| Q49DS8_9HIV1 |
| ID: | 1416818806 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 208 (208) | ||
| Sequences: | 9913 (1657) | ||
| Seq/Len: | 47.659 | ||
| Nf(neff/√len): | 114.9 |
Jackhmmer Results: (2014_04_16)
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: 47.659).
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 |
| 12_I | 166_L | 5.543 | 1.00 |
| 75_K | 78_N | 3.797 | 1.00 |
| 6_I | 79_L | 3.479 | 1.00 |
| 22_I | 64_S | 3.323 | 1.00 |
| 138_N | 145_K | 2.830 | 1.00 |
| 4_E | 11_K | 2.775 | 1.00 |
| 29_Y | 155_R | 2.747 | 1.00 |
| 19_E | 67_K | 2.747 | 1.00 |
| 19_E | 64_S | 2.746 | 1.00 |
| 37_H | 43_A | 2.691 | 1.00 |
| 19_E | 71_Q | 2.660 | 1.00 |
| 4_E | 7_T | 2.428 | 1.00 |
| 22_I | 159_S | 2.289 | 1.00 |
| 24_N | 159_S | 2.193 | 1.00 |
| 142_G | 145_K | 2.102 | 1.00 |
| 2_R | 194_S | 2.082 | 1.00 |
| 18_N | 71_Q | 2.028 | 1.00 |
| 62_G | 125_R | 2.012 | 1.00 |
| 4_E | 8_N | 1.973 | 1.00 |
| 38_V | 44_L | 1.973 | 1.00 |
| 85_V | 180_T | 1.914 | 1.00 |
| 134_K | 137_I | 1.883 | 1.00 |
| 85_V | 178_N | 1.864 | 1.00 |
| 114_N | 130_P | 1.864 | 1.00 |
| 38_V | 42_Q | 1.839 | 1.00 |
| 169_R | 179_E | 1.819 | 1.00 |
| 6_I | 80_F | 1.804 | 1.00 |
| 52_D | 132_R | 1.791 | 1.00 |
| 94_P | 98_T | 1.788 | 1.00 |
| 67_K | 71_Q | 1.782 | 1.00 |
| 73_T | 77_K | 1.764 | 1.00 |
| 37_H | 42_Q | 1.694 | 1.00 |
| 31_N | 35_S | 1.664 | 1.00 |
| 8_N | 11_K | 1.651 | 1.00 |
| 48_E | 153_A | 1.650 | 1.00 |
| 22_I | 26_T | 1.635 | 1.00 |
| 139_M | 142_G | 1.616 | 1.00 |
| 73_T | 118_N | 1.599 | 1.00 |
| 62_G | 66_N | 1.559 | 1.00 |
| 74_A | 77_K | 1.554 | 1.00 |
| 184_G | 187_D | 1.551 | 1.00 |
| 43_A | 46_T | 1.549 | 1.00 |
| 52_D | 55_Q | 1.532 | 1.00 |
| 80_F | 181_F | 1.509 | 1.00 |
| 32_T | 153_A | 1.501 | 1.00 |
| 96_I | 100_S | 1.490 | 1.00 |
| 172_G | 179_E | 1.443 | 1.00 |
| 70_Q | 73_T | 1.419 | 1.00 |
| 34_R | 46_T | 1.414 | 1.00 |
| 57_H | 61_S | 1.410 | 1.00 |
| 1_I | 6_I | 1.376 | 0.99 |
| 57_H | 128_T | 1.369 | 0.99 |
| 120_E | 123_N | 1.357 | 0.99 |
| 29_Y | 50_I | 1.339 | 0.99 |
| 171_G | 179_E | 1.324 | 0.99 |
| 37_H | 44_L | 1.319 | 0.99 |
| 33_R | 48_E | 1.313 | 0.99 |
| 30_N | 50_I | 1.310 | 0.99 |
| 14_I | 166_L | 1.309 | 0.99 |
| 64_S | 67_K | 1.306 | 0.99 |
| 169_R | 172_G | 1.291 | 0.99 |
| 201_V | 206_P | 1.271 | 0.99 |
| 62_G | 114_N | 1.267 | 0.99 |
| 89_P | 96_I | 1.254 | 0.99 |
| 59_N | 63_T | 1.245 | 0.98 |
| 89_P | 97_T | 1.243 | 0.98 |
| 32_T | 35_S | 1.239 | 0.98 |
| 94_P | 137_I | 1.212 | 0.98 |
| 71_Q | 74_A | 1.212 | 0.98 |
| 89_P | 184_G | 1.180 | 0.98 |
| 155_R | 159_S | 1.152 | 0.97 |
| 199_Y | 202_V | 1.151 | 0.97 |
| 18_N | 22_I | 1.141 | 0.97 |
| 24_N | 157_N | 1.136 | 0.97 |
| 94_P | 145_K | 1.135 | 0.97 |
| 70_Q | 74_A | 1.101 | 0.96 |
| 2_R | 16_Q | 1.092 | 0.96 |
| 10_A | 90_S | 1.087 | 0.96 |
| 29_Y | 153_A | 1.086 | 0.96 |
| 94_P | 138_N | 1.084 | 0.96 |
| 40_P | 44_L | 1.071 | 0.95 |
| 35_S | 48_E | 1.065 | 0.95 |
| 4_E | 187_D | 1.064 | 0.95 |
| 31_N | 50_I | 1.062 | 0.95 |
| 94_P | 142_G | 1.062 | 0.95 |
| 200_K | 206_P | 1.061 | 0.95 |
| 24_N | 155_R | 1.044 | 0.94 |
| 199_Y | 206_P | 1.043 | 0.94 |
| 60_I | 129_L | 1.039 | 0.94 |
| 16_Q | 194_S | 1.038 | 0.94 |
| 187_D | 190_D | 1.032 | 0.94 |
| 40_P | 139_M | 1.032 | 0.94 |
| 104_G | 156_I | 1.029 | 0.94 |
| 157_N | 205_E | 1.017 | 0.93 |
| 24_N | 64_S | 1.016 | 0.93 |
| 16_Q | 20_S | 1.015 | 0.93 |
| 30_N | 153_A | 1.014 | 0.93 |
| 175_S | 178_N | 1.009 | 0.93 |
| 114_N | 129_L | 1.009 | 0.93 |
| 75_K | 142_G | 1.009 | 0.93 |
| 141_Q | 146_A | 1.008 | 0.93 |
| 30_N | 35_S | 1.008 | 0.93 |
| 100_S | 165_L | 1.002 | 0.92 |
| 32_T | 50_I | 1.000 | 0.92 |
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
- See coupling matrix (for protein design or mutagenesis)
- 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 | |
| 4ncoA | 3 | 0.9856 | 100 | 0.044 | Contact Map |
| 4jzzA | 1 | 0.8558 | 100 | 0.151 | Contact Map |
| 3lqaG | 1 | 0.8269 | 100 | 0.207 | Contact Map |
| 2bf1A | 1 | 0.8173 | 100 | 0.236 | Contact Map |
| 4i3sG | 1 | 0.7356 | 100 | 0.339 | Contact Map |
| 3tygA | 1 | 0.524 | 100 | 0.558 | Contact Map |
| 4jpkA | 1 | 0.4519 | 100 | 0.625 | Contact Map |
| 3mlzP | 1 | 0.101 | 98.4 | 0.921 | Contact Map |
| 3ujiP | 1 | 0.0865 | 98 | 0.928 | Contact Map |
| 3mlyP | 2 | 0.0577 | 97.9 | 0.929 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)