| T0819 |
| ID: | 1402705425 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 373 (360) | ||
| Sequences: | 5539 (4224.1) | ||
| Seq/Len: | 15.386 | ||
| Nf(neff/√len): | 222.6 |
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: 15.386).
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 |
| 235_I | 265_A | 3.828 | 1.00 |
| 288_R | 357_D | 3.819 | 1.00 |
| 330_H | 365_E | 3.664 | 1.00 |
| 76_A | 270_A | 3.430 | 1.00 |
| 292_I | 360_A | 3.121 | 1.00 |
| 348_I | 359_L | 2.828 | 1.00 |
| 179_V | 214_D | 2.671 | 1.00 |
| 110_A | 158_P | 2.480 | 1.00 |
| 285_S | 288_R | 2.419 | 1.00 |
| 179_V | 183_Q | 2.398 | 1.00 |
| 240_S | 245_A | 2.380 | 1.00 |
| 174_P | 177_R | 2.346 | 1.00 |
| 285_S | 353_D | 2.320 | 1.00 |
| 292_I | 295_D | 2.217 | 1.00 |
| 182_A | 218_V | 2.141 | 1.00 |
| 53_L | 57_Q | 2.141 | 1.00 |
| 289_I | 350_T | 2.141 | 1.00 |
| 101_I | 219_I | 2.118 | 1.00 |
| 83_T | 239_L | 2.109 | 1.00 |
| 219_I | 240_S | 2.073 | 1.00 |
| 285_S | 356_M | 2.069 | 1.00 |
| 91_G | 97_L | 2.060 | 1.00 |
| 101_I | 192_V | 2.052 | 1.00 |
| 296_S | 364_P | 2.042 | 1.00 |
| 70_N | 262_V | 1.954 | 1.00 |
| 352_P | 355_E | 1.947 | 1.00 |
| 118_G | 163_A | 1.944 | 1.00 |
| 48_A | 271_D | 1.902 | 1.00 |
| 111_P | 153_G | 1.891 | 1.00 |
| 126_V | 131_G | 1.877 | 1.00 |
| 290_G | 308_V | 1.876 | 1.00 |
| 123_N | 135_T | 1.856 | 1.00 |
| 145_L | 181_F | 1.832 | 1.00 |
| 330_H | 362_A | 1.791 | 1.00 |
| 182_A | 191_L | 1.784 | 1.00 |
| 289_I | 356_M | 1.781 | 1.00 |
| 111_P | 132_R | 1.780 | 1.00 |
| 77_L | 88_I | 1.757 | 1.00 |
| 86_A | 242_P | 1.749 | 1.00 |
| 17_S | 20_F | 1.749 | 1.00 |
| 288_R | 292_I | 1.740 | 1.00 |
| 80_H | 272_Q | 1.736 | 1.00 |
| 114_T | 133_L | 1.735 | 1.00 |
| 64_K | 355_E | 1.728 | 1.00 |
| 45_F | 281_K | 1.720 | 1.00 |
| 89_A | 245_A | 1.713 | 1.00 |
| 323_V | 326_L | 1.684 | 1.00 |
| 76_A | 266_I | 1.677 | 1.00 |
| 299_A | 311_D | 1.672 | 1.00 |
| 75_Q | 85_P | 1.664 | 1.00 |
| 146_E | 180_A | 1.646 | 1.00 |
| 144_D | 147_G | 1.644 | 1.00 |
| 292_I | 364_P | 1.642 | 1.00 |
| 310_V | 348_I | 1.639 | 1.00 |
| 80_H | 228_Y | 1.625 | 1.00 |
| 111_P | 134_V | 1.615 | 1.00 |
| 84_S | 87_N | 1.611 | 1.00 |
| 55_I | 260_I | 1.610 | 1.00 |
| 152_V | 157_A | 1.602 | 1.00 |
| 175_A | 179_V | 1.589 | 1.00 |
| 161_Y | 192_V | 1.587 | 1.00 |
| 112_V | 126_V | 1.580 | 1.00 |
| 77_L | 237_Y | 1.568 | 1.00 |
| 89_A | 238_T | 1.562 | 1.00 |
| 52_L | 56_R | 1.536 | 1.00 |
| 190_L | 244_T | 1.534 | 1.00 |
| 219_I | 238_T | 1.530 | 1.00 |
| 101_I | 159_L | 1.521 | 1.00 |
| 67_D | 71_H | 1.521 | 1.00 |
| 123_N | 127_A | 1.516 | 1.00 |
| 197_Y | 225_S | 1.515 | 1.00 |
| 106_V | 131_G | 1.509 | 1.00 |
| 272_Q | 276_K | 1.507 | 1.00 |
| 111_P | 157_A | 1.506 | 1.00 |
| 183_Q | 215_K | 1.504 | 1.00 |
| 99_G | 103_R | 1.501 | 1.00 |
| 98_L | 221_A | 1.500 | 1.00 |
| 186_P | 189_T | 1.500 | 1.00 |
| 287_Q | 291_R | 1.496 | 1.00 |
| 288_R | 353_D | 1.471 | 1.00 |
| 81_L | 237_Y | 1.466 | 1.00 |
| 102_V | 161_Y | 1.463 | 1.00 |
| 92_E | 258_S | 1.461 | 1.00 |
| 74_K | 249_D | 1.456 | 1.00 |
| 72_D | 266_I | 1.450 | 1.00 |
| 78_A | 84_S | 1.449 | 1.00 |
| 294_A | 302_P | 1.445 | 1.00 |
| 246_Q | 250_K | 1.424 | 1.00 |
| 325_R | 329_D | 1.417 | 1.00 |
| 139_A | 144_D | 1.415 | 1.00 |
| 353_D | 357_D | 1.409 | 1.00 |
| 111_P | 156_N | 1.403 | 0.99 |
| 196_A | 223_T | 1.382 | 0.99 |
| 247_A | 250_K | 1.374 | 0.99 |
| 358_L | 362_A | 1.372 | 0.99 |
| 280_L | 284_N | 1.372 | 0.99 |
| 200_T | 282_I | 1.366 | 0.99 |
| 36_A | 332_I | 1.366 | 0.99 |
| 98_L | 125_H | 1.362 | 0.99 |
| 96_G | 256_G | 1.360 | 0.99 |
| 311_D | 344_R | 1.359 | 0.99 |
| 113_V | 160_V | 1.359 | 0.99 |
| 55_I | 264_A | 1.354 | 0.99 |
| 310_V | 359_L | 1.343 | 0.99 |
| 47_P | 274_Y | 1.342 | 0.99 |
| 290_G | 300_P | 1.341 | 0.99 |
| 77_L | 269_L | 1.335 | 0.99 |
| 139_A | 142_R | 1.335 | 0.99 |
| 87_N | 242_P | 1.321 | 0.99 |
| 54_A | 267_A | 1.319 | 0.99 |
| 294_A | 300_P | 1.304 | 0.99 |
| 73_L | 77_L | 1.300 | 0.99 |
| 238_T | 248_F | 1.285 | 0.99 |
| 202_P | 283_A | 1.284 | 0.99 |
| 235_I | 261_G | 1.283 | 0.99 |
| 79_R | 270_A | 1.277 | 0.99 |
| 276_K | 280_L | 1.275 | 0.99 |
| 152_V | 185_L | 1.269 | 0.99 |
| 292_I | 296_S | 1.256 | 0.99 |
| 134_V | 153_G | 1.252 | 0.99 |
| 288_R | 360_A | 1.250 | 0.99 |
| 324_D | 329_D | 1.238 | 0.98 |
| 142_R | 177_R | 1.235 | 0.98 |
| 351_A | 355_E | 1.230 | 0.98 |
| 75_Q | 79_R | 1.228 | 0.98 |
| 322_I | 326_L | 1.227 | 0.98 |
| 153_G | 157_A | 1.218 | 0.98 |
| 162_L | 173_W | 1.216 | 0.98 |
| 249_D | 252_R | 1.212 | 0.98 |
| 81_L | 239_L | 1.208 | 0.98 |
| 88_I | 239_L | 1.207 | 0.98 |
| 50_S | 271_D | 1.204 | 0.98 |
| 97_L | 238_T | 1.204 | 0.98 |
| 94_I | 221_A | 1.201 | 0.98 |
| 136_V | 151_A | 1.197 | 0.98 |
| 70_N | 90_I | 1.184 | 0.98 |
| 258_S | 261_G | 1.183 | 0.98 |
| 309_A | 342_L | 1.182 | 0.98 |
| 34_I | 358_L | 1.181 | 0.98 |
| 166_D | 169_M | 1.180 | 0.98 |
| 20_F | 23_P | 1.175 | 0.98 |
| 106_V | 112_V | 1.174 | 0.98 |
| 295_D | 364_P | 1.172 | 0.98 |
| 172_W | 304_A | 1.162 | 0.97 |
| 36_A | 355_E | 1.161 | 0.97 |
| 149_L | 184_A | 1.159 | 0.97 |
| 271_D | 274_Y | 1.154 | 0.97 |
| 180_A | 184_A | 1.153 | 0.97 |
| 100_Q | 252_R | 1.149 | 0.97 |
| 356_M | 360_A | 1.148 | 0.97 |
| 43_S | 278_V | 1.146 | 0.97 |
| 143_E | 148_L | 1.141 | 0.97 |
| 262_V | 266_I | 1.132 | 0.97 |
| 357_D | 361_A | 1.131 | 0.97 |
| 40_A | 255_F | 1.128 | 0.97 |
| 53_L | 56_R | 1.127 | 0.97 |
| 216_P | 243_G | 1.123 | 0.97 |
| 284_N | 353_D | 1.122 | 0.97 |
| 289_I | 308_V | 1.122 | 0.97 |
| 73_L | 265_A | 1.112 | 0.96 |
| 277_E | 281_K | 1.110 | 0.96 |
| 325_R | 366_V | 1.107 | 0.96 |
| 115_S | 143_E | 1.106 | 0.96 |
| 185_L | 191_L | 1.105 | 0.96 |
| 104_L | 251_I | 1.101 | 0.96 |
| 222_R | 237_Y | 1.099 | 0.96 |
| 358_L | 361_A | 1.096 | 0.96 |
| 332_I | 358_L | 1.092 | 0.96 |
| 228_Y | 272_Q | 1.089 | 0.96 |
| 290_G | 294_A | 1.088 | 0.96 |
| 208_P | 211_S | 1.086 | 0.96 |
| 47_P | 52_L | 1.086 | 0.96 |
| 77_L | 90_I | 1.084 | 0.96 |
| 159_L | 192_V | 1.084 | 0.96 |
| 147_G | 150_A | 1.079 | 0.95 |
| 252_R | 256_G | 1.077 | 0.95 |
| 175_A | 210_E | 1.066 | 0.95 |
| 179_V | 215_K | 1.056 | 0.95 |
| 77_L | 81_L | 1.050 | 0.94 |
| 145_L | 149_L | 1.048 | 0.94 |
| 212_L | 239_L | 1.045 | 0.94 |
| 176_E | 179_V | 1.044 | 0.94 |
| 51_V | 267_A | 1.035 | 0.94 |
| 147_G | 151_A | 1.029 | 0.94 |
| 177_R | 180_A | 1.027 | 0.94 |
| 49_P | 53_L | 1.021 | 0.93 |
| 50_S | 53_L | 1.013 | 0.93 |
| 334_I | 346_I | 1.012 | 0.93 |
| 227_A | 279_T | 1.009 | 0.93 |
| 285_S | 357_D | 1.005 | 0.93 |
| 98_L | 161_Y | 1.004 | 0.93 |
| 179_V | 211_S | 1.000 | 0.92 |
| 332_I | 362_A | 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 | |
| 1fg7A | 1 | 0.9223 | 100 | 0.446 | Contact Map |
| 3getA | 2 | 0.9625 | 100 | 0.451 | Contact Map |
| 3ffhA | 2 | 0.9464 | 100 | 0.452 | Contact Map |
| 3hdoA | 2 | 0.9249 | 100 | 0.476 | Contact Map |
| 3ly1A | 4 | 0.9383 | 100 | 0.485 | Contact Map |
| 3eucA | 2 | 0.933 | 100 | 0.49 | Contact Map |
| 3cq5A | 3 | 0.9357 | 100 | 0.491 | Contact Map |
| 1lc5A | 1 | 0.9276 | 100 | 0.5 | Contact Map |
| 3ftbA | 4 | 0.8767 | 100 | 0.501 | Contact Map |
| 3p1tA | 4 | 0.8633 | 100 | 0.504 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)