| T0852 -force run |
| ID: | 1405101109 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 414 (377) | ||
| Sequences: | 116 (106.5) | ||
| Seq/Len: | 0.308 | ||
| Nf(neff/√len): | 5.5 |
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: 0.308).
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 |
| 124_Q | 129_I | 2.208 | 0.83 |
| 56_V | 86_G | 2.117 | 0.80 |
| 41_K | 71_R | 1.818 | 0.63 |
| 28_S | 31_L | 1.812 | 0.63 |
| 190_Y | 226_V | 1.776 | 0.61 |
| 58_N | 233_V | 1.680 | 0.54 |
| 8_V | 11_L | 1.635 | 0.51 |
| 336_A | 372_R | 1.593 | 0.49 |
| 41_K | 164_N | 1.537 | 0.45 |
| 112_F | 148_Y | 1.519 | 0.44 |
| 86_G | 194_A | 1.505 | 0.43 |
| 120_V | 133_K | 1.483 | 0.41 |
| 134_G | 159_M | 1.478 | 0.41 |
| 13_T | 17_A | 1.478 | 0.41 |
| 144_L | 164_N | 1.476 | 0.41 |
| 94_D | 129_I | 1.464 | 0.40 |
| 35_Q | 94_D | 1.464 | 0.40 |
| 63_M | 123_I | 1.454 | 0.39 |
| 58_N | 137_A | 1.448 | 0.39 |
| 34_K | 79_M | 1.420 | 0.37 |
| 58_N | 118_E | 1.410 | 0.36 |
| 45_Y | 128_P | 1.410 | 0.36 |
| 10_A | 16_S | 1.406 | 0.36 |
| 165_P | 348_A | 1.404 | 0.36 |
| 17_A | 54_I | 1.401 | 0.36 |
| 124_Q | 240_G | 1.397 | 0.36 |
| 129_I | 162_S | 1.383 | 0.35 |
| 44_K | 81_K | 1.382 | 0.35 |
| 133_K | 244_A | 1.376 | 0.34 |
| 54_I | 82_C | 1.372 | 0.34 |
| 63_M | 84_V | 1.367 | 0.34 |
| 80_P | 249_F | 1.361 | 0.33 |
| 314_K | 338_Y | 1.359 | 0.33 |
| 131_D | 318_K | 1.353 | 0.33 |
| 336_A | 352_Y | 1.349 | 0.33 |
| 130_A | 235_A | 1.348 | 0.33 |
| 94_D | 111_F | 1.339 | 0.32 |
| 112_F | 283_Y | 1.328 | 0.31 |
| 132_L | 249_F | 1.326 | 0.31 |
| 35_Q | 111_F | 1.321 | 0.31 |
| 119_L | 138_S | 1.321 | 0.31 |
| 108_S | 144_L | 1.318 | 0.31 |
| 143_F | 166_V | 1.316 | 0.31 |
| 189_Y | 313_L | 1.309 | 0.30 |
| 2_K | 33_R | 1.304 | 0.30 |
| 124_Q | 133_K | 1.298 | 0.30 |
| 252_Y | 338_Y | 1.297 | 0.30 |
| 260_F | 371_E | 1.292 | 0.29 |
| 14_L | 18_F | 1.287 | 0.29 |
| 171_M | 295_N | 1.281 | 0.29 |
| 31_L | 114_F | 1.279 | 0.29 |
| 370_N | 374_T | 1.275 | 0.28 |
| 28_S | 118_E | 1.273 | 0.28 |
| 31_L | 111_F | 1.271 | 0.28 |
| 55_V | 87_V | 1.271 | 0.28 |
| 98_V | 193_T | 1.262 | 0.28 |
| 226_V | 243_Q | 1.256 | 0.27 |
| 343_G | 346_K | 1.251 | 0.27 |
| 133_K | 173_E | 1.246 | 0.27 |
| 61_T | 237_K | 1.239 | 0.27 |
| 57_L | 114_F | 1.236 | 0.26 |
| 121_P | 208_F | 1.235 | 0.26 |
| 179_L | 316_L | 1.231 | 0.26 |
| 165_P | 249_F | 1.228 | 0.26 |
| 35_Q | 58_N | 1.226 | 0.26 |
| 39_I | 238_L | 1.225 | 0.26 |
| 192_A | 197_E | 1.222 | 0.26 |
| 340_E | 352_Y | 1.219 | 0.25 |
| 74_E | 187_L | 1.218 | 0.25 |
| 270_G | 307_S | 1.215 | 0.25 |
| 295_N | 314_K | 1.213 | 0.25 |
| 41_K | 134_G | 1.210 | 0.25 |
| 52_P | 87_V | 1.209 | 0.25 |
| 53_L | 301_Y | 1.208 | 0.25 |
| 214_S | 280_N | 1.204 | 0.25 |
| 31_L | 137_A | 1.203 | 0.25 |
| 28_S | 35_Q | 1.203 | 0.25 |
| 68_S | 71_R | 1.193 | 0.24 |
| 127_Y | 149_M | 1.191 | 0.24 |
| 10_A | 18_F | 1.191 | 0.24 |
| 119_L | 125_G | 1.182 | 0.24 |
| 255_I | 275_L | 1.182 | 0.24 |
| 138_S | 233_V | 1.181 | 0.24 |
| 4_Y | 16_S | 1.181 | 0.24 |
| 63_M | 86_G | 1.180 | 0.24 |
| 193_T | 197_E | 1.178 | 0.23 |
| 2_K | 11_L | 1.178 | 0.23 |
| 229_K | 238_L | 1.178 | 0.23 |
| 228_F | 243_Q | 1.177 | 0.23 |
| 8_V | 21_V | 1.173 | 0.23 |
| 161_V | 240_G | 1.172 | 0.23 |
| 91_K | 326_L | 1.167 | 0.23 |
| 244_A | 318_K | 1.164 | 0.23 |
| 232_S | 253_K | 1.164 | 0.23 |
| 280_N | 288_V | 1.160 | 0.23 |
| 89_E | 291_V | 1.159 | 0.23 |
| 19_S | 22_I | 1.156 | 0.22 |
| 305_N | 311_E | 1.155 | 0.22 |
| 35_Q | 118_E | 1.154 | 0.22 |
| 111_F | 114_F | 1.151 | 0.22 |
| 282_I | 290_K | 1.149 | 0.22 |
| 127_Y | 167_A | 1.148 | 0.22 |
| 124_Q | 162_S | 1.146 | 0.22 |
| 220_S | 322_S | 1.145 | 0.22 |
| 326_L | 331_P | 1.144 | 0.22 |
| 58_N | 91_K | 1.143 | 0.22 |
| 133_K | 212_M | 1.142 | 0.22 |
| 108_S | 118_E | 1.141 | 0.22 |
| 49_Q | 128_P | 1.141 | 0.22 |
| 114_F | 118_E | 1.140 | 0.22 |
| 111_F | 118_E | 1.129 | 0.21 |
| 302_T | 317_A | 1.127 | 0.21 |
| 4_Y | 11_L | 1.126 | 0.21 |
| 163_L | 252_Y | 1.125 | 0.21 |
| 224_H | 247_M | 1.124 | 0.21 |
| 298_M | 301_Y | 1.124 | 0.21 |
| 104_P | 149_M | 1.123 | 0.21 |
| 149_M | 160_I | 1.121 | 0.21 |
| 43_E | 46_T | 1.119 | 0.21 |
| 164_N | 192_A | 1.119 | 0.21 |
| 3_K | 12_V | 1.118 | 0.21 |
| 119_L | 335_L | 1.118 | 0.21 |
| 12_V | 15_Q | 1.118 | 0.21 |
| 44_K | 284_K | 1.116 | 0.21 |
| 53_L | 59_A | 1.114 | 0.20 |
| 58_N | 86_G | 1.113 | 0.20 |
| 139_E | 142_G | 1.112 | 0.20 |
| 55_V | 123_I | 1.112 | 0.20 |
| 344_D | 360_N | 1.112 | 0.20 |
| 336_A | 354_K | 1.106 | 0.20 |
| 3_K | 11_L | 1.106 | 0.20 |
| 235_A | 245_L | 1.104 | 0.20 |
| 54_I | 136_I | 1.103 | 0.20 |
| 41_K | 144_L | 1.103 | 0.20 |
| 278_K | 330_M | 1.102 | 0.20 |
| 38_G | 320_V | 1.099 | 0.20 |
| 60_E | 232_S | 1.096 | 0.20 |
| 258_K | 262_T | 1.095 | 0.20 |
| 40_Y | 71_R | 1.093 | 0.20 |
| 225_F | 336_A | 1.091 | 0.19 |
| 59_A | 233_V | 1.086 | 0.19 |
| 133_K | 316_L | 1.085 | 0.19 |
| 109_A | 353_Q | 1.082 | 0.19 |
| 26_F | 123_I | 1.080 | 0.19 |
| 278_K | 333_F | 1.078 | 0.19 |
| 129_I | 240_G | 1.077 | 0.19 |
| 192_A | 228_F | 1.076 | 0.19 |
| 192_A | 240_G | 1.076 | 0.19 |
| 70_V | 84_V | 1.074 | 0.19 |
| 124_Q | 300_T | 1.073 | 0.19 |
| 26_F | 59_A | 1.071 | 0.19 |
| 68_S | 138_S | 1.071 | 0.19 |
| 35_Q | 87_V | 1.070 | 0.19 |
| 45_Y | 81_K | 1.067 | 0.18 |
| 280_N | 339_Y | 1.066 | 0.18 |
| 51_Y | 119_L | 1.066 | 0.18 |
| 10_A | 13_T | 1.064 | 0.18 |
| 138_S | 326_L | 1.064 | 0.18 |
| 31_L | 35_Q | 1.062 | 0.18 |
| 71_R | 154_K | 1.059 | 0.18 |
| 208_F | 354_K | 1.059 | 0.18 |
| 197_E | 236_A | 1.057 | 0.18 |
| 91_K | 233_V | 1.056 | 0.18 |
| 41_K | 355_A | 1.055 | 0.18 |
| 73_Y | 314_K | 1.052 | 0.18 |
| 39_I | 270_G | 1.051 | 0.18 |
| 22_I | 261_K | 1.050 | 0.18 |
| 336_A | 359_P | 1.050 | 0.18 |
| 21_V | 375_H | 1.047 | 0.18 |
| 9_I | 18_F | 1.046 | 0.18 |
| 194_A | 230_G | 1.044 | 0.18 |
| 334_F | 337_E | 1.041 | 0.17 |
| 326_L | 335_L | 1.041 | 0.17 |
| 156_T | 161_V | 1.041 | 0.17 |
| 321_E | 335_L | 1.038 | 0.17 |
| 4_Y | 7_I | 1.036 | 0.17 |
| 319_Y | 356_Y | 1.036 | 0.17 |
| 31_L | 58_N | 1.036 | 0.17 |
| 137_A | 233_V | 1.035 | 0.17 |
| 84_V | 159_M | 1.034 | 0.17 |
| 114_F | 326_L | 1.034 | 0.17 |
| 208_F | 289_K | 1.033 | 0.17 |
| 118_E | 233_V | 1.031 | 0.17 |
| 86_G | 245_L | 1.028 | 0.17 |
| 77_G | 376_L | 1.027 | 0.17 |
| 193_T | 240_G | 1.026 | 0.17 |
| 59_A | 82_C | 1.025 | 0.17 |
| 130_A | 274_Y | 1.025 | 0.17 |
| 138_S | 197_E | 1.022 | 0.17 |
| 19_S | 159_M | 1.021 | 0.17 |
| 127_Y | 279_Y | 1.021 | 0.17 |
| 73_Y | 278_K | 1.019 | 0.17 |
| 137_A | 326_L | 1.018 | 0.17 |
| 31_L | 118_E | 1.018 | 0.17 |
| 142_G | 231_S | 1.018 | 0.17 |
| 133_K | 240_G | 1.018 | 0.17 |
| 197_E | 248_C | 1.017 | 0.17 |
| 39_I | 352_Y | 1.016 | 0.16 |
| 65_P | 108_S | 1.015 | 0.16 |
| 292_P | 337_E | 1.014 | 0.16 |
| 142_G | 188_F | 1.014 | 0.16 |
| 87_V | 111_F | 1.013 | 0.16 |
| 292_P | 324_G | 1.011 | 0.16 |
| 148_Y | 283_Y | 1.009 | 0.16 |
| 210_R | 343_G | 1.009 | 0.16 |
| 84_V | 336_A | 1.009 | 0.16 |
| 41_K | 128_P | 1.009 | 0.16 |
| 208_F | 262_T | 1.009 | 0.16 |
| 34_K | 126_K | 1.007 | 0.16 |
| 244_A | 330_M | 1.007 | 0.16 |
| 35_Q | 52_P | 1.006 | 0.16 |
| 58_N | 138_S | 1.005 | 0.16 |
| 292_P | 376_L | 1.005 | 0.16 |
| 166_V | 194_A | 1.002 | 0.16 |
| 39_I | 346_K | 1.001 | 0.16 |
| 84_V | 289_K | 1.001 | 0.16 |
| 26_F | 249_F | 1.000 | 0.16 |
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 | |
| 4w9rA | 2 | 0.8647 | 100 | 0.505 | Contact Map |
| 3gffA | 2 | 0.7005 | 100 | 0.692 | Contact Map |
| 2gzsA | 1 | 0.5531 | 99.9 | 0.819 | Contact Map |
| 2qm0A | 2 | 0.5821 | 99.9 | 0.828 | Contact Map |
| 1jjfA | 1 | 0.5483 | 99.9 | 0.841 | Contact Map |
| 3ls2A | 4 | 0.57 | 99.9 | 0.842 | Contact Map |
| 3c8dA | 4 | 0.57 | 99.8 | 0.851 | Contact Map |
| 4folA | 4 | 0.5773 | 99.8 | 0.861 | Contact Map |
| 3i6yA | 2 | 0.5749 | 99.7 | 0.866 | Contact Map |
| 3e4dA | 6 | 0.57 | 99.7 | 0.868 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)