| AraC Arm FullAlign |
| ID: | 1496875293 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 50% gaps before running GREMLIN. |
| Length: | 195 (157) | ||
| Sequences: | 13745 (10028.9) | ||
| Seq/Len: | 87.548 | ||
| Nf(neff/√len): | 800.4 |
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: 87.548).
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 |
| 174_P | 177_Q | 3.681 | 1.00 |
| 147_L | 150_T | 3.469 | 1.00 |
| 183_L | 189_P | 3.445 | 1.00 |
| 145_G | 170_I | 3.320 | 1.00 |
| 178_P | 189_P | 2.917 | 1.00 |
| 56_V | 63_Q | 2.730 | 1.00 |
| 178_P | 183_L | 2.719 | 1.00 |
| 45_Y | 76_P | 2.651 | 1.00 |
| 153_D | 156_A | 2.501 | 1.00 |
| 164_D | 168_Q | 2.498 | 1.00 |
| 183_L | 187_Q | 2.482 | 1.00 |
| 179_G | 185_V | 2.380 | 1.00 |
| 174_P | 178_P | 2.344 | 1.00 |
| 52_R | 92_Y | 2.336 | 1.00 |
| 184_P | 187_Q | 2.158 | 1.00 |
| 56_V | 65_V | 2.135 | 1.00 |
| 56_V | 83_G | 2.123 | 1.00 |
| 54_E | 65_V | 2.117 | 1.00 |
| 67_R | 70_D | 2.082 | 1.00 |
| 58_N | 81_H | 2.016 | 1.00 |
| 148_F | 170_I | 2.004 | 1.00 |
| 51_I | 94_Q | 1.999 | 1.00 |
| 58_N | 63_Q | 1.983 | 1.00 |
| 148_F | 174_P | 1.863 | 1.00 |
| 60_H | 78_E | 1.829 | 1.00 |
| 46_I | 80_H | 1.737 | 1.00 |
| 143_G | 147_L | 1.720 | 1.00 |
| 54_E | 67_R | 1.689 | 1.00 |
| 175_A | 190_S | 1.688 | 1.00 |
| 152_G | 157_G | 1.652 | 1.00 |
| 157_G | 163_A | 1.638 | 1.00 |
| 156_A | 159_A | 1.637 | 1.00 |
| 52_R | 68_P | 1.634 | 1.00 |
| 170_I | 174_P | 1.623 | 1.00 |
| 177_Q | 180_A | 1.615 | 1.00 |
| 156_A | 160_A | 1.613 | 1.00 |
| 55_G | 91_W | 1.584 | 1.00 |
| 42_M | 80_H | 1.560 | 1.00 |
| 178_P | 190_S | 1.509 | 1.00 |
| 154_K | 163_A | 1.498 | 1.00 |
| 39_P | 79_I | 1.481 | 1.00 |
| 145_G | 166_G | 1.480 | 1.00 |
| 75_P | 78_E | 1.464 | 1.00 |
| 149_R | 189_P | 1.442 | 1.00 |
| 51_I | 92_Y | 1.382 | 0.99 |
| 155_P | 159_A | 1.372 | 0.99 |
| 143_G | 160_A | 1.371 | 0.99 |
| 45_Y | 73_L | 1.330 | 0.99 |
| 144_G | 167_D | 1.314 | 0.99 |
| 74_F | 80_H | 1.306 | 0.99 |
| 40_L | 80_H | 1.305 | 0.99 |
| 174_P | 190_S | 1.288 | 0.99 |
| 125_Q | 132_E | 1.247 | 0.99 |
| 152_G | 156_A | 1.245 | 0.98 |
| 151_V | 156_A | 1.244 | 0.98 |
| 58_N | 83_G | 1.241 | 0.98 |
| 163_A | 167_D | 1.235 | 0.98 |
| 171_A | 190_S | 1.221 | 0.98 |
| 39_P | 81_H | 1.216 | 0.98 |
| 170_I | 173_S | 1.214 | 0.98 |
| 50_T | 93_H | 1.209 | 0.98 |
| 54_E | 85_H | 1.201 | 0.98 |
| 42_M | 46_I | 1.192 | 0.98 |
| 41_G | 79_I | 1.163 | 0.97 |
| 169_R | 173_S | 1.155 | 0.97 |
| 50_T | 91_W | 1.138 | 0.97 |
| 142_Q | 146_A | 1.128 | 0.97 |
| 144_G | 170_I | 1.127 | 0.97 |
| 152_G | 171_A | 1.120 | 0.96 |
| 52_R | 90_E | 1.110 | 0.96 |
| 151_V | 171_A | 1.101 | 0.96 |
| 129_R | 132_E | 1.083 | 0.96 |
| 165_G | 169_R | 1.080 | 0.95 |
| 147_L | 156_A | 1.080 | 0.95 |
| 150_T | 156_A | 1.079 | 0.95 |
| 44_G | 97_Y | 1.056 | 0.95 |
| 55_G | 66_C | 1.056 | 0.95 |
| 143_G | 161_A | 1.055 | 0.95 |
| 173_S | 176_G | 1.054 | 0.95 |
| 157_G | 160_A | 1.045 | 0.94 |
| 148_F | 167_D | 1.034 | 0.94 |
| 172_A | 176_G | 1.021 | 0.93 |
| 50_T | 53_G | 1.010 | 0.93 |
| 143_G | 157_G | 1.002 | 0.92 |
| 165_G | 168_Q | 1.001 | 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 | |
| 3gbgA | 1 | 0.8974 | 99.6 | 0.562 | Contact Map |
| 2arcA | 2 | 0.8359 | 99.3 | 0.653 | Contact Map |
| 4mv2A | 2 | 0.5487 | 98.6 | 0.729 | Contact Map |
| 4rd7A | 1 | 0.5333 | 98.5 | 0.738 | Contact Map |
| 3cewA | 4 | 0.5538 | 98.1 | 0.767 | Contact Map |
| 1yhfA | 1 | 0.4821 | 98 | 0.771 | Contact Map |
| 3bcwA | 2 | 0.4462 | 98 | 0.774 | Contact Map |
| 2f4pA | 4 | 0.6 | 98 | 0.774 | Contact Map |
| 3es1A | 1 | 0.5385 | 98 | 0.774 | Contact Map |
| 1o4tA | 2 | 0.4667 | 98 | 0.775 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)