| 1gm4 |
| ID: | 1453971264 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 107 (96) | ||
| Sequences: | 114 (102) | ||
| Seq/Len: | 1.188 | ||
| Nf(neff/√len): | 10.4 |
HHblits Results: (2015_06)
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: 1.188).
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 |
| 72_G | 76_H | 2.050 | 0.97 |
| 72_G | 77_T | 1.694 | 0.90 |
| 51_C | 69_H | 1.612 | 0.87 |
| 52_H | 69_H | 1.612 | 0.87 |
| 14_S | 27_K | 1.571 | 0.85 |
| 28_V | 96_D | 1.519 | 0.82 |
| 67_V | 76_H | 1.438 | 0.77 |
| 21_P | 24_P | 1.427 | 0.76 |
| 23_A | 26_E | 1.389 | 0.74 |
| 28_V | 47_G | 1.383 | 0.73 |
| 101_A | 107_P | 1.375 | 0.72 |
| 71_R | 77_T | 1.362 | 0.71 |
| 41_E | 49_S | 1.349 | 0.70 |
| 16_K | 45_K | 1.347 | 0.70 |
| 17_T | 50_G | 1.333 | 0.69 |
| 19_M | 88_A | 1.315 | 0.68 |
| 54_D | 81_A | 1.257 | 0.62 |
| 63_S | 85_K | 1.235 | 0.60 |
| 72_G | 75_K | 1.233 | 0.60 |
| 31_V | 39_G | 1.232 | 0.60 |
| 21_P | 26_E | 1.201 | 0.57 |
| 71_R | 76_H | 1.197 | 0.57 |
| 39_G | 42_S | 1.181 | 0.55 |
| 71_R | 75_K | 1.165 | 0.54 |
| 67_V | 81_A | 1.160 | 0.53 |
| 62_K | 101_A | 1.152 | 0.53 |
| 64_L | 101_A | 1.125 | 0.50 |
| 58_K | 104_K | 1.107 | 0.48 |
| 15_Q | 36_L | 1.095 | 0.47 |
| 68_V | 75_K | 1.088 | 0.46 |
| 69_H | 100_C | 1.074 | 0.45 |
| 31_V | 92_E | 1.065 | 0.44 |
| 59_K | 107_P | 1.064 | 0.44 |
| 57_A | 60_G | 1.063 | 0.44 |
| 28_V | 41_E | 1.062 | 0.44 |
| 17_T | 67_V | 1.054 | 0.43 |
| 19_M | 78_S | 1.049 | 0.43 |
| 28_V | 84_S | 1.047 | 0.42 |
| 32_T | 88_A | 1.041 | 0.42 |
| 87_V | 97_L | 1.039 | 0.42 |
| 27_K | 92_E | 1.039 | 0.42 |
| 27_K | 101_A | 1.029 | 0.41 |
| 65_Y | 78_S | 1.020 | 0.40 |
| 16_K | 29_E | 1.016 | 0.39 |
| 21_P | 99_G | 1.016 | 0.39 |
| 17_T | 89_E | 1.006 | 0.39 |
| 17_T | 88_A | 1.006 | 0.39 |
| 67_V | 94_K | 1.005 | 0.38 |
| 75_K | 90_K | 1.004 | 0.38 |
| 38_D | 58_K | 1.003 | 0.38 |
| 36_L | 99_G | 1.001 | 0.38 |
| 53_D | 84_S | 1.000 | 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 | |
| 1up9A | 1 | 0.9813 | 99.9 | 0.31 | Contact Map |
| 1j0pA | 1 | 0.972 | 99.8 | 0.386 | Contact Map |
| 1wadA | 1 | 0.972 | 99.8 | 0.395 | Contact Map |
| 1czjA | 1 | 0.9252 | 99.7 | 0.425 | Contact Map |
| 2a3mA | 1 | 0.9626 | 99.7 | 0.434 | Contact Map |
| 2cy3A | 1 | 0.8785 | 99.7 | 0.453 | Contact Map |
| 2bq4A | 2 | 0.9065 | 99.7 | 0.458 | Contact Map |
| 1gyoA | 2 | 0.9065 | 99.6 | 0.494 | Contact Map |
| 2e84A | 1 | 0.8037 | 99.5 | 0.522 | Contact Map |
| 2cvcA | 1 | 0.8224 | 99.5 | 0.526 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)