| T0823 |
| ID: | 1403033653 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 296 (281) | ||
| Sequences: | 14089 (10330.8) | ||
| Seq/Len: | 50.139 | ||
| Nf(neff/√len): | 616.3 |
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: 50.139).
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 |
| 94_R | 134_A | 3.207 | 1.00 |
| 37_T | 261_E | 2.981 | 1.00 |
| 28_A | 61_E | 2.753 | 1.00 |
| 64_A | 101_S | 2.746 | 1.00 |
| 93_K | 129_L | 2.717 | 1.00 |
| 73_L | 102_L | 2.522 | 1.00 |
| 229_P | 275_V | 2.501 | 1.00 |
| 75_W | 105_L | 2.451 | 1.00 |
| 90_D | 132_G | 2.432 | 1.00 |
| 37_T | 41_N | 2.430 | 1.00 |
| 228_T | 278_Q | 2.352 | 1.00 |
| 272_P | 275_V | 2.191 | 1.00 |
| 228_T | 275_V | 2.173 | 1.00 |
| 5_P | 12_A | 2.079 | 1.00 |
| 90_D | 128_D | 2.039 | 1.00 |
| 75_W | 96_A | 2.023 | 1.00 |
| 105_L | 135_L | 1.945 | 1.00 |
| 109_L | 158_A | 1.925 | 1.00 |
| 239_G | 269_R | 1.915 | 1.00 |
| 93_K | 108_L | 1.882 | 1.00 |
| 243_T | 276_C | 1.874 | 1.00 |
| 95_S | 99_G | 1.850 | 1.00 |
| 32_R | 62_A | 1.828 | 1.00 |
| 232_S | 262_R | 1.805 | 1.00 |
| 128_D | 132_G | 1.804 | 1.00 |
| 177_Q | 181_N | 1.804 | 1.00 |
| 4_R | 15_A | 1.780 | 1.00 |
| 41_N | 264_A | 1.755 | 1.00 |
| 128_D | 131_K | 1.749 | 1.00 |
| 32_R | 65_S | 1.729 | 1.00 |
| 109_L | 186_I | 1.727 | 1.00 |
| 32_R | 61_E | 1.725 | 1.00 |
| 38_A | 43_V | 1.720 | 1.00 |
| 273_T | 277_A | 1.710 | 1.00 |
| 127_Q | 131_K | 1.706 | 1.00 |
| 231_W | 269_R | 1.705 | 1.00 |
| 178_A | 185_V | 1.699 | 1.00 |
| 17_T | 45_S | 1.665 | 1.00 |
| 223_E | 227_N | 1.662 | 1.00 |
| 184_A | 249_T | 1.655 | 1.00 |
| 46_F | 59_A | 1.652 | 1.00 |
| 257_R | 261_E | 1.649 | 1.00 |
| 244_E | 280_E | 1.638 | 1.00 |
| 224_F | 278_Q | 1.637 | 1.00 |
| 74_T | 109_L | 1.636 | 1.00 |
| 41_N | 261_E | 1.634 | 1.00 |
| 104_Y | 136_R | 1.625 | 1.00 |
| 93_K | 105_L | 1.614 | 1.00 |
| 57_K | 99_G | 1.603 | 1.00 |
| 27_R | 30_D | 1.593 | 1.00 |
| 225_L | 236_I | 1.582 | 1.00 |
| 52_A | 92_L | 1.577 | 1.00 |
| 67_E | 70_L | 1.552 | 1.00 |
| 77_L | 89_L | 1.551 | 1.00 |
| 90_D | 125_G | 1.550 | 1.00 |
| 86_P | 90_D | 1.518 | 1.00 |
| 86_P | 128_D | 1.502 | 1.00 |
| 11_V | 137_G | 1.490 | 1.00 |
| 129_L | 135_L | 1.485 | 1.00 |
| 32_R | 36_F | 1.475 | 1.00 |
| 135_L | 138_L | 1.471 | 1.00 |
| 34_L | 260_I | 1.468 | 1.00 |
| 35_V | 62_A | 1.449 | 1.00 |
| 254_A | 260_I | 1.427 | 1.00 |
| 231_W | 235_D | 1.424 | 1.00 |
| 37_T | 40_E | 1.418 | 1.00 |
| 39_L | 71_L | 1.390 | 0.99 |
| 232_S | 235_D | 1.386 | 0.99 |
| 254_A | 259_E | 1.364 | 0.99 |
| 94_R | 98_E | 1.356 | 0.99 |
| 9_T | 137_G | 1.340 | 0.99 |
| 11_V | 72_F | 1.334 | 0.99 |
| 37_T | 257_R | 1.331 | 0.99 |
| 137_G | 157_T | 1.330 | 0.99 |
| 30_D | 33_A | 1.319 | 0.99 |
| 261_E | 265_A | 1.316 | 0.99 |
| 176_R | 180_Q | 1.310 | 0.99 |
| 90_D | 94_R | 1.304 | 0.99 |
| 239_G | 243_T | 1.301 | 0.99 |
| 125_G | 128_D | 1.299 | 0.99 |
| 57_K | 98_E | 1.298 | 0.99 |
| 148_P | 180_Q | 1.296 | 0.99 |
| 36_F | 40_E | 1.294 | 0.99 |
| 77_L | 108_L | 1.292 | 0.99 |
| 56_L | 96_A | 1.287 | 0.99 |
| 91_A | 95_S | 1.283 | 0.99 |
| 265_A | 268_E | 1.280 | 0.99 |
| 148_P | 152_A | 1.279 | 0.99 |
| 126_L | 138_L | 1.278 | 0.99 |
| 260_I | 264_A | 1.276 | 0.99 |
| 258_Q | 261_E | 1.266 | 0.99 |
| 95_S | 98_E | 1.265 | 0.99 |
| 161_S | 185_V | 1.265 | 0.99 |
| 36_F | 62_A | 1.259 | 0.99 |
| 68_R | 102_L | 1.254 | 0.99 |
| 148_P | 177_Q | 1.249 | 0.99 |
| 86_P | 125_G | 1.246 | 0.98 |
| 173_H | 176_R | 1.241 | 0.98 |
| 165_L | 279_I | 1.235 | 0.98 |
| 222_Y | 233_A | 1.232 | 0.98 |
| 72_F | 107_L | 1.227 | 0.98 |
| 3_Y | 12_A | 1.221 | 0.98 |
| 86_P | 124_S | 1.217 | 0.98 |
| 222_Y | 279_I | 1.212 | 0.98 |
| 86_P | 121_A | 1.202 | 0.98 |
| 241_A | 250_V | 1.187 | 0.98 |
| 130_Q | 154_D | 1.184 | 0.98 |
| 68_R | 104_Y | 1.180 | 0.98 |
| 179_S | 245_P | 1.174 | 0.98 |
| 231_W | 236_I | 1.172 | 0.98 |
| 130_Q | 157_T | 1.169 | 0.97 |
| 277_A | 281_M | 1.165 | 0.97 |
| 238_L | 266_V | 1.164 | 0.97 |
| 236_I | 269_R | 1.161 | 0.97 |
| 28_A | 32_R | 1.158 | 0.97 |
| 107_L | 158_A | 1.139 | 0.97 |
| 165_L | 237_C | 1.136 | 0.97 |
| 228_T | 272_P | 1.134 | 0.97 |
| 36_F | 65_S | 1.133 | 0.97 |
| 229_P | 272_P | 1.133 | 0.97 |
| 45_S | 186_I | 1.123 | 0.97 |
| 239_G | 266_V | 1.122 | 0.97 |
| 221_G | 224_F | 1.113 | 0.96 |
| 100_L | 105_L | 1.110 | 0.96 |
| 94_R | 132_G | 1.104 | 0.96 |
| 57_K | 61_E | 1.100 | 0.96 |
| 224_F | 227_N | 1.091 | 0.96 |
| 61_E | 101_S | 1.090 | 0.96 |
| 97_F | 134_A | 1.089 | 0.96 |
| 60_G | 101_S | 1.088 | 0.96 |
| 74_T | 186_I | 1.081 | 0.95 |
| 148_P | 181_N | 1.077 | 0.95 |
| 110_I | 126_L | 1.074 | 0.95 |
| 278_Q | 281_M | 1.073 | 0.95 |
| 14_S | 43_V | 1.070 | 0.95 |
| 235_D | 262_R | 1.066 | 0.95 |
| 122_F | 125_G | 1.065 | 0.95 |
| 9_T | 157_T | 1.060 | 0.95 |
| 235_D | 265_A | 1.056 | 0.95 |
| 85_G | 88_T | 1.055 | 0.95 |
| 168_G | 171_E | 1.051 | 0.94 |
| 163_Y | 244_E | 1.050 | 0.94 |
| 63_F | 71_L | 1.046 | 0.94 |
| 14_S | 44_N | 1.046 | 0.94 |
| 52_A | 88_T | 1.045 | 0.94 |
| 29_N | 33_A | 1.044 | 0.94 |
| 87_H | 91_A | 1.037 | 0.94 |
| 127_Q | 130_Q | 1.034 | 0.94 |
| 129_L | 132_G | 1.033 | 0.94 |
| 258_Q | 262_R | 1.030 | 0.94 |
| 242_L | 266_V | 1.026 | 0.94 |
| 2_R | 15_A | 1.019 | 0.93 |
| 178_A | 183_F | 1.019 | 0.93 |
| 225_L | 229_P | 1.019 | 0.93 |
| 129_L | 134_A | 1.017 | 0.93 |
| 277_A | 280_E | 1.017 | 0.93 |
| 140_V | 159_V | 1.015 | 0.93 |
| 274_G | 277_A | 1.015 | 0.93 |
| 33_A | 37_T | 1.012 | 0.93 |
| 120_M | 149_G | 1.010 | 0.93 |
| 44_N | 72_F | 1.007 | 0.93 |
| 35_V | 46_F | 1.006 | 0.93 |
| 244_E | 276_C | 1.006 | 0.93 |
| 106_D | 136_R | 1.005 | 0.93 |
| 45_S | 74_T | 1.002 | 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 | |
| 1pyfA | 1 | 0.9561 | 100 | 0.16 | Contact Map |
| 1pz1A | 2 | 0.9932 | 100 | 0.169 | Contact Map |
| 3n2tA | 1 | 0.9797 | 100 | 0.174 | Contact Map |
| 3erpA | 2 | 0.9223 | 100 | 0.176 | Contact Map |
| 3v0sA | 1 | 0.8615 | 100 | 0.176 | Contact Map |
| 1ur3M | 1 | 0.9223 | 100 | 0.181 | Contact Map |
| 1ynpA | 2 | 0.9493 | 100 | 0.184 | Contact Map |
| 1lqaA | 2 | 0.9696 | 100 | 0.185 | Contact Map |
| 3lutA | 1 | 0.9595 | 100 | 0.187 | Contact Map |
| 3n6qA | 8 | 0.9324 | 100 | 0.188 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)