| cdc20 -force run |
| ID: | 1452598384 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 499 (499) | ||
| Sequences: | 55 (34.6) | ||
| Seq/Len: | 0.110 | ||
| Nf(neff/√len): | 1.5 |
Jackhmmer Results: (2015_08)
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: 0.110).
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 |
| 403_C | 408_S | 2.006 | 0.44 |
| 232_V | 393_L | 1.897 | 0.38 |
| 408_S | 425_L | 1.883 | 0.38 |
| 403_C | 425_L | 1.797 | 0.34 |
| 109_K | 237_E | 1.756 | 0.32 |
| 170_S | 183_N | 1.729 | 0.31 |
| 7_E | 163_K | 1.675 | 0.28 |
| 129_K | 137_P | 1.595 | 0.25 |
| 94_L | 183_N | 1.594 | 0.25 |
| 279_Y | 334_N | 1.564 | 0.24 |
| 169_P | 467_L | 1.555 | 0.24 |
| 23_A | 26_A | 1.545 | 0.23 |
| 73_K | 117_A | 1.534 | 0.23 |
| 273_S | 309_S | 1.512 | 0.22 |
| 415_I | 449_L | 1.486 | 0.21 |
| 70_T | 113_Q | 1.477 | 0.21 |
| 138_Q | 356_G | 1.474 | 0.21 |
| 170_S | 448_S | 1.459 | 0.20 |
| 266_S | 356_G | 1.454 | 0.20 |
| 302_V | 337_P | 1.438 | 0.20 |
| 370_V | 443_T | 1.426 | 0.19 |
| 108_T | 266_S | 1.419 | 0.19 |
| 333_V | 373_T | 1.418 | 0.19 |
| 89_E | 383_R | 1.411 | 0.19 |
| 433_M | 469_L | 1.409 | 0.19 |
| 417_G | 449_L | 1.371 | 0.17 |
| 403_C | 424_Q | 1.370 | 0.17 |
| 53_G | 233_A | 1.365 | 0.17 |
| 356_G | 378_S | 1.364 | 0.17 |
| 121_N | 130_I | 1.362 | 0.17 |
| 321_G | 359_K | 1.356 | 0.17 |
| 7_E | 151_L | 1.347 | 0.17 |
| 75_G | 149_K | 1.344 | 0.17 |
| 4_F | 414_L | 1.334 | 0.16 |
| 144_Y | 232_V | 1.327 | 0.16 |
| 151_L | 304_T | 1.326 | 0.16 |
| 290_I | 312_V | 1.324 | 0.16 |
| 210_S | 248_A | 1.321 | 0.16 |
| 58_R | 471_R | 1.318 | 0.16 |
| 107_P | 309_S | 1.315 | 0.16 |
| 44_R | 304_T | 1.308 | 0.16 |
| 144_Y | 281_L | 1.304 | 0.16 |
| 121_N | 298_A | 1.298 | 0.15 |
| 287_S | 319_P | 1.293 | 0.15 |
| 26_A | 133_L | 1.283 | 0.15 |
| 393_L | 422_Q | 1.282 | 0.15 |
| 138_Q | 378_S | 1.279 | 0.15 |
| 285_S | 305_L | 1.273 | 0.15 |
| 2_A | 495_H | 1.272 | 0.15 |
| 350_T | 444_S | 1.272 | 0.15 |
| 122_G | 141_P | 1.266 | 0.15 |
| 389_S | 474_E | 1.256 | 0.14 |
| 307_G | 312_V | 1.253 | 0.14 |
| 9_D | 261_L | 1.253 | 0.14 |
| 384_I | 394_S | 1.251 | 0.14 |
| 268_S | 456_A | 1.243 | 0.14 |
| 455_G | 472_C | 1.242 | 0.14 |
| 134_S | 151_L | 1.240 | 0.14 |
| 298_A | 462_A | 1.240 | 0.14 |
| 348_L | 448_S | 1.240 | 0.14 |
| 30_R | 381_H | 1.240 | 0.14 |
| 119_N | 351_F | 1.238 | 0.14 |
| 53_G | 451_M | 1.236 | 0.14 |
| 370_V | 373_T | 1.236 | 0.14 |
| 42_P | 291_H | 1.235 | 0.14 |
| 243_V | 282_S | 1.233 | 0.14 |
| 149_K | 282_S | 1.231 | 0.14 |
| 133_L | 378_S | 1.230 | 0.14 |
| 19_P | 275_S | 1.223 | 0.14 |
| 237_E | 422_Q | 1.221 | 0.13 |
| 425_L | 458_V | 1.218 | 0.13 |
| 93_F | 351_F | 1.218 | 0.13 |
| 291_H | 298_A | 1.218 | 0.13 |
| 226_G | 415_I | 1.214 | 0.13 |
| 328_G | 466_T | 1.196 | 0.13 |
| 26_A | 137_P | 1.194 | 0.13 |
| 491_S | 494_I | 1.194 | 0.13 |
| 144_Y | 154_Q | 1.189 | 0.13 |
| 305_L | 415_I | 1.189 | 0.13 |
| 186_Y | 191_D | 1.184 | 0.13 |
| 15_Q | 86_A | 1.182 | 0.13 |
| 163_K | 232_V | 1.181 | 0.13 |
| 30_R | 475_L | 1.180 | 0.13 |
| 42_P | 462_A | 1.180 | 0.13 |
| 429_K | 466_T | 1.178 | 0.12 |
| 199_A | 457_T | 1.178 | 0.12 |
| 280_I | 449_L | 1.177 | 0.12 |
| 297_V | 462_A | 1.177 | 0.12 |
| 207_Y | 358_V | 1.176 | 0.12 |
| 207_Y | 234_W | 1.175 | 0.12 |
| 26_A | 356_G | 1.174 | 0.12 |
| 252_L | 457_T | 1.171 | 0.12 |
| 73_K | 373_T | 1.170 | 0.12 |
| 149_K | 243_V | 1.170 | 0.12 |
| 3_Q | 232_V | 1.165 | 0.12 |
| 94_L | 387_V | 1.165 | 0.12 |
| 233_A | 243_V | 1.165 | 0.12 |
| 172_P | 287_S | 1.162 | 0.12 |
| 171_L | 459_A | 1.162 | 0.12 |
| 74_P | 87_Q | 1.159 | 0.12 |
| 349_Q | 368_S | 1.158 | 0.12 |
| 42_P | 443_T | 1.155 | 0.12 |
| 260_R | 367_Q | 1.152 | 0.12 |
| 62_K | 75_G | 1.152 | 0.12 |
| 404_S | 482_E | 1.149 | 0.12 |
| 41_S | 215_D | 1.149 | 0.12 |
| 7_E | 232_V | 1.145 | 0.12 |
| 251_Q | 405_I | 1.144 | 0.12 |
| 54_R | 434_A | 1.144 | 0.12 |
| 285_S | 307_G | 1.141 | 0.12 |
| 138_Q | 266_S | 1.139 | 0.12 |
| 214_G | 421_A | 1.136 | 0.12 |
| 213_S | 282_S | 1.135 | 0.12 |
| 282_S | 299_E | 1.133 | 0.11 |
| 291_H | 462_A | 1.132 | 0.11 |
| 51_S | 99_N | 1.128 | 0.11 |
| 183_N | 378_S | 1.124 | 0.11 |
| 54_R | 59_T | 1.123 | 0.11 |
| 422_Q | 456_A | 1.123 | 0.11 |
| 251_Q | 266_S | 1.123 | 0.11 |
| 297_V | 383_R | 1.123 | 0.11 |
| 106_T | 278_S | 1.120 | 0.11 |
| 151_L | 163_K | 1.116 | 0.11 |
| 291_H | 301_H | 1.116 | 0.11 |
| 347_P | 463_A | 1.116 | 0.11 |
| 53_G | 69_T | 1.116 | 0.11 |
| 87_Q | 133_L | 1.114 | 0.11 |
| 133_L | 356_G | 1.111 | 0.11 |
| 87_Q | 236_K | 1.110 | 0.11 |
| 49_S | 76_G | 1.109 | 0.11 |
| 9_D | 414_L | 1.108 | 0.11 |
| 268_S | 420_F | 1.108 | 0.11 |
| 248_A | 433_M | 1.106 | 0.11 |
| 16_L | 462_A | 1.103 | 0.11 |
| 169_P | 407_W | 1.103 | 0.11 |
| 144_Y | 480_R | 1.101 | 0.11 |
| 333_V | 459_A | 1.100 | 0.11 |
| 7_E | 291_H | 1.100 | 0.11 |
| 82_H | 218_Q | 1.100 | 0.11 |
| 201_A | 272_G | 1.099 | 0.11 |
| 233_A | 236_K | 1.099 | 0.11 |
| 443_T | 467_L | 1.098 | 0.11 |
| 120_L | 304_T | 1.097 | 0.11 |
| 407_W | 467_L | 1.097 | 0.11 |
| 58_R | 248_A | 1.095 | 0.11 |
| 13_L | 193_S | 1.093 | 0.11 |
| 102_E | 415_I | 1.092 | 0.11 |
| 268_S | 349_Q | 1.091 | 0.11 |
| 147_R | 255_V | 1.090 | 0.11 |
| 433_M | 455_G | 1.090 | 0.11 |
| 140_A | 333_V | 1.089 | 0.11 |
| 335_V | 422_Q | 1.089 | 0.11 |
| 121_N | 297_V | 1.088 | 0.11 |
| 92_S | 404_S | 1.087 | 0.11 |
| 259_K | 310_Q | 1.087 | 0.11 |
| 110_K | 299_E | 1.086 | 0.11 |
| 39_A | 427_I | 1.086 | 0.11 |
| 88_M | 384_I | 1.086 | 0.11 |
| 8_S | 21_P | 1.085 | 0.11 |
| 477_P | 492_S | 1.085 | 0.11 |
| 281_L | 436_V | 1.084 | 0.10 |
| 189_L | 199_A | 1.084 | 0.10 |
| 28_W | 31_K | 1.084 | 0.10 |
| 183_N | 448_S | 1.083 | 0.10 |
| 147_R | 298_A | 1.082 | 0.10 |
| 236_K | 255_V | 1.081 | 0.10 |
| 156_A | 378_S | 1.080 | 0.10 |
| 408_S | 424_Q | 1.080 | 0.10 |
| 210_S | 427_I | 1.080 | 0.10 |
| 393_L | 456_A | 1.080 | 0.10 |
| 87_Q | 90_V | 1.079 | 0.10 |
| 361_V | 373_T | 1.076 | 0.10 |
| 61_G | 307_G | 1.076 | 0.10 |
| 93_F | 337_P | 1.075 | 0.10 |
| 200_V | 373_T | 1.075 | 0.10 |
| 103_N | 493_L | 1.075 | 0.10 |
| 426_V | 443_T | 1.074 | 0.10 |
| 415_I | 458_V | 1.074 | 0.10 |
| 323_H | 335_V | 1.073 | 0.10 |
| 189_L | 457_T | 1.072 | 0.10 |
| 175_I | 427_I | 1.072 | 0.10 |
| 36_A | 144_Y | 1.071 | 0.10 |
| 89_E | 297_V | 1.067 | 0.10 |
| 148_L | 298_A | 1.067 | 0.10 |
| 106_T | 432_T | 1.067 | 0.10 |
| 149_K | 183_N | 1.065 | 0.10 |
| 30_R | 197_V | 1.064 | 0.10 |
| 426_V | 438_E | 1.062 | 0.10 |
| 16_L | 298_A | 1.062 | 0.10 |
| 26_A | 138_Q | 1.058 | 0.10 |
| 261_L | 414_L | 1.058 | 0.10 |
| 384_I | 436_V | 1.058 | 0.10 |
| 206_V | 260_R | 1.058 | 0.10 |
| 156_A | 183_N | 1.055 | 0.10 |
| 208_L | 227_E | 1.055 | 0.10 |
| 151_L | 301_H | 1.054 | 0.10 |
| 362_A | 409_P | 1.054 | 0.10 |
| 251_Q | 309_S | 1.053 | 0.10 |
| 11_H | 398_A | 1.052 | 0.10 |
| 169_P | 347_P | 1.052 | 0.10 |
| 89_E | 370_V | 1.051 | 0.10 |
| 285_S | 387_V | 1.051 | 0.10 |
| 73_K | 149_K | 1.050 | 0.10 |
| 157_T | 218_Q | 1.050 | 0.10 |
| 107_P | 407_W | 1.050 | 0.10 |
| 189_L | 219_L | 1.049 | 0.10 |
| 70_T | 213_S | 1.048 | 0.10 |
| 151_L | 291_H | 1.048 | 0.10 |
| 221_Q | 462_A | 1.048 | 0.10 |
| 185_Y | 358_V | 1.047 | 0.10 |
| 285_S | 297_V | 1.047 | 0.10 |
| 58_R | 89_E | 1.047 | 0.10 |
| 30_R | 462_A | 1.044 | 0.10 |
| 14_L | 334_N | 1.043 | 0.10 |
| 437_A | 493_L | 1.041 | 0.10 |
| 183_N | 356_G | 1.041 | 0.10 |
| 98_E | 417_G | 1.041 | 0.10 |
| 133_L | 182_R | 1.041 | 0.10 |
| 347_P | 467_L | 1.041 | 0.10 |
| 261_L | 351_F | 1.040 | 0.10 |
| 163_K | 304_T | 1.039 | 0.10 |
| 335_V | 484_E | 1.038 | 0.10 |
| 148_L | 369_N | 1.038 | 0.10 |
| 2_A | 26_A | 1.038 | 0.10 |
| 134_S | 140_A | 1.036 | 0.10 |
| 492_S | 496_Q | 1.035 | 0.10 |
| 208_L | 362_A | 1.032 | 0.10 |
| 218_Q | 433_M | 1.031 | 0.10 |
| 22_N | 356_G | 1.030 | 0.09 |
| 141_P | 281_L | 1.029 | 0.09 |
| 312_V | 404_S | 1.028 | 0.09 |
| 121_N | 129_K | 1.026 | 0.09 |
| 340_P | 493_L | 1.025 | 0.09 |
| 259_K | 481_R | 1.025 | 0.09 |
| 197_V | 212_S | 1.025 | 0.09 |
| 26_A | 147_R | 1.025 | 0.09 |
| 144_Y | 148_L | 1.024 | 0.09 |
| 214_G | 238_G | 1.023 | 0.09 |
| 211_A | 287_S | 1.023 | 0.09 |
| 66_K | 449_L | 1.022 | 0.09 |
| 249_E | 263_N | 1.022 | 0.09 |
| 261_L | 349_Q | 1.021 | 0.09 |
| 256_Q | 420_F | 1.019 | 0.09 |
| 460_S | 472_C | 1.019 | 0.09 |
| 328_G | 429_K | 1.019 | 0.09 |
| 185_Y | 335_V | 1.018 | 0.09 |
| 82_H | 285_S | 1.017 | 0.09 |
| 121_N | 462_A | 1.015 | 0.09 |
| 170_S | 335_V | 1.015 | 0.09 |
| 285_S | 474_E | 1.015 | 0.09 |
| 266_S | 399_H | 1.015 | 0.09 |
| 89_E | 282_S | 1.014 | 0.09 |
| 79_Y | 361_V | 1.013 | 0.09 |
| 36_A | 232_V | 1.012 | 0.09 |
| 283_S | 293_H | 1.012 | 0.09 |
| 173_D | 451_M | 1.012 | 0.09 |
| 282_S | 368_S | 1.010 | 0.09 |
| 185_Y | 241_L | 1.010 | 0.09 |
| 71_P | 113_Q | 1.009 | 0.09 |
| 20_I | 158_P | 1.009 | 0.09 |
| 138_Q | 183_N | 1.008 | 0.09 |
| 2_A | 137_P | 1.007 | 0.09 |
| 279_Y | 449_L | 1.006 | 0.09 |
| 250_V | 420_F | 1.006 | 0.09 |
| 49_S | 85_A | 1.005 | 0.09 |
| 159_G | 221_Q | 1.005 | 0.09 |
| 280_I | 424_Q | 1.005 | 0.09 |
| 185_Y | 422_Q | 1.005 | 0.09 |
| 171_L | 417_G | 1.004 | 0.09 |
| 61_G | 351_F | 1.004 | 0.09 |
| 251_Q | 322_R | 1.003 | 0.09 |
| 181_I | 457_T | 1.003 | 0.09 |
| 7_E | 304_T | 1.002 | 0.09 |
| 108_T | 485_K | 1.002 | 0.09 |
| 189_L | 427_I | 1.002 | 0.09 |
| 173_D | 410_H | 1.002 | 0.09 |
| 241_L | 466_T | 1.001 | 0.09 |
| 411_Y | 477_P | 1.000 | 0.09 |
| 163_K | 301_H | 1.000 | 0.09 |
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 | |
| 4ggaA | 1 | 0.6293 | 100 | 0.675 | Contact Map |
| 4aezA | 3 | 0.6493 | 100 | 0.714 | Contact Map |
| 4ui9R | 1 | 0 | 100 | 0.748 | Contact Map |
| 4ggcA | 1 | 0.6273 | 100 | 0.752 | Contact Map |
| 4bh6A | 8 | 0.6112 | 100 | 0.774 | Contact Map |
| 1vyhC | 10 | 0.5852 | 100 | 0.847 | Contact Map |
| 4wjuA | 2 | 0.7255 | 100 | 0.86 | Contact Map |
| 1gotB | 1 | 0.6573 | 100 | 0.862 | Contact Map |
| 3dwlC | 2 | 0.5531 | 100 | 0.865 | Contact Map |
| 3ow8A | 4 | 0.5832 | 100 | 0.865 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)