| chen 1-450 1-400 |
| ID: | 1510542060 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 400 (396) | ||
| Sequences: | 1514 (967.4) | ||
| Seq/Len: | 3.823 | ||
| Nf(neff/√len): | 48.6 |
Jackhmmer Results: (2016_04)
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: 3.823).
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 |
| 15_T | 18_D | 5.794 | 1.00 |
| 10_I | 36_L | 4.422 | 1.00 |
| 105_V | 120_I | 3.976 | 1.00 |
| 17_F | 70_E | 3.970 | 1.00 |
| 133_V | 158_F | 3.537 | 1.00 |
| 41_E | 57_R | 3.142 | 1.00 |
| 221_R | 225_E | 3.117 | 1.00 |
| 23_V | 78_R | 3.116 | 1.00 |
| 44_S | 98_A | 3.002 | 1.00 |
| 16_L | 67_G | 2.953 | 1.00 |
| 65_P | 69_A | 2.946 | 1.00 |
| 220_G | 252_L | 2.777 | 1.00 |
| 151_L | 173_H | 2.676 | 1.00 |
| 69_A | 225_E | 2.632 | 1.00 |
| 24_P | 78_R | 2.582 | 1.00 |
| 34_L | 71_L | 2.581 | 1.00 |
| 241_A | 244_D | 2.562 | 1.00 |
| 36_L | 75_A | 2.533 | 1.00 |
| 104_D | 108_R | 2.514 | 1.00 |
| 136_D | 140_E | 2.513 | 1.00 |
| 64_G | 67_G | 2.477 | 1.00 |
| 68_L | 227_L | 2.441 | 1.00 |
| 58_V | 68_L | 2.424 | 1.00 |
| 314_R | 317_E | 2.421 | 1.00 |
| 117_Y | 214_D | 2.345 | 1.00 |
| 8_L | 19_A | 2.272 | 1.00 |
| 41_E | 60_A | 2.272 | 1.00 |
| 27_H | 78_R | 2.225 | 1.00 |
| 23_V | 75_A | 2.220 | 1.00 |
| 135_G | 153_Y | 2.171 | 1.00 |
| 74_A | 78_R | 2.153 | 1.00 |
| 102_W | 202_A | 2.149 | 1.00 |
| 298_E | 302_T | 2.139 | 1.00 |
| 27_H | 80_M | 2.128 | 1.00 |
| 170_R | 174_D | 2.126 | 1.00 |
| 243_G | 273_Q | 2.125 | 1.00 |
| 250_A | 277_A | 2.122 | 1.00 |
| 138_P | 170_R | 2.097 | 1.00 |
| 86_I | 233_V | 2.048 | 1.00 |
| 377_A | 381_A | 2.038 | 1.00 |
| 65_P | 221_R | 2.021 | 1.00 |
| 84_V | 228_V | 2.006 | 1.00 |
| 219_I | 231_L | 2.005 | 1.00 |
| 324_R | 355_E | 1.959 | 1.00 |
| 104_D | 113_E | 1.946 | 1.00 |
| 197_A | 330_I | 1.929 | 1.00 |
| 215_T | 219_I | 1.920 | 1.00 |
| 6_Y | 26_L | 1.918 | 1.00 |
| 93_V | 202_A | 1.914 | 1.00 |
| 16_L | 39_L | 1.895 | 1.00 |
| 116_D | 208_D | 1.889 | 1.00 |
| 218_E | 222_W | 1.874 | 1.00 |
| 146_V | 160_I | 1.857 | 1.00 |
| 136_D | 141_L | 1.830 | 1.00 |
| 101_W | 117_Y | 1.807 | 0.99 |
| 223_I | 256_R | 1.790 | 0.99 |
| 76_H | 229_D | 1.775 | 0.99 |
| 17_F | 20_A | 1.758 | 0.99 |
| 209_P | 248_R | 1.734 | 0.99 |
| 218_E | 221_R | 1.733 | 0.99 |
| 17_F | 67_G | 1.732 | 0.99 |
| 86_I | 219_I | 1.731 | 0.99 |
| 65_P | 218_E | 1.701 | 0.99 |
| 72_S | 227_L | 1.687 | 0.99 |
| 108_R | 162_E | 1.668 | 0.99 |
| 336_R | 350_E | 1.644 | 0.99 |
| 75_A | 80_M | 1.641 | 0.99 |
| 250_A | 258_I | 1.620 | 0.99 |
| 23_V | 71_L | 1.613 | 0.99 |
| 143_A | 154_Y | 1.607 | 0.98 |
| 297_G | 301_L | 1.604 | 0.98 |
| 83_V | 257_P | 1.598 | 0.98 |
| 33_W | 229_D | 1.582 | 0.98 |
| 20_A | 70_E | 1.573 | 0.98 |
| 68_L | 82_V | 1.546 | 0.98 |
| 42_S | 59_D | 1.529 | 0.98 |
| 260_V | 276_I | 1.498 | 0.97 |
| 114_Y | 117_Y | 1.496 | 0.97 |
| 284_A | 288_I | 1.488 | 0.97 |
| 43_E | 200_T | 1.486 | 0.97 |
| 137_G | 182_S | 1.473 | 0.97 |
| 57_R | 60_A | 1.472 | 0.97 |
| 20_A | 23_V | 1.470 | 0.97 |
| 213_D | 252_L | 1.458 | 0.97 |
| 116_D | 210_R | 1.452 | 0.97 |
| 36_L | 82_V | 1.450 | 0.97 |
| 185_R | 189_D | 1.446 | 0.96 |
| 243_G | 247_R | 1.443 | 0.96 |
| 3_A | 32_D | 1.427 | 0.96 |
| 374_L | 381_A | 1.385 | 0.95 |
| 320_P | 324_R | 1.380 | 0.95 |
| 11_S | 14_F | 1.327 | 0.94 |
| 205_R | 208_D | 1.324 | 0.93 |
| 20_A | 74_A | 1.319 | 0.93 |
| 74_A | 77_E | 1.319 | 0.93 |
| 161_A | 177_H | 1.314 | 0.93 |
| 153_Y | 156_H | 1.312 | 0.93 |
| 120_I | 129_L | 1.302 | 0.93 |
| 4_S | 32_D | 1.302 | 0.93 |
| 213_D | 248_R | 1.293 | 0.92 |
| 14_F | 61_A | 1.292 | 0.92 |
| 186_A | 199_N | 1.292 | 0.92 |
| 39_L | 82_V | 1.292 | 0.92 |
| 16_L | 68_L | 1.291 | 0.92 |
| 54_D | 57_R | 1.290 | 0.92 |
| 10_I | 75_A | 1.282 | 0.92 |
| 244_D | 248_R | 1.273 | 0.92 |
| 55_H | 100_R | 1.270 | 0.91 |
| 107_A | 162_E | 1.265 | 0.91 |
| 246_L | 260_V | 1.255 | 0.91 |
| 359_A | 384_A | 1.241 | 0.90 |
| 92_G | 202_A | 1.226 | 0.89 |
| 223_I | 228_V | 1.213 | 0.89 |
| 117_Y | 204_V | 1.211 | 0.89 |
| 136_D | 143_A | 1.208 | 0.89 |
| 19_A | 71_L | 1.206 | 0.88 |
| 220_G | 224_A | 1.198 | 0.88 |
| 139_D | 185_R | 1.195 | 0.88 |
| 236_P | 246_L | 1.194 | 0.88 |
| 130_R | 181_M | 1.194 | 0.88 |
| 75_A | 82_V | 1.193 | 0.88 |
| 324_R | 358_A | 1.184 | 0.87 |
| 44_S | 61_A | 1.182 | 0.87 |
| 23_V | 80_M | 1.182 | 0.87 |
| 73_R | 76_H | 1.173 | 0.86 |
| 186_A | 333_S | 1.171 | 0.86 |
| 151_L | 160_I | 1.169 | 0.86 |
| 69_A | 227_L | 1.169 | 0.86 |
| 320_P | 359_A | 1.166 | 0.86 |
| 55_H | 101_W | 1.165 | 0.86 |
| 328_R | 354_V | 1.162 | 0.86 |
| 22_I | 26_L | 1.160 | 0.86 |
| 152_V | 157_R | 1.160 | 0.86 |
| 39_L | 68_L | 1.148 | 0.85 |
| 378_V | 382_Q | 1.148 | 0.85 |
| 169_P | 172_V | 1.145 | 0.85 |
| 39_L | 84_V | 1.140 | 0.84 |
| 108_R | 113_E | 1.137 | 0.84 |
| 12_A | 59_D | 1.133 | 0.84 |
| 135_G | 154_Y | 1.133 | 0.84 |
| 26_L | 31_A | 1.132 | 0.84 |
| 196_F | 263_I | 1.128 | 0.83 |
| 214_D | 217_R | 1.125 | 0.83 |
| 303_Q | 307_E | 1.122 | 0.83 |
| 72_S | 76_H | 1.122 | 0.83 |
| 10_I | 20_A | 1.120 | 0.83 |
| 152_V | 155_E | 1.113 | 0.82 |
| 58_V | 64_G | 1.108 | 0.82 |
| 264_I | 270_M | 1.099 | 0.81 |
| 137_G | 140_E | 1.098 | 0.81 |
| 73_R | 77_E | 1.096 | 0.81 |
| 73_R | 227_L | 1.094 | 0.81 |
| 138_P | 173_H | 1.093 | 0.81 |
| 373_H | 377_A | 1.086 | 0.80 |
| 385_A | 388_L | 1.073 | 0.79 |
| 320_P | 358_A | 1.067 | 0.78 |
| 40_L | 219_I | 1.057 | 0.78 |
| 327_A | 357_A | 1.054 | 0.77 |
| 93_V | 102_W | 1.053 | 0.77 |
| 223_I | 231_L | 1.050 | 0.77 |
| 356_I | 378_V | 1.044 | 0.76 |
| 264_I | 283_D | 1.038 | 0.76 |
| 181_M | 185_R | 1.036 | 0.76 |
| 374_L | 378_V | 1.036 | 0.76 |
| 10_I | 39_L | 1.033 | 0.75 |
| 66_E | 69_A | 1.031 | 0.75 |
| 380_A | 383_A | 1.026 | 0.75 |
| 33_W | 83_V | 1.026 | 0.75 |
| 84_V | 219_I | 1.024 | 0.74 |
| 372_E | 381_A | 1.024 | 0.74 |
| 18_D | 21_R | 1.022 | 0.74 |
| 130_R | 179_E | 1.018 | 0.74 |
| 72_S | 75_A | 1.010 | 0.73 |
| 110_Q | 123_E | 1.003 | 0.72 |
| 223_I | 253_A | 1.000 | 0.72 |
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 | |
| 1iv8A | 1 | 0.92 | 100 | 0.375 | Contact Map |
| 3hjeA | 1 | 0.9275 | 100 | 0.396 | Contact Map |
| 2wc7A | 1 | 0.8125 | 100 | 0.7 | Contact Map |
| 2z1kA | 4 | 0.825 | 100 | 0.706 | Contact Map |
| 1j0hA | 2 | 0.815 | 100 | 0.709 | Contact Map |
| 1ea9C | 2 | 0.8175 | 100 | 0.711 | Contact Map |
| 1lwjA | 2 | 0.835 | 100 | 0.715 | Contact Map |
| 1wzlA | 2 | 0.8125 | 100 | 0.715 | Contact Map |
| 4aefA | 2 | 0.85 | 100 | 0.717 | Contact Map |
| 4aeeA | 2 | 0.8675 | 100 | 0.719 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)