| T0808 40-330 -force run |
| ID: | 1405184637 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 291 (290) | ||
| Sequences: | 84 (72.7) | ||
| Seq/Len: | 0.290 | ||
| Nf(neff/√len): | 4.3 |
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: 0.290).
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 |
| 22_F | 78_I | 2.275 | 0.84 |
| 135_W | 251_Y | 2.069 | 0.76 |
| 176_L | 219_Q | 2.047 | 0.75 |
| 151_S | 206_V | 1.915 | 0.67 |
| 181_S | 216_S | 1.910 | 0.67 |
| 200_L | 266_F | 1.857 | 0.64 |
| 134_E | 237_Q | 1.847 | 0.63 |
| 187_N | 190_E | 1.826 | 0.62 |
| 222_L | 263_I | 1.801 | 0.60 |
| 135_W | 277_R | 1.777 | 0.59 |
| 238_I | 275_Y | 1.767 | 0.58 |
| 236_M | 250_A | 1.707 | 0.54 |
| 136_F | 278_P | 1.681 | 0.53 |
| 213_N | 262_L | 1.549 | 0.44 |
| 230_N | 254_A | 1.525 | 0.42 |
| 209_G | 213_N | 1.523 | 0.42 |
| 80_L | 261_K | 1.482 | 0.40 |
| 28_T | 100_N | 1.421 | 0.36 |
| 181_S | 188_P | 1.418 | 0.36 |
| 251_Y | 278_P | 1.400 | 0.34 |
| 19_S | 79_D | 1.368 | 0.33 |
| 181_S | 191_I | 1.346 | 0.31 |
| 126_Y | 138_N | 1.343 | 0.31 |
| 160_E | 273_T | 1.341 | 0.31 |
| 23_Y | 93_I | 1.328 | 0.30 |
| 115_W | 197_I | 1.320 | 0.30 |
| 66_G | 264_A | 1.317 | 0.30 |
| 43_K | 50_G | 1.315 | 0.30 |
| 199_L | 255_T | 1.307 | 0.29 |
| 70_I | 165_M | 1.302 | 0.29 |
| 107_Y | 279_H | 1.290 | 0.28 |
| 147_E | 150_H | 1.288 | 0.28 |
| 8_V | 279_H | 1.282 | 0.28 |
| 27_P | 107_Y | 1.272 | 0.27 |
| 118_R | 268_R | 1.269 | 0.27 |
| 119_G | 268_R | 1.262 | 0.27 |
| 150_H | 153_Y | 1.259 | 0.27 |
| 210_E | 248_Y | 1.259 | 0.27 |
| 167_Y | 275_Y | 1.257 | 0.26 |
| 208_I | 276_K | 1.257 | 0.26 |
| 275_Y | 278_P | 1.255 | 0.26 |
| 155_A | 234_F | 1.246 | 0.26 |
| 251_Y | 277_R | 1.244 | 0.26 |
| 108_V | 116_G | 1.238 | 0.25 |
| 150_H | 186_Q | 1.238 | 0.25 |
| 7_G | 136_F | 1.228 | 0.25 |
| 110_D | 113_D | 1.226 | 0.25 |
| 147_E | 167_Y | 1.224 | 0.25 |
| 136_F | 251_Y | 1.222 | 0.25 |
| 222_L | 287_P | 1.219 | 0.24 |
| 68_I | 113_D | 1.217 | 0.24 |
| 238_I | 245_N | 1.214 | 0.24 |
| 13_N | 21_Y | 1.207 | 0.24 |
| 19_S | 77_R | 1.202 | 0.24 |
| 45_S | 104_K | 1.202 | 0.24 |
| 22_F | 98_A | 1.198 | 0.23 |
| 82_G | 90_F | 1.193 | 0.23 |
| 120_P | 143_P | 1.192 | 0.23 |
| 114_Y | 271_T | 1.191 | 0.23 |
| 141_T | 231_T | 1.190 | 0.23 |
| 236_M | 275_Y | 1.187 | 0.23 |
| 55_L | 146_G | 1.181 | 0.23 |
| 120_P | 219_Q | 1.181 | 0.23 |
| 165_M | 175_I | 1.176 | 0.22 |
| 181_S | 185_T | 1.170 | 0.22 |
| 116_G | 266_F | 1.169 | 0.22 |
| 53_V | 221_Y | 1.167 | 0.22 |
| 87_G | 92_E | 1.157 | 0.22 |
| 124_L | 155_A | 1.156 | 0.22 |
| 119_G | 182_P | 1.155 | 0.21 |
| 96_L | 267_L | 1.153 | 0.21 |
| 116_G | 181_S | 1.151 | 0.21 |
| 39_H | 140_I | 1.149 | 0.21 |
| 179_V | 263_I | 1.144 | 0.21 |
| 8_V | 59_D | 1.136 | 0.21 |
| 42_I | 175_I | 1.134 | 0.21 |
| 200_L | 277_R | 1.132 | 0.20 |
| 36_A | 55_L | 1.130 | 0.20 |
| 34_L | 55_L | 1.128 | 0.20 |
| 12_T | 25_H | 1.125 | 0.20 |
| 165_M | 263_I | 1.121 | 0.20 |
| 135_W | 278_P | 1.119 | 0.20 |
| 51_F | 68_I | 1.116 | 0.20 |
| 14_P | 170_P | 1.115 | 0.20 |
| 19_S | 81_Q | 1.113 | 0.20 |
| 24_L | 78_I | 1.111 | 0.20 |
| 172_E | 269_P | 1.107 | 0.19 |
| 137_Y | 233_K | 1.107 | 0.19 |
| 5_Q | 253_Y | 1.106 | 0.19 |
| 9_T | 55_L | 1.103 | 0.19 |
| 165_M | 193_D | 1.103 | 0.19 |
| 134_E | 239_R | 1.100 | 0.19 |
| 172_E | 284_N | 1.099 | 0.19 |
| 188_P | 216_S | 1.098 | 0.19 |
| 171_T | 227_K | 1.097 | 0.19 |
| 17_I | 81_Q | 1.095 | 0.19 |
| 191_I | 216_S | 1.093 | 0.19 |
| 183_F | 216_S | 1.089 | 0.19 |
| 167_Y | 202_Q | 1.087 | 0.19 |
| 19_S | 244_G | 1.084 | 0.18 |
| 116_G | 191_I | 1.077 | 0.18 |
| 154_M | 219_Q | 1.077 | 0.18 |
| 70_I | 73_A | 1.076 | 0.18 |
| 107_Y | 276_K | 1.073 | 0.18 |
| 121_S | 139_E | 1.069 | 0.18 |
| 154_M | 269_P | 1.068 | 0.18 |
| 182_P | 268_R | 1.068 | 0.18 |
| 176_L | 221_Y | 1.067 | 0.18 |
| 174_R | 265_S | 1.066 | 0.18 |
| 19_S | 22_F | 1.063 | 0.18 |
| 145_E | 167_Y | 1.063 | 0.18 |
| 80_L | 183_F | 1.060 | 0.18 |
| 182_P | 218_G | 1.058 | 0.17 |
| 118_R | 182_P | 1.057 | 0.17 |
| 160_E | 183_F | 1.055 | 0.17 |
| 150_H | 236_M | 1.050 | 0.17 |
| 3_I | 18_V | 1.049 | 0.17 |
| 245_N | 267_L | 1.048 | 0.17 |
| 6_R | 89_G | 1.048 | 0.17 |
| 235_L | 260_W | 1.046 | 0.17 |
| 192_P | 213_N | 1.045 | 0.17 |
| 186_Q | 276_K | 1.043 | 0.17 |
| 124_L | 163_F | 1.040 | 0.17 |
| 249_T | 266_F | 1.038 | 0.17 |
| 83_V | 149_M | 1.038 | 0.17 |
| 232_Y | 271_T | 1.038 | 0.17 |
| 76_V | 96_L | 1.038 | 0.17 |
| 222_L | 282_L | 1.036 | 0.17 |
| 143_P | 250_A | 1.035 | 0.17 |
| 15_K | 140_I | 1.035 | 0.17 |
| 125_G | 175_I | 1.034 | 0.17 |
| 120_P | 176_L | 1.034 | 0.17 |
| 24_L | 175_I | 1.033 | 0.16 |
| 30_A | 100_N | 1.031 | 0.16 |
| 169_S | 173_R | 1.031 | 0.16 |
| 137_Y | 260_W | 1.029 | 0.16 |
| 200_L | 249_T | 1.029 | 0.16 |
| 181_S | 262_L | 1.029 | 0.16 |
| 104_K | 140_I | 1.029 | 0.16 |
| 200_L | 209_G | 1.027 | 0.16 |
| 78_I | 113_D | 1.022 | 0.16 |
| 163_F | 173_R | 1.020 | 0.16 |
| 52_K | 128_L | 1.017 | 0.16 |
| 124_L | 213_N | 1.015 | 0.16 |
| 122_V | 282_L | 1.015 | 0.16 |
| 115_W | 129_P | 1.011 | 0.16 |
| 33_S | 247_T | 1.010 | 0.16 |
| 120_P | 282_L | 1.008 | 0.16 |
| 145_E | 231_T | 1.006 | 0.16 |
| 36_A | 251_Y | 1.005 | 0.15 |
| 55_L | 170_P | 1.005 | 0.15 |
| 216_S | 262_L | 1.003 | 0.15 |
| 133_T | 238_I | 1.001 | 0.15 |
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 | |
| 2bgoA | 1 | 0.3436 | 93.3 | 0.953 | Contact Map |
| 2vzsA | 2 | 0 | 91 | 0.956 | Contact Map |
| 4kmqA | 1 | 0.3333 | 89.6 | 0.958 | Contact Map |
| 2vzpA | 2 | 0.323 | 84.8 | 0.961 | Contact Map |
| 2w87A | 2 | 0.3608 | 83.3 | 0.962 | Contact Map |
| 2w47A | 1 | 0.3505 | 77.3 | 0.964 | Contact Map |
| 2w3jA | 1 | 0.3608 | 73.4 | 0.965 | Contact Map |
| 2wz8A | 1 | 0.3333 | 73.2 | 0.965 | Contact Map |
| 2y8kA | 1 | 0.3265 | 69.9 | 0.966 | Contact Map |
| 2xwxA | 2 | 0.3368 | 62.1 | 0.967 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)