| 4mfuoj |
| ID: | 1495077653 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 490 (315) | ||
| Sequences: | 19418 (10978.4) | ||
| Seq/Len: | 61.644 | ||
| Nf(neff/√len): | 618.6 |
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: 61.644).
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 |
| 163_G | 168_L | 3.053 | 1.00 |
| 115_L | 120_V | 2.738 | 1.00 |
| 288_M | 300_F | 2.649 | 1.00 |
| 197_L | 207_L | 2.555 | 1.00 |
| 153_A | 195_I | 2.514 | 1.00 |
| 248_L | 257_F | 2.402 | 1.00 |
| 153_A | 163_G | 2.378 | 1.00 |
| 64_L | 69_A | 2.373 | 1.00 |
| 300_F | 305_G | 2.263 | 1.00 |
| 207_L | 212_G | 2.243 | 1.00 |
| 197_L | 246_S | 2.235 | 1.00 |
| 255_E | 259_K | 2.218 | 1.00 |
| 205_E | 209_E | 2.196 | 1.00 |
| 248_L | 286_H | 2.137 | 1.00 |
| 190_S | 243_S | 2.110 | 1.00 |
| 208_G | 253_N | 2.102 | 1.00 |
| 241_F | 283_V | 2.077 | 1.00 |
| 298_H | 302_D | 2.031 | 1.00 |
| 55_A | 94_E | 1.995 | 1.00 |
| 55_A | 64_L | 1.967 | 1.00 |
| 96_T | 151_N | 1.944 | 1.00 |
| 256_R | 259_K | 1.939 | 1.00 |
| 194_A | 242_D | 1.905 | 1.00 |
| 125_V | 168_L | 1.896 | 1.00 |
| 257_F | 262_G | 1.821 | 1.00 |
| 258_L | 296_N | 1.814 | 1.00 |
| 113_D | 117_D | 1.786 | 1.00 |
| 244_L | 283_V | 1.776 | 1.00 |
| 146_L | 192_V | 1.772 | 1.00 |
| 161_T | 165_Q | 1.735 | 1.00 |
| 116_V | 159_M | 1.718 | 1.00 |
| 204_R | 250_L | 1.676 | 1.00 |
| 245_C | 282_K | 1.658 | 1.00 |
| 177_K | 215_V | 1.656 | 1.00 |
| 62_H | 66_E | 1.648 | 1.00 |
| 73_L | 88_V | 1.645 | 1.00 |
| 217_L | 262_G | 1.643 | 1.00 |
| 124_L | 148_I | 1.611 | 1.00 |
| 186_K | 231_A | 1.609 | 1.00 |
| 221_S | 265_L | 1.587 | 1.00 |
| 266_M | 283_V | 1.587 | 1.00 |
| 267_N | 305_G | 1.584 | 1.00 |
| 78_G | 123_L | 1.584 | 1.00 |
| 96_T | 115_L | 1.576 | 1.00 |
| 242_D | 279_S | 1.561 | 1.00 |
| 173_L | 212_G | 1.556 | 1.00 |
| 183_D | 233_E | 1.549 | 1.00 |
| 129_E | 171_W | 1.543 | 1.00 |
| 187_L | 233_E | 1.541 | 1.00 |
| 299_K | 302_D | 1.532 | 1.00 |
| 147_A | 188_Y | 1.515 | 1.00 |
| 74_L | 120_V | 1.495 | 1.00 |
| 266_M | 280_A | 1.488 | 1.00 |
| 206_L | 209_E | 1.486 | 1.00 |
| 164_A | 203_N | 1.483 | 1.00 |
| 51_M | 91_L | 1.472 | 1.00 |
| 238_E | 275_I | 1.461 | 1.00 |
| 85_S | 130_R | 1.460 | 1.00 |
| 172_L | 192_V | 1.457 | 1.00 |
| 90_D | 144_N | 1.452 | 1.00 |
| 245_C | 248_L | 1.448 | 1.00 |
| 139_A | 182_F | 1.441 | 1.00 |
| 44_L | 47_I | 1.430 | 1.00 |
| 191_E | 239_N | 1.426 | 1.00 |
| 216_L | 240_L | 1.417 | 1.00 |
| 149_V | 192_V | 1.411 | 1.00 |
| 150_E | 153_A | 1.392 | 0.99 |
| 142_V | 180_M | 1.381 | 0.99 |
| 52_H | 87_A | 1.376 | 0.99 |
| 256_R | 260_G | 1.370 | 0.99 |
| 239_N | 242_D | 1.366 | 0.99 |
| 92_L | 148_I | 1.360 | 0.99 |
| 142_V | 145_T | 1.359 | 0.99 |
| 143_H | 182_F | 1.358 | 0.99 |
| 50_E | 53_V | 1.355 | 0.99 |
| 150_E | 191_E | 1.352 | 0.99 |
| 90_D | 94_E | 1.352 | 0.99 |
| 124_L | 145_T | 1.352 | 0.99 |
| 146_L | 189_C | 1.333 | 0.99 |
| 186_K | 189_C | 1.306 | 0.99 |
| 49_Q | 53_V | 1.298 | 0.99 |
| 45_N | 81_N | 1.272 | 0.99 |
| 193_L | 243_S | 1.270 | 0.99 |
| 172_L | 189_C | 1.268 | 0.99 |
| 48_I | 91_L | 1.265 | 0.99 |
| 85_S | 88_V | 1.257 | 0.99 |
| 49_Q | 87_A | 1.253 | 0.99 |
| 44_L | 79_H | 1.247 | 0.99 |
| 93_Q | 96_T | 1.236 | 0.98 |
| 254_R | 290_G | 1.234 | 0.98 |
| 237_M | 272_E | 1.220 | 0.98 |
| 265_L | 268_L | 1.214 | 0.98 |
| 242_D | 245_C | 1.204 | 0.98 |
| 93_Q | 147_A | 1.202 | 0.98 |
| 299_K | 303_I | 1.202 | 0.98 |
| 63_L | 66_E | 1.197 | 0.98 |
| 245_C | 283_V | 1.194 | 0.98 |
| 336_S | 340_S | 1.193 | 0.98 |
| 76_L | 84_V | 1.188 | 0.98 |
| 194_A | 197_L | 1.187 | 0.98 |
| 157_P | 160_C | 1.185 | 0.98 |
| 75_G | 78_G | 1.185 | 0.98 |
| 284_L | 337_I | 1.185 | 0.98 |
| 177_K | 218_Q | 1.184 | 0.98 |
| 216_L | 243_S | 1.178 | 0.98 |
| 85_S | 141_G | 1.173 | 0.98 |
| 125_V | 171_W | 1.172 | 0.98 |
| 237_M | 240_L | 1.164 | 0.97 |
| 237_M | 276_S | 1.161 | 0.97 |
| 191_E | 194_A | 1.159 | 0.97 |
| 221_S | 268_L | 1.157 | 0.97 |
| 82_T | 85_S | 1.155 | 0.97 |
| 288_M | 340_S | 1.145 | 0.97 |
| 123_L | 126_Q | 1.143 | 0.97 |
| 80_D | 84_V | 1.142 | 0.97 |
| 86_I | 138_E | 1.135 | 0.97 |
| 173_L | 215_V | 1.131 | 0.97 |
| 129_E | 174_K | 1.122 | 0.97 |
| 143_H | 184_A | 1.112 | 0.96 |
| 127_N | 141_G | 1.110 | 0.96 |
| 89_V | 145_T | 1.103 | 0.96 |
| 188_Y | 191_E | 1.101 | 0.96 |
| 154_E | 195_I | 1.091 | 0.96 |
| 279_S | 282_K | 1.090 | 0.96 |
| 160_C | 199_D | 1.090 | 0.96 |
| 206_L | 210_L | 1.087 | 0.96 |
| 241_F | 280_A | 1.087 | 0.96 |
| 333_H | 336_S | 1.085 | 0.96 |
| 81_N | 84_V | 1.082 | 0.96 |
| 76_L | 88_V | 1.082 | 0.96 |
| 147_A | 151_N | 1.080 | 0.95 |
| 271_R | 308_T | 1.075 | 0.95 |
| 93_Q | 144_N | 1.073 | 0.95 |
| 162_E | 166_Q | 1.071 | 0.95 |
| 150_E | 188_Y | 1.071 | 0.95 |
| 122_A | 166_Q | 1.066 | 0.95 |
| 73_L | 91_L | 1.063 | 0.95 |
| 99_D | 102_H | 1.063 | 0.95 |
| 180_M | 185_N | 1.058 | 0.95 |
| 58_P | 61_Y | 1.055 | 0.95 |
| 44_L | 48_I | 1.051 | 0.94 |
| 45_N | 49_Q | 1.045 | 0.94 |
| 164_A | 167_G | 1.041 | 0.94 |
| 161_T | 202_E | 1.039 | 0.94 |
| 195_I | 198_Q | 1.038 | 0.94 |
| 55_A | 91_L | 1.038 | 0.94 |
| 89_V | 148_I | 1.037 | 0.94 |
| 126_Q | 129_E | 1.031 | 0.94 |
| 194_A | 243_S | 1.026 | 0.94 |
| 296_N | 299_K | 1.025 | 0.93 |
| 171_W | 174_K | 1.022 | 0.93 |
| 74_L | 123_L | 1.019 | 0.93 |
| 150_E | 192_V | 1.018 | 0.93 |
| 191_E | 195_I | 1.016 | 0.93 |
| 332_E | 336_S | 1.014 | 0.93 |
| 242_D | 246_S | 1.013 | 0.93 |
| 213_I | 244_L | 1.010 | 0.93 |
| 190_S | 240_L | 1.010 | 0.93 |
| 162_E | 165_Q | 1.009 | 0.93 |
| 151_N | 195_I | 1.005 | 0.93 |
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 | |
| 4mfuA | 1 | 0.9939 | 100 | -0.139 | Contact Map |
| 4cb9A | 1 | 0.9837 | 100 | -0.136 | Contact Map |
| 3nmzA | 2 | 0.6408 | 99.9 | 0.662 | Contact Map |
| 3nmwA | 2 | 0.6245 | 99.9 | 0.664 | Contact Map |
| 3opbA | 2 | 0.7265 | 99.9 | 0.668 | Contact Map |
| 4plqA | 1 | 0.5735 | 99.9 | 0.671 | Contact Map |
| 4uaeA | 1 | 0.802 | 99.9 | 0.675 | Contact Map |
| 4rxhB | 1 | 0 | 99.9 | 0.68 | Contact Map |
| 2jdqA | 2 | 0.7367 | 99.9 | 0.682 | Contact Map |
| 4uafB | 1 | 0.7184 | 99.9 | 0.684 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)