| Soj dimer |
| ID: | 1430396061 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 253 (252) | ||
| Sequences: | 10107 (6770.4) | ||
| Seq/Len: | 40.107 | ||
| Nf(neff/√len): | 426.5 |
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: 40.107).
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 |
| 20_S | 123_I | 4.736 | 1.00 |
| 83_D | 119_Y | 4.123 | 1.00 |
| 214_P | 241_V | 3.909 | 1.00 |
| 6_A | 141_S | 3.488 | 1.00 |
| 27_L | 121_Y | 3.332 | 1.00 |
| 19_T | 242_Y | 3.311 | 1.00 |
| 30_I | 247_K | 3.059 | 1.00 |
| 32_K | 121_Y | 3.026 | 1.00 |
| 35_L | 119_Y | 2.921 | 1.00 |
| 228_P | 231_L | 2.869 | 1.00 |
| 149_Q | 185_M | 2.680 | 1.00 |
| 185_M | 215_R | 2.611 | 1.00 |
| 36_L | 45_A | 2.582 | 1.00 |
| 3_K | 143_S | 2.482 | 1.00 |
| 20_S | 36_L | 2.482 | 1.00 |
| 29_Y | 243_L | 2.421 | 1.00 |
| 7_I | 23_L | 2.420 | 1.00 |
| 21_V | 45_A | 2.418 | 1.00 |
| 26_C | 246_A | 2.178 | 1.00 |
| 33_R | 120_D | 2.132 | 1.00 |
| 19_T | 182_L | 2.106 | 1.00 |
| 24_G | 36_L | 2.078 | 1.00 |
| 198_E | 202_K | 2.032 | 1.00 |
| 218_R | 221_E | 1.944 | 1.00 |
| 211_T | 248_E | 1.939 | 1.00 |
| 27_L | 123_I | 1.874 | 1.00 |
| 6_A | 126_C | 1.872 | 1.00 |
| 47_S | 156_E | 1.861 | 1.00 |
| 182_L | 245_L | 1.853 | 1.00 |
| 26_C | 230_I | 1.841 | 1.00 |
| 48_G | 153_Y | 1.820 | 1.00 |
| 187_D | 215_R | 1.808 | 1.00 |
| 32_K | 120_D | 1.787 | 1.00 |
| 4_I | 124_I | 1.760 | 1.00 |
| 7_I | 145_V | 1.758 | 1.00 |
| 19_T | 184_T | 1.729 | 1.00 |
| 24_G | 123_I | 1.720 | 1.00 |
| 30_I | 243_L | 1.697 | 1.00 |
| 236_S | 239_A | 1.669 | 1.00 |
| 21_V | 48_G | 1.644 | 1.00 |
| 23_L | 246_A | 1.610 | 1.00 |
| 183_L | 197_I | 1.601 | 1.00 |
| 24_G | 45_A | 1.565 | 1.00 |
| 210_K | 248_E | 1.553 | 1.00 |
| 7_I | 20_S | 1.542 | 1.00 |
| 216_N | 238_G | 1.477 | 1.00 |
| 23_L | 249_V | 1.477 | 1.00 |
| 211_T | 245_L | 1.473 | 1.00 |
| 151_E | 154_A | 1.462 | 1.00 |
| 143_S | 179_E | 1.459 | 1.00 |
| 240_E | 243_L | 1.450 | 1.00 |
| 15_G | 184_T | 1.450 | 1.00 |
| 76_A | 83_D | 1.431 | 1.00 |
| 49_L | 82_L | 1.419 | 1.00 |
| 28_A | 82_L | 1.406 | 0.99 |
| 71_I | 118_N | 1.404 | 0.99 |
| 44_N | 153_Y | 1.404 | 0.99 |
| 21_V | 49_L | 1.403 | 0.99 |
| 153_Y | 223_P | 1.402 | 0.99 |
| 59_C | 62_D | 1.389 | 0.99 |
| 186_L | 212_V | 1.376 | 0.99 |
| 28_A | 81_N | 1.374 | 0.99 |
| 27_L | 246_A | 1.371 | 0.99 |
| 221_E | 225_H | 1.362 | 0.99 |
| 39_I | 137_A | 1.350 | 0.99 |
| 39_I | 124_I | 1.327 | 0.99 |
| 233_D | 236_S | 1.326 | 0.99 |
| 3_K | 142_D | 1.324 | 0.99 |
| 35_L | 122_I | 1.316 | 0.99 |
| 147_P | 184_T | 1.272 | 0.99 |
| 197_I | 201_K | 1.269 | 0.99 |
| 32_K | 250_A | 1.266 | 0.99 |
| 150_C | 183_L | 1.240 | 0.98 |
| 30_I | 250_A | 1.233 | 0.98 |
| 234_P | 239_A | 1.233 | 0.98 |
| 37_V | 122_I | 1.227 | 0.98 |
| 17_T | 48_G | 1.219 | 0.98 |
| 8_T | 126_C | 1.217 | 0.98 |
| 227_K | 231_L | 1.214 | 0.98 |
| 69_D | 72_D | 1.199 | 0.98 |
| 149_Q | 154_A | 1.197 | 0.98 |
| 19_T | 23_L | 1.192 | 0.98 |
| 143_S | 180_G | 1.182 | 0.98 |
| 49_L | 84_V | 1.177 | 0.98 |
| 199_E | 203_Y | 1.177 | 0.98 |
| 163_N | 166_R | 1.174 | 0.98 |
| 51_I | 84_V | 1.173 | 0.98 |
| 70_V | 85_I | 1.172 | 0.98 |
| 27_L | 34_V | 1.171 | 0.98 |
| 144_V | 165_V | 1.163 | 0.97 |
| 4_I | 122_I | 1.140 | 0.97 |
| 24_G | 82_L | 1.125 | 0.97 |
| 145_V | 182_L | 1.117 | 0.96 |
| 2_G | 122_I | 1.114 | 0.96 |
| 7_I | 123_I | 1.112 | 0.96 |
| 219_L | 238_G | 1.112 | 0.96 |
| 218_R | 233_D | 1.111 | 0.96 |
| 18_T | 219_L | 1.107 | 0.96 |
| 33_R | 118_N | 1.106 | 0.96 |
| 83_D | 117_Q | 1.099 | 0.96 |
| 7_I | 19_T | 1.093 | 0.96 |
| 26_C | 243_L | 1.092 | 0.96 |
| 244_D | 248_E | 1.091 | 0.96 |
| 109_K | 113_E | 1.082 | 0.96 |
| 190_T | 193_G | 1.078 | 0.95 |
| 44_N | 157_G | 1.075 | 0.95 |
| 237_R | 240_E | 1.074 | 0.95 |
| 197_I | 212_V | 1.072 | 0.95 |
| 244_D | 247_K | 1.071 | 0.95 |
| 17_T | 45_A | 1.071 | 0.95 |
| 173_N | 176_L | 1.066 | 0.95 |
| 184_T | 242_Y | 1.065 | 0.95 |
| 39_I | 60_V | 1.064 | 0.95 |
| 19_T | 147_P | 1.061 | 0.95 |
| 113_E | 116_K | 1.050 | 0.94 |
| 5_I | 121_Y | 1.050 | 0.94 |
| 247_K | 251_A | 1.047 | 0.94 |
| 199_E | 202_K | 1.045 | 0.94 |
| 119_Y | 122_I | 1.043 | 0.94 |
| 34_V | 120_D | 1.042 | 0.94 |
| 25_A | 29_Y | 1.041 | 0.94 |
| 151_E | 220_S | 1.039 | 0.94 |
| 245_L | 249_V | 1.028 | 0.94 |
| 183_L | 186_L | 1.027 | 0.94 |
| 121_Y | 250_A | 1.019 | 0.93 |
| 2_G | 116_K | 1.018 | 0.93 |
| 22_N | 25_A | 1.017 | 0.93 |
| 198_E | 212_V | 1.014 | 0.93 |
| 213_I | 238_G | 1.013 | 0.93 |
| 216_N | 236_S | 1.012 | 0.93 |
| 22_N | 230_I | 1.002 | 0.92 |
| 8_T | 161_L | 1.000 | 0.92 |
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 | |
| 4pfsA | 2 | 0.9289 | 100 | 0.179 | Contact Map |
| 1wcv1 | 1 | 0.9565 | 100 | 0.216 | Contact Map |
| 3pg5A | 4 | 0.8893 | 100 | 0.238 | Contact Map |
| 1g3qA | 1 | 0.9328 | 100 | 0.242 | Contact Map |
| 1hyqA | 1 | 0.913 | 100 | 0.248 | Contact Map |
| 3ez2A | 2 | 0.9881 | 100 | 0.266 | Contact Map |
| 3q9lA | 2 | 0.9565 | 100 | 0.267 | Contact Map |
| 4v03A | 2 | 0.8972 | 100 | 0.267 | Contact Map |
| 3ea0A | 2 | 0.9249 | 100 | 0.268 | Contact Map |
| 3ez9A | 2 | 0.8379 | 100 | 0.27 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)