| trp1 |
| ID: | 1491479151 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 313 (298) | ||
| Sequences: | 1895 (1298.5) | ||
| Seq/Len: | 6.359 | ||
| Nf(neff/√len): | 75.2 |
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: 6.359).
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 |
| 109_G | 119_S | 4.150 | 1.00 |
| 208_F | 259_A | 3.648 | 1.00 |
| 119_S | 127_S | 3.419 | 1.00 |
| 109_G | 112_Y | 3.392 | 1.00 |
| 193_D | 279_T | 3.328 | 1.00 |
| 109_G | 127_S | 2.212 | 1.00 |
| 233_K | 240_D | 2.123 | 1.00 |
| 242_E | 245_E | 2.091 | 1.00 |
| 127_S | 130_E | 2.061 | 1.00 |
| 212_V | 256_L | 1.956 | 1.00 |
| 193_D | 197_F | 1.951 | 1.00 |
| 278_E | 281_N | 1.899 | 1.00 |
| 163_A | 207_G | 1.886 | 1.00 |
| 106_F | 138_L | 1.827 | 1.00 |
| 279_T | 282_K | 1.808 | 1.00 |
| 274_A | 280_V | 1.760 | 1.00 |
| 260_Y | 264_T | 1.687 | 1.00 |
| 221_Y | 227_T | 1.670 | 1.00 |
| 231_L | 234_F | 1.580 | 0.99 |
| 227_T | 231_L | 1.557 | 0.99 |
| 91_R | 95_E | 1.557 | 0.99 |
| 90_F | 94_G | 1.547 | 0.99 |
| 93_T | 97_L | 1.529 | 0.99 |
| 13_L | 17_A | 1.508 | 0.99 |
| 63_I | 67_A | 1.498 | 0.99 |
| 275_L | 280_V | 1.497 | 0.99 |
| 273_I | 277_G | 1.480 | 0.99 |
| 221_Y | 234_F | 1.474 | 0.99 |
| 172_Y | 280_V | 1.466 | 0.99 |
| 185_M | 270_N | 1.465 | 0.99 |
| 112_Y | 127_S | 1.463 | 0.99 |
| 279_T | 283_I | 1.399 | 0.98 |
| 276_M | 279_T | 1.392 | 0.98 |
| 290_I | 294_Q | 1.366 | 0.98 |
| 275_L | 278_E | 1.362 | 0.98 |
| 270_N | 273_I | 1.354 | 0.98 |
| 126_D | 130_E | 1.354 | 0.98 |
| 103_V | 107_F | 1.351 | 0.98 |
| 10_N | 15_V | 1.314 | 0.97 |
| 42_K | 46_F | 1.313 | 0.97 |
| 142_V | 146_L | 1.312 | 0.97 |
| 235_T | 266_I | 1.311 | 0.97 |
| 278_E | 284_A | 1.311 | 0.97 |
| 307_L | 310_M | 1.310 | 0.97 |
| 12_V | 19_S | 1.308 | 0.97 |
| 13_L | 16_I | 1.305 | 0.97 |
| 193_D | 275_L | 1.305 | 0.97 |
| 192_R | 195_C | 1.295 | 0.97 |
| 230_E | 234_F | 1.285 | 0.97 |
| 233_K | 236_I | 1.282 | 0.97 |
| 278_E | 282_K | 1.271 | 0.97 |
| 42_K | 47_V | 1.268 | 0.97 |
| 33_E | 36_N | 1.265 | 0.97 |
| 290_I | 293_L | 1.258 | 0.96 |
| 290_I | 295_R | 1.257 | 0.96 |
| 12_V | 16_I | 1.250 | 0.96 |
| 66_T | 69_A | 1.243 | 0.96 |
| 241_L | 257_L | 1.239 | 0.96 |
| 136_Q | 161_S | 1.235 | 0.96 |
| 266_I | 269_L | 1.235 | 0.96 |
| 126_D | 168_N | 1.232 | 0.96 |
| 231_L | 260_Y | 1.227 | 0.96 |
| 122_S | 127_S | 1.225 | 0.96 |
| 42_K | 303_E | 1.222 | 0.96 |
| 103_V | 145_V | 1.208 | 0.95 |
| 175_G | 183_A | 1.202 | 0.95 |
| 266_I | 272_L | 1.197 | 0.95 |
| 274_A | 279_T | 1.192 | 0.95 |
| 271_M | 278_E | 1.184 | 0.94 |
| 62_M | 207_G | 1.183 | 0.94 |
| 122_S | 126_D | 1.174 | 0.94 |
| 283_I | 295_R | 1.152 | 0.93 |
| 14_E | 18_Y | 1.149 | 0.93 |
| 180_G | 193_D | 1.147 | 0.93 |
| 163_A | 256_L | 1.147 | 0.93 |
| 271_M | 274_A | 1.142 | 0.93 |
| 190_I | 276_M | 1.136 | 0.93 |
| 140_M | 224_L | 1.132 | 0.93 |
| 59_C | 63_I | 1.126 | 0.92 |
| 291_W | 294_Q | 1.123 | 0.92 |
| 39_L | 42_K | 1.123 | 0.92 |
| 11_S | 18_Y | 1.119 | 0.92 |
| 294_Q | 298_T | 1.116 | 0.92 |
| 30_L | 33_E | 1.115 | 0.92 |
| 276_M | 291_W | 1.114 | 0.92 |
| 9_K | 16_I | 1.114 | 0.92 |
| 212_V | 216_I | 1.114 | 0.92 |
| 211_A | 287_S | 1.112 | 0.92 |
| 193_D | 274_A | 1.112 | 0.92 |
| 173_T | 182_Y | 1.106 | 0.91 |
| 137_S | 144_V | 1.106 | 0.91 |
| 266_I | 273_I | 1.105 | 0.91 |
| 210_T | 213_V | 1.105 | 0.91 |
| 276_M | 280_V | 1.103 | 0.91 |
| 279_T | 287_S | 1.096 | 0.91 |
| 266_I | 270_N | 1.096 | 0.91 |
| 300_L | 305_S | 1.090 | 0.91 |
| 281_N | 285_Q | 1.090 | 0.91 |
| 159_V | 211_A | 1.088 | 0.90 |
| 96_I | 100_S | 1.087 | 0.90 |
| 293_L | 296_A | 1.084 | 0.90 |
| 215_L | 246_N | 1.078 | 0.90 |
| 204_F | 264_T | 1.078 | 0.90 |
| 48_K | 51_F | 1.075 | 0.90 |
| 133_F | 161_S | 1.074 | 0.90 |
| 295_R | 299_I | 1.072 | 0.90 |
| 92_V | 96_I | 1.071 | 0.89 |
| 163_A | 211_A | 1.069 | 0.89 |
| 197_F | 204_F | 1.068 | 0.89 |
| 89_Y | 93_T | 1.067 | 0.89 |
| 182_Y | 280_V | 1.066 | 0.89 |
| 9_K | 17_A | 1.065 | 0.89 |
| 194_L | 267_L | 1.063 | 0.89 |
| 233_K | 280_V | 1.061 | 0.89 |
| 126_D | 136_Q | 1.060 | 0.89 |
| 80_Y | 85_T | 1.058 | 0.89 |
| 186_I | 280_V | 1.058 | 0.89 |
| 15_V | 18_Y | 1.057 | 0.89 |
| 162_L | 166_W | 1.053 | 0.88 |
| 182_Y | 197_F | 1.052 | 0.88 |
| 169_M | 173_T | 1.048 | 0.88 |
| 96_I | 106_F | 1.043 | 0.88 |
| 13_L | 19_S | 1.040 | 0.88 |
| 267_L | 273_I | 1.037 | 0.87 |
| 136_Q | 157_S | 1.035 | 0.87 |
| 200_V | 275_L | 1.033 | 0.87 |
| 66_T | 166_W | 1.032 | 0.87 |
| 302_T | 305_S | 1.028 | 0.87 |
| 14_E | 17_A | 1.023 | 0.86 |
| 86_V | 255_I | 1.016 | 0.86 |
| 54_N | 262_I | 1.015 | 0.86 |
| 94_G | 97_L | 1.012 | 0.86 |
| 254_I | 257_L | 1.007 | 0.85 |
| 41_D | 45_R | 1.007 | 0.85 |
| 108_R | 130_E | 1.006 | 0.85 |
| 234_F | 237_G | 1.005 | 0.85 |
| 140_M | 144_V | 1.004 | 0.85 |
| 198_M | 209_S | 1.003 | 0.85 |
| 208_F | 242_E | 1.002 | 0.85 |
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 | |
| 3j5pB | 4 | 0.9808 | 100 | 0.246 | Contact Map |
| 3j9pD | 4 | 0.8754 | 100 | 0.32 | Contact Map |
| 4dxwA | 4 | 0.6901 | 99.7 | 0.694 | Contact Map |
| 3rvyA | 2 | 0.6869 | 99.7 | 0.71 | Contact Map |
| 4bgnA | 2 | 0.6677 | 99.6 | 0.718 | Contact Map |
| 3behA | 4 | 0.7029 | 99.2 | 0.784 | Contact Map |
| 4ltoA | 4 | 0.377 | 99.1 | 0.79 | Contact Map |
| 4cbcA | 4 | 0.2716 | 99.1 | 0.794 | Contact Map |
| 2r9rB | 2 | 0.8882 | 99.1 | 0.794 | Contact Map |
| 1orqC | 1 | 0.6773 | 97 | 0.879 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)