| catherine Etchebest |
| ID: | 1487788667 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 278 (244) | ||
| Sequences: | 752 (447.9) | ||
| Seq/Len: | 3.082 | ||
| Nf(neff/√len): | 28.7 |
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: 3.082).
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 |
| 221_K | 227_S | 3.940 | 1.00 |
| 120_E | 132_R | 3.736 | 1.00 |
| 202_C | 229_L | 3.701 | 1.00 |
| 122_I | 132_R | 3.497 | 1.00 |
| 118_D | 135_K | 3.169 | 1.00 |
| 219_T | 223_V | 3.034 | 1.00 |
| 136_D | 225_S | 2.710 | 1.00 |
| 247_C | 252_C | 2.374 | 1.00 |
| 245_C | 252_C | 2.372 | 1.00 |
| 224_P | 227_S | 2.254 | 1.00 |
| 199_E | 251_N | 2.128 | 1.00 |
| 149_E | 159_R | 2.047 | 1.00 |
| 118_D | 134_A | 1.968 | 1.00 |
| 138_P | 222_L | 1.943 | 1.00 |
| 232_D | 253_R | 1.915 | 0.99 |
| 111_F | 216_G | 1.870 | 0.99 |
| 136_D | 224_P | 1.847 | 0.99 |
| 195_N | 198_C | 1.823 | 0.99 |
| 209_V | 214_R | 1.822 | 0.99 |
| 192_R | 195_N | 1.819 | 0.99 |
| 199_E | 249_S | 1.757 | 0.99 |
| 120_E | 134_A | 1.745 | 0.99 |
| 143_V | 202_C | 1.610 | 0.98 |
| 119_V | 131_L | 1.593 | 0.97 |
| 126_K | 246_F | 1.586 | 0.97 |
| 192_R | 198_C | 1.578 | 0.97 |
| 127_K | 170_H | 1.550 | 0.97 |
| 191_S | 194_M | 1.544 | 0.97 |
| 143_V | 219_T | 1.521 | 0.96 |
| 95_E | 112_Q | 1.514 | 0.96 |
| 138_P | 141_T | 1.490 | 0.96 |
| 119_V | 144_L | 1.480 | 0.95 |
| 155_E | 158_A | 1.480 | 0.95 |
| 172_Y | 176_L | 1.467 | 0.95 |
| 144_L | 191_S | 1.466 | 0.95 |
| 137_L | 223_V | 1.466 | 0.95 |
| 133_A | 137_L | 1.442 | 0.95 |
| 112_Q | 122_I | 1.422 | 0.94 |
| 245_C | 248_G | 1.391 | 0.93 |
| 137_L | 219_T | 1.389 | 0.93 |
| 189_N | 232_D | 1.381 | 0.93 |
| 139_S | 222_L | 1.379 | 0.93 |
| 145_E | 214_R | 1.378 | 0.93 |
| 138_P | 219_T | 1.378 | 0.93 |
| 225_S | 229_L | 1.375 | 0.93 |
| 102_N | 142_F | 1.374 | 0.93 |
| 192_R | 196_H | 1.355 | 0.92 |
| 188_G | 192_R | 1.333 | 0.91 |
| 207_W | 216_G | 1.325 | 0.91 |
| 83_C | 87_C | 1.314 | 0.90 |
| 144_L | 189_N | 1.305 | 0.90 |
| 124_T | 132_R | 1.298 | 0.89 |
| 204_T | 215_V | 1.291 | 0.89 |
| 193_F | 196_H | 1.283 | 0.89 |
| 129_W | 229_L | 1.274 | 0.88 |
| 197_S | 200_P | 1.269 | 0.88 |
| 235_F | 238_Y | 1.263 | 0.88 |
| 197_S | 201_N | 1.263 | 0.88 |
| 109_R | 113_R | 1.259 | 0.87 |
| 141_T | 219_T | 1.255 | 0.87 |
| 122_I | 129_W | 1.254 | 0.87 |
| 42_L | 256_L | 1.251 | 0.87 |
| 202_C | 217_F | 1.238 | 0.86 |
| 170_H | 174_M | 1.187 | 0.83 |
| 146_Y | 172_Y | 1.165 | 0.81 |
| 135_K | 225_S | 1.158 | 0.81 |
| 121_V | 190_C | 1.155 | 0.80 |
| 95_E | 109_R | 1.151 | 0.80 |
| 95_E | 110_R | 1.150 | 0.80 |
| 93_M | 232_D | 1.131 | 0.79 |
| 156_F | 256_L | 1.129 | 0.78 |
| 156_F | 170_H | 1.128 | 0.78 |
| 193_F | 198_C | 1.128 | 0.78 |
| 173_F | 231_F | 1.128 | 0.78 |
| 95_E | 228_E | 1.111 | 0.77 |
| 21_F | 25_Q | 1.106 | 0.76 |
| 131_L | 194_M | 1.103 | 0.76 |
| 142_F | 216_G | 1.098 | 0.76 |
| 119_V | 133_A | 1.091 | 0.75 |
| 46_N | 211_G | 1.071 | 0.73 |
| 27_W | 30_C | 1.048 | 0.71 |
| 90_R | 103_G | 1.031 | 0.69 |
| 184_A | 195_N | 1.031 | 0.69 |
| 133_A | 225_S | 1.030 | 0.69 |
| 29_E | 32_K | 1.025 | 0.68 |
| 173_F | 237_R | 1.023 | 0.68 |
| 147_C | 189_N | 1.022 | 0.68 |
| 95_E | 127_K | 1.021 | 0.68 |
| 43_I | 139_S | 1.012 | 0.67 |
| 31_A | 34_G | 1.008 | 0.66 |
| 90_R | 173_F | 1.001 | 0.66 |
| 202_C | 256_L | 1.001 | 0.66 |
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 | |
| 4h12A | 1 | 0.8381 | 100 | 0.224 | Contact Map |
| 4nj5A | 1 | 0.795 | 100 | 0.379 | Contact Map |
| 4qenA | 1 | 0.8273 | 100 | 0.388 | Contact Map |
| 3ooiA | 1 | 0.8309 | 100 | 0.388 | Contact Map |
| 1mvhA | 1 | 0.8273 | 100 | 0.406 | Contact Map |
| 3opeA | 2 | 0.7554 | 100 | 0.408 | Contact Map |
| 3bo5A | 1 | 0.8777 | 100 | 0.409 | Contact Map |
| 3hnaA | 2 | 0.8489 | 100 | 0.41 | Contact Map |
| 1ml9A | 1 | 0.7806 | 100 | 0.411 | Contact Map |
| 2r3aA | 1 | 0.8345 | 100 | 0.417 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)