| RIFIN |
| ID: | 1446560346 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 367 (352) | ||
| Sequences: | 380 (321.1) | ||
| Seq/Len: | 1.080 | ||
| Nf(neff/√len): | 17.1 |
HHblits Results: (2015_06)
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: 1.080).
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 |
| 61_Q | 65_R | 2.904 | 1.00 |
| 61_Q | 64_D | 2.888 | 1.00 |
| 35_N | 39_C | 2.888 | 1.00 |
| 166_A | 169_T | 2.796 | 1.00 |
| 328_I | 332_V | 2.713 | 1.00 |
| 84_C | 91_E | 2.580 | 1.00 |
| 91_E | 97_L | 2.546 | 0.99 |
| 88_C | 91_E | 2.494 | 0.99 |
| 342_V | 347_I | 2.319 | 0.99 |
| 71_H | 74_D | 2.313 | 0.99 |
| 159_I | 165_N | 2.309 | 0.99 |
| 60_Q | 65_R | 2.258 | 0.98 |
| 60_Q | 64_D | 2.232 | 0.98 |
| 6_I | 13_L | 2.227 | 0.98 |
| 43_L | 48_N | 2.163 | 0.98 |
| 324_Y | 329_A | 2.152 | 0.98 |
| 84_C | 88_C | 2.134 | 0.98 |
| 3_D | 7_N | 2.101 | 0.97 |
| 159_I | 163_A | 2.087 | 0.97 |
| 155_V | 163_A | 2.062 | 0.97 |
| 43_L | 46_P | 2.056 | 0.97 |
| 70_F | 74_D | 2.006 | 0.96 |
| 329_A | 332_V | 1.986 | 0.96 |
| 335_V | 338_V | 1.960 | 0.95 |
| 320_T | 329_A | 1.948 | 0.95 |
| 163_A | 166_A | 1.915 | 0.95 |
| 137_V | 140_K | 1.880 | 0.94 |
| 159_I | 166_A | 1.838 | 0.93 |
| 88_C | 97_L | 1.811 | 0.92 |
| 158_E | 164_V | 1.788 | 0.92 |
| 320_T | 324_Y | 1.767 | 0.91 |
| 33_E | 37_S | 1.763 | 0.91 |
| 158_E | 168_K | 1.737 | 0.90 |
| 45_S | 48_N | 1.734 | 0.90 |
| 6_I | 12_A | 1.725 | 0.90 |
| 158_E | 165_N | 1.705 | 0.89 |
| 155_V | 158_E | 1.681 | 0.88 |
| 33_E | 39_C | 1.671 | 0.88 |
| 163_A | 167_W | 1.671 | 0.88 |
| 312_N | 315_A | 1.657 | 0.87 |
| 308_A | 312_N | 1.653 | 0.87 |
| 44_Y | 48_N | 1.651 | 0.87 |
| 54_E | 61_Q | 1.643 | 0.86 |
| 64_D | 67_T | 1.641 | 0.86 |
| 319_A | 322_P | 1.640 | 0.86 |
| 101_I | 106_T | 1.638 | 0.86 |
| 143_Q | 148_I | 1.606 | 0.85 |
| 165_N | 168_K | 1.590 | 0.84 |
| 188_K | 191_G | 1.585 | 0.84 |
| 320_T | 328_I | 1.581 | 0.83 |
| 165_N | 169_T | 1.580 | 0.83 |
| 322_P | 325_T | 1.574 | 0.83 |
| 324_Y | 328_I | 1.564 | 0.82 |
| 142_A | 148_I | 1.551 | 0.82 |
| 311_M | 315_A | 1.550 | 0.82 |
| 152_S | 156_L | 1.536 | 0.81 |
| 198_T | 202_I | 1.528 | 0.80 |
| 320_T | 323_Y | 1.525 | 0.80 |
| 117_T | 120_D | 1.519 | 0.80 |
| 63_V | 67_T | 1.503 | 0.79 |
| 363_I | 367_N | 1.498 | 0.79 |
| 3_D | 6_I | 1.493 | 0.78 |
| 155_V | 159_I | 1.492 | 0.78 |
| 188_K | 192_E | 1.489 | 0.78 |
| 84_C | 97_L | 1.460 | 0.76 |
| 105_F | 108_K | 1.453 | 0.76 |
| 325_T | 328_I | 1.449 | 0.75 |
| 144_N | 148_I | 1.427 | 0.74 |
| 215_T | 218_K | 1.425 | 0.74 |
| 163_A | 169_T | 1.412 | 0.73 |
| 113_Q | 120_D | 1.398 | 0.72 |
| 104_E | 108_K | 1.390 | 0.71 |
| 115_D | 120_D | 1.375 | 0.70 |
| 192_E | 196_V | 1.361 | 0.69 |
| 324_Y | 332_V | 1.359 | 0.68 |
| 88_C | 101_I | 1.356 | 0.68 |
| 320_T | 332_V | 1.350 | 0.68 |
| 80_K | 83_Q | 1.334 | 0.66 |
| 155_V | 166_A | 1.330 | 0.66 |
| 203_L | 207_Y | 1.327 | 0.66 |
| 191_G | 198_T | 1.324 | 0.65 |
| 91_E | 101_I | 1.320 | 0.65 |
| 222_A | 225_H | 1.310 | 0.64 |
| 30_R | 33_E | 1.310 | 0.64 |
| 318_A | 321_T | 1.308 | 0.64 |
| 71_H | 78_Q | 1.306 | 0.64 |
| 87_Q | 91_E | 1.302 | 0.64 |
| 115_D | 118_T | 1.299 | 0.63 |
| 309_I | 313_T | 1.289 | 0.62 |
| 323_Y | 328_I | 1.282 | 0.62 |
| 94_K | 102_E | 1.280 | 0.62 |
| 155_V | 164_V | 1.279 | 0.62 |
| 74_D | 78_Q | 1.278 | 0.61 |
| 54_E | 60_Q | 1.262 | 0.60 |
| 82_K | 88_C | 1.257 | 0.60 |
| 159_I | 169_T | 1.256 | 0.59 |
| 2_K | 8_I | 1.252 | 0.59 |
| 323_Y | 329_A | 1.252 | 0.59 |
| 321_T | 328_I | 1.239 | 0.58 |
| 78_Q | 83_Q | 1.234 | 0.57 |
| 155_V | 169_T | 1.234 | 0.57 |
| 107_E | 110_S | 1.233 | 0.57 |
| 113_Q | 118_T | 1.230 | 0.57 |
| 164_V | 169_T | 1.227 | 0.57 |
| 55_M | 61_Q | 1.222 | 0.56 |
| 94_K | 100_K | 1.213 | 0.55 |
| 78_Q | 82_K | 1.204 | 0.55 |
| 106_T | 110_S | 1.203 | 0.55 |
| 79_S | 83_Q | 1.200 | 0.54 |
| 97_L | 102_E | 1.199 | 0.54 |
| 70_F | 77_L | 1.197 | 0.54 |
| 60_Q | 63_V | 1.188 | 0.53 |
| 296_A | 300_V | 1.186 | 0.53 |
| 60_Q | 67_T | 1.182 | 0.53 |
| 71_H | 77_L | 1.180 | 0.52 |
| 109_L | 118_T | 1.178 | 0.52 |
| 70_F | 78_Q | 1.177 | 0.52 |
| 164_V | 168_K | 1.177 | 0.52 |
| 362_Y | 365_L | 1.177 | 0.52 |
| 158_E | 163_A | 1.169 | 0.51 |
| 321_T | 324_Y | 1.164 | 0.51 |
| 158_E | 169_T | 1.162 | 0.51 |
| 7_N | 10_L | 1.161 | 0.51 |
| 113_Q | 117_T | 1.153 | 0.50 |
| 84_C | 87_Q | 1.147 | 0.49 |
| 12_A | 20_Y | 1.147 | 0.49 |
| 284_N | 287_H | 1.147 | 0.49 |
| 109_L | 120_D | 1.146 | 0.49 |
| 197_E | 202_I | 1.130 | 0.48 |
| 97_L | 104_E | 1.127 | 0.47 |
| 152_S | 155_V | 1.125 | 0.47 |
| 300_V | 304_K | 1.124 | 0.47 |
| 31_H | 35_N | 1.123 | 0.47 |
| 78_Q | 84_C | 1.121 | 0.47 |
| 221_F | 225_H | 1.121 | 0.47 |
| 57_R | 60_Q | 1.115 | 0.46 |
| 144_N | 155_V | 1.114 | 0.46 |
| 159_I | 168_K | 1.113 | 0.46 |
| 317_E | 322_P | 1.108 | 0.46 |
| 109_L | 113_Q | 1.097 | 0.45 |
| 362_Y | 366_L | 1.092 | 0.44 |
| 325_T | 329_A | 1.092 | 0.44 |
| 59_M | 64_D | 1.073 | 0.42 |
| 172_L | 176_I | 1.072 | 0.42 |
| 1_M | 8_I | 1.072 | 0.42 |
| 80_K | 91_E | 1.071 | 0.42 |
| 143_Q | 155_V | 1.066 | 0.42 |
| 31_H | 37_S | 1.063 | 0.41 |
| 5_Y | 15_L | 1.061 | 0.41 |
| 109_L | 117_T | 1.061 | 0.41 |
| 13_L | 16_N | 1.057 | 0.41 |
| 220_F | 223_T | 1.056 | 0.41 |
| 198_T | 203_L | 1.054 | 0.41 |
| 43_L | 53_P | 1.052 | 0.40 |
| 329_A | 336_V | 1.052 | 0.40 |
| 26_Y | 32_T | 1.052 | 0.40 |
| 220_F | 225_H | 1.047 | 0.40 |
| 137_V | 145_L | 1.044 | 0.40 |
| 195_G | 203_L | 1.043 | 0.40 |
| 298_T | 302_A | 1.042 | 0.39 |
| 359_K | 365_L | 1.041 | 0.39 |
| 311_M | 314_E | 1.038 | 0.39 |
| 177_A | 180_Q | 1.037 | 0.39 |
| 155_V | 167_W | 1.033 | 0.39 |
| 83_Q | 86_D | 1.032 | 0.39 |
| 159_I | 167_W | 1.028 | 0.38 |
| 3_D | 10_L | 1.026 | 0.38 |
| 140_K | 145_L | 1.025 | 0.38 |
| 144_N | 153_T | 1.024 | 0.38 |
| 360_L | 363_I | 1.019 | 0.37 |
| 185_A | 188_K | 1.019 | 0.37 |
| 309_I | 312_N | 1.018 | 0.37 |
| 311_M | 317_E | 1.018 | 0.37 |
| 194_K | 197_E | 1.017 | 0.37 |
| 328_I | 336_V | 1.011 | 0.37 |
| 109_L | 115_D | 1.008 | 0.36 |
| 319_A | 323_Y | 1.008 | 0.36 |
| 105_F | 110_S | 1.007 | 0.36 |
| 213_K | 216_P | 1.006 | 0.36 |
| 158_E | 166_A | 1.005 | 0.36 |
| 155_V | 165_N | 1.003 | 0.36 |
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 | |
| 2m20A | 2 | 0.1144 | 86.3 | 0.972 | Contact Map |
| 2jwaA | 2 | 0.1172 | 72.1 | 0.976 | Contact Map |
| 2l2tA | 2 | 0.1172 | 68.9 | 0.976 | Contact Map |
| 2k9yA | 2 | 0.109 | 68.1 | 0.976 | Contact Map |
| 2ks1B | 1 | 0.1172 | 62.5 | 0.977 | Contact Map |
| 2gsmB | 2 | 0.1935 | 60.9 | 0.977 | Contact Map |
| 2k1kA | 2 | 0.1035 | 57.4 | 0.978 | Contact Map |
| 1iijA | 1 | 0.0954 | 52.9 | 0.978 | Contact Map |
| 2rddB | 1 | 0.0981 | 42.7 | 0.98 | Contact Map |
| 2kncB | 1 | 0.1471 | 30.3 | 0.981 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)