| test_c |
| ID: | 1484929519 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 193 (166) | ||
| Sequences: | 32348 (27122) | ||
| Seq/Len: | 194.867 | ||
| Nf(neff/√len): | 2105.1 |
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: 194.867).
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 |
| 61_Q | 65_E | 2.336 | 1.00 |
| 93_Q | 127_Q | 2.243 | 1.00 |
| 92_S | 124_T | 2.220 | 1.00 |
| 60_Q | 94_Q | 2.195 | 1.00 |
| 110_Q | 139_Q | 2.187 | 1.00 |
| 59_S | 91_T | 2.158 | 1.00 |
| 23_S | 26_T | 2.148 | 1.00 |
| 27_R | 58_T | 2.067 | 1.00 |
| 125_S | 157_T | 1.981 | 1.00 |
| 28_E | 61_Q | 1.967 | 1.00 |
| 22_L | 55_L | 1.966 | 1.00 |
| 94_Q | 98_A | 1.919 | 1.00 |
| 127_Q | 131_A | 1.919 | 1.00 |
| 150_F | 162_L | 1.788 | 1.00 |
| 77_Q | 106_Q | 1.777 | 1.00 |
| 72_A | 104_I | 1.773 | 1.00 |
| 110_Q | 118_Y | 1.752 | 1.00 |
| 147_L | 150_F | 1.749 | 1.00 |
| 56_Q | 90_E | 1.734 | 1.00 |
| 26_T | 29_F | 1.727 | 1.00 |
| 45_A | 73_Q | 1.725 | 1.00 |
| 105_A | 137_I | 1.710 | 1.00 |
| 89_Q | 123_E | 1.697 | 1.00 |
| 143_Q | 151_H | 1.661 | 1.00 |
| 126_Q | 160_Q | 1.646 | 1.00 |
| 122_R | 156_E | 1.623 | 1.00 |
| 89_Q | 127_Q | 1.565 | 1.00 |
| 24_L | 61_Q | 1.563 | 1.00 |
| 114_L | 145_Q | 1.548 | 1.00 |
| 87_E | 121_V | 1.546 | 1.00 |
| 29_F | 33_T | 1.541 | 1.00 |
| 45_A | 52_Y | 1.538 | 1.00 |
| 56_Q | 94_Q | 1.519 | 1.00 |
| 54_D | 88_L | 1.519 | 1.00 |
| 120_E | 154_L | 1.515 | 1.00 |
| 122_R | 160_Q | 1.470 | 1.00 |
| 77_Q | 85_H | 1.451 | 1.00 |
| 14_S | 26_T | 1.429 | 1.00 |
| 24_L | 57_E | 1.422 | 1.00 |
| 40_Q | 71_I | 1.415 | 1.00 |
| 48_L | 59_S | 1.374 | 0.99 |
| 113_E | 125_S | 1.360 | 0.99 |
| 49_Q | 82_L | 1.329 | 0.99 |
| 88_L | 91_T | 1.305 | 0.99 |
| 49_Q | 79_Q | 1.285 | 0.99 |
| 81_L | 112_Q | 1.280 | 0.99 |
| 114_L | 148_L | 1.269 | 0.99 |
| 89_Q | 124_T | 1.255 | 0.99 |
| 17_E | 21_E | 1.249 | 0.99 |
| 121_V | 124_T | 1.246 | 0.98 |
| 96_L | 127_Q | 1.237 | 0.98 |
| 129_L | 160_Q | 1.228 | 0.98 |
| 81_L | 115_L | 1.221 | 0.98 |
| 24_L | 28_E | 1.218 | 0.98 |
| 56_Q | 91_T | 1.212 | 0.98 |
| 139_Q | 148_L | 1.205 | 0.98 |
| 80_E | 92_S | 1.190 | 0.98 |
| 110_Q | 115_L | 1.183 | 0.98 |
| 63_L | 94_Q | 1.175 | 0.98 |
| 143_Q | 147_L | 1.174 | 0.98 |
| 122_R | 126_Q | 1.159 | 0.97 |
| 15_I | 27_R | 1.152 | 0.97 |
| 55_L | 58_T | 1.150 | 0.97 |
| 56_Q | 60_Q | 1.138 | 0.97 |
| 89_Q | 93_Q | 1.126 | 0.97 |
| 146_E | 162_L | 1.114 | 0.96 |
| 96_L | 131_A | 1.112 | 0.96 |
| 81_L | 114_L | 1.109 | 0.96 |
| 160_Q | 164_A | 1.107 | 0.96 |
| 61_Q | 64_S | 1.102 | 0.96 |
| 150_F | 158_S | 1.099 | 0.96 |
| 155_Q | 159_Q | 1.084 | 0.96 |
| 126_Q | 130_S | 1.066 | 0.95 |
| 143_Q | 148_L | 1.061 | 0.95 |
| 60_Q | 64_S | 1.061 | 0.95 |
| 110_Q | 114_L | 1.046 | 0.94 |
| 122_R | 157_T | 1.043 | 0.94 |
| 45_A | 49_Q | 1.040 | 0.94 |
| 19_V | 27_R | 1.039 | 0.94 |
| 31_S | 61_Q | 1.029 | 0.94 |
| 146_E | 158_S | 1.024 | 0.93 |
| 134_Q | 137_I | 1.023 | 0.93 |
| 24_L | 58_T | 1.019 | 0.93 |
| 144_A | 147_L | 1.017 | 0.93 |
| 116_A | 125_S | 1.017 | 0.93 |
| 77_Q | 82_L | 1.003 | 0.93 |
| 93_Q | 97_S | 1.002 | 0.92 |
| 32_V | 65_E | 1.000 | 0.92 |
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 | |
| 4rlvA | 1 | 0.8497 | 100 | 0.212 | Contact Map |
| 1ihbA | 2 | 0.8135 | 100 | 0.227 | Contact Map |
| 4rlyA | 1 | 0.9948 | 100 | 0.232 | Contact Map |
| 4oavB | 2 | 0.9534 | 100 | 0.234 | Contact Map |
| 2etbA | 1 | 0.8964 | 100 | 0.241 | Contact Map |
| 2rfmA | 2 | 0.8653 | 100 | 0.245 | Contact Map |
| 4qfvA | 4 | 0 | 100 | 0.247 | Contact Map |
| 1iknD | 1 | 0.9326 | 100 | 0.249 | Contact Map |
| 1n11A | 1 | 0.9275 | 100 | 0.25 | Contact Map |
| 1yyhA | 2 | 0.9689 | 100 | 0.252 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)