| T0793_sub |
| ID: | 1402888278 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 360 (344) | ||
| Sequences: | 452 (368.1) | ||
| Seq/Len: | 1.314 | ||
| Nf(neff/√len): | 19.8 |
Jackhmmer Results: (2014_04_16)
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: 1.314).
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 |
| 76_A | 205_L | 3.496 | 1.00 |
| 62_S | 244_R | 3.148 | 1.00 |
| 90_W | 156_S | 3.087 | 1.00 |
| 20_V | 30_V | 2.916 | 1.00 |
| 29_A | 57_F | 2.873 | 1.00 |
| 17_I | 204_V | 2.838 | 1.00 |
| 55_F | 252_I | 2.825 | 1.00 |
| 11_N | 200_N | 2.605 | 1.00 |
| 56_S | 158_S | 2.544 | 1.00 |
| 61_S | 170_D | 2.487 | 1.00 |
| 28_L | 252_I | 2.452 | 1.00 |
| 9_F | 203_H | 2.432 | 1.00 |
| 31_I | 256_A | 2.360 | 0.99 |
| 34_I | 204_V | 2.325 | 0.99 |
| 96_A | 136_Q | 2.246 | 0.99 |
| 95_N | 138_S | 2.242 | 0.99 |
| 69_A | 155_I | 2.231 | 0.99 |
| 53_I | 248_R | 2.227 | 0.99 |
| 200_N | 203_H | 2.202 | 0.99 |
| 211_Y | 262_V | 2.187 | 0.99 |
| 138_S | 142_G | 2.036 | 0.98 |
| 33_G | 75_V | 2.034 | 0.98 |
| 71_L | 193_I | 2.014 | 0.98 |
| 26_L | 68_A | 2.014 | 0.98 |
| 127_Y | 159_E | 1.986 | 0.97 |
| 260_G | 265_T | 1.982 | 0.97 |
| 177_I | 245_M | 1.977 | 0.97 |
| 91_N | 135_R | 1.970 | 0.97 |
| 66_S | 157_T | 1.929 | 0.97 |
| 260_G | 266_D | 1.923 | 0.96 |
| 159_E | 171_G | 1.894 | 0.96 |
| 69_A | 157_T | 1.888 | 0.96 |
| 95_N | 137_R | 1.832 | 0.95 |
| 106_G | 151_G | 1.818 | 0.95 |
| 342_Q | 346_N | 1.803 | 0.94 |
| 98_E | 134_G | 1.773 | 0.94 |
| 70_A | 194_K | 1.741 | 0.93 |
| 9_F | 207_L | 1.741 | 0.93 |
| 73_V | 110_V | 1.682 | 0.91 |
| 301_V | 335_I | 1.676 | 0.91 |
| 25_L | 279_Y | 1.641 | 0.90 |
| 345_N | 348_Q | 1.640 | 0.90 |
| 9_F | 204_V | 1.636 | 0.90 |
| 115_S | 169_N | 1.609 | 0.89 |
| 300_F | 321_Y | 1.594 | 0.88 |
| 30_V | 34_I | 1.590 | 0.88 |
| 308_F | 322_G | 1.576 | 0.87 |
| 101_L | 109_I | 1.561 | 0.87 |
| 11_N | 203_H | 1.552 | 0.86 |
| 241_T | 289_L | 1.548 | 0.86 |
| 56_S | 113_E | 1.546 | 0.86 |
| 343_M | 346_N | 1.526 | 0.85 |
| 204_V | 264_S | 1.525 | 0.85 |
| 98_E | 137_R | 1.513 | 0.84 |
| 343_M | 348_Q | 1.511 | 0.84 |
| 267_I | 283_T | 1.488 | 0.83 |
| 57_F | 155_I | 1.482 | 0.82 |
| 95_N | 99_G | 1.462 | 0.81 |
| 10_D | 13_F | 1.451 | 0.81 |
| 207_L | 210_K | 1.449 | 0.80 |
| 170_D | 241_T | 1.437 | 0.80 |
| 56_S | 156_S | 1.435 | 0.79 |
| 183_F | 192_N | 1.430 | 0.79 |
| 209_A | 213_I | 1.427 | 0.79 |
| 110_V | 157_T | 1.394 | 0.77 |
| 15_M | 200_N | 1.393 | 0.77 |
| 206_P | 213_I | 1.388 | 0.76 |
| 339_V | 343_M | 1.373 | 0.75 |
| 34_I | 208_V | 1.359 | 0.74 |
| 127_Y | 171_G | 1.355 | 0.74 |
| 92_A | 97_L | 1.323 | 0.71 |
| 276_F | 279_Y | 1.322 | 0.71 |
| 62_S | 190_A | 1.314 | 0.71 |
| 25_L | 53_I | 1.312 | 0.70 |
| 280_H | 283_T | 1.310 | 0.70 |
| 33_G | 76_A | 1.294 | 0.69 |
| 304_N | 308_F | 1.289 | 0.68 |
| 53_I | 153_S | 1.282 | 0.68 |
| 212_L | 255_S | 1.277 | 0.67 |
| 117_T | 122_T | 1.277 | 0.67 |
| 342_Q | 348_Q | 1.266 | 0.66 |
| 304_N | 307_K | 1.260 | 0.66 |
| 69_A | 110_V | 1.260 | 0.66 |
| 195_K | 224_Y | 1.258 | 0.66 |
| 69_A | 92_A | 1.256 | 0.65 |
| 30_V | 204_V | 1.252 | 0.65 |
| 257_K | 270_A | 1.244 | 0.64 |
| 99_G | 138_S | 1.236 | 0.64 |
| 66_S | 192_N | 1.221 | 0.62 |
| 52_G | 132_G | 1.203 | 0.61 |
| 51_A | 244_R | 1.192 | 0.59 |
| 12_W | 204_V | 1.188 | 0.59 |
| 208_V | 211_Y | 1.177 | 0.58 |
| 203_H | 206_P | 1.174 | 0.58 |
| 94_R | 121_D | 1.174 | 0.58 |
| 55_F | 177_I | 1.165 | 0.57 |
| 52_G | 116_S | 1.160 | 0.56 |
| 251_V | 257_K | 1.157 | 0.56 |
| 339_V | 346_N | 1.154 | 0.56 |
| 28_L | 55_F | 1.152 | 0.56 |
| 36_A | 152_T | 1.141 | 0.55 |
| 66_S | 280_H | 1.139 | 0.54 |
| 253_T | 257_K | 1.131 | 0.54 |
| 23_H | 131_E | 1.130 | 0.53 |
| 31_I | 34_I | 1.130 | 0.53 |
| 205_L | 255_S | 1.127 | 0.53 |
| 129_I | 154_V | 1.121 | 0.53 |
| 275_Y | 283_T | 1.114 | 0.52 |
| 267_I | 272_I | 1.112 | 0.52 |
| 267_I | 271_N | 1.110 | 0.51 |
| 170_D | 289_L | 1.107 | 0.51 |
| 52_G | 152_T | 1.101 | 0.51 |
| 300_F | 304_N | 1.101 | 0.51 |
| 61_S | 190_A | 1.098 | 0.50 |
| 51_A | 62_S | 1.098 | 0.50 |
| 66_S | 298_I | 1.097 | 0.50 |
| 5_P | 203_H | 1.097 | 0.50 |
| 36_A | 108_P | 1.094 | 0.50 |
| 56_S | 249_Y | 1.092 | 0.50 |
| 346_N | 352_V | 1.091 | 0.50 |
| 19_E | 183_F | 1.089 | 0.49 |
| 122_T | 292_K | 1.072 | 0.48 |
| 267_I | 276_F | 1.066 | 0.47 |
| 90_W | 158_S | 1.066 | 0.47 |
| 28_L | 128_S | 1.060 | 0.46 |
| 116_S | 245_M | 1.059 | 0.46 |
| 206_P | 209_A | 1.058 | 0.46 |
| 174_V | 241_T | 1.057 | 0.46 |
| 191_D | 194_K | 1.054 | 0.46 |
| 66_S | 70_A | 1.050 | 0.45 |
| 61_S | 241_T | 1.049 | 0.45 |
| 308_F | 335_I | 1.049 | 0.45 |
| 225_K | 233_K | 1.046 | 0.45 |
| 8_T | 203_H | 1.046 | 0.45 |
| 348_Q | 352_V | 1.045 | 0.45 |
| 138_S | 144_V | 1.040 | 0.44 |
| 66_S | 69_A | 1.038 | 0.44 |
| 230_F | 254_T | 1.037 | 0.44 |
| 34_I | 259_L | 1.035 | 0.44 |
| 97_L | 297_I | 1.034 | 0.44 |
| 142_G | 158_S | 1.030 | 0.43 |
| 348_Q | 351_D | 1.024 | 0.43 |
| 98_E | 256_A | 1.024 | 0.43 |
| 267_I | 275_Y | 1.023 | 0.43 |
| 316_N | 319_E | 1.020 | 0.42 |
| 9_F | 13_F | 1.014 | 0.42 |
| 25_L | 181_E | 1.014 | 0.42 |
| 16_Y | 179_I | 1.010 | 0.42 |
| 23_H | 26_L | 1.008 | 0.41 |
| 203_H | 207_L | 1.005 | 0.41 |
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 | |
| 1ofhA | 3 | 0.7694 | 97.5 | 0.914 | Contact Map |
| 4b4tJ | 1 | 0.6417 | 97.3 | 0.918 | Contact Map |
| 3bosA | 2 | 0.6028 | 97.2 | 0.919 | Contact Map |
| 3sylA | 2 | 0.7083 | 97.2 | 0.92 | Contact Map |
| 3vfdA | 1 | 0.65 | 97.2 | 0.92 | Contact Map |
| 1r6bX | 1 | 0.7083 | 97.1 | 0.921 | Contact Map |
| 2r44A | 1 | 0.7722 | 97 | 0.921 | Contact Map |
| 3hwsA | 6 | 0.7889 | 97 | 0.921 | Contact Map |
| 3n70A | 8 | 0.3778 | 97 | 0.922 | Contact Map |
| 4l15A | 1 | 0.7 | 97 | 0.922 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)