| 10_1titpdb |
| ID: | 1516869732 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 89 (87) | ||
| Sequences: | 14808 (10008.8) | ||
| Seq/Len: | 170.207 | ||
| Nf(neff/√len): | 1073.1 |
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: 170.207).
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 |
| 35_K | 74_Q | 3.524 | 1.00 |
| 13_V | 63_C | 2.706 | 1.00 |
| 20_H | 59_I | 2.370 | 1.00 |
| 18_T | 59_I | 2.343 | 1.00 |
| 18_T | 61_H | 2.214 | 1.00 |
| 27_E | 31_H | 2.123 | 1.00 |
| 20_H | 57_I | 2.080 | 1.00 |
| 33_Q | 76_A | 2.050 | 1.00 |
| 33_Q | 40_P | 1.934 | 1.00 |
| 35_K | 72_S | 1.864 | 1.00 |
| 36_L | 71_V | 1.815 | 1.00 |
| 14_F | 17_E | 1.789 | 1.00 |
| 46_D | 67_M | 1.739 | 1.00 |
| 13_V | 19_A | 1.704 | 1.00 |
| 35_K | 40_P | 1.669 | 1.00 |
| 36_L | 69_G | 1.646 | 1.00 |
| 25_L | 75_A | 1.611 | 1.00 |
| 70_E | 83_N | 1.611 | 1.00 |
| 37_K | 72_S | 1.592 | 1.00 |
| 21_F | 84_L | 1.576 | 1.00 |
| 22_E | 57_I | 1.553 | 1.00 |
| 33_Q | 74_Q | 1.507 | 1.00 |
| 15_V | 65_L | 1.487 | 1.00 |
| 3_E | 26_S | 1.472 | 1.00 |
| 25_L | 32_G | 1.458 | 1.00 |
| 32_G | 73_F | 1.405 | 0.99 |
| 51_E | 56_H | 1.401 | 0.99 |
| 48_E | 61_H | 1.269 | 0.99 |
| 23_I | 73_F | 1.248 | 0.99 |
| 19_A | 63_C | 1.234 | 0.98 |
| 37_K | 41_L | 1.231 | 0.98 |
| 77_N | 80_S | 1.230 | 0.98 |
| 19_A | 60_L | 1.193 | 0.98 |
| 50_I | 59_I | 1.185 | 0.98 |
| 4_V | 7_P | 1.179 | 0.98 |
| 64_Q | 67_M | 1.155 | 0.97 |
| 13_V | 17_E | 1.149 | 0.97 |
| 19_A | 84_L | 1.147 | 0.97 |
| 32_G | 56_H | 1.146 | 0.97 |
| 14_F | 87_K | 1.142 | 0.97 |
| 6_K | 24_E | 1.129 | 0.97 |
| 4_V | 25_L | 1.120 | 0.96 |
| 24_E | 55_K | 1.108 | 0.96 |
| 67_M | 71_V | 1.087 | 0.96 |
| 11_V | 19_A | 1.087 | 0.96 |
| 5_E | 24_E | 1.076 | 0.95 |
| 8_L | 80_S | 1.055 | 0.95 |
| 10_G | 83_N | 1.042 | 0.94 |
| 38_G | 72_S | 1.007 | 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 | |
| 1waaA | 4 | 1 | 98.7 | 0.012 | Contact Map |
| 3utoA | 2 | 1 | 98.7 | 0.033 | Contact Map |
| 2edfA | 1 | 1 | 98.7 | 0.041 | Contact Map |
| 2e7bA | 1 | 1 | 98.6 | 0.046 | Contact Map |
| 3b43A | 1 | 1 | 98.6 | 0.057 | Contact Map |
| 2enyA | 1 | 1 | 98.6 | 0.062 | Contact Map |
| 1x44A | 1 | 1 | 98.6 | 0.064 | Contact Map |
| 2edhA | 1 | 0.9888 | 98.6 | 0.065 | Contact Map |
| 2e6pA | 1 | 1 | 98.6 | 0.069 | Contact Map |
| 1pd6A | 1 | 0.9888 | 98.6 | 0.07 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)