| t_coffee_200 -force run |
| ID: | 1446001725 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 398 (384) | ||
| Sequences: | 187 (164) | ||
| Seq/Len: | 0.487 | ||
| Nf(neff/√len): | 8.4 |
HHblits Results: (2015_06)
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: 0.487).
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 |
| 189_Q | 214_N | 2.514 | 0.97 |
| 119_G | 123_E | 2.142 | 0.90 |
| 97_H | 148_S | 2.050 | 0.87 |
| 28_L | 75_R | 2.049 | 0.87 |
| 86_Q | 97_H | 2.009 | 0.86 |
| 114_L | 173_V | 1.929 | 0.82 |
| 103_S | 143_H | 1.899 | 0.81 |
| 126_P | 293_T | 1.898 | 0.81 |
| 96_I | 155_S | 1.819 | 0.77 |
| 30_D | 34_L | 1.755 | 0.73 |
| 103_S | 108_A | 1.720 | 0.71 |
| 75_R | 78_E | 1.669 | 0.68 |
| 198_G | 211_V | 1.659 | 0.67 |
| 145_V | 180_L | 1.647 | 0.66 |
| 25_D | 29_D | 1.645 | 0.66 |
| 354_R | 358_A | 1.636 | 0.65 |
| 149_L | 313_T | 1.616 | 0.64 |
| 152_Y | 193_I | 1.610 | 0.64 |
| 113_L | 146_V | 1.607 | 0.63 |
| 21_V | 28_L | 1.581 | 0.61 |
| 143_H | 182_F | 1.564 | 0.60 |
| 98_F | 112_A | 1.546 | 0.59 |
| 110_P | 177_M | 1.526 | 0.57 |
| 265_V | 268_S | 1.519 | 0.57 |
| 163_D | 316_E | 1.499 | 0.55 |
| 244_F | 248_G | 1.490 | 0.55 |
| 314_Y | 374_H | 1.474 | 0.53 |
| 145_V | 182_F | 1.458 | 0.52 |
| 110_P | 145_V | 1.450 | 0.52 |
| 30_D | 39_K | 1.443 | 0.51 |
| 130_L | 385_K | 1.423 | 0.50 |
| 32_K | 36_R | 1.411 | 0.49 |
| 188_I | 198_G | 1.397 | 0.48 |
| 44_T | 49_Q | 1.394 | 0.47 |
| 114_L | 198_G | 1.393 | 0.47 |
| 380_R | 383_E | 1.380 | 0.46 |
| 123_E | 377_A | 1.376 | 0.46 |
| 118_P | 147_P | 1.373 | 0.46 |
| 34_L | 39_K | 1.372 | 0.46 |
| 147_P | 176_L | 1.354 | 0.44 |
| 110_P | 155_S | 1.350 | 0.44 |
| 152_Y | 313_T | 1.336 | 0.43 |
| 65_R | 69_L | 1.334 | 0.43 |
| 111_I | 388_L | 1.329 | 0.42 |
| 23_I | 74_W | 1.319 | 0.42 |
| 58_S | 264_H | 1.318 | 0.42 |
| 263_G | 280_K | 1.318 | 0.42 |
| 117_W | 177_M | 1.316 | 0.41 |
| 98_F | 180_L | 1.316 | 0.41 |
| 110_P | 182_F | 1.308 | 0.41 |
| 150_P | 172_V | 1.306 | 0.41 |
| 117_W | 373_G | 1.304 | 0.41 |
| 86_Q | 121_F | 1.300 | 0.40 |
| 266_L | 279_E | 1.299 | 0.40 |
| 372_G | 375_F | 1.299 | 0.40 |
| 343_S | 369_H | 1.298 | 0.40 |
| 101_L | 144_L | 1.294 | 0.40 |
| 373_G | 379_E | 1.282 | 0.39 |
| 44_T | 54_F | 1.281 | 0.39 |
| 127_I | 385_K | 1.280 | 0.39 |
| 140_L | 389_T | 1.274 | 0.38 |
| 310_A | 316_E | 1.272 | 0.38 |
| 169_N | 313_T | 1.271 | 0.38 |
| 118_P | 192_D | 1.269 | 0.38 |
| 36_R | 69_L | 1.268 | 0.38 |
| 279_E | 286_D | 1.266 | 0.38 |
| 60_W | 63_T | 1.264 | 0.38 |
| 304_T | 310_A | 1.263 | 0.38 |
| 123_E | 189_Q | 1.262 | 0.38 |
| 110_P | 186_Y | 1.262 | 0.38 |
| 142_F | 145_V | 1.255 | 0.37 |
| 244_F | 249_L | 1.247 | 0.36 |
| 72_F | 296_E | 1.243 | 0.36 |
| 135_Y | 138_E | 1.237 | 0.36 |
| 189_Q | 376_A | 1.231 | 0.35 |
| 40_I | 264_H | 1.231 | 0.35 |
| 28_L | 78_E | 1.230 | 0.35 |
| 214_N | 377_A | 1.229 | 0.35 |
| 174_D | 186_Y | 1.227 | 0.35 |
| 41_A | 58_S | 1.226 | 0.35 |
| 190_G | 379_E | 1.221 | 0.35 |
| 341_G | 391_F | 1.219 | 0.34 |
| 307_F | 311_I | 1.211 | 0.34 |
| 263_G | 308_P | 1.209 | 0.34 |
| 87_F | 100_A | 1.207 | 0.34 |
| 85_P | 101_L | 1.206 | 0.34 |
| 374_H | 379_E | 1.203 | 0.33 |
| 117_W | 192_D | 1.193 | 0.33 |
| 32_K | 236_E | 1.193 | 0.33 |
| 211_V | 340_F | 1.186 | 0.32 |
| 154_F | 372_G | 1.186 | 0.32 |
| 113_L | 144_L | 1.184 | 0.32 |
| 59_E | 62_T | 1.184 | 0.32 |
| 180_L | 270_P | 1.181 | 0.32 |
| 192_D | 314_Y | 1.178 | 0.32 |
| 30_D | 38_S | 1.174 | 0.31 |
| 33_T | 231_S | 1.170 | 0.31 |
| 146_V | 181_G | 1.167 | 0.31 |
| 100_A | 182_F | 1.165 | 0.31 |
| 99_A | 121_F | 1.164 | 0.31 |
| 261_T | 266_L | 1.159 | 0.30 |
| 72_F | 153_T | 1.157 | 0.30 |
| 86_Q | 148_S | 1.153 | 0.30 |
| 270_P | 373_G | 1.149 | 0.30 |
| 119_G | 214_N | 1.146 | 0.30 |
| 119_G | 189_Q | 1.141 | 0.29 |
| 127_I | 288_P | 1.141 | 0.29 |
| 52_G | 56_I | 1.140 | 0.29 |
| 120_S | 154_F | 1.135 | 0.29 |
| 143_H | 288_P | 1.133 | 0.29 |
| 84_F | 146_V | 1.129 | 0.29 |
| 110_P | 372_G | 1.124 | 0.28 |
| 149_L | 364_V | 1.122 | 0.28 |
| 195_S | 216_C | 1.118 | 0.28 |
| 9_P | 12_A | 1.116 | 0.28 |
| 89_T | 98_F | 1.113 | 0.28 |
| 216_C | 338_K | 1.109 | 0.27 |
| 97_H | 121_F | 1.104 | 0.27 |
| 67_K | 292_E | 1.102 | 0.27 |
| 131_F | 176_L | 1.099 | 0.27 |
| 42_P | 65_R | 1.098 | 0.27 |
| 112_A | 266_L | 1.096 | 0.27 |
| 307_F | 342_F | 1.092 | 0.26 |
| 98_F | 110_P | 1.091 | 0.26 |
| 25_D | 75_R | 1.091 | 0.26 |
| 145_V | 371_E | 1.089 | 0.26 |
| 91_I | 110_P | 1.087 | 0.26 |
| 146_V | 170_A | 1.087 | 0.26 |
| 49_Q | 54_F | 1.086 | 0.26 |
| 29_D | 63_T | 1.081 | 0.26 |
| 75_R | 79_A | 1.080 | 0.26 |
| 358_A | 366_F | 1.079 | 0.26 |
| 191_G | 348_D | 1.077 | 0.25 |
| 117_W | 310_A | 1.075 | 0.25 |
| 163_D | 179_D | 1.075 | 0.25 |
| 345_F | 376_A | 1.073 | 0.25 |
| 31_L | 34_L | 1.070 | 0.25 |
| 44_T | 57_T | 1.069 | 0.25 |
| 193_I | 313_T | 1.068 | 0.25 |
| 85_P | 89_T | 1.063 | 0.25 |
| 123_E | 214_N | 1.062 | 0.25 |
| 372_G | 376_A | 1.061 | 0.24 |
| 90_E | 145_V | 1.060 | 0.24 |
| 121_F | 148_S | 1.058 | 0.24 |
| 52_G | 57_T | 1.056 | 0.24 |
| 177_M | 182_F | 1.056 | 0.24 |
| 87_F | 99_A | 1.050 | 0.24 |
| 140_L | 393_E | 1.049 | 0.24 |
| 149_L | 197_V | 1.046 | 0.24 |
| 54_F | 315_R | 1.045 | 0.24 |
| 32_K | 66_E | 1.044 | 0.24 |
| 33_T | 43_P | 1.042 | 0.23 |
| 130_L | 392_V | 1.042 | 0.23 |
| 195_S | 213_L | 1.041 | 0.23 |
| 82_N | 177_M | 1.040 | 0.23 |
| 294_I | 343_S | 1.039 | 0.23 |
| 111_I | 212_H | 1.039 | 0.23 |
| 212_H | 270_P | 1.039 | 0.23 |
| 121_F | 156_S | 1.037 | 0.23 |
| 182_F | 270_P | 1.036 | 0.23 |
| 112_A | 198_G | 1.035 | 0.23 |
| 49_Q | 72_F | 1.034 | 0.23 |
| 89_T | 179_D | 1.033 | 0.23 |
| 142_F | 376_A | 1.033 | 0.23 |
| 145_V | 184_S | 1.031 | 0.23 |
| 237_G | 245_M | 1.030 | 0.23 |
| 113_L | 124_F | 1.029 | 0.23 |
| 16_P | 26_E | 1.028 | 0.23 |
| 34_L | 93_G | 1.028 | 0.23 |
| 25_D | 62_T | 1.026 | 0.23 |
| 190_G | 373_G | 1.026 | 0.23 |
| 193_I | 255_H | 1.025 | 0.23 |
| 53_R | 57_T | 1.023 | 0.22 |
| 82_N | 110_P | 1.023 | 0.22 |
| 166_L | 176_L | 1.021 | 0.22 |
| 72_F | 76_P | 1.020 | 0.22 |
| 9_P | 14_I | 1.019 | 0.22 |
| 135_Y | 139_T | 1.018 | 0.22 |
| 301_Y | 316_E | 1.017 | 0.22 |
| 32_K | 69_L | 1.014 | 0.22 |
| 306_S | 366_F | 1.014 | 0.22 |
| 353_P | 356_W | 1.011 | 0.22 |
| 336_I | 379_E | 1.010 | 0.22 |
| 342_F | 366_F | 1.010 | 0.22 |
| 150_P | 186_Y | 1.009 | 0.22 |
| 301_Y | 373_G | 1.007 | 0.22 |
| 78_E | 136_T | 1.006 | 0.22 |
| 214_N | 376_A | 1.005 | 0.21 |
| 50_A | 243_K | 1.004 | 0.21 |
| 123_E | 155_S | 1.003 | 0.21 |
| 277_I | 301_Y | 1.001 | 0.21 |
| 301_Y | 304_T | 1.000 | 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
- See coupling matrix (for protein design or mutagenesis)
- 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 | |
| 3g02A | 2 | 0.9598 | 100 | 0.34 | Contact Map |
| 4qlaA | 2 | 0.9749 | 100 | 0.371 | Contact Map |
| 4qa9A | 1 | 0.9447 | 100 | 0.371 | Contact Map |
| 1ehyA | 4 | 0.6809 | 100 | 0.668 | Contact Map |
| 4inzA | 2 | 0.701 | 100 | 0.693 | Contact Map |
| 3r40A | 2 | 0.7035 | 100 | 0.694 | Contact Map |
| 5bovA | 4 | 0 | 100 | 0.698 | Contact Map |
| 3qyjA | 2 | 0.7035 | 100 | 0.71 | Contact Map |
| 4psuA | 1 | 0.7085 | 100 | 0.717 | Contact Map |
| 3oosA | 1 | 0.6683 | 100 | 0.727 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)