| T0827 |
| ID: | 1403290367 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 407 (371) | ||
| Sequences: | 382 (299.8) | ||
| Seq/Len: | 1.030 | ||
| Nf(neff/√len): | 15.6 |
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: 1.030).
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 | 3.683 | 1.00 |
| 106_D | 131_S | 3.645 | 1.00 |
| 198_A | 202_A | 2.746 | 1.00 |
| 132_E | 157_K | 2.235 | 0.98 |
| 98_L | 124_I | 2.203 | 0.98 |
| 135_A | 150_L | 2.091 | 0.97 |
| 144_P | 173_A | 2.054 | 0.96 |
| 138_L | 146_V | 1.951 | 0.95 |
| 87_L | 101_S | 1.933 | 0.95 |
| 249_Q | 252_R | 1.819 | 0.92 |
| 15_A | 26_L | 1.772 | 0.90 |
| 140_E | 169_A | 1.769 | 0.90 |
| 32_D | 71_R | 1.761 | 0.90 |
| 130_V | 135_A | 1.739 | 0.89 |
| 93_V | 98_L | 1.705 | 0.88 |
| 78_M | 83_V | 1.685 | 0.87 |
| 153_N | 156_V | 1.672 | 0.87 |
| 127_R | 153_N | 1.645 | 0.86 |
| 80_G | 84_R | 1.641 | 0.85 |
| 129_G | 155_L | 1.640 | 0.85 |
| 135_A | 162_G | 1.640 | 0.85 |
| 130_V | 134_V | 1.627 | 0.85 |
| 113_L | 124_I | 1.598 | 0.83 |
| 65_R | 89_D | 1.591 | 0.83 |
| 373_P | 376_L | 1.576 | 0.82 |
| 241_A | 252_R | 1.543 | 0.80 |
| 267_V | 275_N | 1.538 | 0.80 |
| 372_T | 375_L | 1.529 | 0.79 |
| 136_D | 162_G | 1.497 | 0.77 |
| 62_V | 93_V | 1.486 | 0.77 |
| 79_P | 127_R | 1.484 | 0.76 |
| 158_L | 162_G | 1.479 | 0.76 |
| 91_L | 120_H | 1.471 | 0.76 |
| 150_L | 258_S | 1.460 | 0.75 |
| 101_S | 153_N | 1.420 | 0.72 |
| 103_K | 202_A | 1.387 | 0.69 |
| 64_E | 259_P | 1.370 | 0.68 |
| 89_D | 93_V | 1.368 | 0.68 |
| 135_A | 158_L | 1.368 | 0.68 |
| 56_M | 79_P | 1.363 | 0.67 |
| 101_S | 127_R | 1.352 | 0.66 |
| 376_L | 379_I | 1.334 | 0.65 |
| 10_F | 13_P | 1.323 | 0.64 |
| 124_I | 137_A | 1.319 | 0.64 |
| 11_E | 33_V | 1.317 | 0.63 |
| 375_L | 379_I | 1.311 | 0.63 |
| 348_Y | 351_I | 1.308 | 0.63 |
| 158_L | 186_L | 1.285 | 0.61 |
| 99_V | 131_S | 1.282 | 0.60 |
| 258_S | 281_E | 1.277 | 0.60 |
| 79_P | 153_N | 1.271 | 0.59 |
| 99_V | 126_Q | 1.269 | 0.59 |
| 11_E | 14_E | 1.268 | 0.59 |
| 260_F | 318_C | 1.267 | 0.59 |
| 340_N | 346_T | 1.264 | 0.59 |
| 260_F | 267_V | 1.262 | 0.59 |
| 14_E | 29_R | 1.252 | 0.58 |
| 151_L | 176_L | 1.245 | 0.57 |
| 372_T | 376_L | 1.242 | 0.57 |
| 102_E | 313_G | 1.242 | 0.57 |
| 148_E | 152_R | 1.234 | 0.56 |
| 11_E | 15_A | 1.233 | 0.56 |
| 87_L | 153_N | 1.231 | 0.56 |
| 176_L | 303_E | 1.231 | 0.56 |
| 121_R | 141_V | 1.230 | 0.56 |
| 7_T | 14_E | 1.228 | 0.55 |
| 14_E | 26_L | 1.226 | 0.55 |
| 355_R | 362_Y | 1.218 | 0.55 |
| 27_L | 31_A | 1.217 | 0.54 |
| 27_L | 32_D | 1.217 | 0.54 |
| 90_E | 116_A | 1.211 | 0.54 |
| 98_L | 155_L | 1.208 | 0.54 |
| 8_P | 11_E | 1.207 | 0.53 |
| 122_R | 146_V | 1.206 | 0.53 |
| 305_L | 308_L | 1.203 | 0.53 |
| 124_I | 158_L | 1.203 | 0.53 |
| 125_A | 153_N | 1.203 | 0.53 |
| 110_I | 131_S | 1.203 | 0.53 |
| 122_R | 138_L | 1.195 | 0.52 |
| 159_S | 162_G | 1.194 | 0.52 |
| 321_Q | 342_E | 1.190 | 0.52 |
| 120_H | 170_T | 1.184 | 0.51 |
| 113_L | 155_L | 1.173 | 0.50 |
| 59_D | 64_E | 1.170 | 0.50 |
| 147_I | 151_L | 1.170 | 0.50 |
| 25_T | 28_K | 1.169 | 0.50 |
| 333_R | 337_T | 1.169 | 0.50 |
| 343_R | 346_T | 1.166 | 0.50 |
| 113_L | 121_R | 1.166 | 0.50 |
| 41_I | 296_I | 1.166 | 0.50 |
| 30_L | 162_G | 1.164 | 0.49 |
| 110_I | 150_L | 1.158 | 0.49 |
| 56_M | 256_A | 1.158 | 0.49 |
| 79_P | 101_S | 1.153 | 0.48 |
| 46_R | 186_L | 1.151 | 0.48 |
| 125_A | 191_A | 1.151 | 0.48 |
| 94_A | 117_T | 1.144 | 0.48 |
| 241_A | 249_Q | 1.143 | 0.48 |
| 120_H | 146_V | 1.140 | 0.47 |
| 37_P | 41_I | 1.137 | 0.47 |
| 73_A | 101_S | 1.137 | 0.47 |
| 69_A | 131_S | 1.136 | 0.47 |
| 151_L | 304_P | 1.134 | 0.47 |
| 87_L | 97_L | 1.134 | 0.47 |
| 97_L | 239_R | 1.133 | 0.47 |
| 23_R | 30_L | 1.130 | 0.46 |
| 94_A | 127_R | 1.129 | 0.46 |
| 78_M | 101_S | 1.124 | 0.46 |
| 40_R | 82_L | 1.118 | 0.45 |
| 136_D | 141_V | 1.117 | 0.45 |
| 125_A | 137_A | 1.114 | 0.45 |
| 65_R | 186_L | 1.104 | 0.44 |
| 296_I | 304_P | 1.102 | 0.44 |
| 110_I | 121_R | 1.101 | 0.44 |
| 41_I | 49_T | 1.098 | 0.43 |
| 187_R | 259_P | 1.097 | 0.43 |
| 134_V | 137_A | 1.097 | 0.43 |
| 103_K | 274_F | 1.092 | 0.43 |
| 357_Q | 361_R | 1.091 | 0.43 |
| 358_T | 362_Y | 1.088 | 0.42 |
| 94_A | 153_N | 1.084 | 0.42 |
| 362_Y | 366_S | 1.083 | 0.42 |
| 241_A | 245_I | 1.082 | 0.42 |
| 69_A | 286_S | 1.077 | 0.41 |
| 203_R | 263_L | 1.076 | 0.41 |
| 188_P | 232_G | 1.076 | 0.41 |
| 61_N | 248_R | 1.074 | 0.41 |
| 56_M | 180_L | 1.074 | 0.41 |
| 98_L | 260_F | 1.074 | 0.41 |
| 179_L | 198_A | 1.073 | 0.41 |
| 108_D | 125_A | 1.069 | 0.41 |
| 136_D | 159_S | 1.067 | 0.41 |
| 246_E | 284_Y | 1.066 | 0.40 |
| 357_Q | 364_N | 1.062 | 0.40 |
| 93_V | 110_I | 1.060 | 0.40 |
| 202_A | 267_V | 1.060 | 0.40 |
| 101_S | 124_I | 1.060 | 0.40 |
| 305_L | 357_Q | 1.060 | 0.40 |
| 134_V | 314_L | 1.057 | 0.40 |
| 111_S | 114_Y | 1.057 | 0.40 |
| 228_A | 282_I | 1.057 | 0.40 |
| 146_V | 307_I | 1.053 | 0.39 |
| 131_S | 135_A | 1.053 | 0.39 |
| 141_V | 162_G | 1.051 | 0.39 |
| 260_F | 275_N | 1.051 | 0.39 |
| 126_Q | 149_T | 1.049 | 0.39 |
| 14_E | 17_R | 1.048 | 0.39 |
| 373_P | 379_I | 1.047 | 0.39 |
| 143_E | 337_T | 1.047 | 0.39 |
| 260_F | 263_L | 1.047 | 0.39 |
| 162_G | 198_A | 1.044 | 0.38 |
| 60_A | 125_A | 1.043 | 0.38 |
| 362_Y | 365_W | 1.043 | 0.38 |
| 148_E | 151_L | 1.042 | 0.38 |
| 57_L | 181_L | 1.042 | 0.38 |
| 340_N | 359_V | 1.040 | 0.38 |
| 214_R | 220_A | 1.037 | 0.38 |
| 341_L | 345_L | 1.034 | 0.38 |
| 252_R | 258_S | 1.034 | 0.38 |
| 267_V | 319_V | 1.033 | 0.38 |
| 172_D | 326_L | 1.031 | 0.37 |
| 79_P | 314_L | 1.029 | 0.37 |
| 193_V | 286_S | 1.028 | 0.37 |
| 353_V | 357_Q | 1.026 | 0.37 |
| 147_I | 169_A | 1.024 | 0.37 |
| 257_K | 288_L | 1.023 | 0.37 |
| 252_R | 256_A | 1.020 | 0.36 |
| 93_V | 198_A | 1.020 | 0.36 |
| 138_L | 150_L | 1.020 | 0.36 |
| 87_L | 156_V | 1.016 | 0.36 |
| 158_L | 322_L | 1.015 | 0.36 |
| 21_R | 297_F | 1.014 | 0.36 |
| 79_P | 94_A | 1.013 | 0.36 |
| 373_P | 377_K | 1.011 | 0.36 |
| 351_I | 357_Q | 1.011 | 0.36 |
| 242_L | 245_I | 1.009 | 0.35 |
| 354_D | 361_R | 1.004 | 0.35 |
| 69_A | 110_I | 1.003 | 0.35 |
| 72_L | 198_A | 1.001 | 0.35 |
| 355_R | 364_N | 1.001 | 0.35 |
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 | 0.4816 | 98 | 0.892 | Contact Map |
| 3ltmA | 2 | 0.4275 | 94.8 | 0.925 | Contact Map |
| 4l7mA | 2 | 0.4619 | 94.5 | 0.926 | Contact Map |
| 1oyzA | 1 | 0.4447 | 94 | 0.928 | Contact Map |
| 4g3aA | 2 | 0.5037 | 93.6 | 0.929 | Contact Map |
| 4lacA | 1 | 0.2531 | 92.3 | 0.932 | Contact Map |
| 2jdqA | 2 | 0.3956 | 92.3 | 0.932 | Contact Map |
| 3ltjA | 1 | 0.4423 | 91.7 | 0.933 | Contact Map |
| 4db6A | 1 | 0.3857 | 90.7 | 0.935 | Contact Map |
| 4jw3C | 2 | 0.226 | 90.5 | 0.935 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)