| 1vi4 |
| ID: | 1452701028 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 165 (159) | ||
| Sequences: | 2842 (1757.9) | ||
| Seq/Len: | 17.874 | ||
| Nf(neff/√len): | 139.4 |
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: 17.874).
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 |
| 79_D | 104_A | 3.494 | 1.00 |
| 77_M | 82_A | 2.847 | 1.00 |
| 40_V | 131_N | 2.785 | 1.00 |
| 103_V | 151_W | 2.708 | 1.00 |
| 131_N | 143_P | 2.654 | 1.00 |
| 58_N | 90_W | 2.580 | 1.00 |
| 39_I | 147_L | 2.552 | 1.00 |
| 68_G | 76_L | 2.538 | 1.00 |
| 93_V | 110_L | 2.450 | 1.00 |
| 129_Q | 132_V | 2.396 | 1.00 |
| 147_L | 156_M | 2.315 | 1.00 |
| 59_G | 62_K | 2.114 | 1.00 |
| 43_R | 129_Q | 2.103 | 1.00 |
| 98_A | 116_G | 2.008 | 1.00 |
| 39_I | 141_V | 1.970 | 1.00 |
| 35_F | 92_G | 1.931 | 1.00 |
| 40_V | 62_K | 1.886 | 1.00 |
| 142_E | 160_A | 1.875 | 1.00 |
| 82_A | 105_M | 1.842 | 1.00 |
| 133_T | 142_E | 1.796 | 1.00 |
| 38_E | 62_K | 1.788 | 1.00 |
| 113_K | 149_A | 1.779 | 1.00 |
| 106_S | 151_W | 1.753 | 1.00 |
| 11_L | 148_Y | 1.744 | 1.00 |
| 43_R | 67_D | 1.709 | 1.00 |
| 22_L | 136_M | 1.703 | 1.00 |
| 77_M | 93_V | 1.699 | 1.00 |
| 32_R | 109_D | 1.535 | 1.00 |
| 105_M | 112_I | 1.534 | 1.00 |
| 48_N | 124_K | 1.529 | 1.00 |
| 86_I | 108_M | 1.522 | 1.00 |
| 35_F | 149_A | 1.502 | 1.00 |
| 28_N | 113_K | 1.442 | 1.00 |
| 60_K | 89_D | 1.434 | 1.00 |
| 149_A | 154_I | 1.426 | 1.00 |
| 132_V | 143_P | 1.418 | 1.00 |
| 102_V | 117_T | 1.412 | 1.00 |
| 29_F | 114_A | 1.402 | 0.99 |
| 96_Y | 115_L | 1.400 | 0.99 |
| 94_I | 154_I | 1.388 | 0.99 |
| 25_P | 115_L | 1.377 | 0.99 |
| 32_R | 151_W | 1.375 | 0.99 |
| 39_I | 145_D | 1.375 | 0.99 |
| 99_V | 105_M | 1.374 | 0.99 |
| 57_Q | 130_V | 1.374 | 0.99 |
| 102_V | 152_N | 1.373 | 0.99 |
| 86_I | 109_D | 1.372 | 0.99 |
| 35_F | 63_V | 1.334 | 0.99 |
| 63_V | 91_E | 1.333 | 0.99 |
| 22_L | 141_V | 1.326 | 0.99 |
| 77_M | 85_A | 1.309 | 0.99 |
| 64_L | 90_W | 1.298 | 0.99 |
| 35_F | 113_K | 1.297 | 0.99 |
| 83_I | 87_K | 1.285 | 0.99 |
| 39_I | 156_M | 1.272 | 0.99 |
| 38_E | 159_T | 1.237 | 0.98 |
| 10_D | 13_D | 1.192 | 0.98 |
| 47_D | 126_G | 1.174 | 0.98 |
| 22_L | 156_M | 1.154 | 0.97 |
| 65_V | 147_L | 1.142 | 0.97 |
| 67_D | 96_Y | 1.125 | 0.97 |
| 86_I | 110_L | 1.122 | 0.97 |
| 102_V | 106_S | 1.117 | 0.96 |
| 28_N | 31_Q | 1.115 | 0.96 |
| 148_Y | 157_S | 1.111 | 0.96 |
| 26_L | 154_I | 1.108 | 0.96 |
| 55_L | 85_A | 1.101 | 0.96 |
| 74_K | 122_T | 1.101 | 0.96 |
| 38_E | 61_G | 1.093 | 0.96 |
| 51_V | 66_V | 1.082 | 0.96 |
| 135_T | 140_I | 1.081 | 0.95 |
| 80_Q | 84_L | 1.080 | 0.95 |
| 38_E | 146_Y | 1.079 | 0.95 |
| 145_D | 158_E | 1.069 | 0.95 |
| 7_I | 10_D | 1.055 | 0.95 |
| 31_Q | 106_S | 1.052 | 0.95 |
| 27_Q | 117_T | 1.051 | 0.94 |
| 9_P | 152_N | 1.041 | 0.94 |
| 8_T | 155_L | 1.026 | 0.94 |
| 58_N | 64_L | 1.023 | 0.93 |
| 22_L | 137_Q | 1.020 | 0.93 |
| 62_K | 91_E | 1.015 | 0.93 |
| 72_C | 98_A | 1.015 | 0.93 |
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 | |
| 1vi4A | 1 | 0.9818 | 100 | 0.049 | Contact Map |
| 3nojA | 1 | 0.9939 | 100 | 0.068 | Contact Map |
| 3c8oA | 2 | 0.9758 | 100 | 0.074 | Contact Map |
| 2pcnA | 1 | 0.9697 | 100 | 0.087 | Contact Map |
| 1q5xA | 3 | 0.9697 | 100 | 0.089 | Contact Map |
| 1j3lA | 6 | 0.9758 | 100 | 0.09 | Contact Map |
| 1nxjA | 3 | 0.9394 | 100 | 0.092 | Contact Map |
| 3k4iA | 3 | 0.9758 | 100 | 0.102 | Contact Map |
| 2c5qA | 6 | 0.9939 | 100 | 0.107 | Contact Map |
| 1kblA | 1 | 0.8545 | 32.1 | 0.93 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)