| destab_contacts |
| ID: | 1492953081 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 139 (126) | ||
| Sequences: | 202 (146.7) | ||
| Seq/Len: | 1.603 | ||
| Nf(neff/√len): | 13.1 |
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: 1.603).
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 |
| 71_G | 74_S | 2.090 | 0.99 |
| 55_Y | 83_E | 1.994 | 0.98 |
| 51_S | 58_K | 1.910 | 0.98 |
| 31_C | 37_D | 1.871 | 0.97 |
| 65_C | 85_C | 1.864 | 0.97 |
| 35_G | 58_K | 1.816 | 0.96 |
| 61_Y | 86_V | 1.710 | 0.94 |
| 29_C | 134_C | 1.594 | 0.91 |
| 30_I | 127_Y | 1.579 | 0.91 |
| 106_Q | 131_V | 1.449 | 0.85 |
| 65_C | 86_V | 1.441 | 0.84 |
| 70_G | 74_S | 1.438 | 0.84 |
| 30_I | 35_G | 1.401 | 0.82 |
| 107_D | 111_I | 1.386 | 0.81 |
| 106_Q | 110_R | 1.371 | 0.80 |
| 23_T | 99_G | 1.371 | 0.80 |
| 29_C | 52_C | 1.342 | 0.78 |
| 109_A | 128_W | 1.302 | 0.75 |
| 129_N | 132_Q | 1.300 | 0.75 |
| 45_M | 50_L | 1.289 | 0.74 |
| 86_V | 111_I | 1.282 | 0.74 |
| 97_C | 119_C | 1.265 | 0.72 |
| 93_Y | 116_P | 1.262 | 0.72 |
| 96_F | 107_D | 1.258 | 0.72 |
| 79_K | 83_E | 1.245 | 0.70 |
| 22_F | 87_R | 1.223 | 0.68 |
| 94_G | 107_D | 1.216 | 0.68 |
| 26_C | 81_C | 1.212 | 0.67 |
| 26_C | 52_C | 1.195 | 0.66 |
| 71_G | 116_P | 1.194 | 0.66 |
| 62_W | 107_D | 1.174 | 0.64 |
| 88_A | 131_V | 1.172 | 0.64 |
| 71_G | 97_C | 1.164 | 0.63 |
| 52_C | 112_H | 1.160 | 0.62 |
| 55_Y | 79_K | 1.157 | 0.62 |
| 57_I | 64_D | 1.149 | 0.61 |
| 56_Q | 128_W | 1.143 | 0.61 |
| 34_E | 72_Y | 1.141 | 0.61 |
| 112_H | 127_Y | 1.140 | 0.60 |
| 22_F | 90_M | 1.138 | 0.60 |
| 97_C | 101_R | 1.135 | 0.60 |
| 39_Q | 118_G | 1.129 | 0.59 |
| 88_A | 95_T | 1.123 | 0.59 |
| 64_D | 93_Y | 1.102 | 0.57 |
| 75_C | 81_C | 1.100 | 0.56 |
| 93_Y | 118_G | 1.099 | 0.56 |
| 110_R | 128_W | 1.093 | 0.56 |
| 52_C | 81_C | 1.092 | 0.56 |
| 44_G | 130_K | 1.090 | 0.55 |
| 109_A | 127_Y | 1.089 | 0.55 |
| 57_I | 61_Y | 1.079 | 0.54 |
| 76_T | 114_G | 1.079 | 0.54 |
| 34_E | 54_P | 1.077 | 0.54 |
| 58_K | 113_N | 1.076 | 0.54 |
| 66_G | 89_Y | 1.074 | 0.54 |
| 26_C | 31_C | 1.065 | 0.53 |
| 111_I | 117_R | 1.065 | 0.53 |
| 128_W | 132_Q | 1.062 | 0.52 |
| 34_E | 56_Q | 1.053 | 0.51 |
| 76_T | 79_K | 1.042 | 0.50 |
| 103_P | 107_D | 1.038 | 0.50 |
| 34_E | 110_R | 1.038 | 0.50 |
| 104_T | 108_Y | 1.035 | 0.50 |
| 113_N | 127_Y | 1.030 | 0.49 |
| 26_C | 105_C | 1.021 | 0.48 |
| 92_R | 106_Q | 1.014 | 0.47 |
| 40_I | 95_T | 1.007 | 0.47 |
| 51_S | 56_Q | 1.006 | 0.47 |
| 96_F | 134_C | 1.005 | 0.46 |
| 29_C | 89_Y | 1.000 | 0.46 |
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 | |
| 2dqaA | 2 | 0.8633 | 100 | 0.219 | Contact Map |
| 4pj2C | 2 | 0.8633 | 100 | 0.221 | Contact Map |
| 3b72A | 1 | 0.6259 | 88.9 | 0.906 | Contact Map |
| 2vb1A | 1 | 0.7338 | 83.7 | 0.913 | Contact Map |
| 1lsgA | 1 | 0.8489 | 78.2 | 0.917 | Contact Map |
| 2nwdX | 1 | 0.7266 | 74.5 | 0.92 | Contact Map |
| 2gv0A | 1 | 0.7266 | 69.1 | 0.923 | Contact Map |
| 1hmlA | 1 | 0.6403 | 68.8 | 0.923 | Contact Map |
| 1jugA | 1 | 0.7554 | 66.6 | 0.924 | Contact Map |
| 1lmqA | 1 | 0.7626 | 62 | 0.927 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)