| workingVP2_1B__VP3_1Cfasta |
| ID: | 1489785983 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 439 (436) | ||
| Sequences: | 847 (357.4) | ||
| Seq/Len: | 1.943 | ||
| Nf(neff/√len): | 17.1 |
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: 1.943).
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 |
| 325_L | 378_I | 3.207 | 1.00 |
| 322_T | 427_D | 3.112 | 1.00 |
| 125_M | 160_V | 2.496 | 1.00 |
| 120_C | 147_F | 2.455 | 1.00 |
| 326_H | 373_K | 2.378 | 1.00 |
| 125_M | 158_I | 2.332 | 1.00 |
| 107_V | 160_V | 2.274 | 1.00 |
| 69_W | 183_V | 2.180 | 0.99 |
| 114_N | 193_S | 2.168 | 0.99 |
| 313_A | 430_L | 2.134 | 0.99 |
| 147_F | 184_V | 2.128 | 0.99 |
| 124_A | 180_V | 2.123 | 0.99 |
| 322_T | 425_G | 2.116 | 0.99 |
| 1_D | 4_T | 2.098 | 0.99 |
| 106_D | 204_A | 1.978 | 0.99 |
| 323_I | 422_V | 1.943 | 0.99 |
| 114_N | 117_N | 1.885 | 0.98 |
| 104_G | 207_Y | 1.791 | 0.97 |
| 324_N | 423_S | 1.789 | 0.97 |
| 327_F | 405_I | 1.774 | 0.97 |
| 102_R | 209_H | 1.760 | 0.97 |
| 125_M | 177_W | 1.758 | 0.97 |
| 327_F | 378_I | 1.721 | 0.96 |
| 343_Y | 401_G | 1.705 | 0.96 |
| 122_L | 141_T | 1.691 | 0.96 |
| 123_V | 199_V | 1.662 | 0.95 |
| 71_T | 188_T | 1.651 | 0.95 |
| 320_S | 429_E | 1.621 | 0.94 |
| 158_I | 179_L | 1.609 | 0.94 |
| 109_V | 201_A | 1.581 | 0.93 |
| 337_A | 367_D | 1.579 | 0.93 |
| 405_I | 418_L | 1.573 | 0.93 |
| 121_L | 181_V | 1.567 | 0.93 |
| 148_I | 156_A | 1.560 | 0.93 |
| 106_D | 157_H | 1.556 | 0.93 |
| 341_V | 403_V | 1.554 | 0.93 |
| 272_F | 421_S | 1.545 | 0.92 |
| 84_P | 87_H | 1.537 | 0.92 |
| 108_E | 155_T | 1.535 | 0.92 |
| 271_T | 308_Y | 1.519 | 0.91 |
| 95_V | 210_V | 1.515 | 0.91 |
| 7_T | 45_G | 1.482 | 0.90 |
| 7_T | 48_T | 1.468 | 0.89 |
| 6_E | 45_G | 1.464 | 0.89 |
| 6_E | 48_T | 1.463 | 0.89 |
| 109_V | 123_V | 1.463 | 0.89 |
| 343_Y | 346_P | 1.461 | 0.89 |
| 120_C | 149_S | 1.447 | 0.88 |
| 45_G | 48_T | 1.434 | 0.88 |
| 100_Y | 383_A | 1.433 | 0.88 |
| 76_G | 219_G | 1.411 | 0.87 |
| 405_I | 420_V | 1.403 | 0.86 |
| 4_T | 48_T | 1.399 | 0.86 |
| 226_A | 229_Y | 1.395 | 0.86 |
| 17_T | 30_V | 1.381 | 0.85 |
| 331_G | 334_D | 1.378 | 0.85 |
| 124_A | 140_L | 1.365 | 0.84 |
| 106_D | 159_T | 1.332 | 0.82 |
| 22_T | 44_A | 1.332 | 0.82 |
| 185_S | 419_V | 1.331 | 0.82 |
| 46_P | 50_G | 1.318 | 0.81 |
| 108_E | 157_H | 1.316 | 0.81 |
| 324_N | 426_K | 1.315 | 0.81 |
| 200_Y | 367_D | 1.310 | 0.81 |
| 117_N | 187_L | 1.308 | 0.81 |
| 104_G | 346_P | 1.297 | 0.80 |
| 321_G | 428_F | 1.292 | 0.79 |
| 5_E | 45_G | 1.288 | 0.79 |
| 183_V | 270_P | 1.285 | 0.79 |
| 326_H | 375_T | 1.284 | 0.79 |
| 15_L | 32_V | 1.283 | 0.79 |
| 337_A | 368_T | 1.272 | 0.78 |
| 332_S | 335_S | 1.270 | 0.78 |
| 183_V | 425_G | 1.265 | 0.77 |
| 98_Y | 149_S | 1.263 | 0.77 |
| 44_A | 47_N | 1.260 | 0.77 |
| 424_A | 428_F | 1.255 | 0.77 |
| 4_T | 7_T | 1.245 | 0.76 |
| 4_T | 8_T | 1.245 | 0.76 |
| 49_S | 52_E | 1.245 | 0.76 |
| 177_W | 213_E | 1.245 | 0.76 |
| 25_T | 34_H | 1.239 | 0.75 |
| 139_Q | 271_T | 1.236 | 0.75 |
| 325_L | 403_V | 1.226 | 0.74 |
| 6_E | 85_S | 1.225 | 0.74 |
| 4_T | 45_G | 1.222 | 0.74 |
| 345_P | 382_S | 1.207 | 0.73 |
| 346_P | 366_W | 1.205 | 0.72 |
| 18_R | 23_T | 1.202 | 0.72 |
| 3_K | 7_T | 1.198 | 0.72 |
| 89_G | 92_G | 1.197 | 0.72 |
| 298_S | 378_I | 1.197 | 0.72 |
| 321_G | 427_D | 1.196 | 0.72 |
| 345_P | 401_G | 1.193 | 0.71 |
| 69_W | 121_L | 1.190 | 0.71 |
| 112_V | 116_F | 1.188 | 0.71 |
| 2_K | 5_E | 1.186 | 0.71 |
| 13_R | 27_Q | 1.186 | 0.71 |
| 121_L | 187_L | 1.182 | 0.70 |
| 15_L | 29_S | 1.181 | 0.70 |
| 121_L | 150_P | 1.179 | 0.70 |
| 23_T | 61_F | 1.175 | 0.70 |
| 5_E | 48_T | 1.174 | 0.70 |
| 4_T | 47_N | 1.161 | 0.68 |
| 19_N | 43_V | 1.159 | 0.68 |
| 1_D | 8_T | 1.159 | 0.68 |
| 115_Q | 336_K | 1.149 | 0.67 |
| 386_Y | 431_R | 1.139 | 0.66 |
| 11_E | 16_T | 1.133 | 0.66 |
| 12_D | 27_Q | 1.132 | 0.66 |
| 5_E | 8_T | 1.131 | 0.65 |
| 10_L | 28_S | 1.130 | 0.65 |
| 116_F | 212_G | 1.126 | 0.65 |
| 7_T | 47_N | 1.125 | 0.65 |
| 109_V | 199_V | 1.123 | 0.65 |
| 309_L | 323_I | 1.122 | 0.65 |
| 333_T | 376_F | 1.119 | 0.64 |
| 122_L | 140_L | 1.118 | 0.64 |
| 335_S | 416_D | 1.117 | 0.64 |
| 292_L | 313_A | 1.114 | 0.64 |
| 1_D | 7_T | 1.113 | 0.64 |
| 38_T | 254_N | 1.111 | 0.63 |
| 69_W | 187_L | 1.108 | 0.63 |
| 27_Q | 369_G | 1.107 | 0.63 |
| 93_H | 97_S | 1.106 | 0.63 |
| 81_L | 85_S | 1.106 | 0.63 |
| 113_G | 150_P | 1.105 | 0.63 |
| 160_V | 177_W | 1.104 | 0.63 |
| 34_H | 39_E | 1.102 | 0.62 |
| 115_Q | 338_R | 1.102 | 0.62 |
| 211_A | 316_Y | 1.102 | 0.62 |
| 296_D | 301_A | 1.101 | 0.62 |
| 189_V | 193_S | 1.100 | 0.62 |
| 259_F | 368_T | 1.097 | 0.62 |
| 339_Y | 407_Q | 1.095 | 0.62 |
| 1_D | 9_L | 1.095 | 0.62 |
| 332_S | 380_Y | 1.093 | 0.62 |
| 18_R | 34_H | 1.092 | 0.61 |
| 117_N | 205_P | 1.091 | 0.61 |
| 44_A | 48_T | 1.087 | 0.61 |
| 177_W | 393_T | 1.085 | 0.61 |
| 193_S | 410_H | 1.080 | 0.60 |
| 9_L | 28_S | 1.078 | 0.60 |
| 261_N | 338_R | 1.076 | 0.60 |
| 352_P | 366_W | 1.073 | 0.59 |
| 156_A | 339_Y | 1.072 | 0.59 |
| 35_G | 59_E | 1.067 | 0.59 |
| 167_R | 256_P | 1.067 | 0.59 |
| 11_E | 22_T | 1.066 | 0.59 |
| 3_K | 48_T | 1.066 | 0.59 |
| 273_L | 325_L | 1.065 | 0.59 |
| 59_E | 208_V | 1.065 | 0.59 |
| 149_S | 358_A | 1.064 | 0.58 |
| 94_L | 210_V | 1.064 | 0.58 |
| 69_W | 321_G | 1.063 | 0.58 |
| 1_D | 48_T | 1.062 | 0.58 |
| 17_T | 32_V | 1.057 | 0.58 |
| 39_E | 45_G | 1.054 | 0.57 |
| 7_T | 16_T | 1.052 | 0.57 |
| 48_T | 246_K | 1.046 | 0.56 |
| 196_Q | 378_I | 1.043 | 0.56 |
| 82_E | 85_S | 1.043 | 0.56 |
| 4_T | 32_V | 1.040 | 0.56 |
| 214_L | 217_K | 1.040 | 0.56 |
| 17_T | 28_S | 1.039 | 0.56 |
| 48_T | 52_E | 1.038 | 0.56 |
| 25_T | 31_G | 1.037 | 0.56 |
| 83_L | 86_D | 1.035 | 0.55 |
| 42_H | 46_P | 1.034 | 0.55 |
| 2_K | 219_G | 1.032 | 0.55 |
| 346_P | 352_P | 1.030 | 0.55 |
| 2_K | 6_E | 1.028 | 0.55 |
| 106_D | 206_T | 1.028 | 0.55 |
| 9_L | 16_T | 1.026 | 0.54 |
| 364_A | 376_F | 1.026 | 0.54 |
| 339_Y | 405_I | 1.026 | 0.54 |
| 15_L | 19_N | 1.025 | 0.54 |
| 38_T | 42_H | 1.024 | 0.54 |
| 348_V | 384_A | 1.022 | 0.54 |
| 339_Y | 416_D | 1.020 | 0.54 |
| 142_L | 308_Y | 1.017 | 0.53 |
| 5_E | 47_N | 1.017 | 0.53 |
| 106_D | 415_N | 1.015 | 0.53 |
| 44_A | 49_S | 1.014 | 0.53 |
| 67_F | 199_V | 1.014 | 0.53 |
| 338_R | 367_D | 1.013 | 0.53 |
| 210_V | 261_N | 1.013 | 0.53 |
| 35_G | 41_D | 1.012 | 0.53 |
| 34_H | 38_T | 1.008 | 0.52 |
| 369_G | 387_A | 1.008 | 0.52 |
| 201_A | 348_V | 1.008 | 0.52 |
| 327_F | 420_V | 1.008 | 0.52 |
| 312_I | 430_L | 1.007 | 0.52 |
| 200_Y | 337_A | 1.007 | 0.52 |
| 144_P | 367_D | 1.007 | 0.52 |
| 187_L | 197_I | 1.006 | 0.52 |
| 205_P | 366_W | 1.004 | 0.52 |
| 215_P | 393_T | 1.003 | 0.52 |
| 213_E | 217_K | 1.003 | 0.52 |
| 107_V | 121_L | 1.003 | 0.52 |
| 55_V | 59_E | 1.001 | 0.52 |
| 40_E | 54_R | 1.001 | 0.52 |
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 | |
| 1tme2 | 1 | 0.4761 | 100 | 0.453 | Contact Map |
| 3cjiC | 1 | 0.4761 | 100 | 0.458 | Contact Map |
| 4q4w2 | 1 | 0.4806 | 100 | 0.465 | Contact Map |
| 1ncqB | 1 | 0.4784 | 100 | 0.467 | Contact Map |
| 1bev2 | 1 | 0.4852 | 100 | 0.467 | Contact Map |
| 4gb32 | 1 | 0.4738 | 100 | 0.468 | Contact Map |
| 4wm8B | 1 | 0.4647 | 100 | 0.471 | Contact Map |
| 4rr3G | 5 | 0.4624 | 100 | 0.471 | Contact Map |
| 1pov0 | 1 | 0.4601 | 100 | 0.471 | Contact Map |
| 1aym2 | 1 | 0.4692 | 100 | 0.474 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)