| AraC DD-2 |
| ID: | 1495559203 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 195 (174) | ||
| Sequences: | 1240 (947) | ||
| Seq/Len: | 7.126 | ||
| Nf(neff/√len): | 71.8 |
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: 7.126).
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 |
| 178_P | 182_G | 3.726 | 1.00 |
| 52_R | 92_Y | 2.399 | 1.00 |
| 45_Y | 76_P | 2.337 | 1.00 |
| 42_M | 80_H | 2.066 | 1.00 |
| 40_L | 80_H | 2.053 | 1.00 |
| 140_A | 161_A | 2.035 | 1.00 |
| 54_E | 67_R | 1.801 | 1.00 |
| 60_H | 78_E | 1.778 | 1.00 |
| 46_I | 93_H | 1.767 | 1.00 |
| 55_G | 82_Y | 1.747 | 1.00 |
| 40_L | 46_I | 1.728 | 1.00 |
| 189_P | 192_G | 1.700 | 1.00 |
| 130_F | 155_P | 1.651 | 1.00 |
| 42_M | 46_I | 1.595 | 1.00 |
| 24_T | 30_G | 1.554 | 1.00 |
| 188_R | 194_P | 1.553 | 1.00 |
| 50_T | 55_G | 1.541 | 0.99 |
| 56_V | 83_G | 1.534 | 0.99 |
| 55_G | 72_L | 1.526 | 0.99 |
| 55_G | 91_W | 1.502 | 0.99 |
| 54_E | 89_S | 1.485 | 0.99 |
| 82_Y | 95_W | 1.450 | 0.99 |
| 51_I | 94_Q | 1.442 | 0.99 |
| 52_R | 68_P | 1.432 | 0.99 |
| 74_F | 80_H | 1.411 | 0.99 |
| 70_D | 121_R | 1.410 | 0.99 |
| 54_E | 85_H | 1.388 | 0.99 |
| 75_P | 78_E | 1.379 | 0.99 |
| 58_N | 63_Q | 1.358 | 0.98 |
| 46_I | 80_H | 1.345 | 0.98 |
| 188_R | 191_G | 1.344 | 0.98 |
| 54_E | 65_V | 1.329 | 0.98 |
| 137_I | 141_G | 1.327 | 0.98 |
| 26_I | 30_G | 1.323 | 0.98 |
| 57_I | 82_Y | 1.293 | 0.98 |
| 131_G | 135_G | 1.290 | 0.98 |
| 24_T | 46_I | 1.284 | 0.98 |
| 185_V | 192_G | 1.253 | 0.97 |
| 186_H | 189_P | 1.242 | 0.97 |
| 25_P | 29_Q | 1.239 | 0.97 |
| 72_L | 82_Y | 1.227 | 0.97 |
| 177_Q | 181_R | 1.222 | 0.96 |
| 28_A | 32_L | 1.215 | 0.96 |
| 70_D | 119_F | 1.210 | 0.96 |
| 48_N | 95_W | 1.197 | 0.96 |
| 26_I | 29_Q | 1.160 | 0.95 |
| 21_T | 27_E | 1.153 | 0.95 |
| 49_L | 134_F | 1.145 | 0.94 |
| 129_R | 158_T | 1.143 | 0.94 |
| 91_W | 97_Y | 1.142 | 0.94 |
| 44_G | 97_Y | 1.142 | 0.94 |
| 75_P | 156_A | 1.139 | 0.94 |
| 50_T | 93_H | 1.131 | 0.94 |
| 23_L | 29_Q | 1.116 | 0.93 |
| 23_L | 30_G | 1.107 | 0.93 |
| 24_T | 31_Y | 1.103 | 0.93 |
| 56_V | 65_V | 1.096 | 0.92 |
| 24_T | 33_D | 1.096 | 0.92 |
| 145_G | 161_A | 1.093 | 0.92 |
| 185_V | 194_P | 1.089 | 0.92 |
| 57_I | 95_W | 1.087 | 0.92 |
| 50_T | 91_W | 1.086 | 0.92 |
| 125_Q | 142_Q | 1.084 | 0.92 |
| 56_V | 63_Q | 1.082 | 0.92 |
| 192_G | 195_F | 1.076 | 0.91 |
| 186_H | 192_G | 1.076 | 0.91 |
| 135_G | 139_D | 1.062 | 0.91 |
| 23_L | 32_L | 1.052 | 0.90 |
| 20_V | 28_A | 1.047 | 0.90 |
| 26_I | 32_L | 1.047 | 0.90 |
| 23_L | 27_E | 1.047 | 0.90 |
| 174_P | 189_P | 1.044 | 0.90 |
| 96_V | 137_I | 1.043 | 0.90 |
| 27_E | 33_D | 1.037 | 0.89 |
| 147_L | 161_A | 1.034 | 0.89 |
| 19_L | 23_L | 1.030 | 0.89 |
| 26_I | 80_H | 1.029 | 0.89 |
| 24_T | 38_R | 1.024 | 0.89 |
| 71_M | 159_A | 1.023 | 0.89 |
| 48_N | 93_H | 1.022 | 0.88 |
| 24_T | 29_Q | 1.021 | 0.88 |
| 22_G | 31_Y | 1.006 | 0.87 |
| 44_G | 57_I | 1.006 | 0.87 |
| 30_G | 46_I | 1.005 | 0.87 |
| 131_G | 182_G | 1.005 | 0.87 |
| 49_L | 127_Q | 1.001 | 0.87 |
| 61_G | 165_G | 1.000 | 0.87 |
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 | |
| 2arcA | 2 | 0.8051 | 99.8 | 0.518 | Contact Map |
| 3gbgA | 1 | 0.8564 | 99.6 | 0.603 | Contact Map |
| 4mv2A | 2 | 0.5487 | 99.2 | 0.689 | Contact Map |
| 4rd7A | 1 | 0.5333 | 99.1 | 0.703 | Contact Map |
| 2xlgA | 1 | 0.8359 | 98.9 | 0.725 | Contact Map |
| 3cewA | 4 | 0.559 | 98.9 | 0.733 | Contact Map |
| 1o4tA | 2 | 0.4667 | 98.8 | 0.736 | Contact Map |
| 2f4pA | 4 | 0.6 | 98.8 | 0.736 | Contact Map |
| 4bifA | 8 | 0.5692 | 98.7 | 0.747 | Contact Map |
| 1y3tA | 2 | 0.6769 | 98.7 | 0.747 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)