| kdpB |
| ID: | 1416985031 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 682 (614) | ||
| Sequences: | 3840 (2234.9) | ||
| Seq/Len: | 6.254 | ||
| Nf(neff/√len): | 90.2 |
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: 6.254).
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 |
| 144_G | 189_I | 6.678 | 1.00 |
| 302_D | 511_R | 4.267 | 1.00 |
| 132_V | 144_G | 4.113 | 1.00 |
| 132_V | 189_I | 3.870 | 1.00 |
| 482_A | 490_F | 3.523 | 1.00 |
| 507_Q | 528_Q | 3.263 | 1.00 |
| 534_A | 546_G | 3.260 | 1.00 |
| 336_A | 440_L | 3.226 | 1.00 |
| 144_G | 176_V | 2.983 | 1.00 |
| 142_C | 191_C | 2.902 | 1.00 |
| 504_R | 528_Q | 2.899 | 1.00 |
| 321_E | 426_Q | 2.890 | 1.00 |
| 132_V | 141_P | 2.859 | 1.00 |
| 128_K | 194_N | 2.766 | 1.00 |
| 423_V | 444_A | 2.723 | 1.00 |
| 452_G | 554_N | 2.722 | 1.00 |
| 153_V | 182_I | 2.660 | 1.00 |
| 457_F | 487_V | 2.611 | 1.00 |
| 270_L | 275_G | 2.589 | 1.00 |
| 459_Q | 563_H | 2.536 | 1.00 |
| 82_A | 86_A | 2.518 | 1.00 |
| 271_L | 275_G | 2.516 | 1.00 |
| 83_E | 86_A | 2.463 | 1.00 |
| 153_V | 176_V | 2.461 | 1.00 |
| 314_L | 451_G | 2.424 | 1.00 |
| 144_G | 192_S | 2.405 | 1.00 |
| 416_V | 439_V | 2.379 | 1.00 |
| 285_A | 563_H | 2.349 | 1.00 |
| 105_F | 120_K | 2.347 | 1.00 |
| 131_I | 147_I | 2.335 | 1.00 |
| 37_F | 41_I | 2.321 | 1.00 |
| 267_I | 275_G | 2.301 | 1.00 |
| 109_L | 188_V | 2.295 | 1.00 |
| 176_V | 189_I | 2.281 | 1.00 |
| 134_V | 140_I | 2.269 | 1.00 |
| 107_R | 135_E | 2.268 | 1.00 |
| 179_G | 200_L | 2.228 | 1.00 |
| 148_E | 188_V | 2.210 | 1.00 |
| 140_I | 153_V | 2.210 | 1.00 |
| 107_R | 138_D | 2.206 | 1.00 |
| 289_A | 548_M | 2.173 | 1.00 |
| 458_A | 462_K | 2.150 | 1.00 |
| 126_L | 132_V | 2.146 | 1.00 |
| 252_V | 256_V | 2.130 | 1.00 |
| 370_L | 387_N | 2.123 | 1.00 |
| 121_V | 126_L | 2.111 | 1.00 |
| 285_A | 560_E | 2.100 | 1.00 |
| 86_A | 90_S | 2.052 | 1.00 |
| 419_K | 422_Q | 2.029 | 1.00 |
| 465_I | 562_V | 2.016 | 1.00 |
| 151_A | 187_L | 1.977 | 1.00 |
| 312_I | 485_A | 1.972 | 1.00 |
| 407_A | 410_G | 1.971 | 1.00 |
| 189_I | 192_S | 1.966 | 1.00 |
| 460_L | 559_I | 1.952 | 1.00 |
| 334_A | 355_L | 1.952 | 1.00 |
| 432_V | 439_V | 1.944 | 1.00 |
| 233_L | 237_A | 1.938 | 1.00 |
| 471_T | 478_A | 1.936 | 1.00 |
| 126_L | 191_C | 1.935 | 1.00 |
| 267_I | 271_L | 1.923 | 1.00 |
| 243_S | 251_S | 1.921 | 1.00 |
| 272_S | 275_G | 1.904 | 1.00 |
| 270_L | 276_V | 1.897 | 1.00 |
| 468_V | 506_Y | 1.895 | 1.00 |
| 435_E | 438_R | 1.885 | 1.00 |
| 384_S | 392_M | 1.876 | 1.00 |
| 479_A | 483_A | 1.848 | 1.00 |
| 267_I | 270_L | 1.848 | 1.00 |
| 430_P | 442_V | 1.826 | 1.00 |
| 336_A | 393_I | 1.823 | 1.00 |
| 452_G | 455_E | 1.813 | 1.00 |
| 269_G | 275_G | 1.783 | 1.00 |
| 418_Q | 422_Q | 1.778 | 1.00 |
| 131_I | 190_E | 1.771 | 1.00 |
| 288_I | 551_L | 1.771 | 1.00 |
| 287_V | 557_K | 1.763 | 1.00 |
| 454_K | 458_A | 1.763 | 1.00 |
| 428_A | 444_A | 1.753 | 1.00 |
| 175_S | 192_S | 1.743 | 1.00 |
| 268_G | 275_G | 1.738 | 1.00 |
| 354_I | 358_Q | 1.730 | 1.00 |
| 199_F | 202_R | 1.679 | 1.00 |
| 107_R | 118_A | 1.679 | 1.00 |
| 136_A | 378_T | 1.665 | 1.00 |
| 105_F | 122_P | 1.655 | 1.00 |
| 427_G | 480_A | 1.630 | 1.00 |
| 333_L | 441_G | 1.629 | 1.00 |
| 272_S | 276_V | 1.629 | 1.00 |
| 332_T | 435_E | 1.621 | 1.00 |
| 40_W | 44_L | 1.611 | 1.00 |
| 505_Q | 508_A | 1.601 | 1.00 |
| 176_V | 182_I | 1.593 | 0.99 |
| 316_N | 319_A | 1.590 | 0.99 |
| 32_R | 37_F | 1.575 | 0.99 |
| 82_A | 85_L | 1.572 | 0.99 |
| 338_Q | 356_A | 1.563 | 0.99 |
| 423_V | 428_A | 1.563 | 0.99 |
| 421_D | 476_L | 1.561 | 0.99 |
| 303_V | 468_V | 1.558 | 0.99 |
| 214_K | 222_T | 1.544 | 0.99 |
| 482_A | 487_V | 1.540 | 0.99 |
| 533_V | 558_L | 1.529 | 0.99 |
| 271_L | 276_V | 1.523 | 0.99 |
| 173_F | 177_T | 1.519 | 0.99 |
| 578_F | 582_N | 1.518 | 0.99 |
| 145_E | 190_E | 1.508 | 0.99 |
| 146_V | 187_L | 1.497 | 0.99 |
| 118_A | 133_L | 1.496 | 0.99 |
| 64_F | 68_I | 1.489 | 0.99 |
| 507_Q | 530_D | 1.485 | 0.99 |
| 461_R | 467_T | 1.484 | 0.99 |
| 401_I | 434_V | 1.480 | 0.99 |
| 417_D | 421_D | 1.476 | 0.99 |
| 122_P | 125_Q | 1.465 | 0.99 |
| 152_S | 184_S | 1.465 | 0.99 |
| 266_T | 269_G | 1.464 | 0.99 |
| 182_I | 187_L | 1.463 | 0.99 |
| 452_G | 556_T | 1.460 | 0.99 |
| 364_E | 368_Q | 1.459 | 0.99 |
| 425_R | 476_L | 1.451 | 0.99 |
| 456_R | 556_T | 1.445 | 0.99 |
| 155_E | 167_R | 1.439 | 0.99 |
| 68_I | 79_A | 1.438 | 0.99 |
| 286_N | 551_L | 1.434 | 0.99 |
| 107_R | 120_K | 1.431 | 0.99 |
| 575_L | 579_S | 1.429 | 0.99 |
| 109_L | 118_A | 1.422 | 0.99 |
| 85_L | 89_R | 1.418 | 0.99 |
| 290_T | 546_G | 1.417 | 0.99 |
| 270_L | 274_I | 1.416 | 0.99 |
| 213_R | 507_Q | 1.416 | 0.99 |
| 134_V | 138_D | 1.415 | 0.99 |
| 384_S | 394_R | 1.413 | 0.99 |
| 286_N | 557_K | 1.409 | 0.98 |
| 202_R | 497_E | 1.406 | 0.98 |
| 75_T | 79_A | 1.395 | 0.98 |
| 316_N | 358_Q | 1.388 | 0.98 |
| 271_L | 274_I | 1.381 | 0.98 |
| 518_D | 521_N | 1.363 | 0.98 |
| 491_L | 502_L | 1.362 | 0.98 |
| 531_V | 548_M | 1.360 | 0.98 |
| 449_V | 485_A | 1.356 | 0.98 |
| 146_V | 149_G | 1.351 | 0.98 |
| 470_I | 502_L | 1.348 | 0.98 |
| 460_L | 467_T | 1.346 | 0.98 |
| 121_V | 125_Q | 1.341 | 0.98 |
| 79_A | 83_E | 1.335 | 0.98 |
| 301_V | 514_A | 1.330 | 0.98 |
| 86_A | 89_R | 1.330 | 0.98 |
| 455_E | 459_Q | 1.329 | 0.98 |
| 420_V | 430_P | 1.325 | 0.97 |
| 301_V | 562_V | 1.325 | 0.97 |
| 153_V | 187_L | 1.324 | 0.97 |
| 109_L | 131_I | 1.324 | 0.97 |
| 475_R | 479_A | 1.322 | 0.97 |
| 319_A | 352_I | 1.320 | 0.97 |
| 469_M | 482_A | 1.319 | 0.97 |
| 319_A | 355_L | 1.307 | 0.97 |
| 305_L | 506_Y | 1.303 | 0.97 |
| 86_A | 91_K | 1.303 | 0.97 |
| 34_P | 225_L | 1.300 | 0.97 |
| 420_V | 442_V | 1.298 | 0.97 |
| 422_Q | 426_Q | 1.298 | 0.97 |
| 446_K | 484_E | 1.289 | 0.97 |
| 355_L | 443_I | 1.288 | 0.97 |
| 69_S | 76_V | 1.286 | 0.97 |
| 230_I | 234_L | 1.279 | 0.97 |
| 133_L | 188_V | 1.279 | 0.97 |
| 526_L | 542_A | 1.278 | 0.97 |
| 398_V | 420_V | 1.275 | 0.97 |
| 504_R | 508_A | 1.268 | 0.96 |
| 385_G | 388_I | 1.264 | 0.96 |
| 287_V | 561_V | 1.263 | 0.96 |
| 570_M | 574_S | 1.253 | 0.96 |
| 337_A | 443_I | 1.248 | 0.96 |
| 514_A | 533_V | 1.248 | 0.96 |
| 267_I | 272_S | 1.242 | 0.96 |
| 394_R | 401_I | 1.238 | 0.96 |
| 405_V | 434_V | 1.236 | 0.96 |
| 66_A | 70_G | 1.234 | 0.96 |
| 433_V | 443_I | 1.232 | 0.96 |
| 268_G | 276_V | 1.232 | 0.96 |
| 267_I | 276_V | 1.232 | 0.96 |
| 414_T | 418_Q | 1.231 | 0.96 |
| 127_R | 194_N | 1.231 | 0.96 |
| 320_S | 484_E | 1.222 | 0.95 |
| 269_G | 274_I | 1.217 | 0.95 |
| 63_L | 66_A | 1.215 | 0.95 |
| 268_G | 271_L | 1.213 | 0.95 |
| 315_G | 318_Q | 1.212 | 0.95 |
| 206_M | 497_E | 1.212 | 0.95 |
| 319_A | 445_L | 1.207 | 0.95 |
| 146_V | 189_I | 1.203 | 0.95 |
| 154_D | 157_A | 1.201 | 0.95 |
| 323_I | 419_K | 1.198 | 0.95 |
| 301_V | 531_V | 1.181 | 0.94 |
| 149_G | 176_V | 1.179 | 0.94 |
| 256_V | 262_L | 1.179 | 0.94 |
| 336_A | 433_V | 1.178 | 0.94 |
| 582_N | 586_K | 1.173 | 0.94 |
| 384_S | 388_I | 1.172 | 0.94 |
| 64_F | 79_A | 1.172 | 0.94 |
| 340_A | 460_L | 1.170 | 0.94 |
| 470_I | 494_A | 1.165 | 0.94 |
| 478_A | 492_A | 1.164 | 0.94 |
| 370_L | 385_G | 1.160 | 0.93 |
| 221_L | 274_I | 1.160 | 0.93 |
| 466_K | 489_D | 1.159 | 0.93 |
| 507_Q | 526_L | 1.157 | 0.93 |
| 123_A | 126_L | 1.155 | 0.93 |
| 321_E | 423_V | 1.153 | 0.93 |
| 69_S | 72_L | 1.149 | 0.93 |
| 418_Q | 421_D | 1.148 | 0.93 |
| 146_V | 176_V | 1.143 | 0.93 |
| 31_W | 76_V | 1.140 | 0.93 |
| 401_I | 405_V | 1.137 | 0.93 |
| 401_I | 432_V | 1.137 | 0.93 |
| 377_F | 397_S | 1.137 | 0.93 |
| 321_E | 428_A | 1.129 | 0.92 |
| 151_A | 182_I | 1.128 | 0.92 |
| 460_L | 555_P | 1.127 | 0.92 |
| 110_R | 130_D | 1.126 | 0.92 |
| 318_Q | 358_Q | 1.125 | 0.92 |
| 266_T | 275_G | 1.112 | 0.91 |
| 379_A | 382_R | 1.110 | 0.91 |
| 290_T | 549_V | 1.110 | 0.91 |
| 405_V | 439_V | 1.109 | 0.91 |
| 535_M | 538_G | 1.107 | 0.91 |
| 240_W | 255_L | 1.100 | 0.91 |
| 45_L | 252_V | 1.100 | 0.91 |
| 398_V | 432_V | 1.099 | 0.91 |
| 524_P | 539_T | 1.097 | 0.91 |
| 49_I | 290_T | 1.096 | 0.91 |
| 342_L | 371_H | 1.094 | 0.90 |
| 269_G | 272_S | 1.093 | 0.90 |
| 224_L | 576_T | 1.092 | 0.90 |
| 43_S | 65_S | 1.090 | 0.90 |
| 315_G | 319_A | 1.086 | 0.90 |
| 381_S | 384_S | 1.086 | 0.90 |
| 134_V | 182_I | 1.085 | 0.90 |
| 47_T | 65_S | 1.085 | 0.90 |
| 135_E | 186_W | 1.083 | 0.90 |
| 179_G | 500_L | 1.083 | 0.90 |
| 503_I | 515_M | 1.081 | 0.90 |
| 223_I | 227_A | 1.078 | 0.90 |
| 92_A | 95_N | 1.078 | 0.90 |
| 269_G | 276_V | 1.077 | 0.90 |
| 140_I | 182_I | 1.073 | 0.89 |
| 575_L | 578_F | 1.072 | 0.89 |
| 18_L | 22_V | 1.057 | 0.88 |
| 512_L | 530_D | 1.051 | 0.88 |
| 467_T | 555_P | 1.049 | 0.88 |
| 226_I | 230_I | 1.048 | 0.88 |
| 455_E | 458_A | 1.047 | 0.88 |
| 110_R | 127_R | 1.046 | 0.88 |
| 108_K | 121_V | 1.045 | 0.88 |
| 421_D | 425_R | 1.044 | 0.88 |
| 352_I | 443_I | 1.042 | 0.87 |
| 560_E | 563_H | 1.036 | 0.87 |
| 516_T | 558_L | 1.031 | 0.87 |
| 68_I | 76_V | 1.029 | 0.87 |
| 491_L | 506_Y | 1.027 | 0.86 |
| 332_T | 393_I | 1.027 | 0.86 |
| 267_I | 274_I | 1.025 | 0.86 |
| 523_A | 541_A | 1.020 | 0.86 |
| 85_L | 91_K | 1.019 | 0.86 |
| 306_L | 485_A | 1.017 | 0.86 |
| 88_G | 92_A | 1.017 | 0.86 |
| 148_E | 186_W | 1.017 | 0.86 |
| 108_K | 119_D | 1.016 | 0.86 |
| 71_W | 257_A | 1.011 | 0.85 |
| 82_A | 90_S | 1.009 | 0.85 |
| 97_L | 494_A | 1.008 | 0.85 |
| 303_V | 506_Y | 1.002 | 0.84 |
| 382_R | 397_S | 1.001 | 0.84 |
| 91_K | 95_N | 1.000 | 0.84 |
| 145_E | 175_S | 1.000 | 0.84 |
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 | |
| 3ixzA | 1 | 0.9604 | 100 | 0.326 | Contact Map |
| 2zxeA | 1 | 0.9589 | 100 | 0.328 | Contact Map |
| 3ar4A | 1 | 0.9545 | 100 | 0.329 | Contact Map |
| 3b8cA | 2 | 0.9472 | 100 | 0.341 | Contact Map |
| 1mhsA | 2 | 0.9399 | 100 | 0.35 | Contact Map |
| 4bbjA | 1 | 0.8768 | 100 | 0.431 | Contact Map |
| 4umwA | 1 | 0.8402 | 100 | 0.446 | Contact Map |
| 3j09A | 2 | 0.8812 | 100 | 0.469 | Contact Map |
| 3j08A | 2 | 0.8812 | 100 | 0.47 | Contact Map |
| 3skxA | 1 | 0.3827 | 100 | 0.82 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)