| 4rdq -force run |
| ID: | 1414192142 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 366 (366) | ||
| Sequences: | 191 (134.3) | ||
| Seq/Len: | 0.522 | ||
| Nf(neff/√len): | 7.0 |
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: 0.522).
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 |
| 195_R | 203_S | 2.270 | 0.94 |
| 54_S | 57_Q | 2.016 | 0.87 |
| 1_T | 4_Y | 2.009 | 0.87 |
| 119_Y | 197_E | 1.867 | 0.81 |
| 243_V | 306_T | 1.799 | 0.78 |
| 162_M | 170_F | 1.783 | 0.77 |
| 272_V | 277_F | 1.772 | 0.76 |
| 95_Q | 102_P | 1.706 | 0.72 |
| 307_N | 311_D | 1.702 | 0.72 |
| 24_K | 216_L | 1.697 | 0.71 |
| 50_R | 57_Q | 1.594 | 0.65 |
| 244_Y | 317_S | 1.554 | 0.62 |
| 86_S | 161_L | 1.550 | 0.61 |
| 102_P | 294_I | 1.545 | 0.61 |
| 23_W | 26_S | 1.542 | 0.61 |
| 314_L | 318_L | 1.506 | 0.58 |
| 103_D | 312_R | 1.496 | 0.57 |
| 124_R | 149_R | 1.474 | 0.56 |
| 38_F | 102_P | 1.460 | 0.54 |
| 297_F | 317_S | 1.448 | 0.54 |
| 123_L | 190_L | 1.440 | 0.53 |
| 109_V | 127_L | 1.438 | 0.53 |
| 79_F | 85_V | 1.422 | 0.52 |
| 127_L | 187_F | 1.407 | 0.50 |
| 106_M | 127_L | 1.401 | 0.50 |
| 103_D | 170_F | 1.400 | 0.50 |
| 93_W | 102_P | 1.398 | 0.50 |
| 45_I | 252_I | 1.393 | 0.49 |
| 38_F | 294_I | 1.390 | 0.49 |
| 244_Y | 297_F | 1.387 | 0.49 |
| 322_D | 334_D | 1.384 | 0.49 |
| 127_L | 190_L | 1.382 | 0.48 |
| 336_Y | 345_P | 1.381 | 0.48 |
| 179_K | 195_R | 1.374 | 0.48 |
| 167_H | 171_E | 1.371 | 0.48 |
| 102_P | 230_S | 1.370 | 0.47 |
| 250_C | 257_L | 1.369 | 0.47 |
| 263_Y | 266_H | 1.368 | 0.47 |
| 137_L | 140_R | 1.367 | 0.47 |
| 1_T | 8_V | 1.359 | 0.47 |
| 75_I | 241_V | 1.355 | 0.46 |
| 28_Y | 100_P | 1.352 | 0.46 |
| 28_Y | 38_F | 1.345 | 0.46 |
| 107_N | 180_F | 1.342 | 0.45 |
| 155_H | 347_T | 1.333 | 0.45 |
| 1_T | 16_F | 1.331 | 0.44 |
| 27_I | 68_C | 1.319 | 0.44 |
| 257_L | 263_Y | 1.314 | 0.43 |
| 26_S | 29_K | 1.311 | 0.43 |
| 346_Y | 361_S | 1.310 | 0.43 |
| 93_W | 234_V | 1.307 | 0.43 |
| 103_D | 287_L | 1.304 | 0.42 |
| 1_T | 305_E | 1.302 | 0.42 |
| 136_V | 161_L | 1.302 | 0.42 |
| 129_R | 150_F | 1.301 | 0.42 |
| 346_Y | 360_G | 1.295 | 0.42 |
| 78_S | 238_V | 1.290 | 0.41 |
| 313_N | 321_V | 1.284 | 0.41 |
| 62_E | 274_V | 1.281 | 0.41 |
| 84_Y | 236_T | 1.279 | 0.40 |
| 342_P | 354_K | 1.279 | 0.40 |
| 21_L | 75_I | 1.275 | 0.40 |
| 16_F | 19_L | 1.267 | 0.40 |
| 240_T | 244_Y | 1.251 | 0.38 |
| 213_L | 231_I | 1.248 | 0.38 |
| 105_I | 131_S | 1.248 | 0.38 |
| 37_I | 97_E | 1.245 | 0.38 |
| 190_L | 327_D | 1.243 | 0.38 |
| 28_Y | 78_S | 1.242 | 0.38 |
| 96_Y | 230_S | 1.240 | 0.38 |
| 240_T | 287_L | 1.233 | 0.37 |
| 39_I | 43_F | 1.233 | 0.37 |
| 161_L | 178_N | 1.222 | 0.36 |
| 93_W | 253_G | 1.217 | 0.36 |
| 28_Y | 220_C | 1.213 | 0.36 |
| 64_L | 142_V | 1.206 | 0.35 |
| 8_V | 16_F | 1.204 | 0.35 |
| 156_V | 161_L | 1.202 | 0.35 |
| 300_D | 303_D | 1.199 | 0.35 |
| 351_A | 354_K | 1.186 | 0.34 |
| 48_V | 53_L | 1.186 | 0.34 |
| 151_P | 160_G | 1.180 | 0.33 |
| 85_V | 92_W | 1.180 | 0.33 |
| 352_E | 364_D | 1.178 | 0.33 |
| 254_R | 279_Q | 1.178 | 0.33 |
| 101_W | 225_G | 1.177 | 0.33 |
| 106_M | 320_A | 1.176 | 0.33 |
| 4_Y | 16_F | 1.169 | 0.33 |
| 102_P | 236_T | 1.160 | 0.32 |
| 230_S | 236_T | 1.159 | 0.32 |
| 299_E | 302_D | 1.157 | 0.32 |
| 176_P | 274_V | 1.155 | 0.32 |
| 125_R | 291_E | 1.153 | 0.31 |
| 2_V | 8_V | 1.153 | 0.31 |
| 39_I | 65_A | 1.149 | 0.31 |
| 115_G | 157_V | 1.138 | 0.30 |
| 318_L | 344_P | 1.137 | 0.30 |
| 276_T | 279_Q | 1.136 | 0.30 |
| 132_N | 317_S | 1.135 | 0.30 |
| 89_V | 286_W | 1.135 | 0.30 |
| 17_S | 106_M | 1.134 | 0.30 |
| 27_I | 75_I | 1.133 | 0.30 |
| 199_R | 279_Q | 1.132 | 0.30 |
| 343_Q | 357_S | 1.131 | 0.30 |
| 198_G | 270_L | 1.131 | 0.30 |
| 20_L | 28_Y | 1.129 | 0.30 |
| 313_N | 320_A | 1.128 | 0.30 |
| 347_T | 350_T | 1.127 | 0.30 |
| 258_D | 263_Y | 1.123 | 0.29 |
| 162_M | 189_N | 1.121 | 0.29 |
| 30_L | 100_P | 1.121 | 0.29 |
| 313_N | 317_S | 1.115 | 0.29 |
| 348_A | 354_K | 1.115 | 0.29 |
| 336_Y | 349_A | 1.113 | 0.29 |
| 93_W | 236_T | 1.112 | 0.29 |
| 118_E | 194_A | 1.112 | 0.29 |
| 29_K | 301_D | 1.110 | 0.29 |
| 82_G | 115_G | 1.110 | 0.29 |
| 236_T | 240_T | 1.106 | 0.28 |
| 242_A | 313_N | 1.106 | 0.28 |
| 18_Q | 229_I | 1.104 | 0.28 |
| 84_Y | 240_T | 1.101 | 0.28 |
| 147_Y | 336_Y | 1.101 | 0.28 |
| 9_A | 14_G | 1.099 | 0.28 |
| 148_K | 314_L | 1.098 | 0.28 |
| 294_I | 312_R | 1.095 | 0.28 |
| 140_R | 147_Y | 1.094 | 0.28 |
| 358_F | 362_T | 1.093 | 0.28 |
| 4_Y | 8_V | 1.092 | 0.28 |
| 142_V | 153_M | 1.090 | 0.27 |
| 122_L | 310_I | 1.090 | 0.27 |
| 308_W | 342_P | 1.090 | 0.27 |
| 39_I | 272_V | 1.088 | 0.27 |
| 95_Q | 100_P | 1.086 | 0.27 |
| 118_E | 246_F | 1.085 | 0.27 |
| 100_P | 141_S | 1.085 | 0.27 |
| 247_F | 255_Q | 1.085 | 0.27 |
| 194_A | 290_A | 1.084 | 0.27 |
| 73_E | 252_I | 1.083 | 0.27 |
| 295_N | 307_N | 1.081 | 0.27 |
| 19_L | 23_W | 1.080 | 0.27 |
| 84_Y | 95_Q | 1.077 | 0.27 |
| 236_T | 347_T | 1.073 | 0.26 |
| 244_Y | 287_L | 1.071 | 0.26 |
| 129_R | 151_P | 1.068 | 0.26 |
| 12_R | 96_Y | 1.067 | 0.26 |
| 352_E | 355_R | 1.066 | 0.26 |
| 235_Y | 285_G | 1.065 | 0.26 |
| 250_C | 258_D | 1.064 | 0.26 |
| 255_Q | 288_K | 1.062 | 0.26 |
| 125_R | 322_D | 1.062 | 0.26 |
| 67_Y | 133_L | 1.061 | 0.26 |
| 234_V | 253_G | 1.060 | 0.26 |
| 23_W | 29_K | 1.059 | 0.26 |
| 75_I | 81_L | 1.058 | 0.25 |
| 220_C | 281_F | 1.058 | 0.25 |
| 295_N | 299_E | 1.057 | 0.25 |
| 50_R | 276_T | 1.057 | 0.25 |
| 160_G | 194_A | 1.053 | 0.25 |
| 117_D | 199_R | 1.052 | 0.25 |
| 120_G | 229_I | 1.052 | 0.25 |
| 3_T | 248_L | 1.052 | 0.25 |
| 43_F | 46_S | 1.051 | 0.25 |
| 345_P | 349_A | 1.050 | 0.25 |
| 103_D | 283_Y | 1.048 | 0.25 |
| 285_G | 288_K | 1.048 | 0.25 |
| 121_R | 149_R | 1.048 | 0.25 |
| 235_Y | 255_Q | 1.046 | 0.25 |
| 255_Q | 285_G | 1.044 | 0.25 |
| 100_P | 220_C | 1.043 | 0.25 |
| 245_S | 253_G | 1.043 | 0.25 |
| 115_G | 149_R | 1.039 | 0.24 |
| 238_V | 301_D | 1.038 | 0.24 |
| 199_R | 315_Q | 1.038 | 0.24 |
| 120_G | 199_R | 1.037 | 0.24 |
| 286_W | 302_D | 1.037 | 0.24 |
| 257_L | 266_H | 1.036 | 0.24 |
| 281_F | 308_W | 1.035 | 0.24 |
| 134_C | 140_R | 1.034 | 0.24 |
| 95_Q | 244_Y | 1.032 | 0.24 |
| 4_Y | 19_L | 1.029 | 0.24 |
| 102_P | 135_S | 1.027 | 0.24 |
| 102_P | 317_S | 1.027 | 0.24 |
| 80_V | 281_F | 1.026 | 0.24 |
| 80_V | 98_S | 1.024 | 0.23 |
| 155_H | 236_T | 1.023 | 0.23 |
| 182_I | 231_I | 1.022 | 0.23 |
| 32_Y | 169_K | 1.020 | 0.23 |
| 102_P | 244_Y | 1.019 | 0.23 |
| 351_A | 358_F | 1.018 | 0.23 |
| 351_A | 355_R | 1.016 | 0.23 |
| 125_R | 334_D | 1.014 | 0.23 |
| 255_Q | 282_F | 1.010 | 0.23 |
| 334_D | 337_W | 1.009 | 0.23 |
| 82_G | 88_V | 1.008 | 0.23 |
| 115_G | 124_R | 1.008 | 0.23 |
| 190_L | 335_L | 1.004 | 0.22 |
| 224_Y | 228_W | 1.003 | 0.22 |
| 150_F | 311_D | 1.003 | 0.22 |
| 143_S | 305_E | 1.002 | 0.22 |
| 295_N | 311_D | 1.002 | 0.22 |
| 76_P | 79_F | 1.001 | 0.22 |
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 | |
| 2lmcA | 1 | 0.1311 | 13.3 | 0.982 | Contact Map |
| 2aqeA | 1 | 0.2404 | 10.8 | 0.983 | Contact Map |
| 1dgnA | 1 | 0.2322 | 10.3 | 0.983 | Contact Map |
| 3jroA | 1 | 0.3115 | 7.7 | 0.984 | Contact Map |
| 4mjsB | 12 | 0.2404 | 5.4 | 0.985 | Contact Map |
| 3kyjA | 1 | 0.1475 | 5 | 0.986 | Contact Map |
| 1dulA | 1 | 0.1858 | 4.6 | 0.986 | Contact Map |
| 4g0dW | 4 | 0.071 | 4.5 | 0.986 | Contact Map |
| 1mzbA | 1 | 0.3197 | 4.4 | 0.986 | Contact Map |
| 1hq1A | 1 | 0.2077 | 3.7 | 0.986 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)