| YjhB_MembraneProt |
| ID: | 1517362718 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 405 (373) | ||
| Sequences: | 60956 (36601.9) | ||
| Seq/Len: | 163.421 | ||
| Nf(neff/√len): | 1895.2 |
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: 163.421).
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 |
| 101_T | 105_M | 4.489 | 1.00 |
| 89_I | 116_G | 4.068 | 1.00 |
| 96_L | 109_C | 4.060 | 1.00 |
| 98_G | 173_F | 3.716 | 1.00 |
| 62_A | 111_F | 3.305 | 1.00 |
| 86_A | 119_G | 3.266 | 1.00 |
| 91_S | 179_V | 3.197 | 1.00 |
| 138_S | 276_D | 3.172 | 1.00 |
| 79_R | 130_E | 3.093 | 1.00 |
| 93_G | 109_C | 3.035 | 1.00 |
| 335_F | 343_G | 3.031 | 1.00 |
| 102_N | 105_M | 2.956 | 1.00 |
| 136_L | 139_K | 2.916 | 1.00 |
| 70_F | 119_G | 2.913 | 1.00 |
| 104_Y | 108_V | 2.893 | 1.00 |
| 132_W | 140_A | 2.545 | 1.00 |
| 93_G | 112_I | 2.480 | 1.00 |
| 93_G | 116_G | 2.476 | 1.00 |
| 75_D | 341_G | 2.445 | 1.00 |
| 249_N | 252_V | 2.410 | 1.00 |
| 133_P | 136_L | 2.377 | 1.00 |
| 58_V | 111_F | 2.376 | 1.00 |
| 103_L | 107_A | 2.271 | 1.00 |
| 72_A | 76_K | 2.256 | 1.00 |
| 280_V | 333_D | 2.227 | 1.00 |
| 48_T | 51_Q | 2.207 | 1.00 |
| 66_G | 115_L | 2.192 | 1.00 |
| 336_P | 339_L | 2.180 | 1.00 |
| 80_K | 84_M | 2.148 | 1.00 |
| 74_A | 123_C | 2.082 | 1.00 |
| 13_Q | 136_L | 2.046 | 1.00 |
| 166_Y | 170_N | 2.034 | 1.00 |
| 73_M | 82_M | 2.031 | 1.00 |
| 97_S | 109_C | 2.010 | 1.00 |
| 100_A | 105_M | 2.006 | 1.00 |
| 51_Q | 103_L | 1.971 | 1.00 |
| 100_A | 109_C | 1.932 | 1.00 |
| 97_S | 106_L | 1.875 | 1.00 |
| 58_V | 107_A | 1.865 | 1.00 |
| 95_G | 176_L | 1.840 | 1.00 |
| 273_F | 277_K | 1.830 | 1.00 |
| 21_W | 147_G | 1.795 | 1.00 |
| 105_M | 109_C | 1.758 | 1.00 |
| 78_G | 81_P | 1.751 | 1.00 |
| 55_I | 106_L | 1.743 | 1.00 |
| 167_G | 170_N | 1.729 | 1.00 |
| 40_I | 43_A | 1.719 | 1.00 |
| 47_I | 103_L | 1.709 | 1.00 |
| 279_G | 282_K | 1.677 | 1.00 |
| 66_G | 118_S | 1.677 | 1.00 |
| 66_G | 69_F | 1.633 | 1.00 |
| 23_G | 83_M | 1.626 | 1.00 |
| 73_M | 77_Y | 1.614 | 1.00 |
| 270_F | 273_F | 1.607 | 1.00 |
| 128_A | 144_L | 1.586 | 1.00 |
| 130_E | 340_R | 1.581 | 1.00 |
| 104_Y | 107_A | 1.551 | 1.00 |
| 93_G | 113_V | 1.543 | 1.00 |
| 272_G | 276_D | 1.535 | 1.00 |
| 28_G | 148_F | 1.509 | 1.00 |
| 77_Y | 81_P | 1.505 | 1.00 |
| 75_D | 342_L | 1.499 | 1.00 |
| 81_P | 85_W | 1.473 | 1.00 |
| 281_K | 285_V | 1.471 | 1.00 |
| 47_I | 51_Q | 1.462 | 1.00 |
| 77_Y | 82_M | 1.455 | 1.00 |
| 207_L | 211_R | 1.450 | 1.00 |
| 96_L | 99_I | 1.447 | 1.00 |
| 134_K | 137_Q | 1.430 | 1.00 |
| 42_K | 52_A | 1.422 | 1.00 |
| 71_G | 75_D | 1.411 | 1.00 |
| 139_K | 276_D | 1.410 | 1.00 |
| 16_A | 131_S | 1.405 | 0.99 |
| 282_K | 285_V | 1.405 | 0.99 |
| 40_I | 44_D | 1.380 | 0.99 |
| 162_F | 170_N | 1.380 | 0.99 |
| 50_I | 367_G | 1.376 | 0.99 |
| 274_V | 278_I | 1.364 | 0.99 |
| 199_K | 202_D | 1.357 | 0.99 |
| 38_L | 52_A | 1.353 | 0.99 |
| 84_M | 186_R | 1.350 | 0.99 |
| 139_K | 273_F | 1.347 | 0.99 |
| 62_A | 114_G | 1.344 | 0.99 |
| 86_A | 116_G | 1.342 | 0.99 |
| 244_A | 253_I | 1.328 | 0.99 |
| 81_P | 84_M | 1.325 | 0.99 |
| 139_K | 143_F | 1.320 | 0.99 |
| 184_W | 188_S | 1.318 | 0.99 |
| 62_A | 66_G | 1.318 | 0.99 |
| 364_Y | 368_Y | 1.316 | 0.99 |
| 14_R | 18_F | 1.316 | 0.99 |
| 354_G | 358_A | 1.308 | 0.99 |
| 149_S | 264_T | 1.299 | 0.99 |
| 173_F | 177_L | 1.292 | 0.99 |
| 78_G | 82_M | 1.289 | 0.99 |
| 279_G | 283_A | 1.261 | 0.99 |
| 92_V | 96_L | 1.261 | 0.99 |
| 49_D | 367_G | 1.260 | 0.99 |
| 95_G | 99_I | 1.257 | 0.99 |
| 74_A | 341_G | 1.256 | 0.99 |
| 79_R | 191_E | 1.253 | 0.99 |
| 74_A | 79_R | 1.245 | 0.98 |
| 267_G | 270_F | 1.244 | 0.98 |
| 12_P | 15_K | 1.237 | 0.98 |
| 84_M | 88_F | 1.236 | 0.98 |
| 99_I | 173_F | 1.230 | 0.98 |
| 108_V | 112_I | 1.227 | 0.98 |
| 170_N | 173_F | 1.227 | 0.98 |
| 75_D | 79_R | 1.221 | 0.98 |
| 89_I | 93_G | 1.215 | 0.98 |
| 94_T | 175_G | 1.209 | 0.98 |
| 85_W | 89_I | 1.202 | 0.98 |
| 251_V | 255_T | 1.201 | 0.98 |
| 30_D | 33_M | 1.197 | 0.98 |
| 127_Y | 189_A | 1.197 | 0.98 |
| 71_G | 341_G | 1.195 | 0.98 |
| 61_I | 356_M | 1.191 | 0.98 |
| 137_Q | 333_D | 1.191 | 0.98 |
| 263_G | 267_G | 1.189 | 0.98 |
| 332_Y | 344_T | 1.184 | 0.98 |
| 244_A | 250_T | 1.183 | 0.98 |
| 129_V | 137_Q | 1.181 | 0.98 |
| 363_T | 367_G | 1.167 | 0.97 |
| 98_G | 169_R | 1.164 | 0.97 |
| 59_A | 117_M | 1.161 | 0.97 |
| 44_D | 169_R | 1.160 | 0.97 |
| 25_V | 154_I | 1.160 | 0.97 |
| 69_F | 72_A | 1.158 | 0.97 |
| 266_T | 269_I | 1.156 | 0.97 |
| 17_L | 132_W | 1.150 | 0.97 |
| 331_I | 347_I | 1.146 | 0.97 |
| 88_F | 183_L | 1.139 | 0.97 |
| 79_R | 126_T | 1.138 | 0.97 |
| 242_Y | 246_N | 1.134 | 0.97 |
| 252_V | 255_T | 1.132 | 0.97 |
| 278_I | 283_A | 1.127 | 0.97 |
| 248_V | 252_V | 1.127 | 0.97 |
| 96_L | 105_M | 1.124 | 0.97 |
| 289_I | 293_I | 1.123 | 0.97 |
| 282_K | 286_V | 1.121 | 0.97 |
| 23_G | 120_E | 1.118 | 0.96 |
| 81_P | 191_E | 1.110 | 0.96 |
| 54_L | 360_V | 1.108 | 0.96 |
| 263_G | 314_F | 1.105 | 0.96 |
| 84_M | 183_L | 1.102 | 0.96 |
| 101_T | 104_Y | 1.099 | 0.96 |
| 269_I | 273_F | 1.095 | 0.96 |
| 351_G | 355_G | 1.095 | 0.96 |
| 278_I | 282_K | 1.094 | 0.96 |
| 55_I | 103_L | 1.091 | 0.96 |
| 29_F | 155_A | 1.091 | 0.96 |
| 127_Y | 131_S | 1.080 | 0.95 |
| 57_T | 356_M | 1.074 | 0.95 |
| 95_G | 173_F | 1.073 | 0.95 |
| 105_M | 108_V | 1.071 | 0.95 |
| 58_V | 62_A | 1.068 | 0.95 |
| 146_S | 149_S | 1.068 | 0.95 |
| 286_V | 289_I | 1.066 | 0.95 |
| 30_D | 110_R | 1.060 | 0.95 |
| 55_I | 107_A | 1.059 | 0.95 |
| 25_V | 151_G | 1.056 | 0.95 |
| 97_S | 172_F | 1.056 | 0.95 |
| 129_V | 141_S | 1.055 | 0.95 |
| 50_I | 360_V | 1.048 | 0.94 |
| 146_S | 265_L | 1.044 | 0.94 |
| 183_L | 187_K | 1.040 | 0.94 |
| 157_Q | 258_T | 1.038 | 0.94 |
| 98_G | 176_L | 1.035 | 0.94 |
| 85_W | 88_F | 1.033 | 0.94 |
| 27_D | 120_E | 1.032 | 0.94 |
| 157_Q | 161_Q | 1.032 | 0.94 |
| 82_M | 85_W | 1.029 | 0.94 |
| 305_N | 308_L | 1.027 | 0.94 |
| 53_T | 238_L | 1.021 | 0.93 |
| 21_W | 143_F | 1.015 | 0.93 |
| 91_S | 176_L | 1.013 | 0.93 |
| 72_A | 342_L | 1.012 | 0.93 |
| 138_S | 272_G | 1.011 | 0.93 |
| 337_T | 340_R | 1.009 | 0.93 |
| 126_T | 341_G | 1.005 | 0.93 |
| 170_N | 174_I | 1.002 | 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
- 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 | |
| 1pw4A | 1 | 0.9704 | 100 | 0.243 | Contact Map |
| 4j05A | 2 | 0.9259 | 100 | 0.243 | Contact Map |
| 4pypA | 1 | 0.9481 | 100 | 0.255 | Contact Map |
| 2gfpA | 2 | 0.9136 | 100 | 0.272 | Contact Map |
| 3wdoA | 1 | 0.9679 | 100 | 0.275 | Contact Map |
| 4ldsA | 2 | 0.9481 | 100 | 0.284 | Contact Map |
| 4gc0A | 1 | 0.9778 | 100 | 0.287 | Contact Map |
| 3o7qA | 1 | 0.9309 | 100 | 0.292 | Contact Map |
| 4zw9A | 1 | 0 | 100 | 0.296 | Contact Map |
| 2cfqA | 1 | 0.958 | 100 | 0.321 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)