| 1SS1 |
| ID: | 1429471470 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 59 (53) | ||
| Sequences: | 454 (396.6) | ||
| Seq/Len: | 8.566 | ||
| Nf(neff/√len): | 54.5 |
Jackhmmer Results: (2015_01_07)
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: 8.566).
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 |
| 17_L | 31_I | 2.606 | 1.00 |
| 16_I | 34_L | 2.514 | 1.00 |
| 33_S | 47_E | 2.314 | 1.00 |
| 24_E | 28_N | 2.070 | 1.00 |
| 7_K | 11_N | 1.816 | 1.00 |
| 21_N | 52_N | 1.784 | 1.00 |
| 15_E | 49_K | 1.695 | 1.00 |
| 23_N | 26_Q | 1.602 | 1.00 |
| 30_F | 33_S | 1.598 | 1.00 |
| 30_F | 51_L | 1.583 | 1.00 |
| 13_F | 35_K | 1.573 | 1.00 |
| 26_Q | 51_L | 1.498 | 1.00 |
| 13_F | 31_I | 1.472 | 1.00 |
| 45_L | 49_K | 1.406 | 0.99 |
| 7_K | 10_Q | 1.393 | 0.99 |
| 29_G | 32_Q | 1.261 | 0.98 |
| 33_S | 44_L | 1.253 | 0.98 |
| 40_Q | 43_N | 1.195 | 0.97 |
| 4_K | 8_E | 1.188 | 0.97 |
| 28_N | 32_Q | 1.181 | 0.97 |
| 51_L | 54_A | 1.153 | 0.96 |
| 37_D | 41_S | 1.140 | 0.96 |
| 4_K | 7_K | 1.131 | 0.96 |
| 10_Q | 14_Y | 1.124 | 0.95 |
| 32_Q | 36_D | 1.070 | 0.94 |
| 16_I | 31_I | 1.035 | 0.92 |
| 31_I | 35_K | 1.024 | 0.91 |
| 26_Q | 55_Q | 1.004 | 0.90 |
| 8_E | 12_A | 1.003 | 0.90 |
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 | |
| 2kziA | 1 | 0.9831 | 98.7 | 0.213 | Contact Map |
| 4npfY | 2 | 1 | 98.6 | 0.249 | Contact Map |
| 4gwpC | 1 | 0 | 98.6 | 0.25 | Contact Map |
| 3qwoC | 2 | 0.8983 | 98.5 | 0.273 | Contact Map |
| 4npdA | 1 | 0.9831 | 98.5 | 0.274 | Contact Map |
| 2lr2A | 1 | 0.9831 | 98.4 | 0.294 | Contact Map |
| 1zxgA | 1 | 1 | 98.2 | 0.323 | Contact Map |
| 4kjmA | 2 | 0.8983 | 97.2 | 0.455 | Contact Map |
| 1zdaA | 1 | 0.6271 | 96.4 | 0.508 | Contact Map |
| 2dgjA | 2 | 1 | 96.1 | 0.524 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)