| hGR Question Mark Shorter |
| ID: | 1478530333 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 69 (67) | ||
| Sequences: | 68 (51.1) | ||
| Seq/Len: | 1.015 | ||
| Nf(neff/√len): | 6.2 |
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: 1.015).
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 |
| 6_V | 30_Q | 2.284 | 0.98 |
| 5_S | 10_S | 1.961 | 0.95 |
| 22_N | 57_D | 1.514 | 0.78 |
| 58_D | 62_S | 1.510 | 0.78 |
| 32_Q | 65_T | 1.487 | 0.76 |
| 19_Y | 30_Q | 1.430 | 0.72 |
| 8_G | 11_T | 1.289 | 0.61 |
| 53_Q | 68_F | 1.279 | 0.60 |
| 16_M | 20_D | 1.263 | 0.58 |
| 19_Y | 40_P | 1.247 | 0.57 |
| 36_F | 42_I | 1.242 | 0.56 |
| 3_A | 6_V | 1.242 | 0.56 |
| 20_D | 32_Q | 1.225 | 0.55 |
| 48_N | 54_G | 1.205 | 0.53 |
| 15_Q | 54_G | 1.187 | 0.51 |
| 6_V | 16_M | 1.182 | 0.51 |
| 41_P | 44_V | 1.148 | 0.48 |
| 20_D | 65_T | 1.148 | 0.48 |
| 20_D | 47_E | 1.147 | 0.47 |
| 21_M | 27_S | 1.125 | 0.45 |
| 8_G | 15_Q | 1.120 | 0.45 |
| 23_T | 61_T | 1.103 | 0.43 |
| 20_D | 46_S | 1.101 | 0.43 |
| 7_H | 16_M | 1.077 | 0.41 |
| 10_S | 35_I | 1.075 | 0.41 |
| 36_F | 55_S | 1.071 | 0.41 |
| 13_G | 26_L | 1.068 | 0.40 |
| 20_D | 33_K | 1.065 | 0.40 |
| 41_P | 54_G | 1.064 | 0.40 |
| 29_Q | 37_N | 1.059 | 0.39 |
| 36_F | 40_P | 1.059 | 0.39 |
| 38_V | 62_S | 1.045 | 0.38 |
| 45_G | 58_D | 1.038 | 0.38 |
| 36_F | 47_E | 1.028 | 0.37 |
| 23_T | 43_P | 1.023 | 0.36 |
| 46_S | 58_D | 1.023 | 0.36 |
| 17_Y | 30_Q | 1.014 | 0.36 |
| 42_I | 47_E | 1.004 | 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 | 0.5652 | 12 | 0.921 | Contact Map |
| 1nmbN | 1 | 0.3913 | 1.9 | 0.946 | Contact Map |
| 2b99A | 5 | 0.8841 | 1.8 | 0.947 | Contact Map |
| 3tiaA | 4 | 0.4058 | 1.7 | 0.947 | Contact Map |
| 1qqp3 | 1 | 0.3913 | 1.6 | 0.948 | Contact Map |
| 4rwfB | 1 | 0 | 1.5 | 0.949 | Contact Map |
| 3oskA | 2 | 0.5217 | 1.4 | 0.95 | Contact Map |
| 3cqlA | 2 | 0.3478 | 1.4 | 0.951 | Contact Map |
| 4wa3A | 1 | 0.4058 | 1.3 | 0.951 | Contact Map |
| 4dw1A | 1 | 0.2464 | 1.2 | 0.952 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)