| sonic 20-164 1-80 |
| ID: | 1477517192 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 80 (80) | ||
| Sequences: | 108 (58) | ||
| Seq/Len: | 1.350 | ||
| Nf(neff/√len): | 6.5 |
Jackhmmer Results: (2016_04)
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: 1.350).
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 |
| 1_Y | 4_F | 1.796 | 0.95 |
| 35_P | 54_L | 1.729 | 0.93 |
| 44_K | 51_A | 1.700 | 0.92 |
| 20_E | 56_T | 1.654 | 0.91 |
| 37_Y | 40_D | 1.623 | 0.90 |
| 40_D | 56_T | 1.619 | 0.89 |
| 26_N | 39_P | 1.596 | 0.89 |
| 23_I | 26_N | 1.541 | 0.86 |
| 49_T | 75_P | 1.450 | 0.81 |
| 39_P | 48_N | 1.378 | 0.76 |
| 58_R | 62_K | 1.375 | 0.76 |
| 13_L | 22_K | 1.375 | 0.76 |
| 64_N | 76_G | 1.345 | 0.74 |
| 28_E | 44_K | 1.332 | 0.73 |
| 1_Y | 28_E | 1.313 | 0.71 |
| 8_V | 28_E | 1.308 | 0.71 |
| 4_F | 34_T | 1.292 | 0.69 |
| 58_R | 67_A | 1.273 | 0.68 |
| 1_Y | 29_R | 1.272 | 0.68 |
| 13_L | 18_R | 1.266 | 0.67 |
| 46_E | 78_K | 1.264 | 0.67 |
| 1_Y | 32_E | 1.255 | 0.66 |
| 67_A | 79_L | 1.217 | 0.63 |
| 5_I | 31_K | 1.216 | 0.63 |
| 1_Y | 56_T | 1.203 | 0.61 |
| 4_F | 18_R | 1.202 | 0.61 |
| 27_S | 48_N | 1.201 | 0.61 |
| 33_L | 50_G | 1.200 | 0.61 |
| 5_I | 34_T | 1.175 | 0.59 |
| 16_S | 21_G | 1.160 | 0.57 |
| 25_R | 51_A | 1.159 | 0.57 |
| 5_I | 13_L | 1.156 | 0.57 |
| 18_R | 42_I | 1.151 | 0.56 |
| 45_D | 53_R | 1.149 | 0.56 |
| 64_N | 67_A | 1.145 | 0.56 |
| 30_F | 51_A | 1.119 | 0.53 |
| 30_F | 34_T | 1.116 | 0.53 |
| 45_D | 60_K | 1.096 | 0.51 |
| 9_A | 60_K | 1.095 | 0.51 |
| 29_R | 32_E | 1.090 | 0.50 |
| 20_E | 27_S | 1.038 | 0.45 |
| 13_L | 42_I | 1.032 | 0.44 |
| 40_D | 57_Q | 1.021 | 0.43 |
| 12_T | 18_R | 1.011 | 0.42 |
| 58_R | 76_G | 1.007 | 0.42 |
| 59_C | 77_V | 1.005 | 0.42 |
| 2_K | 18_R | 1.001 | 0.41 |
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 | |
| 2ibgE | 4 | 0.9125 | 100 | 0.394 | Contact Map |
| 3k7iB | 1 | 1 | 100 | 0.399 | Contact Map |
| 3n1gB | 2 | 1 | 99.9 | 0.496 | Contact Map |
| 4k7jA | 2 | 0.975 | 16.4 | 0.938 | Contact Map |
| 2l8dA | 1 | 0.325 | 8.5 | 0.945 | Contact Map |
| 4q9aA | 2 | 0.9375 | 8.4 | 0.945 | Contact Map |
| 1wudA | 3 | 0.5125 | 6.6 | 0.948 | Contact Map |
| 1fxwF | 1 | 0.9375 | 6.2 | 0.948 | Contact Map |
| 2digA | 1 | 0.3625 | 6.1 | 0.949 | Contact Map |
| 1tt9A | 4 | 0.4125 | 5.2 | 0.95 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)