| 4x5m |
| ID: | 1489252477 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 100 (90) | ||
| Sequences: | 745 (614.9) | ||
| Seq/Len: | 8.278 | ||
| Nf(neff/√len): | 64.8 |
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: 8.278).
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 |
| 31_N | 34_G | 3.845 | 1.00 |
| 12_A | 65_A | 2.076 | 1.00 |
| 26_T | 32_T | 2.015 | 1.00 |
| 5_L | 59_D | 1.859 | 1.00 |
| 44_L | 73_A | 1.843 | 1.00 |
| 15_T | 46_G | 1.834 | 1.00 |
| 19_F | 39_M | 1.680 | 1.00 |
| 30_R | 83_N | 1.604 | 1.00 |
| 9_L | 60_F | 1.532 | 1.00 |
| 40_Y | 76_V | 1.484 | 1.00 |
| 54_G | 66_N | 1.439 | 0.99 |
| 16_T | 69_T | 1.401 | 0.99 |
| 51_I | 55_I | 1.386 | 0.99 |
| 32_T | 83_N | 1.378 | 0.99 |
| 15_T | 50_W | 1.344 | 0.99 |
| 19_F | 43_F | 1.330 | 0.99 |
| 47_V | 69_T | 1.295 | 0.98 |
| 10_F | 49_S | 1.283 | 0.98 |
| 60_F | 64_I | 1.271 | 0.98 |
| 79_I | 83_N | 1.268 | 0.98 |
| 25_K | 34_G | 1.267 | 0.98 |
| 26_T | 76_V | 1.267 | 0.98 |
| 48_I | 70_L | 1.265 | 0.98 |
| 44_L | 70_L | 1.264 | 0.98 |
| 27_I | 79_I | 1.263 | 0.98 |
| 19_F | 73_A | 1.255 | 0.98 |
| 11_A | 49_S | 1.236 | 0.98 |
| 43_F | 69_T | 1.231 | 0.97 |
| 23_S | 76_V | 1.228 | 0.97 |
| 54_G | 62_V | 1.225 | 0.97 |
| 50_W | 54_G | 1.211 | 0.97 |
| 25_K | 29_T | 1.204 | 0.97 |
| 48_I | 52_A | 1.200 | 0.97 |
| 37_V | 80_T | 1.177 | 0.96 |
| 14_F | 45_T | 1.157 | 0.96 |
| 20_A | 24_I | 1.150 | 0.96 |
| 43_F | 47_V | 1.114 | 0.95 |
| 57_R | 62_V | 1.111 | 0.95 |
| 8_G | 54_G | 1.095 | 0.94 |
| 52_A | 71_F | 1.090 | 0.94 |
| 72_L | 76_V | 1.080 | 0.94 |
| 51_I | 63_L | 1.080 | 0.94 |
| 44_L | 74_A | 1.079 | 0.94 |
| 18_A | 43_F | 1.074 | 0.93 |
| 51_I | 62_V | 1.073 | 0.93 |
| 55_I | 63_L | 1.056 | 0.93 |
| 26_T | 79_I | 1.055 | 0.93 |
| 5_L | 9_L | 1.049 | 0.92 |
| 32_T | 35_I | 1.042 | 0.92 |
| 40_Y | 73_A | 1.023 | 0.91 |
| 39_M | 73_A | 1.020 | 0.91 |
| 4_I | 63_L | 1.019 | 0.91 |
| 59_D | 62_V | 1.011 | 0.90 |
| 39_M | 43_F | 1.000 | 0.90 |
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 | |
| 4x5mA | 3 | 0.94 | 99.8 | 0.271 | Contact Map |
| 4qncA | 2 | 0.82 | 99.7 | 0.373 | Contact Map |
| 4rngA | 6 | 0.83 | 99.7 | 0.376 | Contact Map |
| 4qndA | 1 | 0.88 | 99.5 | 0.426 | Contact Map |
| 2xijA | 1 | 0.81 | 47.9 | 0.868 | Contact Map |
| 4u4vA | 1 | 0 | 22.2 | 0.889 | Contact Map |
| 4uvmA | 1 | 0.87 | 18.2 | 0.894 | Contact Map |
| 3l1lA | 1 | 0.91 | 16.6 | 0.896 | Contact Map |
| 4b4aA | 1 | 0.55 | 15.7 | 0.897 | Contact Map |
| 3dh4A | 4 | 0.97 | 13.7 | 0.9 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)