| 4HTTAPDBIDCHAINSEQUENCE 2-231 |
| ID: | 1465850577 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 230 (228) | ||
| Sequences: | 3086 (1917.5) | ||
| Seq/Len: | 13.535 | ||
| Nf(neff/√len): | 127.0 |
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: 13.535).
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 |
| 175_Q | 228_G | 3.838 | 1.00 |
| 189_R | 222_E | 3.771 | 1.00 |
| 21_A | 80_V | 3.640 | 1.00 |
| 13_Y | 17_I | 3.507 | 1.00 |
| 186_A | 229_K | 3.240 | 1.00 |
| 83_Y | 87_R | 2.994 | 1.00 |
| 10_E | 14_R | 2.767 | 1.00 |
| 17_I | 80_V | 2.715 | 1.00 |
| 26_S | 73_G | 2.505 | 1.00 |
| 197_F | 214_A | 2.417 | 1.00 |
| 192_F | 221_Y | 2.323 | 1.00 |
| 182_P | 228_G | 2.313 | 1.00 |
| 171_L | 185_L | 2.159 | 1.00 |
| 18_S | 81_I | 2.156 | 1.00 |
| 29_A | 72_V | 2.010 | 1.00 |
| 3_P | 6_E | 1.933 | 1.00 |
| 193_I | 218_L | 1.900 | 1.00 |
| 117_L | 121_F | 1.883 | 1.00 |
| 93_L | 97_E | 1.877 | 1.00 |
| 221_Y | 225_I | 1.855 | 1.00 |
| 112_F | 162_G | 1.851 | 1.00 |
| 60_E | 146_S | 1.832 | 1.00 |
| 27_G | 31_Y | 1.813 | 1.00 |
| 25_G | 73_G | 1.776 | 1.00 |
| 56_L | 146_S | 1.768 | 1.00 |
| 174_L | 179_V | 1.766 | 1.00 |
| 108_S | 166_E | 1.733 | 1.00 |
| 181_T | 184_Q | 1.727 | 1.00 |
| 36_V | 72_V | 1.701 | 1.00 |
| 191_Y | 195_I | 1.696 | 1.00 |
| 186_A | 189_R | 1.682 | 1.00 |
| 14_R | 84_Q | 1.670 | 1.00 |
| 180_I | 185_L | 1.667 | 1.00 |
| 197_F | 210_Q | 1.658 | 1.00 |
| 2_M | 6_E | 1.636 | 1.00 |
| 17_I | 84_Q | 1.635 | 1.00 |
| 42_E | 46_K | 1.616 | 1.00 |
| 77_A | 81_I | 1.600 | 1.00 |
| 105_L | 109_I | 1.595 | 1.00 |
| 175_Q | 182_P | 1.592 | 1.00 |
| 57_S | 60_E | 1.582 | 1.00 |
| 16_I | 20_I | 1.580 | 1.00 |
| 188_F | 191_Y | 1.573 | 1.00 |
| 54_I | 144_Y | 1.571 | 1.00 |
| 15_L | 19_I | 1.555 | 1.00 |
| 21_A | 77_A | 1.544 | 1.00 |
| 186_A | 222_E | 1.540 | 1.00 |
| 73_G | 77_A | 1.536 | 1.00 |
| 184_Q | 188_F | 1.524 | 1.00 |
| 205_P | 210_Q | 1.499 | 1.00 |
| 196_A | 217_L | 1.495 | 1.00 |
| 22_F | 70_L | 1.482 | 1.00 |
| 146_S | 149_M | 1.458 | 1.00 |
| 25_G | 76_I | 1.415 | 1.00 |
| 183_E | 187_S | 1.406 | 0.99 |
| 58_P | 153_F | 1.377 | 0.99 |
| 182_P | 229_K | 1.365 | 0.99 |
| 222_E | 226_F | 1.357 | 0.99 |
| 207_V | 210_Q | 1.354 | 0.99 |
| 22_F | 81_I | 1.350 | 0.99 |
| 58_P | 128_L | 1.348 | 0.99 |
| 52_E | 142_T | 1.346 | 0.99 |
| 171_L | 228_G | 1.336 | 0.99 |
| 201_A | 210_Q | 1.333 | 0.99 |
| 18_S | 77_A | 1.327 | 0.99 |
| 14_R | 87_R | 1.323 | 0.99 |
| 183_E | 186_A | 1.312 | 0.99 |
| 92_A | 97_E | 1.307 | 0.99 |
| 203_I | 213_M | 1.288 | 0.99 |
| 55_T | 61_P | 1.275 | 0.99 |
| 78_S | 82_L | 1.263 | 0.99 |
| 116_A | 158_V | 1.263 | 0.99 |
| 194_V | 198_V | 1.248 | 0.99 |
| 132_L | 143_P | 1.237 | 0.98 |
| 57_S | 149_M | 1.230 | 0.98 |
| 110_L | 114_L | 1.228 | 0.98 |
| 18_S | 21_A | 1.201 | 0.98 |
| 196_A | 218_L | 1.191 | 0.98 |
| 17_I | 20_I | 1.190 | 0.98 |
| 226_F | 230_L | 1.189 | 0.98 |
| 7_H | 11_L | 1.187 | 0.98 |
| 56_L | 144_Y | 1.186 | 0.98 |
| 199_I | 203_I | 1.176 | 0.98 |
| 10_E | 84_Q | 1.164 | 0.97 |
| 211_V | 215_I | 1.162 | 0.97 |
| 88_F | 92_A | 1.157 | 0.97 |
| 58_P | 61_P | 1.139 | 0.97 |
| 182_P | 225_I | 1.131 | 0.97 |
| 200_G | 214_A | 1.123 | 0.97 |
| 137_T | 143_P | 1.122 | 0.97 |
| 182_P | 186_A | 1.112 | 0.96 |
| 59_T | 131_L | 1.109 | 0.96 |
| 90_E | 98_K | 1.089 | 0.96 |
| 65_L | 136_F | 1.086 | 0.96 |
| 39_I | 121_F | 1.079 | 0.95 |
| 116_A | 162_G | 1.073 | 0.95 |
| 102_I | 106_L | 1.064 | 0.95 |
| 32_F | 35_Y | 1.062 | 0.95 |
| 124_L | 128_L | 1.059 | 0.95 |
| 193_I | 222_E | 1.058 | 0.95 |
| 34_K | 38_E | 1.056 | 0.95 |
| 167_M | 196_A | 1.051 | 0.94 |
| 188_F | 192_F | 1.048 | 0.94 |
| 124_L | 154_V | 1.042 | 0.94 |
| 195_I | 198_V | 1.039 | 0.94 |
| 7_H | 97_E | 1.018 | 0.93 |
| 88_F | 91_P | 1.014 | 0.93 |
| 23_L | 27_G | 1.009 | 0.93 |
| 7_H | 10_E | 1.007 | 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 | |
| 4httA | 2 | 0.9696 | 100 | -0.029 | Contact Map |
| 4b4aA | 1 | 0.9783 | 100 | -0.01 | Contact Map |
| 4o93B | 2 | 0.3174 | 3.4 | 0.963 | Contact Map |
| 4o9uB | 2 | 0.3174 | 3.3 | 0.963 | Contact Map |
| 1iv3A | 6 | 0.2174 | 2.8 | 0.964 | Contact Map |
| 2hwvA | 1 | 0.1696 | 2.5 | 0.965 | Contact Map |
| 2ksfA | 1 | 0.2 | 2.2 | 0.966 | Contact Map |
| 2ki9A | 1 | 0.1435 | 2.2 | 0.966 | Contact Map |
| 3rkoM | 2 | 0.2391 | 2.1 | 0.967 | Contact Map |
| 4kf8A | 2 | 0.2391 | 1.7 | 0.968 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)