| T0764 |
| ID: | 1400706461 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 341 (335) | ||
| Sequences: | 379 (292.4) | ||
| Seq/Len: | 1.131 | ||
| Nf(neff/√len): | 16.0 |
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: 1.131).
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 |
| 83_T | 87_R | 3.640 | 1.00 |
| 192_T | 200_G | 3.294 | 1.00 |
| 77_S | 103_L | 3.218 | 1.00 |
| 34_V | 181_L | 2.966 | 1.00 |
| 147_Q | 322_L | 2.883 | 1.00 |
| 104_V | 178_Y | 2.511 | 0.99 |
| 305_H | 308_E | 2.457 | 0.99 |
| 77_S | 111_N | 2.325 | 0.99 |
| 300_D | 338_K | 2.316 | 0.99 |
| 69_F | 191_I | 2.301 | 0.99 |
| 266_D | 269_P | 2.299 | 0.99 |
| 29_Q | 57_Q | 2.298 | 0.99 |
| 76_F | 163_T | 2.274 | 0.99 |
| 109_R | 195_Q | 2.166 | 0.98 |
| 182_F | 188_G | 2.099 | 0.98 |
| 47_F | 123_P | 2.001 | 0.96 |
| 216_Y | 331_L | 1.973 | 0.96 |
| 94_F | 328_A | 1.898 | 0.95 |
| 30_G | 56_Y | 1.847 | 0.94 |
| 294_L | 301_V | 1.825 | 0.93 |
| 73_V | 195_Q | 1.814 | 0.93 |
| 99_F | 332_S | 1.782 | 0.92 |
| 183_D | 206_K | 1.724 | 0.90 |
| 67_L | 191_I | 1.713 | 0.90 |
| 145_G | 267_N | 1.708 | 0.90 |
| 31_S | 81_E | 1.700 | 0.90 |
| 201_W | 215_S | 1.699 | 0.89 |
| 53_Y | 111_N | 1.696 | 0.89 |
| 291_A | 301_V | 1.673 | 0.89 |
| 179_A | 207_T | 1.656 | 0.88 |
| 93_I | 328_A | 1.653 | 0.88 |
| 263_Y | 304_I | 1.640 | 0.87 |
| 314_N | 323_N | 1.636 | 0.87 |
| 106_Q | 109_R | 1.607 | 0.86 |
| 68_V | 185_I | 1.565 | 0.84 |
| 53_Y | 81_E | 1.501 | 0.80 |
| 63_R | 99_F | 1.480 | 0.79 |
| 73_V | 165_T | 1.470 | 0.78 |
| 52_A | 112_A | 1.462 | 0.77 |
| 149_K | 154_T | 1.440 | 0.76 |
| 189_V | 212_A | 1.414 | 0.74 |
| 275_P | 291_A | 1.414 | 0.74 |
| 318_P | 327_V | 1.411 | 0.74 |
| 165_T | 195_Q | 1.401 | 0.73 |
| 37_T | 50_D | 1.400 | 0.73 |
| 58_K | 100_C | 1.387 | 0.72 |
| 315_T | 321_D | 1.385 | 0.72 |
| 153_E | 156_D | 1.378 | 0.71 |
| 214_A | 335_L | 1.371 | 0.71 |
| 93_I | 325_I | 1.350 | 0.69 |
| 311_L | 327_V | 1.342 | 0.68 |
| 216_Y | 318_P | 1.341 | 0.68 |
| 10_I | 13_L | 1.339 | 0.68 |
| 83_T | 324_N | 1.327 | 0.67 |
| 197_G | 218_P | 1.326 | 0.67 |
| 70_A | 196_G | 1.308 | 0.66 |
| 233_A | 242_M | 1.304 | 0.65 |
| 191_I | 331_L | 1.303 | 0.65 |
| 31_S | 53_Y | 1.298 | 0.65 |
| 146_V | 315_T | 1.278 | 0.63 |
| 13_L | 16_C | 1.277 | 0.63 |
| 153_E | 191_I | 1.277 | 0.63 |
| 76_F | 111_N | 1.275 | 0.63 |
| 251_V | 254_E | 1.272 | 0.62 |
| 184_K | 326_E | 1.265 | 0.62 |
| 75_Q | 109_R | 1.258 | 0.61 |
| 80_W | 162_M | 1.257 | 0.61 |
| 69_F | 94_F | 1.256 | 0.61 |
| 76_F | 79_T | 1.255 | 0.61 |
| 182_F | 209_N | 1.248 | 0.60 |
| 291_A | 303_V | 1.245 | 0.60 |
| 80_W | 327_V | 1.244 | 0.60 |
| 70_A | 178_Y | 1.244 | 0.60 |
| 14_V | 17_K | 1.244 | 0.60 |
| 55_F | 91_Q | 1.241 | 0.60 |
| 196_G | 325_I | 1.241 | 0.60 |
| 113_G | 324_N | 1.238 | 0.59 |
| 222_V | 244_G | 1.222 | 0.58 |
| 21_E | 69_F | 1.218 | 0.57 |
| 114_R | 139_W | 1.213 | 0.57 |
| 187_P | 209_N | 1.207 | 0.56 |
| 34_V | 185_I | 1.200 | 0.56 |
| 238_L | 241_K | 1.199 | 0.56 |
| 200_G | 215_S | 1.195 | 0.55 |
| 182_F | 187_P | 1.195 | 0.55 |
| 26_V | 57_Q | 1.194 | 0.55 |
| 106_Q | 195_Q | 1.190 | 0.55 |
| 192_T | 201_W | 1.186 | 0.54 |
| 192_T | 213_I | 1.171 | 0.53 |
| 47_F | 127_E | 1.170 | 0.53 |
| 88_E | 96_R | 1.162 | 0.52 |
| 266_D | 271_T | 1.160 | 0.52 |
| 68_V | 188_G | 1.159 | 0.52 |
| 106_Q | 200_G | 1.153 | 0.51 |
| 223_P | 294_L | 1.152 | 0.51 |
| 54_V | 112_A | 1.144 | 0.50 |
| 158_Y | 193_H | 1.141 | 0.50 |
| 29_Q | 55_F | 1.137 | 0.50 |
| 184_K | 211_K | 1.131 | 0.49 |
| 149_K | 334_W | 1.124 | 0.48 |
| 68_V | 104_V | 1.098 | 0.46 |
| 293_M | 296_D | 1.097 | 0.46 |
| 10_I | 14_V | 1.096 | 0.46 |
| 69_F | 103_L | 1.096 | 0.46 |
| 24_L | 96_R | 1.096 | 0.46 |
| 279_E | 294_L | 1.093 | 0.45 |
| 75_Q | 106_Q | 1.086 | 0.45 |
| 201_W | 218_P | 1.085 | 0.45 |
| 134_F | 161_Q | 1.083 | 0.45 |
| 201_W | 213_I | 1.069 | 0.43 |
| 234_K | 242_M | 1.067 | 0.43 |
| 114_R | 126_D | 1.064 | 0.43 |
| 281_T | 287_M | 1.058 | 0.42 |
| 182_F | 320_S | 1.054 | 0.42 |
| 97_R | 332_S | 1.051 | 0.42 |
| 69_F | 101_V | 1.050 | 0.41 |
| 276_E | 279_E | 1.043 | 0.41 |
| 223_P | 286_L | 1.043 | 0.41 |
| 55_F | 81_E | 1.042 | 0.41 |
| 126_D | 130_W | 1.042 | 0.41 |
| 67_L | 79_T | 1.041 | 0.41 |
| 87_R | 324_N | 1.038 | 0.40 |
| 9_I | 16_C | 1.038 | 0.40 |
| 135_R | 280_W | 1.034 | 0.40 |
| 303_V | 319_M | 1.033 | 0.40 |
| 325_I | 329_D | 1.032 | 0.40 |
| 221_A | 242_M | 1.024 | 0.39 |
| 77_S | 81_E | 1.023 | 0.39 |
| 87_R | 307_P | 1.021 | 0.39 |
| 279_E | 283_R | 1.021 | 0.39 |
| 159_F | 162_M | 1.020 | 0.39 |
| 15_G | 19_R | 1.018 | 0.38 |
| 71_H | 80_W | 1.017 | 0.38 |
| 181_L | 185_I | 1.017 | 0.38 |
| 284_L | 305_H | 1.015 | 0.38 |
| 10_I | 16_C | 1.015 | 0.38 |
| 259_P | 265_G | 1.014 | 0.38 |
| 32_F | 102_Y | 1.013 | 0.38 |
| 9_I | 15_G | 1.006 | 0.37 |
| 107_P | 201_W | 1.005 | 0.37 |
| 83_T | 175_S | 1.001 | 0.37 |
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 | |
| 1qlwA | 2 | 0.8534 | 100 | 0.579 | Contact Map |
| 2rauA | 1 | 0.7537 | 99.7 | 0.853 | Contact Map |
| 3i1iA | 2 | 0.7654 | 99.7 | 0.854 | Contact Map |
| 2hdwA | 2 | 0.7185 | 99.7 | 0.855 | Contact Map |
| 3visA | 2 | 0.6481 | 99.7 | 0.855 | Contact Map |
| 2zyrA | 2 | 0.5953 | 99.7 | 0.855 | Contact Map |
| 3bdiA | 1 | 0.5982 | 99.7 | 0.857 | Contact Map |
| 3vdxA | 3 | 0.654 | 99.7 | 0.858 | Contact Map |
| 1k8qA | 2 | 0.7742 | 99.7 | 0.858 | Contact Map |
| 2z3zA | 1 | 0.7713 | 99.7 | 0.858 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)