| T0780 -force run |
| ID: | 1401909558 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 259 (249) | ||
| Sequences: | 95 (82.4) | ||
| Seq/Len: | 0.382 | ||
| Nf(neff/√len): | 5.2 |
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: 0.382).
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 |
| 100_A | 105_I | 2.200 | 0.87 |
| 95_A | 109_L | 2.173 | 0.87 |
| 88_T | 91_F | 2.013 | 0.80 |
| 61_I | 214_A | 1.954 | 0.77 |
| 48_V | 61_I | 1.918 | 0.76 |
| 52_I | 212_L | 1.763 | 0.66 |
| 59_Y | 209_G | 1.654 | 0.59 |
| 62_S | 100_A | 1.630 | 0.57 |
| 158_E | 226_T | 1.629 | 0.57 |
| 16_C | 174_E | 1.560 | 0.53 |
| 55_N | 102_V | 1.508 | 0.49 |
| 120_A | 134_K | 1.503 | 0.48 |
| 82_S | 89_R | 1.496 | 0.48 |
| 137_K | 140_V | 1.469 | 0.46 |
| 94_T | 226_T | 1.468 | 0.46 |
| 93_V | 109_L | 1.451 | 0.45 |
| 106_E | 126_K | 1.441 | 0.44 |
| 186_L | 225_V | 1.436 | 0.44 |
| 104_T | 225_V | 1.396 | 0.41 |
| 50_I | 64_F | 1.393 | 0.41 |
| 24_A | 142_I | 1.388 | 0.40 |
| 164_D | 234_S | 1.383 | 0.40 |
| 186_L | 223_M | 1.376 | 0.39 |
| 50_I | 80_L | 1.360 | 0.38 |
| 62_S | 213_P | 1.352 | 0.38 |
| 121_V | 129_V | 1.348 | 0.38 |
| 118_L | 188_T | 1.341 | 0.37 |
| 61_I | 219_F | 1.322 | 0.36 |
| 179_I | 232_P | 1.321 | 0.36 |
| 50_I | 129_V | 1.311 | 0.35 |
| 11_S | 116_N | 1.306 | 0.35 |
| 72_L | 76_N | 1.302 | 0.35 |
| 106_E | 227_T | 1.297 | 0.34 |
| 105_I | 223_M | 1.290 | 0.34 |
| 5_S | 8_I | 1.283 | 0.33 |
| 17_V | 177_D | 1.269 | 0.32 |
| 22_A | 75_A | 1.269 | 0.32 |
| 174_E | 207_R | 1.259 | 0.32 |
| 51_D | 92_K | 1.257 | 0.32 |
| 72_L | 86_E | 1.257 | 0.32 |
| 57_D | 200_V | 1.251 | 0.31 |
| 102_V | 128_T | 1.246 | 0.31 |
| 61_I | 135_A | 1.238 | 0.31 |
| 9_I | 169_I | 1.235 | 0.30 |
| 66_S | 120_A | 1.224 | 0.30 |
| 157_I | 216_I | 1.215 | 0.29 |
| 12_L | 141_K | 1.213 | 0.29 |
| 50_I | 176_L | 1.211 | 0.29 |
| 89_R | 132_G | 1.200 | 0.28 |
| 16_C | 55_N | 1.199 | 0.28 |
| 179_I | 234_S | 1.198 | 0.28 |
| 59_Y | 88_T | 1.188 | 0.28 |
| 9_I | 58_K | 1.187 | 0.28 |
| 33_A | 123_T | 1.173 | 0.27 |
| 88_T | 218_P | 1.172 | 0.27 |
| 20_V | 196_Y | 1.171 | 0.27 |
| 169_I | 212_L | 1.169 | 0.26 |
| 149_S | 179_I | 1.163 | 0.26 |
| 18_L | 170_T | 1.161 | 0.26 |
| 219_F | 225_V | 1.160 | 0.26 |
| 148_P | 233_S | 1.150 | 0.25 |
| 43_N | 82_S | 1.149 | 0.25 |
| 144_P | 182_I | 1.145 | 0.25 |
| 58_K | 131_I | 1.143 | 0.25 |
| 65_A | 171_S | 1.135 | 0.25 |
| 205_I | 216_I | 1.134 | 0.25 |
| 79_S | 171_S | 1.134 | 0.25 |
| 59_Y | 78_L | 1.132 | 0.24 |
| 129_V | 147_D | 1.128 | 0.24 |
| 72_L | 118_L | 1.126 | 0.24 |
| 114_L | 134_K | 1.123 | 0.24 |
| 55_N | 190_E | 1.122 | 0.24 |
| 79_S | 90_K | 1.121 | 0.24 |
| 158_E | 179_I | 1.121 | 0.24 |
| 104_T | 130_K | 1.119 | 0.24 |
| 147_D | 151_I | 1.113 | 0.23 |
| 159_N | 179_I | 1.110 | 0.23 |
| 142_I | 179_I | 1.109 | 0.23 |
| 248_S | 251_T | 1.106 | 0.23 |
| 8_I | 45_V | 1.105 | 0.23 |
| 52_I | 136_Q | 1.102 | 0.23 |
| 119_T | 128_T | 1.100 | 0.23 |
| 54_Y | 61_I | 1.092 | 0.22 |
| 34_R | 193_T | 1.089 | 0.22 |
| 70_V | 206_D | 1.084 | 0.22 |
| 44_T | 169_I | 1.084 | 0.22 |
| 182_I | 195_N | 1.083 | 0.22 |
| 132_G | 232_P | 1.082 | 0.22 |
| 104_T | 122_A | 1.081 | 0.22 |
| 65_A | 155_V | 1.080 | 0.22 |
| 13_F | 61_I | 1.078 | 0.22 |
| 21_Y | 179_I | 1.077 | 0.22 |
| 65_A | 214_A | 1.073 | 0.21 |
| 87_S | 200_V | 1.071 | 0.21 |
| 134_K | 213_P | 1.071 | 0.21 |
| 163_S | 200_V | 1.066 | 0.21 |
| 52_I | 169_I | 1.064 | 0.21 |
| 105_I | 155_V | 1.062 | 0.21 |
| 70_V | 252_K | 1.061 | 0.21 |
| 16_C | 178_R | 1.056 | 0.21 |
| 50_I | 127_I | 1.054 | 0.21 |
| 80_L | 94_T | 1.054 | 0.21 |
| 31_T | 115_P | 1.045 | 0.20 |
| 154_R | 183_I | 1.044 | 0.20 |
| 22_A | 171_S | 1.041 | 0.20 |
| 89_R | 130_K | 1.039 | 0.20 |
| 9_I | 125_Q | 1.039 | 0.20 |
| 89_R | 175_T | 1.037 | 0.20 |
| 92_K | 136_Q | 1.030 | 0.19 |
| 132_G | 172_D | 1.029 | 0.19 |
| 54_Y | 134_K | 1.029 | 0.19 |
| 70_V | 125_Q | 1.029 | 0.19 |
| 79_S | 113_D | 1.028 | 0.19 |
| 52_I | 189_S | 1.027 | 0.19 |
| 191_R | 221_T | 1.025 | 0.19 |
| 146_I | 188_T | 1.025 | 0.19 |
| 64_F | 220_D | 1.021 | 0.19 |
| 157_I | 205_I | 1.018 | 0.19 |
| 88_T | 95_A | 1.017 | 0.19 |
| 82_S | 194_G | 1.016 | 0.19 |
| 64_F | 215_V | 1.014 | 0.19 |
| 65_A | 79_S | 1.014 | 0.19 |
| 61_I | 198_G | 1.012 | 0.19 |
| 88_T | 209_G | 1.010 | 0.19 |
| 3_K | 245_S | 1.008 | 0.18 |
| 80_L | 158_E | 1.007 | 0.18 |
| 250_S | 253_A | 1.006 | 0.18 |
| 168_S | 194_G | 1.003 | 0.18 |
| 3_K | 43_N | 1.003 | 0.18 |
| 11_S | 200_V | 1.002 | 0.18 |
| 141_K | 144_P | 1.002 | 0.18 |
| 45_V | 96_D | 1.001 | 0.18 |
| 45_V | 206_D | 1.000 | 0.18 |
| 76_N | 192_I | 1.000 | 0.18 |
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 | |
| 2kq1A | 1 | 0.4556 | 99.9 | 0.753 | Contact Map |
| 2kpsA | 1 | 0.3784 | 99.7 | 0.8 | Contact Map |
| 3lywA | 1 | 0.3243 | 99.6 | 0.819 | Contact Map |
| 2kxyA | 1 | 0.3861 | 99.2 | 0.853 | Contact Map |
| 3pddA | 1 | 0.6834 | 15.1 | 0.968 | Contact Map |
| 4ng0A | 3 | 0.2973 | 14.2 | 0.969 | Contact Map |
| 4l3aA | 2 | 0.8263 | 13.1 | 0.969 | Contact Map |
| 2eecA | 1 | 0.3745 | 7.6 | 0.972 | Contact Map |
| 2dibA | 1 | 0.4633 | 6.8 | 0.973 | Contact Map |
| 2qcpX | 1 | 0.278 | 5.9 | 0.974 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)