| mad3_II |
| ID: | 1414419353 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 68 (65) | ||
| Sequences: | 97 (74) | ||
| Seq/Len: | 1.492 | ||
| Nf(neff/√len): | 9.2 |
HHblits Results: (2013_03)
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: 1.492).
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 |
| 51_A | 54_R | 1.705 | 0.94 |
| 4_I | 52_I | 1.569 | 0.89 |
| 15_V | 32_N | 1.541 | 0.88 |
| 30_D | 36_L | 1.451 | 0.83 |
| 12_S | 28_K | 1.432 | 0.82 |
| 4_I | 7_D | 1.350 | 0.77 |
| 31_C | 49_I | 1.318 | 0.74 |
| 23_G | 38_P | 1.301 | 0.73 |
| 27_E | 37_Y | 1.294 | 0.73 |
| 59_K | 63_K | 1.276 | 0.71 |
| 23_G | 35_L | 1.243 | 0.68 |
| 1_K | 7_D | 1.234 | 0.67 |
| 4_I | 25_K | 1.231 | 0.67 |
| 19_I | 32_N | 1.201 | 0.64 |
| 24_K | 35_L | 1.201 | 0.64 |
| 1_K | 5_F | 1.198 | 0.64 |
| 25_K | 50_L | 1.196 | 0.64 |
| 1_K | 48_E | 1.174 | 0.62 |
| 11_R | 14_P | 1.173 | 0.62 |
| 18_L | 21_N | 1.160 | 0.60 |
| 24_K | 33_F | 1.153 | 0.60 |
| 41_E | 45_S | 1.152 | 0.59 |
| 17_K | 24_K | 1.151 | 0.59 |
| 38_P | 48_E | 1.131 | 0.57 |
| 22_P | 42_E | 1.098 | 0.54 |
| 23_G | 50_L | 1.085 | 0.53 |
| 30_D | 33_F | 1.072 | 0.51 |
| 36_L | 42_E | 1.068 | 0.51 |
| 42_E | 45_S | 1.058 | 0.50 |
| 4_I | 51_A | 1.053 | 0.49 |
| 25_K | 49_I | 1.042 | 0.48 |
| 29_I | 49_I | 1.025 | 0.46 |
| 6_K | 26_P | 1.024 | 0.46 |
| 14_P | 29_I | 1.022 | 0.46 |
| 36_L | 46_L | 1.021 | 0.46 |
| 21_N | 61_K | 1.020 | 0.46 |
| 9_S | 47_E | 1.016 | 0.46 |
| 17_K | 45_S | 1.014 | 0.45 |
| 14_P | 33_F | 1.010 | 0.45 |
| 25_K | 40_D | 1.006 | 0.45 |
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 | |
| 4bl0B | 2 | 0.6765 | 99.9 | 0.102 | Contact Map |
| 2i3tB | 4 | 0.5441 | 99.5 | 0.395 | Contact Map |
| 2i3sB | 3 | 0.5294 | 99.4 | 0.431 | Contact Map |
| 3exmA | 1 | 1 | 7.7 | 0.905 | Contact Map |
| 2v0xA | 2 | 0.3235 | 7 | 0.907 | Contact Map |
| 4mykA | 1 | 0.9412 | 4.6 | 0.915 | Contact Map |
| 2hp0A | 1 | 0.9412 | 4.1 | 0.917 | Contact Map |
| 2kdoA | 1 | 1 | 3.9 | 0.917 | Contact Map |
| 2inrA | 1 | 0.8529 | 3.9 | 0.918 | Contact Map |
| 3tj1A | 2 | 0.3529 | 3.8 | 0.918 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)