| 4n7wA |
| ID: | 1491921369 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 307 (305) | ||
| Sequences: | 5881 (3406) | ||
| Seq/Len: | 19.282 | ||
| Nf(neff/√len): | 195.0 |
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: 19.282).
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 |
| 43_F | 174_I | 6.065 | 1.00 |
| 118_D | 247_T | 5.718 | 1.00 |
| 112_I | 117_G | 2.919 | 1.00 |
| 43_F | 170_A | 2.782 | 1.00 |
| 245_E | 249_R | 2.688 | 1.00 |
| 101_S | 140_L | 2.449 | 1.00 |
| 68_T | 132_V | 2.438 | 1.00 |
| 244_D | 247_T | 2.376 | 1.00 |
| 71_H | 104_S | 2.343 | 1.00 |
| 55_K | 59_S | 2.341 | 1.00 |
| 263_A | 279_G | 2.309 | 1.00 |
| 239_K | 248_C | 2.298 | 1.00 |
| 152_D | 155_G | 2.282 | 1.00 |
| 69_F | 73_L | 2.261 | 1.00 |
| 227_N | 289_S | 2.147 | 1.00 |
| 232_L | 236_W | 2.119 | 1.00 |
| 293_L | 297_W | 2.111 | 1.00 |
| 238_G | 248_C | 2.092 | 1.00 |
| 235_Y | 248_C | 2.075 | 1.00 |
| 79_A | 100_G | 1.999 | 1.00 |
| 52_D | 55_K | 1.999 | 1.00 |
| 72_Y | 136_A | 1.980 | 1.00 |
| 236_W | 240_L | 1.941 | 1.00 |
| 122_S | 250_T | 1.934 | 1.00 |
| 96_M | 222_A | 1.862 | 1.00 |
| 78_T | 229_I | 1.849 | 1.00 |
| 111_M | 253_I | 1.841 | 1.00 |
| 16_L | 198_L | 1.839 | 1.00 |
| 75_M | 230_G | 1.835 | 1.00 |
| 53_D | 56_R | 1.832 | 1.00 |
| 180_K | 184_R | 1.827 | 1.00 |
| 112_I | 250_T | 1.814 | 1.00 |
| 132_V | 136_A | 1.802 | 1.00 |
| 169_T | 173_V | 1.793 | 1.00 |
| 238_G | 251_L | 1.765 | 1.00 |
| 66_A | 251_L | 1.710 | 1.00 |
| 98_L | 267_G | 1.700 | 1.00 |
| 80_W | 84_M | 1.688 | 1.00 |
| 243_F | 251_L | 1.674 | 1.00 |
| 15_L | 19_A | 1.629 | 1.00 |
| 65_A | 69_F | 1.601 | 1.00 |
| 82_L | 222_A | 1.599 | 1.00 |
| 102_V | 263_A | 1.585 | 1.00 |
| 77_L | 81_I | 1.572 | 1.00 |
| 56_R | 59_S | 1.546 | 1.00 |
| 112_I | 122_S | 1.509 | 1.00 |
| 66_A | 241_F | 1.507 | 1.00 |
| 20_A | 27_F | 1.495 | 1.00 |
| 224_I | 285_W | 1.475 | 1.00 |
| 86_F | 222_A | 1.470 | 1.00 |
| 78_T | 230_G | 1.452 | 1.00 |
| 183_K | 186_E | 1.443 | 1.00 |
| 229_I | 233_S | 1.441 | 1.00 |
| 18_V | 22_F | 1.435 | 1.00 |
| 81_I | 84_M | 1.419 | 1.00 |
| 158_K | 162_Q | 1.406 | 0.99 |
| 249_R | 297_W | 1.400 | 0.99 |
| 173_V | 177_T | 1.397 | 0.99 |
| 81_I | 85_L | 1.396 | 0.99 |
| 104_S | 126_S | 1.363 | 0.99 |
| 83_A | 93_S | 1.360 | 0.99 |
| 118_D | 246_S | 1.342 | 0.99 |
| 161_L | 166_I | 1.333 | 0.99 |
| 296_Y | 300_K | 1.326 | 0.99 |
| 94_A | 145_V | 1.319 | 0.99 |
| 18_V | 21_Y | 1.315 | 0.99 |
| 248_C | 252_A | 1.308 | 0.99 |
| 61_P | 65_A | 1.306 | 0.99 |
| 50_R | 53_D | 1.296 | 0.99 |
| 178_F | 181_T | 1.288 | 0.99 |
| 52_D | 56_R | 1.286 | 0.99 |
| 50_R | 175_H | 1.283 | 0.99 |
| 285_W | 289_S | 1.277 | 0.99 |
| 70_L | 74_I | 1.271 | 0.99 |
| 136_A | 139_L | 1.266 | 0.99 |
| 99_V | 282_F | 1.260 | 0.99 |
| 109_N | 254_E | 1.258 | 0.99 |
| 260_S | 283_S | 1.254 | 0.99 |
| 42_M | 46_G | 1.250 | 0.99 |
| 12_W | 198_L | 1.244 | 0.98 |
| 67_A | 125_I | 1.235 | 0.98 |
| 245_E | 300_K | 1.231 | 0.98 |
| 115_A | 294_A | 1.227 | 0.98 |
| 238_G | 243_F | 1.226 | 0.98 |
| 235_Y | 245_E | 1.225 | 0.98 |
| 46_G | 171_G | 1.225 | 0.98 |
| 107_A | 231_L | 1.198 | 0.98 |
| 60_R | 247_T | 1.197 | 0.98 |
| 36_P | 39_M | 1.193 | 0.98 |
| 292_L | 296_Y | 1.190 | 0.98 |
| 296_Y | 299_G | 1.188 | 0.98 |
| 174_I | 178_F | 1.185 | 0.98 |
| 252_A | 297_W | 1.177 | 0.98 |
| 4_K | 8_L | 1.169 | 0.97 |
| 122_S | 254_E | 1.161 | 0.97 |
| 297_W | 300_K | 1.158 | 0.97 |
| 14_L | 18_V | 1.155 | 0.97 |
| 67_A | 251_L | 1.143 | 0.97 |
| 124_T | 127_A | 1.139 | 0.97 |
| 8_L | 12_W | 1.136 | 0.97 |
| 248_C | 297_W | 1.127 | 0.97 |
| 70_L | 255_V | 1.126 | 0.97 |
| 72_Y | 129_S | 1.123 | 0.97 |
| 133_G | 137_T | 1.120 | 0.96 |
| 228_G | 232_L | 1.114 | 0.96 |
| 98_L | 137_T | 1.110 | 0.96 |
| 120_A | 123_V | 1.109 | 0.96 |
| 64_V | 128_V | 1.100 | 0.96 |
| 172_L | 176_H | 1.100 | 0.96 |
| 154_V | 158_K | 1.099 | 0.96 |
| 74_I | 233_S | 1.095 | 0.96 |
| 32_P | 36_P | 1.095 | 0.96 |
| 175_H | 183_K | 1.088 | 0.96 |
| 180_K | 183_K | 1.082 | 0.96 |
| 71_H | 129_S | 1.081 | 0.95 |
| 107_A | 287_N | 1.076 | 0.95 |
| 11_V | 15_L | 1.074 | 0.95 |
| 33_Y | 36_P | 1.074 | 0.95 |
| 295_G | 298_S | 1.074 | 0.95 |
| 89_P | 93_S | 1.070 | 0.95 |
| 83_A | 97_V | 1.068 | 0.95 |
| 12_W | 16_L | 1.063 | 0.95 |
| 70_L | 234_G | 1.061 | 0.95 |
| 104_S | 109_N | 1.059 | 0.95 |
| 301_P | 304_K | 1.057 | 0.95 |
| 140_L | 144_Y | 1.046 | 0.94 |
| 63_P | 243_F | 1.037 | 0.94 |
| 104_S | 122_S | 1.027 | 0.94 |
| 71_H | 126_S | 1.026 | 0.94 |
| 225_L | 229_I | 1.009 | 0.93 |
| 75_M | 100_G | 1.008 | 0.93 |
| 197_I | 201_I | 1.002 | 0.92 |
| 283_S | 287_N | 1.002 | 0.92 |
| 60_R | 118_D | 1.000 | 0.92 |
| 4_K | 7_R | 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 | |
| 4n7wA | 2 | 1 | 100 | 0.146 | Contact Map |
| 3zuxA | 1 | 0.9805 | 100 | 0.181 | Contact Map |
| 4bwzA | 1 | 0.9642 | 95.3 | 0.888 | Contact Map |
| 4czbA | 3 | 0.9446 | 94.9 | 0.891 | Contact Map |
| 4cz8A | 2 | 0.9316 | 70.9 | 0.925 | Contact Map |
| 1zcdA | 2 | 0.9479 | 43.4 | 0.936 | Contact Map |
| 2cfqA | 1 | 0.5961 | 6.7 | 0.957 | Contact Map |
| 3rkoL | 2 | 0.4658 | 6.5 | 0.957 | Contact Map |
| 2xq2A | 1 | 0.2313 | 6 | 0.958 | Contact Map |
| 4he8L | 2 | 0.4593 | 5.2 | 0.959 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)