| P38105 |
| ID: | 1507886928 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 339 (337) | ||
| Sequences: | 74179 (45238.6) | ||
| Seq/Len: | 220.116 | ||
| Nf(neff/√len): | 2464.3 |
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: 220.116).
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 |
| 32_K | 137_D | 3.145 | 1.00 |
| 30_K | 66_D | 3.073 | 1.00 |
| 32_K | 64_V | 2.972 | 1.00 |
| 315_H | 318_D | 2.961 | 1.00 |
| 28_R | 66_D | 2.742 | 1.00 |
| 163_T | 188_N | 2.668 | 1.00 |
| 7_E | 15_V | 2.574 | 1.00 |
| 76_R | 79_E | 2.560 | 1.00 |
| 79_E | 130_K | 2.524 | 1.00 |
| 27_V | 128_A | 2.524 | 1.00 |
| 80_R | 131_I | 2.515 | 1.00 |
| 136_A | 139_Y | 2.500 | 1.00 |
| 181_K | 208_D | 2.430 | 1.00 |
| 138_Q | 310_T | 2.403 | 1.00 |
| 30_K | 64_V | 2.375 | 1.00 |
| 19_I | 120_Y | 2.327 | 1.00 |
| 311_F | 322_L | 2.323 | 1.00 |
| 30_K | 120_Y | 2.319 | 1.00 |
| 164_V | 180_L | 2.256 | 1.00 |
| 309_H | 322_L | 2.224 | 1.00 |
| 310_T | 336_T | 2.221 | 1.00 |
| 61_F | 116_G | 2.215 | 1.00 |
| 221_I | 224_E | 2.205 | 1.00 |
| 200_E | 204_E | 2.202 | 1.00 |
| 7_E | 13_A | 2.195 | 1.00 |
| 61_F | 83_V | 2.171 | 1.00 |
| 199_L | 203_K | 2.170 | 1.00 |
| 188_N | 209_W | 2.156 | 1.00 |
| 294_D | 298_K | 2.142 | 1.00 |
| 24_A | 70_E | 2.135 | 1.00 |
| 169_A | 191_V | 2.123 | 1.00 |
| 5_L | 15_V | 2.099 | 1.00 |
| 74_S | 125_A | 2.057 | 1.00 |
| 23_S | 26_E | 2.055 | 1.00 |
| 80_R | 137_D | 2.041 | 1.00 |
| 177_V | 207_A | 2.038 | 1.00 |
| 159_T | 162_D | 2.029 | 1.00 |
| 62_F | 137_D | 2.000 | 1.00 |
| 134_A | 297_S | 1.984 | 1.00 |
| 321_S | 325_Q | 1.979 | 1.00 |
| 312_D | 315_H | 1.968 | 1.00 |
| 28_R | 122_V | 1.967 | 1.00 |
| 24_A | 71_G | 1.966 | 1.00 |
| 66_D | 120_Y | 1.938 | 1.00 |
| 25_G | 71_G | 1.922 | 1.00 |
| 45_R | 324_E | 1.916 | 1.00 |
| 200_E | 203_K | 1.866 | 1.00 |
| 165_L | 192_A | 1.816 | 1.00 |
| 165_L | 229_P | 1.806 | 1.00 |
| 199_L | 210_A | 1.790 | 1.00 |
| 322_L | 327_Q | 1.770 | 1.00 |
| 146_F | 175_T | 1.768 | 1.00 |
| 21_T | 67_A | 1.767 | 1.00 |
| 131_I | 137_D | 1.748 | 1.00 |
| 230_T | 250_S | 1.737 | 1.00 |
| 318_D | 321_S | 1.735 | 1.00 |
| 254_R | 278_S | 1.733 | 1.00 |
| 196_D | 200_E | 1.714 | 1.00 |
| 190_I | 229_P | 1.713 | 1.00 |
| 318_D | 322_L | 1.708 | 1.00 |
| 311_F | 319_A | 1.683 | 1.00 |
| 193_D | 199_L | 1.660 | 1.00 |
| 201_K | 204_E | 1.639 | 1.00 |
| 254_R | 280_F | 1.637 | 1.00 |
| 28_R | 120_Y | 1.629 | 1.00 |
| 4_I | 316_V | 1.626 | 1.00 |
| 67_A | 77_V | 1.621 | 1.00 |
| 131_I | 140_A | 1.613 | 1.00 |
| 75_A | 130_K | 1.605 | 1.00 |
| 182_G | 300_L | 1.591 | 1.00 |
| 249_A | 255_I | 1.585 | 1.00 |
| 167_Y | 245_A | 1.576 | 1.00 |
| 162_D | 254_R | 1.575 | 1.00 |
| 64_V | 80_R | 1.563 | 1.00 |
| 188_N | 208_D | 1.559 | 1.00 |
| 26_E | 124_P | 1.558 | 1.00 |
| 68_V | 77_V | 1.558 | 1.00 |
| 75_A | 79_E | 1.541 | 1.00 |
| 196_D | 212_N | 1.520 | 1.00 |
| 25_G | 124_P | 1.516 | 1.00 |
| 138_Q | 336_T | 1.510 | 1.00 |
| 117_F | 320_I | 1.509 | 1.00 |
| 28_R | 67_A | 1.505 | 1.00 |
| 31_V | 61_F | 1.499 | 1.00 |
| 69_G | 72_V | 1.484 | 1.00 |
| 26_E | 122_V | 1.473 | 1.00 |
| 2_K | 16_E | 1.473 | 1.00 |
| 249_A | 277_L | 1.469 | 1.00 |
| 232_I | 249_A | 1.461 | 1.00 |
| 249_A | 253_A | 1.450 | 1.00 |
| 216_T | 221_I | 1.450 | 1.00 |
| 80_R | 133_E | 1.449 | 1.00 |
| 212_N | 215_Q | 1.438 | 1.00 |
| 317_A | 321_S | 1.434 | 1.00 |
| 33_L | 138_Q | 1.426 | 1.00 |
| 156_G | 231_L | 1.424 | 1.00 |
| 22_P | 122_V | 1.422 | 1.00 |
| 92_C | 95_C | 1.416 | 1.00 |
| 196_D | 215_Q | 1.413 | 1.00 |
| 232_I | 245_A | 1.396 | 0.99 |
| 217_P | 220_E | 1.395 | 0.99 |
| 3_S | 17_R | 1.391 | 0.99 |
| 308_T | 322_L | 1.390 | 0.99 |
| 27_V | 75_A | 1.368 | 0.99 |
| 44_Y | 320_I | 1.358 | 0.99 |
| 65_I | 75_A | 1.353 | 0.99 |
| 294_D | 297_S | 1.353 | 0.99 |
| 176_I | 233_I | 1.348 | 0.99 |
| 32_K | 80_R | 1.346 | 0.99 |
| 92_C | 103_C | 1.338 | 0.99 |
| 2_K | 314_Q | 1.338 | 0.99 |
| 2_K | 119_E | 1.338 | 0.99 |
| 64_V | 137_D | 1.334 | 0.99 |
| 22_P | 28_R | 1.326 | 0.99 |
| 163_T | 190_I | 1.325 | 0.99 |
| 154_G | 291_I | 1.312 | 0.99 |
| 167_Y | 192_A | 1.305 | 0.99 |
| 177_V | 191_V | 1.300 | 0.99 |
| 194_R | 213_N | 1.295 | 0.99 |
| 33_L | 336_T | 1.294 | 0.99 |
| 31_V | 121_A | 1.272 | 0.99 |
| 4_I | 14_I | 1.269 | 0.99 |
| 196_D | 199_L | 1.263 | 0.99 |
| 95_C | 103_C | 1.249 | 0.99 |
| 154_G | 288_K | 1.243 | 0.98 |
| 220_E | 224_E | 1.236 | 0.98 |
| 89_C | 92_C | 1.227 | 0.98 |
| 19_I | 28_R | 1.217 | 0.98 |
| 313_F | 337_F | 1.187 | 0.98 |
| 75_A | 128_A | 1.186 | 0.98 |
| 25_G | 125_A | 1.175 | 0.98 |
| 163_T | 230_T | 1.164 | 0.97 |
| 199_L | 212_N | 1.157 | 0.97 |
| 8_K | 11_Q | 1.150 | 0.97 |
| 291_I | 294_D | 1.150 | 0.97 |
| 312_D | 336_T | 1.145 | 0.97 |
| 143_I | 296_L | 1.137 | 0.97 |
| 29_V | 63_G | 1.132 | 0.97 |
| 139_Y | 304_E | 1.122 | 0.97 |
| 89_C | 95_C | 1.108 | 0.96 |
| 66_D | 77_V | 1.107 | 0.96 |
| 33_L | 137_D | 1.100 | 0.96 |
| 295_W | 300_L | 1.095 | 0.96 |
| 203_K | 210_A | 1.095 | 0.96 |
| 316_V | 335_L | 1.074 | 0.95 |
| 36_I | 319_A | 1.072 | 0.95 |
| 123_V | 128_A | 1.072 | 0.95 |
| 162_D | 230_T | 1.070 | 0.95 |
| 4_I | 313_F | 1.070 | 0.95 |
| 22_P | 26_E | 1.066 | 0.95 |
| 89_C | 103_C | 1.066 | 0.95 |
| 139_Y | 302_K | 1.064 | 0.95 |
| 178_Q | 302_K | 1.062 | 0.95 |
| 151_N | 288_K | 1.061 | 0.95 |
| 204_E | 305_K | 1.059 | 0.95 |
| 149_A | 176_I | 1.056 | 0.95 |
| 234_D | 237_C | 1.056 | 0.95 |
| 158_P | 186_V | 1.054 | 0.95 |
| 236_A | 241_I | 1.051 | 0.94 |
| 217_P | 221_I | 1.048 | 0.94 |
| 247_T | 271_G | 1.043 | 0.94 |
| 201_K | 330_C | 1.041 | 0.94 |
| 191_V | 207_A | 1.039 | 0.94 |
| 219_G | 247_T | 1.033 | 0.94 |
| 29_V | 81_V | 1.032 | 0.94 |
| 5_L | 17_R | 1.032 | 0.94 |
| 44_Y | 324_E | 1.024 | 0.93 |
| 286_A | 290_P | 1.021 | 0.93 |
| 321_S | 324_E | 1.008 | 0.93 |
| 34_A | 117_F | 1.004 | 0.93 |
| 302_K | 305_K | 1.002 | 0.92 |
| 158_P | 162_D | 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
- See coupling matrix (for protein design or mutagenesis)
- 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 | |
| 4ilkA | 2 | 0.9882 | 100 | 0.043 | Contact Map |
| 4ej6A | 1 | 0.9853 | 100 | 0.071 | Contact Map |
| 2dq4A | 2 | 0.9853 | 100 | 0.074 | Contact Map |
| 4oh1A | 1 | 0.9705 | 100 | 0.089 | Contact Map |
| 3ukoA | 2 | 0.9882 | 100 | 0.09 | Contact Map |
| 3m6iA | 2 | 0.9882 | 100 | 0.093 | Contact Map |
| 4gkvA | 4 | 0.9794 | 100 | 0.093 | Contact Map |
| 4uejA | 2 | 0 | 100 | 0.095 | Contact Map |
| 1e3jA | 1 | 0.9912 | 100 | 0.1 | Contact Map |
| 4cpdA | 4 | 0.9823 | 100 | 0.1 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)