| wdoutCA-Nter |
| ID: | 1382152145 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 226 (205) | ||
| Sequences: | 22318 (18276.1) | ||
| Seq/Len: | 108.868 | ||
| Nf(neff/√len): | 1276.5 |
HHblits Results: (2013_03)
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: 108.868).
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 |
| 31_V | 45_V | 3.789 | 1.00 |
| 174_D | 178_G | 3.775 | 1.00 |
| 180_P | 183_E | 2.977 | 1.00 |
| 130_E | 175_D | 2.888 | 1.00 |
| 28_Q | 49_T | 2.844 | 1.00 |
| 35_Q | 46_E | 2.530 | 1.00 |
| 76_D | 79_E | 2.415 | 1.00 |
| 181_E | 184_R | 2.295 | 1.00 |
| 179_I | 183_E | 2.282 | 1.00 |
| 147_N | 171_Y | 2.258 | 1.00 |
| 35_Q | 43_Y | 2.242 | 1.00 |
| 83_Q | 116_S | 2.231 | 1.00 |
| 179_I | 187_V | 2.183 | 1.00 |
| 75_R | 110_T | 2.140 | 1.00 |
| 28_Q | 50_E | 2.099 | 1.00 |
| 97_R | 143_Q | 2.081 | 1.00 |
| 147_N | 173_E | 2.058 | 1.00 |
| 145_F | 173_E | 2.011 | 1.00 |
| 27_V | 49_T | 2.009 | 1.00 |
| 88_Y | 120_D | 2.003 | 1.00 |
| 74_I | 112_L | 1.887 | 1.00 |
| 183_E | 186_N | 1.801 | 1.00 |
| 32_K | 46_E | 1.799 | 1.00 |
| 111_L | 114_E | 1.797 | 1.00 |
| 186_N | 192_Y | 1.782 | 1.00 |
| 130_E | 142_Q | 1.720 | 1.00 |
| 186_N | 189_D | 1.715 | 1.00 |
| 130_E | 144_L | 1.711 | 1.00 |
| 8_E | 12_Q | 1.661 | 1.00 |
| 124_S | 128_A | 1.658 | 1.00 |
| 114_E | 117_K | 1.653 | 1.00 |
| 110_T | 115_H | 1.649 | 1.00 |
| 143_Q | 175_D | 1.644 | 1.00 |
| 183_E | 192_Y | 1.638 | 1.00 |
| 189_D | 192_Y | 1.636 | 1.00 |
| 53_D | 57_V | 1.623 | 1.00 |
| 99_E | 147_N | 1.617 | 1.00 |
| 31_V | 46_E | 1.617 | 1.00 |
| 94_V | 98_D | 1.609 | 1.00 |
| 99_E | 145_F | 1.607 | 1.00 |
| 30_T | 44_E | 1.605 | 1.00 |
| 46_E | 50_E | 1.598 | 1.00 |
| 78_T | 148_L | 1.587 | 1.00 |
| 97_R | 145_F | 1.562 | 1.00 |
| 34_M | 42_R | 1.552 | 1.00 |
| 92_F | 127_R | 1.535 | 1.00 |
| 199_T | 202_G | 1.517 | 1.00 |
| 119_I | 170_F | 1.500 | 1.00 |
| 27_V | 45_V | 1.489 | 1.00 |
| 31_V | 49_T | 1.479 | 1.00 |
| 26_I | 48_D | 1.470 | 1.00 |
| 73_L | 109_E | 1.458 | 1.00 |
| 28_Q | 53_D | 1.446 | 1.00 |
| 129_G | 193_S | 1.425 | 1.00 |
| 142_Q | 175_D | 1.415 | 1.00 |
| 202_G | 205_I | 1.394 | 0.99 |
| 78_T | 82_E | 1.390 | 0.99 |
| 7_E | 10_T | 1.353 | 0.99 |
| 26_I | 30_T | 1.339 | 0.99 |
| 149_L | 169_G | 1.339 | 0.99 |
| 29_D | 33_F | 1.335 | 0.99 |
| 179_I | 184_R | 1.331 | 0.99 |
| 183_E | 194_T | 1.331 | 0.99 |
| 88_Y | 123_L | 1.324 | 0.99 |
| 207_R | 211_E | 1.324 | 0.99 |
| 7_E | 11_Q | 1.269 | 0.99 |
| 21_R | 57_V | 1.236 | 0.98 |
| 54_R | 113_G | 1.227 | 0.98 |
| 28_Q | 46_E | 1.216 | 0.98 |
| 89_A | 93_N | 1.204 | 0.98 |
| 95_E | 143_Q | 1.204 | 0.98 |
| 149_L | 171_Y | 1.168 | 0.97 |
| 85_L | 89_A | 1.159 | 0.97 |
| 83_Q | 112_L | 1.151 | 0.97 |
| 19_Q | 117_K | 1.144 | 0.97 |
| 44_E | 48_D | 1.137 | 0.97 |
| 21_R | 53_D | 1.134 | 0.97 |
| 179_I | 185_G | 1.132 | 0.97 |
| 12_Q | 15_T | 1.131 | 0.97 |
| 87_R | 120_D | 1.122 | 0.97 |
| 47_V | 83_Q | 1.117 | 0.96 |
| 164_G | 169_G | 1.113 | 0.96 |
| 87_R | 116_S | 1.091 | 0.96 |
| 31_V | 35_Q | 1.089 | 0.96 |
| 202_G | 209_V | 1.088 | 0.96 |
| 79_E | 83_Q | 1.088 | 0.96 |
| 44_E | 47_V | 1.082 | 0.96 |
| 128_A | 195_A | 1.077 | 0.95 |
| 15_T | 190_A | 1.073 | 0.95 |
| 43_Y | 47_V | 1.072 | 0.95 |
| 202_G | 206_V | 1.070 | 0.95 |
| 19_Q | 23_G | 1.069 | 0.95 |
| 106_Y | 150_R | 1.063 | 0.95 |
| 80_R | 84_A | 1.062 | 0.95 |
| 95_E | 98_D | 1.051 | 0.94 |
| 76_D | 107_S | 1.048 | 0.94 |
| 119_I | 123_L | 1.045 | 0.94 |
| 112_L | 116_S | 1.037 | 0.94 |
| 58_E | 114_E | 1.033 | 0.94 |
| 48_D | 51_A | 1.032 | 0.94 |
| 200_G | 203_L | 1.030 | 0.94 |
| 205_I | 209_V | 1.029 | 0.94 |
| 151_N | 169_G | 1.029 | 0.94 |
| 75_R | 109_E | 1.021 | 0.93 |
| 12_Q | 190_A | 1.019 | 0.93 |
| 121_D | 125_L | 1.018 | 0.93 |
| 5_E | 9_V | 1.015 | 0.93 |
| 77_I | 170_F | 1.012 | 0.93 |
| 20_S | 52_G | 1.010 | 0.93 |
| 84_A | 116_S | 1.006 | 0.93 |
| 118_V | 206_V | 1.002 | 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 | |
| 4mpcA | 1 | 0.8982 | 99.9 | 0.363 | Contact Map |
| 4i5sA | 2 | 0.8894 | 99.8 | 0.367 | Contact Map |
| 1y8oA | 1 | 0.9115 | 99.8 | 0.37 | Contact Map |
| 2c2aA | 1 | 0.9071 | 99.8 | 0.375 | Contact Map |
| 3a0rA | 1 | 0.8628 | 99.8 | 0.383 | Contact Map |
| 2e0aA | 2 | 0.9292 | 99.8 | 0.387 | Contact Map |
| 2q8gA | 1 | 0.8938 | 99.8 | 0.393 | Contact Map |
| 4ew8A | 2 | 0.9027 | 99.8 | 0.398 | Contact Map |
| 4gczA | 2 | 0.9027 | 99.8 | 0.402 | Contact Map |
| 3d36A | 2 | 0.8673 | 99.8 | 0.404 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)