| 3OOD |
| ID: | 1486992730 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 301 (289) | ||
| Sequences: | 1095 (801.9) | ||
| Seq/Len: | 3.789 | ||
| Nf(neff/√len): | 47.2 |
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: 3.789).
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 |
| 172_G | 184_V | 3.773 | 1.00 |
| 165_G | 186_T | 3.725 | 1.00 |
| 120_C | 123_C | 3.562 | 1.00 |
| 265_C | 273_C | 3.228 | 1.00 |
| 94_V | 97_D | 2.716 | 1.00 |
| 166_A | 192_V | 2.525 | 1.00 |
| 76_H | 154_Y | 2.508 | 1.00 |
| 189_Q | 244_C | 2.474 | 1.00 |
| 169_L | 189_Q | 2.412 | 1.00 |
| 133_Y | 174_N | 2.273 | 1.00 |
| 169_L | 197_F | 2.180 | 1.00 |
| 85_I | 171_F | 2.119 | 1.00 |
| 195_A | 199_N | 2.076 | 1.00 |
| 81_I | 148_I | 2.039 | 1.00 |
| 231_I | 285_V | 2.003 | 1.00 |
| 79_K | 153_D | 1.920 | 1.00 |
| 199_N | 268_Q | 1.909 | 1.00 |
| 186_T | 224_R | 1.895 | 1.00 |
| 72_L | 143_K | 1.889 | 1.00 |
| 88_T | 94_V | 1.872 | 1.00 |
| 137_Y | 174_N | 1.866 | 1.00 |
| 129_F | 190_P | 1.838 | 1.00 |
| 125_V | 170_L | 1.828 | 1.00 |
| 104_P | 124_L | 1.792 | 0.99 |
| 71_Y | 84_V | 1.765 | 0.99 |
| 286_I | 290_L | 1.756 | 0.99 |
| 21_Y | 80_Q | 1.720 | 0.99 |
| 86_R | 93_D | 1.715 | 0.99 |
| 103_A | 127_N | 1.696 | 0.99 |
| 79_K | 154_Y | 1.647 | 0.99 |
| 72_L | 83_L | 1.645 | 0.99 |
| 29_Y | 87_G | 1.640 | 0.99 |
| 18_F | 225_I | 1.637 | 0.99 |
| 202_D | 245_S | 1.630 | 0.99 |
| 21_Y | 187_L | 1.622 | 0.99 |
| 169_L | 201_V | 1.619 | 0.99 |
| 165_G | 189_Q | 1.603 | 0.98 |
| 169_L | 192_V | 1.575 | 0.98 |
| 52_N | 75_D | 1.568 | 0.98 |
| 133_Y | 167_A | 1.562 | 0.98 |
| 24_L | 53_V | 1.552 | 0.98 |
| 25_A | 159_T | 1.551 | 0.98 |
| 59_F | 70_G | 1.547 | 0.98 |
| 56_I | 147_V | 1.524 | 0.98 |
| 156_I | 182_P | 1.519 | 0.98 |
| 30_C | 43_C | 1.506 | 0.97 |
| 193_G | 197_F | 1.488 | 0.97 |
| 75_D | 78_S | 1.475 | 0.97 |
| 88_T | 97_D | 1.448 | 0.96 |
| 99_R | 127_N | 1.445 | 0.96 |
| 28_G | 84_V | 1.445 | 0.96 |
| 72_L | 144_L | 1.437 | 0.96 |
| 156_I | 180_H | 1.432 | 0.96 |
| 249_F | 276_G | 1.417 | 0.96 |
| 55_L | 58_E | 1.412 | 0.96 |
| 15_Y | 18_F | 1.395 | 0.95 |
| 80_Q | 157_A | 1.386 | 0.95 |
| 43_C | 47_C | 1.374 | 0.95 |
| 24_L | 75_D | 1.372 | 0.95 |
| 54_E | 151_Y | 1.371 | 0.95 |
| 166_A | 190_P | 1.362 | 0.94 |
| 99_R | 241_Y | 1.356 | 0.94 |
| 102_Q | 241_Y | 1.354 | 0.94 |
| 148_I | 180_H | 1.347 | 0.94 |
| 173_I | 201_V | 1.342 | 0.94 |
| 73_A | 298_V | 1.333 | 0.94 |
| 146_S | 150_Q | 1.329 | 0.94 |
| 137_Y | 141_G | 1.325 | 0.93 |
| 229_G | 288_N | 1.325 | 0.93 |
| 234_Q | 274_S | 1.311 | 0.93 |
| 81_I | 156_I | 1.309 | 0.93 |
| 289_H | 299_C | 1.307 | 0.93 |
| 12_Q | 16_N | 1.307 | 0.93 |
| 94_V | 98_I | 1.301 | 0.93 |
| 245_S | 268_Q | 1.298 | 0.92 |
| 129_F | 166_A | 1.295 | 0.92 |
| 21_Y | 157_A | 1.281 | 0.92 |
| 136_T | 140_I | 1.274 | 0.91 |
| 28_G | 71_Y | 1.270 | 0.91 |
| 67_D | 90_S | 1.265 | 0.91 |
| 287_G | 290_L | 1.262 | 0.91 |
| 119_T | 123_C | 1.261 | 0.91 |
| 52_N | 77_A | 1.251 | 0.90 |
| 110_L | 116_S | 1.247 | 0.90 |
| 202_D | 222_L | 1.242 | 0.90 |
| 136_T | 250_I | 1.237 | 0.90 |
| 184_V | 222_L | 1.236 | 0.90 |
| 80_Q | 155_Q | 1.229 | 0.89 |
| 99_R | 131_Q | 1.220 | 0.89 |
| 195_A | 242_Q | 1.211 | 0.89 |
| 223_Y | 248_V | 1.210 | 0.88 |
| 102_Q | 124_L | 1.197 | 0.88 |
| 158_V | 172_G | 1.196 | 0.88 |
| 10_I | 14_S | 1.188 | 0.87 |
| 123_C | 200_W | 1.186 | 0.87 |
| 145_D | 149_E | 1.183 | 0.87 |
| 11_D | 14_S | 1.180 | 0.87 |
| 155_Q | 183_L | 1.179 | 0.87 |
| 97_D | 163_L | 1.154 | 0.85 |
| 88_T | 162_S | 1.149 | 0.85 |
| 125_V | 130_I | 1.147 | 0.85 |
| 54_E | 76_H | 1.143 | 0.84 |
| 57_E | 143_K | 1.138 | 0.84 |
| 145_D | 155_Q | 1.137 | 0.84 |
| 158_V | 168_A | 1.131 | 0.83 |
| 25_A | 28_G | 1.128 | 0.83 |
| 94_V | 232_V | 1.126 | 0.83 |
| 74_V | 154_Y | 1.124 | 0.83 |
| 192_V | 197_F | 1.116 | 0.82 |
| 226_T | 245_S | 1.116 | 0.82 |
| 188_G | 193_G | 1.113 | 0.82 |
| 61_D | 135_N | 1.109 | 0.82 |
| 188_G | 191_I | 1.106 | 0.82 |
| 195_A | 268_Q | 1.104 | 0.81 |
| 116_S | 217_S | 1.098 | 0.81 |
| 126_H | 129_F | 1.091 | 0.80 |
| 222_L | 244_C | 1.087 | 0.80 |
| 246_G | 267_G | 1.086 | 0.80 |
| 186_T | 189_Q | 1.082 | 0.80 |
| 122_D | 196_G | 1.071 | 0.79 |
| 143_K | 147_V | 1.063 | 0.78 |
| 95_I | 99_R | 1.061 | 0.78 |
| 168_A | 186_T | 1.057 | 0.77 |
| 76_H | 151_Y | 1.057 | 0.77 |
| 119_T | 200_W | 1.051 | 0.77 |
| 22_A | 187_L | 1.049 | 0.77 |
| 68_V | 132_S | 1.048 | 0.76 |
| 47_C | 289_H | 1.047 | 0.76 |
| 263_V | 272_Q | 1.043 | 0.76 |
| 105_L | 126_H | 1.040 | 0.76 |
| 56_I | 151_Y | 1.038 | 0.75 |
| 271_K | 274_S | 1.036 | 0.75 |
| 202_D | 268_Q | 1.030 | 0.75 |
| 197_F | 201_V | 1.029 | 0.75 |
| 234_Q | 275_A | 1.029 | 0.75 |
| 224_R | 289_H | 1.026 | 0.74 |
| 130_I | 134_N | 1.025 | 0.74 |
| 169_L | 244_C | 1.023 | 0.74 |
| 19_E | 293_F | 1.020 | 0.74 |
| 285_V | 288_N | 1.020 | 0.74 |
| 97_D | 162_S | 1.015 | 0.73 |
| 158_V | 175_L | 1.011 | 0.73 |
| 85_I | 136_T | 1.005 | 0.72 |
| 202_D | 246_G | 1.003 | 0.72 |
| 172_G | 182_P | 1.001 | 0.72 |
| 285_V | 289_H | 1.001 | 0.72 |
| 53_V | 73_A | 1.001 | 0.72 |
| 13_E | 16_N | 1.001 | 0.72 |
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 | |
| 3o0dA | 7 | 1 | 100 | 0.215 | Contact Map |
| 3ngmA | 4 | 0.8671 | 100 | 0.287 | Contact Map |
| 1tiaA | 1 | 0.8771 | 100 | 0.292 | Contact Map |
| 1tibA | 1 | 0.8738 | 100 | 0.304 | Contact Map |
| 4l3wA | 1 | 0.8505 | 100 | 0.307 | Contact Map |
| 3g7nA | 2 | 0.8272 | 100 | 0.322 | Contact Map |
| 1uwcA | 2 | 0.8538 | 100 | 0.323 | Contact Map |
| 1tglA | 1 | 0.8538 | 100 | 0.365 | Contact Map |
| 3uueA | 1 | 0.8571 | 100 | 0.366 | Contact Map |
| 2yijA | 2 | 0.8605 | 100 | 0.46 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)