| MAD1L1 |
| ID: | 1493975373 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 50% gaps before running GREMLIN. |
| Length: | 162 (125) | ||
| Sequences: | 432 (304.5) | ||
| Seq/Len: | 3.456 | ||
| Nf(neff/√len): | 27.2 |
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: 3.456).
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 |
| 21_V | 24_R | 2.549 | 1.00 |
| 20_V | 25_D | 2.089 | 1.00 |
| 43_R | 76_F | 1.975 | 1.00 |
| 29_L | 33_E | 1.890 | 1.00 |
| 26_K | 30_R | 1.875 | 1.00 |
| 141_W | 150_G | 1.861 | 0.99 |
| 1_M | 4_R | 1.679 | 0.99 |
| 47_S | 69_D | 1.660 | 0.99 |
| 4_R | 8_E | 1.625 | 0.98 |
| 15_D | 18_E | 1.610 | 0.98 |
| 63_R | 73_S | 1.585 | 0.98 |
| 11_E | 16_A | 1.554 | 0.97 |
| 141_W | 155_V | 1.519 | 0.97 |
| 148_I | 152_M | 1.474 | 0.96 |
| 30_R | 34_V | 1.470 | 0.96 |
| 41_E | 152_M | 1.470 | 0.96 |
| 47_S | 67_Q | 1.469 | 0.96 |
| 141_W | 145_E | 1.447 | 0.96 |
| 14_R | 17_L | 1.399 | 0.95 |
| 140_Y | 145_E | 1.395 | 0.94 |
| 74_F | 155_V | 1.379 | 0.94 |
| 147_C | 150_G | 1.372 | 0.94 |
| 156_T | 162_K | 1.342 | 0.93 |
| 35_F | 42_F | 1.328 | 0.92 |
| 141_W | 154_S | 1.322 | 0.92 |
| 49_I | 152_M | 1.313 | 0.92 |
| 44_E | 53_K | 1.312 | 0.92 |
| 52_F | 159_C | 1.287 | 0.91 |
| 38_K | 41_E | 1.260 | 0.89 |
| 47_S | 160_Y | 1.249 | 0.89 |
| 7_W | 10_M | 1.222 | 0.87 |
| 24_R | 28_L | 1.213 | 0.87 |
| 34_V | 38_K | 1.193 | 0.86 |
| 13_E | 18_E | 1.192 | 0.86 |
| 61_Q | 77_Q | 1.178 | 0.85 |
| 137_L | 141_W | 1.177 | 0.85 |
| 139_E | 144_G | 1.174 | 0.84 |
| 20_V | 24_R | 1.172 | 0.84 |
| 16_A | 20_V | 1.168 | 0.84 |
| 141_W | 144_G | 1.157 | 0.83 |
| 142_V | 147_C | 1.154 | 0.83 |
| 33_E | 45_A | 1.153 | 0.83 |
| 52_F | 74_F | 1.126 | 0.81 |
| 129_G | 138_V | 1.112 | 0.80 |
| 49_I | 155_V | 1.095 | 0.78 |
| 56_F | 141_W | 1.093 | 0.78 |
| 81_L | 118_G | 1.081 | 0.77 |
| 137_L | 159_C | 1.078 | 0.77 |
| 19_E | 22_R | 1.077 | 0.77 |
| 158_E | 161_E | 1.075 | 0.77 |
| 135_G | 139_E | 1.066 | 0.76 |
| 30_R | 35_F | 1.066 | 0.76 |
| 38_K | 56_F | 1.057 | 0.75 |
| 44_E | 48_S | 1.034 | 0.73 |
| 7_W | 11_E | 1.033 | 0.72 |
| 26_K | 35_F | 1.031 | 0.72 |
| 20_V | 23_Q | 1.030 | 0.72 |
| 39_S | 63_R | 1.030 | 0.72 |
| 147_C | 151_L | 1.025 | 0.72 |
| 56_F | 62_V | 1.025 | 0.72 |
| 150_G | 160_Y | 1.018 | 0.71 |
| 26_K | 31_L | 1.010 | 0.70 |
| 14_R | 22_R | 1.000 | 0.69 |
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 | |
| 4dzoA | 2 | 0.7099 | 100 | 0.285 | Contact Map |
| 2ve7A | 2 | 0.7469 | 91.2 | 0.877 | Contact Map |
| 2zxxA | 4 | 0.3086 | 38.6 | 0.92 | Contact Map |
| 2akfA | 3 | 0.1975 | 34.3 | 0.923 | Contact Map |
| 1hjbA | 4 | 0.2407 | 33.5 | 0.923 | Contact Map |
| 4gfhA | 2 | 0.3395 | 30.5 | 0.925 | Contact Map |
| 3w92A | 3 | 0.1914 | 28.3 | 0.926 | Contact Map |
| 4dznA | 3 | 0.1914 | 25.9 | 0.927 | Contact Map |
| 1deqA | 4 | 0.6173 | 25.9 | 0.927 | Contact Map |
| 3ra3A | 2 | 0.1667 | 24.6 | 0.928 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)