| Sergey |
| ID: | 1446896922 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 332 (309) | ||
| Sequences: | 628 (436.2) | ||
| Seq/Len: | 2.032 | ||
| Nf(neff/√len): | 24.8 |
HHblits Results: (2015_06)
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: 2.032).
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 |
| 57_A | 62_V | 3.181 | 1.00 |
| 82_E | 86_A | 2.915 | 1.00 |
| 180_A | 215_Y | 2.897 | 1.00 |
| 304_R | 310_Q | 2.891 | 1.00 |
| 132_A | 163_V | 2.679 | 1.00 |
| 167_T | 179_Q | 2.608 | 1.00 |
| 309_P | 312_T | 2.464 | 1.00 |
| 158_S | 188_L | 2.321 | 1.00 |
| 135_I | 154_A | 2.304 | 1.00 |
| 261_K | 315_G | 2.279 | 1.00 |
| 119_R | 123_Y | 2.241 | 1.00 |
| 5_N | 10_P | 2.220 | 1.00 |
| 208_T | 257_Q | 2.212 | 1.00 |
| 152_K | 186_E | 2.197 | 1.00 |
| 121_I | 163_V | 2.178 | 1.00 |
| 81_A | 85_R | 2.148 | 0.99 |
| 168_H | 268_D | 2.129 | 0.99 |
| 260_M | 315_G | 2.122 | 0.99 |
| 222_I | 299_V | 2.088 | 0.99 |
| 310_Q | 314_A | 2.087 | 0.99 |
| 209_A | 212_A | 2.083 | 0.99 |
| 181_A | 213_R | 2.022 | 0.99 |
| 158_S | 165_V | 2.010 | 0.99 |
| 114_T | 118_L | 1.988 | 0.99 |
| 184_E | 213_R | 1.954 | 0.99 |
| 92_V | 133_G | 1.953 | 0.99 |
| 145_P | 148_E | 1.933 | 0.99 |
| 300_I | 304_R | 1.892 | 0.98 |
| 253_A | 257_Q | 1.856 | 0.98 |
| 197_H | 268_D | 1.853 | 0.98 |
| 314_A | 319_T | 1.746 | 0.97 |
| 319_T | 322_A | 1.728 | 0.97 |
| 60_A | 297_L | 1.702 | 0.96 |
| 118_L | 161_T | 1.681 | 0.96 |
| 113_L | 153_A | 1.617 | 0.95 |
| 75_R | 120_E | 1.611 | 0.95 |
| 168_H | 197_H | 1.569 | 0.93 |
| 190_P | 193_V | 1.562 | 0.93 |
| 118_L | 157_A | 1.561 | 0.93 |
| 8_R | 90_H | 1.534 | 0.92 |
| 253_A | 256_D | 1.518 | 0.92 |
| 51_V | 83_V | 1.489 | 0.91 |
| 148_E | 152_K | 1.488 | 0.91 |
| 314_A | 318_V | 1.487 | 0.91 |
| 51_V | 87_A | 1.485 | 0.91 |
| 68_V | 94_A | 1.477 | 0.90 |
| 51_V | 86_A | 1.464 | 0.90 |
| 114_T | 156_R | 1.459 | 0.90 |
| 68_V | 166_T | 1.456 | 0.90 |
| 167_T | 195_I | 1.450 | 0.89 |
| 64_T | 90_H | 1.448 | 0.89 |
| 216_L | 264_L | 1.416 | 0.88 |
| 43_R | 82_E | 1.390 | 0.87 |
| 152_K | 156_R | 1.385 | 0.86 |
| 156_R | 186_E | 1.384 | 0.86 |
| 136_K | 139_T | 1.368 | 0.85 |
| 184_E | 190_P | 1.367 | 0.85 |
| 194_C | 324_F | 1.358 | 0.85 |
| 118_L | 160_A | 1.355 | 0.85 |
| 4_I | 11_I | 1.351 | 0.84 |
| 11_I | 19_T | 1.331 | 0.83 |
| 166_T | 196_G | 1.329 | 0.83 |
| 255_I | 316_I | 1.316 | 0.82 |
| 303_L | 308_V | 1.313 | 0.82 |
| 16_A | 64_T | 1.311 | 0.82 |
| 143_A | 178_Q | 1.308 | 0.82 |
| 8_R | 85_R | 1.284 | 0.80 |
| 179_Q | 195_I | 1.279 | 0.80 |
| 216_L | 262_Q | 1.273 | 0.79 |
| 176_G | 206_Y | 1.270 | 0.79 |
| 121_I | 132_A | 1.266 | 0.79 |
| 252_K | 255_I | 1.260 | 0.78 |
| 296_P | 300_I | 1.259 | 0.78 |
| 115_Q | 119_R | 1.251 | 0.78 |
| 62_V | 296_P | 1.248 | 0.77 |
| 181_A | 185_S | 1.245 | 0.77 |
| 155_A | 183_F | 1.243 | 0.77 |
| 134_I | 166_T | 1.216 | 0.75 |
| 180_A | 195_I | 1.203 | 0.74 |
| 23_E | 266_S | 1.192 | 0.73 |
| 308_V | 312_T | 1.184 | 0.72 |
| 308_V | 314_A | 1.183 | 0.72 |
| 138_A | 141_G | 1.181 | 0.72 |
| 81_A | 130_I | 1.162 | 0.70 |
| 21_T | 317_T | 1.157 | 0.69 |
| 152_K | 185_S | 1.150 | 0.69 |
| 25_I | 91_I | 1.139 | 0.68 |
| 185_S | 261_K | 1.135 | 0.67 |
| 265_V | 316_I | 1.134 | 0.67 |
| 158_S | 215_Y | 1.130 | 0.67 |
| 54_L | 83_V | 1.129 | 0.67 |
| 294_F | 299_V | 1.120 | 0.66 |
| 6_T | 9_G | 1.103 | 0.64 |
| 157_A | 163_V | 1.100 | 0.64 |
| 20_L | 266_S | 1.097 | 0.63 |
| 264_L | 324_F | 1.096 | 0.63 |
| 315_G | 319_T | 1.091 | 0.63 |
| 123_Y | 132_A | 1.090 | 0.63 |
| 139_T | 179_Q | 1.089 | 0.62 |
| 20_L | 296_P | 1.083 | 0.62 |
| 82_E | 85_R | 1.073 | 0.61 |
| 180_A | 213_R | 1.069 | 0.60 |
| 21_T | 66_V | 1.068 | 0.60 |
| 132_A | 157_A | 1.062 | 0.60 |
| 221_H | 270_L | 1.060 | 0.59 |
| 4_I | 64_T | 1.059 | 0.59 |
| 220_D | 268_D | 1.058 | 0.59 |
| 84_S | 248_A | 1.058 | 0.59 |
| 262_Q | 323_R | 1.056 | 0.59 |
| 260_M | 312_T | 1.055 | 0.59 |
| 70_T | 136_K | 1.055 | 0.59 |
| 105_M | 149_L | 1.051 | 0.58 |
| 57_A | 89_V | 1.050 | 0.58 |
| 196_G | 247_R | 1.042 | 0.57 |
| 95_T | 132_A | 1.040 | 0.57 |
| 248_A | 251_I | 1.040 | 0.57 |
| 53_G | 291_G | 1.034 | 0.57 |
| 148_E | 186_E | 1.032 | 0.56 |
| 207_L | 219_L | 1.029 | 0.56 |
| 54_L | 87_A | 1.029 | 0.56 |
| 222_I | 294_F | 1.026 | 0.56 |
| 151_L | 179_Q | 1.025 | 0.56 |
| 67_D | 206_Y | 1.025 | 0.56 |
| 212_A | 259_Y | 1.024 | 0.55 |
| 95_T | 120_E | 1.024 | 0.55 |
| 95_T | 125_I | 1.021 | 0.55 |
| 176_G | 210_L | 1.020 | 0.55 |
| 200_D | 221_H | 1.016 | 0.55 |
| 20_L | 23_E | 1.015 | 0.54 |
| 262_Q | 314_A | 1.014 | 0.54 |
| 249_L | 306_K | 1.012 | 0.54 |
| 177_E | 209_A | 1.010 | 0.54 |
| 24_H | 268_D | 1.010 | 0.54 |
| 26_C | 83_V | 1.007 | 0.54 |
| 169_T | 179_Q | 1.002 | 0.53 |
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 | |
| 3k2gA | 4 | 0.9398 | 100 | 0.415 | Contact Map |
| 3rhgA | 1 | 0.9337 | 100 | 0.426 | Contact Map |
| 3pnzA | 6 | 0.8976 | 100 | 0.547 | Contact Map |
| 3gtxA | 1 | 0.9277 | 100 | 0.562 | Contact Map |
| 2ob3A | 2 | 0.9488 | 100 | 0.566 | Contact Map |
| 3ovgA | 6 | 0.9096 | 100 | 0.57 | Contact Map |
| 3tn4A | 2 | 0.9277 | 100 | 0.573 | Contact Map |
| 4if2A | 1 | 0.9398 | 100 | 0.575 | Contact Map |
| 4kezA | 4 | 0.9217 | 100 | 0.603 | Contact Map |
| 1bf6A | 2 | 0.8645 | 100 | 0.61 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)