| AraC minus 30-200 |
| ID: | 1497389476 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 179 (146) | ||
| Sequences: | 5764 (4128.5) | ||
| Seq/Len: | 39.479 | ||
| Nf(neff/√len): | 341.7 |
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: 39.479).
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 |
| 152_F | 163_F | 3.644 | 1.00 |
| 108_I | 116_D | 3.246 | 1.00 |
| 119_I | 156_T | 3.093 | 1.00 |
| 123_K | 156_T | 3.038 | 1.00 |
| 116_D | 155_C | 2.718 | 1.00 |
| 74_S | 117_Q | 2.572 | 1.00 |
| 121_Q | 124_L | 2.434 | 1.00 |
| 85_A | 95_P | 2.368 | 1.00 |
| 73_I | 114_R | 2.318 | 1.00 |
| 122_A | 148_F | 2.245 | 1.00 |
| 131_M | 139_N | 2.229 | 1.00 |
| 93_L | 98_L | 2.198 | 1.00 |
| 76_H | 80_S | 2.194 | 1.00 |
| 131_M | 135_T | 2.010 | 1.00 |
| 102_F | 113_W | 1.962 | 1.00 |
| 119_I | 155_C | 1.895 | 1.00 |
| 72_Y | 90_H | 1.860 | 1.00 |
| 72_Y | 76_H | 1.850 | 1.00 |
| 97_R | 101_L | 1.794 | 1.00 |
| 123_K | 163_F | 1.751 | 1.00 |
| 134_A | 145_Q | 1.739 | 1.00 |
| 125_L | 139_N | 1.735 | 1.00 |
| 129_T | 164_R | 1.715 | 1.00 |
| 149_S | 159_S | 1.678 | 1.00 |
| 126_L | 133_I | 1.619 | 1.00 |
| 69_A | 87_V | 1.596 | 1.00 |
| 96_S | 100_H | 1.589 | 1.00 |
| 129_T | 136_V | 1.564 | 1.00 |
| 93_L | 97_R | 1.563 | 1.00 |
| 69_A | 91_V | 1.559 | 1.00 |
| 125_L | 131_M | 1.509 | 1.00 |
| 83_D | 86_S | 1.502 | 1.00 |
| 161_S | 165_A | 1.495 | 1.00 |
| 124_L | 128_T | 1.482 | 1.00 |
| 76_H | 79_D | 1.383 | 0.99 |
| 132_P | 135_T | 1.381 | 0.99 |
| 72_Y | 91_V | 1.376 | 0.99 |
| 69_A | 98_L | 1.373 | 0.99 |
| 135_T | 139_N | 1.371 | 0.99 |
| 147_Y | 151_V | 1.333 | 0.99 |
| 41_N | 44_E | 1.314 | 0.99 |
| 109_S | 112_S | 1.311 | 0.99 |
| 108_I | 112_S | 1.306 | 0.99 |
| 80_S | 86_S | 1.305 | 0.99 |
| 158_A | 166_G | 1.295 | 0.99 |
| 158_A | 162_E | 1.288 | 0.99 |
| 71_Q | 75_D | 1.274 | 0.99 |
| 42_L | 45_Q | 1.258 | 0.99 |
| 120_S | 123_K | 1.249 | 0.99 |
| 121_Q | 125_L | 1.244 | 0.98 |
| 131_M | 136_V | 1.235 | 0.98 |
| 135_T | 138_R | 1.216 | 0.98 |
| 73_I | 117_Q | 1.201 | 0.98 |
| 136_V | 140_V | 1.188 | 0.98 |
| 98_L | 110_V | 1.182 | 0.98 |
| 95_P | 99_S | 1.181 | 0.98 |
| 145_Q | 149_S | 1.179 | 0.98 |
| 123_K | 152_F | 1.178 | 0.98 |
| 70_C | 106_L | 1.168 | 0.97 |
| 72_Y | 82_F | 1.143 | 0.97 |
| 97_R | 100_H | 1.129 | 0.97 |
| 125_L | 140_V | 1.118 | 0.96 |
| 127_S | 167_C | 1.094 | 0.96 |
| 82_F | 87_V | 1.083 | 0.96 |
| 70_C | 113_W | 1.079 | 0.95 |
| 116_D | 120_S | 1.077 | 0.95 |
| 85_A | 89_Q | 1.063 | 0.95 |
| 162_E | 166_G | 1.062 | 0.95 |
| 115_E | 151_V | 1.051 | 0.94 |
| 94_S | 97_R | 1.048 | 0.94 |
| 126_L | 163_F | 1.041 | 0.94 |
| 142_F | 147_Y | 1.038 | 0.94 |
| 73_I | 87_V | 1.024 | 0.93 |
| 117_Q | 120_S | 1.021 | 0.93 |
| 117_Q | 121_Q | 1.020 | 0.93 |
| 66_V | 106_L | 1.013 | 0.93 |
| 151_V | 154_K | 1.006 | 0.93 |
| 149_S | 161_S | 1.006 | 0.93 |
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 | |
| 3gbgA | 1 | 0.8939 | 100 | 0.353 | Contact Map |
| 3oioA | 1 | 0.6257 | 100 | 0.406 | Contact Map |
| 1bl0A | 1 | 0.648 | 100 | 0.409 | Contact Map |
| 3oouA | 1 | 0.5866 | 99.9 | 0.409 | Contact Map |
| 3mn2A | 2 | 0.5922 | 99.9 | 0.413 | Contact Map |
| 2k9sA | 1 | 0.5922 | 99.9 | 0.417 | Contact Map |
| 3mklA | 2 | 0.6201 | 99.9 | 0.424 | Contact Map |
| 3w6vA | 1 | 0.6201 | 99.9 | 0.425 | Contact Map |
| 3lsgA | 5 | 0.5754 | 99.9 | 0.426 | Contact Map |
| 4fe7A | 1 | 0.9274 | 99.9 | 0.428 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)