| HD TGS low coverage |
| ID: | 1425311079 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 50% gaps before running GREMLIN. |
| Length: | 287 (284) | ||
| Sequences: | 1160 (584.8) | ||
| Seq/Len: | 4.085 | ||
| Nf(neff/√len): | 34.7 |
HHblits Results: (2013_03)
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: 4.085).
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 |
| 39_L | 112_L | 4.713 | 1.00 |
| 246_Y | 254_D | 4.612 | 1.00 |
| 53_I | 60_K | 4.269 | 1.00 |
| 64_A | 69_D | 3.824 | 1.00 |
| 129_K | 132_A | 3.549 | 1.00 |
| 261_I | 266_K | 3.389 | 1.00 |
| 125_L | 168_H | 3.358 | 1.00 |
| 262_N | 276_D | 2.944 | 1.00 |
| 60_K | 76_E | 2.677 | 1.00 |
| 42_A | 70_E | 2.631 | 1.00 |
| 123_R | 160_E | 2.610 | 1.00 |
| 74_L | 113_V | 2.508 | 1.00 |
| 272_L | 278_V | 2.318 | 1.00 |
| 7_Y | 58_V | 2.315 | 1.00 |
| 261_I | 270_T | 2.276 | 1.00 |
| 139_R | 143_D | 2.272 | 1.00 |
| 170_N | 173_A | 2.188 | 1.00 |
| 3_R | 66_L | 2.162 | 1.00 |
| 1_M | 44_I | 2.158 | 1.00 |
| 260_K | 279_E | 2.042 | 1.00 |
| 53_I | 63_I | 2.021 | 1.00 |
| 227_T | 233_V | 2.005 | 1.00 |
| 53_I | 76_E | 1.997 | 1.00 |
| 8_A | 24_Y | 1.982 | 1.00 |
| 270_T | 273_N | 1.970 | 1.00 |
| 225_V | 272_L | 1.960 | 1.00 |
| 2_N | 6_V | 1.927 | 1.00 |
| 176_A | 180_R | 1.915 | 1.00 |
| 34_L | 47_A | 1.879 | 1.00 |
| 31_A | 44_I | 1.876 | 1.00 |
| 134_R | 168_H | 1.858 | 1.00 |
| 131_Q | 135_E | 1.853 | 1.00 |
| 73_E | 106_K | 1.802 | 1.00 |
| 166_F | 170_N | 1.797 | 1.00 |
| 46_T | 113_V | 1.794 | 1.00 |
| 252_V | 282_R | 1.778 | 0.99 |
| 122_M | 164_L | 1.774 | 0.99 |
| 104_I | 108_V | 1.740 | 0.99 |
| 131_Q | 134_R | 1.735 | 0.99 |
| 250_T | 254_D | 1.723 | 0.99 |
| 46_T | 74_L | 1.711 | 0.99 |
| 10_R | 13_G | 1.687 | 0.99 |
| 159_T | 185_R | 1.674 | 0.99 |
| 18_A | 128_I | 1.666 | 0.99 |
| 53_I | 72_G | 1.662 | 0.99 |
| 34_L | 43_T | 1.535 | 0.98 |
| 241_P | 259_V | 1.528 | 0.98 |
| 175_N | 178_I | 1.527 | 0.98 |
| 223_V | 274_N | 1.498 | 0.98 |
| 5_Y | 9_M | 1.485 | 0.97 |
| 33_I | 123_R | 1.484 | 0.97 |
| 41_T | 45_V | 1.454 | 0.97 |
| 6_V | 9_M | 1.437 | 0.97 |
| 60_K | 72_G | 1.432 | 0.97 |
| 39_L | 43_T | 1.375 | 0.96 |
| 113_V | 150_R | 1.374 | 0.95 |
| 256_C | 268_L | 1.349 | 0.95 |
| 128_I | 137_I | 1.334 | 0.94 |
| 166_F | 173_A | 1.329 | 0.94 |
| 7_Y | 66_L | 1.306 | 0.94 |
| 125_L | 138_A | 1.290 | 0.93 |
| 61_E | 65_K | 1.254 | 0.92 |
| 122_M | 125_L | 1.243 | 0.91 |
| 13_G | 16_T | 1.238 | 0.91 |
| 143_D | 215_K | 1.235 | 0.91 |
| 222_Q | 234_S | 1.223 | 0.90 |
| 184_L | 187_E | 1.221 | 0.90 |
| 120_H | 124_T | 1.196 | 0.89 |
| 241_P | 261_I | 1.189 | 0.89 |
| 31_A | 47_A | 1.176 | 0.88 |
| 53_I | 79_T | 1.168 | 0.87 |
| 125_L | 137_I | 1.161 | 0.87 |
| 55_D | 80_K | 1.157 | 0.87 |
| 11_M | 62_E | 1.154 | 0.87 |
| 55_D | 121_N | 1.150 | 0.86 |
| 263_G | 279_E | 1.139 | 0.86 |
| 45_V | 71_I | 1.137 | 0.85 |
| 64_A | 72_G | 1.136 | 0.85 |
| 56_T | 59_T | 1.130 | 0.85 |
| 260_K | 265_L | 1.129 | 0.85 |
| 101_I | 145_Y | 1.126 | 0.85 |
| 61_E | 64_A | 1.123 | 0.85 |
| 118_R | 141_T | 1.117 | 0.84 |
| 75_V | 197_L | 1.116 | 0.84 |
| 60_K | 64_A | 1.115 | 0.84 |
| 7_Y | 11_M | 1.110 | 0.84 |
| 11_M | 57_P | 1.105 | 0.83 |
| 54_E | 121_N | 1.105 | 0.83 |
| 62_E | 65_K | 1.091 | 0.82 |
| 167_E | 175_N | 1.084 | 0.82 |
| 133_K | 137_I | 1.079 | 0.81 |
| 1_M | 224_F | 1.078 | 0.81 |
| 11_M | 58_V | 1.075 | 0.81 |
| 78_V | 269_R | 1.064 | 0.80 |
| 9_M | 24_Y | 1.060 | 0.80 |
| 238_G | 271_L | 1.059 | 0.79 |
| 78_V | 81_L | 1.058 | 0.79 |
| 81_L | 218_M | 1.054 | 0.79 |
| 122_M | 242_L | 1.048 | 0.78 |
| 80_K | 121_N | 1.045 | 0.78 |
| 174_R | 178_I | 1.031 | 0.77 |
| 184_L | 189_G | 1.031 | 0.77 |
| 46_T | 75_V | 1.030 | 0.77 |
| 187_E | 191_A | 1.028 | 0.77 |
| 81_L | 287_V | 1.025 | 0.76 |
| 40_D | 221_D | 1.023 | 0.76 |
| 53_I | 62_E | 1.022 | 0.76 |
| 51_D | 54_E | 1.006 | 0.74 |
| 17_R | 121_N | 1.004 | 0.74 |
| 100_F | 202_E | 1.002 | 0.74 |
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 | |
| 1vj7A | 2 | 0.9303 | 100 | 0.47 | Contact Map |
| 3nr1A | 2 | 0.5854 | 100 | 0.663 | Contact Map |
| 3nqwA | 2 | 0.5714 | 100 | 0.672 | Contact Map |
| 2ekiA | 1 | 0.2857 | 99.8 | 0.845 | Contact Map |
| 3hvzA | 6 | 0.223 | 99.7 | 0.869 | Contact Map |
| 3l9dA | 2 | 0.2195 | 99.6 | 0.875 | Contact Map |
| 1wxqA | 1 | 0.8432 | 99.6 | 0.88 | Contact Map |
| 1nyrA | 2 | 0.2369 | 99.6 | 0.881 | Contact Map |
| 3j7y7 | 1 | 0.3415 | 99.5 | 0.883 | Contact Map |
| 2kmmA | 1 | 0.2334 | 99.4 | 0.894 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)