| qrrm3 |
| ID: | 1444164749 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 106 (85) | ||
| Sequences: | 8180 (4913.6) | ||
| Seq/Len: | 96.235 | ||
| Nf(neff/√len): | 533.0 |
HHblits Results: (2015_06)
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: 96.235).
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 |
| 53_S | 56_R | 2.659 | 1.00 |
| 26_T | 52_K | 2.599 | 1.00 |
| 16_D | 70_K | 2.435 | 1.00 |
| 10_Y | 72_R | 2.427 | 1.00 |
| 13_T | 16_D | 2.308 | 1.00 |
| 59_M | 63_K | 2.177 | 1.00 |
| 69_M | 74_V | 1.922 | 1.00 |
| 58_F | 78_Q | 1.878 | 1.00 |
| 3_I | 57_A | 1.673 | 1.00 |
| 36_V | 46_D | 1.646 | 1.00 |
| 18_L | 22_G | 1.644 | 1.00 |
| 24_F | 63_K | 1.644 | 1.00 |
| 5_L | 21_L | 1.634 | 1.00 |
| 2_C | 50_Q | 1.537 | 1.00 |
| 35_M | 43_P | 1.518 | 1.00 |
| 20_F | 67_K | 1.510 | 1.00 |
| 57_A | 78_Q | 1.502 | 1.00 |
| 6_R | 75_E | 1.501 | 1.00 |
| 28_I | 50_Q | 1.478 | 1.00 |
| 68_N | 73_Y | 1.472 | 1.00 |
| 19_D | 22_G | 1.451 | 1.00 |
| 24_F | 64_C | 1.451 | 1.00 |
| 58_F | 62_Q | 1.446 | 1.00 |
| 54_A | 58_F | 1.434 | 1.00 |
| 3_I | 61_A | 1.434 | 1.00 |
| 28_I | 52_K | 1.419 | 1.00 |
| 52_K | 56_R | 1.407 | 0.99 |
| 66_K | 73_Y | 1.407 | 0.99 |
| 68_N | 71_D | 1.383 | 0.99 |
| 55_D | 59_M | 1.346 | 0.99 |
| 26_T | 56_R | 1.285 | 0.99 |
| 14_I | 18_L | 1.265 | 0.99 |
| 17_I | 47_A | 1.263 | 0.99 |
| 9_P | 12_A | 1.261 | 0.99 |
| 54_A | 78_Q | 1.240 | 0.98 |
| 64_C | 67_K | 1.231 | 0.98 |
| 21_L | 49_I | 1.218 | 0.98 |
| 11_A | 70_K | 1.211 | 0.98 |
| 10_Y | 42_R | 1.157 | 0.97 |
| 15_E | 19_D | 1.148 | 0.97 |
| 6_R | 77_F | 1.143 | 0.97 |
| 36_V | 48_F | 1.141 | 0.97 |
| 59_M | 62_Q | 1.124 | 0.97 |
| 12_A | 70_K | 1.115 | 0.96 |
| 20_F | 69_M | 1.095 | 0.96 |
| 15_E | 18_L | 1.074 | 0.95 |
| 9_P | 70_K | 1.068 | 0.95 |
| 20_F | 64_C | 1.032 | 0.94 |
| 5_L | 17_I | 1.020 | 0.93 |
| 12_A | 69_M | 1.018 | 0.93 |
| 33_V | 47_A | 1.001 | 0.92 |
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 | |
| 1rk8A | 1 | 0.7547 | 99.7 | 0.252 | Contact Map |
| 2hglA | 1 | 0.8396 | 99.7 | 0.257 | Contact Map |
| 3pgwS | 2 | 0.7547 | 99.7 | 0.261 | Contact Map |
| 3q2sC | 2 | 0.8491 | 99.7 | 0.261 | Contact Map |
| 2lmiA | 1 | 0.8774 | 99.7 | 0.266 | Contact Map |
| 3n9uC | 2 | 0.8774 | 99.7 | 0.267 | Contact Map |
| 2kn4A | 1 | 0.8208 | 99.7 | 0.271 | Contact Map |
| 4wikA | 2 | 0.9717 | 99.7 | 0.273 | Contact Map |
| 2dhaA | 1 | 0.9057 | 99.7 | 0.274 | Contact Map |
| 2lcwA | 1 | 0.8679 | 99.7 | 0.275 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)