| fjx1 |
| ID: | 1510685045 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 353 (312) | ||
| Sequences: | 2071 (1102.3) | ||
| Seq/Len: | 6.638 | ||
| Nf(neff/√len): | 62.4 |
Jackhmmer Results: (2016_04)
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: 6.638).
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 |
| 211_F | 215_T | 2.717 | 1.00 |
| 95_V | 156_V | 2.545 | 1.00 |
| 287_T | 290_R | 2.401 | 1.00 |
| 113_L | 215_T | 2.275 | 1.00 |
| 214_L | 291_V | 2.107 | 1.00 |
| 115_R | 120_Q | 2.045 | 1.00 |
| 117_L | 290_R | 1.976 | 1.00 |
| 295_H | 334_D | 1.958 | 1.00 |
| 117_L | 214_L | 1.925 | 1.00 |
| 168_V | 171_P | 1.879 | 1.00 |
| 110_S | 211_F | 1.809 | 1.00 |
| 284_R | 287_T | 1.801 | 1.00 |
| 214_L | 333_L | 1.732 | 1.00 |
| 283_F | 287_T | 1.704 | 1.00 |
| 122_H | 208_L | 1.683 | 1.00 |
| 290_R | 293_E | 1.677 | 1.00 |
| 274_E | 278_Q | 1.663 | 1.00 |
| 174_W | 177_E | 1.659 | 1.00 |
| 181_L | 185_R | 1.633 | 1.00 |
| 132_E | 152_E | 1.629 | 1.00 |
| 185_R | 188_G | 1.619 | 1.00 |
| 108_A | 128_L | 1.603 | 1.00 |
| 181_L | 184_L | 1.597 | 1.00 |
| 182_R | 185_R | 1.582 | 1.00 |
| 187_A | 191_L | 1.532 | 0.99 |
| 126_L | 159_T | 1.520 | 0.99 |
| 105_Q | 320_A | 1.504 | 0.99 |
| 326_A | 330_Q | 1.500 | 0.99 |
| 102_E | 105_Q | 1.497 | 0.99 |
| 183_P | 186_D | 1.473 | 0.99 |
| 290_R | 294_L | 1.471 | 0.99 |
| 312_E | 315_F | 1.460 | 0.99 |
| 131_V | 152_E | 1.446 | 0.99 |
| 208_L | 252_F | 1.429 | 0.99 |
| 225_L | 250_L | 1.425 | 0.99 |
| 331_R | 335_F | 1.423 | 0.99 |
| 169_V | 172_A | 1.422 | 0.99 |
| 62_E | 66_G | 1.412 | 0.99 |
| 69_M | 72_L | 1.412 | 0.99 |
| 125_P | 160_R | 1.401 | 0.99 |
| 184_L | 191_L | 1.392 | 0.99 |
| 168_V | 175_R | 1.383 | 0.98 |
| 85_A | 93_A | 1.377 | 0.98 |
| 169_V | 176_S | 1.373 | 0.98 |
| 67_A | 71_A | 1.370 | 0.98 |
| 173_P | 177_E | 1.367 | 0.98 |
| 97_Y | 100_N | 1.357 | 0.98 |
| 173_P | 176_S | 1.349 | 0.98 |
| 302_A | 305_L | 1.346 | 0.98 |
| 174_W | 180_R | 1.337 | 0.98 |
| 192_A | 195_S | 1.323 | 0.98 |
| 228_L | 247_G | 1.318 | 0.98 |
| 240_S | 243_H | 1.308 | 0.98 |
| 286_R | 289_R | 1.307 | 0.98 |
| 171_P | 175_R | 1.306 | 0.97 |
| 37_G | 40_W | 1.305 | 0.97 |
| 184_L | 188_G | 1.292 | 0.97 |
| 226_F | 253_L | 1.289 | 0.97 |
| 215_T | 258_G | 1.287 | 0.97 |
| 176_S | 179_G | 1.273 | 0.97 |
| 68_R | 72_L | 1.271 | 0.97 |
| 234_V | 237_R | 1.271 | 0.97 |
| 188_G | 192_A | 1.268 | 0.97 |
| 285_E | 289_R | 1.264 | 0.97 |
| 68_R | 71_A | 1.255 | 0.97 |
| 308_Y | 313_P | 1.250 | 0.97 |
| 174_W | 179_G | 1.249 | 0.96 |
| 288_A | 292_L | 1.239 | 0.96 |
| 218_F | 257_A | 1.238 | 0.96 |
| 123_V | 211_F | 1.218 | 0.96 |
| 145_L | 148_A | 1.217 | 0.96 |
| 126_L | 157_S | 1.215 | 0.96 |
| 114_A | 122_H | 1.211 | 0.96 |
| 177_E | 180_R | 1.210 | 0.96 |
| 171_P | 174_W | 1.202 | 0.95 |
| 183_P | 191_L | 1.201 | 0.95 |
| 110_S | 215_T | 1.201 | 0.95 |
| 283_F | 290_R | 1.198 | 0.95 |
| 334_D | 338_K | 1.193 | 0.95 |
| 168_V | 172_A | 1.193 | 0.95 |
| 40_W | 50_P | 1.190 | 0.95 |
| 169_V | 174_W | 1.184 | 0.95 |
| 72_L | 86_R | 1.182 | 0.95 |
| 184_L | 187_A | 1.179 | 0.95 |
| 168_V | 180_R | 1.179 | 0.95 |
| 183_P | 188_G | 1.174 | 0.95 |
| 333_L | 337_A | 1.167 | 0.94 |
| 114_A | 211_F | 1.164 | 0.94 |
| 303_R | 306_R | 1.164 | 0.94 |
| 141_V | 145_L | 1.160 | 0.94 |
| 104_I | 128_L | 1.158 | 0.94 |
| 119_L | 207_D | 1.154 | 0.94 |
| 207_D | 290_R | 1.152 | 0.94 |
| 176_S | 180_R | 1.151 | 0.94 |
| 285_E | 292_L | 1.149 | 0.94 |
| 219_D | 254_D | 1.145 | 0.94 |
| 170_V | 174_W | 1.137 | 0.93 |
| 186_D | 189_G | 1.132 | 0.93 |
| 283_F | 295_H | 1.129 | 0.93 |
| 321_L | 326_A | 1.127 | 0.93 |
| 259_L | 321_L | 1.120 | 0.93 |
| 63_A | 66_G | 1.115 | 0.92 |
| 283_F | 288_A | 1.114 | 0.92 |
| 108_A | 112_Y | 1.107 | 0.92 |
| 284_R | 295_H | 1.106 | 0.92 |
| 272_Y | 276_L | 1.103 | 0.92 |
| 63_A | 67_A | 1.102 | 0.92 |
| 117_L | 287_T | 1.101 | 0.92 |
| 139_A | 142_Q | 1.097 | 0.92 |
| 187_A | 192_A | 1.090 | 0.91 |
| 334_D | 337_A | 1.082 | 0.91 |
| 119_L | 210_L | 1.079 | 0.91 |
| 207_D | 287_T | 1.079 | 0.91 |
| 273_N | 276_L | 1.078 | 0.91 |
| 35_H | 41_S | 1.076 | 0.90 |
| 63_A | 87_F | 1.073 | 0.90 |
| 223_S | 226_F | 1.071 | 0.90 |
| 188_G | 191_L | 1.069 | 0.90 |
| 291_V | 333_L | 1.069 | 0.90 |
| 78_G | 82_N | 1.067 | 0.90 |
| 306_R | 309_R | 1.054 | 0.89 |
| 117_L | 213_Y | 1.053 | 0.89 |
| 114_A | 123_V | 1.052 | 0.89 |
| 114_A | 126_L | 1.051 | 0.89 |
| 86_R | 92_R | 1.048 | 0.89 |
| 170_V | 175_R | 1.047 | 0.89 |
| 292_L | 337_A | 1.046 | 0.89 |
| 228_L | 251_V | 1.045 | 0.89 |
| 77_C | 82_N | 1.042 | 0.88 |
| 221_L | 224_N | 1.042 | 0.88 |
| 53_S | 56_Q | 1.040 | 0.88 |
| 93_A | 157_S | 1.038 | 0.88 |
| 40_W | 43_G | 1.038 | 0.88 |
| 217_N | 220_R | 1.034 | 0.88 |
| 300_A | 303_R | 1.031 | 0.88 |
| 169_V | 173_P | 1.027 | 0.88 |
| 180_R | 183_P | 1.026 | 0.87 |
| 170_V | 173_P | 1.023 | 0.87 |
| 233_R | 236_Q | 1.022 | 0.87 |
| 84_L | 92_R | 1.022 | 0.87 |
| 174_W | 178_D | 1.022 | 0.87 |
| 289_R | 292_L | 1.017 | 0.87 |
| 114_A | 120_Q | 1.017 | 0.87 |
| 100_N | 322_A | 1.014 | 0.87 |
| 34_V | 38_V | 1.013 | 0.87 |
| 112_Y | 316_P | 1.013 | 0.87 |
| 55_A | 59_A | 1.007 | 0.86 |
| 44_L | 47_Q | 1.006 | 0.86 |
| 172_A | 175_R | 1.002 | 0.86 |
| 280_V | 283_F | 1.002 | 0.86 |
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 | |
| 4kqaA | 4 | 0.9292 | 100 | 0.28 | Contact Map |
| 4hneA | 2 | 0.8612 | 100 | 0.596 | Contact Map |
| 4wtvA | 2 | 0 | 99.9 | 0.663 | Contact Map |
| 3akjA | 2 | 0.6771 | 99.5 | 0.798 | Contact Map |
| 1cjaA | 2 | 0.7875 | 99.4 | 0.808 | Contact Map |
| 4pu5A | 1 | 0.8952 | 98.8 | 0.852 | Contact Map |
| 3tpdA | 1 | 0.8187 | 98.8 | 0.853 | Contact Map |
| 4yknA | 1 | 0 | 92.3 | 0.929 | Contact Map |
| 1e7uA | 1 | 0.8187 | 92 | 0.929 | Contact Map |
| 4bfrA | 2 | 0.8159 | 91.1 | 0.931 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)