| p5cr |
| ID: | 1505113320 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 263 (260) | ||
| Sequences: | 13232 (8345.7) | ||
| Seq/Len: | 50.892 | ||
| Nf(neff/√len): | 517.6 |
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: 50.892).
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 |
| 139_D | 143_K | 3.478 | 1.00 |
| 105_R | 134_D | 3.172 | 1.00 |
| 71_E | 95_T | 2.740 | 1.00 |
| 4_Y | 58_D | 2.712 | 1.00 |
| 2_N | 26_R | 2.631 | 1.00 |
| 70_M | 88_A | 2.570 | 1.00 |
| 188_D | 191_E | 2.541 | 1.00 |
| 4_Y | 54_E | 2.186 | 1.00 |
| 132_E | 136_R | 2.167 | 1.00 |
| 109_V | 122_S | 2.025 | 1.00 |
| 8_G | 29_I | 2.018 | 1.00 |
| 149_V | 194_A | 2.015 | 1.00 |
| 2_N | 28_Y | 1.999 | 1.00 |
| 31_N | 36_K | 1.959 | 1.00 |
| 171_V | 200_F | 1.919 | 1.00 |
| 2_N | 59_D | 1.901 | 1.00 |
| 139_D | 150_W | 1.887 | 1.00 |
| 64_A | 87_V | 1.881 | 1.00 |
| 63_L | 84_V | 1.877 | 1.00 |
| 131_S | 134_D | 1.854 | 1.00 |
| 147_L | 194_A | 1.853 | 1.00 |
| 119_L | 205_A | 1.830 | 1.00 |
| 34_A | 38_E | 1.822 | 1.00 |
| 179_Q | 193_R | 1.820 | 1.00 |
| 136_R | 139_D | 1.810 | 1.00 |
| 71_E | 75_K | 1.808 | 1.00 |
| 60_V | 83_L | 1.803 | 1.00 |
| 41_E | 49_S | 1.797 | 1.00 |
| 174_L | 244_I | 1.796 | 1.00 |
| 183_I | 189_M | 1.791 | 1.00 |
| 126_A | 135_R | 1.788 | 1.00 |
| 121_V | 147_L | 1.734 | 1.00 |
| 29_I | 46_V | 1.692 | 1.00 |
| 135_R | 150_W | 1.672 | 1.00 |
| 85_L | 138_A | 1.665 | 1.00 |
| 5_F | 16_A | 1.657 | 1.00 |
| 205_A | 209_Q | 1.652 | 1.00 |
| 249_C | 253_R | 1.638 | 1.00 |
| 69_D | 72_A | 1.607 | 1.00 |
| 83_L | 138_A | 1.604 | 1.00 |
| 172_F | 203_A | 1.592 | 1.00 |
| 83_L | 134_D | 1.581 | 1.00 |
| 37_R | 49_S | 1.573 | 1.00 |
| 175_L | 207_A | 1.571 | 1.00 |
| 28_Y | 50_A | 1.564 | 1.00 |
| 167_G | 199_T | 1.554 | 1.00 |
| 28_Y | 47_E | 1.554 | 1.00 |
| 216_K | 220_N | 1.545 | 1.00 |
| 197_L | 208_E | 1.526 | 1.00 |
| 250_A | 253_R | 1.525 | 1.00 |
| 201_K | 205_A | 1.516 | 1.00 |
| 28_Y | 57_S | 1.512 | 1.00 |
| 38_E | 42_K | 1.510 | 1.00 |
| 63_L | 70_M | 1.509 | 1.00 |
| 15_V | 145_V | 1.496 | 1.00 |
| 190_A | 194_A | 1.480 | 1.00 |
| 143_K | 148_T | 1.461 | 1.00 |
| 11_M | 87_V | 1.423 | 1.00 |
| 30_A | 52_L | 1.411 | 1.00 |
| 36_K | 39_R | 1.408 | 1.00 |
| 65_V | 73_A | 1.406 | 0.99 |
| 5_F | 12_A | 1.379 | 0.99 |
| 62_I | 85_L | 1.375 | 0.99 |
| 109_V | 142_M | 1.367 | 0.99 |
| 212_E | 220_N | 1.365 | 0.99 |
| 140_R | 143_K | 1.336 | 0.99 |
| 132_E | 150_W | 1.336 | 0.99 |
| 5_F | 62_I | 1.335 | 0.99 |
| 236_R | 241_A | 1.331 | 0.99 |
| 158_H | 255_S | 1.325 | 0.99 |
| 2_N | 57_S | 1.319 | 0.99 |
| 38_E | 41_E | 1.317 | 0.99 |
| 254_R | 257_E | 1.315 | 0.99 |
| 17_G | 43_E | 1.313 | 0.99 |
| 54_E | 58_D | 1.304 | 0.99 |
| 16_A | 27_I | 1.302 | 0.99 |
| 86_S | 96_L | 1.302 | 0.99 |
| 31_N | 37_R | 1.294 | 0.99 |
| 35_E | 38_E | 1.282 | 0.99 |
| 60_V | 85_L | 1.257 | 0.99 |
| 174_L | 240_V | 1.254 | 0.99 |
| 229_H | 233_E | 1.253 | 0.99 |
| 97_S | 101_G | 1.250 | 0.99 |
| 135_R | 139_D | 1.248 | 0.99 |
| 107_V | 138_A | 1.238 | 0.98 |
| 123_G | 160_I | 1.209 | 0.98 |
| 216_K | 219_K | 1.208 | 0.98 |
| 242_E | 246_E | 1.197 | 0.98 |
| 246_E | 250_A | 1.194 | 0.98 |
| 62_I | 87_V | 1.190 | 0.98 |
| 28_Y | 58_D | 1.190 | 0.98 |
| 213_D | 216_K | 1.188 | 0.98 |
| 32_R | 69_D | 1.186 | 0.98 |
| 182_A | 192_A | 1.184 | 0.98 |
| 149_V | 191_E | 1.169 | 0.97 |
| 72_A | 75_K | 1.168 | 0.97 |
| 237_R | 246_E | 1.168 | 0.97 |
| 153_D | 156_K | 1.165 | 0.97 |
| 60_V | 137_I | 1.162 | 0.97 |
| 33_G | 36_K | 1.158 | 0.97 |
| 18_G | 21_K | 1.155 | 0.97 |
| 3_V | 19_L | 1.150 | 0.97 |
| 75_K | 99_Y | 1.148 | 0.97 |
| 205_A | 208_E | 1.123 | 0.97 |
| 252_V | 256_Q | 1.119 | 0.96 |
| 18_G | 145_V | 1.117 | 0.96 |
| 253_R | 257_E | 1.115 | 0.96 |
| 4_Y | 30_A | 1.113 | 0.96 |
| 17_G | 44_L | 1.091 | 0.96 |
| 39_R | 42_K | 1.080 | 0.95 |
| 230_E | 233_E | 1.079 | 0.95 |
| 234_A | 237_R | 1.078 | 0.95 |
| 15_V | 19_L | 1.070 | 0.95 |
| 15_V | 64_A | 1.069 | 0.95 |
| 12_A | 16_A | 1.066 | 0.95 |
| 180_N | 189_M | 1.065 | 0.95 |
| 13_A | 36_K | 1.063 | 0.95 |
| 193_R | 197_L | 1.061 | 0.95 |
| 74_C | 84_V | 1.060 | 0.95 |
| 13_A | 39_R | 1.059 | 0.95 |
| 137_I | 140_R | 1.056 | 0.95 |
| 180_N | 241_A | 1.055 | 0.95 |
| 180_N | 183_I | 1.045 | 0.94 |
| 130_V | 134_D | 1.042 | 0.94 |
| 65_V | 88_A | 1.040 | 0.94 |
| 158_H | 256_Q | 1.038 | 0.94 |
| 182_A | 187_F | 1.036 | 0.94 |
| 63_L | 74_C | 1.036 | 0.94 |
| 114_P | 120_G | 1.035 | 0.94 |
| 198_A | 201_K | 1.033 | 0.94 |
| 53_P | 56_H | 1.032 | 0.94 |
| 55_L | 61_L | 1.029 | 0.94 |
| 191_E | 194_A | 1.026 | 0.94 |
| 170_Y | 231_A | 1.024 | 0.93 |
| 98_R | 102_G | 1.022 | 0.93 |
| 171_V | 174_L | 1.021 | 0.93 |
| 184_R | 245_S | 1.020 | 0.93 |
| 152_D | 156_K | 1.010 | 0.93 |
| 1_M | 25_Y | 1.004 | 0.93 |
| 75_K | 78_R | 1.002 | 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 | |
| 2ahrA | 5 | 0.9658 | 100 | 0.241 | Contact Map |
| 1yqgA | 1 | 0.9924 | 100 | 0.245 | Contact Map |
| 2izzA | 5 | 0.9886 | 100 | 0.247 | Contact Map |
| 2rcyA | 5 | 0.9582 | 100 | 0.255 | Contact Map |
| 3triA | 2 | 0.9924 | 100 | 0.265 | Contact Map |
| 3gt0A | 1 | 0.7833 | 100 | 0.313 | Contact Map |
| 4kqwA | 2 | 0.9696 | 100 | 0.393 | Contact Map |
| 4wjiA | 1 | 0.962 | 100 | 0.403 | Contact Map |
| 4d3sA | 8 | 0.9658 | 99.9 | 0.411 | Contact Map |
| 4d3dA | 2 | 0.962 | 99.9 | 0.413 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)