| ss |
| ID: | 1516464400 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 168 (134) | ||
| Sequences: | 2261 (1704.9) | ||
| Seq/Len: | 16.873 | ||
| Nf(neff/√len): | 147.3 |
HHblits Results: (2016_02)
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: 16.873).
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 |
| 121_Q | 129_G | 3.495 | 1.00 |
| 48_A | 128_T | 3.419 | 1.00 |
| 44_I | 68_E | 2.473 | 1.00 |
| 27_I | 122_L | 2.459 | 1.00 |
| 25_E | 29_L | 2.317 | 1.00 |
| 99_R | 116_I | 2.292 | 1.00 |
| 39_D | 42_K | 2.137 | 1.00 |
| 24_D | 90_S | 2.096 | 1.00 |
| 96_Y | 119_V | 1.960 | 1.00 |
| 86_F | 100_V | 1.923 | 1.00 |
| 63_G | 66_A | 1.919 | 1.00 |
| 25_E | 91_S | 1.897 | 1.00 |
| 49_E | 64_R | 1.892 | 1.00 |
| 38_N | 75_F | 1.872 | 1.00 |
| 123_T | 128_T | 1.870 | 1.00 |
| 42_K | 45_E | 1.816 | 1.00 |
| 51_T | 67_V | 1.792 | 1.00 |
| 54_Q | 131_R | 1.749 | 1.00 |
| 24_D | 122_L | 1.720 | 1.00 |
| 26_K | 30_E | 1.682 | 1.00 |
| 102_V | 113_N | 1.680 | 1.00 |
| 100_V | 113_N | 1.660 | 1.00 |
| 118_G | 130_W | 1.603 | 1.00 |
| 50_D | 123_T | 1.592 | 1.00 |
| 98_E | 131_R | 1.557 | 1.00 |
| 23_P | 26_K | 1.553 | 1.00 |
| 54_Q | 129_G | 1.512 | 1.00 |
| 47_F | 51_T | 1.509 | 1.00 |
| 93_G | 121_Q | 1.488 | 1.00 |
| 29_L | 33_D | 1.481 | 1.00 |
| 28_V | 122_L | 1.481 | 1.00 |
| 87_H | 98_E | 1.460 | 1.00 |
| 99_R | 118_G | 1.423 | 1.00 |
| 28_V | 120_F | 1.407 | 0.99 |
| 49_E | 126_K | 1.374 | 0.99 |
| 33_D | 37_S | 1.333 | 0.99 |
| 41_A | 68_E | 1.331 | 0.99 |
| 30_E | 46_Y | 1.302 | 0.99 |
| 52_M | 129_G | 1.259 | 0.99 |
| 34_A | 42_K | 1.253 | 0.99 |
| 30_E | 45_E | 1.253 | 0.99 |
| 36_T | 83_V | 1.240 | 0.98 |
| 29_L | 88_I | 1.221 | 0.98 |
| 87_H | 94_L | 1.209 | 0.98 |
| 35_L | 71_L | 1.203 | 0.98 |
| 25_E | 90_S | 1.198 | 0.98 |
| 72_A | 76_T | 1.182 | 0.98 |
| 79_S | 104_R | 1.177 | 0.98 |
| 51_T | 64_R | 1.161 | 0.97 |
| 24_D | 27_I | 1.118 | 0.96 |
| 98_E | 117_L | 1.102 | 0.96 |
| 118_G | 132_D | 1.096 | 0.96 |
| 36_T | 82_A | 1.090 | 0.96 |
| 33_D | 36_T | 1.086 | 0.96 |
| 96_Y | 117_L | 1.081 | 0.95 |
| 22_T | 26_K | 1.070 | 0.95 |
| 55_N | 132_D | 1.059 | 0.95 |
| 28_V | 32_M | 1.058 | 0.95 |
| 117_L | 133_Y | 1.027 | 0.94 |
| 120_F | 130_W | 1.021 | 0.93 |
| 68_E | 72_A | 1.019 | 0.93 |
| 80_I | 103_L | 1.010 | 0.93 |
| 53_Y | 118_G | 1.005 | 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 | |
| 4r9kA | 3 | 0.9464 | 99.9 | 0.247 | Contact Map |
| 1nwwA | 2 | 0.8631 | 99.9 | 0.32 | Contact Map |
| 2f99A | 4 | 0.7857 | 99.9 | 0.328 | Contact Map |
| 3k0zA | 2 | 0.8631 | 99.8 | 0.345 | Contact Map |
| 2gexA | 2 | 0.8155 | 99.8 | 0.353 | Contact Map |
| 3kkgA | 1 | 0.7857 | 99.8 | 0.353 | Contact Map |
| 1sjwA | 1 | 0.7857 | 99.8 | 0.36 | Contact Map |
| 3ebtA | 1 | 0.7381 | 99.8 | 0.362 | Contact Map |
| 3f9sA | 2 | 0.7738 | 99.8 | 0.364 | Contact Map |
| 4lgqA | 4 | 0.7381 | 99.8 | 0.365 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)