| 4HPad-AE |
| ID: | 1415306471 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 316 (296) | ||
| Sequences: | 774 (571.6) | ||
| Seq/Len: | 2.615 | ||
| Nf(neff/√len): | 33.2 |
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: 2.615).
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 |
| 141_F | 153_L | 4.341 | 1.00 |
| 199_R | 209_Y | 3.356 | 1.00 |
| 139_V | 160_C | 3.010 | 1.00 |
| 202_H | 210_N | 2.938 | 1.00 |
| 12_F | 46_S | 2.804 | 1.00 |
| 166_H | 189_F | 2.718 | 1.00 |
| 11_I | 31_L | 2.703 | 1.00 |
| 173_A | 192_I | 2.528 | 1.00 |
| 157_L | 167_T | 2.507 | 1.00 |
| 126_I | 160_C | 2.452 | 1.00 |
| 159_K | 162_E | 2.286 | 1.00 |
| 119_V | 159_K | 2.254 | 1.00 |
| 233_V | 261_I | 2.228 | 1.00 |
| 15_Q | 18_S | 2.182 | 1.00 |
| 298_Q | 302_L | 2.175 | 1.00 |
| 125_V | 128_R | 2.170 | 1.00 |
| 161_H | 188_D | 2.167 | 1.00 |
| 42_A | 170_E | 2.130 | 1.00 |
| 96_C | 101_C | 2.089 | 1.00 |
| 93_C | 96_C | 2.047 | 1.00 |
| 127_K | 163_V | 2.035 | 1.00 |
| 192_I | 217_I | 2.022 | 1.00 |
| 120_D | 159_K | 1.973 | 0.99 |
| 9_G | 149_Q | 1.972 | 0.99 |
| 93_C | 101_C | 1.964 | 0.99 |
| 199_R | 211_D | 1.936 | 0.99 |
| 35_P | 172_S | 1.914 | 0.99 |
| 289_V | 294_L | 1.884 | 0.99 |
| 117_Y | 122_L | 1.874 | 0.99 |
| 177_N | 219_N | 1.842 | 0.99 |
| 123_V | 160_C | 1.839 | 0.99 |
| 197_M | 252_F | 1.796 | 0.99 |
| 250_I | 301_F | 1.774 | 0.98 |
| 181_N | 219_N | 1.747 | 0.98 |
| 170_E | 230_V | 1.727 | 0.98 |
| 158_L | 186_D | 1.709 | 0.98 |
| 201_K | 204_E | 1.697 | 0.98 |
| 9_G | 152_F | 1.659 | 0.97 |
| 146_P | 153_L | 1.622 | 0.97 |
| 73_C | 96_C | 1.611 | 0.97 |
| 243_D | 247_S | 1.586 | 0.96 |
| 122_L | 156_V | 1.548 | 0.95 |
| 217_I | 252_F | 1.547 | 0.95 |
| 243_D | 296_E | 1.510 | 0.95 |
| 205_Q | 239_F | 1.500 | 0.94 |
| 251_S | 304_N | 1.499 | 0.94 |
| 146_P | 169_I | 1.474 | 0.94 |
| 32_N | 52_H | 1.464 | 0.93 |
| 245_N | 249_I | 1.454 | 0.93 |
| 154_H | 182_K | 1.453 | 0.93 |
| 159_K | 163_V | 1.444 | 0.93 |
| 36_L | 213_I | 1.433 | 0.92 |
| 43_N | 273_K | 1.431 | 0.92 |
| 141_F | 156_V | 1.419 | 0.92 |
| 60_C | 66_C | 1.413 | 0.92 |
| 31_L | 146_P | 1.411 | 0.92 |
| 231_L | 253_M | 1.410 | 0.92 |
| 73_C | 101_C | 1.409 | 0.92 |
| 123_V | 159_K | 1.400 | 0.91 |
| 211_D | 215_E | 1.397 | 0.91 |
| 202_H | 208_V | 1.389 | 0.91 |
| 36_L | 172_S | 1.387 | 0.91 |
| 203_K | 209_Y | 1.361 | 0.90 |
| 10_M | 116_P | 1.358 | 0.89 |
| 214_L | 252_F | 1.351 | 0.89 |
| 27_T | 129_D | 1.334 | 0.88 |
| 241_D | 293_H | 1.327 | 0.88 |
| 39_K | 205_Q | 1.313 | 0.87 |
| 130_S | 134_R | 1.312 | 0.87 |
| 190_A | 217_I | 1.311 | 0.87 |
| 170_E | 191_F | 1.309 | 0.87 |
| 250_I | 304_N | 1.307 | 0.87 |
| 233_V | 249_I | 1.291 | 0.86 |
| 73_C | 93_C | 1.284 | 0.86 |
| 235_V | 294_L | 1.280 | 0.85 |
| 122_L | 126_I | 1.277 | 0.85 |
| 35_P | 174_C | 1.268 | 0.85 |
| 177_N | 181_N | 1.260 | 0.84 |
| 9_G | 31_L | 1.253 | 0.84 |
| 235_V | 263_L | 1.252 | 0.84 |
| 52_H | 279_K | 1.237 | 0.83 |
| 230_V | 260_E | 1.237 | 0.83 |
| 190_A | 220_L | 1.226 | 0.82 |
| 119_V | 152_F | 1.225 | 0.82 |
| 35_P | 148_L | 1.220 | 0.81 |
| 47_W | 279_K | 1.214 | 0.81 |
| 60_C | 105_C | 1.212 | 0.81 |
| 23_P | 189_F | 1.211 | 0.81 |
| 47_W | 274_W | 1.208 | 0.81 |
| 61_Q | 107_Y | 1.201 | 0.80 |
| 28_T | 142_S | 1.194 | 0.79 |
| 69_C | 105_C | 1.188 | 0.79 |
| 118_T | 121_E | 1.188 | 0.79 |
| 9_G | 119_V | 1.187 | 0.79 |
| 197_M | 245_N | 1.186 | 0.79 |
| 246_I | 249_I | 1.183 | 0.79 |
| 126_I | 139_V | 1.169 | 0.77 |
| 196_H | 245_N | 1.162 | 0.77 |
| 147_L | 183_I | 1.151 | 0.76 |
| 202_H | 213_I | 1.150 | 0.76 |
| 40_W | 234_P | 1.147 | 0.76 |
| 77_A | 96_C | 1.146 | 0.75 |
| 202_H | 266_F | 1.143 | 0.75 |
| 147_L | 175_V | 1.137 | 0.75 |
| 66_C | 69_C | 1.126 | 0.74 |
| 78_L | 86_P | 1.125 | 0.74 |
| 177_N | 215_E | 1.123 | 0.73 |
| 60_C | 69_C | 1.117 | 0.73 |
| 240_N | 245_N | 1.115 | 0.73 |
| 187_I | 190_A | 1.113 | 0.72 |
| 29_V | 126_I | 1.107 | 0.72 |
| 126_I | 156_V | 1.103 | 0.71 |
| 169_I | 190_A | 1.101 | 0.71 |
| 250_I | 306_I | 1.100 | 0.71 |
| 190_A | 227_G | 1.079 | 0.69 |
| 75_N | 94_K | 1.073 | 0.68 |
| 141_F | 146_P | 1.072 | 0.68 |
| 17_F | 25_C | 1.070 | 0.68 |
| 210_N | 213_I | 1.068 | 0.68 |
| 8_E | 116_P | 1.067 | 0.68 |
| 66_C | 105_C | 1.066 | 0.68 |
| 28_T | 170_E | 1.064 | 0.67 |
| 275_T | 284_S | 1.059 | 0.67 |
| 89_D | 92_I | 1.058 | 0.67 |
| 208_V | 213_I | 1.056 | 0.67 |
| 218_S | 252_F | 1.053 | 0.66 |
| 194_I | 214_L | 1.044 | 0.65 |
| 268_R | 297_L | 1.035 | 0.64 |
| 191_F | 265_P | 1.033 | 0.64 |
| 157_L | 187_I | 1.032 | 0.64 |
| 39_K | 282_E | 1.031 | 0.64 |
| 45_E | 216_N | 1.029 | 0.64 |
| 174_C | 212_L | 1.029 | 0.64 |
| 39_K | 204_E | 1.025 | 0.63 |
| 16_S | 32_N | 1.024 | 0.63 |
| 280_E | 284_S | 1.024 | 0.63 |
| 299_D | 303_D | 1.023 | 0.63 |
| 238_G | 241_D | 1.022 | 0.63 |
| 161_H | 186_D | 1.009 | 0.61 |
| 42_A | 269_L | 1.008 | 0.61 |
| 170_E | 192_I | 1.007 | 0.61 |
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 | |
| 3c8fA | 1 | 0.7627 | 100 | 0.671 | Contact Map |
| 3c8yA | 1 | 0.8513 | 100 | 0.73 | Contact Map |
| 3canA | 1 | 0.4968 | 100 | 0.741 | Contact Map |
| 1hfeL | 2 | 0.8165 | 100 | 0.743 | Contact Map |
| 2z2uA | 1 | 0.6646 | 100 | 0.769 | Contact Map |
| 3rfaA | 2 | 0.7373 | 100 | 0.783 | Contact Map |
| 2yx0A | 1 | 0.7405 | 100 | 0.797 | Contact Map |
| 1oltA | 1 | 0.7563 | 99.9 | 0.816 | Contact Map |
| 2qgqA | 8 | 0.6361 | 99.9 | 0.819 | Contact Map |
| 4u0oB | 1 | 0.7437 | 99.9 | 0.821 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)