| T0830 1-340 |
| ID: | 1405373854 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 340 (317) | ||
| Sequences: | 2621 (2122.3) | ||
| Seq/Len: | 8.268 | ||
| Nf(neff/√len): | 119.2 |
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: 8.268).
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 |
| 121_V | 167_C | 3.457 | 1.00 |
| 117_L | 163_G | 3.324 | 1.00 |
| 126_A | 135_A | 3.143 | 1.00 |
| 96_G | 106_Q | 2.948 | 1.00 |
| 167_C | 195_A | 2.931 | 1.00 |
| 199_A | 207_G | 2.819 | 1.00 |
| 114_S | 163_G | 2.679 | 1.00 |
| 142_L | 148_W | 2.608 | 1.00 |
| 193_W | 236_G | 2.536 | 1.00 |
| 113_L | 117_L | 2.512 | 1.00 |
| 103_G | 106_Q | 2.408 | 1.00 |
| 197_G | 243_I | 2.350 | 1.00 |
| 118_G | 166_S | 2.288 | 1.00 |
| 158_D | 203_K | 2.189 | 1.00 |
| 97_Y | 107_A | 2.178 | 1.00 |
| 200_I | 240_M | 2.134 | 1.00 |
| 88_F | 202_T | 2.128 | 1.00 |
| 61_E | 64_R | 2.111 | 1.00 |
| 171_F | 195_A | 2.059 | 1.00 |
| 96_G | 110_A | 1.991 | 1.00 |
| 125_A | 173_L | 1.986 | 1.00 |
| 119_I | 139_G | 1.973 | 1.00 |
| 126_A | 138_T | 1.938 | 1.00 |
| 114_S | 160_T | 1.904 | 1.00 |
| 67_F | 98_E | 1.879 | 1.00 |
| 226_G | 229_R | 1.875 | 1.00 |
| 308_R | 311_V | 1.855 | 1.00 |
| 97_Y | 102_L | 1.850 | 1.00 |
| 164_V | 202_T | 1.825 | 1.00 |
| 128_R | 174_M | 1.813 | 1.00 |
| 123_M | 139_G | 1.809 | 1.00 |
| 131_G | 134_A | 1.803 | 1.00 |
| 115_G | 152_A | 1.782 | 1.00 |
| 171_F | 188_W | 1.776 | 1.00 |
| 96_G | 100_F | 1.761 | 1.00 |
| 175_G | 189_M | 1.756 | 1.00 |
| 119_I | 142_L | 1.756 | 1.00 |
| 135_A | 139_G | 1.749 | 1.00 |
| 193_W | 197_G | 1.734 | 1.00 |
| 118_G | 163_G | 1.733 | 1.00 |
| 67_F | 94_V | 1.713 | 1.00 |
| 207_G | 211_P | 1.710 | 1.00 |
| 171_F | 191_A | 1.701 | 1.00 |
| 95_V | 99_L | 1.698 | 1.00 |
| 62_I | 82_Y | 1.668 | 1.00 |
| 127_R | 135_A | 1.645 | 1.00 |
| 64_R | 68_A | 1.633 | 1.00 |
| 144_A | 296_W | 1.587 | 1.00 |
| 43_F | 116_L | 1.576 | 1.00 |
| 56_E | 108_R | 1.574 | 1.00 |
| 71_D | 254_R | 1.554 | 1.00 |
| 105_W | 109_L | 1.518 | 1.00 |
| 122_S | 142_L | 1.486 | 1.00 |
| 127_R | 132_A | 1.480 | 0.99 |
| 38_A | 119_I | 1.449 | 0.99 |
| 85_K | 91_W | 1.449 | 0.99 |
| 43_F | 112_A | 1.439 | 0.99 |
| 326_I | 330_A | 1.427 | 0.99 |
| 173_L | 323_M | 1.416 | 0.99 |
| 85_K | 203_K | 1.412 | 0.99 |
| 305_T | 309_A | 1.411 | 0.99 |
| 194_A | 243_I | 1.409 | 0.99 |
| 121_V | 163_G | 1.406 | 0.99 |
| 283_F | 287_P | 1.404 | 0.99 |
| 85_K | 270_R | 1.394 | 0.99 |
| 46_L | 112_A | 1.392 | 0.99 |
| 249_Y | 253_V | 1.388 | 0.99 |
| 86_P | 203_K | 1.385 | 0.99 |
| 92_V | 160_T | 1.381 | 0.99 |
| 164_V | 198_V | 1.378 | 0.99 |
| 238_V | 242_V | 1.368 | 0.99 |
| 271_Y | 334_F | 1.364 | 0.99 |
| 118_G | 148_W | 1.364 | 0.99 |
| 160_T | 202_T | 1.357 | 0.99 |
| 128_R | 177_H | 1.354 | 0.99 |
| 59_Y | 157_L | 1.345 | 0.99 |
| 190_V | 235_L | 1.334 | 0.99 |
| 63_S | 93_T | 1.332 | 0.99 |
| 119_I | 143_L | 1.331 | 0.99 |
| 152_A | 159_M | 1.331 | 0.99 |
| 96_G | 109_L | 1.326 | 0.99 |
| 61_E | 65_E | 1.310 | 0.98 |
| 135_A | 138_T | 1.299 | 0.98 |
| 26_A | 29_G | 1.267 | 0.98 |
| 248_F | 262_F | 1.260 | 0.98 |
| 170_A | 174_M | 1.259 | 0.98 |
| 115_G | 148_W | 1.257 | 0.98 |
| 168_V | 196_M | 1.253 | 0.98 |
| 65_E | 76_R | 1.251 | 0.98 |
| 195_A | 198_V | 1.251 | 0.98 |
| 280_G | 284_Y | 1.241 | 0.98 |
| 246_P | 250_L | 1.240 | 0.98 |
| 176_Q | 218_Y | 1.227 | 0.97 |
| 123_M | 135_A | 1.227 | 0.97 |
| 129_W | 173_L | 1.226 | 0.97 |
| 106_Q | 110_A | 1.223 | 0.97 |
| 245_V | 249_Y | 1.223 | 0.97 |
| 304_W | 308_R | 1.216 | 0.97 |
| 84_E | 266_E | 1.206 | 0.97 |
| 88_F | 198_V | 1.203 | 0.97 |
| 124_M | 170_A | 1.202 | 0.97 |
| 89_H | 157_L | 1.197 | 0.97 |
| 40_V | 44_V | 1.191 | 0.97 |
| 89_H | 160_T | 1.180 | 0.97 |
| 82_Y | 266_E | 1.173 | 0.96 |
| 71_D | 76_R | 1.173 | 0.96 |
| 82_Y | 157_L | 1.166 | 0.96 |
| 165_M | 207_G | 1.160 | 0.96 |
| 243_I | 246_P | 1.148 | 0.96 |
| 122_S | 138_T | 1.147 | 0.96 |
| 227_L | 230_R | 1.146 | 0.96 |
| 39_L | 43_F | 1.140 | 0.96 |
| 115_G | 142_L | 1.130 | 0.95 |
| 125_A | 166_S | 1.130 | 0.95 |
| 188_W | 191_A | 1.128 | 0.95 |
| 164_V | 199_A | 1.125 | 0.95 |
| 122_S | 126_A | 1.109 | 0.95 |
| 75_I | 90_M | 1.106 | 0.95 |
| 242_V | 246_P | 1.105 | 0.94 |
| 100_F | 109_L | 1.105 | 0.94 |
| 107_A | 155_N | 1.101 | 0.94 |
| 126_A | 129_W | 1.095 | 0.94 |
| 186_R | 190_V | 1.086 | 0.94 |
| 29_G | 32_V | 1.084 | 0.94 |
| 106_Q | 109_L | 1.083 | 0.94 |
| 201_L | 247_W | 1.082 | 0.94 |
| 223_R | 226_G | 1.079 | 0.94 |
| 124_M | 128_R | 1.077 | 0.93 |
| 72_W | 94_V | 1.067 | 0.93 |
| 34_F | 38_A | 1.063 | 0.93 |
| 63_S | 97_Y | 1.059 | 0.93 |
| 92_V | 96_G | 1.058 | 0.93 |
| 226_G | 230_R | 1.052 | 0.92 |
| 102_L | 107_A | 1.044 | 0.92 |
| 287_P | 290_I | 1.040 | 0.92 |
| 126_A | 130_F | 1.032 | 0.91 |
| 91_W | 201_L | 1.026 | 0.91 |
| 89_H | 93_T | 1.020 | 0.91 |
| 222_T | 322_L | 1.015 | 0.90 |
| 85_K | 247_W | 1.013 | 0.90 |
| 271_Y | 338_S | 1.013 | 0.90 |
| 169_L | 323_M | 1.012 | 0.90 |
| 83_F | 255_N | 1.009 | 0.90 |
| 69_S | 76_R | 1.009 | 0.90 |
| 329_I | 333_V | 1.009 | 0.90 |
| 320_P | 324_A | 1.008 | 0.90 |
| 308_R | 312_E | 1.006 | 0.90 |
| 280_G | 285_F | 1.006 | 0.90 |
| 97_Y | 106_Q | 1.006 | 0.90 |
| 298_G | 302_K | 1.005 | 0.90 |
| 172_M | 215_L | 1.005 | 0.90 |
| 111_V | 155_N | 1.003 | 0.90 |
| 239_V | 243_I | 1.002 | 0.90 |
| 286_L | 332_F | 1.002 | 0.90 |
| 164_V | 195_A | 1.001 | 0.90 |
| 94_V | 98_E | 1.001 | 0.90 |
| 262_F | 267_H | 1.000 | 0.90 |
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 | |
| 3wajA | 1 | 0.8294 | 100 | 0.617 | Contact Map |
| 3rceA | 1 | 0.7971 | 99.9 | 0.67 | Contact Map |
| 3dh4A | 4 | 0.1412 | 6.9 | 0.967 | Contact Map |
| 2xq2A | 1 | 0.1824 | 6.6 | 0.967 | Contact Map |
| 2z73A | 2 | 0.7059 | 4.7 | 0.969 | Contact Map |
| 1zrtD | 2 | 0.1765 | 3.5 | 0.971 | Contact Map |
| 2m8rA | 1 | 0.1529 | 3.2 | 0.972 | Contact Map |
| 3rkoL | 2 | 0.3882 | 2.8 | 0.973 | Contact Map |
| 1fftA | 2 | 0 | 2.6 | 0.973 | Contact Map |
| 4p02B | 1 | 0.3294 | 2.3 | 0.974 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)