| CC_parB |
| ID: | 1488368715 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 304 (285) | ||
| Sequences: | 3395 (2240.5) | ||
| Seq/Len: | 11.912 | ||
| Nf(neff/√len): | 132.7 |
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: 11.912).
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 |
| 46_E | 115_T | 4.510 | 1.00 |
| 219_I | 229_T | 4.001 | 1.00 |
| 218_Q | 222_G | 3.985 | 1.00 |
| 192_Y | 216_A | 3.982 | 1.00 |
| 172_S | 175_H | 3.916 | 1.00 |
| 152_K | 156_E | 3.477 | 1.00 |
| 162_Q | 177_A | 3.426 | 1.00 |
| 98_I | 105_W | 3.357 | 1.00 |
| 53_Q | 95_E | 3.109 | 1.00 |
| 52_L | 98_I | 2.862 | 1.00 |
| 153_V | 157_K | 2.849 | 1.00 |
| 84_I | 116_V | 2.816 | 1.00 |
| 224_L | 232_L | 2.769 | 1.00 |
| 72_S | 110_R | 2.734 | 1.00 |
| 80_V | 108_A | 2.624 | 1.00 |
| 145_L | 190_Q | 2.569 | 1.00 |
| 48_P | 51_I | 2.493 | 1.00 |
| 84_I | 98_I | 2.486 | 1.00 |
| 69_E | 73_N | 2.412 | 1.00 |
| 47_A | 118_I | 2.410 | 1.00 |
| 149_L | 190_Q | 2.383 | 1.00 |
| 228_E | 231_A | 2.349 | 1.00 |
| 69_E | 110_R | 2.277 | 1.00 |
| 81_L | 85_L | 2.247 | 1.00 |
| 202_H | 226_V | 2.204 | 1.00 |
| 192_Y | 220_I | 2.169 | 1.00 |
| 215_L | 232_L | 2.154 | 1.00 |
| 295_D | 299_R | 2.148 | 1.00 |
| 49_I | 105_W | 2.144 | 1.00 |
| 68_L | 110_R | 2.121 | 1.00 |
| 155_M | 165_I | 2.115 | 1.00 |
| 65_E | 110_R | 2.107 | 1.00 |
| 47_A | 86_V | 2.105 | 1.00 |
| 253_K | 261_E | 2.082 | 1.00 |
| 123_L | 131_I | 1.972 | 1.00 |
| 191_S | 195_S | 1.959 | 1.00 |
| 105_W | 109_Q | 1.952 | 1.00 |
| 67_D | 140_A | 1.947 | 1.00 |
| 292_Q | 295_D | 1.931 | 1.00 |
| 64_R | 67_D | 1.869 | 1.00 |
| 65_E | 69_E | 1.828 | 1.00 |
| 174_S | 177_A | 1.805 | 1.00 |
| 87_R | 97_Q | 1.799 | 1.00 |
| 164_N | 167_Q | 1.798 | 1.00 |
| 86_V | 118_I | 1.784 | 1.00 |
| 53_Q | 97_Q | 1.760 | 1.00 |
| 99_V | 123_L | 1.757 | 1.00 |
| 179_T | 200_A | 1.753 | 1.00 |
| 189_V | 216_A | 1.746 | 1.00 |
| 205_A | 229_T | 1.725 | 1.00 |
| 163_E | 167_Q | 1.694 | 1.00 |
| 290_L | 294_D | 1.693 | 1.00 |
| 205_A | 226_V | 1.651 | 1.00 |
| 193_L | 203_A | 1.611 | 1.00 |
| 202_H | 205_A | 1.590 | 1.00 |
| 209_A | 215_L | 1.585 | 1.00 |
| 51_I | 95_E | 1.569 | 1.00 |
| 89_S | 97_Q | 1.565 | 1.00 |
| 216_A | 220_I | 1.555 | 1.00 |
| 108_A | 113_L | 1.524 | 1.00 |
| 84_I | 118_I | 1.523 | 1.00 |
| 87_R | 125_D | 1.498 | 1.00 |
| 225_S | 228_E | 1.478 | 1.00 |
| 73_N | 76_R | 1.478 | 1.00 |
| 192_Y | 197_E | 1.475 | 1.00 |
| 124_D | 127_A | 1.468 | 1.00 |
| 59_P | 132_G | 1.468 | 1.00 |
| 108_A | 111_A | 1.462 | 1.00 |
| 224_L | 229_T | 1.448 | 1.00 |
| 263_D | 301_T | 1.443 | 1.00 |
| 48_P | 115_T | 1.435 | 1.00 |
| 294_D | 298_N | 1.416 | 1.00 |
| 52_L | 86_V | 1.404 | 0.99 |
| 143_N | 194_V | 1.398 | 0.99 |
| 68_L | 72_S | 1.396 | 0.99 |
| 219_I | 224_L | 1.357 | 0.99 |
| 165_I | 176_V | 1.357 | 0.99 |
| 87_R | 128_V | 1.355 | 0.99 |
| 149_L | 194_V | 1.350 | 0.99 |
| 289_T | 292_Q | 1.343 | 0.99 |
| 73_N | 77_E | 1.329 | 0.99 |
| 80_V | 117_P | 1.320 | 0.99 |
| 75_I | 108_A | 1.313 | 0.99 |
| 198_L | 216_A | 1.298 | 0.99 |
| 200_A | 204_R | 1.295 | 0.99 |
| 218_Q | 232_L | 1.289 | 0.99 |
| 77_E | 167_Q | 1.279 | 0.99 |
| 55_N | 128_V | 1.272 | 0.99 |
| 229_T | 233_A | 1.266 | 0.99 |
| 201_G | 227_R | 1.260 | 0.99 |
| 217_K | 221_E | 1.258 | 0.99 |
| 52_L | 116_V | 1.244 | 0.98 |
| 80_V | 116_V | 1.244 | 0.98 |
| 227_R | 230_E | 1.235 | 0.98 |
| 187_D | 190_Q | 1.229 | 0.98 |
| 155_M | 177_A | 1.227 | 0.98 |
| 288_A | 292_Q | 1.205 | 0.98 |
| 275_D | 284_T | 1.195 | 0.98 |
| 69_E | 72_S | 1.191 | 0.98 |
| 231_A | 234_R | 1.186 | 0.98 |
| 191_S | 194_V | 1.169 | 0.97 |
| 151_Y | 169_I | 1.168 | 0.97 |
| 224_L | 228_E | 1.156 | 0.97 |
| 75_I | 80_V | 1.153 | 0.97 |
| 50_E | 109_Q | 1.146 | 0.97 |
| 130_E | 168_T | 1.134 | 0.97 |
| 88_P | 94_G | 1.115 | 0.96 |
| 85_L | 100_A | 1.105 | 0.96 |
| 147_E | 171_K | 1.102 | 0.96 |
| 21_G | 25_L | 1.099 | 0.96 |
| 215_L | 236_A | 1.097 | 0.96 |
| 54_R | 105_W | 1.095 | 0.96 |
| 155_M | 162_Q | 1.094 | 0.96 |
| 188_E | 217_K | 1.092 | 0.96 |
| 268_L | 285_I | 1.076 | 0.95 |
| 68_L | 111_A | 1.069 | 0.95 |
| 147_E | 179_T | 1.068 | 0.95 |
| 256_D | 259_A | 1.065 | 0.95 |
| 187_D | 191_S | 1.065 | 0.95 |
| 53_Q | 89_S | 1.061 | 0.95 |
| 281_G | 287_Y | 1.059 | 0.95 |
| 51_I | 94_G | 1.058 | 0.95 |
| 145_L | 193_L | 1.056 | 0.95 |
| 193_L | 199_T | 1.054 | 0.95 |
| 276_H | 287_Y | 1.052 | 0.95 |
| 208_A | 237_P | 1.046 | 0.94 |
| 56_P | 97_Q | 1.041 | 0.94 |
| 192_Y | 198_L | 1.037 | 0.94 |
| 80_V | 84_I | 1.034 | 0.94 |
| 200_A | 205_A | 1.025 | 0.93 |
| 193_L | 198_L | 1.021 | 0.93 |
| 147_E | 151_Y | 1.019 | 0.93 |
| 126_L | 130_E | 1.016 | 0.93 |
| 270_L | 285_I | 1.015 | 0.93 |
| 72_S | 75_I | 1.007 | 0.93 |
| 219_I | 232_L | 1.001 | 0.92 |
| 78_K | 130_E | 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 | |
| 4umkA | 4 | 0 | 100 | 0.381 | Contact Map |
| 1vz0A | 8 | 0.625 | 100 | 0.395 | Contact Map |
| 3mkyB | 2 | 0.3487 | 100 | 0.663 | Contact Map |
| 1r71A | 4 | 0.3553 | 100 | 0.669 | Contact Map |
| 1vk1A | 1 | 0.648 | 99.9 | 0.713 | Contact Map |
| 1xw3A | 1 | 0.3454 | 99.9 | 0.728 | Contact Map |
| 1yzsA | 1 | 0.3816 | 99.9 | 0.731 | Contact Map |
| 1zx4A | 2 | 0.5263 | 99.4 | 0.827 | Contact Map |
| 1rzsA | 1 | 0.1842 | 94 | 0.932 | Contact Map |
| 3vwbA | 1 | 0.375 | 94 | 0.932 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)