| hGR Question Mark Shorter |
| ID: | 1478554379 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 63 (62) | ||
| Sequences: | 72 (54.6) | ||
| Seq/Len: | 1.161 | ||
| Nf(neff/√len): | 6.9 |
Jackhmmer Results: (2016_04)
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: 1.161).
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 |
| 4_Y | 15_Q | 1.642 | 0.88 |
| 29_V | 54_P | 1.517 | 0.82 |
| 3_H | 56_R | 1.476 | 0.79 |
| 11_L | 31_S | 1.368 | 0.71 |
| 13_Q | 54_P | 1.319 | 0.67 |
| 3_H | 33_N | 1.313 | 0.67 |
| 17_Q | 55_G | 1.306 | 0.66 |
| 14_Q | 22_N | 1.288 | 0.65 |
| 6_M | 12_S | 1.280 | 0.64 |
| 38_Q | 53_F | 1.274 | 0.63 |
| 43_D | 47_S | 1.269 | 0.63 |
| 33_N | 37_C | 1.243 | 0.61 |
| 9_A | 46_T | 1.242 | 0.60 |
| 21_F | 40_S | 1.215 | 0.58 |
| 56_R | 60_S | 1.196 | 0.56 |
| 5_D | 17_Q | 1.179 | 0.54 |
| 16_D | 55_G | 1.163 | 0.53 |
| 26_P | 29_V | 1.156 | 0.52 |
| 8_T | 46_T | 1.155 | 0.52 |
| 2_Y | 19_P | 1.152 | 0.52 |
| 30_G | 49_G | 1.146 | 0.51 |
| 31_S | 43_D | 1.144 | 0.51 |
| 7_N | 42_D | 1.142 | 0.51 |
| 3_H | 19_P | 1.136 | 0.50 |
| 25_P | 46_T | 1.129 | 0.50 |
| 16_D | 50_T | 1.127 | 0.49 |
| 11_L | 21_F | 1.125 | 0.49 |
| 5_D | 18_K | 1.102 | 0.47 |
| 17_Q | 50_T | 1.093 | 0.46 |
| 4_Y | 56_R | 1.082 | 0.45 |
| 5_D | 26_P | 1.079 | 0.45 |
| 37_C | 48_L | 1.067 | 0.44 |
| 8_T | 41_G | 1.062 | 0.43 |
| 21_F | 25_P | 1.059 | 0.43 |
| 48_L | 51_L | 1.056 | 0.43 |
| 33_N | 39_G | 1.051 | 0.42 |
| 42_D | 51_L | 1.045 | 0.42 |
| 4_Y | 25_P | 1.034 | 0.41 |
| 32_E | 57_T | 1.024 | 0.40 |
| 19_P | 33_N | 1.022 | 0.39 |
| 29_V | 50_T | 1.015 | 0.39 |
| 42_D | 52_N | 1.010 | 0.38 |
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 | |
| 2z37A | 4 | 0.3333 | 2 | 0.935 | Contact Map |
| 3w3eA | 2 | 0.3333 | 1.9 | 0.935 | Contact Map |
| 3cqlA | 2 | 0.3333 | 1.9 | 0.935 | Contact Map |
| 1tlqA | 1 | 0.1429 | 1.8 | 0.936 | Contact Map |
| 3abhA | 2 | 0.0476 | 1.6 | 0.938 | Contact Map |
| 4kbxA | 1 | 0.9206 | 1.5 | 0.939 | Contact Map |
| 2hevF | 1 | 0.6984 | 1.5 | 0.94 | Contact Map |
| 2vqaA | 3 | 0.4286 | 1.4 | 0.94 | Contact Map |
| 3bboL | 1 | 0 | 1.4 | 0.94 | Contact Map |
| 1zm8A | 1 | 0.4762 | 1.4 | 0.94 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)