| 4HTTAPDBIDCHAINSEQUENCE |
| ID: | 1465839101 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 231 (228) | ||
| Sequences: | 3092 (1924.1) | ||
| Seq/Len: | 13.561 | ||
| Nf(neff/√len): | 127.4 |
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: 13.561).
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 |
| 176_Q | 229_G | 3.865 | 1.00 |
| 22_A | 81_V | 3.664 | 1.00 |
| 190_R | 223_E | 3.650 | 1.00 |
| 14_Y | 18_I | 3.492 | 1.00 |
| 187_A | 230_K | 3.242 | 1.00 |
| 84_Y | 88_R | 2.955 | 1.00 |
| 11_E | 15_R | 2.786 | 1.00 |
| 18_I | 81_V | 2.678 | 1.00 |
| 27_S | 74_G | 2.519 | 1.00 |
| 198_F | 215_A | 2.418 | 1.00 |
| 193_F | 222_Y | 2.315 | 1.00 |
| 183_P | 229_G | 2.267 | 1.00 |
| 19_S | 82_I | 2.177 | 1.00 |
| 172_L | 186_L | 2.139 | 1.00 |
| 30_A | 73_V | 1.997 | 1.00 |
| 194_I | 219_L | 1.909 | 1.00 |
| 113_F | 163_G | 1.884 | 1.00 |
| 222_Y | 226_I | 1.878 | 1.00 |
| 118_L | 122_F | 1.876 | 1.00 |
| 94_L | 98_E | 1.841 | 1.00 |
| 61_E | 147_S | 1.832 | 1.00 |
| 4_P | 7_E | 1.816 | 1.00 |
| 28_G | 32_Y | 1.791 | 1.00 |
| 175_L | 180_V | 1.779 | 1.00 |
| 182_T | 185_Q | 1.773 | 1.00 |
| 43_E | 47_K | 1.766 | 1.00 |
| 26_G | 74_G | 1.760 | 1.00 |
| 109_S | 167_E | 1.757 | 1.00 |
| 57_L | 147_S | 1.742 | 1.00 |
| 192_Y | 196_I | 1.726 | 1.00 |
| 15_R | 85_Q | 1.697 | 1.00 |
| 181_I | 186_L | 1.637 | 1.00 |
| 18_I | 85_Q | 1.635 | 1.00 |
| 16_L | 20_I | 1.634 | 1.00 |
| 78_A | 82_I | 1.633 | 1.00 |
| 187_A | 190_R | 1.633 | 1.00 |
| 198_F | 211_Q | 1.617 | 1.00 |
| 3_M | 7_E | 1.614 | 1.00 |
| 37_V | 73_V | 1.611 | 1.00 |
| 17_I | 21_I | 1.610 | 1.00 |
| 58_S | 61_E | 1.607 | 1.00 |
| 106_L | 110_I | 1.596 | 1.00 |
| 55_I | 145_Y | 1.586 | 1.00 |
| 22_A | 78_A | 1.576 | 1.00 |
| 74_G | 78_A | 1.571 | 1.00 |
| 189_F | 192_Y | 1.565 | 1.00 |
| 176_Q | 183_P | 1.560 | 1.00 |
| 185_Q | 189_F | 1.542 | 1.00 |
| 197_A | 218_L | 1.502 | 1.00 |
| 187_A | 223_E | 1.493 | 1.00 |
| 206_P | 211_Q | 1.485 | 1.00 |
| 23_F | 71_L | 1.476 | 1.00 |
| 147_S | 150_M | 1.474 | 1.00 |
| 184_E | 187_A | 1.392 | 0.99 |
| 53_E | 143_T | 1.390 | 0.99 |
| 183_P | 230_K | 1.381 | 0.99 |
| 184_E | 188_S | 1.379 | 0.99 |
| 223_E | 227_F | 1.357 | 0.99 |
| 59_P | 129_L | 1.345 | 0.99 |
| 208_V | 211_Q | 1.335 | 0.99 |
| 172_L | 229_G | 1.327 | 0.99 |
| 26_G | 77_I | 1.320 | 0.99 |
| 202_A | 211_Q | 1.318 | 0.99 |
| 59_P | 154_F | 1.309 | 0.99 |
| 23_F | 82_I | 1.308 | 0.99 |
| 204_I | 214_M | 1.308 | 0.99 |
| 19_S | 78_A | 1.301 | 0.99 |
| 195_V | 199_V | 1.296 | 0.99 |
| 15_R | 88_R | 1.292 | 0.99 |
| 79_S | 83_L | 1.279 | 0.99 |
| 56_T | 62_P | 1.268 | 0.99 |
| 133_L | 144_P | 1.265 | 0.99 |
| 93_A | 98_E | 1.256 | 0.99 |
| 117_A | 159_V | 1.253 | 0.99 |
| 58_S | 150_M | 1.249 | 0.99 |
| 227_F | 231_L | 1.223 | 0.98 |
| 57_L | 145_Y | 1.215 | 0.98 |
| 197_A | 219_L | 1.211 | 0.98 |
| 111_L | 115_L | 1.202 | 0.98 |
| 212_V | 216_I | 1.187 | 0.98 |
| 18_I | 21_I | 1.176 | 0.98 |
| 89_F | 93_A | 1.166 | 0.97 |
| 200_I | 204_I | 1.164 | 0.97 |
| 183_P | 187_A | 1.163 | 0.97 |
| 19_S | 22_A | 1.157 | 0.97 |
| 8_H | 12_L | 1.154 | 0.97 |
| 11_E | 85_Q | 1.147 | 0.97 |
| 138_T | 144_P | 1.144 | 0.97 |
| 117_A | 163_G | 1.126 | 0.97 |
| 59_P | 62_P | 1.112 | 0.96 |
| 24_L | 28_G | 1.109 | 0.96 |
| 60_T | 132_L | 1.103 | 0.96 |
| 183_P | 226_I | 1.099 | 0.96 |
| 35_K | 39_E | 1.098 | 0.96 |
| 201_G | 215_A | 1.097 | 0.96 |
| 103_I | 107_L | 1.097 | 0.96 |
| 66_L | 137_F | 1.090 | 0.96 |
| 91_E | 99_K | 1.077 | 0.95 |
| 8_H | 11_E | 1.038 | 0.94 |
| 33_F | 36_Y | 1.038 | 0.94 |
| 194_I | 223_E | 1.033 | 0.94 |
| 196_I | 199_V | 1.030 | 0.94 |
| 40_I | 122_F | 1.026 | 0.94 |
| 189_F | 193_F | 1.021 | 0.93 |
| 114_M | 118_L | 1.016 | 0.93 |
| 8_H | 98_E | 1.008 | 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 | 0.9654 | 100 | -0.035 | Contact Map |
| 4b4aA | 1 | 0.974 | 100 | -0.011 | Contact Map |
| 2qarB | 2 | 0.1342 | 3.5 | 0.963 | Contact Map |
| 2a7wA | 12 | 0.0736 | 2.8 | 0.964 | Contact Map |
| 2ksfA | 1 | 0.1991 | 2.5 | 0.965 | Contact Map |
| 2ki9A | 1 | 0.1429 | 2.4 | 0.965 | Contact Map |
| 4o93B | 2 | 0.316 | 2.3 | 0.966 | Contact Map |
| 4o9uB | 2 | 0.316 | 2.2 | 0.966 | Contact Map |
| 1yvwA | 4 | 0.0823 | 2.1 | 0.967 | Contact Map |
| 3rkoM | 2 | 0.2424 | 2.1 | 0.967 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)