| mic60 |
| ID: | 1445514859 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 180 (169) | ||
| Sequences: | 550 (399.2) | ||
| Seq/Len: | 3.254 | ||
| Nf(neff/√len): | 30.7 |
Jackhmmer Results: (2015_08)
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: 3.254).
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 |
| 134_N | 137_D | 3.615 | 1.00 |
| 126_V | 142_V | 3.267 | 1.00 |
| 125_R | 141_E | 2.756 | 1.00 |
| 21_C | 25_N | 2.053 | 1.00 |
| 92_G | 95_G | 1.945 | 1.00 |
| 78_A | 127_G | 1.854 | 0.99 |
| 30_K | 34_I | 1.839 | 0.99 |
| 163_K | 167_Q | 1.810 | 0.99 |
| 156_W | 160_A | 1.800 | 0.99 |
| 116_A | 141_E | 1.666 | 0.98 |
| 15_D | 19_C | 1.656 | 0.98 |
| 81_F | 153_C | 1.655 | 0.98 |
| 88_P | 92_G | 1.633 | 0.98 |
| 121_S | 125_R | 1.606 | 0.98 |
| 143_V | 161_R | 1.550 | 0.97 |
| 13_C | 16_G | 1.488 | 0.96 |
| 31_E | 34_I | 1.471 | 0.96 |
| 16_G | 19_C | 1.447 | 0.95 |
| 67_N | 71_Y | 1.416 | 0.94 |
| 81_F | 123_Y | 1.374 | 0.93 |
| 70_I | 160_A | 1.372 | 0.93 |
| 139_V | 157_I | 1.361 | 0.93 |
| 86_L | 118_D | 1.334 | 0.92 |
| 116_A | 121_S | 1.321 | 0.91 |
| 36_C | 91_S | 1.304 | 0.91 |
| 16_G | 20_S | 1.294 | 0.90 |
| 106_L | 109_K | 1.292 | 0.90 |
| 113_P | 124_A | 1.292 | 0.90 |
| 73_R | 159_D | 1.283 | 0.90 |
| 78_A | 108_T | 1.280 | 0.89 |
| 21_C | 24_G | 1.279 | 0.89 |
| 17_D | 24_G | 1.274 | 0.89 |
| 149_P | 153_C | 1.242 | 0.87 |
| 12_C | 15_D | 1.237 | 0.87 |
| 34_I | 37_K | 1.234 | 0.87 |
| 39_K | 53_D | 1.213 | 0.86 |
| 112_N | 128_D | 1.211 | 0.86 |
| 118_D | 142_V | 1.211 | 0.86 |
| 34_I | 41_K | 1.203 | 0.85 |
| 147_G | 153_C | 1.196 | 0.85 |
| 41_K | 48_L | 1.188 | 0.84 |
| 47_L | 176_E | 1.187 | 0.84 |
| 124_A | 141_E | 1.186 | 0.84 |
| 121_S | 141_E | 1.180 | 0.84 |
| 13_C | 17_D | 1.144 | 0.81 |
| 122_V | 125_R | 1.144 | 0.81 |
| 99_A | 140_E | 1.143 | 0.81 |
| 175_C | 179_T | 1.130 | 0.80 |
| 92_G | 96_Q | 1.130 | 0.80 |
| 17_D | 26_K | 1.128 | 0.80 |
| 18_C | 22_K | 1.125 | 0.79 |
| 122_V | 145_L | 1.125 | 0.79 |
| 81_F | 126_V | 1.124 | 0.79 |
| 14_D | 17_D | 1.119 | 0.79 |
| 57_S | 84_A | 1.106 | 0.78 |
| 19_C | 23_K | 1.104 | 0.78 |
| 145_L | 164_L | 1.094 | 0.77 |
| 116_A | 125_R | 1.093 | 0.77 |
| 48_L | 52_L | 1.089 | 0.76 |
| 45_P | 176_E | 1.075 | 0.75 |
| 44_P | 49_S | 1.069 | 0.74 |
| 63_K | 74_W | 1.068 | 0.74 |
| 118_D | 164_L | 1.066 | 0.74 |
| 170_V | 174_D | 1.060 | 0.73 |
| 23_K | 26_K | 1.055 | 0.73 |
| 11_S | 18_C | 1.051 | 0.73 |
| 126_V | 156_W | 1.051 | 0.73 |
| 139_V | 160_A | 1.050 | 0.72 |
| 11_S | 15_D | 1.043 | 0.72 |
| 24_G | 27_N | 1.039 | 0.71 |
| 136_N | 155_S | 1.035 | 0.71 |
| 31_E | 35_S | 1.028 | 0.70 |
| 88_P | 102_F | 1.026 | 0.70 |
| 89_P | 99_A | 1.022 | 0.70 |
| 85_S | 89_P | 1.021 | 0.69 |
| 43_N | 115_N | 1.020 | 0.69 |
| 21_C | 28_E | 1.019 | 0.69 |
| 28_E | 31_E | 1.018 | 0.69 |
| 155_S | 165_E | 1.016 | 0.69 |
| 73_R | 164_L | 1.015 | 0.69 |
| 17_D | 20_S | 1.011 | 0.68 |
| 82_K | 120_D | 1.011 | 0.68 |
| 11_S | 14_D | 1.007 | 0.68 |
| 31_E | 170_V | 1.006 | 0.68 |
| 13_C | 18_C | 1.004 | 0.68 |
| 81_F | 119_F | 1.003 | 0.67 |
| 15_D | 18_C | 1.000 | 0.67 |
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 | |
| 4ynvA | 2 | 0 | 41.3 | 0.918 | Contact Map |
| 4bujB | 2 | 0.3722 | 40.1 | 0.919 | Contact Map |
| 2pziA | 2 | 0.9167 | 27.9 | 0.925 | Contact Map |
| 3urzA | 2 | 0.3556 | 27.6 | 0.925 | Contact Map |
| 4r7sA | 1 | 0.3611 | 23.4 | 0.928 | Contact Map |
| 2lniA | 1 | 0.4278 | 22.7 | 0.928 | Contact Map |
| 4ui9J | 1 | 0 | 21.9 | 0.929 | Contact Map |
| 3cv0A | 1 | 0.4556 | 21.7 | 0.929 | Contact Map |
| 4ja7A | 1 | 0.3722 | 20.8 | 0.929 | Contact Map |
| 2c2lA | 4 | 0.5111 | 20.1 | 0.93 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)