| lphkopen |
| ID: | 1409215709 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 195 (195) | ||
| Sequences: | 50805 (41398.3) | ||
| Seq/Len: | 260.538 | ||
| Nf(neff/√len): | 2964.6 |
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: 260.538).
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 |
| 167_K | 171_Q | 3.008 | 1.00 |
| 178_W | 190_Y | 2.930 | 1.00 |
| 18_I | 39_T | 2.893 | 1.00 |
| 71_V | 103_I | 2.853 | 1.00 |
| 103_I | 173_L | 2.598 | 1.00 |
| 182_V | 185_K | 2.417 | 1.00 |
| 134_P | 137_D | 2.397 | 1.00 |
| 166_S | 177_I | 2.281 | 1.00 |
| 111_V | 170_V | 2.235 | 1.00 |
| 138_L | 181_S | 2.191 | 1.00 |
| 138_L | 179_V | 2.160 | 1.00 |
| 15_R | 44_D | 2.097 | 1.00 |
| 170_V | 175_G | 2.090 | 1.00 |
| 179_V | 189_F | 2.086 | 1.00 |
| 69_E | 105_T | 2.071 | 1.00 |
| 111_V | 169_V | 2.059 | 1.00 |
| 15_R | 43_T | 2.058 | 1.00 |
| 142_F | 177_I | 2.029 | 1.00 |
| 22_S | 40_Q | 1.994 | 1.00 |
| 70_L | 102_E | 1.936 | 1.00 |
| 79_Y | 109_T | 1.926 | 1.00 |
| 181_S | 187_S | 1.847 | 1.00 |
| 22_S | 37_K | 1.839 | 1.00 |
| 14_L | 43_T | 1.820 | 1.00 |
| 72_N | 75_E | 1.817 | 1.00 |
| 170_V | 191_I | 1.786 | 1.00 |
| 133_I | 137_D | 1.764 | 1.00 |
| 126_Q | 192_S | 1.712 | 1.00 |
| 103_I | 108_F | 1.707 | 1.00 |
| 133_I | 141_V | 1.705 | 1.00 |
| 111_V | 166_S | 1.700 | 1.00 |
| 135_R | 138_L | 1.684 | 1.00 |
| 180_D | 188_T | 1.673 | 1.00 |
| 88_Y | 120_I | 1.625 | 1.00 |
| 140_H | 143_D | 1.597 | 1.00 |
| 180_D | 190_Y | 1.589 | 1.00 |
| 140_H | 146_F | 1.571 | 1.00 |
| 117_N | 121_K | 1.564 | 1.00 |
| 70_L | 100_W | 1.563 | 1.00 |
| 169_V | 173_L | 1.543 | 1.00 |
| 19_E | 40_Q | 1.541 | 1.00 |
| 176_R | 192_S | 1.539 | 1.00 |
| 47_I | 51_N | 1.538 | 1.00 |
| 137_D | 140_H | 1.498 | 1.00 |
| 171_Q | 176_R | 1.493 | 1.00 |
| 128_I | 192_S | 1.486 | 1.00 |
| 84_F | 113_D | 1.483 | 1.00 |
| 133_I | 187_S | 1.479 | 1.00 |
| 128_I | 190_Y | 1.456 | 1.00 |
| 181_S | 185_K | 1.419 | 1.00 |
| 137_D | 146_F | 1.392 | 0.99 |
| 107_K | 110_Q | 1.391 | 0.99 |
| 18_I | 40_Q | 1.380 | 0.99 |
| 6_E | 110_Q | 1.348 | 0.99 |
| 134_P | 183_E | 1.335 | 0.99 |
| 72_N | 98_D | 1.318 | 0.99 |
| 15_R | 47_I | 1.306 | 0.99 |
| 142_F | 179_V | 1.286 | 0.99 |
| 14_L | 39_T | 1.282 | 0.99 |
| 181_S | 184_G | 1.269 | 0.99 |
| 132_G | 187_S | 1.267 | 0.99 |
| 17_Y | 35_F | 1.256 | 0.99 |
| 8_R | 51_N | 1.222 | 0.98 |
| 175_G | 193_L | 1.221 | 0.98 |
| 2_N | 144_R | 1.220 | 0.98 |
| 178_W | 192_S | 1.219 | 0.98 |
| 68_M | 102_E | 1.218 | 0.98 |
| 104_D | 107_K | 1.214 | 0.98 |
| 122_Y | 147_R | 1.205 | 0.98 |
| 79_Y | 105_T | 1.204 | 0.98 |
| 18_I | 43_T | 1.176 | 0.98 |
| 40_Q | 44_D | 1.167 | 0.97 |
| 143_D | 146_F | 1.166 | 0.97 |
| 114_N | 166_S | 1.164 | 0.97 |
| 141_V | 179_V | 1.157 | 0.97 |
| 48_R | 106_D | 1.155 | 0.97 |
| 132_G | 186_G | 1.150 | 0.97 |
| 72_N | 100_W | 1.147 | 0.97 |
| 15_R | 40_Q | 1.140 | 0.97 |
| 66_V | 104_D | 1.140 | 0.97 |
| 137_D | 148_V | 1.135 | 0.97 |
| 17_Y | 38_V | 1.122 | 0.97 |
| 107_K | 169_V | 1.113 | 0.96 |
| 18_I | 36_L | 1.095 | 0.96 |
| 89_T | 92_R | 1.091 | 0.96 |
| 21_L | 36_L | 1.088 | 0.96 |
| 111_V | 191_I | 1.086 | 0.96 |
| 168_E | 171_Q | 1.080 | 0.95 |
| 74_N | 78_N | 1.066 | 0.95 |
| 142_F | 189_F | 1.065 | 0.95 |
| 107_K | 172_M | 1.056 | 0.95 |
| 170_V | 177_I | 1.046 | 0.94 |
| 178_W | 191_I | 1.045 | 0.94 |
| 22_S | 33_P | 1.045 | 0.94 |
| 68_M | 173_L | 1.037 | 0.94 |
| 13_S | 42_E | 1.026 | 0.94 |
| 13_S | 17_Y | 1.025 | 0.93 |
| 77_F | 112_L | 1.019 | 0.93 |
| 138_L | 142_F | 1.006 | 0.93 |
| 76_M | 80_V | 1.004 | 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 | |
| 4i5sA | 2 | 0.959 | 100 | 0.14 | Contact Map |
| 2c2aA | 1 | 0.9538 | 100 | 0.152 | Contact Map |
| 4bixA | 2 | 0.9282 | 100 | 0.197 | Contact Map |
| 4mpcA | 1 | 0.9231 | 100 | 0.201 | Contact Map |
| 3jz3A | 2 | 0.7282 | 100 | 0.201 | Contact Map |
| 1y8oA | 1 | 0.9436 | 100 | 0.209 | Contact Map |
| 4ew8A | 2 | 0.9641 | 100 | 0.209 | Contact Map |
| 2e0aA | 2 | 0.9846 | 100 | 0.213 | Contact Map |
| 4e01A | 1 | 0.9487 | 100 | 0.222 | Contact Map |
| 3a0rA | 1 | 0.9077 | 99.9 | 0.228 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)