| workingVP4_1A__VP2_1Bfasta |
| ID: | 1489786056 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 303 (290) | ||
| Sequences: | 294 (114) | ||
| Seq/Len: | 1.014 | ||
| Nf(neff/√len): | 6.7 |
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: 1.014).
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 |
| 210_M | 245_V | 4.097 | 1.00 |
| 156_T | 273_T | 2.951 | 1.00 |
| 210_M | 243_I | 2.824 | 1.00 |
| 245_V | 262_W | 2.531 | 0.99 |
| 205_C | 232_F | 2.492 | 0.99 |
| 233_I | 241_A | 2.392 | 0.99 |
| 207_L | 226_T | 2.245 | 0.98 |
| 232_F | 269_V | 2.005 | 0.96 |
| 144_E | 293_V | 1.998 | 0.96 |
| 243_I | 262_W | 1.873 | 0.93 |
| 243_I | 264_L | 1.851 | 0.93 |
| 210_M | 262_W | 1.848 | 0.92 |
| 209_A | 265_V | 1.815 | 0.92 |
| 211_V | 225_L | 1.805 | 0.91 |
| 194_V | 208_V | 1.784 | 0.91 |
| 213_E | 259_H | 1.682 | 0.87 |
| 134_S | 137_E | 1.672 | 0.86 |
| 248_L | 262_W | 1.662 | 0.86 |
| 199_N | 278_S | 1.636 | 0.85 |
| 245_V | 248_L | 1.614 | 0.84 |
| 146_F | 289_A | 1.593 | 0.83 |
| 191_D | 244_T | 1.564 | 0.81 |
| 15_S | 26_Y | 1.548 | 0.80 |
| 209_A | 225_L | 1.529 | 0.79 |
| 86_D | 89_T | 1.518 | 0.78 |
| 208_V | 284_V | 1.487 | 0.76 |
| 196_A | 206_L | 1.487 | 0.76 |
| 111_T | 193_E | 1.477 | 0.76 |
| 120_G | 144_E | 1.442 | 0.73 |
| 6_S | 9_T | 1.434 | 0.72 |
| 134_S | 298_E | 1.411 | 0.71 |
| 184_A | 274_V | 1.410 | 0.71 |
| 225_L | 265_V | 1.409 | 0.71 |
| 67_W | 73_S | 1.375 | 0.68 |
| 1_G | 5_S | 1.373 | 0.68 |
| 199_N | 277_T | 1.362 | 0.67 |
| 198_G | 235_P | 1.359 | 0.67 |
| 180_V | 256_Y | 1.355 | 0.66 |
| 266_V | 288_I | 1.344 | 0.65 |
| 175_V | 296_A | 1.338 | 0.65 |
| 239_M | 242_H | 1.332 | 0.64 |
| 67_W | 70_K | 1.331 | 0.64 |
| 21_I | 114_S | 1.315 | 0.63 |
| 174_G | 177_G | 1.299 | 0.61 |
| 102_T | 115_V | 1.297 | 0.61 |
| 209_A | 226_T | 1.290 | 0.61 |
| 138_T | 248_L | 1.287 | 0.60 |
| 274_V | 278_S | 1.287 | 0.60 |
| 30_Y | 90_E | 1.286 | 0.60 |
| 269_V | 276_N | 1.285 | 0.60 |
| 97_D | 231_Q | 1.271 | 0.59 |
| 196_A | 284_V | 1.268 | 0.59 |
| 190_W | 257_K | 1.243 | 0.56 |
| 183_Y | 197_V | 1.243 | 0.56 |
| 40_D | 161_G | 1.238 | 0.56 |
| 91_E | 170_S | 1.227 | 0.55 |
| 106_H | 298_E | 1.202 | 0.53 |
| 106_H | 174_G | 1.198 | 0.52 |
| 144_E | 215_K | 1.196 | 0.52 |
| 96_E | 185_Y | 1.193 | 0.52 |
| 208_V | 238_N | 1.187 | 0.51 |
| 4_Q | 7_P | 1.171 | 0.50 |
| 120_G | 188_N | 1.167 | 0.49 |
| 250_V | 269_V | 1.163 | 0.49 |
| 87_K | 233_I | 1.156 | 0.48 |
| 243_I | 248_L | 1.155 | 0.48 |
| 192_V | 245_V | 1.153 | 0.48 |
| 206_L | 284_V | 1.142 | 0.47 |
| 23_N | 144_E | 1.138 | 0.47 |
| 54_T | 172_H | 1.136 | 0.46 |
| 40_D | 57_T | 1.133 | 0.46 |
| 121_Y | 202_N | 1.131 | 0.46 |
| 110_T | 119_H | 1.119 | 0.45 |
| 133_T | 287_N | 1.118 | 0.45 |
| 199_N | 223_Y | 1.114 | 0.44 |
| 54_T | 68_F | 1.110 | 0.44 |
| 147_Y | 285_Y | 1.108 | 0.44 |
| 24_N | 32_N | 1.108 | 0.44 |
| 211_V | 245_V | 1.107 | 0.44 |
| 151_L | 227_L | 1.107 | 0.44 |
| 98_R | 231_Q | 1.105 | 0.44 |
| 24_N | 91_E | 1.104 | 0.43 |
| 245_V | 264_L | 1.102 | 0.43 |
| 111_T | 236_R | 1.101 | 0.43 |
| 225_L | 267_M | 1.100 | 0.43 |
| 195_S | 285_Y | 1.097 | 0.43 |
| 26_Y | 29_Q | 1.096 | 0.43 |
| 87_K | 242_H | 1.095 | 0.43 |
| 168_L | 263_T | 1.092 | 0.42 |
| 248_L | 265_V | 1.082 | 0.41 |
| 227_L | 232_F | 1.081 | 0.41 |
| 128_V | 258_K | 1.081 | 0.41 |
| 203_G | 273_T | 1.079 | 0.41 |
| 3_G | 10_G | 1.079 | 0.41 |
| 168_L | 262_W | 1.078 | 0.41 |
| 210_M | 248_L | 1.078 | 0.41 |
| 19_G | 26_Y | 1.075 | 0.41 |
| 210_M | 214_W | 1.074 | 0.41 |
| 12_Q | 37_Q | 1.073 | 0.41 |
| 140_V | 144_E | 1.066 | 0.40 |
| 147_Y | 287_N | 1.060 | 0.40 |
| 86_D | 268_V | 1.060 | 0.40 |
| 232_F | 281_Q | 1.059 | 0.39 |
| 113_S | 239_M | 1.059 | 0.39 |
| 39_G | 80_F | 1.054 | 0.39 |
| 53_D | 70_K | 1.052 | 0.39 |
| 223_Y | 256_Y | 1.052 | 0.39 |
| 86_D | 242_H | 1.042 | 0.38 |
| 34_M | 224_Q | 1.039 | 0.38 |
| 81_G | 99_I | 1.039 | 0.38 |
| 237_T | 264_L | 1.034 | 0.37 |
| 88_K | 293_V | 1.033 | 0.37 |
| 194_V | 284_V | 1.032 | 0.37 |
| 132_N | 184_A | 1.028 | 0.37 |
| 108_T | 146_F | 1.027 | 0.37 |
| 100_L | 114_S | 1.026 | 0.37 |
| 184_A | 203_G | 1.024 | 0.36 |
| 120_G | 281_Q | 1.022 | 0.36 |
| 29_Q | 68_F | 1.022 | 0.36 |
| 221_E | 224_Q | 1.020 | 0.36 |
| 63_Q | 168_L | 1.019 | 0.36 |
| 134_S | 299_L | 1.018 | 0.36 |
| 97_D | 112_Q | 1.018 | 0.36 |
| 137_E | 179_L | 1.014 | 0.35 |
| 54_T | 67_W | 1.011 | 0.35 |
| 81_G | 91_E | 1.011 | 0.35 |
| 203_G | 279_A | 1.000 | 0.34 |
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 | |
| 1pov0 | 1 | 0.8053 | 100 | 0.14 | Contact Map |
| 4rr3G | 5 | 0.67 | 100 | 0.174 | Contact Map |
| 3cjiC | 1 | 0.6832 | 100 | 0.264 | Contact Map |
| 4q4w2 | 1 | 0.6832 | 100 | 0.269 | Contact Map |
| 1tme2 | 1 | 0.6832 | 100 | 0.272 | Contact Map |
| 4gb32 | 1 | 0.6832 | 100 | 0.273 | Contact Map |
| 1ncqB | 1 | 0.6832 | 100 | 0.275 | Contact Map |
| 1aym2 | 1 | 0.6733 | 100 | 0.286 | Contact Map |
| 1bev2 | 1 | 0.6931 | 100 | 0.298 | Contact Map |
| 4wm8B | 1 | 0.67 | 100 | 0.302 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)