| rnf144a |
| ID: | 1504859966 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 292 (275) | ||
| Sequences: | 373 (227.6) | ||
| Seq/Len: | 1.356 | ||
| Nf(neff/√len): | 13.7 |
HHblits Results: (2016_02)
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: 1.356).
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 |
| 20_C | 23_C | 2.319 | 0.99 |
| 226_H | 232_C | 2.095 | 0.98 |
| 231_P | 234_N | 2.022 | 0.98 |
| 105_D | 108_R | 1.905 | 0.96 |
| 138_C | 156_C | 1.854 | 0.96 |
| 143_C | 146_C | 1.818 | 0.95 |
| 211_C | 214_C | 1.782 | 0.94 |
| 38_C | 43_C | 1.752 | 0.94 |
| 229_K | 232_C | 1.715 | 0.93 |
| 20_C | 43_C | 1.703 | 0.92 |
| 138_C | 143_C | 1.695 | 0.92 |
| 199_A | 213_Y | 1.686 | 0.92 |
| 228_D | 231_P | 1.661 | 0.91 |
| 20_C | 38_C | 1.659 | 0.91 |
| 141_E | 251_V | 1.657 | 0.91 |
| 23_C | 38_C | 1.634 | 0.90 |
| 268_L | 272_T | 1.611 | 0.89 |
| 194_R | 199_A | 1.582 | 0.88 |
| 65_C | 116_C | 1.533 | 0.86 |
| 203_C | 206_C | 1.529 | 0.86 |
| 31_Q | 48_K | 1.526 | 0.85 |
| 206_C | 211_C | 1.523 | 0.85 |
| 143_C | 156_C | 1.523 | 0.85 |
| 23_C | 43_C | 1.508 | 0.85 |
| 70_C | 232_C | 1.500 | 0.84 |
| 162_I | 166_P | 1.481 | 0.83 |
| 92_R | 96_L | 1.480 | 0.83 |
| 227_Y | 232_C | 1.478 | 0.83 |
| 60_E | 100_R | 1.475 | 0.83 |
| 43_C | 46_C | 1.468 | 0.82 |
| 206_C | 214_C | 1.454 | 0.81 |
| 63_I | 139_R | 1.445 | 0.81 |
| 226_H | 234_N | 1.432 | 0.80 |
| 226_H | 231_P | 1.431 | 0.80 |
| 203_C | 211_C | 1.425 | 0.80 |
| 151_H | 156_C | 1.400 | 0.78 |
| 185_C | 206_C | 1.395 | 0.78 |
| 38_C | 46_C | 1.392 | 0.77 |
| 117_Q | 205_N | 1.389 | 0.77 |
| 146_C | 150_W | 1.388 | 0.77 |
| 226_H | 230_G | 1.355 | 0.75 |
| 203_C | 214_C | 1.351 | 0.74 |
| 138_C | 146_C | 1.350 | 0.74 |
| 222_F | 226_H | 1.346 | 0.74 |
| 116_C | 146_C | 1.330 | 0.73 |
| 116_C | 156_C | 1.327 | 0.72 |
| 185_C | 211_C | 1.304 | 0.71 |
| 185_C | 203_C | 1.303 | 0.71 |
| 222_F | 227_Y | 1.282 | 0.69 |
| 263_V | 270_L | 1.274 | 0.68 |
| 225_I | 228_D | 1.268 | 0.67 |
| 168_E | 173_F | 1.266 | 0.67 |
| 243_V | 270_L | 1.260 | 0.67 |
| 212_W | 215_L | 1.259 | 0.67 |
| 88_E | 168_E | 1.257 | 0.67 |
| 20_C | 46_C | 1.257 | 0.67 |
| 185_C | 214_C | 1.250 | 0.66 |
| 94_K | 99_E | 1.237 | 0.65 |
| 238_H | 247_R | 1.235 | 0.65 |
| 23_C | 46_C | 1.229 | 0.64 |
| 226_H | 236_L | 1.225 | 0.64 |
| 146_C | 156_C | 1.212 | 0.62 |
| 170_S | 173_F | 1.210 | 0.62 |
| 230_G | 236_L | 1.205 | 0.62 |
| 198_C | 206_C | 1.204 | 0.62 |
| 138_C | 151_H | 1.198 | 0.61 |
| 138_C | 203_C | 1.197 | 0.61 |
| 276_L | 282_C | 1.195 | 0.61 |
| 183_K | 212_W | 1.194 | 0.61 |
| 186_P | 206_C | 1.192 | 0.60 |
| 198_C | 203_C | 1.183 | 0.60 |
| 225_I | 231_P | 1.177 | 0.59 |
| 244_I | 248_T | 1.175 | 0.59 |
| 10_W | 14_L | 1.171 | 0.58 |
| 254_F | 257_F | 1.170 | 0.58 |
| 232_C | 236_L | 1.165 | 0.58 |
| 278_C | 281_K | 1.160 | 0.57 |
| 61_T | 76_L | 1.157 | 0.57 |
| 109_T | 196_E | 1.152 | 0.57 |
| 223_L | 226_H | 1.147 | 0.56 |
| 186_P | 203_C | 1.146 | 0.56 |
| 234_N | 238_H | 1.140 | 0.55 |
| 111_C | 116_C | 1.136 | 0.55 |
| 232_C | 238_H | 1.135 | 0.55 |
| 263_V | 267_F | 1.133 | 0.55 |
| 71_P | 139_R | 1.133 | 0.55 |
| 50_Y | 54_L | 1.130 | 0.54 |
| 200_Q | 209_A | 1.126 | 0.54 |
| 11_D | 15_D | 1.125 | 0.54 |
| 147_K | 157_P | 1.123 | 0.54 |
| 171_A | 174_K | 1.122 | 0.54 |
| 40_C | 199_A | 1.119 | 0.53 |
| 232_C | 239_S | 1.115 | 0.53 |
| 116_C | 138_C | 1.114 | 0.53 |
| 228_D | 232_C | 1.114 | 0.53 |
| 109_T | 144_S | 1.112 | 0.53 |
| 198_C | 211_C | 1.108 | 0.52 |
| 22_L | 42_F | 1.103 | 0.52 |
| 271_A | 277_C | 1.100 | 0.51 |
| 116_C | 143_C | 1.099 | 0.51 |
| 263_V | 268_L | 1.098 | 0.51 |
| 261_L | 264_A | 1.096 | 0.51 |
| 186_P | 211_C | 1.092 | 0.51 |
| 278_C | 283_S | 1.089 | 0.50 |
| 54_L | 64_S | 1.088 | 0.50 |
| 27_Y | 49_Q | 1.085 | 0.50 |
| 197_G | 254_F | 1.085 | 0.50 |
| 270_L | 275_V | 1.078 | 0.49 |
| 45_L | 57_E | 1.072 | 0.49 |
| 12_L | 15_D | 1.072 | 0.49 |
| 231_P | 236_L | 1.067 | 0.48 |
| 230_G | 233_R | 1.063 | 0.48 |
| 102_V | 200_Q | 1.060 | 0.47 |
| 166_P | 170_S | 1.056 | 0.47 |
| 36_A | 39_Q | 1.049 | 0.46 |
| 55_I | 190_V | 1.049 | 0.46 |
| 262_L | 274_F | 1.046 | 0.46 |
| 112_P | 201_M | 1.046 | 0.46 |
| 82_E | 90_M | 1.045 | 0.46 |
| 198_C | 214_C | 1.043 | 0.46 |
| 109_T | 147_K | 1.042 | 0.46 |
| 135_C | 197_G | 1.039 | 0.45 |
| 242_S | 253_I | 1.038 | 0.45 |
| 78_E | 94_K | 1.037 | 0.45 |
| 229_K | 234_N | 1.037 | 0.45 |
| 135_C | 156_C | 1.035 | 0.45 |
| 258_G | 269_L | 1.030 | 0.44 |
| 265_S | 268_L | 1.030 | 0.44 |
| 228_D | 233_R | 1.027 | 0.44 |
| 186_P | 214_C | 1.027 | 0.44 |
| 265_S | 269_L | 1.025 | 0.44 |
| 209_A | 216_E | 1.024 | 0.44 |
| 16_P | 26_E | 1.023 | 0.44 |
| 108_R | 119_V | 1.020 | 0.43 |
| 35_I | 164_F | 1.019 | 0.43 |
| 195_D | 212_W | 1.017 | 0.43 |
| 194_R | 201_M | 1.017 | 0.43 |
| 44_T | 84_M | 1.015 | 0.43 |
| 199_A | 212_W | 1.014 | 0.43 |
| 232_C | 240_R | 1.014 | 0.43 |
| 226_H | 229_K | 1.013 | 0.43 |
| 102_V | 105_D | 1.009 | 0.42 |
| 272_T | 275_V | 1.009 | 0.42 |
| 29_V | 48_K | 1.008 | 0.42 |
| 168_E | 171_A | 1.006 | 0.42 |
| 242_S | 248_T | 1.005 | 0.42 |
| 156_C | 203_C | 1.004 | 0.42 |
| 31_Q | 44_T | 1.002 | 0.42 |
| 105_D | 200_Q | 1.001 | 0.41 |
| 227_Y | 230_G | 1.000 | 0.41 |
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
- See coupling matrix (for protein design or mutagenesis)
- 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 | |
| 4i1fA | 1 | 0.7158 | 100 | 0.522 | Contact Map |
| 5c1zA | 2 | 0 | 100 | 0.525 | Contact Map |
| 4k95A | 12 | 0.6815 | 100 | 0.532 | Contact Map |
| 5cawA | 2 | 0 | 100 | 0.535 | Contact Map |
| 4kblA | 2 | 0.8253 | 100 | 0.562 | Contact Map |
| 2m48A | 1 | 0.4281 | 100 | 0.678 | Contact Map |
| 4ljoA | 1 | 0.4075 | 99.7 | 0.8 | Contact Map |
| 2ct7A | 1 | 0.2842 | 99.7 | 0.802 | Contact Map |
| 1wimA | 1 | 0.3219 | 99.5 | 0.818 | Contact Map |
| 3hcsA | 2 | 0.5068 | 99.1 | 0.854 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)