| T0794 - roll -force run |
| ID: | 1384277130 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 470 (469) | ||
| Sequences: | 158 (111.8) | ||
| Seq/Len: | 0.337 | ||
| Nf(neff/√len): | 5.2 |
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: 0.337).
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 |
| 336_C | 341_C | 2.585 | 0.94 |
| 120_D | 156_H | 2.177 | 0.84 |
| 76_E | 156_H | 2.122 | 0.82 |
| 215_T | 226_A | 2.118 | 0.82 |
| 124_C | 131_C | 1.975 | 0.75 |
| 224_L | 451_T | 1.954 | 0.74 |
| 280_L | 321_F | 1.833 | 0.67 |
| 230_H | 243_A | 1.805 | 0.65 |
| 174_E | 241_F | 1.796 | 0.65 |
| 51_A | 112_I | 1.757 | 0.62 |
| 103_L | 408_G | 1.748 | 0.62 |
| 76_E | 120_D | 1.700 | 0.58 |
| 236_G | 419_V | 1.688 | 0.58 |
| 159_N | 224_L | 1.670 | 0.56 |
| 51_A | 110_N | 1.665 | 0.56 |
| 31_L | 340_L | 1.650 | 0.55 |
| 367_T | 370_G | 1.634 | 0.54 |
| 234_A | 340_L | 1.632 | 0.54 |
| 103_L | 379_L | 1.601 | 0.52 |
| 105_C | 202_L | 1.578 | 0.50 |
| 104_S | 217_W | 1.561 | 0.49 |
| 142_D | 187_I | 1.560 | 0.49 |
| 234_A | 363_D | 1.554 | 0.48 |
| 256_S | 259_Y | 1.539 | 0.47 |
| 139_Y | 378_T | 1.535 | 0.47 |
| 236_G | 361_A | 1.517 | 0.46 |
| 39_L | 56_T | 1.512 | 0.46 |
| 194_L | 420_L | 1.505 | 0.45 |
| 420_L | 451_T | 1.478 | 0.43 |
| 7_A | 51_A | 1.474 | 0.43 |
| 449_V | 452_V | 1.454 | 0.42 |
| 98_P | 340_L | 1.453 | 0.42 |
| 245_N | 366_H | 1.452 | 0.41 |
| 244_S | 387_L | 1.442 | 0.41 |
| 223_H | 452_V | 1.439 | 0.41 |
| 213_F | 226_A | 1.437 | 0.40 |
| 102_R | 422_S | 1.434 | 0.40 |
| 7_A | 11_H | 1.432 | 0.40 |
| 256_S | 279_L | 1.429 | 0.40 |
| 53_I | 144_V | 1.426 | 0.40 |
| 258_I | 279_L | 1.426 | 0.40 |
| 358_A | 414_Y | 1.424 | 0.40 |
| 440_F | 451_T | 1.421 | 0.39 |
| 213_F | 217_W | 1.409 | 0.39 |
| 213_F | 241_F | 1.387 | 0.37 |
| 331_G | 428_P | 1.373 | 0.36 |
| 147_S | 181_T | 1.363 | 0.36 |
| 161_F | 220_V | 1.363 | 0.36 |
| 113_Y | 154_R | 1.362 | 0.36 |
| 142_D | 156_H | 1.357 | 0.35 |
| 193_I | 213_F | 1.334 | 0.34 |
| 88_C | 105_C | 1.329 | 0.33 |
| 189_T | 214_P | 1.322 | 0.33 |
| 7_A | 212_V | 1.319 | 0.33 |
| 60_A | 216_A | 1.319 | 0.33 |
| 108_K | 175_I | 1.311 | 0.32 |
| 185_F | 198_P | 1.308 | 0.32 |
| 7_A | 110_N | 1.307 | 0.32 |
| 208_V | 241_F | 1.306 | 0.32 |
| 188_F | 199_A | 1.303 | 0.32 |
| 180_T | 186_G | 1.302 | 0.32 |
| 42_A | 54_I | 1.301 | 0.32 |
| 87_P | 104_S | 1.288 | 0.31 |
| 78_I | 357_Y | 1.288 | 0.31 |
| 335_V | 361_A | 1.287 | 0.31 |
| 186_G | 192_D | 1.282 | 0.31 |
| 340_L | 456_G | 1.276 | 0.30 |
| 199_A | 224_L | 1.272 | 0.30 |
| 177_T | 207_H | 1.266 | 0.30 |
| 161_F | 369_E | 1.266 | 0.30 |
| 2_D | 175_I | 1.264 | 0.30 |
| 35_N | 46_A | 1.262 | 0.29 |
| 160_L | 190_C | 1.261 | 0.29 |
| 186_G | 202_L | 1.255 | 0.29 |
| 170_P | 245_N | 1.253 | 0.29 |
| 4_F | 9_Y | 1.251 | 0.29 |
| 108_K | 326_L | 1.251 | 0.29 |
| 135_G | 221_L | 1.250 | 0.29 |
| 199_A | 239_V | 1.250 | 0.29 |
| 39_L | 252_K | 1.244 | 0.28 |
| 46_A | 279_L | 1.239 | 0.28 |
| 220_V | 384_T | 1.237 | 0.28 |
| 88_C | 202_L | 1.232 | 0.28 |
| 4_F | 8_V | 1.218 | 0.27 |
| 281_S | 384_T | 1.213 | 0.27 |
| 86_I | 98_P | 1.203 | 0.26 |
| 7_A | 216_A | 1.196 | 0.26 |
| 153_A | 187_I | 1.194 | 0.26 |
| 153_A | 457_R | 1.192 | 0.26 |
| 96_Q | 139_Y | 1.190 | 0.25 |
| 7_A | 10_E | 1.187 | 0.25 |
| 246_I | 259_Y | 1.184 | 0.25 |
| 6_A | 242_L | 1.183 | 0.25 |
| 103_L | 202_L | 1.182 | 0.25 |
| 448_P | 455_F | 1.180 | 0.25 |
| 144_V | 391_G | 1.178 | 0.25 |
| 194_L | 391_G | 1.177 | 0.25 |
| 4_F | 12_A | 1.175 | 0.25 |
| 200_V | 368_V | 1.173 | 0.25 |
| 321_F | 361_A | 1.170 | 0.24 |
| 228_E | 283_L | 1.168 | 0.24 |
| 46_A | 132_P | 1.167 | 0.24 |
| 114_V | 415_V | 1.166 | 0.24 |
| 58_E | 87_P | 1.166 | 0.24 |
| 213_F | 246_I | 1.164 | 0.24 |
| 88_C | 186_G | 1.160 | 0.24 |
| 170_P | 366_H | 1.160 | 0.24 |
| 375_Q | 414_Y | 1.159 | 0.24 |
| 176_V | 392_D | 1.158 | 0.24 |
| 234_A | 240_N | 1.157 | 0.24 |
| 44_T | 282_Q | 1.156 | 0.24 |
| 177_T | 239_V | 1.156 | 0.24 |
| 120_D | 264_S | 1.148 | 0.23 |
| 148_Q | 361_A | 1.145 | 0.23 |
| 150_K | 203_V | 1.145 | 0.23 |
| 60_A | 245_N | 1.143 | 0.23 |
| 87_P | 217_W | 1.143 | 0.23 |
| 188_F | 233_W | 1.143 | 0.23 |
| 196_H | 415_V | 1.143 | 0.23 |
| 162_M | 233_W | 1.142 | 0.23 |
| 346_Y | 375_Q | 1.140 | 0.23 |
| 255_G | 259_Y | 1.140 | 0.23 |
| 199_A | 225_S | 1.138 | 0.23 |
| 152_V | 179_N | 1.136 | 0.23 |
| 159_N | 163_G | 1.135 | 0.23 |
| 159_N | 190_C | 1.135 | 0.23 |
| 391_G | 420_L | 1.135 | 0.23 |
| 209_D | 218_M | 1.135 | 0.23 |
| 46_A | 256_S | 1.134 | 0.23 |
| 61_I | 134_D | 1.127 | 0.22 |
| 214_P | 217_W | 1.126 | 0.22 |
| 26_E | 144_V | 1.126 | 0.22 |
| 75_L | 340_L | 1.125 | 0.22 |
| 340_L | 389_T | 1.121 | 0.22 |
| 240_N | 401_F | 1.121 | 0.22 |
| 100_Q | 379_L | 1.118 | 0.22 |
| 463_W | 466_N | 1.118 | 0.22 |
| 153_A | 399_T | 1.117 | 0.22 |
| 335_V | 363_D | 1.106 | 0.21 |
| 153_A | 176_V | 1.106 | 0.21 |
| 232_A | 259_Y | 1.104 | 0.21 |
| 175_I | 347_K | 1.103 | 0.21 |
| 80_D | 246_I | 1.103 | 0.21 |
| 6_A | 35_N | 1.103 | 0.21 |
| 181_T | 454_L | 1.102 | 0.21 |
| 174_E | 213_F | 1.102 | 0.21 |
| 168_N | 196_H | 1.101 | 0.21 |
| 225_S | 358_A | 1.097 | 0.21 |
| 10_E | 117_N | 1.095 | 0.21 |
| 46_A | 51_A | 1.095 | 0.21 |
| 219_N | 452_V | 1.094 | 0.21 |
| 218_M | 253_M | 1.093 | 0.21 |
| 4_F | 78_I | 1.093 | 0.21 |
| 194_L | 276_G | 1.091 | 0.21 |
| 54_I | 87_P | 1.090 | 0.21 |
| 142_D | 239_V | 1.090 | 0.21 |
| 69_D | 284_D | 1.090 | 0.21 |
| 147_S | 404_F | 1.089 | 0.21 |
| 58_E | 61_I | 1.088 | 0.20 |
| 58_E | 190_C | 1.087 | 0.20 |
| 264_S | 452_V | 1.083 | 0.20 |
| 43_I | 164_E | 1.080 | 0.20 |
| 189_T | 218_M | 1.080 | 0.20 |
| 6_A | 10_E | 1.078 | 0.20 |
| 132_P | 258_I | 1.077 | 0.20 |
| 259_Y | 279_L | 1.077 | 0.20 |
| 183_G | 214_P | 1.076 | 0.20 |
| 273_T | 437_G | 1.075 | 0.20 |
| 55_V | 58_E | 1.072 | 0.20 |
| 409_T | 421_L | 1.072 | 0.20 |
| 59_D | 116_A | 1.069 | 0.20 |
| 140_N | 255_G | 1.068 | 0.20 |
| 32_M | 61_I | 1.068 | 0.20 |
| 114_V | 327_T | 1.068 | 0.20 |
| 208_V | 408_G | 1.066 | 0.20 |
| 27_E | 361_A | 1.064 | 0.19 |
| 323_F | 358_A | 1.061 | 0.19 |
| 53_I | 178_F | 1.060 | 0.19 |
| 40_E | 152_V | 1.060 | 0.19 |
| 446_S | 459_Y | 1.054 | 0.19 |
| 145_F | 207_H | 1.054 | 0.19 |
| 190_C | 213_F | 1.053 | 0.19 |
| 103_L | 194_L | 1.052 | 0.19 |
| 120_D | 219_N | 1.052 | 0.19 |
| 152_V | 215_T | 1.051 | 0.19 |
| 80_D | 156_H | 1.050 | 0.19 |
| 296_T | 299_A | 1.049 | 0.19 |
| 190_C | 226_A | 1.048 | 0.19 |
| 111_S | 409_T | 1.046 | 0.19 |
| 245_N | 252_K | 1.046 | 0.19 |
| 76_E | 256_S | 1.045 | 0.19 |
| 276_G | 312_F | 1.043 | 0.19 |
| 76_E | 219_N | 1.041 | 0.18 |
| 219_N | 261_P | 1.041 | 0.18 |
| 159_N | 370_G | 1.041 | 0.18 |
| 160_L | 199_A | 1.041 | 0.18 |
| 287_P | 339_D | 1.040 | 0.18 |
| 181_T | 261_P | 1.039 | 0.18 |
| 341_C | 426_L | 1.039 | 0.18 |
| 11_H | 110_N | 1.037 | 0.18 |
| 52_H | 219_N | 1.036 | 0.18 |
| 43_I | 234_A | 1.035 | 0.18 |
| 4_F | 219_N | 1.035 | 0.18 |
| 7_A | 35_N | 1.035 | 0.18 |
| 105_C | 233_W | 1.032 | 0.18 |
| 10_E | 390_C | 1.032 | 0.18 |
| 337_Q | 361_A | 1.031 | 0.18 |
| 91_R | 128_D | 1.031 | 0.18 |
| 178_F | 185_F | 1.030 | 0.18 |
| 75_L | 253_M | 1.029 | 0.18 |
| 224_L | 420_L | 1.028 | 0.18 |
| 334_T | 409_T | 1.028 | 0.18 |
| 365_L | 373_Y | 1.027 | 0.18 |
| 327_T | 340_L | 1.027 | 0.18 |
| 75_L | 136_R | 1.026 | 0.18 |
| 415_V | 419_V | 1.025 | 0.18 |
| 77_D | 118_I | 1.025 | 0.18 |
| 56_T | 230_H | 1.023 | 0.18 |
| 161_F | 193_I | 1.023 | 0.18 |
| 113_Y | 142_D | 1.023 | 0.18 |
| 14_I | 28_A | 1.023 | 0.18 |
| 232_A | 258_I | 1.022 | 0.18 |
| 208_V | 406_L | 1.022 | 0.18 |
| 336_C | 426_L | 1.022 | 0.18 |
| 212_V | 381_K | 1.022 | 0.18 |
| 75_L | 97_T | 1.022 | 0.18 |
| 267_F | 344_L | 1.021 | 0.18 |
| 238_R | 284_D | 1.021 | 0.18 |
| 54_I | 212_V | 1.021 | 0.18 |
| 103_L | 116_A | 1.019 | 0.18 |
| 159_N | 372_Y | 1.015 | 0.17 |
| 208_V | 334_T | 1.014 | 0.17 |
| 325_K | 378_T | 1.014 | 0.17 |
| 218_M | 408_G | 1.014 | 0.17 |
| 142_D | 376_I | 1.012 | 0.17 |
| 24_S | 52_H | 1.012 | 0.17 |
| 183_G | 224_L | 1.011 | 0.17 |
| 5_I | 13_A | 1.011 | 0.17 |
| 263_S | 347_K | 1.011 | 0.17 |
| 234_A | 397_A | 1.010 | 0.17 |
| 216_A | 253_M | 1.008 | 0.17 |
| 133_P | 386_N | 1.003 | 0.17 |
| 11_H | 170_P | 1.003 | 0.17 |
| 98_P | 320_E | 1.002 | 0.17 |
| 136_R | 145_F | 1.002 | 0.17 |
| 389_T | 408_G | 1.001 | 0.17 |
| 180_T | 192_D | 1.001 | 0.17 |
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 | |
| 4cyfA | 2 | 0.9809 | 100 | 0.403 | Contact Map |
| 2dyuA | 2 | 0.6723 | 100 | 0.809 | Contact Map |
| 3ivzA | 2 | 0.5447 | 100 | 0.838 | Contact Map |
| 4izuA | 1 | 0.5319 | 100 | 0.842 | Contact Map |
| 2w1vA | 2 | 0.5511 | 100 | 0.845 | Contact Map |
| 2vhhA | 4 | 0.617 | 100 | 0.845 | Contact Map |
| 3p8kA | 2 | 0.5468 | 100 | 0.848 | Contact Map |
| 4lf0A | 1 | 0.683 | 100 | 0.848 | Contact Map |
| 1f89A | 2 | 0.5468 | 100 | 0.85 | Contact Map |
| 1uf5A | 2 | 0.5915 | 100 | 0.851 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)