| AtfA alignment |
| ID: | 1512634646 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 458 (424) | ||
| Sequences: | 19932 (16502.7) | ||
| Seq/Len: | 47.009 | ||
| Nf(neff/√len): | 801.4 |
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: 47.009).
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 |
| 283_P | 309_N | 3.455 | 1.00 |
| 28_L | 124_R | 3.342 | 1.00 |
| 61_K | 70_D | 3.205 | 1.00 |
| 315_D | 323_I | 2.887 | 1.00 |
| 266_S | 310_L | 2.805 | 1.00 |
| 250_A | 260_V | 2.724 | 1.00 |
| 208_D | 327_S | 2.719 | 1.00 |
| 272_Y | 436_H | 2.625 | 1.00 |
| 317_P | 444_F | 2.559 | 1.00 |
| 253_L | 318_L | 2.544 | 1.00 |
| 44_V | 48_R | 2.463 | 1.00 |
| 420_L | 434_L | 2.403 | 1.00 |
| 54_P | 147_K | 2.368 | 1.00 |
| 268_A | 440_E | 2.346 | 1.00 |
| 50_S | 156_K | 2.304 | 1.00 |
| 30_Q | 124_R | 2.302 | 1.00 |
| 131_I | 136_V | 2.301 | 1.00 |
| 263_A | 320_R | 2.246 | 1.00 |
| 48_R | 53_I | 2.189 | 1.00 |
| 201_L | 334_R | 2.150 | 1.00 |
| 316_D | 319_Q | 2.113 | 1.00 |
| 61_K | 109_K | 2.087 | 1.00 |
| 438_E | 442_Q | 2.082 | 1.00 |
| 51_K | 148_S | 2.075 | 1.00 |
| 55_V | 147_K | 2.074 | 1.00 |
| 283_P | 311_A | 2.072 | 1.00 |
| 47_I | 114_C | 2.051 | 1.00 |
| 259_D | 325_R | 2.037 | 1.00 |
| 285_I | 307_L | 2.031 | 1.00 |
| 239_Q | 418_V | 2.012 | 1.00 |
| 51_K | 151_H | 2.006 | 1.00 |
| 237_A | 431_Q | 1.961 | 1.00 |
| 120_I | 123_N | 1.936 | 1.00 |
| 50_S | 53_I | 1.908 | 1.00 |
| 50_S | 151_H | 1.908 | 1.00 |
| 43_L | 148_S | 1.904 | 1.00 |
| 265_C | 407_I | 1.882 | 1.00 |
| 34_N | 42_D | 1.866 | 1.00 |
| 409_M | 418_V | 1.856 | 1.00 |
| 100_E | 115_N | 1.852 | 1.00 |
| 265_C | 369_F | 1.815 | 1.00 |
| 326_R | 330_N | 1.812 | 1.00 |
| 28_L | 126_A | 1.804 | 1.00 |
| 267_G | 320_R | 1.795 | 1.00 |
| 146_E | 297_S | 1.790 | 1.00 |
| 203_Q | 207_K | 1.756 | 1.00 |
| 422_A | 430_M | 1.749 | 1.00 |
| 248_N | 252_S | 1.734 | 1.00 |
| 144_L | 299_V | 1.733 | 1.00 |
| 240_S | 415_K | 1.731 | 1.00 |
| 263_A | 324_I | 1.728 | 1.00 |
| 253_L | 322_E | 1.718 | 1.00 |
| 235_R | 424_R | 1.710 | 1.00 |
| 420_L | 430_M | 1.709 | 1.00 |
| 202_S | 337_R | 1.708 | 1.00 |
| 407_I | 420_L | 1.705 | 1.00 |
| 240_S | 417_E | 1.696 | 1.00 |
| 57_P | 60_N | 1.686 | 1.00 |
| 235_R | 429_R | 1.682 | 1.00 |
| 247_R | 411_S | 1.681 | 1.00 |
| 30_Q | 389_K | 1.660 | 1.00 |
| 82_I | 115_N | 1.657 | 1.00 |
| 92_E | 95_I | 1.648 | 1.00 |
| 267_G | 440_E | 1.645 | 1.00 |
| 202_S | 345_N | 1.632 | 1.00 |
| 201_L | 336_K | 1.631 | 1.00 |
| 204_T | 331_S | 1.610 | 1.00 |
| 264_V | 441_I | 1.607 | 1.00 |
| 63_N | 68_D | 1.603 | 1.00 |
| 270_R | 312_T | 1.600 | 1.00 |
| 32_P | 123_N | 1.589 | 1.00 |
| 310_L | 324_I | 1.586 | 1.00 |
| 202_S | 206_F | 1.582 | 1.00 |
| 255_V | 321_L | 1.570 | 1.00 |
| 30_Q | 391_D | 1.561 | 1.00 |
| 83_A | 118_E | 1.544 | 1.00 |
| 113_T | 130_K | 1.530 | 1.00 |
| 222_P | 428_P | 1.529 | 1.00 |
| 431_Q | 435_T | 1.524 | 1.00 |
| 118_E | 125_F | 1.520 | 1.00 |
| 249_I | 253_L | 1.512 | 1.00 |
| 146_E | 150_S | 1.506 | 1.00 |
| 199_Q | 203_Q | 1.505 | 1.00 |
| 246_F | 257_I | 1.498 | 1.00 |
| 114_C | 127_M | 1.497 | 1.00 |
| 16_K | 64_G | 1.491 | 1.00 |
| 111_L | 135_M | 1.474 | 1.00 |
| 206_F | 345_N | 1.466 | 1.00 |
| 26_L | 128_Y | 1.464 | 1.00 |
| 26_L | 126_A | 1.455 | 1.00 |
| 81_H | 118_E | 1.451 | 1.00 |
| 42_D | 156_K | 1.440 | 1.00 |
| 257_I | 416_L | 1.438 | 1.00 |
| 45_N | 156_K | 1.432 | 1.00 |
| 266_S | 286_A | 1.431 | 1.00 |
| 96_Y | 117_I | 1.431 | 1.00 |
| 432_N | 436_H | 1.416 | 1.00 |
| 4_L | 65_L | 1.414 | 1.00 |
| 246_F | 260_V | 1.405 | 0.99 |
| 119_G | 126_A | 1.405 | 0.99 |
| 42_D | 157_S | 1.398 | 0.99 |
| 328_V | 332_K | 1.391 | 0.99 |
| 62_L | 134_A | 1.388 | 0.99 |
| 56_P | 178_G | 1.387 | 0.99 |
| 95_I | 99_Q | 1.385 | 0.99 |
| 287_M | 367_Q | 1.380 | 0.99 |
| 100_E | 103_T | 1.379 | 0.99 |
| 204_T | 208_D | 1.370 | 0.99 |
| 439_E | 443_L | 1.368 | 0.99 |
| 245_R | 442_Q | 1.367 | 0.99 |
| 100_E | 130_K | 1.360 | 0.99 |
| 199_Q | 202_S | 1.354 | 0.99 |
| 140_A | 299_V | 1.349 | 0.99 |
| 203_Q | 206_F | 1.341 | 0.99 |
| 62_L | 135_M | 1.341 | 0.99 |
| 40_I | 44_V | 1.335 | 0.99 |
| 272_Y | 433_L | 1.334 | 0.99 |
| 208_D | 330_N | 1.334 | 0.99 |
| 28_L | 391_D | 1.331 | 0.99 |
| 117_I | 128_Y | 1.329 | 0.99 |
| 34_N | 152_D | 1.329 | 0.99 |
| 43_L | 127_M | 1.317 | 0.99 |
| 268_A | 437_L | 1.316 | 0.99 |
| 249_I | 445_E | 1.314 | 0.99 |
| 319_Q | 322_E | 1.309 | 0.99 |
| 262_L | 286_A | 1.302 | 0.99 |
| 323_I | 327_S | 1.292 | 0.99 |
| 40_I | 81_H | 1.280 | 0.99 |
| 245_R | 248_N | 1.270 | 0.99 |
| 239_Q | 438_E | 1.261 | 0.99 |
| 40_I | 116_I | 1.261 | 0.99 |
| 245_R | 445_E | 1.258 | 0.99 |
| 258_N | 288_V | 1.256 | 0.99 |
| 136_V | 140_A | 1.255 | 0.99 |
| 24_G | 130_K | 1.254 | 0.99 |
| 435_T | 438_E | 1.254 | 0.99 |
| 42_D | 152_D | 1.254 | 0.99 |
| 236_F | 421_I | 1.250 | 0.99 |
| 341_D | 344_L | 1.249 | 0.99 |
| 238_A | 419_G | 1.244 | 0.98 |
| 93_L | 126_A | 1.244 | 0.98 |
| 233_S | 425_N | 1.242 | 0.98 |
| 447_V | 450_K | 1.238 | 0.98 |
| 239_Q | 434_L | 1.233 | 0.98 |
| 298_D | 302_R | 1.225 | 0.98 |
| 318_L | 449_A | 1.214 | 0.98 |
| 43_L | 152_D | 1.212 | 0.98 |
| 262_L | 328_V | 1.211 | 0.98 |
| 33_D | 43_L | 1.209 | 0.98 |
| 339_T | 343_I | 1.205 | 0.98 |
| 271_A | 436_H | 1.200 | 0.98 |
| 133_H | 138_G | 1.198 | 0.98 |
| 139_V | 291_S | 1.194 | 0.98 |
| 151_H | 156_K | 1.193 | 0.98 |
| 112_W | 129_F | 1.192 | 0.98 |
| 46_D | 151_H | 1.189 | 0.98 |
| 315_D | 319_Q | 1.189 | 0.98 |
| 237_A | 434_L | 1.189 | 0.98 |
| 255_V | 259_D | 1.186 | 0.98 |
| 54_P | 151_H | 1.183 | 0.98 |
| 264_V | 444_F | 1.181 | 0.98 |
| 33_D | 125_F | 1.175 | 0.98 |
| 231_S | 425_N | 1.175 | 0.98 |
| 245_R | 446_G | 1.172 | 0.98 |
| 307_L | 342_Q | 1.170 | 0.97 |
| 114_C | 129_F | 1.165 | 0.97 |
| 264_V | 437_L | 1.164 | 0.97 |
| 311_A | 315_D | 1.162 | 0.97 |
| 136_V | 141_G | 1.159 | 0.97 |
| 427_L | 430_M | 1.157 | 0.97 |
| 261_V | 437_L | 1.157 | 0.97 |
| 255_V | 325_R | 1.156 | 0.97 |
| 250_A | 255_V | 1.156 | 0.97 |
| 261_V | 416_L | 1.153 | 0.97 |
| 45_N | 48_R | 1.150 | 0.97 |
| 268_A | 436_H | 1.148 | 0.97 |
| 244_D | 248_N | 1.135 | 0.97 |
| 237_A | 429_R | 1.135 | 0.97 |
| 261_V | 409_M | 1.132 | 0.97 |
| 231_S | 423_C | 1.131 | 0.97 |
| 22_H | 130_K | 1.131 | 0.97 |
| 325_R | 329_Q | 1.129 | 0.97 |
| 53_I | 72_E | 1.126 | 0.97 |
| 347_S | 352_G | 1.125 | 0.97 |
| 235_R | 422_A | 1.123 | 0.97 |
| 162_W | 165_E | 1.111 | 0.96 |
| 186_G | 189_S | 1.110 | 0.96 |
| 149_L | 154_T | 1.109 | 0.96 |
| 40_I | 118_E | 1.106 | 0.96 |
| 34_N | 41_Q | 1.105 | 0.96 |
| 175_P | 178_G | 1.105 | 0.96 |
| 265_C | 437_L | 1.103 | 0.96 |
| 11_F | 301_N | 1.100 | 0.96 |
| 98_S | 102_S | 1.099 | 0.96 |
| 372_V | 375_N | 1.096 | 0.96 |
| 45_N | 50_S | 1.095 | 0.96 |
| 44_V | 81_H | 1.095 | 0.96 |
| 406_N | 421_I | 1.094 | 0.96 |
| 341_D | 345_N | 1.093 | 0.96 |
| 270_R | 273_L | 1.093 | 0.96 |
| 356_L | 359_I | 1.091 | 0.96 |
| 61_K | 110_P | 1.089 | 0.96 |
| 265_C | 371_L | 1.086 | 0.96 |
| 439_E | 442_Q | 1.085 | 0.96 |
| 218_S | 221_A | 1.081 | 0.95 |
| 268_A | 272_Y | 1.081 | 0.95 |
| 5_H | 8_D | 1.080 | 0.95 |
| 116_I | 125_F | 1.076 | 0.95 |
| 259_D | 329_Q | 1.076 | 0.95 |
| 259_D | 328_V | 1.074 | 0.95 |
| 120_I | 124_R | 1.074 | 0.95 |
| 65_L | 69_E | 1.070 | 0.95 |
| 94_L | 98_S | 1.064 | 0.95 |
| 136_V | 144_L | 1.062 | 0.95 |
| 56_P | 59_N | 1.060 | 0.95 |
| 4_L | 62_L | 1.058 | 0.95 |
| 155_E | 158_I | 1.051 | 0.94 |
| 255_V | 260_V | 1.051 | 0.94 |
| 96_Y | 115_N | 1.051 | 0.94 |
| 52_S | 112_W | 1.047 | 0.94 |
| 167_K | 172_L | 1.043 | 0.94 |
| 236_F | 419_G | 1.040 | 0.94 |
| 97_I | 128_Y | 1.040 | 0.94 |
| 51_K | 144_L | 1.036 | 0.94 |
| 42_D | 46_D | 1.035 | 0.94 |
| 179_K | 182_K | 1.034 | 0.94 |
| 48_R | 74_D | 1.030 | 0.94 |
| 174_E | 178_G | 1.028 | 0.94 |
| 249_I | 252_S | 1.026 | 0.94 |
| 249_I | 260_V | 1.022 | 0.93 |
| 290_A | 306_I | 1.022 | 0.93 |
| 90_I | 94_L | 1.015 | 0.93 |
| 312_T | 320_R | 1.014 | 0.93 |
| 46_D | 152_D | 1.013 | 0.93 |
| 312_T | 315_D | 1.007 | 0.93 |
| 80_R | 115_N | 1.007 | 0.93 |
| 209_I | 213_P | 1.004 | 0.93 |
| 47_I | 148_S | 1.002 | 0.92 |
| 7_I | 10_I | 1.001 | 0.92 |
| 89_R | 92_E | 1.001 | 0.92 |
| 66_F | 69_E | 1.000 | 0.92 |
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 | |
| 2vsqA | 1 | 0.8821 | 100 | 0.142 | Contact Map |
| 2jgpA | 1 | 0.8843 | 100 | 0.145 | Contact Map |
| 1l5aA | 3 | 0.8777 | 100 | 0.165 | Contact Map |
| 4jn3A | 2 | 0.8843 | 100 | 0.169 | Contact Map |
| 4znmA | 2 | 0 | 100 | 0.172 | Contact Map |
| 4tx3B | 1 | 0.8952 | 100 | 0.172 | Contact Map |
| 2xhgA | 1 | 0.9083 | 100 | 0.214 | Contact Map |
| 4hvmA | 4 | 0.81 | 100 | 0.217 | Contact Map |
| 1q9jA | 2 | 0.7882 | 100 | 0.263 | Contact Map |
| 3fotA | 1 | 0.9039 | 100 | 0.352 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)