| T0774 -force run |
| ID: | 1399913328 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 379 (351) | ||
| Sequences: | 167 (134.4) | ||
| Seq/Len: | 0.476 | ||
| Nf(neff/√len): | 7.2 |
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: 0.476).
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 |
| 339_F | 347_Y | 2.795 | 0.98 |
| 61_G | 119_Y | 2.372 | 0.95 |
| 86_N | 116_Y | 2.297 | 0.93 |
| 189_T | 345_H | 1.990 | 0.84 |
| 9_V | 12_T | 1.869 | 0.79 |
| 61_G | 86_N | 1.862 | 0.78 |
| 60_F | 104_W | 1.859 | 0.78 |
| 163_D | 184_F | 1.847 | 0.78 |
| 215_L | 334_L | 1.713 | 0.70 |
| 114_F | 230_F | 1.704 | 0.69 |
| 148_V | 160_L | 1.615 | 0.63 |
| 197_K | 346_T | 1.613 | 0.63 |
| 36_L | 113_F | 1.613 | 0.63 |
| 86_N | 119_Y | 1.598 | 0.62 |
| 340_K | 343_T | 1.560 | 0.59 |
| 21_N | 355_A | 1.554 | 0.59 |
| 17_G | 43_Q | 1.553 | 0.59 |
| 142_P | 311_Y | 1.549 | 0.58 |
| 17_G | 234_T | 1.548 | 0.58 |
| 113_F | 290_F | 1.546 | 0.58 |
| 61_G | 117_A | 1.528 | 0.57 |
| 20_Q | 114_F | 1.510 | 0.55 |
| 15_I | 361_E | 1.484 | 0.54 |
| 17_G | 198_P | 1.475 | 0.53 |
| 196_V | 213_L | 1.464 | 0.52 |
| 14_T | 38_V | 1.454 | 0.51 |
| 61_G | 118_P | 1.451 | 0.51 |
| 4_K | 22_E | 1.435 | 0.50 |
| 104_W | 113_F | 1.431 | 0.50 |
| 62_I | 196_V | 1.411 | 0.48 |
| 28_P | 62_I | 1.410 | 0.48 |
| 67_T | 306_K | 1.406 | 0.48 |
| 34_I | 45_R | 1.394 | 0.47 |
| 115_A | 182_F | 1.387 | 0.46 |
| 21_N | 213_L | 1.386 | 0.46 |
| 21_N | 144_I | 1.383 | 0.46 |
| 182_F | 311_Y | 1.381 | 0.46 |
| 11_A | 22_E | 1.379 | 0.46 |
| 64_A | 84_M | 1.363 | 0.44 |
| 189_T | 291_I | 1.359 | 0.44 |
| 290_F | 311_Y | 1.354 | 0.44 |
| 61_G | 116_Y | 1.353 | 0.44 |
| 54_L | 240_P | 1.349 | 0.43 |
| 4_K | 14_T | 1.341 | 0.43 |
| 38_V | 161_V | 1.336 | 0.42 |
| 60_F | 235_W | 1.318 | 0.41 |
| 102_R | 289_Y | 1.307 | 0.40 |
| 184_F | 187_V | 1.294 | 0.39 |
| 235_W | 339_F | 1.288 | 0.39 |
| 176_N | 345_H | 1.288 | 0.39 |
| 310_N | 313_I | 1.283 | 0.38 |
| 44_T | 313_I | 1.280 | 0.38 |
| 190_Q | 344_K | 1.275 | 0.38 |
| 330_K | 334_L | 1.271 | 0.38 |
| 242_A | 349_L | 1.270 | 0.38 |
| 84_M | 142_P | 1.254 | 0.36 |
| 60_F | 184_F | 1.252 | 0.36 |
| 104_W | 235_W | 1.248 | 0.36 |
| 114_F | 345_H | 1.247 | 0.36 |
| 160_L | 235_W | 1.240 | 0.35 |
| 19_S | 40_T | 1.238 | 0.35 |
| 8_M | 60_F | 1.237 | 0.35 |
| 5_S | 13_L | 1.225 | 0.34 |
| 10_M | 206_T | 1.225 | 0.34 |
| 7_L | 26_M | 1.222 | 0.34 |
| 4_K | 21_N | 1.215 | 0.34 |
| 15_I | 57_N | 1.213 | 0.34 |
| 115_A | 329_N | 1.212 | 0.33 |
| 189_T | 343_T | 1.212 | 0.33 |
| 114_F | 162_T | 1.207 | 0.33 |
| 199_D | 348_V | 1.204 | 0.33 |
| 54_L | 241_D | 1.203 | 0.33 |
| 8_M | 16_A | 1.199 | 0.33 |
| 65_Y | 142_P | 1.196 | 0.32 |
| 184_F | 346_T | 1.194 | 0.32 |
| 113_F | 311_Y | 1.192 | 0.32 |
| 14_T | 21_N | 1.185 | 0.32 |
| 224_N | 339_F | 1.182 | 0.31 |
| 101_L | 280_A | 1.180 | 0.31 |
| 34_I | 349_L | 1.176 | 0.31 |
| 62_I | 89_A | 1.174 | 0.31 |
| 309_I | 360_V | 1.172 | 0.31 |
| 34_I | 67_T | 1.171 | 0.31 |
| 89_A | 210_V | 1.167 | 0.31 |
| 17_G | 37_D | 1.166 | 0.30 |
| 89_A | 98_Y | 1.163 | 0.30 |
| 187_V | 312_D | 1.161 | 0.30 |
| 54_L | 188_L | 1.157 | 0.30 |
| 41_E | 45_R | 1.155 | 0.30 |
| 113_F | 180_V | 1.153 | 0.30 |
| 230_F | 311_Y | 1.151 | 0.29 |
| 45_R | 281_L | 1.149 | 0.29 |
| 75_E | 369_D | 1.148 | 0.29 |
| 105_P | 111_I | 1.147 | 0.29 |
| 96_W | 115_A | 1.145 | 0.29 |
| 116_Y | 244_Y | 1.145 | 0.29 |
| 60_F | 162_T | 1.135 | 0.28 |
| 60_F | 89_A | 1.134 | 0.28 |
| 104_W | 162_T | 1.129 | 0.28 |
| 76_K | 144_I | 1.126 | 0.28 |
| 40_T | 114_F | 1.125 | 0.28 |
| 118_P | 161_V | 1.121 | 0.28 |
| 9_V | 13_L | 1.121 | 0.28 |
| 188_L | 339_F | 1.119 | 0.28 |
| 291_I | 307_L | 1.115 | 0.27 |
| 196_V | 309_I | 1.114 | 0.27 |
| 9_V | 108_D | 1.113 | 0.27 |
| 60_F | 293_V | 1.110 | 0.27 |
| 21_N | 117_A | 1.110 | 0.27 |
| 64_A | 111_I | 1.108 | 0.27 |
| 191_I | 203_G | 1.108 | 0.27 |
| 190_Q | 348_V | 1.108 | 0.27 |
| 10_M | 13_L | 1.107 | 0.27 |
| 21_N | 113_F | 1.104 | 0.27 |
| 103_F | 235_W | 1.102 | 0.26 |
| 28_P | 333_S | 1.099 | 0.26 |
| 176_N | 210_V | 1.095 | 0.26 |
| 5_S | 332_V | 1.093 | 0.26 |
| 226_A | 235_W | 1.092 | 0.26 |
| 64_A | 83_F | 1.092 | 0.26 |
| 90_T | 138_A | 1.088 | 0.26 |
| 133_L | 294_N | 1.087 | 0.26 |
| 114_F | 290_F | 1.086 | 0.26 |
| 13_L | 47_T | 1.083 | 0.25 |
| 62_I | 180_V | 1.082 | 0.25 |
| 289_Y | 349_L | 1.082 | 0.25 |
| 133_L | 225_K | 1.079 | 0.25 |
| 348_V | 360_V | 1.076 | 0.25 |
| 2_E | 347_Y | 1.076 | 0.25 |
| 36_L | 62_I | 1.075 | 0.25 |
| 84_M | 98_Y | 1.073 | 0.25 |
| 17_G | 121_S | 1.072 | 0.25 |
| 17_G | 304_D | 1.070 | 0.25 |
| 308_K | 333_S | 1.068 | 0.25 |
| 94_D | 351_I | 1.068 | 0.25 |
| 65_Y | 146_F | 1.067 | 0.24 |
| 190_Q | 350_T | 1.067 | 0.24 |
| 64_A | 150_T | 1.066 | 0.24 |
| 84_M | 105_P | 1.065 | 0.24 |
| 10_M | 64_A | 1.064 | 0.24 |
| 182_F | 289_Y | 1.060 | 0.24 |
| 10_M | 14_T | 1.057 | 0.24 |
| 67_T | 84_M | 1.052 | 0.24 |
| 17_G | 25_E | 1.052 | 0.24 |
| 116_Y | 251_L | 1.051 | 0.24 |
| 294_N | 351_I | 1.050 | 0.24 |
| 229_K | 232_N | 1.049 | 0.23 |
| 189_T | 272_V | 1.044 | 0.23 |
| 236_E | 307_L | 1.039 | 0.23 |
| 8_M | 180_V | 1.039 | 0.23 |
| 17_G | 21_N | 1.037 | 0.23 |
| 114_F | 311_Y | 1.036 | 0.23 |
| 63_F | 161_V | 1.036 | 0.23 |
| 374_D | 377_V | 1.034 | 0.23 |
| 52_S | 368_T | 1.033 | 0.23 |
| 41_E | 116_Y | 1.032 | 0.23 |
| 60_F | 146_F | 1.031 | 0.22 |
| 311_Y | 347_Y | 1.029 | 0.22 |
| 13_L | 215_L | 1.026 | 0.22 |
| 159_D | 186_H | 1.026 | 0.22 |
| 280_A | 375_I | 1.025 | 0.22 |
| 142_P | 289_Y | 1.024 | 0.22 |
| 185_S | 233_D | 1.024 | 0.22 |
| 16_A | 101_L | 1.023 | 0.22 |
| 69_S | 90_T | 1.022 | 0.22 |
| 94_D | 205_D | 1.022 | 0.22 |
| 116_Y | 212_G | 1.021 | 0.22 |
| 93_S | 342_G | 1.021 | 0.22 |
| 9_V | 34_I | 1.018 | 0.22 |
| 99_T | 198_P | 1.017 | 0.22 |
| 54_L | 67_T | 1.012 | 0.22 |
| 60_F | 196_V | 1.011 | 0.21 |
| 83_F | 105_P | 1.011 | 0.21 |
| 358_I | 365_E | 1.009 | 0.21 |
| 156_D | 358_I | 1.008 | 0.21 |
| 131_I | 251_L | 1.007 | 0.21 |
| 20_Q | 25_E | 1.006 | 0.21 |
| 6_L | 304_D | 1.006 | 0.21 |
| 33_T | 103_F | 1.005 | 0.21 |
| 84_M | 89_A | 1.004 | 0.21 |
| 160_L | 228_Y | 1.004 | 0.21 |
| 142_P | 230_F | 1.003 | 0.21 |
| 104_W | 160_L | 1.003 | 0.21 |
| 6_L | 255_L | 1.002 | 0.21 |
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 | |
| 4qb7A | 1 | 0.8681 | 100 | 0.312 | Contact Map |
| 3sy6A | 2 | 0.6807 | 100 | 0.552 | Contact Map |
| 3t2lA | 1 | 0.6992 | 100 | 0.554 | Contact Map |
| 3ufiA | 1 | 0.6491 | 100 | 0.58 | Contact Map |
| 4k4kA | 2 | 0.6438 | 100 | 0.583 | Contact Map |
| 4epsA | 1 | 0.6781 | 100 | 0.645 | Contact Map |
| 4dguA | 2 | 0.5937 | 99.8 | 0.761 | Contact Map |
| 4jg5A | 1 | 0.7546 | 95.9 | 0.922 | Contact Map |
| 4h40A | 2 | 0.6966 | 93.2 | 0.933 | Contact Map |
| 4gpvA | 2 | 0.7441 | 90.9 | 0.937 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)