| uraa |
| ID: | 1428403626 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 429 (408) | ||
| Sequences: | 5520 (3132.3) | ||
| Seq/Len: | 13.529 | ||
| Nf(neff/√len): | 155.1 |
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: 13.529).
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 |
| 95_I | 278_G | 4.539 | 1.00 |
| 144_A | 162_S | 3.421 | 1.00 |
| 53_G | 273_S | 3.243 | 1.00 |
| 169_T | 188_G | 3.132 | 1.00 |
| 7_G | 10_E | 3.129 | 1.00 |
| 99_V | 103_L | 2.738 | 1.00 |
| 99_V | 275_V | 2.662 | 1.00 |
| 131_V | 395_A | 2.656 | 1.00 |
| 160_I | 164_T | 2.629 | 1.00 |
| 105_S | 268_F | 2.581 | 1.00 |
| 164_T | 168_V | 2.557 | 1.00 |
| 168_V | 191_V | 2.536 | 1.00 |
| 102_C | 275_V | 2.511 | 1.00 |
| 21_S | 308_G | 2.431 | 1.00 |
| 67_A | 287_T | 2.378 | 1.00 |
| 194_A | 198_A | 2.279 | 1.00 |
| 256_D | 259_R | 2.272 | 1.00 |
| 166_L | 340_L | 2.260 | 1.00 |
| 60_I | 306_I | 2.250 | 1.00 |
| 164_T | 195_L | 2.170 | 1.00 |
| 8_V | 303_T | 2.118 | 1.00 |
| 172_G | 187_I | 2.109 | 1.00 |
| 408_L | 411_V | 2.040 | 1.00 |
| 190_L | 194_A | 2.036 | 1.00 |
| 20_L | 299_R | 2.025 | 1.00 |
| 187_I | 191_V | 2.013 | 1.00 |
| 8_V | 14_L | 1.982 | 1.00 |
| 102_C | 268_F | 1.976 | 1.00 |
| 98_G | 274_T | 1.961 | 1.00 |
| 212_W | 321_K | 1.930 | 1.00 |
| 55_L | 309_A | 1.908 | 1.00 |
| 165_T | 336_G | 1.898 | 1.00 |
| 375_I | 394_L | 1.894 | 1.00 |
| 32_T | 47_L | 1.796 | 1.00 |
| 299_R | 304_W | 1.785 | 1.00 |
| 102_C | 271_G | 1.775 | 1.00 |
| 205_T | 209_N | 1.770 | 1.00 |
| 100_L | 232_L | 1.759 | 1.00 |
| 86_G | 89_V | 1.744 | 1.00 |
| 192_G | 333_V | 1.739 | 1.00 |
| 401_G | 405_I | 1.734 | 1.00 |
| 49_F | 285_N | 1.730 | 1.00 |
| 25_L | 312_F | 1.728 | 1.00 |
| 409_I | 412_L | 1.724 | 1.00 |
| 49_F | 280_F | 1.720 | 1.00 |
| 18_I | 307_G | 1.712 | 1.00 |
| 51_G | 313_A | 1.711 | 1.00 |
| 14_L | 303_T | 1.694 | 1.00 |
| 403_S | 411_V | 1.683 | 1.00 |
| 98_G | 275_V | 1.642 | 1.00 |
| 114_G | 264_H | 1.637 | 1.00 |
| 249_T | 295_M | 1.633 | 1.00 |
| 169_T | 337_V | 1.602 | 1.00 |
| 204_T | 207_I | 1.593 | 1.00 |
| 51_G | 55_L | 1.590 | 1.00 |
| 161_I | 196_S | 1.580 | 1.00 |
| 371_V | 398_V | 1.580 | 1.00 |
| 123_A | 365_N | 1.570 | 1.00 |
| 18_I | 22_L | 1.568 | 1.00 |
| 251_N | 357_K | 1.564 | 1.00 |
| 52_I | 276_I | 1.532 | 1.00 |
| 262_G | 265_R | 1.515 | 1.00 |
| 276_I | 280_F | 1.489 | 1.00 |
| 54_T | 309_A | 1.477 | 1.00 |
| 246_L | 266_S | 1.475 | 1.00 |
| 152_Q | 155_D | 1.451 | 1.00 |
| 154_P | 159_I | 1.451 | 1.00 |
| 166_L | 339_L | 1.437 | 1.00 |
| 138_G | 384_I | 1.435 | 1.00 |
| 275_V | 278_G | 1.432 | 1.00 |
| 48_L | 317_S | 1.430 | 1.00 |
| 52_I | 280_F | 1.427 | 1.00 |
| 168_V | 188_G | 1.425 | 1.00 |
| 193_Y | 328_M | 1.416 | 1.00 |
| 310_A | 314_I | 1.415 | 1.00 |
| 169_T | 340_L | 1.404 | 0.99 |
| 56_L | 276_I | 1.404 | 0.99 |
| 95_I | 275_V | 1.400 | 0.99 |
| 88_E | 219_Y | 1.398 | 0.99 |
| 35_V | 73_F | 1.398 | 0.99 |
| 353_L | 373_L | 1.385 | 0.99 |
| 3_R | 9_S | 1.385 | 0.99 |
| 60_I | 272_L | 1.383 | 0.99 |
| 56_L | 269_A | 1.369 | 0.99 |
| 3_R | 8_V | 1.366 | 0.99 |
| 106_F | 268_F | 1.360 | 0.99 |
| 106_F | 111_A | 1.358 | 0.99 |
| 55_L | 307_G | 1.357 | 0.99 |
| 92_G | 222_R | 1.356 | 0.99 |
| 245_H | 289_G | 1.356 | 0.99 |
| 130_A | 373_L | 1.337 | 0.99 |
| 13_P | 16_Q | 1.331 | 0.99 |
| 208_I | 211_H | 1.329 | 0.99 |
| 164_T | 191_V | 1.315 | 0.99 |
| 307_G | 310_A | 1.311 | 0.99 |
| 194_A | 197_F | 1.307 | 0.99 |
| 168_V | 172_G | 1.305 | 0.99 |
| 166_L | 336_G | 1.304 | 0.99 |
| 94_F | 278_G | 1.302 | 0.99 |
| 372_I | 399_G | 1.297 | 0.99 |
| 393_A | 397_I | 1.294 | 0.99 |
| 188_G | 337_V | 1.293 | 0.99 |
| 88_E | 222_R | 1.290 | 0.99 |
| 100_L | 235_A | 1.282 | 0.99 |
| 140_A | 339_L | 1.282 | 0.99 |
| 65_I | 260_D | 1.279 | 0.99 |
| 363_A | 367_I | 1.275 | 0.99 |
| 161_I | 192_G | 1.274 | 0.99 |
| 242_H | 246_L | 1.266 | 0.99 |
| 168_V | 195_L | 1.261 | 0.99 |
| 161_I | 199_M | 1.260 | 0.99 |
| 18_I | 308_G | 1.250 | 0.99 |
| 97_C | 234_A | 1.247 | 0.99 |
| 20_L | 304_W | 1.247 | 0.99 |
| 28_M | 68_Y | 1.244 | 0.98 |
| 97_C | 235_A | 1.242 | 0.98 |
| 172_G | 184_P | 1.242 | 0.98 |
| 89_V | 222_R | 1.234 | 0.98 |
| 213_F | 216_P | 1.230 | 0.98 |
| 191_V | 195_L | 1.230 | 0.98 |
| 55_L | 310_A | 1.227 | 0.98 |
| 311_I | 315_L | 1.227 | 0.98 |
| 92_G | 223_F | 1.227 | 0.98 |
| 171_L | 175_L | 1.223 | 0.98 |
| 14_L | 18_I | 1.221 | 0.98 |
| 193_Y | 329_I | 1.215 | 0.98 |
| 185_I | 337_V | 1.209 | 0.98 |
| 364_Q | 406_F | 1.208 | 0.98 |
| 252_I | 296_A | 1.207 | 0.98 |
| 198_A | 201_I | 1.203 | 0.98 |
| 31_A | 35_V | 1.202 | 0.98 |
| 105_S | 271_G | 1.195 | 0.98 |
| 161_I | 201_I | 1.187 | 0.98 |
| 242_H | 287_T | 1.181 | 0.98 |
| 249_T | 292_I | 1.172 | 0.98 |
| 169_T | 173_S | 1.170 | 0.97 |
| 238_V | 284_P | 1.167 | 0.97 |
| 307_G | 311_I | 1.165 | 0.97 |
| 398_V | 402_L | 1.163 | 0.97 |
| 241_E | 286_T | 1.161 | 0.97 |
| 17_T | 308_G | 1.157 | 0.97 |
| 164_T | 199_M | 1.156 | 0.97 |
| 62_K | 265_R | 1.155 | 0.97 |
| 176_F | 180_L | 1.152 | 0.97 |
| 55_L | 306_I | 1.151 | 0.97 |
| 193_Y | 202_V | 1.148 | 0.97 |
| 364_Q | 403_S | 1.145 | 0.97 |
| 300_V | 305_V | 1.140 | 0.97 |
| 404_L | 409_I | 1.140 | 0.97 |
| 195_L | 199_M | 1.139 | 0.97 |
| 41_I | 87_Y | 1.138 | 0.97 |
| 210_A | 321_K | 1.137 | 0.97 |
| 47_L | 51_G | 1.135 | 0.97 |
| 162_S | 336_G | 1.135 | 0.97 |
| 7_G | 64_K | 1.132 | 0.97 |
| 173_S | 184_P | 1.129 | 0.97 |
| 165_T | 188_G | 1.120 | 0.96 |
| 51_G | 314_I | 1.119 | 0.96 |
| 171_L | 405_I | 1.118 | 0.96 |
| 165_T | 192_G | 1.117 | 0.96 |
| 350_I | 373_L | 1.115 | 0.96 |
| 98_G | 271_G | 1.111 | 0.96 |
| 371_V | 394_L | 1.107 | 0.96 |
| 34_L | 37_V | 1.105 | 0.96 |
| 6_I | 10_E | 1.103 | 0.96 |
| 163_I | 167_A | 1.099 | 0.96 |
| 65_I | 266_S | 1.094 | 0.96 |
| 104_V | 235_A | 1.086 | 0.96 |
| 224_E | 227_A | 1.084 | 0.96 |
| 196_S | 201_I | 1.083 | 0.96 |
| 187_I | 190_L | 1.083 | 0.96 |
| 79_V | 83_L | 1.080 | 0.95 |
| 8_V | 64_K | 1.079 | 0.95 |
| 391_G | 395_A | 1.077 | 0.95 |
| 365_N | 403_S | 1.073 | 0.95 |
| 104_V | 239_I | 1.070 | 0.95 |
| 103_L | 106_F | 1.067 | 0.95 |
| 169_T | 185_I | 1.067 | 0.95 |
| 78_P | 81_L | 1.065 | 0.95 |
| 157_K | 160_I | 1.065 | 0.95 |
| 28_M | 288_Y | 1.060 | 0.95 |
| 170_V | 367_I | 1.060 | 0.95 |
| 273_S | 276_I | 1.059 | 0.95 |
| 67_A | 249_T | 1.054 | 0.95 |
| 8_V | 12_P | 1.051 | 0.94 |
| 383_N | 388_E | 1.050 | 0.94 |
| 195_L | 198_A | 1.048 | 0.94 |
| 172_G | 176_F | 1.046 | 0.94 |
| 8_V | 11_R | 1.046 | 0.94 |
| 68_Y | 308_G | 1.045 | 0.94 |
| 277_S | 282_S | 1.043 | 0.94 |
| 35_V | 46_V | 1.043 | 0.94 |
| 348_S | 351_R | 1.034 | 0.94 |
| 179_F | 183_I | 1.032 | 0.94 |
| 114_G | 118_V | 1.032 | 0.94 |
| 346_G | 349_G | 1.030 | 0.94 |
| 127_A | 372_I | 1.030 | 0.94 |
| 176_F | 181_A | 1.029 | 0.94 |
| 15_L | 19_P | 1.022 | 0.93 |
| 303_T | 306_I | 1.022 | 0.93 |
| 58_L | 307_G | 1.022 | 0.93 |
| 306_I | 310_A | 1.014 | 0.93 |
| 5_A | 9_S | 1.005 | 0.93 |
| 24_H | 291_N | 1.001 | 0.92 |
| 51_G | 309_A | 1.001 | 0.92 |
| 97_C | 238_V | 1.000 | 0.92 |
| 94_F | 284_P | 1.000 | 0.92 |
| 351_R | 356_S | 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 | |
| 3qe7A | 1 | 0.9487 | 100 | 0.166 | Contact Map |
| 1pw4A | 1 | 0.4732 | 12.6 | 0.97 | Contact Map |
| 2gfpA | 2 | 0.4336 | 9.9 | 0.972 | Contact Map |
| 2kluA | 1 | 0.1142 | 8.1 | 0.973 | Contact Map |
| 3o7qA | 1 | 0.4476 | 8 | 0.973 | Contact Map |
| 2jlnA | 1 | 0.8765 | 7.8 | 0.973 | Contact Map |
| 4cz8A | 2 | 0.5758 | 5.9 | 0.974 | Contact Map |
| 4f35D | 4 | 0.4802 | 2.6 | 0.978 | Contact Map |
| 2ksfA | 1 | 0.2494 | 2.6 | 0.978 | Contact Map |
| 1s5lX | 2 | 0.0932 | 2.3 | 0.979 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)