| AraC NoMid |
| ID: | 1497369903 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 201 (175) | ||
| Sequences: | 14899 (11041.1) | ||
| Seq/Len: | 85.137 | ||
| Nf(neff/√len): | 834.6 |
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: 85.137).
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 |
| 130_I | 138_D | 3.338 | 1.00 |
| 145_K | 178_T | 3.126 | 1.00 |
| 153_M | 161_N | 2.969 | 1.00 |
| 96_S | 139_Q | 2.891 | 1.00 |
| 141_I | 178_T | 2.810 | 1.00 |
| 174_F | 185_F | 2.627 | 1.00 |
| 98_H | 102_S | 2.581 | 1.00 |
| 143_Q | 146_L | 2.481 | 1.00 |
| 180_A | 188_G | 2.448 | 1.00 |
| 144_A | 170_F | 2.446 | 1.00 |
| 94_Y | 98_H | 2.395 | 1.00 |
| 147_L | 161_N | 2.394 | 1.00 |
| 105_D | 108_S | 2.268 | 1.00 |
| 138_D | 177_C | 2.228 | 1.00 |
| 94_Y | 112_H | 2.151 | 1.00 |
| 107_A | 117_P | 2.071 | 1.00 |
| 124_F | 135_W | 1.909 | 1.00 |
| 153_M | 157_T | 1.810 | 1.00 |
| 95_I | 136_R | 1.808 | 1.00 |
| 145_K | 185_F | 1.753 | 1.00 |
| 119_R | 122_H | 1.737 | 1.00 |
| 148_L | 155_I | 1.734 | 1.00 |
| 183_S | 187_A | 1.715 | 1.00 |
| 147_L | 153_M | 1.670 | 1.00 |
| 167_Q | 171_S | 1.667 | 1.00 |
| 169_Y | 173_V | 1.656 | 1.00 |
| 146_L | 150_T | 1.641 | 1.00 |
| 119_R | 123_L | 1.639 | 1.00 |
| 63_N | 66_E | 1.614 | 1.00 |
| 180_A | 184_E | 1.599 | 1.00 |
| 154_P | 157_T | 1.561 | 1.00 |
| 93_Q | 97_D | 1.551 | 1.00 |
| 91_A | 120_L | 1.550 | 1.00 |
| 133_L | 137_E | 1.545 | 1.00 |
| 157_T | 160_R | 1.531 | 1.00 |
| 115_L | 120_L | 1.522 | 1.00 |
| 143_Q | 147_L | 1.497 | 1.00 |
| 98_H | 101_D | 1.490 | 1.00 |
| 130_I | 134_S | 1.451 | 1.00 |
| 108_S | 112_H | 1.447 | 1.00 |
| 147_L | 162_V | 1.442 | 1.00 |
| 94_Y | 104_F | 1.438 | 1.00 |
| 156_A | 167_Q | 1.438 | 1.00 |
| 88_V | 128_L | 1.438 | 1.00 |
| 151_T | 186_R | 1.415 | 1.00 |
| 141_I | 177_C | 1.404 | 0.99 |
| 118_S | 122_H | 1.390 | 0.99 |
| 115_L | 119_R | 1.378 | 0.99 |
| 120_L | 132_V | 1.368 | 0.99 |
| 91_A | 113_V | 1.358 | 0.99 |
| 153_M | 158_V | 1.358 | 0.99 |
| 106_I | 121_S | 1.351 | 0.99 |
| 107_A | 111_Q | 1.346 | 0.99 |
| 139_Q | 142_S | 1.326 | 0.99 |
| 139_Q | 143_Q | 1.322 | 0.99 |
| 92_C | 128_L | 1.285 | 0.99 |
| 168_L | 171_S | 1.282 | 0.99 |
| 171_S | 181_S | 1.271 | 0.99 |
| 157_T | 161_N | 1.269 | 0.99 |
| 138_D | 142_S | 1.244 | 0.98 |
| 164_F | 173_V | 1.238 | 0.98 |
| 149_S | 189_C | 1.234 | 0.98 |
| 109_V | 132_V | 1.222 | 0.98 |
| 106_I | 132_V | 1.215 | 0.98 |
| 173_V | 176_K | 1.213 | 0.98 |
| 64_L | 67_Q | 1.200 | 0.98 |
| 49_A | 74_E | 1.197 | 0.98 |
| 102_S | 108_S | 1.186 | 0.98 |
| 147_L | 158_V | 1.185 | 0.98 |
| 121_S | 132_V | 1.181 | 0.98 |
| 40_S | 44_G | 1.170 | 0.97 |
| 143_Q | 162_V | 1.156 | 0.97 |
| 104_F | 109_V | 1.154 | 0.97 |
| 181_S | 184_E | 1.151 | 0.97 |
| 95_I | 139_Q | 1.140 | 0.97 |
| 156_A | 160_R | 1.139 | 0.97 |
| 116_S | 119_R | 1.138 | 0.97 |
| 91_A | 109_V | 1.116 | 0.96 |
| 131_S | 134_S | 1.113 | 0.96 |
| 144_A | 162_V | 1.106 | 0.96 |
| 99_L | 139_Q | 1.102 | 0.96 |
| 91_A | 124_F | 1.097 | 0.96 |
| 137_E | 173_V | 1.079 | 0.95 |
| 142_S | 145_K | 1.074 | 0.95 |
| 133_L | 169_Y | 1.072 | 0.95 |
| 124_F | 128_L | 1.058 | 0.95 |
| 60_L | 67_Q | 1.056 | 0.95 |
| 184_E | 187_A | 1.053 | 0.95 |
| 172_R | 176_K | 1.050 | 0.94 |
| 87_R | 115_L | 1.042 | 0.94 |
| 137_E | 177_C | 1.040 | 0.94 |
| 148_L | 158_V | 1.032 | 0.94 |
| 117_P | 121_S | 1.030 | 0.94 |
| 151_T | 158_V | 1.019 | 0.93 |
| 85_D | 127_Q | 1.015 | 0.93 |
| 41_D | 44_G | 1.003 | 0.93 |
| 166_D | 169_Y | 1.002 | 0.92 |
| 145_K | 149_S | 1.002 | 0.92 |
| 140_R | 162_V | 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 | 0.8706 | 100 | 0.3 | Contact Map |
| 3oouA | 1 | 0.5224 | 99.9 | 0.357 | Contact Map |
| 3oioA | 1 | 0.5572 | 99.9 | 0.357 | Contact Map |
| 1bl0A | 1 | 0.5771 | 99.9 | 0.36 | Contact Map |
| 2k9sA | 1 | 0.5323 | 99.9 | 0.363 | Contact Map |
| 3mn2A | 2 | 0.5274 | 99.9 | 0.364 | Contact Map |
| 3mklA | 2 | 0.5522 | 99.9 | 0.369 | Contact Map |
| 3lsgA | 5 | 0.5124 | 99.9 | 0.375 | Contact Map |
| 3w6vA | 1 | 0.5522 | 99.9 | 0.376 | Contact Map |
| 4fe7A | 1 | 0.9104 | 99.9 | 0.39 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)