| 1r5m |
| ID: | 1454883347 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 351 (328) | ||
| Sequences: | 52077 (34274.1) | ||
| Seq/Len: | 158.771 | ||
| Nf(neff/√len): | 1892.5 |
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: 158.771).
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 |
| 68_C | 81_G | 2.481 | 1.00 |
| 109_S | 122_M | 2.437 | 1.00 |
| 192_V | 205_A | 2.423 | 1.00 |
| 275_A | 288_A | 2.386 | 1.00 |
| 70_A | 111_K | 2.368 | 1.00 |
| 17_S | 31_G | 2.286 | 1.00 |
| 151_D | 163_P | 2.241 | 1.00 |
| 234_S | 246_C | 2.175 | 1.00 |
| 120_I | 130_L | 2.153 | 1.00 |
| 79_V | 112_W | 2.150 | 1.00 |
| 103_H | 121_S | 2.109 | 1.00 |
| 62_S | 80_T | 2.104 | 1.00 |
| 244_I | 254_L | 2.091 | 1.00 |
| 88_R | 96_L | 2.072 | 1.00 |
| 203_L | 237_W | 2.064 | 1.00 |
| 111_K | 153_E | 2.050 | 1.00 |
| 203_L | 213_I | 2.028 | 1.00 |
| 79_V | 89_L | 2.028 | 1.00 |
| 80_T | 90_W | 2.026 | 1.00 |
| 286_A | 296_V | 2.014 | 1.00 |
| 79_V | 119_I | 2.001 | 1.00 |
| 129_I | 138_V | 1.994 | 1.00 |
| 11_K | 30_Y | 1.982 | 1.00 |
| 325_D | 338_A | 1.973 | 1.00 |
| 121_S | 131_W | 1.973 | 1.00 |
| 244_I | 278_I | 1.965 | 1.00 |
| 204_S | 214_W | 1.947 | 1.00 |
| 212_R | 221_S | 1.928 | 1.00 |
| 186_H | 204_S | 1.915 | 1.00 |
| 194_E | 236_S | 1.902 | 1.00 |
| 253_R | 262_L | 1.882 | 1.00 |
| 236_S | 277_R | 1.877 | 1.00 |
| 153_E | 194_E | 1.871 | 1.00 |
| 245_S | 255_W | 1.862 | 1.00 |
| 287_V | 297_Y | 1.849 | 1.00 |
| 269_D | 287_V | 1.849 | 1.00 |
| 161_V | 195_F | 1.848 | 1.00 |
| 87_L | 121_S | 1.841 | 1.00 |
| 30_Y | 40_A | 1.836 | 1.00 |
| 169_I | 204_S | 1.814 | 1.00 |
| 19_T | 70_A | 1.812 | 1.00 |
| 108_V | 124_V | 1.808 | 1.00 |
| 29_A | 71_W | 1.783 | 1.00 |
| 29_A | 78_I | 1.780 | 1.00 |
| 238_V | 278_I | 1.777 | 1.00 |
| 212_R | 224_C | 1.759 | 1.00 |
| 339_Y | 343_E | 1.748 | 1.00 |
| 161_V | 171_V | 1.746 | 1.00 |
| 203_L | 243_V | 1.742 | 1.00 |
| 170_F | 179_P | 1.734 | 1.00 |
| 162_I | 172_Y | 1.707 | 1.00 |
| 228_H | 245_S | 1.706 | 1.00 |
| 67_T | 83_E | 1.706 | 1.00 |
| 211_L | 245_S | 1.706 | 1.00 |
| 252_V | 287_V | 1.689 | 1.00 |
| 253_R | 265_L | 1.684 | 1.00 |
| 170_F | 182_K | 1.678 | 1.00 |
| 155_V | 195_F | 1.677 | 1.00 |
| 256_S | 259_Q | 1.671 | 1.00 |
| 128_T | 162_I | 1.665 | 1.00 |
| 129_I | 141_H | 1.655 | 1.00 |
| 132_N | 135_S | 1.652 | 1.00 |
| 196_N | 237_W | 1.624 | 1.00 |
| 113_N | 154_W | 1.624 | 1.00 |
| 37_A | 80_T | 1.624 | 1.00 |
| 88_R | 99_V | 1.623 | 1.00 |
| 29_A | 39_L | 1.613 | 1.00 |
| 286_A | 328_W | 1.604 | 1.00 |
| 317_S | 337_V | 1.597 | 1.00 |
| 120_I | 154_W | 1.584 | 1.00 |
| 274_F | 290_M | 1.553 | 1.00 |
| 161_V | 202_L | 1.550 | 1.00 |
| 319_D | 337_V | 1.548 | 1.00 |
| 233_V | 248_M | 1.544 | 1.00 |
| 173_Q | 176_E | 1.533 | 1.00 |
| 215_H | 218_N | 1.533 | 1.00 |
| 79_V | 110_V | 1.533 | 1.00 |
| 41_R | 44_E | 1.517 | 1.00 |
| 150_V | 165_P | 1.512 | 1.00 |
| 16_V | 33_K | 1.492 | 1.00 |
| 191_S | 207_D | 1.489 | 1.00 |
| 120_I | 160_F | 1.488 | 1.00 |
| 72_S | 112_W | 1.483 | 1.00 |
| 23_L | 26_S | 1.461 | 1.00 |
| 236_S | 276_G | 1.415 | 1.00 |
| 145_K | 162_I | 1.413 | 1.00 |
| 244_I | 285_Y | 1.409 | 1.00 |
| 38_R | 47_W | 1.379 | 0.99 |
| 205_A | 232_I | 1.361 | 0.99 |
| 277_R | 327_S | 1.353 | 0.99 |
| 337_V | 349_I | 1.337 | 0.99 |
| 29_A | 69_L | 1.333 | 0.99 |
| 194_E | 235_A | 1.331 | 0.99 |
| 246_C | 273_I | 1.306 | 0.99 |
| 62_S | 82_V | 1.303 | 0.99 |
| 120_I | 152_V | 1.289 | 0.99 |
| 234_S | 275_A | 1.283 | 0.99 |
| 298_D | 301_K | 1.273 | 0.99 |
| 138_V | 141_H | 1.270 | 0.99 |
| 288_A | 323_I | 1.270 | 0.99 |
| 203_L | 235_A | 1.257 | 0.99 |
| 81_G | 110_V | 1.250 | 0.99 |
| 295_N | 313_S | 1.248 | 0.99 |
| 294_V | 337_V | 1.246 | 0.98 |
| 161_V | 193_L | 1.244 | 0.98 |
| 244_I | 276_G | 1.243 | 0.98 |
| 77_S | 89_L | 1.242 | 0.98 |
| 117_T | 134_I | 1.228 | 0.98 |
| 279_S | 328_W | 1.228 | 0.98 |
| 336_S | 348_A | 1.225 | 0.98 |
| 239_G | 282_G | 1.200 | 0.98 |
| 179_P | 182_K | 1.198 | 0.98 |
| 205_A | 235_A | 1.195 | 0.98 |
| 68_C | 109_S | 1.190 | 0.98 |
| 70_A | 110_V | 1.185 | 0.98 |
| 109_S | 151_D | 1.181 | 0.98 |
| 38_R | 54_E | 1.175 | 0.98 |
| 103_H | 123_D | 1.162 | 0.97 |
| 163_P | 190_I | 1.153 | 0.97 |
| 286_A | 335_I | 1.151 | 0.97 |
| 118_H | 130_L | 1.150 | 0.97 |
| 91_N | 97_L | 1.139 | 0.97 |
| 153_E | 193_L | 1.128 | 0.97 |
| 122_M | 152_V | 1.117 | 0.96 |
| 27_I | 39_L | 1.116 | 0.96 |
| 96_L | 99_V | 1.114 | 0.96 |
| 200_K | 217_G | 1.114 | 0.96 |
| 221_S | 224_C | 1.111 | 0.96 |
| 186_H | 206_S | 1.105 | 0.96 |
| 246_C | 276_G | 1.103 | 0.96 |
| 324_F | 342_Q | 1.101 | 0.96 |
| 11_K | 32_E | 1.095 | 0.96 |
| 68_C | 110_V | 1.093 | 0.96 |
| 262_L | 265_L | 1.091 | 0.96 |
| 204_S | 212_R | 1.084 | 0.96 |
| 103_H | 125_E | 1.083 | 0.96 |
| 192_V | 234_S | 1.082 | 0.96 |
| 122_M | 149_G | 1.081 | 0.95 |
| 228_H | 247_S | 1.075 | 0.95 |
| 242_K | 263_L | 1.074 | 0.95 |
| 20_W | 28_L | 1.069 | 0.95 |
| 295_N | 310_L | 1.066 | 0.95 |
| 287_V | 295_N | 1.065 | 0.95 |
| 251_S | 265_L | 1.064 | 0.95 |
| 73_H | 116_G | 1.047 | 0.94 |
| 279_S | 284_K | 1.044 | 0.94 |
| 118_H | 139_M | 1.042 | 0.94 |
| 163_P | 193_L | 1.041 | 0.94 |
| 32_E | 36_V | 1.033 | 0.94 |
| 80_T | 88_R | 1.027 | 0.94 |
| 72_S | 76_N | 1.027 | 0.94 |
| 238_V | 242_K | 1.026 | 0.94 |
| 310_L | 313_S | 1.025 | 0.93 |
| 121_S | 129_I | 1.023 | 0.93 |
| 201_L | 213_I | 1.019 | 0.93 |
| 242_K | 254_L | 1.016 | 0.93 |
| 111_K | 152_V | 1.012 | 0.93 |
| 62_S | 66_V | 1.011 | 0.93 |
| 236_S | 278_I | 1.010 | 0.93 |
| 279_S | 283_Q | 1.010 | 0.93 |
| 168_A | 182_K | 1.007 | 0.93 |
| 301_K | 309_P | 1.005 | 0.93 |
| 112_W | 133_V | 1.002 | 0.92 |
| 21_N | 26_S | 1.001 | 0.92 |
| 72_S | 77_S | 1.001 | 0.92 |
| 277_R | 326_L | 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 | |
| 4lg9A | 1 | 0.943 | 100 | 0.034 | Contact Map |
| 4wjuA | 2 | 0.9487 | 100 | 0.039 | Contact Map |
| 4wjsA | 1 | 0.9487 | 100 | 0.055 | Contact Map |
| 3sfzA | 1 | 0.9316 | 100 | 0.059 | Contact Map |
| 4nsxA | 1 | 0.943 | 100 | 0.081 | Contact Map |
| 1r5mA | 1 | 0.943 | 100 | 0.084 | Contact Map |
| 2ymuA | 2 | 0.9288 | 100 | 0.094 | Contact Map |
| 1vyhC | 10 | 0.8234 | 100 | 0.1 | Contact Map |
| 4ci8A | 2 | 0.9487 | 100 | 0.112 | Contact Map |
| 4zoyA | 1 | 0 | 100 | 0.119 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)