| 220930_soal4b_rrepeppre_fused_320_50-50 |
| ID: | 1666470713 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 50% gaps before running GREMLIN. |
| Length: | 268 (244) | ||
| Sequences: | 1102 (950.8) | ||
| Seq/Len: | 4.516 | ||
| Nf(neff/√len): | 60.9 |
HHblits Results: (2016_02)
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 |
| 34_D | 243_S | 3.227 | 1.00 |
| 203_Q | 206_S | 3.109 | 1.00 |
| 189_F | 200_C | 2.796 | 1.00 |
| 158_R | 170_D | 2.545 | 1.00 |
| 21_R | 26_A | 2.293 | 1.00 |
| 208_V | 211_D | 2.230 | 1.00 |
| 211_D | 215_K | 2.221 | 1.00 |
| 211_D | 216_V | 2.203 | 1.00 |
| 174_Y | 178_A | 2.149 | 1.00 |
| 35_R | 238_D | 2.118 | 1.00 |
| 162_P | 165_P | 2.074 | 1.00 |
| 31_V | 132_L | 2.072 | 1.00 |
| 14_A | 17_V | 2.048 | 1.00 |
| 34_D | 242_A | 1.952 | 1.00 |
| 175_A | 185_V | 1.917 | 1.00 |
| 171_A | 210_T | 1.895 | 1.00 |
| 150_H | 178_A | 1.888 | 1.00 |
| 203_Q | 221_V | 1.816 | 1.00 |
| 16_G | 32_R | 1.795 | 1.00 |
| 127_P | 131_V | 1.794 | 1.00 |
| 179_R | 184_A | 1.764 | 1.00 |
| 27_V | 191_V | 1.741 | 1.00 |
| 36_Y | 198_A | 1.735 | 0.99 |
| 150_H | 177_V | 1.733 | 0.99 |
| 171_A | 202_V | 1.731 | 0.99 |
| 175_A | 187_L | 1.726 | 0.99 |
| 20_A | 222_V | 1.722 | 0.99 |
| 31_V | 128_L | 1.715 | 0.99 |
| 17_V | 71_L | 1.693 | 0.99 |
| 208_V | 216_V | 1.693 | 0.99 |
| 178_A | 185_V | 1.686 | 0.99 |
| 19_V | 28_V | 1.666 | 0.99 |
| 175_A | 202_V | 1.637 | 0.99 |
| 123_L | 172_L | 1.604 | 0.99 |
| 135_L | 175_A | 1.580 | 0.99 |
| 191_V | 222_V | 1.571 | 0.99 |
| 18_G | 223_L | 1.571 | 0.99 |
| 165_P | 170_D | 1.568 | 0.99 |
| 186_D | 224_A | 1.544 | 0.99 |
| 36_Y | 196_F | 1.528 | 0.98 |
| 64_R | 68_R | 1.522 | 0.98 |
| 34_D | 241_T | 1.513 | 0.98 |
| 22_I | 193_L | 1.509 | 0.98 |
| 197_E | 219_F | 1.502 | 0.98 |
| 25_K | 193_L | 1.479 | 0.98 |
| 27_V | 193_L | 1.477 | 0.98 |
| 174_Y | 209_L | 1.474 | 0.98 |
| 151_A | 174_Y | 1.471 | 0.98 |
| 153_A | 177_V | 1.459 | 0.98 |
| 20_A | 220_E | 1.424 | 0.97 |
| 92_T | 206_S | 1.423 | 0.97 |
| 69_N | 72_L | 1.421 | 0.97 |
| 183_F | 204_S | 1.399 | 0.97 |
| 192_K | 197_E | 1.390 | 0.97 |
| 21_R | 48_L | 1.373 | 0.96 |
| 203_Q | 224_A | 1.345 | 0.96 |
| 162_P | 170_D | 1.341 | 0.96 |
| 238_D | 241_T | 1.338 | 0.96 |
| 93_A | 206_S | 1.335 | 0.95 |
| 122_D | 176_R | 1.334 | 0.95 |
| 241_T | 244_I | 1.309 | 0.95 |
| 166_R | 169_P | 1.292 | 0.94 |
| 28_V | 47_L | 1.289 | 0.94 |
| 169_P | 202_V | 1.251 | 0.93 |
| 147_L | 183_F | 1.238 | 0.92 |
| 36_Y | 246_T | 1.233 | 0.92 |
| 111_A | 181_E | 1.227 | 0.92 |
| 241_T | 248_G | 1.211 | 0.91 |
| 25_K | 38_M | 1.195 | 0.91 |
| 93_A | 96_V | 1.179 | 0.90 |
| 12_R | 15_A | 1.174 | 0.90 |
| 38_M | 187_L | 1.160 | 0.89 |
| 159_R | 193_L | 1.160 | 0.89 |
| 128_L | 132_L | 1.140 | 0.88 |
| 154_F | 170_D | 1.133 | 0.87 |
| 175_A | 179_R | 1.121 | 0.86 |
| 122_D | 126_A | 1.121 | 0.86 |
| 168_L | 188_V | 1.120 | 0.86 |
| 186_D | 208_V | 1.115 | 0.86 |
| 158_R | 162_P | 1.104 | 0.85 |
| 74_K | 145_R | 1.102 | 0.85 |
| 17_V | 33_H | 1.097 | 0.85 |
| 263_P | 267_R | 1.094 | 0.85 |
| 150_H | 181_E | 1.083 | 0.84 |
| 70_G | 113_V | 1.080 | 0.84 |
| 13_I | 17_V | 1.066 | 0.82 |
| 21_R | 24_D | 1.061 | 0.82 |
| 14_A | 32_R | 1.060 | 0.82 |
| 208_V | 242_A | 1.060 | 0.82 |
| 39_W | 47_L | 1.057 | 0.82 |
| 211_D | 226_M | 1.057 | 0.82 |
| 143_T | 146_D | 1.055 | 0.82 |
| 18_G | 31_V | 1.053 | 0.81 |
| 123_L | 131_V | 1.051 | 0.81 |
| 188_V | 222_V | 1.048 | 0.81 |
| 71_L | 236_V | 1.046 | 0.81 |
| 192_K | 218_R | 1.046 | 0.81 |
| 203_Q | 208_V | 1.042 | 0.80 |
| 66_L | 71_L | 1.041 | 0.80 |
| 29_L | 242_A | 1.039 | 0.80 |
| 242_A | 246_T | 1.035 | 0.80 |
| 135_L | 187_L | 1.034 | 0.80 |
| 236_V | 259_L | 1.034 | 0.80 |
| 15_A | 146_D | 1.028 | 0.79 |
| 211_D | 214_D | 1.021 | 0.78 |
| 122_D | 171_A | 1.020 | 0.78 |
| 135_L | 179_R | 1.019 | 0.78 |
| 119_A | 123_L | 1.012 | 0.78 |
| 171_A | 178_A | 1.011 | 0.78 |
| 204_S | 209_L | 1.006 | 0.77 |
| 127_P | 130_Q | 1.004 | 0.77 |
| 188_V | 221_V | 1.004 | 0.77 |
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 | |
| 2hlyA | 1 | 0.4739 | 48.5 | 0.933 | Contact Map |
| 3g2bA | 1 | 0.3284 | 38.5 | 0.936 | Contact Map |
| 2f4mA | 1 | 0.7649 | 23.3 | 0.943 | Contact Map |
| 2q3zA | 1 | 0.8284 | 16.1 | 0.947 | Contact Map |
| 3isrA | 4 | 0.8433 | 14.6 | 0.948 | Contact Map |
| 1x3zA | 1 | 0.7612 | 13.5 | 0.949 | Contact Map |
| 4fgqA | 2 | 0.5485 | 11.5 | 0.95 | Contact Map |
| 4u65E | 2 | 0.5149 | 10.4 | 0.952 | Contact Map |
| 3l48A | 5 | 0.1978 | 1.7 | 0.967 | Contact Map |
| 1hx6A | 3 | 0.2239 | 1.6 | 0.967 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)