30_I | 1.462 | 1.00 |
| 112_I | 132_N | 1.457 | 1.00 |
| 7_W | 80_G | 1.432 | 1.00 |
| 31_R | 117_S | 1.426 | 1.00 |
| 33_F | 43_F | 1.409 | 1.00 |
| 8_Q | 12_H | 1.372 | 0.99 |
| 27_D | 31_R | 1.323 | 0.99 |
| 116_H | 125_A | 1.287 | 0.99 |
| 36_H | 110_A | 1.247 | 0.99 |
| 71_A | 74_A | 1.245 | 0.98 |
| 31_R | 35_S | 1.227 | 0.98 |
| 3_S | 133_K | 1.204 | 0.98 |
| 73_G | 77_K | 1.179 | 0.98 |
| 132_N | 136_E | 1.176 | 0.98 |
| 28_I | 111_I | 1.172 | 0.98 |
| 64_H | 68_V | 1.171 | 0.98 |
| 139_R | 143_A | 1.164 | 0.97 |
| 92_S | 96_K | 1.155 | 0.97 |
| 109_E | 113_H | 1.145 | 0.97 |
| 36_H | 39_T | 1.136 | 0.97 |
| 35_S | 109_E | 1.130 | 0.97 |
| 112_I | 128_Q | 1.126 | 0.97 |
| 43_F | 93_H | 1.121 | 0.97 |
| 105_E | 143_A | 1.105 | 0.96 |
| 123_F | 127_A | 1.094 | 0.96 |
| 114_V | 118_R | 1.089 | 0.96 |
| 26_Q | 65_G | 1.083 | 0.96 |
| 135_L | 139_R | 1.080 | 0.95 |
| 31_R | 114_V | 1.070 | 0.95 |
| 66_V | 70_T | 1.055 | 0.95 |
| 50_K | 57_A | 1.054 | 0.95 |
| 4_E | 7_W | 1.039 | 0.94 |
| 78_K | 81_H | 1.038 | 0.94 |
| 136_E | 140_K | 1.032 | 0.94 |
| 14_W | 17_V | 1.009 | 0.93 |
| 29_L | 68_V | 1.005 | 0.93 |
| 111_I | 135_L | 1.001 | 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 | |
| 1a6mA | 1 | 0.9869 | 100 | 0.057 | Contact Map |
| 1lhsA | 1 | 1 | 100 | 0.06 | Contact Map |
| 2dc3A | 2 | 1 | 100 | 0.073 | Contact Map |
| 1v4xB | 2 | 0.9412 | 100 | 0.094 | Contact Map |
| 2r80B | 2 | 0.9412 | 100 | 0.094 | Contact Map |
| 2aa1B | 2 | 0.9477 | 100 | 0.096 | Contact Map |
| 1outB | 1 | 0.9412 | 100 | 0.097 | Contact Map |
| 3d1kB | 1 | 0.9412 | 100 | 0.097 | Contact Map |
| 3bomB | 2 | 0.9412 | 100 | 0.1 | Contact Map |
| 2w72B | 2 | 0.9477 | 100 | 0.101 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)