| sub_b |
| ID: | 1502119673 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 105 (105) | ||
| Sequences: | 4252 (3024.5) | ||
| Seq/Len: | 40.495 | ||
| Nf(neff/√len): | 295.2 |
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: 40.495).
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 |
| 7_D | 11_N | 2.428 | 1.00 |
| 17_L | 21_R | 2.195 | 1.00 |
| 25_E | 29_K | 2.123 | 1.00 |
| 10_D | 14_Q | 2.096 | 1.00 |
| 24_E | 28_G | 2.028 | 1.00 |
| 50_Q | 54_N | 2.014 | 1.00 |
| 18_N | 22_N | 1.981 | 1.00 |
| 65_N | 69_S | 1.878 | 1.00 |
| 14_Q | 18_N | 1.863 | 1.00 |
| 89_Q | 93_I | 1.729 | 1.00 |
| 32_E | 36_K | 1.728 | 1.00 |
| 70_T | 74_L | 1.710 | 1.00 |
| 13_K | 17_L | 1.629 | 1.00 |
| 62_E | 65_N | 1.627 | 1.00 |
| 21_R | 25_E | 1.581 | 1.00 |
| 34_L | 38_R | 1.558 | 1.00 |
| 53_V | 57_S | 1.556 | 1.00 |
| 86_Q | 90_Q | 1.531 | 1.00 |
| 60_E | 64_M | 1.513 | 1.00 |
| 64_M | 68_N | 1.500 | 1.00 |
| 43_K | 47_D | 1.495 | 1.00 |
| 11_N | 15_R | 1.470 | 1.00 |
| 75_E | 79_N | 1.449 | 1.00 |
| 57_S | 61_R | 1.448 | 1.00 |
| 39_A | 43_K | 1.440 | 1.00 |
| 78_E | 82_N | 1.424 | 1.00 |
| 74_L | 77_F | 1.411 | 1.00 |
| 69_S | 73_T | 1.382 | 0.99 |
| 36_K | 40_R | 1.378 | 0.99 |
| 79_N | 83_E | 1.367 | 0.99 |
| 28_G | 32_E | 1.358 | 0.99 |
| 35_E | 39_A | 1.356 | 0.99 |
| 76_Q | 80_Y | 1.323 | 0.99 |
| 10_D | 13_K | 1.320 | 0.99 |
| 68_N | 71_Y | 1.319 | 0.99 |
| 53_V | 56_Y | 1.293 | 0.99 |
| 72_K | 76_Q | 1.289 | 0.99 |
| 15_R | 19_T | 1.279 | 0.99 |
| 43_K | 46_M | 1.244 | 0.98 |
| 71_Y | 75_E | 1.243 | 0.98 |
| 49_D | 53_V | 1.233 | 0.98 |
| 88_E | 91_K | 1.224 | 0.98 |
| 72_K | 75_E | 1.221 | 0.98 |
| 35_E | 38_R | 1.210 | 0.98 |
| 47_D | 50_Q | 1.205 | 0.98 |
| 60_E | 63_K | 1.179 | 0.98 |
| 63_K | 66_L | 1.161 | 0.97 |
| 31_I | 35_E | 1.161 | 0.97 |
| 27_R | 31_I | 1.156 | 0.97 |
| 95_Q | 99_R | 1.150 | 0.97 |
| 22_N | 26_L | 1.145 | 0.97 |
| 80_Y | 83_E | 1.136 | 0.97 |
| 4_V | 7_D | 1.122 | 0.97 |
| 68_N | 72_K | 1.102 | 0.96 |
| 28_G | 31_I | 1.095 | 0.96 |
| 11_N | 14_Q | 1.086 | 0.96 |
| 90_Q | 94_N | 1.078 | 0.95 |
| 62_E | 66_L | 1.068 | 0.95 |
| 44_V | 48_A | 1.057 | 0.95 |
| 63_K | 67_I | 1.054 | 0.95 |
| 87_F | 91_K | 1.045 | 0.94 |
| 29_K | 32_E | 1.038 | 0.94 |
| 40_R | 43_K | 1.038 | 0.94 |
| 37_A | 40_R | 1.027 | 0.94 |
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 | |
| 2khkA | 1 | 0.5048 | 96.8 | 0.511 | Contact Map |
| 1l2pA | 1 | 0.581 | 94.7 | 0.585 | Contact Map |
| 2dm9A | 2 | 0.0667 | 89.5 | 0.647 | Contact Map |
| 3v6iA | 2 | 0.7905 | 76.5 | 0.699 | Contact Map |
| 4efaG | 1 | 0.8476 | 41 | 0.76 | Contact Map |
| 2clyA | 2 | 0.9524 | 28.2 | 0.78 | Contact Map |
| 4cfgA | 2 | 0.9238 | 24.4 | 0.787 | Contact Map |
| 4efaE | 1 | 0.8381 | 23.5 | 0.789 | Contact Map |
| 4aurA | 1 | 1 | 20.5 | 0.794 | Contact Map |
| 3v6iB | 2 | 0.8762 | 19.2 | 0.797 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)