| 25 |
| ID: | 1508441372 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 123 (116) | ||
| Sequences: | 3218 (1949.2) | ||
| Seq/Len: | 27.741 | ||
| Nf(neff/√len): | 181.0 |
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: 27.741).
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 |
| 59_H | 100_F | 4.011 | 1.00 |
| 91_E | 94_K | 3.535 | 1.00 |
| 13_I | 16_G | 2.244 | 1.00 |
| 30_F | 49_P | 2.178 | 1.00 |
| 34_S | 45_N | 2.087 | 1.00 |
| 56_Q | 74_L | 2.054 | 1.00 |
| 18_V | 27_P | 2.010 | 1.00 |
| 98_N | 102_Q | 1.994 | 1.00 |
| 11_A | 105_L | 1.829 | 1.00 |
| 16_G | 90_M | 1.779 | 1.00 |
| 65_C | 115_A | 1.774 | 1.00 |
| 105_L | 116_L | 1.766 | 1.00 |
| 94_K | 98_N | 1.749 | 1.00 |
| 59_H | 63_S | 1.717 | 1.00 |
| 50_R | 55_F | 1.678 | 1.00 |
| 61_K | 64_E | 1.670 | 1.00 |
| 33_V | 46_W | 1.662 | 1.00 |
| 27_P | 90_M | 1.662 | 1.00 |
| 32_M | 45_N | 1.576 | 1.00 |
| 51_R | 93_S | 1.556 | 1.00 |
| 66_V | 113_S | 1.550 | 1.00 |
| 57_N | 61_K | 1.520 | 1.00 |
| 55_F | 97_L | 1.475 | 1.00 |
| 107_D | 110_L | 1.460 | 1.00 |
| 19_T | 28_C | 1.438 | 1.00 |
| 59_H | 74_L | 1.437 | 1.00 |
| 28_C | 49_P | 1.430 | 1.00 |
| 31_V | 101_L | 1.427 | 1.00 |
| 17_E | 49_P | 1.401 | 0.99 |
| 10_K | 34_S | 1.368 | 0.99 |
| 29_Y | 93_S | 1.343 | 0.99 |
| 32_M | 47_T | 1.325 | 0.99 |
| 97_L | 100_F | 1.318 | 0.99 |
| 56_Q | 77_L | 1.316 | 0.99 |
| 116_L | 120_L | 1.305 | 0.99 |
| 29_Y | 90_M | 1.298 | 0.99 |
| 118_A | 122_P | 1.284 | 0.99 |
| 26_L | 51_R | 1.265 | 0.99 |
| 104_L | 110_L | 1.251 | 0.99 |
| 51_R | 77_L | 1.239 | 0.98 |
| 78_S | 89_F | 1.237 | 0.98 |
| 14_T | 32_M | 1.230 | 0.98 |
| 30_F | 47_T | 1.223 | 0.98 |
| 77_L | 93_S | 1.223 | 0.98 |
| 99_K | 103_N | 1.215 | 0.98 |
| 56_Q | 60_R | 1.193 | 0.98 |
| 66_V | 110_L | 1.156 | 0.97 |
| 90_M | 93_S | 1.150 | 0.97 |
| 114_E | 118_A | 1.139 | 0.97 |
| 27_P | 85_I | 1.113 | 0.96 |
| 11_A | 98_N | 1.105 | 0.96 |
| 65_C | 113_S | 1.102 | 0.96 |
| 74_L | 100_F | 1.096 | 0.96 |
| 55_F | 58_L | 1.081 | 0.95 |
| 29_Y | 51_R | 1.072 | 0.95 |
| 53_S | 56_Q | 1.071 | 0.95 |
| 33_V | 48_V | 1.037 | 0.94 |
| 57_N | 118_A | 1.027 | 0.94 |
| 113_S | 116_L | 1.024 | 0.93 |
| 52_L | 93_S | 1.016 | 0.93 |
| 14_T | 94_K | 1.016 | 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
- See coupling matrix (for protein design or mutagenesis)
- 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 | |
| 4akvA | 2 | 0.8049 | 99.9 | 0.134 | Contact Map |
| 3dytA | 1 | 0.8293 | 99.9 | 0.142 | Contact Map |
| 1ocsA | 1 | 0.9593 | 99.9 | 0.147 | Contact Map |
| 3iq2A | 2 | 0.9593 | 99.9 | 0.155 | Contact Map |
| 4on3A | 2 | 0.935 | 99.9 | 0.169 | Contact Map |
| 4hasA | 2 | 0.8455 | 99.9 | 0.178 | Contact Map |
| 4bgjA | 1 | 0.935 | 99.9 | 0.178 | Contact Map |
| 4ikdA | 1 | 0.8943 | 99.9 | 0.181 | Contact Map |
| 2i4kA | 1 | 0.935 | 99.9 | 0.194 | Contact Map |
| 2cskA | 1 | 0.9756 | 99.9 | 0.194 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)