| hGR Question Mark Increase Iter |
| ID: | 1478544314 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 78 (76) | ||
| Sequences: | 79 (47.1) | ||
| Seq/Len: | 1.039 | ||
| Nf(neff/√len): | 5.4 |
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: 1.039).
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 |
| 19_Y | 40_P | 1.872 | 0.93 |
| 5_S | 10_S | 1.722 | 0.89 |
| 70_G | 73_V | 1.441 | 0.74 |
| 20_D | 47_E | 1.429 | 0.73 |
| 71_R | 75_S | 1.427 | 0.73 |
| 8_G | 12_S | 1.412 | 0.72 |
| 6_V | 30_Q | 1.407 | 0.71 |
| 34_P | 37_N | 1.371 | 0.68 |
| 8_G | 11_T | 1.363 | 0.68 |
| 72_T | 77_G | 1.315 | 0.64 |
| 54_G | 69_P | 1.309 | 0.63 |
| 14_G | 18_H | 1.284 | 0.61 |
| 23_T | 61_T | 1.236 | 0.56 |
| 63_L | 66_L | 1.215 | 0.55 |
| 71_R | 77_G | 1.206 | 0.54 |
| 12_S | 15_Q | 1.194 | 0.53 |
| 2_S | 18_H | 1.189 | 0.52 |
| 8_G | 15_Q | 1.188 | 0.52 |
| 45_G | 58_D | 1.185 | 0.52 |
| 32_Q | 56_G | 1.176 | 0.51 |
| 53_Q | 68_F | 1.165 | 0.50 |
| 39_I | 46_S | 1.140 | 0.48 |
| 36_F | 42_I | 1.133 | 0.47 |
| 9_V | 12_S | 1.126 | 0.46 |
| 70_G | 75_S | 1.109 | 0.45 |
| 71_R | 74_F | 1.109 | 0.45 |
| 5_S | 17_Y | 1.099 | 0.44 |
| 70_G | 77_G | 1.091 | 0.43 |
| 14_G | 49_W | 1.071 | 0.41 |
| 70_G | 74_F | 1.067 | 0.41 |
| 40_P | 43_P | 1.066 | 0.41 |
| 57_D | 62_S | 1.065 | 0.41 |
| 3_A | 39_I | 1.061 | 0.40 |
| 11_T | 15_Q | 1.058 | 0.40 |
| 18_H | 64_G | 1.057 | 0.40 |
| 17_Y | 30_Q | 1.056 | 0.40 |
| 34_P | 56_G | 1.051 | 0.39 |
| 4_I | 11_T | 1.039 | 0.38 |
| 34_P | 54_G | 1.034 | 0.38 |
| 2_S | 64_G | 1.029 | 0.37 |
| 42_I | 45_G | 1.023 | 0.37 |
| 22_N | 57_D | 1.010 | 0.36 |
| 7_H | 19_Y | 1.009 | 0.36 |
| 19_Y | 31_D | 1.004 | 0.35 |
| 37_N | 59_N | 1.001 | 0.35 |
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 | |
| 3phzA | 2 | 0.5 | 8.1 | 0.923 | Contact Map |
| 3oa3A | 2 | 0.3718 | 3.5 | 0.936 | Contact Map |
| 1nscA | 2 | 0.3333 | 1.9 | 0.944 | Contact Map |
| 2qdrA | 2 | 0.3974 | 1.8 | 0.945 | Contact Map |
| 4cpyA | 2 | 0.3333 | 1.6 | 0.946 | Contact Map |
| 3fldA | 2 | 0.6282 | 1.5 | 0.948 | Contact Map |
| 2kuyA | 1 | 0.2308 | 1.3 | 0.95 | Contact Map |
| 4wa3A | 1 | 0.359 | 1.2 | 0.951 | Contact Map |
| 4atdA | 2 | 0.1795 | 1.2 | 0.951 | Contact Map |
| 2hsiA | 2 | 0.4744 | 1.2 | 0.951 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)