| HIV CACTD |
| ID: | 1445327923 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 74 (74) | ||
| Sequences: | 353 (173.4) | ||
| Seq/Len: | 4.770 | ||
| Nf(neff/√len): | 20.2 |
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: 4.770).
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 |
| 13_F | 16_Y | 1.911 | 1.00 |
| 43_V | 46_A | 1.804 | 1.00 |
| 47_N | 50_C | 1.763 | 1.00 |
| 70_C | 73_V | 1.752 | 1.00 |
| 7_Q | 11_E | 1.686 | 0.99 |
| 2_I | 7_Q | 1.541 | 0.99 |
| 67_M | 70_C | 1.511 | 0.98 |
| 47_N | 51_K | 1.469 | 0.98 |
| 4_D | 7_Q | 1.439 | 0.98 |
| 46_A | 50_C | 1.437 | 0.98 |
| 16_Y | 20_F | 1.429 | 0.98 |
| 68_T | 71_Q | 1.409 | 0.97 |
| 11_E | 17_V | 1.375 | 0.97 |
| 3_L | 7_Q | 1.360 | 0.96 |
| 61_A | 67_M | 1.355 | 0.96 |
| 11_E | 16_Y | 1.354 | 0.96 |
| 5_I | 9_P | 1.354 | 0.96 |
| 28_Q | 33_V | 1.334 | 0.96 |
| 1_S | 5_I | 1.290 | 0.95 |
| 1_S | 7_Q | 1.261 | 0.94 |
| 63_L | 66_M | 1.227 | 0.93 |
| 42_L | 45_N | 1.219 | 0.92 |
| 11_E | 15_D | 1.213 | 0.92 |
| 56_A | 59_P | 1.212 | 0.92 |
| 4_D | 9_P | 1.197 | 0.91 |
| 52_T | 59_P | 1.189 | 0.91 |
| 64_E | 67_M | 1.184 | 0.91 |
| 46_A | 49_D | 1.179 | 0.91 |
| 33_V | 37_M | 1.156 | 0.89 |
| 33_V | 36_W | 1.151 | 0.89 |
| 51_K | 54_L | 1.144 | 0.89 |
| 39_E | 42_L | 1.143 | 0.89 |
| 32_E | 35_N | 1.139 | 0.89 |
| 12_P | 17_V | 1.136 | 0.88 |
| 53_I | 56_A | 1.131 | 0.88 |
| 57_L | 61_A | 1.126 | 0.88 |
| 26_A | 29_A | 1.119 | 0.87 |
| 14_R | 17_V | 1.099 | 0.86 |
| 20_F | 25_R | 1.095 | 0.86 |
| 68_T | 73_V | 1.093 | 0.86 |
| 38_T | 41_L | 1.066 | 0.84 |
| 22_K | 26_A | 1.062 | 0.83 |
| 13_F | 17_V | 1.037 | 0.81 |
| 4_D | 8_G | 1.030 | 0.81 |
| 20_F | 23_T | 1.018 | 0.80 |
| 56_A | 60_G | 1.017 | 0.80 |
| 23_T | 26_A | 1.015 | 0.79 |
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 | |
| 2jylA | 1 | 1 | 99.9 | -0.066 | Contact Map |
| 3ds4A | 2 | 1 | 99.9 | -0.062 | Contact Map |
| 1bajA | 1 | 0.9459 | 99.9 | -0.058 | Contact Map |
| 4ph1A | 3 | 0 | 99.9 | -0.045 | Contact Map |
| 1eiaA | 1 | 1 | 99.9 | -0.041 | Contact Map |
| 4u0cA | 1 | 0.9189 | 99.9 | -0.036 | Contact Map |
| 1d1dA | 1 | 1 | 99.9 | -0.015 | Contact Map |
| 4ph0A | 6 | 0 | 99.9 | -0.013 | Contact Map |
| 1qrjA | 1 | 1 | 99.9 | -0.013 | Contact Map |
| 3g1gA | 2 | 1 | 99.9 | 0.031 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)