| Rv3835 81-339 -force run |
| ID: | 1443027286 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 259 (254) | ||
| Sequences: | 197 (155.1) | ||
| Seq/Len: | 0.776 | ||
| Nf(neff/√len): | 9.7 |
HHblits Results: (2015_06)
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: 0.776).
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 |
| 45_A | 82_V | 2.157 | 0.96 |
| 43_E | 108_W | 2.072 | 0.94 |
| 42_F | 119_G | 1.714 | 0.83 |
| 230_L | 234_S | 1.695 | 0.82 |
| 177_G | 206_M | 1.686 | 0.81 |
| 57_E | 69_R | 1.591 | 0.76 |
| 176_S | 256_L | 1.575 | 0.75 |
| 199_I | 225_Y | 1.538 | 0.72 |
| 135_K | 138_D | 1.507 | 0.70 |
| 175_V | 243_S | 1.497 | 0.69 |
| 108_W | 114_R | 1.474 | 0.68 |
| 85_Y | 190_P | 1.474 | 0.68 |
| 226_P | 256_L | 1.466 | 0.67 |
| 21_L | 44_V | 1.453 | 0.66 |
| 51_R | 250_N | 1.439 | 0.65 |
| 214_L | 218_T | 1.437 | 0.65 |
| 123_P | 129_Q | 1.437 | 0.65 |
| 191_S | 194_E | 1.428 | 0.64 |
| 176_S | 202_A | 1.413 | 0.63 |
| 120_L | 165_V | 1.410 | 0.63 |
| 174_E | 210_Y | 1.409 | 0.63 |
| 253_W | 258_N | 1.409 | 0.63 |
| 112_G | 190_P | 1.343 | 0.57 |
| 42_F | 140_D | 1.326 | 0.56 |
| 84_R | 138_D | 1.321 | 0.55 |
| 40_H | 85_Y | 1.319 | 0.55 |
| 90_F | 174_E | 1.318 | 0.55 |
| 120_L | 136_V | 1.317 | 0.55 |
| 40_H | 108_W | 1.316 | 0.55 |
| 40_H | 112_G | 1.312 | 0.54 |
| 218_T | 246_A | 1.311 | 0.54 |
| 43_E | 114_R | 1.308 | 0.54 |
| 23_W | 92_P | 1.306 | 0.54 |
| 40_H | 43_E | 1.302 | 0.54 |
| 119_G | 140_D | 1.299 | 0.53 |
| 7_K | 250_N | 1.290 | 0.52 |
| 39_E | 131_A | 1.261 | 0.50 |
| 240_V | 251_G | 1.260 | 0.50 |
| 89_K | 130_L | 1.259 | 0.50 |
| 117_L | 173_M | 1.259 | 0.50 |
| 226_P | 243_S | 1.256 | 0.50 |
| 44_V | 119_G | 1.254 | 0.49 |
| 41_R | 82_V | 1.252 | 0.49 |
| 49_D | 141_Q | 1.250 | 0.49 |
| 9_N | 14_R | 1.239 | 0.48 |
| 43_E | 91_D | 1.237 | 0.48 |
| 181_L | 232_S | 1.233 | 0.48 |
| 221_L | 237_S | 1.211 | 0.46 |
| 54_P | 211_L | 1.197 | 0.44 |
| 85_Y | 108_W | 1.197 | 0.44 |
| 176_S | 207_T | 1.193 | 0.44 |
| 96_F | 238_R | 1.192 | 0.44 |
| 125_P | 164_P | 1.184 | 0.43 |
| 142_S | 153_I | 1.183 | 0.43 |
| 52_T | 56_M | 1.182 | 0.43 |
| 15_V | 44_V | 1.167 | 0.42 |
| 50_M | 241_A | 1.167 | 0.42 |
| 54_P | 58_Y | 1.161 | 0.41 |
| 40_H | 114_R | 1.157 | 0.41 |
| 11_S | 83_R | 1.153 | 0.41 |
| 43_E | 85_Y | 1.152 | 0.41 |
| 233_W | 236_G | 1.150 | 0.40 |
| 35_S | 201_D | 1.146 | 0.40 |
| 95_K | 189_L | 1.144 | 0.40 |
| 186_P | 251_G | 1.144 | 0.40 |
| 42_F | 92_P | 1.144 | 0.40 |
| 91_D | 119_G | 1.141 | 0.40 |
| 91_D | 212_A | 1.141 | 0.40 |
| 35_S | 197_G | 1.140 | 0.40 |
| 96_F | 136_V | 1.139 | 0.40 |
| 65_P | 210_Y | 1.135 | 0.39 |
| 96_F | 132_F | 1.131 | 0.39 |
| 180_N | 183_E | 1.131 | 0.39 |
| 246_A | 254_A | 1.128 | 0.39 |
| 141_Q | 210_Y | 1.125 | 0.38 |
| 108_W | 174_E | 1.122 | 0.38 |
| 94_S | 199_I | 1.114 | 0.37 |
| 211_L | 240_V | 1.110 | 0.37 |
| 49_D | 54_P | 1.108 | 0.37 |
| 138_D | 247_T | 1.107 | 0.37 |
| 28_P | 170_P | 1.102 | 0.37 |
| 139_I | 198_F | 1.100 | 0.36 |
| 15_V | 119_G | 1.098 | 0.36 |
| 23_W | 42_F | 1.092 | 0.36 |
| 141_Q | 237_S | 1.091 | 0.36 |
| 44_V | 111_A | 1.090 | 0.36 |
| 136_V | 139_I | 1.089 | 0.35 |
| 142_S | 237_S | 1.089 | 0.35 |
| 107_A | 116_M | 1.082 | 0.35 |
| 151_L | 226_P | 1.078 | 0.35 |
| 38_D | 156_T | 1.076 | 0.34 |
| 121_Q | 195_Q | 1.076 | 0.34 |
| 6_A | 206_M | 1.076 | 0.34 |
| 55_G | 126_N | 1.072 | 0.34 |
| 17_S | 177_G | 1.070 | 0.34 |
| 137_A | 179_V | 1.069 | 0.34 |
| 121_Q | 148_G | 1.068 | 0.34 |
| 19_D | 175_V | 1.067 | 0.34 |
| 10_A | 168_A | 1.067 | 0.34 |
| 54_P | 57_E | 1.065 | 0.34 |
| 14_R | 188_A | 1.061 | 0.33 |
| 128_Q | 230_L | 1.058 | 0.33 |
| 7_K | 67_P | 1.056 | 0.33 |
| 141_Q | 232_S | 1.056 | 0.33 |
| 11_S | 55_G | 1.055 | 0.33 |
| 5_G | 35_S | 1.054 | 0.33 |
| 76_E | 204_T | 1.054 | 0.33 |
| 30_S | 107_A | 1.052 | 0.33 |
| 87_G | 249_G | 1.049 | 0.32 |
| 54_P | 62_A | 1.048 | 0.32 |
| 161_I | 187_D | 1.047 | 0.32 |
| 31_A | 241_A | 1.043 | 0.32 |
| 55_G | 160_P | 1.039 | 0.32 |
| 23_W | 121_Q | 1.036 | 0.31 |
| 210_Y | 215_K | 1.033 | 0.31 |
| 7_K | 51_R | 1.030 | 0.31 |
| 87_G | 208_D | 1.024 | 0.30 |
| 154_D | 176_S | 1.022 | 0.30 |
| 61_N | 170_P | 1.020 | 0.30 |
| 6_A | 9_N | 1.016 | 0.30 |
| 211_L | 253_W | 1.016 | 0.30 |
| 87_G | 214_L | 1.014 | 0.30 |
| 229_T | 240_V | 1.014 | 0.30 |
| 56_M | 251_G | 1.013 | 0.30 |
| 48_I | 56_M | 1.011 | 0.30 |
| 70_I | 253_W | 1.011 | 0.30 |
| 121_Q | 174_E | 1.010 | 0.29 |
| 193_P | 207_T | 1.010 | 0.29 |
| 7_K | 138_D | 1.009 | 0.29 |
| 164_P | 174_E | 1.005 | 0.29 |
| 52_T | 109_R | 1.000 | 0.29 |
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 | |
| 2hvqA | 1 | 0.2664 | 1.8 | 0.977 | Contact Map |
| 1mhmB | 1 | 0.1815 | 1.7 | 0.977 | Contact Map |
| 2c3gA | 1 | 0.1506 | 1.5 | 0.978 | Contact Map |
| 3d24B | 2 | 0.0541 | 1.2 | 0.979 | Contact Map |
| 3c5tB | 1 | 0.0965 | 1.2 | 0.979 | Contact Map |
| 4a3pA | 1 | 0.2278 | 1 | 0.98 | Contact Map |
| 3eb8A | 2 | 0.2471 | 0.9 | 0.981 | Contact Map |
| 3ee1A | 2 | 0.2548 | 0.9 | 0.981 | Contact Map |
| 4uebB | 3 | 0.1544 | 0.8 | 0.981 | Contact Map |
| 1t0pB | 1 | 0.1467 | 0.8 | 0.981 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)