| HIV Vif |
| ID: | 1443430419 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 192 (160) | ||
| Sequences: | 1768 (74) | ||
| Seq/Len: | 11.050 | ||
| Nf(neff/√len): | 5.9 |
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: 11.050).
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 |
| 64_L | 98_V | 3.374 | 1.00 |
| 13_V | 18_I | 2.036 | 1.00 |
| 120_I | 127_R | 1.980 | 1.00 |
| 23_R | 26_K | 1.879 | 1.00 |
| 139_H | 142_V | 1.566 | 1.00 |
| 41_R | 124_I | 1.561 | 1.00 |
| 119_A | 122_N | 1.536 | 1.00 |
| 113_D | 122_N | 1.533 | 1.00 |
| 121_R | 125_L | 1.525 | 1.00 |
| 69_Y | 118_S | 1.518 | 1.00 |
| 106_L | 144_S | 1.499 | 1.00 |
| 14_D | 125_L | 1.453 | 1.00 |
| 127_R | 130_S | 1.448 | 1.00 |
| 38_W | 57_I | 1.406 | 0.99 |
| 64_L | 89_W | 1.403 | 0.99 |
| 27_H | 31_I | 1.395 | 0.99 |
| 64_L | 116_S | 1.392 | 0.99 |
| 124_I | 128_I | 1.380 | 0.99 |
| 66_I | 141_K | 1.371 | 0.99 |
| 66_I | 151_A | 1.361 | 0.99 |
| 117_E | 120_I | 1.343 | 0.99 |
| 124_I | 130_S | 1.305 | 0.99 |
| 32_S | 120_I | 1.304 | 0.99 |
| 21_W | 70_W | 1.295 | 0.99 |
| 81_L | 84_G | 1.272 | 0.99 |
| 50_K | 71_G | 1.262 | 0.99 |
| 102_L | 105_Q | 1.257 | 0.99 |
| 117_E | 141_K | 1.245 | 0.98 |
| 35_A | 68_T | 1.245 | 0.98 |
| 53_S | 135_Y | 1.237 | 0.98 |
| 160_K | 169_L | 1.234 | 0.98 |
| 99_D | 102_L | 1.231 | 0.98 |
| 120_I | 168_K | 1.224 | 0.98 |
| 50_K | 78_D | 1.224 | 0.98 |
| 40_Y | 142_V | 1.215 | 0.98 |
| 63_K | 125_L | 1.203 | 0.98 |
| 34_K | 88_E | 1.187 | 0.98 |
| 28_H | 90_R | 1.171 | 0.98 |
| 102_L | 147_Y | 1.168 | 0.97 |
| 141_K | 144_S | 1.157 | 0.97 |
| 15_R | 125_L | 1.149 | 0.97 |
| 91_K | 98_V | 1.149 | 0.97 |
| 130_S | 152_A | 1.140 | 0.97 |
| 59_L | 64_L | 1.138 | 0.97 |
| 105_Q | 150_L | 1.128 | 0.97 |
| 50_K | 67_T | 1.126 | 0.97 |
| 120_I | 125_L | 1.126 | 0.97 |
| 122_N | 130_S | 1.123 | 0.97 |
| 163_L | 173_R | 1.117 | 0.96 |
| 64_L | 105_Q | 1.108 | 0.96 |
| 141_K | 149_A | 1.108 | 0.96 |
| 59_L | 79_W | 1.103 | 0.96 |
| 79_W | 87_I | 1.102 | 0.96 |
| 57_I | 99_D | 1.100 | 0.96 |
| 59_L | 141_K | 1.095 | 0.96 |
| 40_Y | 149_A | 1.094 | 0.96 |
| 96_T | 103_A | 1.087 | 0.96 |
| 98_V | 134_E | 1.087 | 0.96 |
| 56_H | 106_L | 1.082 | 0.96 |
| 60_G | 137_A | 1.071 | 0.95 |
| 35_A | 129_V | 1.064 | 0.95 |
| 170_T | 173_R | 1.063 | 0.95 |
| 38_W | 138_G | 1.063 | 0.95 |
| 23_R | 30_Y | 1.051 | 0.94 |
| 20_T | 78_D | 1.050 | 0.94 |
| 98_V | 122_N | 1.048 | 0.94 |
| 122_N | 153_L | 1.047 | 0.94 |
| 66_I | 130_S | 1.046 | 0.94 |
| 127_R | 150_L | 1.046 | 0.94 |
| 15_R | 28_H | 1.042 | 0.94 |
| 165_S | 169_L | 1.032 | 0.94 |
| 48_N | 173_R | 1.027 | 0.94 |
| 146_Q | 150_L | 1.022 | 0.93 |
| 165_S | 171_E | 1.021 | 0.93 |
| 29_M | 113_D | 1.019 | 0.93 |
| 163_L | 166_V | 1.018 | 0.93 |
| 59_L | 135_Y | 1.013 | 0.93 |
| 117_E | 124_I | 1.010 | 0.93 |
| 117_E | 136_Q | 1.006 | 0.93 |
| 142_V | 153_L | 1.002 | 0.92 |
| 164_P | 173_R | 1.001 | 0.92 |
| 43_H | 149_A | 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 | |
| 4n9fb | 12 | 0.8958 | 100 | 0.028 | Contact Map |
| 3dcgE | 2 | 0.0885 | 99.6 | 0.817 | Contact Map |
| 4a17X | 1 | 0.224 | 4.2 | 0.975 | Contact Map |
| 3v9rB | 2 | 0.2917 | 3.1 | 0.976 | Contact Map |
| 4ne3B | 1 | 0.2917 | 2.7 | 0.977 | Contact Map |
| 4w20e | 1 | 0.2344 | 2.4 | 0.978 | Contact Map |
| 1co4A | 1 | 0.2188 | 2.2 | 0.978 | Contact Map |
| 4htpA | 2 | 0.2969 | 2.2 | 0.978 | Contact Map |
| 2ygvE | 4 | 0.1042 | 2.1 | 0.978 | Contact Map |
| 2rlwA | 1 | 0.1771 | 1.7 | 0.98 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)