| scEMC5 |
| ID: | 1504851149 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 141 (135) | ||
| Sequences: | 152 (108.1) | ||
| Seq/Len: | 1.126 | ||
| Nf(neff/√len): | 9.3 |
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: 1.126).
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 |
| 11_V | 15_V | 2.104 | 0.98 |
| 1_M | 5_S | 1.848 | 0.94 |
| 6_K | 68_F | 1.675 | 0.89 |
| 51_Y | 56_G | 1.672 | 0.88 |
| 21_F | 116_T | 1.662 | 0.88 |
| 76_I | 83_I | 1.612 | 0.86 |
| 19_S | 49_I | 1.609 | 0.86 |
| 106_G | 111_G | 1.553 | 0.83 |
| 47_K | 59_L | 1.527 | 0.81 |
| 12_S | 19_S | 1.527 | 0.81 |
| 43_S | 58_I | 1.525 | 0.81 |
| 57_L | 127_K | 1.450 | 0.77 |
| 24_Y | 57_L | 1.450 | 0.77 |
| 108_N | 114_I | 1.356 | 0.69 |
| 22_S | 25_E | 1.352 | 0.69 |
| 8_L | 47_K | 1.324 | 0.67 |
| 25_E | 121_D | 1.316 | 0.66 |
| 59_L | 98_A | 1.314 | 0.66 |
| 11_V | 14_L | 1.292 | 0.64 |
| 15_V | 55_A | 1.291 | 0.64 |
| 76_I | 84_I | 1.291 | 0.64 |
| 29_L | 53_T | 1.273 | 0.62 |
| 28_H | 31_K | 1.268 | 0.62 |
| 29_L | 66_T | 1.237 | 0.59 |
| 2_S | 14_L | 1.235 | 0.59 |
| 1_M | 109_P | 1.232 | 0.59 |
| 87_G | 125_K | 1.204 | 0.56 |
| 34_S | 110_N | 1.197 | 0.55 |
| 83_I | 86_Q | 1.190 | 0.55 |
| 2_S | 11_V | 1.181 | 0.54 |
| 36_N | 39_Q | 1.174 | 0.53 |
| 12_S | 16_L | 1.168 | 0.52 |
| 62_L | 118_S | 1.154 | 0.51 |
| 59_L | 115_F | 1.141 | 0.50 |
| 26_F | 32_L | 1.133 | 0.49 |
| 89_Y | 95_L | 1.129 | 0.49 |
| 127_K | 131_E | 1.129 | 0.49 |
| 6_K | 97_K | 1.110 | 0.47 |
| 83_I | 90_L | 1.103 | 0.46 |
| 74_L | 91_K | 1.102 | 0.46 |
| 7_L | 40_G | 1.098 | 0.46 |
| 71_L | 82_K | 1.098 | 0.46 |
| 116_T | 129_C | 1.097 | 0.46 |
| 77_E | 122_V | 1.091 | 0.45 |
| 13_A | 135_N | 1.086 | 0.45 |
| 83_I | 91_K | 1.085 | 0.45 |
| 17_F | 124_M | 1.083 | 0.44 |
| 126_R | 132_W | 1.082 | 0.44 |
| 93_I | 120_V | 1.081 | 0.44 |
| 4_V | 100_N | 1.081 | 0.44 |
| 43_S | 135_N | 1.080 | 0.44 |
| 70_K | 111_G | 1.074 | 0.44 |
| 8_L | 11_V | 1.070 | 0.43 |
| 38_A | 42_I | 1.069 | 0.43 |
| 30_L | 33_N | 1.057 | 0.42 |
| 60_F | 68_F | 1.057 | 0.42 |
| 128_I | 131_E | 1.057 | 0.42 |
| 67_S | 111_G | 1.055 | 0.42 |
| 22_S | 52_E | 1.053 | 0.42 |
| 73_Y | 76_I | 1.045 | 0.41 |
| 77_E | 80_D | 1.043 | 0.41 |
| 51_Y | 59_L | 1.042 | 0.41 |
| 8_L | 67_S | 1.042 | 0.41 |
| 44_K | 58_I | 1.041 | 0.40 |
| 91_K | 94_A | 1.039 | 0.40 |
| 38_A | 41_A | 1.037 | 0.40 |
| 71_L | 118_S | 1.036 | 0.40 |
| 108_N | 132_W | 1.029 | 0.39 |
| 131_E | 134_S | 1.027 | 0.39 |
| 86_Q | 89_Y | 1.027 | 0.39 |
| 51_Y | 55_A | 1.022 | 0.39 |
| 61_V | 102_D | 1.019 | 0.38 |
| 27_H | 125_K | 1.018 | 0.38 |
| 5_S | 66_T | 1.015 | 0.38 |
| 117_P | 120_V | 1.014 | 0.38 |
| 18_H | 25_E | 1.011 | 0.38 |
| 8_L | 32_L | 1.010 | 0.38 |
| 20_G | 122_V | 1.009 | 0.38 |
| 19_S | 26_F | 1.000 | 0.37 |
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 | |
| 4ezcA | 3 | 0.1489 | 10.5 | 0.951 | Contact Map |
| 4hvtA | 1 | 0.1986 | 8.4 | 0.953 | Contact Map |
| 1yr2A | 1 | 0.3262 | 7.3 | 0.954 | Contact Map |
| 1rijA | 1 | 0.1277 | 5.7 | 0.956 | Contact Map |
| 1ciiA | 1 | 0.4752 | 5.7 | 0.956 | Contact Map |
| 2xdwA | 1 | 0.3404 | 4.5 | 0.958 | Contact Map |
| 3g21A | 1 | 0.1844 | 3.9 | 0.96 | Contact Map |
| 2pk2A | 4 | 0.2837 | 3.2 | 0.961 | Contact Map |
| 3sjaC | 5 | 0.2624 | 3 | 0.962 | Contact Map |
| 3g9wC | 2 | 0.1844 | 2.8 | 0.962 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)