| nterm |
| ID: | 1512674019 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 50% gaps before running GREMLIN. |
| Length: | 111 (106) | ||
| Sequences: | 508 (161.2) | ||
| Seq/Len: | 4.792 | ||
| Nf(neff/√len): | 15.7 |
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: 4.792).
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 |
| 86_A | 92_V | 2.136 | 1.00 |
| 97_E | 102_I | 1.847 | 1.00 |
| 95_Y | 98_K | 1.796 | 1.00 |
| 72_S | 75_R | 1.728 | 1.00 |
| 8_I | 24_L | 1.698 | 0.99 |
| 74_S | 77_A | 1.685 | 0.99 |
| 94_S | 105_W | 1.673 | 0.99 |
| 75_R | 78_H | 1.668 | 0.99 |
| 66_R | 69_D | 1.623 | 0.99 |
| 37_R | 102_I | 1.612 | 0.99 |
| 17_K | 21_L | 1.595 | 0.99 |
| 84_Q | 92_V | 1.558 | 0.99 |
| 55_Q | 58_G | 1.508 | 0.98 |
| 102_I | 105_W | 1.506 | 0.98 |
| 12_K | 47_T | 1.424 | 0.97 |
| 20_A | 50_L | 1.418 | 0.97 |
| 69_D | 80_H | 1.391 | 0.97 |
| 38_I | 102_I | 1.356 | 0.96 |
| 10_Y | 13_C | 1.319 | 0.96 |
| 61_K | 64_N | 1.308 | 0.95 |
| 19_E | 22_S | 1.285 | 0.95 |
| 72_S | 78_H | 1.235 | 0.93 |
| 43_H | 49_H | 1.233 | 0.93 |
| 75_R | 81_P | 1.232 | 0.93 |
| 62_C | 67_F | 1.231 | 0.93 |
| 37_R | 97_E | 1.216 | 0.92 |
| 9_T | 12_K | 1.201 | 0.92 |
| 20_A | 23_Q | 1.195 | 0.91 |
| 3_S | 6_Y | 1.194 | 0.91 |
| 97_E | 104_D | 1.188 | 0.91 |
| 60_F | 67_F | 1.172 | 0.90 |
| 53_L | 96_I | 1.167 | 0.90 |
| 33_K | 44_E | 1.166 | 0.90 |
| 52_V | 81_P | 1.157 | 0.90 |
| 88_S | 93_K | 1.142 | 0.89 |
| 27_I | 31_T | 1.140 | 0.89 |
| 80_H | 95_Y | 1.138 | 0.89 |
| 29_T | 67_F | 1.138 | 0.89 |
| 96_I | 105_W | 1.138 | 0.89 |
| 80_H | 98_K | 1.137 | 0.88 |
| 38_I | 41_E | 1.123 | 0.88 |
| 77_A | 81_P | 1.110 | 0.87 |
| 93_K | 97_E | 1.105 | 0.87 |
| 7_F | 55_Q | 1.100 | 0.86 |
| 96_I | 99_D | 1.095 | 0.86 |
| 45_D | 51_H | 1.092 | 0.86 |
| 90_S | 99_D | 1.065 | 0.84 |
| 36_I | 43_H | 1.063 | 0.84 |
| 3_S | 59_K | 1.048 | 0.82 |
| 88_S | 94_S | 1.045 | 0.82 |
| 18_E | 21_L | 1.040 | 0.82 |
| 56_F | 60_F | 1.037 | 0.81 |
| 51_H | 55_Q | 1.034 | 0.81 |
| 13_C | 17_K | 1.030 | 0.81 |
| 76_S | 80_H | 1.029 | 0.81 |
| 13_C | 21_L | 1.001 | 0.78 |
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 | |
| 1l2mA | 1 | 1 | 100 | -0.026 | Contact Map |
| 2hwtA | 1 | 0.7838 | 99.8 | 0.56 | Contact Map |
| 2hw0A | 1 | 0.8829 | 99.6 | 0.63 | Contact Map |
| 3dkxA | 3 | 0.9189 | 45 | 0.919 | Contact Map |
| 4pp4A | 1 | 0.8288 | 12.8 | 0.938 | Contact Map |
| 2nq5A | 1 | 0.3243 | 6.8 | 0.945 | Contact Map |
| 2ww6A | 3 | 0.2252 | 5.9 | 0.947 | Contact Map |
| 4mmsB | 3 | 0.3243 | 5.1 | 0.948 | Contact Map |
| 4lviA | 1 | 0.8378 | 4.1 | 0.951 | Contact Map |
| 1ypxA | 1 | 0.3243 | 3.2 | 0.953 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)