| sea4 |
| ID: | 1503438371 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 108 (100) | ||
| Sequences: | 2534 (1541.2) | ||
| Seq/Len: | 25.340 | ||
| Nf(neff/√len): | 154.1 |
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: 25.340).
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 |
| 14_S | 22_Y | 4.319 | 1.00 |
| 44_L | 64_R | 2.724 | 1.00 |
| 15_L | 51_F | 2.538 | 1.00 |
| 18_P | 23_Y | 2.515 | 1.00 |
| 52_R | 58_Q | 2.343 | 1.00 |
| 12_N | 15_L | 2.309 | 1.00 |
| 11_F | 16_E | 2.115 | 1.00 |
| 21_D | 25_E | 1.916 | 1.00 |
| 23_Y | 27_Q | 1.789 | 1.00 |
| 35_L | 46_L | 1.677 | 1.00 |
| 38_Y | 43_F | 1.629 | 1.00 |
| 43_F | 46_L | 1.494 | 1.00 |
| 70_V | 74_E | 1.491 | 1.00 |
| 49_I | 60_T | 1.463 | 1.00 |
| 34_F | 59_L | 1.442 | 1.00 |
| 13_S | 16_E | 1.405 | 0.99 |
| 26_L | 30_I | 1.388 | 0.99 |
| 73_V | 76_Q | 1.372 | 0.99 |
| 73_V | 77_F | 1.340 | 0.99 |
| 46_L | 61_L | 1.324 | 0.99 |
| 35_L | 43_F | 1.308 | 0.99 |
| 32_E | 36_Q | 1.283 | 0.99 |
| 26_L | 51_F | 1.256 | 0.99 |
| 12_N | 22_Y | 1.256 | 0.99 |
| 25_E | 28_R | 1.255 | 0.99 |
| 74_E | 81_K | 1.244 | 0.98 |
| 27_Q | 31_S | 1.243 | 0.98 |
| 22_Y | 26_L | 1.236 | 0.98 |
| 18_P | 28_R | 1.236 | 0.98 |
| 48_N | 59_L | 1.228 | 0.98 |
| 30_I | 34_F | 1.213 | 0.98 |
| 76_Q | 81_K | 1.132 | 0.97 |
| 26_L | 63_F | 1.122 | 0.97 |
| 34_F | 38_Y | 1.118 | 0.96 |
| 15_L | 23_Y | 1.108 | 0.96 |
| 34_F | 40_Q | 1.106 | 0.96 |
| 75_T | 79_Q | 1.100 | 0.96 |
| 50_K | 58_Q | 1.092 | 0.96 |
| 26_L | 38_Y | 1.073 | 0.95 |
| 57_V | 61_L | 1.054 | 0.95 |
| 45_G | 62_A | 1.047 | 0.94 |
| 93_S | 98_S | 1.044 | 0.94 |
| 17_D | 101_P | 1.042 | 0.94 |
| 70_V | 81_K | 1.022 | 0.93 |
| 48_N | 51_F | 1.018 | 0.93 |
| 31_S | 48_N | 1.002 | 0.92 |
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 | |
| 2e7vA | 1 | 0.9074 | 99.7 | 0.365 | Contact Map |
| 1ivzA | 1 | 0.963 | 99.5 | 0.432 | Contact Map |
| 2acmA | 1 | 0.5 | 98.5 | 0.627 | Contact Map |
| 2acmB | 1 | 0.4352 | 96.1 | 0.758 | Contact Map |
| 1wh9A | 1 | 0.787 | 15.7 | 0.896 | Contact Map |
| 2rpbA | 1 | 0.75 | 10.2 | 0.904 | Contact Map |
| 3bk6A | 3 | 0.7778 | 8 | 0.909 | Contact Map |
| 1winA | 1 | 0.8148 | 6.8 | 0.912 | Contact Map |
| 4fvgA | 1 | 0.75 | 6.7 | 0.912 | Contact Map |
| 2o3bB | 1 | 0.6481 | 5 | 0.917 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)