| T0794 - roll 1-300 -force run |
| ID: | 1401228723 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 300 (296) | ||
| Sequences: | 128 (61.8) | ||
| Seq/Len: | 0.432 | ||
| Nf(neff/√len): | 3.6 |
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: 0.432).
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 |
| 43_I | 106_L | 1.907 | 0.78 |
| 19_T | 282_Q | 1.839 | 0.75 |
| 160_L | 192_D | 1.728 | 0.68 |
| 47_A | 50_G | 1.713 | 0.67 |
| 120_D | 156_H | 1.699 | 0.66 |
| 183_G | 214_P | 1.694 | 0.66 |
| 43_I | 114_V | 1.690 | 0.65 |
| 144_V | 154_R | 1.632 | 0.61 |
| 130_Q | 206_F | 1.605 | 0.60 |
| 53_I | 121_K | 1.594 | 0.59 |
| 90_N | 114_V | 1.562 | 0.56 |
| 129_P | 211_I | 1.547 | 0.55 |
| 4_F | 130_Q | 1.525 | 0.54 |
| 45_S | 280_L | 1.519 | 0.53 |
| 47_A | 261_P | 1.508 | 0.52 |
| 115_V | 180_T | 1.501 | 0.52 |
| 103_L | 216_A | 1.501 | 0.52 |
| 89_N | 266_A | 1.472 | 0.50 |
| 180_T | 183_G | 1.471 | 0.50 |
| 213_F | 236_G | 1.444 | 0.48 |
| 19_T | 114_V | 1.439 | 0.47 |
| 287_P | 290_S | 1.437 | 0.47 |
| 4_F | 241_F | 1.430 | 0.47 |
| 125_D | 128_D | 1.423 | 0.46 |
| 260_A | 280_L | 1.398 | 0.44 |
| 188_F | 198_P | 1.381 | 0.43 |
| 55_V | 107_A | 1.370 | 0.42 |
| 245_N | 253_M | 1.362 | 0.42 |
| 130_Q | 172_E | 1.346 | 0.41 |
| 189_T | 255_G | 1.329 | 0.39 |
| 3_T | 21_T | 1.317 | 0.39 |
| 115_V | 242_L | 1.316 | 0.38 |
| 145_F | 159_N | 1.313 | 0.38 |
| 192_D | 296_T | 1.309 | 0.38 |
| 56_T | 237_M | 1.304 | 0.38 |
| 240_N | 284_D | 1.299 | 0.37 |
| 205_D | 283_L | 1.298 | 0.37 |
| 161_F | 236_G | 1.280 | 0.36 |
| 20_L | 205_D | 1.276 | 0.36 |
| 26_E | 283_L | 1.269 | 0.35 |
| 155_Y | 193_I | 1.268 | 0.35 |
| 96_Q | 108_K | 1.267 | 0.35 |
| 126_T | 130_Q | 1.238 | 0.33 |
| 53_I | 212_V | 1.228 | 0.32 |
| 52_H | 112_I | 1.222 | 0.32 |
| 233_W | 237_M | 1.222 | 0.32 |
| 243_A | 249_P | 1.218 | 0.32 |
| 140_N | 192_D | 1.215 | 0.32 |
| 140_N | 195_F | 1.208 | 0.31 |
| 192_D | 199_A | 1.205 | 0.31 |
| 179_N | 184_S | 1.195 | 0.30 |
| 203_V | 249_P | 1.190 | 0.30 |
| 8_V | 11_H | 1.184 | 0.30 |
| 147_S | 283_L | 1.184 | 0.30 |
| 142_D | 202_L | 1.183 | 0.30 |
| 202_L | 213_F | 1.180 | 0.29 |
| 186_G | 263_S | 1.177 | 0.29 |
| 4_F | 30_A | 1.168 | 0.29 |
| 107_A | 140_N | 1.161 | 0.28 |
| 161_F | 296_T | 1.156 | 0.28 |
| 36_L | 43_I | 1.156 | 0.28 |
| 58_E | 190_C | 1.154 | 0.28 |
| 24_S | 206_F | 1.152 | 0.28 |
| 189_T | 207_H | 1.151 | 0.28 |
| 160_L | 199_A | 1.151 | 0.28 |
| 127_S | 130_Q | 1.149 | 0.28 |
| 208_V | 279_L | 1.148 | 0.28 |
| 159_N | 192_D | 1.147 | 0.27 |
| 271_M | 280_L | 1.147 | 0.27 |
| 165_N | 169_V | 1.143 | 0.27 |
| 168_N | 192_D | 1.143 | 0.27 |
| 4_F | 64_W | 1.140 | 0.27 |
| 3_T | 207_H | 1.140 | 0.27 |
| 141_T | 251_K | 1.138 | 0.27 |
| 102_R | 178_F | 1.134 | 0.27 |
| 236_G | 252_K | 1.129 | 0.26 |
| 135_G | 242_L | 1.129 | 0.26 |
| 181_T | 207_H | 1.125 | 0.26 |
| 161_F | 192_D | 1.125 | 0.26 |
| 35_N | 195_F | 1.125 | 0.26 |
| 122_K | 139_Y | 1.125 | 0.26 |
| 168_N | 263_S | 1.119 | 0.26 |
| 24_S | 207_H | 1.117 | 0.26 |
| 165_N | 206_F | 1.112 | 0.25 |
| 192_D | 197_D | 1.111 | 0.25 |
| 2_D | 82_E | 1.110 | 0.25 |
| 161_F | 168_N | 1.110 | 0.25 |
| 108_K | 184_S | 1.106 | 0.25 |
| 36_L | 212_V | 1.106 | 0.25 |
| 192_D | 195_F | 1.105 | 0.25 |
| 155_Y | 158_Q | 1.094 | 0.24 |
| 35_N | 193_I | 1.090 | 0.24 |
| 178_F | 290_S | 1.090 | 0.24 |
| 161_F | 248_Y | 1.088 | 0.24 |
| 165_N | 191_F | 1.087 | 0.24 |
| 178_F | 242_L | 1.086 | 0.24 |
| 64_W | 281_S | 1.086 | 0.24 |
| 265_R | 283_L | 1.081 | 0.24 |
| 4_F | 271_M | 1.080 | 0.24 |
| 196_H | 263_S | 1.079 | 0.24 |
| 101_E | 139_Y | 1.079 | 0.24 |
| 44_T | 112_I | 1.078 | 0.24 |
| 42_A | 106_L | 1.078 | 0.24 |
| 143_V | 153_A | 1.077 | 0.24 |
| 161_F | 199_A | 1.072 | 0.23 |
| 214_P | 261_P | 1.071 | 0.23 |
| 4_F | 206_F | 1.069 | 0.23 |
| 76_E | 156_H | 1.068 | 0.23 |
| 36_L | 280_L | 1.068 | 0.23 |
| 195_F | 203_V | 1.067 | 0.23 |
| 240_N | 285_S | 1.066 | 0.23 |
| 24_S | 165_N | 1.065 | 0.23 |
| 65_N | 161_F | 1.061 | 0.23 |
| 213_F | 217_W | 1.059 | 0.23 |
| 152_V | 177_T | 1.057 | 0.22 |
| 140_N | 193_I | 1.055 | 0.22 |
| 95_G | 108_K | 1.055 | 0.22 |
| 4_F | 20_L | 1.053 | 0.22 |
| 54_I | 112_I | 1.053 | 0.22 |
| 151_L | 183_G | 1.052 | 0.22 |
| 63_G | 217_W | 1.051 | 0.22 |
| 13_A | 112_I | 1.049 | 0.22 |
| 120_D | 161_F | 1.048 | 0.22 |
| 160_L | 197_D | 1.048 | 0.22 |
| 5_I | 207_H | 1.047 | 0.22 |
| 57_P | 183_G | 1.045 | 0.22 |
| 185_F | 218_M | 1.042 | 0.22 |
| 20_L | 206_F | 1.041 | 0.22 |
| 155_Y | 192_D | 1.037 | 0.21 |
| 153_A | 259_Y | 1.036 | 0.21 |
| 2_D | 84_N | 1.036 | 0.21 |
| 61_I | 184_S | 1.034 | 0.21 |
| 194_L | 218_M | 1.033 | 0.21 |
| 189_T | 226_A | 1.027 | 0.21 |
| 134_D | 145_F | 1.027 | 0.21 |
| 64_W | 271_M | 1.025 | 0.21 |
| 154_R | 215_T | 1.024 | 0.21 |
| 167_F | 292_V | 1.023 | 0.21 |
| 140_N | 294_N | 1.022 | 0.21 |
| 24_S | 117_N | 1.022 | 0.21 |
| 104_S | 145_F | 1.022 | 0.21 |
| 211_I | 249_P | 1.021 | 0.21 |
| 21_T | 206_F | 1.020 | 0.21 |
| 90_N | 212_V | 1.019 | 0.21 |
| 10_E | 73_P | 1.019 | 0.21 |
| 39_L | 280_L | 1.018 | 0.21 |
| 48_D | 101_E | 1.015 | 0.20 |
| 181_T | 281_S | 1.015 | 0.20 |
| 165_N | 234_A | 1.014 | 0.20 |
| 234_A | 288_S | 1.013 | 0.20 |
| 49_Q | 282_Q | 1.013 | 0.20 |
| 4_F | 280_L | 1.011 | 0.20 |
| 139_Y | 230_H | 1.011 | 0.20 |
| 42_A | 181_T | 1.011 | 0.20 |
| 127_S | 241_F | 1.010 | 0.20 |
| 37_D | 40_E | 1.010 | 0.20 |
| 57_P | 189_T | 1.009 | 0.20 |
| 115_V | 215_T | 1.008 | 0.20 |
| 160_L | 296_T | 1.007 | 0.20 |
| 12_A | 16_P | 1.007 | 0.20 |
| 202_L | 217_W | 1.006 | 0.20 |
| 36_L | 89_N | 1.006 | 0.20 |
| 21_T | 171_K | 1.006 | 0.20 |
| 172_E | 283_L | 1.006 | 0.20 |
| 96_Q | 145_F | 1.005 | 0.20 |
| 89_N | 108_K | 1.004 | 0.20 |
| 61_I | 159_N | 1.004 | 0.20 |
| 215_T | 243_A | 1.002 | 0.20 |
| 93_R | 207_H | 1.002 | 0.20 |
| 107_A | 149_G | 1.002 | 0.20 |
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 | |
| 4cyfA | 2 | 0.99 | 100 | 0.405 | Contact Map |
| 3wuyA | 2 | 0.89 | 100 | 0.519 | Contact Map |
| 2vhhA | 4 | 0.9133 | 100 | 0.536 | Contact Map |
| 2dyuA | 2 | 0.8433 | 100 | 0.551 | Contact Map |
| 3ivzA | 2 | 0.8233 | 100 | 0.554 | Contact Map |
| 1emsA | 2 | 0.85 | 100 | 0.554 | Contact Map |
| 4izuA | 1 | 0.7967 | 100 | 0.561 | Contact Map |
| 1uf5A | 2 | 0.88 | 100 | 0.563 | Contact Map |
| 2w1vA | 2 | 0.83 | 100 | 0.566 | Contact Map |
| 4lf0A | 1 | 0.87 | 100 | 0.566 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)