| SIGSAS |
| ID: | 1465672903 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 123 (116) | ||
| Sequences: | 12268 (8607) | ||
| Seq/Len: | 105.759 | ||
| Nf(neff/√len): | 799.1 |
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: 105.759).
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 |
| 27_C | 104_F | 3.612 | 1.00 |
| 17_V | 94_A | 3.513 | 1.00 |
| 47_F | 105_R | 2.751 | 1.00 |
| 24_I | 90_V | 2.482 | 1.00 |
| 48_K | 100_A | 2.443 | 1.00 |
| 49_G | 53_P | 2.380 | 1.00 |
| 22_C | 92_R | 2.221 | 1.00 |
| 26_S | 88_S | 2.194 | 1.00 |
| 101_W | 118_S | 2.149 | 1.00 |
| 23_V | 119_N | 2.091 | 1.00 |
| 18_P | 21_L | 2.076 | 1.00 |
| 75_R | 98_D | 2.045 | 1.00 |
| 22_C | 90_V | 2.011 | 1.00 |
| 24_I | 88_S | 1.954 | 1.00 |
| 101_W | 116_F | 1.879 | 1.00 |
| 107_E | 112_V | 1.874 | 1.00 |
| 103_F | 114_H | 1.704 | 1.00 |
| 103_F | 116_F | 1.630 | 1.00 |
| 31_Y | 42_A | 1.556 | 1.00 |
| 44_G | 87_C | 1.552 | 1.00 |
| 26_S | 86_S | 1.518 | 1.00 |
| 45_Y | 105_R | 1.486 | 1.00 |
| 47_F | 103_F | 1.481 | 1.00 |
| 17_V | 23_V | 1.479 | 1.00 |
| 29_L | 106_V | 1.438 | 1.00 |
| 49_G | 103_F | 1.409 | 1.00 |
| 18_P | 122_F | 1.398 | 0.99 |
| 72_T | 76_F | 1.397 | 0.99 |
| 45_Y | 107_E | 1.394 | 0.99 |
| 29_L | 44_G | 1.377 | 0.99 |
| 8_S | 11_V | 1.344 | 0.99 |
| 16_P | 120_A | 1.334 | 0.99 |
| 19_E | 96_R | 1.273 | 0.99 |
| 33_R | 42_A | 1.265 | 0.99 |
| 22_C | 93_D | 1.258 | 0.99 |
| 23_V | 91_I | 1.257 | 0.99 |
| 5_P | 9_L | 1.216 | 0.98 |
| 95_Q | 98_D | 1.214 | 0.98 |
| 14_Q | 118_S | 1.212 | 0.98 |
| 23_V | 94_A | 1.182 | 0.98 |
| 44_G | 104_F | 1.168 | 0.97 |
| 48_K | 102_Y | 1.167 | 0.97 |
| 28_N | 86_S | 1.156 | 0.97 |
| 108_R | 111_R | 1.147 | 0.97 |
| 46_W | 89_L | 1.141 | 0.97 |
| 70_M | 73_R | 1.132 | 0.97 |
| 58_P | 62_N | 1.105 | 0.96 |
| 105_R | 112_V | 1.078 | 0.95 |
| 50_R | 53_P | 1.077 | 0.95 |
| 6_S | 9_L | 1.071 | 0.95 |
| 25_V | 119_N | 1.064 | 0.95 |
| 57_A | 60_A | 1.063 | 0.95 |
| 87_C | 104_F | 1.055 | 0.95 |
| 72_T | 75_R | 1.053 | 0.95 |
| 57_A | 62_N | 1.033 | 0.94 |
| 77_Q | 92_R | 1.027 | 0.94 |
| 49_G | 101_W | 1.017 | 0.93 |
| 48_K | 51_T | 1.015 | 0.93 |
| 77_Q | 90_V | 1.014 | 0.93 |
| 49_G | 52_S | 1.008 | 0.93 |
| 58_P | 61_T | 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 | |
| 1nkoA | 1 | 0.9512 | 99.5 | 0.279 | Contact Map |
| 3oaiA | 2 | 0.9268 | 99.4 | 0.287 | Contact Map |
| 3utoA | 2 | 0.7805 | 99.4 | 0.306 | Contact Map |
| 4l1dA | 3 | 0.8374 | 99.4 | 0.314 | Contact Map |
| 2ocwA | 1 | 0.9024 | 99.4 | 0.315 | Contact Map |
| 3zkxC | 1 | 0.8862 | 99.4 | 0.317 | Contact Map |
| 2zg1A | 1 | 0.9593 | 99.3 | 0.327 | Contact Map |
| 1dlfH | 1 | 0.9106 | 99.3 | 0.333 | Contact Map |
| 4qo1A | 1 | 0.9106 | 99.3 | 0.334 | Contact Map |
| 4nobA | 1 | 0.878 | 99.3 | 0.334 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)