| E coli UvrD |
| ID: | 1515937872 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 720 (642) | ||
| Sequences: | 8832 (5782.1) | ||
| Seq/Len: | 13.757 | ||
| Nf(neff/√len): | 228.2 |
HHblits Results: (2016_02)
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: 13.757).
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 |
| 56_S | 215_T | 4.632 | 1.00 |
| 333_V | 573_V | 4.469 | 1.00 |
| 559_L | 602_G | 4.365 | 1.00 |
| 575_M | 612_L | 3.974 | 1.00 |
| 15_R | 19_A | 3.781 | 1.00 |
| 568_P | 608_Q | 3.778 | 1.00 |
| 336_R | 339_T | 3.735 | 1.00 |
| 201_L | 231_A | 3.659 | 1.00 |
| 372_M | 554_V | 3.633 | 1.00 |
| 336_R | 571_F | 3.186 | 1.00 |
| 577_E | 631_R | 3.144 | 1.00 |
| 345_G | 569_Q | 3.131 | 1.00 |
| 572_I | 602_G | 3.099 | 1.00 |
| 16_E | 275_E | 3.040 | 1.00 |
| 569_Q | 609_K | 3.021 | 1.00 |
| 13_K | 16_E | 3.009 | 1.00 |
| 10_L | 18_V | 2.978 | 1.00 |
| 349_E | 568_P | 2.907 | 1.00 |
| 568_P | 607_M | 2.901 | 1.00 |
| 230_Y | 270_D | 2.891 | 1.00 |
| 348_A | 552_D | 2.885 | 1.00 |
| 11_N | 283_Y | 2.881 | 1.00 |
| 341_Q | 347_L | 2.865 | 1.00 |
| 195_R | 198_E | 2.796 | 1.00 |
| 198_E | 202_N | 2.793 | 1.00 |
| 287_S | 291_S | 2.756 | 1.00 |
| 346_A | 552_D | 2.709 | 1.00 |
| 20_A | 25_L | 2.707 | 1.00 |
| 176_A | 179_E | 2.689 | 1.00 |
| 86_W | 214_F | 2.629 | 1.00 |
| 337_I | 350_C | 2.575 | 1.00 |
| 336_R | 611_T | 2.511 | 1.00 |
| 94_A | 196_A | 2.401 | 1.00 |
| 234_R | 270_D | 2.393 | 1.00 |
| 334_V | 370_A | 2.367 | 1.00 |
| 347_L | 373_P | 2.277 | 1.00 |
| 355_R | 595_E | 2.275 | 1.00 |
| 338_K | 370_A | 2.244 | 1.00 |
| 481_T | 516_T | 2.242 | 1.00 |
| 407_F | 411_V | 2.228 | 1.00 |
| 126_L | 180_A | 2.226 | 1.00 |
| 354_Y | 556_L | 2.226 | 1.00 |
| 200_W | 207_L | 2.203 | 1.00 |
| 53_S | 56_S | 2.194 | 1.00 |
| 147_N | 190_A | 2.191 | 1.00 |
| 571_F | 611_T | 2.190 | 1.00 |
| 569_Q | 611_T | 2.187 | 1.00 |
| 88_G | 93_L | 2.168 | 1.00 |
| 187_V | 195_R | 2.125 | 1.00 |
| 101_H | 209_H | 2.100 | 1.00 |
| 352_I | 367_L | 2.087 | 1.00 |
| 193_L | 228_I | 2.079 | 1.00 |
| 25_L | 277_I | 2.074 | 1.00 |
| 41_H | 77_L | 2.050 | 1.00 |
| 320_L | 614_Y | 2.048 | 1.00 |
| 180_A | 183_R | 2.043 | 1.00 |
| 262_E | 266_R | 2.031 | 1.00 |
| 299_N | 635_E | 2.029 | 1.00 |
| 346_A | 349_E | 2.026 | 1.00 |
| 160_Q | 175_Q | 2.014 | 1.00 |
| 329_E | 613_T | 2.013 | 1.00 |
| 557_M | 567_F | 1.994 | 1.00 |
| 207_L | 211_R | 1.992 | 1.00 |
| 482_D | 513_V | 1.988 | 1.00 |
| 114_L | 186_L | 1.986 | 1.00 |
| 345_G | 350_C | 1.986 | 1.00 |
| 104_D | 206_I | 1.985 | 1.00 |
| 101_H | 210_Y | 1.985 | 1.00 |
| 204_P | 207_L | 1.983 | 1.00 |
| 335_N | 370_A | 1.975 | 1.00 |
| 323_A | 332_F | 1.971 | 1.00 |
| 5_Y | 8_D | 1.963 | 1.00 |
| 559_L | 580_F | 1.949 | 1.00 |
| 363_L | 573_V | 1.949 | 1.00 |
| 603_V | 610_L | 1.942 | 1.00 |
| 43_I | 59_A | 1.936 | 1.00 |
| 332_F | 613_T | 1.934 | 1.00 |
| 491_R | 506_I | 1.930 | 1.00 |
| 341_Q | 350_C | 1.916 | 1.00 |
| 572_I | 612_L | 1.906 | 1.00 |
| 340_W | 571_F | 1.896 | 1.00 |
| 179_E | 183_R | 1.895 | 1.00 |
| 102_H | 187_V | 1.877 | 1.00 |
| 231_A | 234_R | 1.866 | 1.00 |
| 155_R | 158_H | 1.864 | 1.00 |
| 519_F | 533_A | 1.864 | 1.00 |
| 37_R | 41_H | 1.858 | 1.00 |
| 208_Q | 212_E | 1.855 | 1.00 |
| 129_A | 176_A | 1.828 | 1.00 |
| 13_K | 281_Q | 1.822 | 1.00 |
| 250_D | 303_R | 1.818 | 1.00 |
| 345_G | 608_Q | 1.809 | 1.00 |
| 483_R | 487_D | 1.804 | 1.00 |
| 201_L | 235_L | 1.801 | 1.00 |
| 403_D | 406_A | 1.788 | 1.00 |
| 387_E | 508_N | 1.762 | 1.00 |
| 180_A | 184_A | 1.738 | 1.00 |
| 153_G | 228_I | 1.717 | 1.00 |
| 27_V | 244_M | 1.713 | 1.00 |
| 197_H | 232_W | 1.708 | 1.00 |
| 366_A | 370_A | 1.702 | 1.00 |
| 340_W | 350_C | 1.701 | 1.00 |
| 340_W | 569_Q | 1.695 | 1.00 |
| 322_C | 614_Y | 1.689 | 1.00 |
| 178_Q | 181_C | 1.688 | 1.00 |
| 175_Q | 179_E | 1.680 | 1.00 |
| 295_A | 637_P | 1.678 | 1.00 |
| 227_N | 260_Q | 1.670 | 1.00 |
| 176_A | 180_A | 1.650 | 1.00 |
| 58_M | 217_I | 1.650 | 1.00 |
| 331_R | 370_A | 1.649 | 1.00 |
| 467_A | 487_D | 1.644 | 1.00 |
| 397_L | 410_V | 1.639 | 1.00 |
| 25_L | 244_M | 1.634 | 1.00 |
| 281_Q | 309_W | 1.633 | 1.00 |
| 333_V | 363_L | 1.619 | 1.00 |
| 126_L | 173_V | 1.613 | 1.00 |
| 122_L | 180_A | 1.613 | 1.00 |
| 129_A | 180_A | 1.611 | 1.00 |
| 125_R | 180_A | 1.610 | 1.00 |
| 72_H | 76_Q | 1.610 | 1.00 |
| 123_L | 143_M | 1.610 | 1.00 |
| 629_P | 633_I | 1.609 | 1.00 |
| 354_Y | 360_S | 1.607 | 1.00 |
| 149_Q | 159_I | 1.606 | 1.00 |
| 478_H | 520_S | 1.598 | 1.00 |
| 69_E | 73_R | 1.596 | 1.00 |
| 296_L | 603_V | 1.595 | 1.00 |
| 292_A | 318_I | 1.591 | 1.00 |
| 219_V | 233_I | 1.588 | 1.00 |
| 97_L | 196_A | 1.585 | 1.00 |
| 340_W | 609_K | 1.584 | 1.00 |
| 575_M | 599_A | 1.584 | 1.00 |
| 319_S | 336_R | 1.582 | 1.00 |
| 489_G | 492_T | 1.582 | 1.00 |
| 46_L | 216_N | 1.574 | 1.00 |
| 268_L | 276_T | 1.573 | 1.00 |
| 292_A | 603_V | 1.567 | 1.00 |
| 241_G | 273_G | 1.561 | 1.00 |
| 19_A | 45_W | 1.558 | 1.00 |
| 492_T | 495_E | 1.558 | 1.00 |
| 319_S | 609_K | 1.557 | 1.00 |
| 97_L | 210_Y | 1.544 | 1.00 |
| 200_W | 235_L | 1.542 | 1.00 |
| 130_M | 176_A | 1.539 | 1.00 |
| 390_D | 409_R | 1.537 | 1.00 |
| 157_H | 175_Q | 1.527 | 1.00 |
| 334_V | 366_A | 1.522 | 1.00 |
| 123_L | 173_V | 1.518 | 1.00 |
| 490_L | 494_Y | 1.518 | 1.00 |
| 43_I | 74_I | 1.513 | 1.00 |
| 333_V | 571_F | 1.511 | 1.00 |
| 210_Y | 214_F | 1.506 | 1.00 |
| 391_A | 509_L | 1.506 | 1.00 |
| 91_H | 192_L | 1.505 | 1.00 |
| 407_F | 441_C | 1.498 | 1.00 |
| 222_F | 230_Y | 1.497 | 1.00 |
| 331_R | 366_A | 1.488 | 1.00 |
| 412_N | 416_R | 1.482 | 1.00 |
| 126_L | 176_A | 1.472 | 1.00 |
| 126_L | 130_M | 1.464 | 1.00 |
| 516_T | 534_F | 1.463 | 1.00 |
| 204_P | 208_Q | 1.461 | 1.00 |
| 282_N | 285_S | 1.459 | 1.00 |
| 393_S | 409_R | 1.456 | 1.00 |
| 45_W | 49_V | 1.453 | 1.00 |
| 97_L | 200_W | 1.450 | 1.00 |
| 596_R | 635_E | 1.438 | 1.00 |
| 197_H | 231_A | 1.431 | 1.00 |
| 599_A | 603_V | 1.430 | 1.00 |
| 323_A | 613_T | 1.428 | 1.00 |
| 336_R | 340_W | 1.421 | 1.00 |
| 347_L | 350_C | 1.419 | 1.00 |
| 203_K | 206_I | 1.418 | 1.00 |
| 340_W | 345_G | 1.413 | 1.00 |
| 208_Q | 211_R | 1.398 | 0.99 |
| 7_L | 15_R | 1.391 | 0.99 |
| 74_I | 87_V | 1.389 | 0.99 |
| 375_R | 553_A | 1.387 | 0.99 |
| 329_E | 574_G | 1.386 | 0.99 |
| 44_A | 77_L | 1.381 | 0.99 |
| 216_N | 242_K | 1.380 | 0.99 |
| 338_K | 347_L | 1.379 | 0.99 |
| 13_K | 280_E | 1.379 | 0.99 |
| 47_M | 78_M | 1.377 | 0.99 |
| 491_R | 510_E | 1.370 | 0.99 |
| 217_I | 237_A | 1.364 | 0.99 |
| 252_S | 255_G | 1.359 | 0.99 |
| 345_G | 568_P | 1.359 | 0.99 |
| 352_I | 363_L | 1.358 | 0.99 |
| 337_I | 554_V | 1.352 | 0.99 |
| 31_A | 294_N | 1.351 | 0.99 |
| 158_H | 161_S | 1.343 | 0.99 |
| 12_D | 15_R | 1.343 | 0.99 |
| 366_A | 369_Q | 1.336 | 0.99 |
| 93_L | 97_L | 1.336 | 0.99 |
| 337_I | 347_L | 1.328 | 0.99 |
| 207_L | 235_L | 1.323 | 0.99 |
| 12_D | 16_E | 1.320 | 0.99 |
| 367_L | 556_L | 1.316 | 0.99 |
| 340_W | 611_T | 1.316 | 0.99 |
| 98_L | 196_A | 1.314 | 0.99 |
| 426_V | 437_L | 1.313 | 0.99 |
| 17_A | 27_V | 1.313 | 0.99 |
| 58_M | 214_F | 1.310 | 0.99 |
| 337_I | 571_F | 1.305 | 0.99 |
| 421_R | 425_V | 1.305 | 0.99 |
| 266_R | 270_D | 1.295 | 0.99 |
| 575_M | 580_F | 1.288 | 0.99 |
| 396_R | 539_A | 1.287 | 0.99 |
| 316_E | 609_K | 1.284 | 0.99 |
| 150_K | 191_E | 1.267 | 0.99 |
| 399_A | 532_Q | 1.247 | 0.99 |
| 347_L | 372_M | 1.246 | 0.98 |
| 569_Q | 608_Q | 1.242 | 0.98 |
| 169_T | 172_K | 1.232 | 0.98 |
| 530_P | 533_A | 1.231 | 0.98 |
| 116_S | 119_Q | 1.222 | 0.98 |
| 182_D | 195_R | 1.221 | 0.98 |
| 178_Q | 182_D | 1.220 | 0.98 |
| 108_P | 185_G | 1.220 | 0.98 |
| 429_T | 440_A | 1.214 | 0.98 |
| 196_A | 232_W | 1.212 | 0.98 |
| 387_E | 505_R | 1.209 | 0.98 |
| 193_L | 232_W | 1.207 | 0.98 |
| 491_R | 495_E | 1.204 | 0.98 |
| 172_K | 175_Q | 1.199 | 0.98 |
| 419_G | 422_T | 1.196 | 0.98 |
| 359_Q | 574_G | 1.196 | 0.98 |
| 320_L | 641_V | 1.191 | 0.98 |
| 391_A | 512_L | 1.187 | 0.98 |
| 391_A | 481_T | 1.184 | 0.98 |
| 636_L | 640_C | 1.182 | 0.98 |
| 60_V | 93_L | 1.175 | 0.98 |
| 104_D | 203_K | 1.175 | 0.98 |
| 127_I | 132_L | 1.166 | 0.97 |
| 576_E | 615_A | 1.163 | 0.97 |
| 350_C | 569_Q | 1.154 | 0.97 |
| 334_V | 554_V | 1.153 | 0.97 |
| 354_Y | 573_V | 1.152 | 0.97 |
| 571_F | 613_T | 1.152 | 0.97 |
| 233_I | 243_V | 1.150 | 0.97 |
| 154_L | 159_I | 1.149 | 0.97 |
| 8_D | 15_R | 1.148 | 0.97 |
| 375_R | 555_Q | 1.145 | 0.97 |
| 6_L | 41_H | 1.144 | 0.97 |
| 397_L | 407_F | 1.139 | 0.97 |
| 197_H | 235_L | 1.135 | 0.97 |
| 100_A | 213_R | 1.128 | 0.97 |
| 86_W | 96_R | 1.127 | 0.97 |
| 26_L | 276_T | 1.127 | 0.97 |
| 325_N | 328_D | 1.125 | 0.97 |
| 23_S | 242_K | 1.124 | 0.97 |
| 321_Y | 332_F | 1.121 | 0.97 |
| 16_E | 19_A | 1.119 | 0.96 |
| 46_L | 52_C | 1.119 | 0.96 |
| 326_E | 362_V | 1.115 | 0.96 |
| 225_T | 263_N | 1.115 | 0.96 |
| 361_R | 365_E | 1.114 | 0.96 |
| 345_G | 349_E | 1.107 | 0.96 |
| 42_R | 244_M | 1.106 | 0.96 |
| 328_D | 331_R | 1.105 | 0.96 |
| 350_C | 571_F | 1.102 | 0.96 |
| 234_R | 271_F | 1.101 | 0.96 |
| 156_P | 174_Y | 1.101 | 0.96 |
| 396_R | 406_A | 1.100 | 0.96 |
| 336_R | 609_K | 1.099 | 0.96 |
| 96_R | 100_A | 1.094 | 0.96 |
| 288_N | 318_I | 1.091 | 0.96 |
| 566_E | 607_M | 1.091 | 0.96 |
| 125_R | 408_E | 1.089 | 0.96 |
| 196_A | 200_W | 1.089 | 0.96 |
| 218_L | 244_M | 1.088 | 0.96 |
| 374_Y | 556_L | 1.087 | 0.96 |
| 330_A | 363_L | 1.081 | 0.95 |
| 9_S | 41_H | 1.074 | 0.95 |
| 478_H | 482_D | 1.074 | 0.95 |
| 476_P | 479_V | 1.072 | 0.95 |
| 293_A | 603_V | 1.066 | 0.95 |
| 322_C | 616_E | 1.063 | 0.95 |
| 123_L | 139_P | 1.059 | 0.95 |
| 436_T | 439_Q | 1.059 | 0.95 |
| 332_F | 336_R | 1.058 | 0.95 |
| 28_L | 249_D | 1.057 | 0.95 |
| 93_L | 210_Y | 1.055 | 0.95 |
| 168_Q | 172_K | 1.049 | 0.94 |
| 557_M | 562_A | 1.048 | 0.94 |
| 402_N | 436_T | 1.047 | 0.94 |
| 39_L | 218_L | 1.046 | 0.94 |
| 398_I | 484_V | 1.044 | 0.94 |
| 515_A | 534_F | 1.044 | 0.94 |
| 105_A | 199_L | 1.038 | 0.94 |
| 267_F | 274_A | 1.031 | 0.94 |
| 391_A | 485_I | 1.030 | 0.94 |
| 68_A | 72_H | 1.030 | 0.94 |
| 95_H | 99_R | 1.028 | 0.94 |
| 160_Q | 171_Q | 1.028 | 0.94 |
| 293_A | 604_T | 1.025 | 0.93 |
| 52_C | 56_S | 1.023 | 0.93 |
| 266_R | 269_N | 1.022 | 0.93 |
| 317_P | 642_E | 1.022 | 0.93 |
| 227_N | 231_A | 1.017 | 0.93 |
| 65_K | 69_E | 1.015 | 0.93 |
| 150_K | 178_Q | 1.014 | 0.93 |
| 20_A | 23_S | 1.014 | 0.93 |
| 367_L | 554_V | 1.013 | 0.93 |
| 194_L | 228_I | 1.012 | 0.93 |
| 298_E | 307_K | 1.010 | 0.93 |
| 268_L | 304_L | 1.009 | 0.93 |
| 386_Q | 413_T | 1.008 | 0.93 |
| 439_Q | 443_E | 1.007 | 0.93 |
| 296_L | 599_A | 1.007 | 0.93 |
| 288_N | 640_C | 1.006 | 0.93 |
| 187_V | 192_L | 1.005 | 0.93 |
| 200_W | 210_Y | 1.005 | 0.93 |
| 381_R | 384_E | 1.005 | 0.93 |
| 26_L | 245_I | 1.003 | 0.93 |
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 | |
| 1pjrA | 1 | 0.8597 | 100 | 0.094 | Contact Map |
| 4c2tA | 4 | 0.8931 | 100 | 0.094 | Contact Map |
| 1uaaA | 2 | 0.8764 | 100 | 0.274 | Contact Map |
| 3lfuA | 1 | 0.8792 | 100 | 0.287 | Contact Map |
| 4c2uA | 2 | 0.8917 | 100 | 0.298 | Contact Map |
| 3u4qA | 1 | 0.9083 | 100 | 0.321 | Contact Map |
| 1w36B | 2 | 0.9333 | 100 | 0.38 | Contact Map |
| 3u4qB | 1 | 0.9097 | 100 | 0.465 | Contact Map |
| 4pj3A | 1 | 0.7 | 100 | 0.633 | Contact Map |
| 2xzlA | 1 | 0.5667 | 100 | 0.706 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)