| GerAA |
| ID: | 1488063683 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 482 (452) | ||
| Sequences: | 2220 (1792.7) | ||
| Seq/Len: | 4.912 | ||
| Nf(neff/√len): | 84.3 |
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: 4.912).
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 |
| 162_K | 192_K | 6.365 | 1.00 |
| 233_V | 243_A | 5.857 | 1.00 |
| 411_S | 423_F | 5.332 | 1.00 |
| 100_C | 115_T | 4.026 | 1.00 |
| 183_A | 188_I | 3.884 | 1.00 |
| 168_E | 199_Q | 3.722 | 1.00 |
| 366_Q | 370_E | 3.420 | 1.00 |
| 214_E | 272_R | 3.362 | 1.00 |
| 166_I | 195_L | 3.103 | 1.00 |
| 298_I | 409_M | 2.925 | 1.00 |
| 292_F | 424_M | 2.765 | 1.00 |
| 161_T | 175_A | 2.726 | 1.00 |
| 205_D | 249_S | 2.684 | 1.00 |
| 224_I | 255_V | 2.656 | 1.00 |
| 245_L | 252_V | 2.620 | 1.00 |
| 179_I | 182_K | 2.608 | 1.00 |
| 202_D | 238_F | 2.592 | 1.00 |
| 95_I | 101_A | 2.536 | 1.00 |
| 87_T | 90_K | 2.520 | 1.00 |
| 14_L | 41_Y | 2.512 | 1.00 |
| 144_D | 147_L | 2.510 | 1.00 |
| 176_I | 192_K | 2.500 | 1.00 |
| 150_I | 245_L | 2.486 | 1.00 |
| 161_T | 177_M | 2.443 | 1.00 |
| 331_A | 378_L | 2.439 | 1.00 |
| 169_N | 181_G | 2.428 | 1.00 |
| 158_K | 181_G | 2.413 | 1.00 |
| 85_V | 112_I | 2.369 | 1.00 |
| 137_V | 153_R | 2.341 | 1.00 |
| 408_S | 423_F | 2.295 | 1.00 |
| 160_I | 180_E | 2.278 | 1.00 |
| 91_T | 101_A | 2.273 | 1.00 |
| 190_E | 194_R | 2.244 | 1.00 |
| 101_A | 112_I | 2.165 | 1.00 |
| 432_T | 442_F | 2.126 | 1.00 |
| 150_I | 177_M | 2.109 | 1.00 |
| 156_H | 169_N | 2.092 | 1.00 |
| 408_S | 427_V | 2.086 | 1.00 |
| 331_A | 409_M | 2.078 | 1.00 |
| 24_N | 160_I | 2.073 | 1.00 |
| 295_S | 412_A | 2.064 | 1.00 |
| 8_E | 13_N | 2.063 | 1.00 |
| 164_I | 196_K | 2.037 | 1.00 |
| 84_P | 109_K | 2.016 | 1.00 |
| 227_T | 233_V | 2.016 | 1.00 |
| 22_K | 160_I | 1.996 | 1.00 |
| 335_E | 405_R | 1.990 | 1.00 |
| 188_I | 242_V | 1.953 | 1.00 |
| 102_V | 113_L | 1.942 | 1.00 |
| 412_A | 420_I | 1.939 | 1.00 |
| 135_P | 270_Y | 1.927 | 1.00 |
| 7_K | 13_N | 1.894 | 1.00 |
| 194_R | 215_D | 1.832 | 1.00 |
| 46_S | 144_D | 1.805 | 1.00 |
| 278_L | 403_V | 1.789 | 1.00 |
| 27_L | 45_F | 1.786 | 1.00 |
| 179_I | 237_L | 1.760 | 1.00 |
| 94_S | 112_I | 1.758 | 1.00 |
| 11_H | 39_V | 1.750 | 1.00 |
| 328_I | 413_A | 1.740 | 1.00 |
| 85_V | 90_K | 1.735 | 1.00 |
| 189_K | 193_A | 1.723 | 1.00 |
| 418_Y | 422_L | 1.722 | 1.00 |
| 277_S | 281_S | 1.716 | 1.00 |
| 180_E | 185_K | 1.716 | 1.00 |
| 263_M | 287_I | 1.708 | 1.00 |
| 191_V | 242_V | 1.702 | 0.99 |
| 190_E | 193_A | 1.690 | 0.99 |
| 126_P | 138_A | 1.670 | 0.99 |
| 191_V | 244_I | 1.669 | 0.99 |
| 99_N | 116_G | 1.669 | 0.99 |
| 269_Y | 455_D | 1.663 | 0.99 |
| 444_P | 447_F | 1.661 | 0.99 |
| 93_E | 171_L | 1.658 | 0.99 |
| 200_L | 212_L | 1.653 | 0.99 |
| 103_F | 110_A | 1.640 | 0.99 |
| 154_T | 234_S | 1.627 | 0.99 |
| 281_S | 285_A | 1.624 | 0.99 |
| 236_A | 254_L | 1.620 | 0.99 |
| 143_I | 175_A | 1.618 | 0.99 |
| 150_I | 159_L | 1.609 | 0.99 |
| 166_I | 174_A | 1.608 | 0.99 |
| 49_T | 54_V | 1.605 | 0.99 |
| 174_A | 246_V | 1.603 | 0.99 |
| 18_L | 29_K | 1.601 | 0.99 |
| 448_F | 453_T | 1.597 | 0.99 |
| 193_A | 197_N | 1.562 | 0.99 |
| 286_S | 340_L | 1.558 | 0.99 |
| 164_I | 192_K | 1.550 | 0.99 |
| 170_K | 202_D | 1.527 | 0.99 |
| 287_I | 401_F | 1.502 | 0.98 |
| 244_I | 255_V | 1.496 | 0.98 |
| 31_K | 39_V | 1.489 | 0.98 |
| 206_S | 246_V | 1.478 | 0.98 |
| 74_K | 84_P | 1.475 | 0.98 |
| 185_K | 189_K | 1.462 | 0.98 |
| 191_V | 255_V | 1.457 | 0.98 |
| 198_I | 209_L | 1.456 | 0.98 |
| 241_R | 261_I | 1.454 | 0.98 |
| 94_S | 99_N | 1.440 | 0.98 |
| 290_T | 392_V | 1.434 | 0.98 |
| 47_E | 147_L | 1.421 | 0.98 |
| 326_P | 329_F | 1.417 | 0.98 |
| 164_I | 176_I | 1.412 | 0.97 |
| 257_V | 262_L | 1.404 | 0.97 |
| 29_K | 41_Y | 1.388 | 0.97 |
| 21_L | 96_L | 1.386 | 0.97 |
| 170_K | 238_F | 1.380 | 0.97 |
| 243_A | 254_L | 1.375 | 0.97 |
| 143_I | 245_L | 1.350 | 0.96 |
| 14_L | 31_K | 1.347 | 0.96 |
| 23_E | 162_K | 1.347 | 0.96 |
| 163_K | 173_P | 1.337 | 0.96 |
| 81_D | 114_T | 1.335 | 0.96 |
| 47_E | 148_A | 1.333 | 0.96 |
| 86_E | 109_K | 1.332 | 0.96 |
| 219_S | 223_Q | 1.331 | 0.96 |
| 91_T | 110_A | 1.307 | 0.95 |
| 154_T | 238_F | 1.307 | 0.95 |
| 182_K | 201_E | 1.303 | 0.95 |
| 158_K | 180_E | 1.302 | 0.95 |
| 286_S | 391_T | 1.302 | 0.95 |
| 125_E | 138_A | 1.298 | 0.95 |
| 337_T | 363_V | 1.279 | 0.95 |
| 14_L | 18_L | 1.276 | 0.95 |
| 147_L | 161_T | 1.275 | 0.95 |
| 430_H | 434_Q | 1.270 | 0.94 |
| 123_L | 137_V | 1.267 | 0.94 |
| 9_Y | 12_D | 1.260 | 0.94 |
| 299_T | 420_I | 1.259 | 0.94 |
| 42_Y | 102_V | 1.250 | 0.94 |
| 183_A | 242_V | 1.245 | 0.94 |
| 33_M | 39_V | 1.242 | 0.94 |
| 52_N | 56_E | 1.238 | 0.93 |
| 131_V | 265_S | 1.236 | 0.93 |
| 48_M | 148_A | 1.230 | 0.93 |
| 431_L | 442_F | 1.227 | 0.93 |
| 369_V | 380_I | 1.224 | 0.93 |
| 223_Q | 272_R | 1.222 | 0.93 |
| 99_N | 112_I | 1.221 | 0.93 |
| 164_I | 195_L | 1.217 | 0.93 |
| 6_F | 103_F | 1.209 | 0.92 |
| 189_K | 192_K | 1.208 | 0.92 |
| 338_I | 386_A | 1.202 | 0.92 |
| 176_I | 242_V | 1.197 | 0.92 |
| 254_L | 261_I | 1.189 | 0.92 |
| 243_A | 252_V | 1.187 | 0.91 |
| 165_M | 171_L | 1.185 | 0.91 |
| 125_E | 136_K | 1.185 | 0.91 |
| 177_M | 252_V | 1.184 | 0.91 |
| 291_L | 404_L | 1.181 | 0.91 |
| 137_V | 149_L | 1.174 | 0.91 |
| 263_M | 284_F | 1.173 | 0.91 |
| 262_L | 397_M | 1.171 | 0.91 |
| 303_F | 414_I | 1.169 | 0.91 |
| 23_E | 160_I | 1.169 | 0.91 |
| 327_P | 378_L | 1.164 | 0.90 |
| 30_N | 82_A | 1.164 | 0.90 |
| 345_G | 353_G | 1.161 | 0.90 |
| 97_N | 155_S | 1.156 | 0.90 |
| 169_N | 201_E | 1.150 | 0.90 |
| 235_S | 239_N | 1.148 | 0.90 |
| 285_A | 336_V | 1.138 | 0.89 |
| 233_V | 252_V | 1.136 | 0.89 |
| 130_K | 350_N | 1.132 | 0.89 |
| 407_I | 411_S | 1.128 | 0.88 |
| 54_V | 115_T | 1.127 | 0.88 |
| 339_E | 406_F | 1.121 | 0.88 |
| 137_V | 248_S | 1.120 | 0.88 |
| 292_F | 408_S | 1.119 | 0.88 |
| 338_I | 357_G | 1.119 | 0.88 |
| 23_E | 180_E | 1.118 | 0.88 |
| 127_T | 136_K | 1.116 | 0.88 |
| 204_Q | 208_T | 1.099 | 0.87 |
| 118_K | 152_Q | 1.096 | 0.86 |
| 169_N | 182_K | 1.092 | 0.86 |
| 10_I | 105_N | 1.091 | 0.86 |
| 83_R | 94_S | 1.086 | 0.86 |
| 190_E | 215_D | 1.083 | 0.86 |
| 43_L | 103_F | 1.082 | 0.85 |
| 13_N | 103_F | 1.081 | 0.85 |
| 132_V | 267_D | 1.078 | 0.85 |
| 10_I | 103_F | 1.077 | 0.85 |
| 278_L | 339_E | 1.076 | 0.85 |
| 165_M | 173_P | 1.073 | 0.85 |
| 280_R | 455_D | 1.067 | 0.84 |
| 12_D | 15_A | 1.056 | 0.84 |
| 99_N | 114_T | 1.051 | 0.83 |
| 219_S | 430_H | 1.051 | 0.83 |
| 239_N | 269_Y | 1.051 | 0.83 |
| 225_Q | 261_I | 1.048 | 0.83 |
| 8_E | 108_D | 1.044 | 0.83 |
| 221_F | 431_L | 1.044 | 0.83 |
| 140_V | 146_N | 1.040 | 0.82 |
| 27_L | 43_L | 1.039 | 0.82 |
| 213_I | 437_F | 1.036 | 0.82 |
| 194_R | 213_I | 1.035 | 0.82 |
| 54_V | 100_C | 1.034 | 0.82 |
| 7_K | 12_D | 1.031 | 0.81 |
| 139_F | 150_I | 1.030 | 0.81 |
| 148_A | 152_Q | 1.025 | 0.81 |
| 319_N | 377_I | 1.025 | 0.81 |
| 335_E | 342_R | 1.024 | 0.81 |
| 50_D | 117_K | 1.023 | 0.81 |
| 124_T | 138_A | 1.023 | 0.81 |
| 257_V | 261_I | 1.018 | 0.80 |
| 224_I | 253_L | 1.018 | 0.80 |
| 101_A | 110_A | 1.015 | 0.80 |
| 221_F | 430_H | 1.015 | 0.80 |
| 29_K | 43_L | 1.015 | 0.80 |
| 118_K | 142_D | 1.014 | 0.80 |
| 137_V | 152_Q | 1.012 | 0.80 |
| 409_M | 413_A | 1.008 | 0.79 |
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 | |
| 4g3oA | 1 | 0.0913 | 17.9 | 0.982 | Contact Map |
| 3kpeA | 1 | 0.1017 | 17.4 | 0.982 | Contact Map |
| 4bemA | 9 | 0.166 | 14.2 | 0.983 | Contact Map |
| 3hh1A | 4 | 0.2116 | 14.1 | 0.983 | Contact Map |
| 2xquA | 5 | 0.166 | 9.3 | 0.984 | Contact Map |
| 2xndJ | 8 | 0.1494 | 8.8 | 0.985 | Contact Map |
| 2qwvA | 2 | 0.3257 | 8.5 | 0.985 | Contact Map |
| 4f4sA | 10 | 0.1535 | 7.3 | 0.985 | Contact Map |
| 1xtiA | 1 | 0.3631 | 7.2 | 0.985 | Contact Map |
| 3zk1A | 22 | 0.1846 | 7.2 | 0.985 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)