| HD Helical low coverage |
| ID: | 1425311194 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 50% gaps before running GREMLIN. |
| Length: | 234 (232) | ||
| Sequences: | 1227 (624.2) | ||
| Seq/Len: | 5.289 | ||
| Nf(neff/√len): | 41.0 |
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: 5.289).
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 |
| 39_L | 112_L | 4.422 | 1.00 |
| 53_I | 60_K | 4.101 | 1.00 |
| 64_A | 69_D | 3.974 | 1.00 |
| 125_L | 168_H | 3.466 | 1.00 |
| 129_K | 132_A | 3.432 | 1.00 |
| 123_R | 160_E | 2.856 | 1.00 |
| 42_A | 70_E | 2.792 | 1.00 |
| 60_K | 76_E | 2.593 | 1.00 |
| 7_Y | 58_V | 2.466 | 1.00 |
| 3_R | 66_L | 2.434 | 1.00 |
| 139_R | 143_D | 2.293 | 1.00 |
| 170_N | 173_A | 2.266 | 1.00 |
| 74_L | 113_V | 2.257 | 1.00 |
| 2_N | 6_V | 2.178 | 1.00 |
| 122_M | 164_L | 2.068 | 1.00 |
| 176_A | 180_R | 2.023 | 1.00 |
| 104_I | 108_V | 1.965 | 1.00 |
| 31_A | 44_I | 1.963 | 1.00 |
| 1_M | 44_I | 1.945 | 1.00 |
| 8_A | 24_Y | 1.944 | 1.00 |
| 166_F | 170_N | 1.879 | 1.00 |
| 53_I | 63_I | 1.877 | 1.00 |
| 46_T | 74_L | 1.860 | 1.00 |
| 73_E | 106_K | 1.842 | 1.00 |
| 134_R | 168_H | 1.842 | 1.00 |
| 53_I | 72_G | 1.833 | 1.00 |
| 131_Q | 134_R | 1.825 | 1.00 |
| 202_T | 205_A | 1.818 | 1.00 |
| 34_L | 47_A | 1.785 | 1.00 |
| 131_Q | 135_E | 1.748 | 1.00 |
| 46_T | 113_V | 1.727 | 1.00 |
| 53_I | 76_E | 1.721 | 1.00 |
| 18_A | 128_I | 1.707 | 1.00 |
| 34_L | 43_T | 1.701 | 1.00 |
| 94_A | 205_A | 1.673 | 1.00 |
| 159_T | 185_R | 1.667 | 0.99 |
| 175_N | 178_I | 1.627 | 0.99 |
| 10_R | 13_G | 1.622 | 0.99 |
| 41_T | 45_V | 1.596 | 0.99 |
| 166_F | 173_A | 1.566 | 0.99 |
| 33_I | 123_R | 1.545 | 0.99 |
| 212_H | 216_T | 1.539 | 0.99 |
| 39_L | 43_T | 1.524 | 0.99 |
| 60_K | 72_G | 1.488 | 0.99 |
| 6_V | 9_M | 1.477 | 0.98 |
| 113_V | 150_R | 1.446 | 0.98 |
| 125_L | 138_A | 1.435 | 0.98 |
| 7_Y | 66_L | 1.400 | 0.98 |
| 5_Y | 9_M | 1.389 | 0.98 |
| 217_E | 220_E | 1.373 | 0.97 |
| 128_I | 137_I | 1.371 | 0.97 |
| 62_E | 65_K | 1.369 | 0.97 |
| 7_Y | 11_M | 1.368 | 0.97 |
| 56_T | 59_T | 1.258 | 0.95 |
| 13_G | 16_T | 1.247 | 0.95 |
| 122_M | 125_L | 1.245 | 0.94 |
| 112_L | 166_F | 1.231 | 0.94 |
| 61_E | 64_A | 1.227 | 0.94 |
| 211_R | 215_Q | 1.222 | 0.94 |
| 98_R | 192_V | 1.219 | 0.94 |
| 194_P | 213_I | 1.213 | 0.93 |
| 31_A | 47_A | 1.207 | 0.93 |
| 120_H | 124_T | 1.191 | 0.93 |
| 118_R | 141_T | 1.185 | 0.92 |
| 184_L | 187_E | 1.184 | 0.92 |
| 53_I | 79_T | 1.180 | 0.92 |
| 11_M | 57_P | 1.163 | 0.91 |
| 64_A | 72_G | 1.151 | 0.91 |
| 174_R | 178_I | 1.146 | 0.91 |
| 60_K | 64_A | 1.138 | 0.90 |
| 60_K | 73_E | 1.135 | 0.90 |
| 55_D | 121_N | 1.132 | 0.90 |
| 11_M | 62_E | 1.125 | 0.89 |
| 99_K | 110_V | 1.122 | 0.89 |
| 61_E | 65_K | 1.120 | 0.89 |
| 55_D | 80_K | 1.118 | 0.89 |
| 58_V | 62_E | 1.117 | 0.89 |
| 125_L | 137_I | 1.114 | 0.89 |
| 54_E | 121_N | 1.112 | 0.89 |
| 93_Q | 96_N | 1.105 | 0.88 |
| 184_L | 189_G | 1.092 | 0.88 |
| 11_M | 58_V | 1.078 | 0.87 |
| 45_V | 71_I | 1.072 | 0.86 |
| 78_V | 81_L | 1.064 | 0.86 |
| 36_E | 156_R | 1.064 | 0.86 |
| 101_I | 145_Y | 1.064 | 0.86 |
| 223_R | 226_R | 1.057 | 0.85 |
| 94_A | 97_L | 1.054 | 0.85 |
| 58_V | 66_L | 1.052 | 0.85 |
| 173_A | 176_A | 1.052 | 0.85 |
| 97_L | 180_R | 1.046 | 0.84 |
| 1_M | 41_T | 1.039 | 0.84 |
| 133_K | 137_I | 1.026 | 0.83 |
| 33_I | 160_E | 1.024 | 0.83 |
| 9_M | 13_G | 1.016 | 0.82 |
| 51_D | 54_E | 1.008 | 0.81 |
| 111_L | 148_L | 1.008 | 0.81 |
| 80_K | 121_N | 1.003 | 0.81 |
| 17_R | 121_N | 1.003 | 0.81 |
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 | |
| 1vj7A | 2 | 0.9231 | 100 | 0.307 | Contact Map |
| 3nr1A | 2 | 0.7179 | 100 | 0.569 | Contact Map |
| 3nqwA | 2 | 0.7009 | 100 | 0.581 | Contact Map |
| 3l9dA | 2 | 0.3034 | 99.5 | 0.857 | Contact Map |
| 2qgsA | 2 | 0.765 | 81.6 | 0.957 | Contact Map |
| 4n6wA | 1 | 0.6581 | 77.8 | 0.958 | Contact Map |
| 4mlmA | 2 | 0.6368 | 72.7 | 0.96 | Contact Map |
| 2pq7A | 1 | 0.5983 | 71.1 | 0.96 | Contact Map |
| 3dtoA | 4 | 0.6838 | 70.3 | 0.961 | Contact Map |
| 2cqzA | 6 | 0.6197 | 67.3 | 0.961 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)