| workingVP3_1C__VP1_1Dfasta |
| ID: | 1489785927 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 432 (413) | ||
| Sequences: | 722 (332.1) | ||
| Seq/Len: | 1.748 | ||
| Nf(neff/√len): | 16.3 |
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: 1.748).
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 |
| 40_R | 404_E | 4.672 | 1.00 |
| 107_L | 160_I | 2.967 | 1.00 |
| 108_H | 155_K | 2.855 | 1.00 |
| 104_T | 209_D | 2.088 | 0.99 |
| 296_D | 402_R | 2.075 | 0.99 |
| 53_T | 90_Y | 2.070 | 0.99 |
| 6_A | 20_K | 1.990 | 0.99 |
| 121_Y | 187_I | 1.955 | 0.98 |
| 34_R | 404_E | 1.910 | 0.98 |
| 107_L | 185_V | 1.894 | 0.98 |
| 75_A | 187_I | 1.875 | 0.98 |
| 125_Y | 183_G | 1.830 | 0.97 |
| 47_V | 53_T | 1.823 | 0.97 |
| 95_A | 212_L | 1.813 | 0.97 |
| 94_I | 212_L | 1.798 | 0.97 |
| 54_F | 203_S | 1.789 | 0.97 |
| 29_V | 32_P | 1.744 | 0.96 |
| 234_T | 238_N | 1.738 | 0.96 |
| 298_E | 399_R | 1.712 | 0.95 |
| 299_I | 338_L | 1.710 | 0.95 |
| 42_T | 46_D | 1.708 | 0.95 |
| 6_A | 23_D | 1.687 | 0.95 |
| 34_R | 40_R | 1.646 | 0.94 |
| 66_T | 189_Q | 1.629 | 0.93 |
| 55_L | 202_V | 1.610 | 0.93 |
| 298_E | 401_K | 1.595 | 0.92 |
| 100_Q | 343_P | 1.570 | 0.92 |
| 47_V | 90_Y | 1.517 | 0.90 |
| 2_I | 28_K | 1.516 | 0.90 |
| 8_A | 11_Y | 1.502 | 0.89 |
| 8_A | 20_K | 1.447 | 0.87 |
| 120_R | 149_D | 1.434 | 0.86 |
| 328_Y | 376_V | 1.430 | 0.86 |
| 309_W | 312_N | 1.416 | 0.85 |
| 346_V | 406_Y | 1.395 | 0.84 |
| 7_C | 11_Y | 1.389 | 0.83 |
| 2_I | 30_Y | 1.385 | 0.83 |
| 223_T | 273_D | 1.380 | 0.83 |
| 287_L | 405_L | 1.363 | 0.82 |
| 237_E | 243_T | 1.359 | 0.81 |
| 20_K | 23_D | 1.350 | 0.81 |
| 161_P | 339_P | 1.346 | 0.81 |
| 337_A | 401_K | 1.344 | 0.80 |
| 18_D | 23_D | 1.342 | 0.80 |
| 45_L | 49_E | 1.341 | 0.80 |
| 69_D | 72_R | 1.336 | 0.80 |
| 28_K | 365_R | 1.336 | 0.80 |
| 223_T | 263_I | 1.334 | 0.80 |
| 73_L | 76_K | 1.323 | 0.79 |
| 98_Y | 149_D | 1.322 | 0.79 |
| 293_Y | 405_L | 1.317 | 0.79 |
| 6_A | 34_R | 1.314 | 0.78 |
| 2_I | 238_N | 1.308 | 0.78 |
| 259_R | 362_S | 1.302 | 0.77 |
| 66_T | 200_L | 1.302 | 0.77 |
| 214_L | 287_L | 1.297 | 0.77 |
| 41_F | 46_D | 1.296 | 0.77 |
| 55_L | 185_V | 1.284 | 0.76 |
| 260_F | 300_V | 1.275 | 0.75 |
| 79_L | 174_D | 1.268 | 0.75 |
| 91_L | 105_I | 1.263 | 0.74 |
| 28_K | 366_G | 1.253 | 0.74 |
| 11_Y | 20_K | 1.247 | 0.73 |
| 52_P | 205_S | 1.246 | 0.73 |
| 250_H | 259_R | 1.244 | 0.73 |
| 190_I | 194_K | 1.239 | 0.72 |
| 5_V | 79_L | 1.235 | 0.72 |
| 6_A | 18_D | 1.232 | 0.72 |
| 28_K | 31_N | 1.230 | 0.72 |
| 291_T | 313_G | 1.227 | 0.71 |
| 125_Y | 128_P | 1.223 | 0.71 |
| 100_Q | 112_T | 1.222 | 0.71 |
| 129_G | 409_R | 1.216 | 0.70 |
| 68_T | 192_H | 1.215 | 0.70 |
| 221_Q | 263_I | 1.211 | 0.70 |
| 67_R | 290_A | 1.203 | 0.69 |
| 19_P | 26_Y | 1.201 | 0.69 |
| 114_S | 117_S | 1.198 | 0.69 |
| 136_T | 139_R | 1.197 | 0.69 |
| 269_T | 362_S | 1.193 | 0.68 |
| 28_K | 234_T | 1.193 | 0.68 |
| 117_S | 301_V | 1.191 | 0.68 |
| 236_V | 366_G | 1.188 | 0.68 |
| 6_A | 15_V | 1.187 | 0.68 |
| 221_Q | 366_G | 1.183 | 0.67 |
| 234_T | 366_G | 1.182 | 0.67 |
| 32_P | 366_G | 1.178 | 0.67 |
| 20_K | 336_L | 1.177 | 0.67 |
| 51_C | 236_V | 1.162 | 0.65 |
| 297_L | 371_L | 1.160 | 0.65 |
| 234_T | 240_G | 1.158 | 0.65 |
| 111_F | 404_E | 1.158 | 0.65 |
| 234_T | 365_R | 1.156 | 0.65 |
| 301_V | 394_H | 1.155 | 0.65 |
| 134_P | 140_A | 1.151 | 0.64 |
| 6_A | 11_Y | 1.147 | 0.64 |
| 45_L | 251_T | 1.138 | 0.63 |
| 90_Y | 300_V | 1.138 | 0.63 |
| 106_N | 205_S | 1.135 | 0.63 |
| 131_E | 373_A | 1.132 | 0.62 |
| 136_T | 394_H | 1.127 | 0.62 |
| 119_A | 150_T | 1.125 | 0.62 |
| 263_I | 398_V | 1.124 | 0.62 |
| 100_Q | 198_D | 1.122 | 0.61 |
| 253_I | 405_L | 1.115 | 0.61 |
| 103_G | 140_A | 1.115 | 0.61 |
| 232_V | 237_E | 1.114 | 0.60 |
| 294_F | 408_P | 1.112 | 0.60 |
| 109_F | 185_V | 1.111 | 0.60 |
| 236_V | 246_Q | 1.110 | 0.60 |
| 373_A | 394_H | 1.107 | 0.60 |
| 103_G | 183_G | 1.107 | 0.60 |
| 167_D | 342_A | 1.107 | 0.60 |
| 134_P | 213_R | 1.107 | 0.60 |
| 110_M | 327_A | 1.106 | 0.60 |
| 119_A | 290_A | 1.106 | 0.60 |
| 126_I | 399_R | 1.106 | 0.60 |
| 299_I | 336_L | 1.102 | 0.59 |
| 53_T | 219_R | 1.100 | 0.59 |
| 2_I | 234_T | 1.100 | 0.59 |
| 108_H | 157_T | 1.097 | 0.59 |
| 127_P | 161_P | 1.097 | 0.59 |
| 232_V | 242_E | 1.095 | 0.59 |
| 107_L | 202_V | 1.094 | 0.58 |
| 107_L | 114_S | 1.092 | 0.58 |
| 259_R | 263_I | 1.084 | 0.57 |
| 259_R | 269_T | 1.083 | 0.57 |
| 230_D | 241_G | 1.081 | 0.57 |
| 52_P | 202_V | 1.080 | 0.57 |
| 77_F | 85_H | 1.079 | 0.57 |
| 106_N | 157_T | 1.079 | 0.57 |
| 289_A | 411_L | 1.073 | 0.56 |
| 299_I | 396_L | 1.071 | 0.56 |
| 27_G | 30_Y | 1.071 | 0.56 |
| 287_L | 297_L | 1.066 | 0.55 |
| 65_T | 197_N | 1.066 | 0.55 |
| 193_G | 198_D | 1.065 | 0.55 |
| 113_G | 116_D | 1.064 | 0.55 |
| 221_Q | 272_I | 1.063 | 0.55 |
| 251_T | 258_D | 1.061 | 0.55 |
| 389_K | 396_L | 1.060 | 0.55 |
| 254_G | 308_T | 1.058 | 0.55 |
| 22_A | 300_V | 1.056 | 0.54 |
| 212_L | 392_A | 1.056 | 0.54 |
| 80_S | 83_A | 1.055 | 0.54 |
| 233_T | 366_G | 1.055 | 0.54 |
| 291_T | 409_R | 1.054 | 0.54 |
| 7_C | 12_G | 1.054 | 0.54 |
| 21_T | 413_A | 1.054 | 0.54 |
| 147_E | 190_I | 1.053 | 0.54 |
| 220_Q | 391_D | 1.050 | 0.54 |
| 126_I | 140_A | 1.049 | 0.54 |
| 41_F | 290_A | 1.048 | 0.54 |
| 8_A | 24_P | 1.047 | 0.53 |
| 128_P | 148_W | 1.047 | 0.53 |
| 149_D | 321_N | 1.047 | 0.53 |
| 6_A | 12_G | 1.045 | 0.53 |
| 121_Y | 377_K | 1.044 | 0.53 |
| 215_P | 411_L | 1.044 | 0.53 |
| 102_S | 260_F | 1.037 | 0.52 |
| 242_E | 250_H | 1.037 | 0.52 |
| 134_P | 311_P | 1.036 | 0.52 |
| 108_H | 211_E | 1.035 | 0.52 |
| 130_V | 166_A | 1.032 | 0.52 |
| 301_V | 373_A | 1.028 | 0.51 |
| 3_F | 182_Q | 1.027 | 0.51 |
| 37_Y | 346_V | 1.026 | 0.51 |
| 300_V | 401_K | 1.025 | 0.51 |
| 250_H | 309_W | 1.024 | 0.51 |
| 254_G | 362_S | 1.023 | 0.51 |
| 121_Y | 227_E | 1.023 | 0.51 |
| 122_M | 141_A | 1.022 | 0.51 |
| 31_N | 249_H | 1.021 | 0.51 |
| 149_D | 339_P | 1.021 | 0.51 |
| 328_Y | 336_L | 1.020 | 0.51 |
| 8_A | 18_D | 1.018 | 0.50 |
| 232_V | 250_H | 1.017 | 0.50 |
| 154_S | 313_G | 1.013 | 0.50 |
| 149_D | 161_P | 1.012 | 0.50 |
| 11_Y | 23_D | 1.011 | 0.50 |
| 81_L | 101_Y | 1.011 | 0.50 |
| 232_V | 235_T | 1.010 | 0.49 |
| 263_I | 309_W | 1.008 | 0.49 |
| 106_N | 208_K | 1.008 | 0.49 |
| 146_A | 281_G | 1.007 | 0.49 |
| 12_G | 20_K | 1.007 | 0.49 |
| 243_T | 250_H | 1.005 | 0.49 |
| 78_D | 181_V | 1.003 | 0.49 |
| 171_T | 212_L | 1.002 | 0.49 |
| 103_G | 210_F | 1.002 | 0.49 |
| 115_T | 150_T | 1.000 | 0.48 |
| 149_D | 183_G | 1.000 | 0.48 |
| 248_R | 251_T | 1.000 | 0.48 |
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 | |
| 2mev3 | 1 | 0.5139 | 100 | 0.5 | Contact Map |
| 3cjiB | 1 | 0.5093 | 100 | 0.501 | Contact Map |
| 1tme3 | 1 | 0.5093 | 100 | 0.506 | Contact Map |
| 4q4w3 | 1 | 0.5069 | 100 | 0.507 | Contact Map |
| 1qqp3 | 1 | 0.5 | 100 | 0.507 | Contact Map |
| 3vbhC | 1 | 0.5208 | 100 | 0.51 | Contact Map |
| 4wm8C | 1 | 0.537 | 100 | 0.51 | Contact Map |
| 1bev3 | 1 | 0.5208 | 100 | 0.511 | Contact Map |
| 2ws93 | 1 | 0.5069 | 100 | 0.511 | Contact Map |
| 1ncqC | 1 | 0.5162 | 100 | 0.512 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)