| armad2 |
| ID: | 1431622381 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 73 (72) | ||
| Sequences: | 2415 (1394.4) | ||
| Seq/Len: | 33.542 | ||
| Nf(neff/√len): | 164.3 |
HHblits Results: (2013_03)
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: 33.542).
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 |
| 1_I | 5_D | 2.981 | 1.00 |
| 38_A | 42_S | 2.479 | 1.00 |
| 29_R | 67_V | 2.094 | 1.00 |
| 17_N | 51_K | 1.896 | 1.00 |
| 11_P | 14_Q | 1.867 | 1.00 |
| 49_L | 68_A | 1.717 | 1.00 |
| 29_R | 32_G | 1.686 | 1.00 |
| 67_V | 70_G | 1.625 | 1.00 |
| 15_L | 23_V | 1.611 | 1.00 |
| 26_Q | 29_R | 1.536 | 1.00 |
| 9_I | 39_Q | 1.514 | 1.00 |
| 35_C | 40_L | 1.492 | 1.00 |
| 17_N | 48_T | 1.463 | 1.00 |
| 31_L | 68_A | 1.448 | 1.00 |
| 40_L | 45_V | 1.352 | 0.99 |
| 13_V | 45_V | 1.347 | 0.99 |
| 39_Q | 43_M | 1.328 | 0.99 |
| 32_G | 67_V | 1.319 | 0.99 |
| 32_G | 64_M | 1.308 | 0.99 |
| 57_H | 61_L | 1.274 | 0.99 |
| 26_Q | 32_G | 1.273 | 0.99 |
| 25_L | 58_N | 1.269 | 0.99 |
| 29_R | 33_N | 1.219 | 0.98 |
| 51_K | 54_G | 1.210 | 0.98 |
| 21_Q | 24_L | 1.184 | 0.98 |
| 25_L | 60_A | 1.177 | 0.98 |
| 52_L | 56_C | 1.158 | 0.97 |
| 29_R | 37_Q | 1.143 | 0.97 |
| 19_K | 23_V | 1.132 | 0.97 |
| 29_R | 70_G | 1.124 | 0.97 |
| 26_Q | 64_M | 1.121 | 0.97 |
| 25_L | 64_M | 1.105 | 0.96 |
| 64_M | 67_V | 1.101 | 0.96 |
| 12_L | 30_A | 1.082 | 0.96 |
| 3_C | 8_L | 1.070 | 0.95 |
| 52_L | 61_L | 1.061 | 0.95 |
| 59_A | 62_T | 1.041 | 0.94 |
| 23_V | 34_I | 1.030 | 0.94 |
| 70_G | 73_A | 1.029 | 0.94 |
| 64_M | 70_G | 1.019 | 0.93 |
| 9_I | 43_M | 1.012 | 0.93 |
| 33_N | 67_V | 1.011 | 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 | |
| 3opbA | 2 | 0.9863 | 99.3 | 0.204 | Contact Map |
| 3grlA | 1 | 0.9863 | 99.1 | 0.268 | Contact Map |
| 4db6A | 1 | 0.9863 | 99 | 0.297 | Contact Map |
| 3tt9A | 1 | 1 | 99 | 0.304 | Contact Map |
| 2jdqA | 2 | 0.9863 | 99 | 0.307 | Contact Map |
| 4wv6A | 1 | 0.9863 | 99 | 0.31 | Contact Map |
| 3l6xA | 1 | 0.9863 | 99 | 0.31 | Contact Map |
| 1xm9A | 1 | 1 | 99 | 0.313 | Contact Map |
| 1xqrA | 2 | 0.9863 | 99 | 0.318 | Contact Map |
| 3nmwA | 2 | 0.9863 | 99 | 0.321 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)