| HORMA |
| ID: | 1517417060 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 50% gaps before running GREMLIN. |
| Length: | 233 (202) | ||
| Sequences: | 1261 (834.7) | ||
| Seq/Len: | 6.243 | ||
| Nf(neff/√len): | 58.7 |
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: 6.243).
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 |
| 83_L | 91_A | 3.055 | 1.00 |
| 194_P | 197_Y | 2.960 | 1.00 |
| 76_K | 79_S | 2.809 | 1.00 |
| 80_V | 85_E | 1.972 | 1.00 |
| 30_E | 67_K | 1.942 | 1.00 |
| 107_D | 110_N | 1.910 | 1.00 |
| 17_F | 28_F | 1.900 | 1.00 |
| 87_G | 91_A | 1.897 | 1.00 |
| 88_I | 100_V | 1.883 | 1.00 |
| 185_I | 191_Q | 1.842 | 1.00 |
| 106_V | 110_N | 1.792 | 1.00 |
| 193_C | 197_Y | 1.785 | 1.00 |
| 20_R | 116_E | 1.779 | 1.00 |
| 106_V | 109_E | 1.755 | 1.00 |
| 182_F | 185_I | 1.709 | 1.00 |
| 83_L | 86_H | 1.704 | 1.00 |
| 186_H | 189_Y | 1.684 | 1.00 |
| 151_K | 159_G | 1.655 | 1.00 |
| 198_E | 204_P | 1.634 | 1.00 |
| 80_V | 84_L | 1.625 | 1.00 |
| 118_Y | 167_L | 1.624 | 1.00 |
| 90_D | 94_K | 1.564 | 0.99 |
| 185_I | 188_F | 1.551 | 0.99 |
| 88_I | 91_A | 1.521 | 0.99 |
| 185_I | 190_T | 1.521 | 0.99 |
| 86_H | 91_A | 1.476 | 0.99 |
| 80_V | 83_L | 1.459 | 0.99 |
| 80_V | 87_G | 1.446 | 0.99 |
| 107_D | 111_P | 1.409 | 0.98 |
| 183_L | 190_T | 1.406 | 0.98 |
| 72_G | 78_D | 1.382 | 0.98 |
| 81_L | 87_G | 1.348 | 0.98 |
| 197_Y | 202_F | 1.334 | 0.98 |
| 12_S | 163_I | 1.313 | 0.97 |
| 13_F | 102_L | 1.293 | 0.97 |
| 83_L | 89_F | 1.286 | 0.97 |
| 183_L | 188_F | 1.270 | 0.96 |
| 64_Q | 67_K | 1.258 | 0.96 |
| 92_L | 122_F | 1.257 | 0.96 |
| 222_T | 231_G | 1.250 | 0.96 |
| 4_F | 7_I | 1.229 | 0.96 |
| 186_H | 190_T | 1.229 | 0.96 |
| 152_T | 155_T | 1.226 | 0.95 |
| 81_L | 85_E | 1.224 | 0.95 |
| 165_R | 173_F | 1.214 | 0.95 |
| 81_L | 86_H | 1.213 | 0.95 |
| 9_L | 120_F | 1.212 | 0.95 |
| 77_A | 83_L | 1.206 | 0.95 |
| 181_R | 189_Y | 1.199 | 0.95 |
| 7_I | 10_H | 1.192 | 0.94 |
| 14_G | 23_L | 1.187 | 0.94 |
| 214_R | 217_N | 1.186 | 0.94 |
| 78_D | 81_L | 1.182 | 0.94 |
| 14_G | 71_R | 1.179 | 0.94 |
| 118_Y | 175_P | 1.177 | 0.94 |
| 17_F | 23_L | 1.175 | 0.94 |
| 169_T | 172_T | 1.174 | 0.94 |
| 181_R | 185_I | 1.171 | 0.94 |
| 7_I | 11_A | 1.170 | 0.94 |
| 132_L | 136_L | 1.162 | 0.93 |
| 24_P | 28_F | 1.146 | 0.93 |
| 156_A | 164_I | 1.142 | 0.93 |
| 85_E | 89_F | 1.134 | 0.92 |
| 9_L | 100_V | 1.134 | 0.92 |
| 91_A | 118_Y | 1.133 | 0.92 |
| 71_R | 78_D | 1.131 | 0.92 |
| 81_L | 97_L | 1.130 | 0.92 |
| 224_S | 231_G | 1.113 | 0.91 |
| 6_Q | 93_E | 1.112 | 0.91 |
| 77_A | 80_V | 1.103 | 0.91 |
| 9_L | 24_P | 1.102 | 0.91 |
| 65_P | 71_R | 1.100 | 0.91 |
| 20_R | 174_L | 1.095 | 0.91 |
| 6_Q | 84_L | 1.091 | 0.90 |
| 188_F | 191_Q | 1.090 | 0.90 |
| 132_L | 135_G | 1.090 | 0.90 |
| 74_N | 78_D | 1.090 | 0.90 |
| 133_K | 136_L | 1.088 | 0.90 |
| 213_P | 217_N | 1.086 | 0.90 |
| 183_L | 189_Y | 1.081 | 0.90 |
| 19_L | 172_T | 1.079 | 0.90 |
| 225_C | 228_M | 1.076 | 0.89 |
| 23_L | 33_L | 1.070 | 0.89 |
| 7_I | 33_L | 1.070 | 0.89 |
| 89_F | 93_E | 1.068 | 0.89 |
| 74_N | 77_A | 1.067 | 0.89 |
| 79_S | 86_H | 1.058 | 0.88 |
| 197_Y | 200_R | 1.054 | 0.88 |
| 20_R | 28_F | 1.052 | 0.88 |
| 219_K | 227_I | 1.050 | 0.88 |
| 11_A | 64_Q | 1.049 | 0.88 |
| 83_L | 185_I | 1.048 | 0.88 |
| 185_I | 189_Y | 1.046 | 0.88 |
| 187_L | 190_T | 1.037 | 0.87 |
| 118_Y | 166_R | 1.028 | 0.86 |
| 71_R | 82_N | 1.027 | 0.86 |
| 166_R | 171_S | 1.026 | 0.86 |
| 167_L | 175_P | 1.019 | 0.86 |
| 189_Y | 198_E | 1.018 | 0.86 |
| 134_K | 138_A | 1.013 | 0.85 |
| 97_L | 124_Y | 1.011 | 0.85 |
| 66_L | 167_L | 1.010 | 0.85 |
| 12_S | 120_F | 1.008 | 0.85 |
| 136_L | 139_V | 1.006 | 0.85 |
| 69_I | 73_R | 1.002 | 0.84 |
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 | |
| 4trkA | 1 | 0.824 | 100 | 0.243 | Contact Map |
| 4tzmA | 2 | 0.8069 | 100 | 0.252 | Contact Map |
| 3abdA | 2 | 0.7382 | 100 | 0.382 | Contact Map |
| 2vfxA | 12 | 0.7554 | 100 | 0.387 | Contact Map |
| 4aezB | 3 | 0.7296 | 100 | 0.402 | Contact Map |
| 4wzgA | 1 | 0 | 87.4 | 0.907 | Contact Map |
| 4yk8A | 1 | 0 | 81.4 | 0.914 | Contact Map |
| 2qyfB | 2 | 0.6738 | 79.7 | 0.916 | Contact Map |
| 4yk8B | 1 | 0 | 59.6 | 0.927 | Contact Map |
| 4j2gA | 2 | 0.6223 | 20.2 | 0.944 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)