| gp120gp41corr |
| ID: | 1392360019 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 133 (133) | ||
| Sequences: | 211 (6) | ||
| Seq/Len: | 1.586 | ||
| Nf(neff/√len): | 0.5 |
HHblits Results: (2013_03)
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: 1.586).
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 |
| 95_Q | 112_M | 3.747 | 1.00 |
| 67_V | 72_L | 1.934 | 0.98 |
| 19_T | 40_Q | 1.789 | 0.96 |
| 116_R | 124_K | 1.748 | 0.95 |
| 93_L | 118_I | 1.713 | 0.94 |
| 92_H | 95_Q | 1.709 | 0.94 |
| 64_T | 120_D | 1.660 | 0.93 |
| 2_A | 111_V | 1.658 | 0.93 |
| 81_N | 95_Q | 1.599 | 0.91 |
| 19_T | 42_E | 1.577 | 0.90 |
| 95_Q | 118_I | 1.536 | 0.89 |
| 54_K | 57_V | 1.514 | 0.88 |
| 63_I | 73_L | 1.497 | 0.87 |
| 20_T | 106_A | 1.433 | 0.84 |
| 115_D | 118_I | 1.415 | 0.83 |
| 46_I | 57_V | 1.415 | 0.83 |
| 106_A | 127_Q | 1.399 | 0.82 |
| 30_E | 95_Q | 1.396 | 0.82 |
| 72_L | 120_D | 1.389 | 0.81 |
| 3_N | 51_Q | 1.385 | 0.81 |
| 42_E | 133_A | 1.371 | 0.80 |
| 113_Q | 116_R | 1.356 | 0.79 |
| 46_I | 119_L | 1.350 | 0.78 |
| 26_Q | 37_P | 1.349 | 0.78 |
| 63_I | 115_D | 1.346 | 0.78 |
| 26_Q | 72_L | 1.333 | 0.77 |
| 28_V | 120_D | 1.329 | 0.77 |
| 67_V | 82_N | 1.329 | 0.77 |
| 115_D | 133_A | 1.320 | 0.76 |
| 19_T | 115_D | 1.317 | 0.76 |
| 74_S | 95_Q | 1.315 | 0.76 |
| 68_Q | 74_S | 1.314 | 0.76 |
| 2_A | 51_Q | 1.308 | 0.75 |
| 41_I | 44_L | 1.305 | 0.75 |
| 1_A | 106_A | 1.254 | 0.71 |
| 40_Q | 133_A | 1.234 | 0.69 |
| 50_K | 120_D | 1.230 | 0.69 |
| 19_T | 131_K | 1.199 | 0.66 |
| 95_Q | 115_D | 1.191 | 0.65 |
| 1_A | 19_T | 1.183 | 0.64 |
| 31_L | 34_Q | 1.183 | 0.64 |
| 93_L | 133_A | 1.179 | 0.64 |
| 26_Q | 128_E | 1.178 | 0.64 |
| 111_V | 131_K | 1.176 | 0.64 |
| 85_R | 112_M | 1.168 | 0.63 |
| 93_L | 123_E | 1.146 | 0.61 |
| 40_Q | 44_L | 1.131 | 0.59 |
| 64_T | 131_K | 1.123 | 0.58 |
| 49_T | 111_V | 1.123 | 0.58 |
| 67_V | 133_A | 1.122 | 0.58 |
| 17_E | 41_I | 1.119 | 0.58 |
| 93_L | 119_L | 1.113 | 0.57 |
| 50_K | 133_A | 1.111 | 0.57 |
| 9_Y | 123_E | 1.097 | 0.56 |
| 42_E | 106_A | 1.093 | 0.55 |
| 16_K | 20_T | 1.087 | 0.55 |
| 1_A | 115_D | 1.073 | 0.53 |
| 52_R | 131_K | 1.071 | 0.53 |
| 50_K | 124_K | 1.067 | 0.53 |
| 85_R | 95_Q | 1.061 | 0.52 |
| 56_A | 91_Q | 1.051 | 0.51 |
| 42_E | 116_R | 1.041 | 0.50 |
| 93_L | 108_V | 1.039 | 0.50 |
| 4_L | 16_K | 1.034 | 0.49 |
| 40_Q | 119_L | 1.032 | 0.49 |
| 2_A | 119_L | 1.031 | 0.49 |
| 2_A | 19_T | 1.028 | 0.49 |
| 61_A | 72_L | 1.018 | 0.47 |
| 28_V | 51_Q | 1.016 | 0.47 |
| 44_L | 118_I | 1.006 | 0.46 |
| 2_A | 63_I | 1.006 | 0.46 |
| 130_D | 133_A | 1.003 | 0.46 |
| 36_A | 81_N | 1.003 | 0.46 |
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 | |
| 3p30A | 1 | 0.4887 | 100 | 0.597 | Contact Map |
| 1envA | 1 | 0.7068 | 100 | 0.621 | Contact Map |
| 3k9aA | 1 | 0.4286 | 100 | 0.634 | Contact Map |
| 1qbzA | 3 | 0.4962 | 99.9 | 0.65 | Contact Map |
| 1jq0A | 1 | 0.406 | 99.9 | 0.656 | Contact Map |
| 2cmrA | 1 | 0.4511 | 99.9 | 0.667 | Contact Map |
| 3o3xA | 1 | 0.4511 | 99.9 | 0.692 | Contact Map |
| 1df4A | 1 | 0.4211 | 99.8 | 0.734 | Contact Map |
| 2x7rA | 3 | 0.3835 | 99.7 | 0.754 | Contact Map |
| 2zfcA | 3 | 0.3308 | 99.7 | 0.765 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)