| VV_TRAP_Small_subunit |
| ID: | 1515972590 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 172 (157) | ||
| Sequences: | 7837 (6091.6) | ||
| Seq/Len: | 49.917 | ||
| Nf(neff/√len): | 486.2 |
HHblits Results: (2016_02)
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: 49.917).
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 |
| 82_P | 85_I | 2.685 | 1.00 |
| 75_T | 79_D | 2.604 | 1.00 |
| 97_V | 145_Q | 2.396 | 1.00 |
| 31_W | 43_S | 2.274 | 1.00 |
| 65_A | 70_T | 2.169 | 1.00 |
| 98_L | 142_V | 2.111 | 1.00 |
| 34_A | 39_L | 2.103 | 1.00 |
| 109_Y | 113_E | 1.966 | 1.00 |
| 81_L | 85_I | 1.893 | 1.00 |
| 29_L | 50_A | 1.890 | 1.00 |
| 81_L | 89_L | 1.849 | 1.00 |
| 91_L | 149_M | 1.840 | 1.00 |
| 91_L | 153_V | 1.823 | 1.00 |
| 84_K | 87_L | 1.819 | 1.00 |
| 56_Y | 133_S | 1.814 | 1.00 |
| 105_I | 142_V | 1.813 | 1.00 |
| 102_F | 106_Y | 1.812 | 1.00 |
| 101_I | 138_G | 1.741 | 1.00 |
| 14_E | 144_R | 1.737 | 1.00 |
| 106_Y | 110_Q | 1.705 | 1.00 |
| 34_A | 38_L | 1.658 | 1.00 |
| 101_I | 141_M | 1.614 | 1.00 |
| 102_F | 142_V | 1.614 | 1.00 |
| 112_V | 132_Y | 1.612 | 1.00 |
| 66_I | 141_M | 1.572 | 1.00 |
| 126_S | 129_W | 1.570 | 1.00 |
| 35_T | 39_L | 1.563 | 1.00 |
| 144_R | 147_Q | 1.556 | 1.00 |
| 31_W | 35_T | 1.551 | 1.00 |
| 85_I | 88_L | 1.545 | 1.00 |
| 62_C | 141_M | 1.543 | 1.00 |
| 116_A | 128_K | 1.538 | 1.00 |
| 120_L | 123_L | 1.508 | 1.00 |
| 84_K | 88_L | 1.450 | 1.00 |
| 98_L | 149_M | 1.424 | 1.00 |
| 94_E | 152_I | 1.423 | 1.00 |
| 115_T | 131_N | 1.406 | 0.99 |
| 69_G | 148_K | 1.405 | 0.99 |
| 78_S | 90_V | 1.393 | 0.99 |
| 35_T | 43_S | 1.376 | 0.99 |
| 12_N | 16_I | 1.368 | 0.99 |
| 105_I | 139_L | 1.355 | 0.99 |
| 88_L | 92_S | 1.348 | 0.99 |
| 101_I | 142_V | 1.311 | 0.99 |
| 150_V | 154_T | 1.306 | 0.99 |
| 120_L | 127_S | 1.303 | 0.99 |
| 48_E | 120_L | 1.281 | 0.99 |
| 66_I | 145_Q | 1.277 | 0.99 |
| 87_L | 156_F | 1.275 | 0.99 |
| 113_E | 117_F | 1.257 | 0.99 |
| 108_G | 138_G | 1.252 | 0.99 |
| 112_V | 135_P | 1.236 | 0.98 |
| 105_I | 138_G | 1.235 | 0.98 |
| 21_L | 53_L | 1.232 | 0.98 |
| 52_V | 120_L | 1.230 | 0.98 |
| 15_E | 64_I | 1.224 | 0.98 |
| 104_I | 138_G | 1.214 | 0.98 |
| 105_I | 109_Y | 1.213 | 0.98 |
| 108_G | 135_P | 1.210 | 0.98 |
| 63_A | 137_G | 1.187 | 0.98 |
| 12_N | 15_E | 1.180 | 0.98 |
| 64_I | 68_R | 1.173 | 0.98 |
| 32_Q | 47_E | 1.153 | 0.97 |
| 63_A | 144_R | 1.145 | 0.97 |
| 54_F | 58_S | 1.145 | 0.97 |
| 52_V | 130_M | 1.140 | 0.97 |
| 132_Y | 136_L | 1.127 | 0.97 |
| 30_T | 34_A | 1.126 | 0.97 |
| 47_E | 51_R | 1.121 | 0.97 |
| 69_G | 73_N | 1.112 | 0.96 |
| 5_M | 8_K | 1.108 | 0.96 |
| 110_Q | 114_R | 1.107 | 0.96 |
| 9_I | 12_N | 1.103 | 0.96 |
| 28_V | 53_L | 1.097 | 0.96 |
| 101_I | 145_Q | 1.093 | 0.96 |
| 94_E | 149_M | 1.087 | 0.96 |
| 24_A | 53_L | 1.084 | 0.96 |
| 23_A | 27_V | 1.079 | 0.95 |
| 108_G | 134_L | 1.070 | 0.95 |
| 63_A | 140_F | 1.060 | 0.95 |
| 49_L | 123_L | 1.056 | 0.95 |
| 33_I | 37_W | 1.053 | 0.95 |
| 98_L | 145_Q | 1.049 | 0.94 |
| 25_L | 57_M | 1.030 | 0.94 |
| 22_M | 57_M | 1.027 | 0.94 |
| 87_L | 155_E | 1.017 | 0.93 |
| 27_V | 31_W | 1.015 | 0.93 |
| 32_Q | 46_S | 1.011 | 0.93 |
| 52_V | 127_S | 1.006 | 0.93 |
| 91_L | 152_I | 1.003 | 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
- 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 | |
| 2wswA | 1 | 0.5291 | 10.2 | 0.924 | Contact Map |
| 4c7rA | 3 | 0.936 | 10 | 0.925 | Contact Map |
| 2kncA | 1 | 0.314 | 7.8 | 0.928 | Contact Map |
| 2ov2I | 8 | 0.186 | 6.8 | 0.93 | Contact Map |
| 4xp4A | 1 | 0 | 6.7 | 0.93 | Contact Map |
| 2odbB | 1 | 0.186 | 6.5 | 0.931 | Contact Map |
| 4uvmA | 1 | 0.8547 | 4.9 | 0.935 | Contact Map |
| 2l8sA | 1 | 0.2558 | 4.9 | 0.935 | Contact Map |
| 3w4tA | 1 | 0.7733 | 4.4 | 0.936 | Contact Map |
| 4ysxC | 2 | 0 | 3.7 | 0.938 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)