| radfl_jack |
| ID: | 1508962952 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 409 (392) | ||
| Sequences: | 1007 (892.5) | ||
| Seq/Len: | 2.569 | ||
| Nf(neff/√len): | 45.1 |
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: 2.569).
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 |
| 193_V | 226_H | 3.235 | 1.00 |
| 186_K | 220_Q | 3.107 | 1.00 |
| 138_I | 217_I | 3.104 | 1.00 |
| 193_V | 202_F | 2.594 | 1.00 |
| 211_A | 236_M | 2.567 | 1.00 |
| 148_Y | 207_F | 2.441 | 1.00 |
| 193_V | 224_L | 2.367 | 1.00 |
| 196_Q | 202_F | 2.227 | 1.00 |
| 137_L | 205_G | 2.153 | 1.00 |
| 147_T | 207_F | 2.092 | 1.00 |
| 190_D | 224_L | 1.998 | 0.99 |
| 182_P | 220_Q | 1.978 | 0.99 |
| 151_L | 400_M | 1.885 | 0.99 |
| 216_E | 219_R | 1.884 | 0.99 |
| 140_D | 207_F | 1.866 | 0.99 |
| 134_P | 160_T | 1.865 | 0.99 |
| 136_Y | 202_F | 1.845 | 0.99 |
| 234_I | 387_L | 1.771 | 0.98 |
| 139_A | 207_F | 1.717 | 0.98 |
| 189_V | 217_I | 1.697 | 0.98 |
| 189_V | 193_V | 1.694 | 0.98 |
| 216_E | 220_Q | 1.690 | 0.98 |
| 198_Q | 226_H | 1.683 | 0.97 |
| 139_A | 188_I | 1.661 | 0.97 |
| 94_Q | 97_A | 1.641 | 0.97 |
| 203_W | 230_S | 1.637 | 0.97 |
| 202_F | 226_H | 1.620 | 0.97 |
| 203_W | 229_D | 1.614 | 0.97 |
| 98_P | 101_P | 1.609 | 0.96 |
| 185_A | 216_E | 1.593 | 0.96 |
| 199_G | 202_F | 1.575 | 0.96 |
| 383_D | 386_E | 1.568 | 0.96 |
| 134_P | 199_G | 1.565 | 0.96 |
| 180_G | 183_G | 1.544 | 0.95 |
| 27_F | 37_I | 1.541 | 0.95 |
| 232_L | 400_M | 1.529 | 0.95 |
| 219_R | 223_A | 1.522 | 0.95 |
| 98_P | 102_R | 1.505 | 0.94 |
| 107_G | 111_A | 1.501 | 0.94 |
| 93_K | 98_P | 1.500 | 0.94 |
| 85_V | 89_S | 1.493 | 0.94 |
| 109_E | 112_V | 1.489 | 0.94 |
| 134_P | 162_Y | 1.475 | 0.94 |
| 89_S | 93_K | 1.470 | 0.93 |
| 97_A | 102_R | 1.438 | 0.92 |
| 208_S | 235_D | 1.435 | 0.92 |
| 135_F | 203_W | 1.411 | 0.91 |
| 31_Y | 40_A | 1.409 | 0.91 |
| 196_Q | 199_G | 1.405 | 0.91 |
| 87_T | 93_K | 1.400 | 0.91 |
| 140_D | 148_Y | 1.395 | 0.91 |
| 92_T | 95_R | 1.389 | 0.91 |
| 85_V | 88_G | 1.381 | 0.90 |
| 258_A | 262_N | 1.377 | 0.90 |
| 136_Y | 199_G | 1.377 | 0.90 |
| 143_G | 151_L | 1.375 | 0.90 |
| 86_V | 89_S | 1.374 | 0.90 |
| 26_M | 30_E | 1.374 | 0.90 |
| 166_S | 188_I | 1.370 | 0.90 |
| 141_G | 237_C | 1.358 | 0.89 |
| 86_V | 90_I | 1.355 | 0.89 |
| 108_P | 111_A | 1.344 | 0.89 |
| 220_Q | 223_A | 1.341 | 0.88 |
| 311_K | 383_D | 1.339 | 0.88 |
| 71_V | 74_V | 1.323 | 0.87 |
| 209_G | 213_I | 1.320 | 0.87 |
| 16_P | 22_Q | 1.311 | 0.87 |
| 382_A | 392_F | 1.304 | 0.86 |
| 185_A | 220_Q | 1.302 | 0.86 |
| 94_Q | 98_P | 1.298 | 0.86 |
| 192_L | 217_I | 1.290 | 0.86 |
| 136_Y | 195_R | 1.286 | 0.85 |
| 108_P | 112_V | 1.280 | 0.85 |
| 71_V | 75_P | 1.279 | 0.85 |
| 233_L | 236_M | 1.277 | 0.85 |
| 11_S | 15_V | 1.275 | 0.85 |
| 87_T | 91_T | 1.270 | 0.84 |
| 99_Q | 102_R | 1.269 | 0.84 |
| 185_A | 217_I | 1.269 | 0.84 |
| 90_I | 95_R | 1.268 | 0.84 |
| 85_V | 90_I | 1.266 | 0.84 |
| 86_V | 98_P | 1.261 | 0.84 |
| 82_L | 85_V | 1.261 | 0.84 |
| 158_K | 401_D | 1.260 | 0.84 |
| 60_D | 64_D | 1.259 | 0.84 |
| 88_G | 92_T | 1.241 | 0.83 |
| 320_S | 323_F | 1.240 | 0.82 |
| 90_I | 93_K | 1.234 | 0.82 |
| 191_E | 194_K | 1.228 | 0.82 |
| 79_S | 84_A | 1.227 | 0.82 |
| 197_P | 226_H | 1.226 | 0.81 |
| 167_P | 184_I | 1.225 | 0.81 |
| 107_G | 110_P | 1.224 | 0.81 |
| 168_Y | 175_L | 1.221 | 0.81 |
| 363_P | 367_D | 1.221 | 0.81 |
| 135_F | 161_I | 1.218 | 0.81 |
| 142_T | 207_F | 1.211 | 0.80 |
| 110_P | 113_R | 1.210 | 0.80 |
| 142_T | 239_P | 1.205 | 0.80 |
| 102_R | 105_G | 1.205 | 0.80 |
| 134_P | 159_M | 1.204 | 0.80 |
| 197_P | 202_F | 1.200 | 0.80 |
| 159_M | 401_D | 1.198 | 0.79 |
| 82_L | 87_T | 1.197 | 0.79 |
| 212_M | 285_V | 1.196 | 0.79 |
| 93_K | 102_R | 1.193 | 0.79 |
| 59_Y | 63_E | 1.190 | 0.79 |
| 82_L | 86_V | 1.186 | 0.78 |
| 24_T | 27_F | 1.181 | 0.78 |
| 24_T | 37_I | 1.180 | 0.78 |
| 136_Y | 196_Q | 1.176 | 0.78 |
| 102_R | 106_D | 1.171 | 0.77 |
| 90_I | 98_P | 1.170 | 0.77 |
| 130_A | 160_T | 1.170 | 0.77 |
| 83_E | 87_T | 1.165 | 0.77 |
| 83_E | 86_V | 1.162 | 0.76 |
| 196_Q | 201_P | 1.159 | 0.76 |
| 89_S | 95_R | 1.156 | 0.76 |
| 71_V | 76_S | 1.155 | 0.76 |
| 156_N | 401_D | 1.152 | 0.76 |
| 98_P | 103_S | 1.151 | 0.75 |
| 91_T | 95_R | 1.147 | 0.75 |
| 255_M | 258_A | 1.144 | 0.75 |
| 393_V | 397_G | 1.141 | 0.75 |
| 86_V | 93_K | 1.139 | 0.74 |
| 259_I | 262_N | 1.138 | 0.74 |
| 98_P | 105_G | 1.135 | 0.74 |
| 139_A | 145_I | 1.135 | 0.74 |
| 90_I | 94_Q | 1.133 | 0.74 |
| 208_S | 384_H | 1.132 | 0.74 |
| 85_V | 94_Q | 1.131 | 0.74 |
| 345_K | 348_P | 1.126 | 0.73 |
| 79_S | 82_L | 1.122 | 0.73 |
| 212_M | 239_P | 1.120 | 0.73 |
| 11_S | 14_L | 1.117 | 0.72 |
| 93_K | 99_Q | 1.117 | 0.72 |
| 94_Q | 102_R | 1.116 | 0.72 |
| 70_A | 73_H | 1.116 | 0.72 |
| 139_A | 184_I | 1.115 | 0.72 |
| 114_F | 119_G | 1.114 | 0.72 |
| 92_T | 97_A | 1.113 | 0.72 |
| 96_D | 100_Q | 1.111 | 0.72 |
| 87_T | 90_I | 1.107 | 0.71 |
| 136_Y | 145_I | 1.099 | 0.71 |
| 218_A | 231_L | 1.095 | 0.70 |
| 381_E | 395_L | 1.095 | 0.70 |
| 81_S | 85_V | 1.093 | 0.70 |
| 89_S | 99_Q | 1.090 | 0.70 |
| 331_G | 334_T | 1.089 | 0.70 |
| 227_V | 295_K | 1.081 | 0.69 |
| 139_A | 211_A | 1.081 | 0.69 |
| 199_G | 226_H | 1.079 | 0.69 |
| 13_G | 22_Q | 1.076 | 0.68 |
| 101_P | 104_I | 1.073 | 0.68 |
| 93_K | 101_P | 1.072 | 0.68 |
| 41_F | 148_Y | 1.071 | 0.68 |
| 57_E | 61_L | 1.069 | 0.67 |
| 98_P | 108_P | 1.067 | 0.67 |
| 85_V | 93_K | 1.066 | 0.67 |
| 217_I | 220_Q | 1.063 | 0.67 |
| 215_Y | 219_R | 1.057 | 0.66 |
| 348_P | 351_W | 1.056 | 0.66 |
| 91_T | 96_D | 1.049 | 0.65 |
| 142_T | 237_C | 1.045 | 0.65 |
| 89_S | 97_A | 1.045 | 0.65 |
| 296_G | 299_P | 1.044 | 0.65 |
| 230_S | 404_F | 1.043 | 0.65 |
| 80_T | 84_A | 1.042 | 0.65 |
| 330_R | 333_V | 1.042 | 0.65 |
| 134_P | 139_A | 1.040 | 0.64 |
| 248_D | 252_G | 1.039 | 0.64 |
| 97_A | 100_Q | 1.036 | 0.64 |
| 78_S | 83_E | 1.035 | 0.64 |
| 82_L | 101_P | 1.034 | 0.64 |
| 202_F | 228_I | 1.033 | 0.64 |
| 86_V | 92_T | 1.032 | 0.64 |
| 80_T | 85_V | 1.030 | 0.63 |
| 126_Q | 129_Q | 1.030 | 0.63 |
| 69_E | 72_V | 1.029 | 0.63 |
| 141_G | 184_I | 1.027 | 0.63 |
| 94_Q | 100_Q | 1.025 | 0.63 |
| 152_P | 234_I | 1.024 | 0.63 |
| 88_G | 94_Q | 1.021 | 0.62 |
| 32_P | 285_V | 1.018 | 0.62 |
| 80_T | 86_V | 1.016 | 0.62 |
| 84_A | 91_T | 1.015 | 0.62 |
| 84_A | 88_G | 1.012 | 0.61 |
| 88_G | 91_T | 1.012 | 0.61 |
| 364_N | 367_D | 1.006 | 0.61 |
| 70_A | 74_V | 1.005 | 0.60 |
| 181_I | 185_A | 1.004 | 0.60 |
| 81_S | 84_A | 1.004 | 0.60 |
| 90_I | 96_D | 1.003 | 0.60 |
| 84_A | 90_I | 1.001 | 0.60 |
| 98_P | 106_D | 1.000 | 0.60 |
| 146_A | 163_G | 1.000 | 0.60 |
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 | |
| 2vz8A | 2 | 0 | 100 | 0.462 | Contact Map |
| 3tejA | 2 | 0.6944 | 100 | 0.6 | Contact Map |
| 2cb9A | 1 | 0.511 | 100 | 0.62 | Contact Map |
| 1jmkC | 2 | 0.5575 | 100 | 0.638 | Contact Map |
| 2vsqA | 1 | 0.6235 | 100 | 0.642 | Contact Map |
| 1kezA | 3 | 0.6455 | 100 | 0.643 | Contact Map |
| 3ilsA | 1 | 0.6259 | 100 | 0.648 | Contact Map |
| 2k2qB | 1 | 0.577 | 99.9 | 0.676 | Contact Map |
| 2px6A | 2 | 0.6112 | 99.9 | 0.691 | Contact Map |
| 3lcrA | 2 | 0.665 | 99.9 | 0.702 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)