| 4noaA |
| ID: | 1491921441 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 108 (100) | ||
| Sequences: | 1185 (941.4) | ||
| Seq/Len: | 11.850 | ||
| Nf(neff/√len): | 94.1 |
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: 11.850).
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_N | 90_E | 3.899 | 1.00 |
| 6_N | 51_L | 3.210 | 1.00 |
| 24_Y | 28_N | 2.898 | 1.00 |
| 16_D | 20_R | 2.544 | 1.00 |
| 80_C | 106_C | 2.529 | 1.00 |
| 70_P | 81_G | 2.524 | 1.00 |
| 84_T | 92_G | 2.381 | 1.00 |
| 9_E | 13_L | 2.124 | 1.00 |
| 1_F | 4_R | 2.053 | 1.00 |
| 21_Q | 25_Y | 1.899 | 1.00 |
| 18_A | 64_Y | 1.893 | 1.00 |
| 14_L | 66_L | 1.823 | 1.00 |
| 55_T | 67_T | 1.758 | 1.00 |
| 55_T | 69_T | 1.748 | 1.00 |
| 60_T | 63_T | 1.667 | 1.00 |
| 53_N | 71_I | 1.602 | 1.00 |
| 7_R | 52_Y | 1.567 | 1.00 |
| 7_R | 77_D | 1.497 | 1.00 |
| 63_T | 87_Q | 1.455 | 1.00 |
| 52_Y | 81_G | 1.424 | 1.00 |
| 21_Q | 36_D | 1.372 | 0.99 |
| 67_T | 82_K | 1.339 | 0.99 |
| 13_L | 17_A | 1.300 | 0.99 |
| 13_L | 54_L | 1.297 | 0.99 |
| 14_L | 85_L | 1.278 | 0.99 |
| 9_E | 49_N | 1.233 | 0.98 |
| 9_E | 16_D | 1.229 | 0.98 |
| 64_Y | 87_Q | 1.213 | 0.98 |
| 93_A | 103_V | 1.207 | 0.98 |
| 6_N | 9_E | 1.193 | 0.98 |
| 7_R | 70_P | 1.185 | 0.98 |
| 1_F | 5_S | 1.183 | 0.98 |
| 85_L | 92_G | 1.182 | 0.98 |
| 11_Q | 83_L | 1.177 | 0.98 |
| 23_R | 26_S | 1.174 | 0.98 |
| 80_C | 93_A | 1.155 | 0.97 |
| 37_V | 40_L | 1.147 | 0.97 |
| 72_N | 77_D | 1.143 | 0.97 |
| 57_A | 65_T | 1.126 | 0.97 |
| 21_Q | 37_V | 1.095 | 0.96 |
| 7_R | 81_G | 1.090 | 0.96 |
| 18_A | 85_L | 1.085 | 0.96 |
| 10_G | 13_L | 1.052 | 0.95 |
| 56_I | 59_P | 1.033 | 0.94 |
| 32_G | 35_K | 1.022 | 0.93 |
| 17_A | 54_L | 1.019 | 0.93 |
| 23_R | 29_P | 1.014 | 0.93 |
| 8_T | 12_A | 1.007 | 0.93 |
| 45_A | 48_P | 1.001 | 0.92 |
| 77_D | 80_C | 1.000 | 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 | |
| 4d40A | 2 | 0 | 99.8 | 0.198 | Contact Map |
| 2m3kA | 1 | 0.8981 | 99.8 | 0.203 | Contact Map |
| 4noaA | 1 | 1 | 99.7 | 0.227 | Contact Map |
| 2opeA | 4 | 0.9444 | 96.1 | 0.718 | Contact Map |
| 3g20A | 2 | 0.8611 | 94.1 | 0.752 | Contact Map |
| 1x6zA | 1 | 0.9444 | 94 | 0.752 | Contact Map |
| 3sokA | 2 | 0.9815 | 90.5 | 0.778 | Contact Map |
| 2hi2A | 1 | 0.9537 | 86.1 | 0.794 | Contact Map |
| 2m7gA | 1 | 0.3241 | 85.4 | 0.796 | Contact Map |
| 1oqwA | 2 | 0.9537 | 81.6 | 0.805 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)