| T0827 |
| ID: | 1403288143 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 407 (365) | ||
| Sequences: | 365 (294) | ||
| Seq/Len: | 1.000 | ||
| Nf(neff/√len): | 15.4 |
Jackhmmer Results: (2014_04_16)
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: 1.000).
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 |
| 130_V | 155_L | 4.296 | 1.00 |
| 106_D | 131_S | 3.800 | 1.00 |
| 198_A | 202_A | 2.536 | 0.99 |
| 144_P | 173_A | 2.345 | 0.99 |
| 93_V | 98_L | 2.344 | 0.99 |
| 132_E | 157_K | 2.260 | 0.98 |
| 98_L | 124_I | 2.202 | 0.98 |
| 135_A | 150_L | 1.904 | 0.94 |
| 32_D | 71_R | 1.892 | 0.93 |
| 62_V | 93_V | 1.799 | 0.91 |
| 255_I | 260_F | 1.782 | 0.90 |
| 130_V | 135_A | 1.778 | 0.90 |
| 138_L | 146_V | 1.771 | 0.90 |
| 15_A | 26_L | 1.763 | 0.90 |
| 136_D | 162_G | 1.754 | 0.89 |
| 80_G | 84_R | 1.748 | 0.89 |
| 135_A | 162_G | 1.731 | 0.89 |
| 129_G | 155_L | 1.696 | 0.87 |
| 140_E | 169_A | 1.679 | 0.86 |
| 65_R | 89_D | 1.660 | 0.86 |
| 251_N | 260_F | 1.645 | 0.85 |
| 78_M | 83_V | 1.586 | 0.82 |
| 130_V | 134_V | 1.552 | 0.80 |
| 151_L | 176_L | 1.545 | 0.80 |
| 259_P | 262_S | 1.535 | 0.79 |
| 270_G | 278_I | 1.523 | 0.78 |
| 87_L | 101_S | 1.517 | 0.78 |
| 135_A | 158_L | 1.517 | 0.78 |
| 321_Q | 342_E | 1.507 | 0.77 |
| 362_Y | 365_W | 1.493 | 0.76 |
| 113_L | 124_I | 1.491 | 0.76 |
| 259_P | 288_L | 1.485 | 0.76 |
| 14_E | 29_R | 1.481 | 0.75 |
| 113_L | 155_L | 1.463 | 0.74 |
| 305_L | 308_L | 1.458 | 0.74 |
| 99_V | 126_Q | 1.447 | 0.73 |
| 158_L | 162_G | 1.432 | 0.72 |
| 89_D | 93_V | 1.418 | 0.71 |
| 93_V | 110_I | 1.414 | 0.71 |
| 91_L | 120_H | 1.411 | 0.70 |
| 153_N | 156_V | 1.386 | 0.68 |
| 110_I | 131_S | 1.372 | 0.67 |
| 124_I | 137_A | 1.372 | 0.67 |
| 98_L | 155_L | 1.371 | 0.67 |
| 30_L | 113_L | 1.363 | 0.66 |
| 176_L | 303_E | 1.322 | 0.63 |
| 87_L | 97_L | 1.320 | 0.63 |
| 59_D | 64_E | 1.311 | 0.62 |
| 335_G | 340_N | 1.303 | 0.61 |
| 251_N | 258_S | 1.299 | 0.61 |
| 254_A | 281_E | 1.294 | 0.61 |
| 93_V | 261_N | 1.290 | 0.60 |
| 202_A | 206_I | 1.286 | 0.60 |
| 41_I | 296_I | 1.281 | 0.59 |
| 83_V | 101_S | 1.276 | 0.59 |
| 90_E | 116_A | 1.274 | 0.59 |
| 34_V | 356_A | 1.272 | 0.59 |
| 136_D | 141_V | 1.263 | 0.58 |
| 340_N | 346_T | 1.262 | 0.58 |
| 23_R | 30_L | 1.255 | 0.57 |
| 138_L | 353_V | 1.253 | 0.57 |
| 244_F | 251_N | 1.252 | 0.57 |
| 358_T | 362_Y | 1.251 | 0.57 |
| 195_F | 199_D | 1.246 | 0.56 |
| 136_D | 206_I | 1.245 | 0.56 |
| 27_L | 31_A | 1.243 | 0.56 |
| 25_T | 283_S | 1.238 | 0.55 |
| 110_I | 121_R | 1.236 | 0.55 |
| 146_V | 307_I | 1.225 | 0.54 |
| 21_R | 297_F | 1.223 | 0.54 |
| 124_I | 158_L | 1.221 | 0.54 |
| 180_L | 266_A | 1.218 | 0.54 |
| 270_G | 319_V | 1.215 | 0.53 |
| 340_N | 345_L | 1.214 | 0.53 |
| 121_R | 141_V | 1.213 | 0.53 |
| 256_A | 259_P | 1.213 | 0.53 |
| 98_L | 146_V | 1.211 | 0.53 |
| 103_K | 202_A | 1.209 | 0.53 |
| 98_L | 262_S | 1.209 | 0.53 |
| 69_A | 309_C | 1.205 | 0.52 |
| 122_R | 138_L | 1.201 | 0.52 |
| 53_L | 146_V | 1.197 | 0.52 |
| 266_A | 294_A | 1.195 | 0.52 |
| 122_R | 146_V | 1.192 | 0.51 |
| 41_I | 49_T | 1.192 | 0.51 |
| 14_E | 26_L | 1.187 | 0.51 |
| 69_A | 255_I | 1.184 | 0.50 |
| 364_N | 367_L | 1.181 | 0.50 |
| 158_L | 322_L | 1.166 | 0.49 |
| 151_L | 166_I | 1.165 | 0.49 |
| 93_V | 326_L | 1.165 | 0.49 |
| 348_Y | 351_I | 1.161 | 0.48 |
| 125_A | 364_N | 1.158 | 0.48 |
| 362_Y | 366_S | 1.157 | 0.48 |
| 97_L | 281_E | 1.151 | 0.47 |
| 14_E | 17_R | 1.150 | 0.47 |
| 202_A | 278_I | 1.149 | 0.47 |
| 151_L | 304_P | 1.147 | 0.47 |
| 37_P | 41_I | 1.145 | 0.47 |
| 159_S | 162_G | 1.145 | 0.47 |
| 94_A | 117_T | 1.144 | 0.47 |
| 268_A | 305_L | 1.143 | 0.47 |
| 140_E | 171_R | 1.125 | 0.45 |
| 76_N | 103_K | 1.122 | 0.45 |
| 97_L | 101_S | 1.121 | 0.45 |
| 150_L | 270_G | 1.117 | 0.44 |
| 66_E | 92_P | 1.117 | 0.44 |
| 145_A | 286_S | 1.116 | 0.44 |
| 252_R | 256_A | 1.116 | 0.44 |
| 148_E | 151_L | 1.111 | 0.44 |
| 27_L | 32_D | 1.110 | 0.44 |
| 186_L | 283_S | 1.107 | 0.43 |
| 43_A | 138_L | 1.104 | 0.43 |
| 340_N | 343_R | 1.104 | 0.43 |
| 177_I | 202_A | 1.097 | 0.42 |
| 114_Y | 158_L | 1.096 | 0.42 |
| 178_P | 282_I | 1.094 | 0.42 |
| 113_L | 141_V | 1.092 | 0.42 |
| 113_L | 121_R | 1.088 | 0.42 |
| 355_R | 362_Y | 1.085 | 0.41 |
| 82_L | 285_L | 1.085 | 0.41 |
| 98_L | 123_L | 1.083 | 0.41 |
| 357_Q | 361_R | 1.082 | 0.41 |
| 61_N | 116_A | 1.078 | 0.41 |
| 179_L | 198_A | 1.077 | 0.41 |
| 27_L | 64_E | 1.076 | 0.41 |
| 203_R | 293_G | 1.076 | 0.41 |
| 98_L | 310_K | 1.070 | 0.40 |
| 104_L | 283_S | 1.070 | 0.40 |
| 120_H | 146_V | 1.069 | 0.40 |
| 286_S | 293_G | 1.069 | 0.40 |
| 111_S | 114_Y | 1.068 | 0.40 |
| 35_C | 301_G | 1.068 | 0.40 |
| 57_L | 223_D | 1.066 | 0.40 |
| 166_I | 224_V | 1.065 | 0.40 |
| 138_L | 150_L | 1.065 | 0.40 |
| 24_S | 32_D | 1.064 | 0.40 |
| 104_L | 155_L | 1.057 | 0.39 |
| 105_S | 312_T | 1.056 | 0.39 |
| 72_L | 198_A | 1.055 | 0.39 |
| 25_T | 28_K | 1.053 | 0.39 |
| 11_E | 31_A | 1.053 | 0.39 |
| 341_L | 345_L | 1.053 | 0.39 |
| 14_E | 18_A | 1.052 | 0.38 |
| 64_E | 186_L | 1.050 | 0.38 |
| 353_V | 357_Q | 1.049 | 0.38 |
| 258_S | 281_E | 1.049 | 0.38 |
| 53_L | 68_V | 1.049 | 0.38 |
| 150_L | 158_L | 1.047 | 0.38 |
| 69_A | 293_G | 1.046 | 0.38 |
| 141_V | 162_G | 1.045 | 0.38 |
| 268_A | 285_L | 1.043 | 0.38 |
| 117_T | 159_S | 1.038 | 0.37 |
| 69_A | 236_P | 1.036 | 0.37 |
| 118_T | 143_E | 1.036 | 0.37 |
| 130_V | 150_L | 1.033 | 0.37 |
| 101_S | 124_I | 1.033 | 0.37 |
| 143_E | 155_L | 1.031 | 0.37 |
| 148_E | 152_R | 1.028 | 0.36 |
| 69_A | 178_P | 1.028 | 0.36 |
| 61_N | 149_T | 1.025 | 0.36 |
| 158_L | 186_L | 1.022 | 0.36 |
| 40_R | 82_L | 1.022 | 0.36 |
| 147_I | 173_A | 1.021 | 0.36 |
| 52_L | 309_C | 1.019 | 0.36 |
| 102_E | 313_G | 1.016 | 0.35 |
| 120_H | 170_T | 1.013 | 0.35 |
| 69_A | 131_S | 1.013 | 0.35 |
| 93_V | 96_A | 1.011 | 0.35 |
| 64_E | 261_N | 1.007 | 0.35 |
| 121_R | 278_I | 1.005 | 0.34 |
| 354_D | 357_Q | 1.004 | 0.34 |
| 151_L | 266_A | 1.000 | 0.34 |
| 46_R | 186_L | 1.000 | 0.34 |
| 18_A | 56_M | 1.000 | 0.34 |
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 | |
| 1lrvA | 1 | 0.3636 | 90.6 | 0.944 | Contact Map |
| 2jdqA | 2 | 0.4128 | 37.3 | 0.964 | Contact Map |
| 4lacA | 1 | 0.2531 | 36.7 | 0.964 | Contact Map |
| 3ltmA | 2 | 0.43 | 35.1 | 0.964 | Contact Map |
| 1oyzA | 1 | 0.4398 | 33.9 | 0.965 | Contact Map |
| 4g3aA | 2 | 0.5307 | 29.1 | 0.966 | Contact Map |
| 3ltjA | 1 | 0.4423 | 26.5 | 0.967 | Contact Map |
| 1b3uA | 2 | 0.1843 | 25.5 | 0.967 | Contact Map |
| 4db6A | 1 | 0.2924 | 22.2 | 0.968 | Contact Map |
| 1te4A | 1 | 0.258 | 20.6 | 0.968 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)