| GerAB |
| ID: | 1488041914 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 365 (350) | ||
| Sequences: | 17224 (8987) | ||
| Seq/Len: | 49.211 | ||
| Nf(neff/√len): | 480.4 |
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: 49.211).
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 |
| 52_G | 229_I | 4.410 | 1.00 |
| 216_Y | 219_R | 2.986 | 1.00 |
| 16_I | 223_L | 2.828 | 1.00 |
| 15_G | 211_M | 2.767 | 1.00 |
| 136_Y | 140_G | 2.686 | 1.00 |
| 11_N | 14_Q | 2.684 | 1.00 |
| 14_Q | 150_P | 2.628 | 1.00 |
| 16_I | 227_I | 2.597 | 1.00 |
| 20_A | 227_I | 2.568 | 1.00 |
| 12_T | 223_L | 2.544 | 1.00 |
| 11_N | 212_K | 2.510 | 1.00 |
| 247_E | 261_S | 2.447 | 1.00 |
| 79_K | 87_G | 2.390 | 1.00 |
| 79_K | 84_K | 2.363 | 1.00 |
| 143_S | 147_R | 2.360 | 1.00 |
| 219_R | 223_L | 2.340 | 1.00 |
| 10_L | 14_Q | 2.232 | 1.00 |
| 257_S | 260_Q | 2.176 | 1.00 |
| 244_T | 247_E | 2.168 | 1.00 |
| 14_Q | 146_S | 2.162 | 1.00 |
| 210_H | 297_N | 2.128 | 1.00 |
| 78_L | 90_I | 2.105 | 1.00 |
| 64_L | 67_K | 2.077 | 1.00 |
| 47_T | 190_S | 2.069 | 1.00 |
| 183_G | 186_P | 2.040 | 1.00 |
| 154_T | 158_I | 1.997 | 1.00 |
| 171_F | 241_G | 1.954 | 1.00 |
| 167_S | 238_I | 1.938 | 1.00 |
| 43_D | 180_L | 1.938 | 1.00 |
| 109_M | 130_F | 1.906 | 1.00 |
| 23_M | 228_P | 1.901 | 1.00 |
| 12_T | 16_I | 1.844 | 1.00 |
| 113_V | 126_I | 1.841 | 1.00 |
| 213_K | 216_Y | 1.780 | 1.00 |
| 19_V | 224_G | 1.734 | 1.00 |
| 106_T | 288_F | 1.732 | 1.00 |
| 12_T | 219_R | 1.710 | 1.00 |
| 122_P | 125_V | 1.698 | 1.00 |
| 222_S | 226_L | 1.696 | 1.00 |
| 158_I | 162_I | 1.695 | 1.00 |
| 59_I | 221_A | 1.695 | 1.00 |
| 257_S | 261_S | 1.679 | 1.00 |
| 66_Q | 77_Y | 1.662 | 1.00 |
| 79_K | 88_S | 1.651 | 1.00 |
| 135_I | 139_V | 1.645 | 1.00 |
| 180_L | 187_I | 1.634 | 1.00 |
| 176_L | 241_G | 1.624 | 1.00 |
| 6_T | 9_K | 1.613 | 1.00 |
| 148_L | 152_Y | 1.611 | 1.00 |
| 59_I | 225_F | 1.597 | 1.00 |
| 268_F | 275_F | 1.592 | 1.00 |
| 134_G | 288_F | 1.584 | 1.00 |
| 226_L | 230_I | 1.548 | 1.00 |
| 22_T | 291_Y | 1.538 | 1.00 |
| 53_F | 57_F | 1.535 | 1.00 |
| 85_W | 89_I | 1.524 | 1.00 |
| 106_T | 131_I | 1.515 | 1.00 |
| 229_I | 233_I | 1.512 | 1.00 |
| 164_F | 234_L | 1.500 | 1.00 |
| 51_E | 194_V | 1.495 | 1.00 |
| 207_L | 293_Y | 1.489 | 1.00 |
| 110_A | 127_I | 1.468 | 1.00 |
| 83_G | 86_I | 1.458 | 1.00 |
| 213_K | 219_R | 1.447 | 1.00 |
| 35_L | 44_G | 1.445 | 1.00 |
| 138_M | 289_V | 1.441 | 1.00 |
| 260_Q | 270_E | 1.429 | 1.00 |
| 76_E | 301_K | 1.418 | 1.00 |
| 69_H | 80_E | 1.402 | 0.99 |
| 82_L | 86_I | 1.388 | 0.99 |
| 242_A | 258_L | 1.384 | 0.99 |
| 18_I | 207_L | 1.379 | 0.99 |
| 49_I | 233_I | 1.375 | 0.99 |
| 110_A | 126_I | 1.361 | 0.99 |
| 157_I | 161_L | 1.351 | 0.99 |
| 43_D | 179_V | 1.345 | 0.99 |
| 146_S | 150_P | 1.344 | 0.99 |
| 124_Q | 128_L | 1.342 | 0.99 |
| 15_G | 220_Y | 1.340 | 0.99 |
| 10_L | 146_S | 1.323 | 0.99 |
| 147_R | 150_P | 1.319 | 0.99 |
| 9_K | 212_K | 1.300 | 0.99 |
| 137_L | 148_L | 1.295 | 0.99 |
| 91_G | 302_T | 1.286 | 0.99 |
| 75_F | 298_G | 1.283 | 0.99 |
| 105_E | 287_T | 1.283 | 0.99 |
| 239_V | 258_L | 1.279 | 0.99 |
| 173_I | 241_G | 1.277 | 0.99 |
| 107_R | 111_E | 1.267 | 0.99 |
| 43_D | 187_I | 1.260 | 0.99 |
| 75_F | 91_G | 1.249 | 0.99 |
| 62_N | 74_L | 1.237 | 0.98 |
| 60_Y | 222_S | 1.236 | 0.98 |
| 5_Q | 8_L | 1.232 | 0.98 |
| 17_S | 150_P | 1.224 | 0.98 |
| 34_A | 37_T | 1.222 | 0.98 |
| 56_I | 222_S | 1.220 | 0.98 |
| 140_G | 144_D | 1.212 | 0.98 |
| 13_F | 150_P | 1.211 | 0.98 |
| 13_F | 17_S | 1.205 | 0.98 |
| 147_R | 151_F | 1.200 | 0.98 |
| 164_F | 238_I | 1.200 | 0.98 |
| 21_N | 153_L | 1.189 | 0.98 |
| 72_P | 80_E | 1.174 | 0.98 |
| 167_S | 242_A | 1.173 | 0.98 |
| 19_V | 204_M | 1.168 | 0.97 |
| 327_D | 330_Q | 1.166 | 0.97 |
| 66_Q | 208_P | 1.160 | 0.97 |
| 230_I | 234_L | 1.156 | 0.97 |
| 172_D | 175_N | 1.154 | 0.97 |
| 218_F | 221_A | 1.152 | 0.97 |
| 35_L | 39_A | 1.150 | 0.97 |
| 17_S | 153_L | 1.150 | 0.97 |
| 10_L | 142_L | 1.149 | 0.97 |
| 12_T | 220_Y | 1.137 | 0.97 |
| 215_K | 219_R | 1.136 | 0.97 |
| 64_L | 68_K | 1.133 | 0.97 |
| 206_F | 294_F | 1.133 | 0.97 |
| 150_P | 154_T | 1.129 | 0.97 |
| 14_Q | 147_R | 1.128 | 0.97 |
| 152_Y | 286_T | 1.128 | 0.97 |
| 203_V | 294_F | 1.127 | 0.97 |
| 83_G | 87_G | 1.126 | 0.97 |
| 128_L | 132_C | 1.121 | 0.97 |
| 121_T | 125_V | 1.121 | 0.97 |
| 76_E | 80_E | 1.117 | 0.96 |
| 30_T | 108_A | 1.116 | 0.96 |
| 144_D | 147_R | 1.111 | 0.96 |
| 95_C | 299_L | 1.109 | 0.96 |
| 39_A | 47_T | 1.105 | 0.96 |
| 65_I | 81_G | 1.104 | 0.96 |
| 48_L | 236_Y | 1.102 | 0.96 |
| 50_L | 191_L | 1.100 | 0.96 |
| 142_L | 146_S | 1.098 | 0.96 |
| 251_L | 257_S | 1.089 | 0.96 |
| 49_I | 53_F | 1.083 | 0.96 |
| 137_L | 285_F | 1.082 | 0.96 |
| 45_W | 240_V | 1.080 | 0.95 |
| 78_L | 82_L | 1.074 | 0.95 |
| 66_Q | 205_L | 1.064 | 0.95 |
| 104_F | 196_I | 1.062 | 0.95 |
| 292_G | 296_A | 1.061 | 0.95 |
| 38_K | 193_V | 1.056 | 0.95 |
| 136_Y | 139_V | 1.056 | 0.95 |
| 22_T | 290_I | 1.054 | 0.95 |
| 152_Y | 282_I | 1.053 | 0.95 |
| 307_T | 310_S | 1.053 | 0.95 |
| 223_L | 226_L | 1.053 | 0.95 |
| 126_I | 129_T | 1.051 | 0.94 |
| 161_L | 165_G | 1.050 | 0.94 |
| 109_M | 281_I | 1.049 | 0.94 |
| 16_I | 220_Y | 1.047 | 0.94 |
| 130_F | 285_F | 1.040 | 0.94 |
| 28_L | 160_L | 1.031 | 0.94 |
| 95_C | 99_L | 1.030 | 0.94 |
| 125_V | 129_T | 1.027 | 0.94 |
| 78_L | 91_G | 1.027 | 0.94 |
| 44_G | 236_Y | 1.026 | 0.94 |
| 74_L | 202_E | 1.024 | 0.93 |
| 84_K | 88_S | 1.019 | 0.93 |
| 4_K | 7_P | 1.019 | 0.93 |
| 52_G | 198_F | 1.015 | 0.93 |
| 243_L | 258_L | 1.014 | 0.93 |
| 102_A | 292_G | 1.014 | 0.93 |
| 112_M | 256_I | 1.013 | 0.93 |
| 185_G | 189_N | 1.010 | 0.93 |
| 184_L | 187_I | 1.009 | 0.93 |
| 189_N | 193_V | 1.008 | 0.93 |
| 159_I | 279_V | 1.002 | 0.92 |
| 300_K | 304_G | 1.001 | 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 | |
| 3l1lA | 1 | 0.937 | 100 | 0.384 | Contact Map |
| 3giaA | 1 | 0.9644 | 100 | 0.423 | Contact Map |
| 4djkA | 2 | 0.926 | 100 | 0.475 | Contact Map |
| 3dh4A | 4 | 0.9205 | 98.7 | 0.787 | Contact Map |
| 2xq2A | 1 | 0.9178 | 98.6 | 0.795 | Contact Map |
| 2jlnA | 1 | 0.9534 | 98.4 | 0.811 | Contact Map |
| 4us3A | 1 | 0.9342 | 97.9 | 0.832 | Contact Map |
| 4wgvA | 2 | 0.8877 | 97.8 | 0.837 | Contact Map |
| 2a65A | 1 | 0.9534 | 97.4 | 0.85 | Contact Map |
| 4xp4A | 1 | 0 | 96.2 | 0.871 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)