| ss |
| ID: | 1518193630 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 56 (48) | ||
| Sequences: | 1501 (1219.1) | ||
| Seq/Len: | 31.271 | ||
| Nf(neff/√len): | 176.0 |
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: 31.271).
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 |
| 15_L | 29_I | 3.007 | 1.00 |
| 11_F | 33_K | 2.977 | 1.00 |
| 21_N | 24_Q | 2.302 | 1.00 |
| 26_N | 30_Q | 2.280 | 1.00 |
| 22_A | 26_N | 2.269 | 1.00 |
| 30_Q | 34_D | 2.163 | 1.00 |
| 31_S | 45_E | 1.705 | 1.00 |
| 14_V | 32_L | 1.676 | 1.00 |
| 19_N | 50_N | 1.614 | 1.00 |
| 37_S | 40_A | 1.555 | 1.00 |
| 27_G | 31_S | 1.551 | 1.00 |
| 8_Q | 12_Y | 1.470 | 1.00 |
| 28_F | 49_L | 1.449 | 1.00 |
| 27_G | 30_Q | 1.375 | 0.99 |
| 6_A | 38_Q | 1.317 | 0.99 |
| 13_Q | 47_Q | 1.313 | 0.99 |
| 28_F | 42_V | 1.309 | 0.99 |
| 44_G | 48_K | 1.306 | 0.99 |
| 5_E | 9_N | 1.298 | 0.99 |
| 41_N | 44_G | 1.282 | 0.99 |
| 12_Y | 16_N | 1.129 | 0.97 |
| 42_V | 45_E | 1.068 | 0.95 |
| 9_N | 12_Y | 1.065 | 0.95 |
| 43_L | 47_Q | 1.050 | 0.94 |
| 5_E | 8_Q | 1.021 | 0.93 |
| 11_F | 29_I | 1.016 | 0.93 |
| 10_A | 43_L | 1.013 | 0.93 |
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 | |
| 4gwpC | 1 | 0 | 98.5 | 0.266 | Contact Map |
| 2kziA | 1 | 1 | 98.2 | 0.312 | Contact Map |
| 3qwoC | 2 | 0.9464 | 98 | 0.349 | Contact Map |
| 4npfY | 2 | 1 | 97.9 | 0.372 | Contact Map |
| 2lr2A | 1 | 1 | 97.8 | 0.379 | Contact Map |
| 4npdA | 1 | 1 | 97.7 | 0.392 | Contact Map |
| 4kjmA | 2 | 0.9107 | 97.2 | 0.447 | Contact Map |
| 1zxgA | 1 | 1 | 97.1 | 0.452 | Contact Map |
| 2dgjA | 2 | 0.8929 | 94.6 | 0.561 | Contact Map |
| 1zdaA | 1 | 0.625 | 89.9 | 0.622 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)