| AraC 1-100 |
| ID: | 1496932255 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 100 (97) | ||
| Sequences: | 314 (202) | ||
| Seq/Len: | 3.237 | ||
| Nf(neff/√len): | 20.5 |
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: 3.237).
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 |
| 55_G | 91_W | 2.095 | 1.00 |
| 7_D | 10_L | 2.017 | 1.00 |
| 82_Y | 98_F | 1.939 | 1.00 |
| 7_D | 18_H | 1.842 | 0.99 |
| 47_L | 73_L | 1.798 | 0.99 |
| 38_R | 81_H | 1.700 | 0.99 |
| 22_G | 91_W | 1.686 | 0.99 |
| 22_G | 55_G | 1.644 | 0.98 |
| 54_Q | 85_H | 1.541 | 0.97 |
| 40_L | 80_H | 1.518 | 0.97 |
| 14_S | 17_A | 1.475 | 0.96 |
| 82_Y | 95_W | 1.442 | 0.95 |
| 54_Q | 65_V | 1.428 | 0.95 |
| 91_W | 95_W | 1.347 | 0.92 |
| 6_N | 17_A | 1.332 | 0.92 |
| 52_R | 92_Y | 1.324 | 0.91 |
| 8_P | 13_Y | 1.316 | 0.91 |
| 69_G | 96_V | 1.306 | 0.91 |
| 7_D | 13_Y | 1.304 | 0.90 |
| 42_M | 74_F | 1.301 | 0.90 |
| 10_L | 13_Y | 1.261 | 0.88 |
| 61_G | 78_E | 1.232 | 0.87 |
| 34_F | 44_G | 1.223 | 0.86 |
| 48_N | 93_H | 1.207 | 0.85 |
| 10_L | 18_H | 1.204 | 0.85 |
| 33_D | 37_D | 1.203 | 0.85 |
| 14_S | 18_H | 1.189 | 0.84 |
| 68_P | 96_V | 1.175 | 0.83 |
| 26_I | 80_H | 1.174 | 0.83 |
| 24_T | 33_D | 1.170 | 0.83 |
| 23_L | 45_Y | 1.158 | 0.82 |
| 44_G | 97_Y | 1.157 | 0.82 |
| 36_I | 50_T | 1.155 | 0.82 |
| 4_A | 14_S | 1.137 | 0.80 |
| 20_V | 97_Y | 1.124 | 0.79 |
| 56_V | 83_G | 1.106 | 0.78 |
| 42_M | 84_R | 1.103 | 0.77 |
| 41_G | 50_T | 1.100 | 0.77 |
| 6_N | 18_H | 1.083 | 0.76 |
| 67_R | 87_E | 1.081 | 0.75 |
| 55_G | 95_W | 1.071 | 0.74 |
| 7_D | 14_S | 1.053 | 0.73 |
| 67_R | 70_D | 1.042 | 0.71 |
| 38_R | 95_W | 1.041 | 0.71 |
| 10_L | 14_S | 1.029 | 0.70 |
| 40_L | 79_I | 1.028 | 0.70 |
| 29_N | 61_G | 1.026 | 0.70 |
| 22_G | 95_W | 1.019 | 0.69 |
| 6_N | 14_S | 1.016 | 0.69 |
| 63_E | 86_P | 1.015 | 0.69 |
| 85_H | 89_R | 1.014 | 0.68 |
| 84_R | 97_Y | 1.012 | 0.68 |
| 82_Y | 91_W | 1.012 | 0.68 |
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 | 0.94 | 99.6 | 0.446 | Contact Map |
| 4mv2A | 2 | 0.94 | 98.8 | 0.63 | Contact Map |
| 3gbgA | 1 | 0.82 | 98.7 | 0.64 | Contact Map |
| 4rd7A | 1 | 0.94 | 98.6 | 0.648 | Contact Map |
| 2f4pA | 4 | 0.94 | 98.4 | 0.671 | Contact Map |
| 3cewA | 4 | 0.94 | 98.3 | 0.678 | Contact Map |
| 3kgzA | 2 | 0.92 | 98.3 | 0.684 | Contact Map |
| 3nw4A | 1 | 0.94 | 98.3 | 0.685 | Contact Map |
| 4bifA | 8 | 0.91 | 98.2 | 0.688 | Contact Map |
| 1o4tA | 2 | 0.94 | 98.2 | 0.689 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)