| student |
| ID: | 1504547736 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 166 (150) | ||
| Sequences: | 3552 (1965.7) | ||
| Seq/Len: | 23.680 | ||
| Nf(neff/√len): | 160.5 |
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: 23.680).
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 |
| 18_Q | 149_E | 4.117 | 1.00 |
| 23_L | 90_R | 2.792 | 1.00 |
| 91_K | 94_K | 2.566 | 1.00 |
| 30_K | 87_A | 2.528 | 1.00 |
| 131_K | 144_K | 2.528 | 1.00 |
| 106_G | 161_E | 2.498 | 1.00 |
| 115_G | 118_H | 2.338 | 1.00 |
| 39_R | 132_E | 2.296 | 1.00 |
| 43_K | 128_D | 2.137 | 1.00 |
| 47_V | 125_A | 2.002 | 1.00 |
| 44_I | 121_V | 2.002 | 1.00 |
| 25_S | 147_W | 1.990 | 1.00 |
| 26_W | 83_C | 1.953 | 1.00 |
| 103_K | 161_E | 1.945 | 1.00 |
| 15_S | 18_Q | 1.920 | 1.00 |
| 47_V | 128_D | 1.909 | 1.00 |
| 34_A | 76_M | 1.796 | 1.00 |
| 25_S | 143_M | 1.779 | 1.00 |
| 156_A | 160_Q | 1.757 | 1.00 |
| 21_L | 146_A | 1.752 | 1.00 |
| 32_D | 35_N | 1.744 | 1.00 |
| 16_E | 20_A | 1.731 | 1.00 |
| 123_K | 151_Y | 1.693 | 1.00 |
| 19_E | 90_R | 1.692 | 1.00 |
| 139_W | 144_K | 1.691 | 1.00 |
| 18_Q | 145_S | 1.676 | 1.00 |
| 85_A | 154_L | 1.651 | 1.00 |
| 17_E | 20_A | 1.642 | 1.00 |
| 140_S | 143_M | 1.611 | 1.00 |
| 144_K | 148_S | 1.560 | 1.00 |
| 22_V | 150_A | 1.559 | 1.00 |
| 41_F | 74_H | 1.542 | 1.00 |
| 39_R | 42_L | 1.533 | 1.00 |
| 17_E | 142_A | 1.532 | 1.00 |
| 145_S | 149_E | 1.531 | 1.00 |
| 21_L | 143_M | 1.531 | 1.00 |
| 43_K | 132_E | 1.526 | 1.00 |
| 20_A | 24_K | 1.509 | 1.00 |
| 37_A | 79_F | 1.495 | 1.00 |
| 106_G | 158_I | 1.472 | 1.00 |
| 28_I | 138_M | 1.405 | 0.99 |
| 123_K | 152_D | 1.400 | 0.99 |
| 39_R | 43_K | 1.395 | 0.99 |
| 43_K | 125_A | 1.386 | 0.99 |
| 131_K | 141_P | 1.327 | 0.99 |
| 127_L | 148_S | 1.322 | 0.99 |
| 15_S | 149_E | 1.308 | 0.99 |
| 108_T | 112_Y | 1.274 | 0.99 |
| 48_A | 51_A | 1.223 | 0.98 |
| 48_A | 125_A | 1.218 | 0.98 |
| 88_Q | 91_K | 1.207 | 0.98 |
| 44_I | 125_A | 1.199 | 0.98 |
| 83_C | 87_A | 1.187 | 0.98 |
| 26_W | 29_L | 1.168 | 0.97 |
| 148_S | 152_D | 1.167 | 0.97 |
| 81_M | 84_E | 1.155 | 0.97 |
| 107_A | 161_E | 1.135 | 0.97 |
| 76_M | 80_V | 1.126 | 0.97 |
| 124_F | 128_D | 1.119 | 0.96 |
| 40_F | 126_L | 1.119 | 0.96 |
| 43_K | 47_V | 1.085 | 0.96 |
| 127_L | 144_K | 1.077 | 0.95 |
| 135_P | 138_M | 1.069 | 0.95 |
| 45_F | 55_F | 1.069 | 0.95 |
| 19_E | 23_L | 1.063 | 0.95 |
| 55_F | 109_H | 1.060 | 0.95 |
| 38_L | 75_A | 1.037 | 0.94 |
| 151_Y | 155_V | 1.022 | 0.93 |
| 86_A | 89_L | 1.021 | 0.93 |
| 125_A | 128_D | 1.016 | 0.93 |
| 139_W | 143_M | 1.015 | 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 | |
| 1hlbA | 1 | 0.9398 | 100 | 0.211 | Contact Map |
| 1q1fA | 1 | 0.8735 | 100 | 0.218 | Contact Map |
| 2dc3A | 2 | 0.9578 | 100 | 0.22 | Contact Map |
| 1hlmA | 1 | 0.9458 | 100 | 0.225 | Contact Map |
| 2oifA | 8 | 0.9096 | 100 | 0.227 | Contact Map |
| 1a6mA | 1 | 0.8855 | 100 | 0.236 | Contact Map |
| 2aa1B | 2 | 0.8614 | 100 | 0.24 | Contact Map |
| 2c0kA | 2 | 0.8795 | 100 | 0.242 | Contact Map |
| 1outB | 1 | 0.8614 | 100 | 0.242 | Contact Map |
| 1v4xB | 2 | 0.8614 | 100 | 0.243 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)