| A2_AG_Cter |
| ID: | 1485877987 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 50% gaps before running GREMLIN. |
| Length: | 334 (171) | ||
| Sequences: | 3440 (2487.6) | ||
| Seq/Len: | 20.117 | ||
| Nf(neff/√len): | 190.2 |
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: 20.117).
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 |
| 178_D | 181_N | 6.490 | 1.00 |
| 125_V | 140_Y | 2.994 | 1.00 |
| 106_D | 109_E | 2.552 | 1.00 |
| 126_T | 186_V | 2.325 | 1.00 |
| 188_E | 192_D | 2.291 | 1.00 |
| 188_E | 191_R | 2.125 | 1.00 |
| 173_V | 189_N | 2.090 | 1.00 |
| 185_W | 189_N | 2.066 | 1.00 |
| 82_D | 85_Q | 1.929 | 1.00 |
| 80_G | 85_Q | 1.878 | 1.00 |
| 130_V | 139_Y | 1.783 | 1.00 |
| 176_Q | 182_C | 1.768 | 1.00 |
| 54_A | 187_Y | 1.739 | 1.00 |
| 128_V | 193_I | 1.714 | 1.00 |
| 80_G | 83_G | 1.626 | 1.00 |
| 55_A | 190_A | 1.625 | 1.00 |
| 111_D | 132_Q | 1.606 | 1.00 |
| 119_V | 125_V | 1.601 | 1.00 |
| 135_N | 139_Y | 1.600 | 1.00 |
| 45_W | 48_T | 1.582 | 1.00 |
| 118_N | 122_R | 1.575 | 1.00 |
| 114_I | 126_T | 1.537 | 1.00 |
| 112_R | 128_V | 1.511 | 1.00 |
| 49_H | 52_F | 1.505 | 1.00 |
| 98_I | 101_F | 1.504 | 1.00 |
| 129_I | 136_Y | 1.502 | 1.00 |
| 118_N | 121_N | 1.475 | 1.00 |
| 145_G | 175_Q | 1.451 | 1.00 |
| 113_L | 129_I | 1.444 | 1.00 |
| 191_R | 195_Q | 1.419 | 1.00 |
| 181_N | 185_W | 1.403 | 0.99 |
| 71_H | 111_D | 1.365 | 0.99 |
| 130_V | 133_N | 1.350 | 0.99 |
| 29_D | 47_Q | 1.341 | 0.99 |
| 91_R | 94_L | 1.334 | 0.99 |
| 181_N | 184_I | 1.325 | 0.99 |
| 112_R | 130_V | 1.301 | 0.99 |
| 178_D | 182_C | 1.280 | 0.99 |
| 79_V | 82_D | 1.278 | 0.99 |
| 154_I | 157_A | 1.276 | 0.99 |
| 47_Q | 50_D | 1.266 | 0.99 |
| 72_Y | 75_E | 1.249 | 0.99 |
| 190_A | 193_I | 1.237 | 0.98 |
| 73_G | 76_I | 1.233 | 0.98 |
| 31_L | 34_D | 1.228 | 0.98 |
| 94_L | 97_H | 1.219 | 0.98 |
| 140_Y | 148_S | 1.165 | 0.97 |
| 126_T | 190_A | 1.159 | 0.97 |
| 114_I | 125_V | 1.147 | 0.97 |
| 28_H | 32_A | 1.141 | 0.97 |
| 52_F | 77_T | 1.125 | 0.97 |
| 26_D | 32_A | 1.125 | 0.97 |
| 151_D | 154_I | 1.122 | 0.97 |
| 114_I | 128_V | 1.119 | 0.96 |
| 187_Y | 190_A | 1.119 | 0.96 |
| 50_D | 54_A | 1.118 | 0.96 |
| 54_A | 58_Y | 1.108 | 0.96 |
| 184_I | 188_E | 1.094 | 0.96 |
| 141_A | 173_V | 1.093 | 0.96 |
| 81_V | 85_Q | 1.090 | 0.96 |
| 192_D | 195_Q | 1.088 | 0.96 |
| 27_V | 30_L | 1.075 | 0.95 |
| 153_N | 157_A | 1.075 | 0.95 |
| 46_L | 184_I | 1.071 | 0.95 |
| 30_L | 34_D | 1.054 | 0.95 |
| 27_V | 31_L | 1.051 | 0.94 |
| 151_D | 155_R | 1.037 | 0.94 |
| 123_H | 126_T | 1.018 | 0.93 |
| 116_I | 186_V | 1.016 | 0.93 |
| 141_A | 193_I | 1.006 | 0.93 |
| 125_V | 148_S | 1.002 | 0.92 |
| 152_N | 156_G | 1.001 | 0.92 |
| 78_S | 81_V | 1.001 | 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
- 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 | |
| 3eayA | 1 | 0.6257 | 100 | 0.572 | Contact Map |
| 2bkrA | 1 | 0.6018 | 100 | 0.58 | Contact Map |
| 1euvA | 1 | 0.5988 | 100 | 0.593 | Contact Map |
| 2oixA | 1 | 0.518 | 100 | 0.605 | Contact Map |
| 2xphA | 2 | 0.6108 | 100 | 0.606 | Contact Map |
| 3zo5A | 1 | 0.6078 | 100 | 0.614 | Contact Map |
| 4ekfA | 1 | 0.5389 | 86.5 | 0.936 | Contact Map |
| 4kp3C | 2 | 0.0749 | 7.3 | 0.968 | Contact Map |
| 4ry2A | 2 | 0 | 5.5 | 0.97 | Contact Map |
| 1q1vA | 1 | 0.1707 | 4.5 | 0.971 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)