| workingVP2_1B__VP1_1Dfasta |
| ID: | 1489785956 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 429 (411) | ||
| Sequences: | 518 (241.5) | ||
| Seq/Len: | 1.260 | ||
| Nf(neff/√len): | 11.9 |
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: 1.260).
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 |
| 125_M | 160_V | 3.515 | 1.00 |
| 125_M | 158_I | 2.934 | 1.00 |
| 120_C | 147_F | 2.897 | 1.00 |
| 125_M | 177_W | 2.526 | 1.00 |
| 71_T | 188_T | 2.520 | 1.00 |
| 124_A | 180_V | 2.515 | 1.00 |
| 158_I | 179_L | 2.434 | 0.99 |
| 122_L | 141_T | 2.362 | 0.99 |
| 148_I | 156_A | 2.303 | 0.99 |
| 293_D | 399_R | 2.301 | 0.99 |
| 295_E | 396_R | 2.215 | 0.99 |
| 1_D | 4_T | 2.053 | 0.98 |
| 106_D | 204_A | 2.051 | 0.98 |
| 295_E | 398_K | 2.029 | 0.97 |
| 147_F | 184_V | 1.946 | 0.96 |
| 109_V | 123_V | 1.915 | 0.96 |
| 160_V | 177_W | 1.897 | 0.96 |
| 163_L | 404_C | 1.773 | 0.93 |
| 114_N | 193_S | 1.747 | 0.93 |
| 117_N | 205_P | 1.695 | 0.91 |
| 69_W | 183_V | 1.666 | 0.90 |
| 306_W | 309_N | 1.625 | 0.89 |
| 109_V | 201_A | 1.623 | 0.88 |
| 288_T | 406_R | 1.610 | 0.88 |
| 63_K | 200_Y | 1.594 | 0.87 |
| 158_I | 177_W | 1.591 | 0.87 |
| 145_H | 212_G | 1.589 | 0.87 |
| 69_W | 121_L | 1.574 | 0.86 |
| 334_A | 398_K | 1.567 | 0.86 |
| 106_D | 159_T | 1.553 | 0.85 |
| 343_V | 403_Y | 1.527 | 0.84 |
| 69_W | 187_L | 1.521 | 0.84 |
| 335_L | 393_L | 1.519 | 0.84 |
| 257_F | 297_V | 1.517 | 0.83 |
| 59_E | 208_V | 1.484 | 0.82 |
| 83_L | 177_W | 1.478 | 0.81 |
| 114_N | 117_N | 1.469 | 0.81 |
| 126_V | 160_V | 1.458 | 0.80 |
| 83_L | 136_E | 1.441 | 0.79 |
| 104_G | 207_Y | 1.432 | 0.78 |
| 124_A | 141_T | 1.430 | 0.78 |
| 299_R | 394_L | 1.424 | 0.78 |
| 296_I | 335_L | 1.415 | 0.77 |
| 325_Y | 373_V | 1.397 | 0.76 |
| 102_R | 209_H | 1.381 | 0.75 |
| 61_F | 204_A | 1.380 | 0.75 |
| 128_E | 174_H | 1.374 | 0.74 |
| 110_S | 200_Y | 1.374 | 0.74 |
| 156_A | 306_W | 1.350 | 0.72 |
| 124_A | 248_T | 1.350 | 0.72 |
| 4_T | 8_T | 1.345 | 0.72 |
| 49_S | 98_Y | 1.341 | 0.72 |
| 83_L | 178_T | 1.340 | 0.71 |
| 13_R | 27_Q | 1.340 | 0.71 |
| 276_Q | 368_L | 1.336 | 0.71 |
| 254_M | 290_Y | 1.335 | 0.71 |
| 69_W | 149_S | 1.327 | 0.70 |
| 296_I | 333_L | 1.316 | 0.69 |
| 98_Y | 213_E | 1.310 | 0.69 |
| 124_A | 140_L | 1.309 | 0.69 |
| 12_D | 27_Q | 1.307 | 0.69 |
| 278_G | 337_Y | 1.306 | 0.69 |
| 25_T | 34_H | 1.297 | 0.68 |
| 125_M | 163_L | 1.289 | 0.67 |
| 12_D | 146_Q | 1.267 | 0.65 |
| 22_T | 44_A | 1.267 | 0.65 |
| 20_G | 228_P | 1.262 | 0.65 |
| 118_G | 298_V | 1.257 | 0.64 |
| 127_P | 213_E | 1.256 | 0.64 |
| 298_V | 391_H | 1.255 | 0.64 |
| 286_A | 408_L | 1.253 | 0.64 |
| 264_S | 393_L | 1.244 | 0.63 |
| 118_G | 194_A | 1.242 | 0.63 |
| 102_R | 161_P | 1.242 | 0.63 |
| 106_D | 157_H | 1.239 | 0.63 |
| 105_W | 143_F | 1.238 | 0.63 |
| 1_D | 9_L | 1.235 | 0.62 |
| 17_T | 30_V | 1.232 | 0.62 |
| 60_R | 228_P | 1.230 | 0.62 |
| 19_N | 43_V | 1.229 | 0.62 |
| 308_P | 405_P | 1.226 | 0.61 |
| 23_T | 61_F | 1.225 | 0.61 |
| 126_V | 180_V | 1.222 | 0.61 |
| 143_F | 407_P | 1.222 | 0.61 |
| 49_S | 57_Q | 1.222 | 0.61 |
| 184_V | 351_T | 1.221 | 0.61 |
| 49_S | 213_E | 1.219 | 0.61 |
| 255_D | 294_L | 1.218 | 0.61 |
| 254_M | 345_A | 1.218 | 0.61 |
| 123_V | 181_V | 1.218 | 0.61 |
| 298_V | 335_L | 1.214 | 0.60 |
| 191_N | 298_V | 1.213 | 0.60 |
| 298_V | 368_L | 1.212 | 0.60 |
| 98_Y | 149_S | 1.211 | 0.60 |
| 35_G | 59_E | 1.210 | 0.60 |
| 98_Y | 112_V | 1.204 | 0.59 |
| 228_P | 366_G | 1.204 | 0.59 |
| 154_M | 208_V | 1.199 | 0.59 |
| 25_T | 47_N | 1.195 | 0.59 |
| 174_H | 205_P | 1.194 | 0.58 |
| 294_L | 304_L | 1.182 | 0.57 |
| 139_Q | 396_R | 1.180 | 0.57 |
| 27_Q | 145_H | 1.170 | 0.56 |
| 27_Q | 149_S | 1.169 | 0.56 |
| 1_D | 8_T | 1.169 | 0.56 |
| 55_V | 59_E | 1.169 | 0.56 |
| 201_A | 226_A | 1.167 | 0.56 |
| 112_V | 192_T | 1.154 | 0.55 |
| 149_S | 213_E | 1.154 | 0.55 |
| 127_P | 161_P | 1.151 | 0.54 |
| 342_R | 402_L | 1.149 | 0.54 |
| 113_G | 150_P | 1.148 | 0.54 |
| 161_P | 336_P | 1.148 | 0.54 |
| 15_L | 32_V | 1.138 | 0.53 |
| 120_C | 149_S | 1.138 | 0.53 |
| 189_V | 193_S | 1.132 | 0.52 |
| 128_E | 205_P | 1.130 | 0.52 |
| 60_R | 336_P | 1.129 | 0.52 |
| 306_W | 366_G | 1.129 | 0.52 |
| 304_L | 328_A | 1.129 | 0.52 |
| 55_V | 208_V | 1.124 | 0.52 |
| 15_L | 29_S | 1.123 | 0.51 |
| 162_Y | 405_P | 1.123 | 0.51 |
| 3_K | 11_E | 1.121 | 0.51 |
| 5_E | 12_D | 1.111 | 0.50 |
| 99_A | 118_G | 1.111 | 0.50 |
| 112_V | 116_F | 1.107 | 0.50 |
| 260_I | 395_V | 1.107 | 0.50 |
| 13_R | 146_Q | 1.106 | 0.50 |
| 104_G | 162_Y | 1.105 | 0.50 |
| 109_V | 199_V | 1.103 | 0.50 |
| 115_Q | 120_C | 1.102 | 0.49 |
| 107_V | 111_A | 1.102 | 0.49 |
| 107_V | 160_V | 1.101 | 0.49 |
| 295_E | 334_A | 1.100 | 0.49 |
| 105_W | 179_L | 1.099 | 0.49 |
| 297_V | 398_K | 1.098 | 0.49 |
| 114_N | 138_Y | 1.097 | 0.49 |
| 25_T | 153_N | 1.094 | 0.49 |
| 18_R | 23_T | 1.094 | 0.49 |
| 29_S | 48_T | 1.085 | 0.48 |
| 116_F | 212_G | 1.082 | 0.47 |
| 264_S | 370_A | 1.080 | 0.47 |
| 291_F | 401_E | 1.077 | 0.47 |
| 183_V | 186_P | 1.073 | 0.47 |
| 2_K | 9_L | 1.072 | 0.46 |
| 118_G | 188_T | 1.072 | 0.46 |
| 311_A | 395_V | 1.071 | 0.46 |
| 264_S | 388_D | 1.063 | 0.46 |
| 294_L | 368_L | 1.063 | 0.46 |
| 292_S | 400_A | 1.060 | 0.45 |
| 102_R | 168_Y | 1.060 | 0.45 |
| 310_G | 406_R | 1.057 | 0.45 |
| 300_H | 304_L | 1.053 | 0.45 |
| 95_V | 101_M | 1.053 | 0.45 |
| 116_F | 228_P | 1.051 | 0.44 |
| 119_G | 336_P | 1.051 | 0.44 |
| 46_P | 50_G | 1.048 | 0.44 |
| 275_H | 352_S | 1.046 | 0.44 |
| 98_Y | 212_G | 1.042 | 0.44 |
| 146_Q | 152_T | 1.042 | 0.44 |
| 104_G | 144_P | 1.042 | 0.44 |
| 112_V | 200_Y | 1.041 | 0.43 |
| 160_V | 163_L | 1.040 | 0.43 |
| 210_V | 214_L | 1.040 | 0.43 |
| 11_E | 22_T | 1.038 | 0.43 |
| 153_N | 371_R | 1.037 | 0.43 |
| 136_E | 410_A | 1.033 | 0.43 |
| 181_V | 207_Y | 1.032 | 0.43 |
| 293_D | 398_K | 1.032 | 0.43 |
| 98_Y | 146_Q | 1.031 | 0.42 |
| 11_E | 16_T | 1.028 | 0.42 |
| 174_H | 406_R | 1.027 | 0.42 |
| 325_Y | 333_L | 1.023 | 0.42 |
| 49_S | 110_S | 1.021 | 0.41 |
| 148_I | 197_I | 1.019 | 0.41 |
| 37_S | 52_E | 1.016 | 0.41 |
| 109_V | 156_A | 1.014 | 0.41 |
| 123_V | 199_V | 1.014 | 0.41 |
| 33_T | 102_R | 1.013 | 0.41 |
| 144_P | 149_S | 1.013 | 0.41 |
| 149_S | 212_G | 1.011 | 0.41 |
| 146_Q | 202_N | 1.011 | 0.41 |
| 311_A | 335_L | 1.009 | 0.40 |
| 22_T | 27_Q | 1.009 | 0.40 |
| 36_Y | 288_T | 1.007 | 0.40 |
| 287_A | 402_L | 1.005 | 0.40 |
| 333_L | 337_Y | 1.004 | 0.40 |
| 70_T | 192_T | 1.003 | 0.40 |
| 149_S | 322_P | 1.003 | 0.40 |
| 155_T | 202_N | 1.002 | 0.40 |
| 261_Q | 393_L | 1.001 | 0.40 |
| 117_N | 174_H | 1.000 | 0.39 |
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 | |
| 3cjiC | 1 | 0.4872 | 100 | 0.426 | Contact Map |
| 1tme2 | 1 | 0.4872 | 100 | 0.433 | Contact Map |
| 4q4w2 | 1 | 0.4918 | 100 | 0.439 | Contact Map |
| 1ncqB | 1 | 0.4895 | 100 | 0.44 | Contact Map |
| 1pov0 | 1 | 0.4709 | 100 | 0.443 | Contact Map |
| 4gb32 | 1 | 0.4848 | 100 | 0.447 | Contact Map |
| 1aym2 | 1 | 0.4802 | 100 | 0.447 | Contact Map |
| 1bev2 | 1 | 0.4965 | 100 | 0.448 | Contact Map |
| 4rr3G | 5 | 0.4732 | 100 | 0.452 | Contact Map |
| 4wm8B | 1 | 0.4755 | 100 | 0.453 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)