| CCT1_yeast |
| ID: | 1402323378 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 559 (528) | ||
| Sequences: | 4617 (2144.1) | ||
| Seq/Len: | 8.744 | ||
| Nf(neff/√len): | 93.3 |
Jackhmmer Results: (2014_04_16)
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: 8.744).
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 |
| 145_S | 521_T | 4.302 | 1.00 |
| 511_D | 514_H | 4.230 | 1.00 |
| 140_I | 521_T | 4.222 | 1.00 |
| 135_E | 138_R | 4.093 | 1.00 |
| 503_D | 506_R | 3.795 | 1.00 |
| 153_K | 182_D | 3.535 | 1.00 |
| 139_F | 142_E | 3.420 | 1.00 |
| 311_V | 366_F | 3.290 | 1.00 |
| 503_D | 510_V | 3.287 | 1.00 |
| 440_V | 448_I | 3.043 | 1.00 |
| 473_L | 509_I | 3.023 | 1.00 |
| 178_N | 182_D | 3.011 | 1.00 |
| 157_I | 178_N | 2.843 | 1.00 |
| 359_D | 376_G | 2.840 | 1.00 |
| 510_V | 515_A | 2.755 | 1.00 |
| 502_L | 507_G | 2.742 | 1.00 |
| 459_P | 477_L | 2.657 | 1.00 |
| 426_E | 524_K | 2.637 | 1.00 |
| 64_N | 69_I | 2.621 | 1.00 |
| 499_N | 511_D | 2.587 | 1.00 |
| 131_V | 444_E | 2.483 | 1.00 |
| 133_L | 528_L | 2.446 | 1.00 |
| 433_L | 448_I | 2.445 | 1.00 |
| 111_R | 453_A | 2.441 | 1.00 |
| 108_L | 129_F | 2.424 | 1.00 |
| 130_R | 536_V | 2.413 | 1.00 |
| 129_F | 532_L | 2.394 | 1.00 |
| 468_K | 502_L | 2.392 | 1.00 |
| 216_S | 387_L | 2.321 | 1.00 |
| 249_L | 252_Q | 2.315 | 1.00 |
| 153_K | 185_L | 2.277 | 1.00 |
| 140_I | 425_V | 2.240 | 1.00 |
| 252_Q | 257_A | 2.205 | 1.00 |
| 133_L | 532_L | 2.190 | 1.00 |
| 252_Q | 256_M | 2.163 | 1.00 |
| 247_L | 252_Q | 2.126 | 1.00 |
| 138_R | 142_E | 2.112 | 1.00 |
| 476_K | 479_S | 2.104 | 1.00 |
| 253_K | 257_A | 2.085 | 1.00 |
| 456_L | 478_R | 2.082 | 1.00 |
| 247_L | 250_N | 2.070 | 1.00 |
| 434_D | 452_A | 2.057 | 1.00 |
| 250_N | 253_K | 2.041 | 1.00 |
| 152_G | 155_T | 2.001 | 1.00 |
| 480_Y | 500_Y | 1.993 | 1.00 |
| 286_K | 290_D | 1.983 | 1.00 |
| 358_C | 374_I | 1.979 | 1.00 |
| 422_G | 512_E | 1.955 | 1.00 |
| 247_L | 251_L | 1.925 | 1.00 |
| 242_V | 245_A | 1.921 | 1.00 |
| 81_K | 84_V | 1.918 | 1.00 |
| 252_Q | 255_R | 1.916 | 1.00 |
| 245_A | 252_Q | 1.916 | 1.00 |
| 34_M | 38_N | 1.907 | 1.00 |
| 136_A | 429_L | 1.905 | 1.00 |
| 400_R | 403_H | 1.899 | 1.00 |
| 302_I | 317_G | 1.878 | 1.00 |
| 245_A | 250_N | 1.877 | 1.00 |
| 34_M | 106_S | 1.873 | 1.00 |
| 246_C | 252_Q | 1.856 | 1.00 |
| 367_S | 370_E | 1.849 | 1.00 |
| 250_N | 257_A | 1.846 | 1.00 |
| 250_N | 255_R | 1.833 | 1.00 |
| 135_E | 436_F | 1.826 | 1.00 |
| 108_L | 451_F | 1.808 | 1.00 |
| 250_N | 254_A | 1.794 | 1.00 |
| 380_H | 384_S | 1.773 | 1.00 |
| 451_F | 532_L | 1.768 | 1.00 |
| 287_K | 290_D | 1.767 | 1.00 |
| 249_L | 254_A | 1.763 | 1.00 |
| 456_L | 460_K | 1.762 | 1.00 |
| 298_T | 329_I | 1.756 | 1.00 |
| 155_T | 158_N | 1.753 | 1.00 |
| 41_K | 106_S | 1.747 | 1.00 |
| 379_K | 382_S | 1.746 | 1.00 |
| 109_L | 538_I | 1.743 | 1.00 |
| 253_K | 256_M | 1.729 | 1.00 |
| 418_V | 518_L | 1.729 | 1.00 |
| 336_T | 354_Y | 1.723 | 1.00 |
| 30_V | 34_M | 1.714 | 1.00 |
| 254_A | 257_A | 1.711 | 1.00 |
| 279_G | 283_E | 1.708 | 1.00 |
| 468_K | 507_G | 1.697 | 1.00 |
| 179_M | 385_I | 1.696 | 1.00 |
| 427_A | 478_R | 1.692 | 1.00 |
| 250_N | 256_M | 1.679 | 1.00 |
| 433_L | 452_A | 1.671 | 1.00 |
| 134_R | 138_R | 1.671 | 1.00 |
| 100_S | 527_S | 1.658 | 1.00 |
| 91_D | 400_R | 1.654 | 1.00 |
| 126_I | 130_R | 1.653 | 1.00 |
| 184_L | 413_L | 1.650 | 1.00 |
| 139_F | 432_Y | 1.639 | 1.00 |
| 174_D | 178_N | 1.636 | 1.00 |
| 141_N | 525_V | 1.629 | 1.00 |
| 180_V | 402_L | 1.621 | 1.00 |
| 324_E | 327_R | 1.618 | 1.00 |
| 510_V | 517_V | 1.616 | 1.00 |
| 236_R | 360_E | 1.603 | 1.00 |
| 427_A | 459_P | 1.600 | 1.00 |
| 436_F | 448_I | 1.600 | 1.00 |
| 61_T | 400_R | 1.589 | 1.00 |
| 503_D | 515_A | 1.587 | 1.00 |
| 161_K | 174_D | 1.585 | 1.00 |
| 124_T | 444_E | 1.570 | 1.00 |
| 246_C | 250_N | 1.557 | 1.00 |
| 245_A | 249_L | 1.556 | 1.00 |
| 19_K | 543_T | 1.543 | 1.00 |
| 179_M | 216_S | 1.538 | 1.00 |
| 186_A | 220_P | 1.531 | 1.00 |
| 115_L | 120_I | 1.529 | 1.00 |
| 139_F | 143_V | 1.528 | 1.00 |
| 64_N | 400_R | 1.528 | 1.00 |
| 28_Q | 31_L | 1.525 | 1.00 |
| 463_A | 468_K | 1.520 | 1.00 |
| 31_L | 35_A | 1.517 | 1.00 |
| 129_F | 451_F | 1.516 | 1.00 |
| 23_D | 27_N | 1.512 | 1.00 |
| 135_E | 432_Y | 1.501 | 1.00 |
| 237_I | 242_V | 1.497 | 1.00 |
| 338_V | 350_F | 1.487 | 1.00 |
| 136_A | 433_L | 1.484 | 1.00 |
| 91_D | 407_S | 1.476 | 1.00 |
| 247_L | 255_R | 1.475 | 1.00 |
| 266_D | 269_Q | 1.469 | 1.00 |
| 110_K | 457_I | 1.469 | 1.00 |
| 115_L | 446_L | 1.467 | 1.00 |
| 59_D | 393_Y | 1.462 | 1.00 |
| 136_A | 455_L | 1.458 | 0.99 |
| 432_Y | 435_N | 1.453 | 0.99 |
| 211_K | 215_E | 1.449 | 0.99 |
| 153_K | 178_N | 1.449 | 0.99 |
| 249_L | 253_K | 1.446 | 0.99 |
| 245_A | 253_K | 1.442 | 0.99 |
| 359_D | 375_K | 1.434 | 0.99 |
| 138_R | 141_N | 1.434 | 0.99 |
| 436_F | 439_T | 1.430 | 0.99 |
| 137_I | 141_N | 1.418 | 0.99 |
| 146_T | 513_I | 1.414 | 0.99 |
| 246_C | 249_L | 1.396 | 0.99 |
| 210_G | 213_A | 1.391 | 0.99 |
| 287_K | 351_E | 1.389 | 0.99 |
| 463_A | 470_S | 1.384 | 0.99 |
| 428_A | 498_R | 1.384 | 0.99 |
| 37_A | 106_S | 1.382 | 0.99 |
| 107_E | 110_K | 1.379 | 0.99 |
| 389_G | 395_L | 1.377 | 0.99 |
| 242_V | 250_N | 1.373 | 0.99 |
| 425_V | 429_L | 1.371 | 0.99 |
| 207_K | 396_D | 1.370 | 0.99 |
| 132_A | 451_F | 1.369 | 0.99 |
| 265_D | 269_Q | 1.364 | 0.99 |
| 64_N | 165_S | 1.364 | 0.99 |
| 476_K | 508_K | 1.357 | 0.99 |
| 244_I | 252_Q | 1.338 | 0.99 |
| 249_L | 256_M | 1.323 | 0.99 |
| 251_L | 255_R | 1.322 | 0.99 |
| 457_I | 461_T | 1.321 | 0.99 |
| 351_E | 354_Y | 1.318 | 0.99 |
| 112_A | 129_F | 1.302 | 0.99 |
| 247_L | 253_K | 1.295 | 0.99 |
| 245_A | 255_R | 1.294 | 0.99 |
| 246_C | 335_A | 1.292 | 0.99 |
| 184_L | 203_V | 1.286 | 0.98 |
| 34_M | 110_K | 1.286 | 0.98 |
| 249_L | 255_R | 1.279 | 0.98 |
| 247_L | 254_A | 1.273 | 0.98 |
| 476_K | 480_Y | 1.265 | 0.98 |
| 424_C | 428_A | 1.265 | 0.98 |
| 247_L | 256_M | 1.260 | 0.98 |
| 246_C | 251_L | 1.256 | 0.98 |
| 282_L | 286_K | 1.245 | 0.98 |
| 248_D | 254_A | 1.241 | 0.98 |
| 269_Q | 272_Q | 1.240 | 0.98 |
| 243_K | 250_N | 1.237 | 0.98 |
| 269_Q | 273_I | 1.223 | 0.98 |
| 455_L | 528_L | 1.218 | 0.98 |
| 248_D | 252_Q | 1.217 | 0.98 |
| 91_D | 403_H | 1.211 | 0.97 |
| 38_N | 106_S | 1.210 | 0.97 |
| 243_K | 252_Q | 1.201 | 0.97 |
| 246_C | 255_R | 1.196 | 0.97 |
| 238_A | 241_N | 1.192 | 0.97 |
| 63_T | 397_E | 1.192 | 0.97 |
| 297_L | 374_I | 1.191 | 0.97 |
| 245_A | 251_L | 1.180 | 0.97 |
| 137_I | 529_K | 1.177 | 0.97 |
| 18_E | 546_T | 1.169 | 0.97 |
| 242_V | 252_Q | 1.165 | 0.97 |
| 111_R | 114_E | 1.164 | 0.97 |
| 149_D | 155_T | 1.164 | 0.97 |
| 415_S | 522_I | 1.155 | 0.96 |
| 441_G | 448_I | 1.151 | 0.96 |
| 512_E | 517_V | 1.135 | 0.96 |
| 127_T | 444_E | 1.134 | 0.96 |
| 288_I | 291_A | 1.133 | 0.96 |
| 135_E | 139_F | 1.133 | 0.96 |
| 207_K | 399_E | 1.124 | 0.96 |
| 249_L | 257_A | 1.119 | 0.95 |
| 156_L | 160_A | 1.117 | 0.95 |
| 244_I | 250_N | 1.109 | 0.95 |
| 400_R | 407_S | 1.106 | 0.95 |
| 135_E | 448_I | 1.106 | 0.95 |
| 107_E | 457_I | 1.099 | 0.95 |
| 244_I | 247_L | 1.098 | 0.95 |
| 244_I | 358_C | 1.097 | 0.95 |
| 445_Q | 449_A | 1.095 | 0.95 |
| 215_E | 386_I | 1.095 | 0.95 |
| 345_E | 349_T | 1.088 | 0.94 |
| 146_T | 155_T | 1.086 | 0.94 |
| 431_I | 435_N | 1.085 | 0.94 |
| 132_A | 448_I | 1.081 | 0.94 |
| 140_I | 525_V | 1.078 | 0.94 |
| 414_E | 522_I | 1.076 | 0.94 |
| 538_I | 544_M | 1.074 | 0.94 |
| 208_A | 395_L | 1.073 | 0.94 |
| 293_A | 357_L | 1.072 | 0.94 |
| 435_N | 438_T | 1.072 | 0.94 |
| 30_V | 109_L | 1.071 | 0.94 |
| 42_S | 51_K | 1.070 | 0.94 |
| 430_N | 478_R | 1.070 | 0.94 |
| 33_T | 538_I | 1.069 | 0.94 |
| 69_I | 400_R | 1.062 | 0.93 |
| 217_L | 386_I | 1.061 | 0.93 |
| 245_A | 344_L | 1.055 | 0.93 |
| 251_L | 256_M | 1.055 | 0.93 |
| 310_F | 317_G | 1.053 | 0.93 |
| 332_A | 377_T | 1.053 | 0.93 |
| 159_I | 418_V | 1.051 | 0.93 |
| 484_S | 497_Y | 1.051 | 0.93 |
| 248_D | 251_L | 1.045 | 0.93 |
| 484_S | 500_Y | 1.045 | 0.93 |
| 428_A | 499_N | 1.041 | 0.93 |
| 359_D | 377_T | 1.038 | 0.92 |
| 289_I | 315_I | 1.031 | 0.92 |
| 462_L | 504_L | 1.031 | 0.92 |
| 459_P | 463_A | 1.030 | 0.92 |
| 420_P | 513_I | 1.030 | 0.92 |
| 251_L | 254_A | 1.025 | 0.92 |
| 385_I | 402_L | 1.022 | 0.92 |
| 420_P | 424_C | 1.021 | 0.92 |
| 149_D | 152_G | 1.017 | 0.91 |
| 143_V | 429_L | 1.012 | 0.91 |
| 318_V | 372_I | 1.011 | 0.91 |
| 267_P | 271_E | 1.011 | 0.91 |
| 248_D | 255_R | 1.010 | 0.91 |
| 330_A | 337_L | 1.008 | 0.91 |
| 242_V | 247_L | 1.007 | 0.91 |
| 344_L | 354_Y | 1.005 | 0.91 |
| 44_L | 103_I | 1.003 | 0.91 |
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 | |
| 3p9dA | 2 | 0.9732 | 100 | 0.056 | Contact Map |
| 3ko1A | 9 | 0.9016 | 100 | 0.071 | Contact Map |
| 1q3qA | 4 | 0.9267 | 100 | 0.074 | Contact Map |
| 1a6dB | 1 | 0.898 | 100 | 0.074 | Contact Map |
| 3ruvA | 4 | 0.9213 | 100 | 0.077 | Contact Map |
| 3j1bA | 16 | 0.9123 | 100 | 0.077 | Contact Map |
| 1a6dA | 1 | 0.8998 | 100 | 0.081 | Contact Map |
| 3p9dF | 2 | 0.9445 | 100 | 0.09 | Contact Map |
| 3p9dD | 2 | 0.9177 | 100 | 0.09 | Contact Map |
| 3iygA | 1 | 0.9463 | 100 | 0.091 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)