| uniqcapsids_via_tblastnlongestgt100mafftfasta ntax5403 nchar948 |
| ID: | 1489766613 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 50% gaps before running GREMLIN. |
| Length: | 211 (182) | ||
| Sequences: | 1158 (392) | ||
| Seq/Len: | 6.363 | ||
| Nf(neff/√len): | 29.1 |
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: 6.363).
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 |
| 88_W | 91_N | 1.959 | 1.00 |
| 196_S | 199_D | 1.933 | 1.00 |
| 146_D | 150_L | 1.823 | 1.00 |
| 178_R | 190_L | 1.667 | 1.00 |
| 77_E | 180_K | 1.667 | 1.00 |
| 196_S | 204_K | 1.639 | 1.00 |
| 72_Y | 184_L | 1.625 | 1.00 |
| 197_S | 202_K | 1.585 | 0.99 |
| 29_H | 37_D | 1.556 | 0.99 |
| 29_H | 38_R | 1.529 | 0.99 |
| 135_K | 138_V | 1.508 | 0.99 |
| 52_D | 55_Q | 1.452 | 0.99 |
| 71_Y | 75_D | 1.435 | 0.99 |
| 34_F | 37_D | 1.435 | 0.99 |
| 32_V | 36_M | 1.429 | 0.99 |
| 200_R | 205_I | 1.404 | 0.98 |
| 197_S | 200_R | 1.396 | 0.98 |
| 79_V | 180_K | 1.388 | 0.98 |
| 199_D | 204_K | 1.367 | 0.98 |
| 66_L | 76_L | 1.364 | 0.98 |
| 196_S | 202_K | 1.352 | 0.98 |
| 63_G | 73_F | 1.340 | 0.98 |
| 198_Q | 203_Q | 1.333 | 0.98 |
| 34_F | 47_S | 1.332 | 0.98 |
| 196_S | 201_H | 1.321 | 0.98 |
| 201_H | 205_I | 1.318 | 0.97 |
| 148_G | 152_A | 1.312 | 0.97 |
| 197_S | 201_H | 1.305 | 0.97 |
| 28_H | 32_V | 1.302 | 0.97 |
| 151_A | 154_V | 1.297 | 0.97 |
| 39_F | 79_V | 1.293 | 0.97 |
| 142_S | 199_D | 1.284 | 0.97 |
| 146_D | 151_A | 1.277 | 0.97 |
| 147_L | 202_K | 1.271 | 0.97 |
| 198_Q | 201_H | 1.271 | 0.97 |
| 197_S | 204_K | 1.254 | 0.96 |
| 138_V | 141_S | 1.253 | 0.96 |
| 106_A | 124_R | 1.240 | 0.96 |
| 202_K | 205_I | 1.232 | 0.96 |
| 31_D | 34_F | 1.227 | 0.96 |
| 32_V | 38_R | 1.223 | 0.96 |
| 70_T | 188_R | 1.212 | 0.95 |
| 141_S | 149_A | 1.207 | 0.95 |
| 64_A | 67_R | 1.202 | 0.95 |
| 27_R | 41_K | 1.191 | 0.95 |
| 201_H | 204_K | 1.190 | 0.95 |
| 49_H | 57_H | 1.182 | 0.94 |
| 99_S | 191_L | 1.176 | 0.94 |
| 81_R | 176_L | 1.168 | 0.94 |
| 70_T | 90_P | 1.167 | 0.94 |
| 197_S | 205_I | 1.163 | 0.94 |
| 32_V | 37_D | 1.155 | 0.93 |
| 116_A | 180_K | 1.155 | 0.93 |
| 142_S | 197_S | 1.152 | 0.93 |
| 61_L | 65_L | 1.152 | 0.93 |
| 27_R | 30_T | 1.147 | 0.93 |
| 38_R | 42_I | 1.145 | 0.93 |
| 199_D | 205_I | 1.145 | 0.93 |
| 198_Q | 202_K | 1.143 | 0.93 |
| 196_S | 205_I | 1.140 | 0.93 |
| 35_I | 85_N | 1.137 | 0.93 |
| 32_V | 184_L | 1.132 | 0.93 |
| 82_H | 173_H | 1.131 | 0.92 |
| 51_I | 54_M | 1.127 | 0.92 |
| 142_S | 149_A | 1.121 | 0.92 |
| 196_S | 203_Q | 1.120 | 0.92 |
| 150_L | 156_K | 1.119 | 0.92 |
| 181_R | 185_Y | 1.111 | 0.92 |
| 68_A | 190_L | 1.107 | 0.91 |
| 198_Q | 204_K | 1.099 | 0.91 |
| 89_V | 106_A | 1.097 | 0.91 |
| 31_D | 183_E | 1.096 | 0.91 |
| 69_A | 79_V | 1.095 | 0.91 |
| 37_D | 43_N | 1.094 | 0.91 |
| 58_Q | 167_I | 1.086 | 0.90 |
| 79_V | 115_L | 1.085 | 0.90 |
| 116_A | 182_A | 1.085 | 0.90 |
| 198_Q | 205_I | 1.085 | 0.90 |
| 152_A | 165_G | 1.069 | 0.89 |
| 53_L | 98_L | 1.061 | 0.89 |
| 73_F | 87_T | 1.061 | 0.89 |
| 78_I | 128_T | 1.056 | 0.89 |
| 46_K | 170_D | 1.053 | 0.88 |
| 125_V | 185_Y | 1.048 | 0.88 |
| 71_Y | 132_G | 1.048 | 0.88 |
| 107_Y | 176_L | 1.039 | 0.88 |
| 200_R | 204_K | 1.038 | 0.87 |
| 28_H | 62_V | 1.036 | 0.87 |
| 196_S | 200_R | 1.034 | 0.87 |
| 42_I | 61_L | 1.033 | 0.87 |
| 152_A | 177_V | 1.030 | 0.87 |
| 139_S | 142_S | 1.025 | 0.87 |
| 141_S | 200_R | 1.023 | 0.86 |
| 35_I | 38_R | 1.019 | 0.86 |
| 108_K | 121_A | 1.015 | 0.86 |
| 49_H | 56_T | 1.012 | 0.86 |
| 121_A | 136_Y | 1.010 | 0.85 |
| 77_E | 81_R | 1.009 | 0.85 |
| 90_P | 130_Y | 1.007 | 0.85 |
| 197_S | 203_Q | 1.006 | 0.85 |
| 74_S | 185_Y | 1.004 | 0.85 |
| 148_G | 153_R | 1.003 | 0.85 |
| 65_L | 73_F | 1.002 | 0.85 |
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 | |
| 1qqp1 | 1 | 0.891 | 100 | 0.066 | Contact Map |
| 1zba1 | 1 | 0.9052 | 100 | 0.067 | Contact Map |
| 1fmd1 | 1 | 0.8863 | 100 | 0.068 | Contact Map |
| 2wzr1 | 1 | 0.891 | 100 | 0.075 | Contact Map |
| 1hxs1 | 1 | 0.9431 | 100 | 0.207 | Contact Map |
| 1d4m1 | 1 | 0.9479 | 100 | 0.21 | Contact Map |
| 4gb31 | 1 | 0.9479 | 100 | 0.211 | Contact Map |
| 3vbhA | 1 | 0.9479 | 100 | 0.217 | Contact Map |
| 1ncqA | 1 | 0.9431 | 100 | 0.218 | Contact Map |
| 1ev11 | 1 | 0.9479 | 100 | 0.218 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)