| lntEco |
| ID: | 1488186353 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 512 (479) | ||
| Sequences: | 1970 (1328.4) | ||
| Seq/Len: | 4.113 | ||
| Nf(neff/√len): | 60.7 |
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: 4.113).
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 |
| 167_M | 171_A | 5.965 | 1.00 |
| 453_G | 457_E | 5.234 | 1.00 |
| 462_I | 468_E | 4.479 | 1.00 |
| 426_F | 450_A | 4.002 | 1.00 |
| 229_G | 249_Y | 3.751 | 1.00 |
| 316_I | 410_I | 3.626 | 1.00 |
| 436_L | 484_A | 3.534 | 1.00 |
| 57_A | 106_G | 3.503 | 1.00 |
| 483_Y | 488_N | 3.206 | 1.00 |
| 411_S | 444_T | 3.195 | 1.00 |
| 161_K | 434_L | 3.155 | 1.00 |
| 432_R | 435_E | 3.036 | 1.00 |
| 226_M | 449_T | 2.797 | 1.00 |
| 125_A | 129_P | 2.784 | 1.00 |
| 253_T | 265_W | 2.775 | 1.00 |
| 155_Q | 176_L | 2.740 | 1.00 |
| 382_L | 406_Y | 2.622 | 1.00 |
| 315_T | 334_N | 2.588 | 1.00 |
| 225_S | 260_S | 2.566 | 1.00 |
| 433_A | 440_L | 2.563 | 1.00 |
| 25_T | 70_S | 2.411 | 1.00 |
| 61_F | 99_A | 2.391 | 1.00 |
| 71_G | 149_L | 2.365 | 1.00 |
| 248_I | 467_R | 2.325 | 1.00 |
| 348_E | 364_S | 2.308 | 1.00 |
| 407_L | 440_L | 2.251 | 1.00 |
| 426_F | 458_I | 2.227 | 1.00 |
| 440_L | 452_I | 2.177 | 1.00 |
| 426_F | 452_I | 2.169 | 1.00 |
| 153_Y | 431_M | 2.169 | 1.00 |
| 225_S | 471_T | 2.139 | 1.00 |
| 164_A | 431_M | 2.080 | 1.00 |
| 78_S | 416_F | 2.028 | 1.00 |
| 301_D | 334_N | 2.011 | 1.00 |
| 152_G | 169_V | 2.002 | 1.00 |
| 439_P | 454_P | 1.999 | 1.00 |
| 253_T | 263_I | 1.984 | 1.00 |
| 164_A | 172_I | 1.977 | 1.00 |
| 165_P | 437_A | 1.957 | 1.00 |
| 133_Q | 174_F | 1.957 | 1.00 |
| 224_V | 441_L | 1.947 | 1.00 |
| 437_A | 481_T | 1.912 | 1.00 |
| 482_P | 486_T | 1.897 | 1.00 |
| 112_L | 128_A | 1.896 | 1.00 |
| 300_V | 365_F | 1.891 | 1.00 |
| 449_T | 462_I | 1.882 | 1.00 |
| 390_I | 440_L | 1.882 | 1.00 |
| 397_R | 487_G | 1.856 | 1.00 |
| 137_F | 141_W | 1.839 | 1.00 |
| 18_L | 62_C | 1.835 | 1.00 |
| 24_G | 43_G | 1.827 | 1.00 |
| 296_V | 318_T | 1.793 | 1.00 |
| 17_A | 59_I | 1.793 | 1.00 |
| 385_A | 396_V | 1.789 | 1.00 |
| 316_I | 384_A | 1.779 | 0.99 |
| 60_G | 106_G | 1.778 | 0.99 |
| 423_W | 448_I | 1.776 | 0.99 |
| 226_M | 443_S | 1.774 | 0.99 |
| 413_D | 425_H | 1.756 | 0.99 |
| 225_S | 469_V | 1.720 | 0.99 |
| 260_S | 471_T | 1.656 | 0.99 |
| 153_Y | 428_M | 1.648 | 0.99 |
| 380_I | 405_D | 1.644 | 0.99 |
| 60_G | 64_G | 1.643 | 0.99 |
| 14_L | 62_C | 1.639 | 0.99 |
| 299_I | 317_I | 1.619 | 0.99 |
| 65_F | 69_G | 1.611 | 0.99 |
| 390_I | 409_T | 1.600 | 0.99 |
| 288_L | 295_L | 1.582 | 0.99 |
| 337_H | 395_Q | 1.566 | 0.98 |
| 235_L | 241_Q | 1.559 | 0.98 |
| 45_Q | 128_A | 1.543 | 0.98 |
| 72_I | 146_F | 1.539 | 0.98 |
| 413_D | 442_R | 1.526 | 0.98 |
| 249_Y | 269_A | 1.518 | 0.98 |
| 165_P | 434_L | 1.516 | 0.98 |
| 17_A | 21_G | 1.516 | 0.98 |
| 491_L | 495_T | 1.506 | 0.98 |
| 452_I | 458_I | 1.495 | 0.98 |
| 381_E | 405_D | 1.485 | 0.98 |
| 155_Q | 172_I | 1.476 | 0.97 |
| 247_K | 251_N | 1.474 | 0.97 |
| 43_G | 63_W | 1.474 | 0.97 |
| 17_A | 48_T | 1.468 | 0.97 |
| 56_S | 60_G | 1.462 | 0.97 |
| 385_A | 390_I | 1.460 | 0.97 |
| 133_Q | 173_N | 1.453 | 0.97 |
| 48_T | 109_A | 1.449 | 0.97 |
| 460_A | 470_L | 1.437 | 0.97 |
| 264_I | 441_L | 1.434 | 0.97 |
| 224_V | 451_V | 1.426 | 0.97 |
| 129_P | 178_M | 1.407 | 0.96 |
| 62_C | 66_G | 1.403 | 0.96 |
| 296_V | 408_L | 1.403 | 0.96 |
| 429_A | 440_L | 1.402 | 0.96 |
| 233_Q | 236_K | 1.397 | 0.96 |
| 243_L | 247_K | 1.388 | 0.96 |
| 230_D | 467_R | 1.370 | 0.95 |
| 226_M | 470_L | 1.350 | 0.95 |
| 150_Q | 153_Y | 1.349 | 0.95 |
| 262_L | 296_V | 1.345 | 0.95 |
| 65_F | 102_S | 1.338 | 0.95 |
| 226_M | 441_L | 1.331 | 0.94 |
| 230_D | 446_N | 1.328 | 0.94 |
| 224_V | 264_I | 1.319 | 0.94 |
| 439_P | 474_V | 1.318 | 0.94 |
| 69_G | 98_A | 1.301 | 0.94 |
| 406_Y | 474_V | 1.298 | 0.93 |
| 268_S | 300_V | 1.286 | 0.93 |
| 53_P | 110_G | 1.285 | 0.93 |
| 130_A | 495_T | 1.282 | 0.93 |
| 46_A | 184_A | 1.279 | 0.93 |
| 383_T | 407_L | 1.273 | 0.93 |
| 320_G | 326_S | 1.270 | 0.92 |
| 22_A | 70_S | 1.270 | 0.92 |
| 270_I | 299_I | 1.259 | 0.92 |
| 275_I | 302_A | 1.256 | 0.92 |
| 138_L | 142_V | 1.252 | 0.92 |
| 301_D | 315_T | 1.252 | 0.92 |
| 157_D | 430_R | 1.251 | 0.92 |
| 75_V | 94_V | 1.241 | 0.91 |
| 75_V | 269_A | 1.234 | 0.91 |
| 441_L | 449_T | 1.232 | 0.91 |
| 21_G | 66_G | 1.227 | 0.91 |
| 406_Y | 441_L | 1.219 | 0.90 |
| 68_F | 139_R | 1.219 | 0.90 |
| 480_L | 485_R | 1.215 | 0.90 |
| 430_R | 458_I | 1.211 | 0.90 |
| 423_W | 464_Q | 1.205 | 0.90 |
| 425_H | 442_R | 1.198 | 0.89 |
| 236_K | 268_S | 1.194 | 0.89 |
| 225_S | 256_L | 1.192 | 0.89 |
| 163_L | 207_P | 1.190 | 0.89 |
| 100_Y | 105_T | 1.187 | 0.89 |
| 245_T | 271_T | 1.187 | 0.89 |
| 139_R | 145_G | 1.186 | 0.89 |
| 56_S | 113_S | 1.186 | 0.89 |
| 273_L | 300_V | 1.185 | 0.89 |
| 407_L | 436_L | 1.183 | 0.88 |
| 315_T | 332_R | 1.174 | 0.88 |
| 422_P | 464_Q | 1.170 | 0.88 |
| 24_G | 63_W | 1.156 | 0.87 |
| 268_S | 445_N | 1.155 | 0.87 |
| 13_R | 59_I | 1.153 | 0.87 |
| 454_P | 477_T | 1.145 | 0.86 |
| 162_G | 165_P | 1.144 | 0.86 |
| 24_G | 27_A | 1.144 | 0.86 |
| 73_N | 420_I | 1.141 | 0.86 |
| 162_G | 434_L | 1.134 | 0.85 |
| 314_N | 415_W | 1.130 | 0.85 |
| 262_L | 406_Y | 1.129 | 0.85 |
| 405_D | 476_P | 1.128 | 0.85 |
| 232_P | 235_L | 1.127 | 0.85 |
| 103_L | 107_L | 1.127 | 0.85 |
| 426_F | 440_L | 1.119 | 0.84 |
| 24_G | 151_F | 1.119 | 0.84 |
| 221_T | 475_T | 1.110 | 0.84 |
| 179_V | 202_F | 1.105 | 0.83 |
| 140_G | 170_E | 1.105 | 0.83 |
| 150_Q | 173_N | 1.104 | 0.83 |
| 241_Q | 245_T | 1.102 | 0.83 |
| 413_D | 422_P | 1.100 | 0.83 |
| 227_V | 469_V | 1.098 | 0.83 |
| 105_T | 132_W | 1.095 | 0.83 |
| 166_I | 482_P | 1.085 | 0.82 |
| 262_L | 408_L | 1.084 | 0.82 |
| 36_A | 43_G | 1.083 | 0.82 |
| 294_S | 318_T | 1.079 | 0.81 |
| 129_P | 181_G | 1.077 | 0.81 |
| 18_L | 66_G | 1.077 | 0.81 |
| 410_I | 443_S | 1.072 | 0.81 |
| 161_K | 165_P | 1.072 | 0.81 |
| 179_V | 204_L | 1.072 | 0.81 |
| 441_L | 451_V | 1.070 | 0.81 |
| 172_I | 431_M | 1.068 | 0.80 |
| 134_V | 138_L | 1.068 | 0.80 |
| 89_V | 92_F | 1.063 | 0.80 |
| 32_D | 427_Q | 1.059 | 0.80 |
| 136_E | 173_N | 1.057 | 0.79 |
| 412_N | 442_R | 1.053 | 0.79 |
| 100_Y | 103_L | 1.050 | 0.79 |
| 16_L | 20_F | 1.048 | 0.79 |
| 394_E | 488_N | 1.048 | 0.79 |
| 458_I | 461_M | 1.046 | 0.78 |
| 425_H | 429_A | 1.045 | 0.78 |
| 383_T | 404_T | 1.040 | 0.78 |
| 303_R | 493_V | 1.040 | 0.78 |
| 100_Y | 104_Y | 1.039 | 0.78 |
| 236_K | 269_A | 1.039 | 0.78 |
| 124_V | 129_P | 1.033 | 0.77 |
| 66_G | 71_G | 1.029 | 0.77 |
| 439_P | 451_V | 1.029 | 0.77 |
| 439_P | 475_T | 1.028 | 0.77 |
| 86_P | 411_S | 1.024 | 0.76 |
| 199_V | 203_A | 1.022 | 0.76 |
| 79_I | 358_F | 1.021 | 0.76 |
| 390_I | 429_A | 1.019 | 0.76 |
| 129_P | 133_Q | 1.019 | 0.76 |
| 125_A | 181_G | 1.017 | 0.76 |
| 303_R | 311_D | 1.004 | 0.74 |
| 73_N | 419_S | 1.002 | 0.74 |
| 353_P | 356_P | 1.000 | 0.74 |
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 | |
| 1uf5A | 2 | 0.5078 | 100 | 0.685 | Contact Map |
| 3p8kA | 2 | 0.4746 | 100 | 0.709 | Contact Map |
| 2w1vA | 2 | 0.4805 | 100 | 0.71 | Contact Map |
| 1f89A | 2 | 0.4766 | 100 | 0.717 | Contact Map |
| 2e11A | 4 | 0.4668 | 100 | 0.718 | Contact Map |
| 3ivzA | 2 | 0.4531 | 100 | 0.719 | Contact Map |
| 2dyuA | 2 | 0.4961 | 100 | 0.719 | Contact Map |
| 4izuA | 1 | 0.4453 | 100 | 0.719 | Contact Map |
| 4lf0A | 1 | 0.5332 | 100 | 0.719 | Contact Map |
| 4f4hA | 2 | 0.5059 | 100 | 0.721 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)