| VX 50-329 |
| ID: | 1414450125 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 280 (247) | ||
| Sequences: | 4140 (2993.3) | ||
| Seq/Len: | 16.761 | ||
| Nf(neff/√len): | 190.5 |
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: 16.761).
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 |
| 64_T | 110_A | 3.958 | 1.00 |
| 102_K | 135_S | 3.897 | 1.00 |
| 91_G | 128_Q | 3.778 | 1.00 |
| 105_A | 115_V | 3.277 | 1.00 |
| 98_E | 128_Q | 2.663 | 1.00 |
| 269_T | 273_R | 2.450 | 1.00 |
| 35_R | 69_R | 2.252 | 1.00 |
| 106_R | 136_E | 2.227 | 1.00 |
| 154_L | 207_Q | 2.184 | 1.00 |
| 67_F | 75_I | 2.147 | 1.00 |
| 5_R | 9_A | 2.138 | 1.00 |
| 87_V | 104_A | 2.110 | 1.00 |
| 44_A | 74_G | 2.097 | 1.00 |
| 119_T | 129_Q | 2.077 | 1.00 |
| 102_K | 136_E | 2.054 | 1.00 |
| 134_E | 159_A | 2.049 | 1.00 |
| 158_T | 162_A | 2.044 | 1.00 |
| 210_M | 266_I | 1.976 | 1.00 |
| 258_V | 263_L | 1.952 | 1.00 |
| 166_L | 212_Q | 1.940 | 1.00 |
| 248_R | 251_P | 1.906 | 1.00 |
| 127_E | 131_A | 1.905 | 1.00 |
| 203_A | 206_D | 1.889 | 1.00 |
| 87_V | 115_V | 1.887 | 1.00 |
| 265_G | 269_T | 1.882 | 1.00 |
| 159_A | 162_A | 1.881 | 1.00 |
| 268_V | 271_P | 1.879 | 1.00 |
| 32_E | 36_A | 1.875 | 1.00 |
| 14_T | 272_A | 1.847 | 1.00 |
| 134_E | 163_R | 1.845 | 1.00 |
| 214_L | 274_F | 1.844 | 1.00 |
| 210_M | 256_K | 1.844 | 1.00 |
| 44_A | 116_T | 1.819 | 1.00 |
| 259_P | 262_T | 1.819 | 1.00 |
| 148_S | 170_D | 1.786 | 1.00 |
| 158_T | 207_Q | 1.744 | 1.00 |
| 169_L | 205_I | 1.739 | 1.00 |
| 18_V | 116_T | 1.714 | 1.00 |
| 7_A | 15_I | 1.650 | 1.00 |
| 153_D | 156_Y | 1.649 | 1.00 |
| 199_L | 202_K | 1.631 | 1.00 |
| 102_K | 132_I | 1.629 | 1.00 |
| 43_A | 72_Q | 1.628 | 1.00 |
| 103_A | 106_R | 1.613 | 1.00 |
| 119_T | 126_G | 1.601 | 1.00 |
| 91_G | 98_E | 1.597 | 1.00 |
| 154_L | 158_T | 1.591 | 1.00 |
| 157_L | 167_I | 1.581 | 1.00 |
| 67_F | 111_T | 1.571 | 1.00 |
| 98_E | 102_K | 1.570 | 1.00 |
| 161_A | 212_Q | 1.563 | 1.00 |
| 210_M | 258_V | 1.550 | 1.00 |
| 109_L | 136_E | 1.548 | 1.00 |
| 51_P | 93_A | 1.547 | 1.00 |
| 98_E | 131_A | 1.546 | 1.00 |
| 131_A | 135_S | 1.535 | 1.00 |
| 199_L | 203_A | 1.535 | 1.00 |
| 112_G | 142_R | 1.533 | 1.00 |
| 267_T | 271_P | 1.525 | 1.00 |
| 101_L | 129_Q | 1.502 | 1.00 |
| 8_R | 40_H | 1.495 | 1.00 |
| 146_G | 160_L | 1.486 | 1.00 |
| 99_L | 103_A | 1.477 | 1.00 |
| 246_P | 260_Q | 1.467 | 1.00 |
| 202_K | 255_E | 1.459 | 1.00 |
| 169_L | 213_I | 1.446 | 1.00 |
| 62_E | 65_Q | 1.426 | 1.00 |
| 6_R | 237_V | 1.425 | 1.00 |
| 32_E | 35_R | 1.417 | 1.00 |
| 28_S | 62_E | 1.408 | 1.00 |
| 202_K | 248_R | 1.404 | 0.99 |
| 64_T | 111_T | 1.398 | 0.99 |
| 127_E | 156_Y | 1.375 | 0.99 |
| 247_L | 260_Q | 1.368 | 0.99 |
| 127_E | 159_A | 1.361 | 0.99 |
| 130_A | 159_A | 1.360 | 0.99 |
| 143_V | 165_Y | 1.354 | 0.99 |
| 166_L | 273_R | 1.350 | 0.99 |
| 34_S | 43_A | 1.337 | 0.99 |
| 268_V | 272_A | 1.332 | 0.99 |
| 17_D | 30_L | 1.321 | 0.99 |
| 14_T | 42_V | 1.310 | 0.99 |
| 126_G | 156_Y | 1.294 | 0.99 |
| 101_L | 117_T | 1.285 | 0.99 |
| 7_A | 12_V | 1.275 | 0.99 |
| 203_A | 207_Q | 1.249 | 0.99 |
| 117_T | 129_Q | 1.248 | 0.99 |
| 4_L | 37_A | 1.246 | 0.98 |
| 16_V | 73_Y | 1.238 | 0.98 |
| 30_L | 34_S | 1.227 | 0.98 |
| 226_Y | 229_N | 1.225 | 0.98 |
| 98_E | 132_I | 1.223 | 0.98 |
| 154_L | 204_L | 1.208 | 0.98 |
| 209_Y | 212_Q | 1.205 | 0.98 |
| 247_L | 251_P | 1.164 | 0.97 |
| 205_I | 249_V | 1.152 | 0.97 |
| 145_I | 274_F | 1.147 | 0.97 |
| 109_L | 137_G | 1.141 | 0.97 |
| 106_R | 110_A | 1.136 | 0.97 |
| 35_R | 71_I | 1.122 | 0.97 |
| 262_T | 265_G | 1.120 | 0.96 |
| 21_F | 26_D | 1.116 | 0.96 |
| 18_V | 44_A | 1.112 | 0.96 |
| 236_R | 239_P | 1.103 | 0.96 |
| 258_V | 262_T | 1.099 | 0.96 |
| 117_T | 146_G | 1.097 | 0.96 |
| 130_A | 160_L | 1.091 | 0.96 |
| 144_C | 165_Y | 1.090 | 0.96 |
| 263_L | 267_T | 1.087 | 0.96 |
| 152_D | 156_Y | 1.085 | 0.96 |
| 237_V | 241_G | 1.085 | 0.96 |
| 45_T | 72_Q | 1.085 | 0.96 |
| 191_I | 222_G | 1.082 | 0.96 |
| 246_P | 250_I | 1.075 | 0.95 |
| 30_L | 43_A | 1.073 | 0.95 |
| 37_A | 40_H | 1.068 | 0.95 |
| 107_A | 111_T | 1.064 | 0.95 |
| 244_F | 247_L | 1.063 | 0.95 |
| 15_I | 41_I | 1.062 | 0.95 |
| 126_G | 152_D | 1.060 | 0.95 |
| 167_I | 208_G | 1.059 | 0.95 |
| 205_I | 256_K | 1.058 | 0.95 |
| 31_A | 35_R | 1.053 | 0.95 |
| 249_V | 252_F | 1.051 | 0.94 |
| 155_S | 158_T | 1.048 | 0.94 |
| 64_T | 68_L | 1.041 | 0.94 |
| 27_V | 45_T | 1.029 | 0.94 |
| 19_S | 27_V | 1.026 | 0.94 |
| 6_R | 238_N | 1.020 | 0.93 |
| 205_I | 255_E | 1.005 | 0.93 |
| 53_L | 100_V | 1.002 | 0.92 |
| 4_L | 15_I | 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
- 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 | |
| 3k2gA | 4 | 0.9321 | 100 | 0.337 | Contact Map |
| 3rhgA | 1 | 0.9214 | 100 | 0.377 | Contact Map |
| 3e2vA | 2 | 0.8357 | 100 | 0.403 | Contact Map |
| 1yixA | 2 | 0.8321 | 100 | 0.467 | Contact Map |
| 3ipwA | 1 | 0.8321 | 100 | 0.475 | Contact Map |
| 3pnzA | 6 | 0.9036 | 100 | 0.477 | Contact Map |
| 1j6oA | 1 | 0.8357 | 100 | 0.479 | Contact Map |
| 3ovgA | 6 | 0.925 | 100 | 0.48 | Contact Map |
| 3gg7A | 1 | 0.7929 | 100 | 0.492 | Contact Map |
| 2xioA | 1 | 0.8393 | 100 | 0.498 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)