| T0827 -force run |
| ID: | 1403287202 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 407 (343) | ||
| Sequences: | 142 (107.7) | ||
| Seq/Len: | 0.414 | ||
| Nf(neff/√len): | 5.8 |
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: 0.414).
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 |
| 106_D | 131_S | 2.898 | 0.98 |
| 132_E | 157_K | 2.444 | 0.94 |
| 121_R | 141_V | 2.159 | 0.88 |
| 136_D | 159_S | 1.941 | 0.79 |
| 125_A | 191_A | 1.728 | 0.67 |
| 198_A | 202_A | 1.717 | 0.66 |
| 125_A | 149_T | 1.681 | 0.64 |
| 287_G | 321_Q | 1.660 | 0.62 |
| 135_A | 150_L | 1.646 | 0.61 |
| 49_T | 113_L | 1.580 | 0.56 |
| 93_V | 288_L | 1.576 | 0.56 |
| 21_R | 69_A | 1.564 | 0.55 |
| 283_S | 286_S | 1.564 | 0.55 |
| 158_L | 186_L | 1.563 | 0.55 |
| 138_L | 146_V | 1.558 | 0.55 |
| 113_L | 146_V | 1.540 | 0.54 |
| 120_H | 159_S | 1.526 | 0.52 |
| 37_P | 41_I | 1.524 | 0.52 |
| 135_A | 162_G | 1.523 | 0.52 |
| 139_I | 142_G | 1.516 | 0.52 |
| 125_A | 364_N | 1.506 | 0.51 |
| 159_S | 162_G | 1.495 | 0.50 |
| 305_L | 349_D | 1.491 | 0.50 |
| 108_D | 311_A | 1.480 | 0.49 |
| 176_L | 224_V | 1.465 | 0.48 |
| 48_M | 121_R | 1.463 | 0.48 |
| 108_D | 309_C | 1.462 | 0.48 |
| 124_I | 137_A | 1.445 | 0.47 |
| 28_K | 293_G | 1.442 | 0.46 |
| 117_T | 287_G | 1.434 | 0.46 |
| 89_D | 167_V | 1.415 | 0.44 |
| 93_V | 112_C | 1.397 | 0.43 |
| 136_D | 141_V | 1.394 | 0.43 |
| 143_E | 155_L | 1.377 | 0.42 |
| 58_R | 235_D | 1.376 | 0.42 |
| 122_R | 146_V | 1.370 | 0.41 |
| 61_N | 198_A | 1.368 | 0.41 |
| 98_L | 123_L | 1.361 | 0.41 |
| 110_I | 150_L | 1.359 | 0.40 |
| 267_V | 363_W | 1.354 | 0.40 |
| 94_A | 98_L | 1.341 | 0.39 |
| 137_A | 158_L | 1.339 | 0.39 |
| 117_T | 143_E | 1.339 | 0.39 |
| 82_L | 167_V | 1.333 | 0.39 |
| 253_A | 262_S | 1.324 | 0.38 |
| 158_L | 355_R | 1.324 | 0.38 |
| 82_L | 100_D | 1.318 | 0.38 |
| 79_P | 109_L | 1.302 | 0.36 |
| 83_V | 103_K | 1.301 | 0.36 |
| 146_V | 151_L | 1.292 | 0.36 |
| 69_A | 309_C | 1.289 | 0.36 |
| 248_R | 281_E | 1.282 | 0.35 |
| 49_T | 121_R | 1.280 | 0.35 |
| 101_S | 124_I | 1.280 | 0.35 |
| 177_I | 316_R | 1.279 | 0.35 |
| 140_E | 309_C | 1.276 | 0.35 |
| 277_E | 304_P | 1.254 | 0.33 |
| 65_R | 304_P | 1.254 | 0.33 |
| 122_R | 229_S | 1.251 | 0.33 |
| 104_L | 138_L | 1.244 | 0.33 |
| 104_L | 283_S | 1.228 | 0.32 |
| 146_V | 162_G | 1.225 | 0.31 |
| 48_M | 141_V | 1.223 | 0.31 |
| 69_A | 249_Q | 1.222 | 0.31 |
| 262_S | 328_R | 1.222 | 0.31 |
| 88_R | 313_G | 1.222 | 0.31 |
| 241_A | 322_L | 1.221 | 0.31 |
| 67_K | 303_E | 1.218 | 0.31 |
| 270_G | 306_A | 1.210 | 0.30 |
| 279_A | 313_G | 1.209 | 0.30 |
| 89_D | 348_Y | 1.207 | 0.30 |
| 128_R | 267_V | 1.205 | 0.30 |
| 127_R | 153_N | 1.203 | 0.30 |
| 162_G | 306_A | 1.190 | 0.29 |
| 118_T | 125_A | 1.187 | 0.29 |
| 105_S | 309_C | 1.185 | 0.29 |
| 51_D | 328_R | 1.182 | 0.29 |
| 113_L | 121_R | 1.180 | 0.29 |
| 33_V | 50_A | 1.180 | 0.29 |
| 105_S | 108_D | 1.179 | 0.29 |
| 87_L | 127_R | 1.176 | 0.28 |
| 253_A | 328_R | 1.174 | 0.28 |
| 64_E | 202_A | 1.162 | 0.28 |
| 202_A | 278_I | 1.161 | 0.27 |
| 78_M | 101_S | 1.161 | 0.27 |
| 106_D | 234_Q | 1.159 | 0.27 |
| 94_A | 127_R | 1.156 | 0.27 |
| 244_F | 360_L | 1.155 | 0.27 |
| 34_V | 49_T | 1.154 | 0.27 |
| 134_V | 241_A | 1.153 | 0.27 |
| 27_L | 31_A | 1.153 | 0.27 |
| 122_R | 138_L | 1.147 | 0.27 |
| 31_A | 125_A | 1.145 | 0.27 |
| 181_L | 306_A | 1.138 | 0.26 |
| 178_P | 296_I | 1.137 | 0.26 |
| 69_A | 274_F | 1.136 | 0.26 |
| 166_I | 354_D | 1.136 | 0.26 |
| 87_L | 101_S | 1.135 | 0.26 |
| 90_E | 309_C | 1.132 | 0.26 |
| 254_A | 262_S | 1.132 | 0.26 |
| 136_D | 162_G | 1.126 | 0.25 |
| 135_A | 146_V | 1.119 | 0.25 |
| 288_L | 357_Q | 1.117 | 0.25 |
| 27_L | 303_E | 1.110 | 0.25 |
| 93_V | 110_I | 1.107 | 0.24 |
| 98_L | 155_L | 1.106 | 0.24 |
| 65_R | 93_V | 1.105 | 0.24 |
| 40_R | 351_I | 1.097 | 0.24 |
| 124_I | 150_L | 1.097 | 0.24 |
| 69_A | 343_R | 1.095 | 0.24 |
| 167_V | 172_D | 1.091 | 0.24 |
| 61_N | 91_L | 1.089 | 0.23 |
| 111_S | 208_Q | 1.087 | 0.23 |
| 117_T | 292_T | 1.086 | 0.23 |
| 176_L | 348_Y | 1.085 | 0.23 |
| 29_R | 270_G | 1.085 | 0.23 |
| 192_Y | 309_C | 1.085 | 0.23 |
| 53_L | 117_T | 1.084 | 0.23 |
| 121_R | 285_L | 1.082 | 0.23 |
| 30_L | 65_R | 1.077 | 0.23 |
| 139_I | 159_S | 1.077 | 0.23 |
| 289_K | 363_W | 1.074 | 0.23 |
| 356_A | 363_W | 1.073 | 0.23 |
| 32_D | 225_F | 1.071 | 0.23 |
| 125_A | 362_Y | 1.069 | 0.22 |
| 199_D | 350_A | 1.065 | 0.22 |
| 130_V | 283_S | 1.062 | 0.22 |
| 158_L | 348_Y | 1.059 | 0.22 |
| 202_A | 316_R | 1.057 | 0.22 |
| 119_E | 132_E | 1.055 | 0.22 |
| 31_A | 158_L | 1.054 | 0.22 |
| 162_G | 186_L | 1.054 | 0.22 |
| 110_I | 277_E | 1.052 | 0.22 |
| 120_H | 194_M | 1.051 | 0.22 |
| 140_E | 169_A | 1.049 | 0.21 |
| 248_R | 306_A | 1.049 | 0.21 |
| 128_R | 357_Q | 1.048 | 0.21 |
| 93_V | 98_L | 1.047 | 0.21 |
| 83_V | 101_S | 1.044 | 0.21 |
| 23_R | 203_R | 1.041 | 0.21 |
| 57_L | 301_G | 1.040 | 0.21 |
| 168_A | 333_R | 1.038 | 0.21 |
| 118_T | 191_A | 1.038 | 0.21 |
| 357_Q | 361_R | 1.036 | 0.21 |
| 218_Q | 293_G | 1.036 | 0.21 |
| 26_L | 282_I | 1.036 | 0.21 |
| 65_R | 309_C | 1.034 | 0.21 |
| 248_R | 262_S | 1.034 | 0.21 |
| 198_A | 222_G | 1.032 | 0.21 |
| 200_S | 351_I | 1.029 | 0.20 |
| 64_E | 198_A | 1.028 | 0.20 |
| 53_L | 310_K | 1.028 | 0.20 |
| 105_S | 147_I | 1.026 | 0.20 |
| 217_L | 312_T | 1.025 | 0.20 |
| 66_E | 331_V | 1.023 | 0.20 |
| 263_L | 293_G | 1.023 | 0.20 |
| 60_A | 187_R | 1.022 | 0.20 |
| 215_E | 218_Q | 1.022 | 0.20 |
| 321_Q | 348_Y | 1.021 | 0.20 |
| 138_L | 341_L | 1.019 | 0.20 |
| 170_T | 183_R | 1.019 | 0.20 |
| 238_S | 282_I | 1.018 | 0.20 |
| 151_L | 200_S | 1.018 | 0.20 |
| 78_M | 83_V | 1.017 | 0.20 |
| 349_D | 357_Q | 1.017 | 0.20 |
| 19_S | 61_N | 1.016 | 0.20 |
| 25_T | 283_S | 1.013 | 0.20 |
| 39_S | 106_D | 1.013 | 0.20 |
| 132_E | 310_K | 1.011 | 0.20 |
| 313_G | 354_D | 1.010 | 0.20 |
| 83_V | 360_L | 1.010 | 0.20 |
| 29_R | 301_G | 1.010 | 0.20 |
| 18_A | 214_R | 1.009 | 0.20 |
| 176_L | 206_I | 1.009 | 0.20 |
| 99_V | 328_R | 1.008 | 0.19 |
| 128_R | 221_V | 1.007 | 0.19 |
| 288_L | 361_R | 1.007 | 0.19 |
| 113_L | 141_V | 1.003 | 0.19 |
| 56_M | 159_S | 1.002 | 0.19 |
| 121_R | 185_E | 1.002 | 0.19 |
| 218_Q | 358_T | 1.001 | 0.19 |
| 26_L | 348_Y | 1.001 | 0.19 |
| 201_E | 311_A | 1.001 | 0.19 |
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 | |
| 1lrvA | 1 | 0.4742 | 31 | 0.972 | Contact Map |
| 1b0nA | 1 | 0.2383 | 29.8 | 0.972 | Contact Map |
| 2o71A | 1 | 0.2211 | 26 | 0.973 | Contact Map |
| 4o6xA | 2 | 0.2334 | 22.4 | 0.974 | Contact Map |
| 3qwgA | 2 | 0.1941 | 19.3 | 0.974 | Contact Map |
| 2of5A | 7 | 0.2211 | 19.3 | 0.974 | Contact Map |
| 4jcyA | 2 | 0.2088 | 18.5 | 0.975 | Contact Map |
| 3r1fA | 18 | 0.285 | 16 | 0.975 | Contact Map |
| 3fmyA | 1 | 0.1548 | 15.7 | 0.975 | Contact Map |
| 3bd1A | 3 | 0.1499 | 14.1 | 0.976 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)