| 1ORQ |
| ID: | 1461695027 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 223 (214) | ||
| Sequences: | 6073 (4082) | ||
| Seq/Len: | 28.379 | ||
| Nf(neff/√len): | 279.0 |
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: 28.379).
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 |
| 53_W | 84_G | 3.304 | 1.00 |
| 175_V | 200_M | 2.721 | 1.00 |
| 145_L | 149_F | 2.414 | 1.00 |
| 176_T | 182_Y | 2.332 | 1.00 |
| 79_A | 82_P | 2.142 | 1.00 |
| 154_V | 195_I | 2.139 | 1.00 |
| 43_L | 47_I | 2.102 | 1.00 |
| 168_D | 193_K | 2.085 | 1.00 |
| 60_A | 66_P | 2.081 | 1.00 |
| 56_Y | 77_I | 2.077 | 1.00 |
| 189_T | 192_G | 2.056 | 1.00 |
| 70_V | 73_T | 2.020 | 1.00 |
| 69_Y | 73_T | 1.782 | 1.00 |
| 67_A | 71_K | 1.766 | 1.00 |
| 152_Y | 165_S | 1.766 | 1.00 |
| 212_G | 215_S | 1.727 | 1.00 |
| 10_V | 55_D | 1.694 | 1.00 |
| 46_L | 50_I | 1.624 | 1.00 |
| 179_T | 183_G | 1.616 | 1.00 |
| 21_S | 48_L | 1.570 | 1.00 |
| 53_W | 80_L | 1.561 | 1.00 |
| 74_L | 78_P | 1.549 | 1.00 |
| 180_V | 183_G | 1.544 | 1.00 |
| 165_S | 168_D | 1.541 | 1.00 |
| 150_A | 195_I | 1.536 | 1.00 |
| 40_R | 43_L | 1.514 | 1.00 |
| 56_Y | 73_T | 1.497 | 1.00 |
| 21_S | 25_V | 1.461 | 1.00 |
| 56_Y | 70_V | 1.458 | 1.00 |
| 100_R | 103_R | 1.457 | 1.00 |
| 144_V | 148_A | 1.439 | 1.00 |
| 61_Y | 66_P | 1.420 | 1.00 |
| 60_A | 70_V | 1.409 | 1.00 |
| 55_D | 59_R | 1.409 | 1.00 |
| 56_Y | 80_L | 1.406 | 0.99 |
| 179_T | 184_D | 1.346 | 0.99 |
| 17_A | 48_L | 1.339 | 0.99 |
| 57_A | 61_Y | 1.305 | 0.99 |
| 26_V | 30_T | 1.296 | 0.99 |
| 40_R | 44_V | 1.293 | 0.99 |
| 181_G | 184_D | 1.283 | 0.99 |
| 172_W | 176_T | 1.279 | 0.99 |
| 11_E | 14_V | 1.278 | 0.99 |
| 178_T | 200_M | 1.271 | 0.99 |
| 179_T | 182_Y | 1.267 | 0.99 |
| 12_L | 16_Y | 1.261 | 0.99 |
| 60_A | 73_T | 1.256 | 0.99 |
| 109_R | 113_I | 1.250 | 0.99 |
| 50_I | 54_A | 1.249 | 0.99 |
| 46_L | 49_V | 1.235 | 0.98 |
| 164_K | 168_D | 1.235 | 0.98 |
| 160_N | 164_K | 1.226 | 0.98 |
| 76_E | 109_R | 1.220 | 0.98 |
| 176_T | 183_G | 1.218 | 0.98 |
| 39_V | 43_L | 1.216 | 0.98 |
| 13_G | 17_A | 1.215 | 0.98 |
| 172_W | 196_G | 1.209 | 0.98 |
| 145_L | 166_V | 1.206 | 0.98 |
| 146_Y | 149_F | 1.206 | 0.98 |
| 175_V | 182_Y | 1.203 | 0.98 |
| 49_V | 53_W | 1.203 | 0.98 |
| 103_R | 106_R | 1.202 | 0.98 |
| 166_V | 170_L | 1.196 | 0.98 |
| 154_V | 191_I | 1.193 | 0.98 |
| 10_V | 14_V | 1.192 | 0.98 |
| 18_A | 21_S | 1.192 | 0.98 |
| 190_P | 193_K | 1.190 | 0.98 |
| 176_T | 184_D | 1.190 | 0.98 |
| 196_G | 200_M | 1.184 | 0.98 |
| 213_T | 217_M | 1.180 | 0.98 |
| 187_P | 196_G | 1.167 | 0.97 |
| 59_R | 69_Y | 1.156 | 0.97 |
| 56_Y | 60_A | 1.153 | 0.97 |
| 71_K | 74_L | 1.152 | 0.97 |
| 14_V | 51_I | 1.145 | 0.97 |
| 20_L | 48_L | 1.145 | 0.97 |
| 23_I | 26_V | 1.144 | 0.97 |
| 47_I | 51_I | 1.141 | 0.97 |
| 43_L | 46_L | 1.134 | 0.97 |
| 183_G | 187_P | 1.131 | 0.97 |
| 34_S | 37_Y | 1.130 | 0.97 |
| 77_I | 81_V | 1.127 | 0.97 |
| 180_V | 200_M | 1.125 | 0.97 |
| 147_G | 199_V | 1.125 | 0.97 |
| 17_A | 51_I | 1.124 | 0.97 |
| 119_K | 122_S | 1.124 | 0.97 |
| 161_S | 164_K | 1.118 | 0.96 |
| 176_T | 181_G | 1.110 | 0.96 |
| 176_T | 180_V | 1.106 | 0.96 |
| 39_V | 42_Y | 1.104 | 0.96 |
| 171_W | 183_G | 1.102 | 0.96 |
| 42_Y | 46_L | 1.088 | 0.96 |
| 171_W | 185_V | 1.084 | 0.96 |
| 44_V | 48_L | 1.083 | 0.96 |
| 171_W | 184_D | 1.082 | 0.96 |
| 207_L | 211_I | 1.078 | 0.95 |
| 208_T | 212_G | 1.066 | 0.95 |
| 96_L | 100_R | 1.060 | 0.95 |
| 151_I | 155_E | 1.059 | 0.95 |
| 16_Y | 20_L | 1.057 | 0.95 |
| 142_L | 149_F | 1.057 | 0.95 |
| 47_I | 50_I | 1.055 | 0.95 |
| 175_V | 184_D | 1.052 | 0.95 |
| 94_A | 97_G | 1.049 | 0.94 |
| 68_G | 71_K | 1.028 | 0.94 |
| 171_W | 179_T | 1.026 | 0.94 |
| 208_T | 211_I | 1.025 | 0.93 |
| 178_T | 181_G | 1.025 | 0.93 |
| 123_A | 127_A | 1.022 | 0.93 |
| 176_T | 179_T | 1.020 | 0.93 |
| 175_V | 179_T | 1.017 | 0.93 |
| 158_D | 189_T | 1.013 | 0.93 |
| 34_S | 38_L | 1.009 | 0.93 |
| 149_F | 166_V | 1.007 | 0.93 |
| 155_E | 171_W | 1.006 | 0.93 |
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 | |
| 1orqC | 1 | 0.9955 | 100 | 0.153 | Contact Map |
| 2r9rB | 2 | 0.991 | 100 | 0.293 | Contact Map |
| 4bgnA | 2 | 0.9013 | 100 | 0.312 | Contact Map |
| 3behA | 4 | 0.9507 | 99.9 | 0.34 | Contact Map |
| 3rvyA | 2 | 0.9372 | 99.9 | 0.377 | Contact Map |
| 4dxwA | 4 | 0.9552 | 99.8 | 0.461 | Contact Map |
| 2ih3C | 1 | 0.426 | 99.7 | 0.524 | Contact Map |
| 2a9hA | 4 | 0.435 | 99.7 | 0.533 | Contact Map |
| 3pjsK | 4 | 0.4395 | 99.6 | 0.58 | Contact Map |
| 3effK | 4 | 0.4395 | 99.5 | 0.61 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)