| AraC 1-100 |
| ID: | 1496934866 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 50% gaps before running GREMLIN. |
| Length: | 150 (125) | ||
| Sequences: | 482 (361.2) | ||
| Seq/Len: | 3.856 | ||
| Nf(neff/√len): | 32.3 |
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: 3.856).
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 |
| 42_M | 74_F | 2.116 | 1.00 |
| 42_M | 80_H | 2.082 | 1.00 |
| 45_Y | 76_P | 1.941 | 1.00 |
| 46_I | 93_H | 1.890 | 1.00 |
| 70_D | 119_F | 1.881 | 1.00 |
| 55_G | 91_W | 1.717 | 0.99 |
| 40_L | 80_H | 1.562 | 0.98 |
| 131_S | 135_G | 1.555 | 0.98 |
| 54_Q | 67_R | 1.550 | 0.98 |
| 52_R | 92_Y | 1.520 | 0.98 |
| 96_V | 137_I | 1.450 | 0.97 |
| 50_T | 91_W | 1.420 | 0.96 |
| 36_I | 97_Y | 1.376 | 0.95 |
| 54_Q | 85_H | 1.358 | 0.95 |
| 33_D | 37_D | 1.336 | 0.94 |
| 24_T | 46_I | 1.336 | 0.94 |
| 56_V | 83_G | 1.312 | 0.93 |
| 87_E | 146_R | 1.280 | 0.92 |
| 32_L | 145_G | 1.267 | 0.91 |
| 74_F | 80_H | 1.227 | 0.90 |
| 24_T | 93_H | 1.224 | 0.89 |
| 52_R | 128_P | 1.219 | 0.89 |
| 56_V | 65_V | 1.212 | 0.89 |
| 49_L | 134_F | 1.211 | 0.89 |
| 35_F | 146_R | 1.204 | 0.88 |
| 35_F | 83_G | 1.190 | 0.88 |
| 96_V | 134_F | 1.189 | 0.88 |
| 47_L | 73_L | 1.181 | 0.87 |
| 32_L | 37_D | 1.180 | 0.87 |
| 82_Y | 91_W | 1.166 | 0.86 |
| 68_P | 111_P | 1.161 | 0.86 |
| 44_G | 97_Y | 1.155 | 0.85 |
| 32_L | 87_E | 1.155 | 0.85 |
| 62_R | 136_Q | 1.150 | 0.85 |
| 82_Y | 98_F | 1.149 | 0.85 |
| 58_K | 81_H | 1.146 | 0.85 |
| 36_I | 93_H | 1.143 | 0.85 |
| 57_V | 64_F | 1.143 | 0.85 |
| 54_Q | 65_V | 1.133 | 0.84 |
| 23_L | 92_Y | 1.129 | 0.84 |
| 59_N | 75_P | 1.127 | 0.84 |
| 19_L | 100_P | 1.126 | 0.83 |
| 20_V | 44_G | 1.126 | 0.83 |
| 35_F | 144_E | 1.117 | 0.83 |
| 129_H | 139_N | 1.106 | 0.82 |
| 37_D | 145_G | 1.103 | 0.82 |
| 58_K | 77_G | 1.103 | 0.82 |
| 19_L | 50_T | 1.099 | 0.81 |
| 47_L | 85_H | 1.097 | 0.81 |
| 71_I | 119_F | 1.095 | 0.81 |
| 37_D | 87_E | 1.091 | 0.81 |
| 50_T | 55_G | 1.084 | 0.80 |
| 80_H | 91_W | 1.074 | 0.79 |
| 33_D | 97_Y | 1.069 | 0.79 |
| 59_N | 80_H | 1.064 | 0.78 |
| 55_G | 84_R | 1.048 | 0.77 |
| 47_L | 98_F | 1.043 | 0.76 |
| 39_P | 79_I | 1.041 | 0.76 |
| 95_W | 115_A | 1.040 | 0.76 |
| 66_C | 96_V | 1.039 | 0.76 |
| 67_R | 119_F | 1.035 | 0.76 |
| 34_F | 44_G | 1.032 | 0.75 |
| 33_D | 44_G | 1.028 | 0.75 |
| 133_L | 136_Q | 1.027 | 0.75 |
| 31_Y | 130_F | 1.026 | 0.75 |
| 58_K | 115_A | 1.024 | 0.75 |
| 22_G | 95_W | 1.022 | 0.74 |
| 48_N | 66_C | 1.016 | 0.74 |
| 128_P | 132_D | 1.014 | 0.74 |
| 49_L | 92_Y | 1.004 | 0.73 |
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 | 0.96 | 99.7 | 0.52 | Contact Map |
| 3gbgA | 1 | 0.7933 | 98.6 | 0.729 | Contact Map |
| 4mv2A | 2 | 0.7133 | 98.6 | 0.731 | Contact Map |
| 4rd7A | 1 | 0.6867 | 98.4 | 0.744 | Contact Map |
| 1o4tA | 2 | 0.6133 | 98.2 | 0.757 | Contact Map |
| 2f4pA | 4 | 0.78 | 98.2 | 0.757 | Contact Map |
| 3h8uA | 2 | 0.6867 | 98.2 | 0.76 | Contact Map |
| 3ht1A | 1 | 0.8067 | 98.1 | 0.761 | Contact Map |
| 2gu9A | 2 | 0.6933 | 98.1 | 0.766 | Contact Map |
| 4bifA | 8 | 0.74 | 98 | 0.768 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)