| T0848 -force run |
| ID: | 1404967707 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 354 (351) | ||
| Sequences: | 52 (47.4) | ||
| Seq/Len: | 0.148 | ||
| Nf(neff/√len): | 2.5 |
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: 0.148).
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 |
| 276_L | 327_M | 2.106 | 0.58 |
| 80_K | 85_V | 1.866 | 0.45 |
| 50_V | 71_V | 1.846 | 0.44 |
| 47_I | 173_D | 1.782 | 0.40 |
| 20_A | 109_E | 1.708 | 0.36 |
| 177_A | 189_K | 1.693 | 0.35 |
| 345_A | 351_F | 1.679 | 0.35 |
| 123_E | 346_E | 1.531 | 0.28 |
| 176_K | 283_K | 1.527 | 0.27 |
| 263_I | 282_D | 1.519 | 0.27 |
| 93_Y | 120_K | 1.512 | 0.27 |
| 347_L | 351_F | 1.475 | 0.25 |
| 39_S | 174_S | 1.463 | 0.25 |
| 126_L | 341_D | 1.437 | 0.24 |
| 346_E | 351_F | 1.436 | 0.24 |
| 132_K | 247_N | 1.434 | 0.24 |
| 5_K | 29_A | 1.434 | 0.24 |
| 126_L | 179_S | 1.427 | 0.23 |
| 113_G | 153_V | 1.407 | 0.22 |
| 80_K | 146_G | 1.383 | 0.22 |
| 39_S | 180_A | 1.378 | 0.21 |
| 247_N | 316_P | 1.372 | 0.21 |
| 4_K | 198_T | 1.366 | 0.21 |
| 69_L | 93_Y | 1.355 | 0.20 |
| 71_V | 252_A | 1.355 | 0.20 |
| 81_D | 311_F | 1.339 | 0.20 |
| 121_S | 304_L | 1.312 | 0.19 |
| 348_V | 351_F | 1.310 | 0.19 |
| 271_V | 301_K | 1.293 | 0.18 |
| 51_S | 200_A | 1.276 | 0.18 |
| 177_A | 180_A | 1.271 | 0.18 |
| 23_S | 207_N | 1.267 | 0.17 |
| 98_K | 140_Y | 1.267 | 0.17 |
| 45_V | 72_N | 1.267 | 0.17 |
| 232_A | 272_D | 1.265 | 0.17 |
| 175_A | 178_L | 1.264 | 0.17 |
| 190_D | 198_T | 1.260 | 0.17 |
| 267_T | 315_G | 1.256 | 0.17 |
| 116_I | 311_F | 1.255 | 0.17 |
| 217_Y | 316_P | 1.253 | 0.17 |
| 83_L | 325_V | 1.239 | 0.17 |
| 94_Q | 334_Q | 1.235 | 0.16 |
| 326_K | 351_F | 1.229 | 0.16 |
| 176_K | 192_A | 1.229 | 0.16 |
| 79_G | 267_T | 1.228 | 0.16 |
| 46_K | 123_E | 1.228 | 0.16 |
| 229_D | 300_V | 1.227 | 0.16 |
| 215_D | 309_E | 1.226 | 0.16 |
| 21_A | 324_E | 1.224 | 0.16 |
| 135_Q | 158_D | 1.223 | 0.16 |
| 97_T | 273_A | 1.220 | 0.16 |
| 80_K | 188_G | 1.220 | 0.16 |
| 11_L | 196_K | 1.217 | 0.16 |
| 151_K | 209_F | 1.210 | 0.16 |
| 207_N | 301_K | 1.206 | 0.16 |
| 137_E | 156_K | 1.204 | 0.16 |
| 68_V | 334_Q | 1.201 | 0.15 |
| 23_S | 126_L | 1.200 | 0.15 |
| 284_V | 337_L | 1.195 | 0.15 |
| 45_V | 193_D | 1.194 | 0.15 |
| 71_V | 297_E | 1.194 | 0.15 |
| 32_K | 209_F | 1.193 | 0.15 |
| 265_E | 269_K | 1.193 | 0.15 |
| 50_V | 268_V | 1.189 | 0.15 |
| 50_V | 252_A | 1.187 | 0.15 |
| 157_I | 247_N | 1.186 | 0.15 |
| 68_V | 217_Y | 1.186 | 0.15 |
| 47_I | 126_L | 1.184 | 0.15 |
| 16_M | 116_I | 1.178 | 0.15 |
| 185_L | 244_L | 1.172 | 0.15 |
| 65_D | 114_S | 1.169 | 0.15 |
| 50_V | 162_K | 1.164 | 0.14 |
| 118_A | 202_K | 1.161 | 0.14 |
| 92_L | 262_A | 1.160 | 0.14 |
| 145_Y | 309_E | 1.156 | 0.14 |
| 229_D | 235_N | 1.150 | 0.14 |
| 118_A | 125_N | 1.149 | 0.14 |
| 96_D | 121_S | 1.148 | 0.14 |
| 71_V | 268_V | 1.145 | 0.14 |
| 83_L | 138_L | 1.144 | 0.14 |
| 89_D | 156_K | 1.142 | 0.14 |
| 38_K | 43_A | 1.140 | 0.14 |
| 227_Y | 230_S | 1.138 | 0.14 |
| 92_L | 96_D | 1.137 | 0.14 |
| 79_G | 99_M | 1.135 | 0.14 |
| 89_D | 296_Y | 1.134 | 0.14 |
| 42_I | 128_F | 1.134 | 0.14 |
| 47_I | 109_E | 1.134 | 0.14 |
| 96_D | 126_L | 1.133 | 0.14 |
| 169_D | 299_A | 1.130 | 0.14 |
| 88_M | 116_I | 1.130 | 0.14 |
| 4_K | 196_K | 1.130 | 0.14 |
| 99_M | 276_L | 1.129 | 0.13 |
| 98_K | 329_K | 1.127 | 0.13 |
| 53_T | 179_S | 1.127 | 0.13 |
| 243_G | 271_V | 1.124 | 0.13 |
| 14_L | 17_M | 1.119 | 0.13 |
| 43_A | 325_V | 1.118 | 0.13 |
| 167_T | 268_V | 1.116 | 0.13 |
| 197_I | 318_S | 1.114 | 0.13 |
| 124_G | 199_G | 1.111 | 0.13 |
| 106_D | 138_L | 1.107 | 0.13 |
| 148_K | 349_E | 1.105 | 0.13 |
| 265_E | 322_T | 1.105 | 0.13 |
| 75_V | 125_N | 1.104 | 0.13 |
| 53_T | 126_L | 1.103 | 0.13 |
| 61_S | 172_Q | 1.102 | 0.13 |
| 26_K | 33_E | 1.101 | 0.13 |
| 96_D | 211_E | 1.100 | 0.13 |
| 50_V | 280_I | 1.100 | 0.13 |
| 14_L | 235_N | 1.099 | 0.13 |
| 9_V | 271_V | 1.094 | 0.13 |
| 100_S | 250_I | 1.093 | 0.13 |
| 173_D | 231_K | 1.092 | 0.13 |
| 271_V | 324_E | 1.091 | 0.13 |
| 69_L | 76_K | 1.090 | 0.12 |
| 70_K | 117_N | 1.089 | 0.12 |
| 39_S | 47_I | 1.089 | 0.12 |
| 73_V | 256_S | 1.089 | 0.12 |
| 327_M | 342_Y | 1.088 | 0.12 |
| 121_S | 158_D | 1.088 | 0.12 |
| 21_A | 151_K | 1.085 | 0.12 |
| 127_F | 177_A | 1.078 | 0.12 |
| 51_S | 116_I | 1.078 | 0.12 |
| 71_V | 162_K | 1.077 | 0.12 |
| 38_K | 324_E | 1.076 | 0.12 |
| 249_S | 255_T | 1.075 | 0.12 |
| 146_G | 198_T | 1.075 | 0.12 |
| 171_L | 178_L | 1.074 | 0.12 |
| 128_F | 202_K | 1.074 | 0.12 |
| 128_F | 162_K | 1.072 | 0.12 |
| 133_G | 152_S | 1.071 | 0.12 |
| 101_D | 298_E | 1.071 | 0.12 |
| 154_T | 172_Q | 1.069 | 0.12 |
| 125_N | 248_S | 1.069 | 0.12 |
| 128_F | 219_S | 1.068 | 0.12 |
| 47_I | 107_Y | 1.067 | 0.12 |
| 244_L | 259_K | 1.067 | 0.12 |
| 98_K | 120_K | 1.062 | 0.12 |
| 190_D | 208_D | 1.061 | 0.12 |
| 50_V | 117_N | 1.058 | 0.12 |
| 182_V | 302_Y | 1.057 | 0.12 |
| 119_D | 147_D | 1.055 | 0.12 |
| 176_K | 188_G | 1.055 | 0.12 |
| 146_G | 338_D | 1.054 | 0.12 |
| 47_I | 152_S | 1.050 | 0.12 |
| 183_D | 191_N | 1.049 | 0.12 |
| 128_F | 283_K | 1.048 | 0.12 |
| 236_I | 316_P | 1.046 | 0.11 |
| 43_A | 140_Y | 1.046 | 0.11 |
| 171_L | 177_A | 1.046 | 0.11 |
| 41_D | 264_V | 1.046 | 0.11 |
| 14_L | 293_S | 1.043 | 0.11 |
| 30_E | 37_E | 1.043 | 0.11 |
| 72_N | 134_K | 1.043 | 0.11 |
| 154_T | 249_S | 1.041 | 0.11 |
| 171_L | 174_S | 1.040 | 0.11 |
| 81_D | 146_G | 1.039 | 0.11 |
| 41_D | 87_S | 1.039 | 0.11 |
| 116_I | 250_I | 1.038 | 0.11 |
| 177_A | 259_K | 1.036 | 0.11 |
| 41_D | 86_D | 1.035 | 0.11 |
| 90_F | 116_I | 1.034 | 0.11 |
| 308_P | 311_F | 1.033 | 0.11 |
| 269_K | 322_T | 1.033 | 0.11 |
| 180_A | 265_E | 1.031 | 0.11 |
| 229_D | 302_Y | 1.030 | 0.11 |
| 93_Y | 137_E | 1.029 | 0.11 |
| 148_K | 267_T | 1.027 | 0.11 |
| 64_D | 309_E | 1.027 | 0.11 |
| 73_V | 327_M | 1.027 | 0.11 |
| 123_E | 199_G | 1.027 | 0.11 |
| 255_T | 324_E | 1.026 | 0.11 |
| 162_K | 254_T | 1.025 | 0.11 |
| 294_A | 305_Q | 1.024 | 0.11 |
| 342_Y | 351_F | 1.024 | 0.11 |
| 187_F | 247_N | 1.023 | 0.11 |
| 43_A | 83_L | 1.022 | 0.11 |
| 284_V | 287_Y | 1.022 | 0.11 |
| 162_K | 333_D | 1.020 | 0.11 |
| 126_L | 152_S | 1.020 | 0.11 |
| 49_D | 56_S | 1.019 | 0.11 |
| 291_N | 323_V | 1.014 | 0.11 |
| 242_E | 283_K | 1.012 | 0.11 |
| 20_A | 193_D | 1.012 | 0.11 |
| 71_V | 259_K | 1.012 | 0.11 |
| 236_I | 245_S | 1.012 | 0.11 |
| 325_V | 340_D | 1.012 | 0.11 |
| 87_S | 264_V | 1.011 | 0.11 |
| 67_L | 349_E | 1.009 | 0.11 |
| 318_S | 323_V | 1.008 | 0.11 |
| 32_K | 151_K | 1.006 | 0.11 |
| 67_L | 122_V | 1.004 | 0.11 |
| 93_Y | 140_Y | 1.004 | 0.11 |
| 325_V | 333_D | 1.002 | 0.11 |
| 75_V | 287_Y | 1.002 | 0.11 |
| 67_L | 133_G | 1.001 | 0.10 |
| 97_T | 240_I | 1.001 | 0.10 |
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 | |
| 3cfuA | 2 | 0.3644 | 99.5 | 0.855 | Contact Map |
| 4lesA | 1 | 0.3249 | 98.9 | 0.886 | Contact Map |
| 2llgA | 1 | 0.3672 | 96.5 | 0.934 | Contact Map |
| 3qfgA | 2 | 0.3418 | 96.3 | 0.935 | Contact Map |
| 3o0lA | 2 | 0.3107 | 78.3 | 0.957 | Contact Map |
| 2x3cA | 1 | 0.5763 | 78.1 | 0.957 | Contact Map |
| 3zbiC | 14 | 0.0763 | 77 | 0.957 | Contact Map |
| 3nrfA | 2 | 0.2853 | 67.6 | 0.96 | Contact Map |
| 3isyA | 1 | 0.2938 | 66.6 | 0.961 | Contact Map |
| 4eaeA | 2 | 0.4294 | 46.6 | 0.965 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)