| SRFlum |
| ID: | 1424830406 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 146 (126) | ||
| Sequences: | 189 (129) | ||
| Seq/Len: | 1.500 | ||
| Nf(neff/√len): | 11.5 |
Jackhmmer Results: (2015_01_07)
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: 1.500).
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 |
| 52_I | 78_F | 2.508 | 1.00 |
| 8_M | 96_V | 2.479 | 1.00 |
| 52_I | 103_L | 2.304 | 0.99 |
| 78_F | 103_L | 1.950 | 0.98 |
| 60_D | 65_Q | 1.890 | 0.97 |
| 26_S | 31_P | 1.888 | 0.97 |
| 36_K | 104_E | 1.760 | 0.95 |
| 47_Y | 72_L | 1.728 | 0.94 |
| 11_R | 15_A | 1.624 | 0.91 |
| 35_L | 52_I | 1.622 | 0.91 |
| 56_N | 64_V | 1.593 | 0.90 |
| 33_P | 36_K | 1.519 | 0.87 |
| 20_Y | 48_T | 1.501 | 0.86 |
| 32_I | 102_G | 1.501 | 0.86 |
| 52_I | 81_T | 1.477 | 0.85 |
| 19_H | 49_P | 1.436 | 0.83 |
| 10_L | 56_N | 1.417 | 0.82 |
| 42_A | 108_D | 1.405 | 0.81 |
| 81_T | 103_L | 1.397 | 0.80 |
| 110_T | 113_G | 1.390 | 0.80 |
| 47_Y | 70_T | 1.384 | 0.79 |
| 29_L | 75_A | 1.341 | 0.76 |
| 90_S | 94_Q | 1.341 | 0.76 |
| 14_K | 64_V | 1.314 | 0.74 |
| 11_R | 59_W | 1.290 | 0.72 |
| 73_D | 76_Y | 1.268 | 0.70 |
| 35_L | 103_L | 1.267 | 0.70 |
| 26_S | 29_L | 1.266 | 0.70 |
| 11_R | 78_F | 1.256 | 0.69 |
| 33_P | 104_E | 1.241 | 0.68 |
| 72_L | 76_Y | 1.235 | 0.68 |
| 15_A | 96_V | 1.221 | 0.66 |
| 22_R | 60_D | 1.219 | 0.66 |
| 7_R | 89_E | 1.218 | 0.66 |
| 19_H | 106_N | 1.208 | 0.65 |
| 109_Y | 113_G | 1.196 | 0.64 |
| 24_T | 28_R | 1.189 | 0.63 |
| 41_T | 96_V | 1.177 | 0.62 |
| 74_I | 112_L | 1.168 | 0.61 |
| 57_K | 67_E | 1.162 | 0.61 |
| 49_P | 90_S | 1.160 | 0.60 |
| 18_L | 110_T | 1.151 | 0.60 |
| 16_L | 111_E | 1.146 | 0.59 |
| 39_G | 43_G | 1.145 | 0.59 |
| 19_H | 51_V | 1.135 | 0.58 |
| 120_S | 123_Q | 1.132 | 0.58 |
| 22_R | 104_E | 1.131 | 0.58 |
| 87_G | 93_D | 1.131 | 0.58 |
| 9_L | 109_Y | 1.126 | 0.57 |
| 106_N | 114_L | 1.112 | 0.56 |
| 8_M | 45_D | 1.101 | 0.54 |
| 41_T | 67_E | 1.096 | 0.54 |
| 44_C | 48_T | 1.083 | 0.53 |
| 18_L | 27_R | 1.071 | 0.51 |
| 23_Y | 31_P | 1.061 | 0.50 |
| 6_D | 23_Y | 1.059 | 0.50 |
| 23_Y | 65_Q | 1.049 | 0.49 |
| 78_F | 81_T | 1.041 | 0.48 |
| 6_D | 29_L | 1.030 | 0.47 |
| 7_R | 40_G | 1.029 | 0.47 |
| 49_P | 61_G | 1.025 | 0.47 |
| 20_Y | 50_K | 1.025 | 0.47 |
| 27_R | 93_D | 1.025 | 0.47 |
| 39_G | 76_Y | 1.012 | 0.45 |
| 113_G | 118_K | 1.010 | 0.45 |
| 42_A | 95_Y | 1.001 | 0.44 |
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
- See coupling matrix (for protein design or mutagenesis)
- 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 | |
| 3bl9A | 2 | 0.3288 | 2.4 | 0.969 | Contact Map |
| 1kqhA | 1 | 0.1644 | 2.4 | 0.969 | Contact Map |
| 1oqwA | 2 | 0.5548 | 2.2 | 0.97 | Contact Map |
| 1fizL | 1 | 0.089 | 2.2 | 0.97 | Contact Map |
| 1iooA | 2 | 0.4726 | 2.1 | 0.97 | Contact Map |
| 1fiwL | 1 | 0.0959 | 2 | 0.971 | Contact Map |
| 1ewsA | 1 | 0.2192 | 1.9 | 0.971 | Contact Map |
| 2ekoA | 1 | 0.1986 | 1.7 | 0.972 | Contact Map |
| 3nkgA | 2 | 0.3151 | 1.6 | 0.972 | Contact Map |
| 1s29A | 1 | 0.2192 | 1.5 | 0.973 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)