| AC1_rep |
| ID: | 1512072998 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 50% gaps before running GREMLIN. |
| Length: | 362 (349) | ||
| Sequences: | 590 (225.1) | ||
| Seq/Len: | 1.691 | ||
| Nf(neff/√len): | 12.0 |
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: 1.691).
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 |
| 135_T | 152_L | 2.505 | 1.00 |
| 153_A | 159_L | 2.241 | 0.99 |
| 44_R | 109_I | 2.069 | 0.99 |
| 104_E | 109_I | 1.927 | 0.98 |
| 158_V | 168_L | 1.917 | 0.98 |
| 142_K | 165_N | 1.896 | 0.98 |
| 133_Y | 159_L | 1.892 | 0.98 |
| 153_A | 156_D | 1.869 | 0.97 |
| 79_S | 85_H | 1.852 | 0.97 |
| 142_K | 169_D | 1.847 | 0.97 |
| 141_S | 144_E | 1.838 | 0.97 |
| 104_E | 111_D | 1.824 | 0.97 |
| 174_E | 177_A | 1.809 | 0.97 |
| 7_G | 68_K | 1.784 | 0.96 |
| 44_R | 104_E | 1.739 | 0.95 |
| 133_Y | 153_A | 1.733 | 0.95 |
| 152_L | 158_V | 1.695 | 0.95 |
| 79_S | 82_R | 1.686 | 0.94 |
| 44_R | 111_D | 1.671 | 0.94 |
| 220_G | 226_K | 1.665 | 0.94 |
| 161_F | 165_N | 1.662 | 0.94 |
| 133_Y | 155_K | 1.652 | 0.94 |
| 13_Y | 69_C | 1.546 | 0.90 |
| 274_M | 300_F | 1.544 | 0.90 |
| 82_R | 85_H | 1.519 | 0.89 |
| 231_R | 236_H | 1.515 | 0.89 |
| 42_Y | 111_D | 1.503 | 0.89 |
| 346_S | 349_Q | 1.486 | 0.88 |
| 93_A | 99_V | 1.480 | 0.87 |
| 280_W | 289_P | 1.459 | 0.86 |
| 233_L | 236_H | 1.453 | 0.86 |
| 49_L | 55_P | 1.452 | 0.86 |
| 212_R | 215_S | 1.441 | 0.86 |
| 220_G | 225_G | 1.417 | 0.84 |
| 109_I | 112_W | 1.402 | 0.83 |
| 8_F | 13_Y | 1.400 | 0.83 |
| 273_F | 300_F | 1.392 | 0.83 |
| 139_A | 148_V | 1.389 | 0.83 |
| 101_S | 112_W | 1.374 | 0.82 |
| 51_E | 59_V | 1.372 | 0.82 |
| 245_L | 273_F | 1.370 | 0.81 |
| 91_Q | 99_V | 1.368 | 0.81 |
| 212_R | 226_K | 1.365 | 0.81 |
| 148_V | 152_L | 1.365 | 0.81 |
| 237_N | 244_D | 1.361 | 0.81 |
| 283_N | 288_K | 1.338 | 0.79 |
| 156_D | 159_L | 1.333 | 0.79 |
| 156_D | 168_L | 1.321 | 0.78 |
| 149_I | 153_A | 1.314 | 0.78 |
| 344_N | 348_A | 1.299 | 0.76 |
| 81_S | 85_H | 1.298 | 0.76 |
| 38_T | 74_F | 1.298 | 0.76 |
| 120_R | 123_R | 1.295 | 0.76 |
| 39_S | 70_Q | 1.293 | 0.76 |
| 101_S | 116_Q | 1.291 | 0.76 |
| 279_D | 282_S | 1.287 | 0.75 |
| 218_I | 301_L | 1.283 | 0.75 |
| 174_E | 178_P | 1.276 | 0.75 |
| 45_I | 109_I | 1.275 | 0.74 |
| 342_G | 346_S | 1.270 | 0.74 |
| 60_L | 103_I | 1.265 | 0.74 |
| 252_N | 290_V | 1.259 | 0.73 |
| 257_N | 294_G | 1.259 | 0.73 |
| 307_N | 318_K | 1.249 | 0.72 |
| 165_N | 169_D | 1.242 | 0.72 |
| 212_R | 220_G | 1.238 | 0.71 |
| 192_P | 199_V | 1.233 | 0.71 |
| 78_V | 85_H | 1.229 | 0.71 |
| 149_I | 156_D | 1.227 | 0.70 |
| 273_F | 306_P | 1.227 | 0.70 |
| 270_F | 273_F | 1.226 | 0.70 |
| 230_A | 234_G | 1.225 | 0.70 |
| 240_C | 270_F | 1.221 | 0.70 |
| 27_A | 30_Q | 1.216 | 0.69 |
| 132_A | 153_A | 1.213 | 0.69 |
| 223_R | 226_K | 1.212 | 0.69 |
| 221_D | 228_M | 1.211 | 0.69 |
| 19_K | 54_T | 1.211 | 0.69 |
| 270_F | 284_T | 1.207 | 0.69 |
| 240_C | 298_T | 1.203 | 0.68 |
| 222_S | 328_K | 1.203 | 0.68 |
| 102_Y | 105_K | 1.201 | 0.68 |
| 51_E | 64_E | 1.197 | 0.68 |
| 290_V | 340_Y | 1.197 | 0.68 |
| 67_F | 74_F | 1.190 | 0.67 |
| 274_M | 298_T | 1.185 | 0.67 |
| 192_P | 198_W | 1.185 | 0.67 |
| 245_L | 298_T | 1.183 | 0.66 |
| 27_A | 57_L | 1.182 | 0.66 |
| 270_F | 306_P | 1.182 | 0.66 |
| 239_L | 249_V | 1.181 | 0.66 |
| 135_T | 153_A | 1.178 | 0.66 |
| 246_S | 284_T | 1.175 | 0.66 |
| 69_C | 74_F | 1.173 | 0.65 |
| 155_K | 158_V | 1.170 | 0.65 |
| 152_L | 159_L | 1.168 | 0.65 |
| 188_F | 192_P | 1.167 | 0.65 |
| 344_N | 349_Q | 1.158 | 0.64 |
| 224_T | 228_M | 1.157 | 0.64 |
| 272_E | 282_S | 1.154 | 0.63 |
| 268_K | 282_S | 1.151 | 0.63 |
| 139_A | 147_R | 1.149 | 0.63 |
| 50_H | 56_H | 1.148 | 0.63 |
| 226_K | 229_W | 1.143 | 0.62 |
| 34_I | 74_F | 1.143 | 0.62 |
| 103_I | 112_W | 1.141 | 0.62 |
| 312_E | 316_E | 1.133 | 0.61 |
| 226_K | 230_A | 1.130 | 0.61 |
| 270_F | 326_A | 1.127 | 0.61 |
| 165_N | 168_L | 1.122 | 0.60 |
| 41_K | 47_R | 1.121 | 0.60 |
| 284_T | 300_F | 1.121 | 0.60 |
| 240_C | 245_L | 1.120 | 0.60 |
| 279_D | 283_N | 1.118 | 0.60 |
| 70_Q | 74_F | 1.114 | 0.59 |
| 13_Y | 38_T | 1.111 | 0.59 |
| 239_L | 243_L | 1.109 | 0.59 |
| 196_E | 201_E | 1.105 | 0.59 |
| 78_V | 81_S | 1.105 | 0.59 |
| 153_A | 161_F | 1.097 | 0.58 |
| 15_I | 31_L | 1.096 | 0.58 |
| 325_W | 329_N | 1.094 | 0.57 |
| 140_G | 168_L | 1.094 | 0.57 |
| 268_K | 305_G | 1.093 | 0.57 |
| 68_K | 71_N | 1.090 | 0.57 |
| 237_N | 257_N | 1.089 | 0.57 |
| 125_G | 130_N | 1.089 | 0.57 |
| 237_N | 250_Y | 1.088 | 0.57 |
| 81_S | 84_A | 1.081 | 0.56 |
| 5_R | 70_Q | 1.078 | 0.56 |
| 160_Q | 163_N | 1.078 | 0.56 |
| 316_E | 341_S | 1.076 | 0.55 |
| 39_S | 54_T | 1.076 | 0.55 |
| 280_W | 283_N | 1.076 | 0.55 |
| 270_F | 300_F | 1.067 | 0.55 |
| 38_T | 69_C | 1.064 | 0.54 |
| 45_I | 59_V | 1.063 | 0.54 |
| 36_T | 74_F | 1.061 | 0.54 |
| 143_S | 161_F | 1.059 | 0.54 |
| 109_I | 114_Q | 1.057 | 0.53 |
| 217_V | 270_F | 1.056 | 0.53 |
| 341_S | 344_N | 1.056 | 0.53 |
| 231_R | 238_Y | 1.054 | 0.53 |
| 306_P | 316_E | 1.054 | 0.53 |
| 50_H | 58_H | 1.052 | 0.53 |
| 344_N | 347_T | 1.051 | 0.53 |
| 237_N | 283_N | 1.049 | 0.53 |
| 300_F | 326_A | 1.047 | 0.52 |
| 270_F | 274_M | 1.044 | 0.52 |
| 123_R | 127_Q | 1.043 | 0.52 |
| 279_D | 296_I | 1.042 | 0.52 |
| 125_G | 128_T | 1.040 | 0.52 |
| 260_D | 329_N | 1.037 | 0.51 |
| 153_A | 158_V | 1.036 | 0.51 |
| 149_I | 161_F | 1.035 | 0.51 |
| 7_G | 69_C | 1.035 | 0.51 |
| 285_K | 288_K | 1.032 | 0.51 |
| 215_S | 220_G | 1.028 | 0.50 |
| 189_D | 196_E | 1.027 | 0.50 |
| 284_T | 289_P | 1.027 | 0.50 |
| 25_E | 110_L | 1.027 | 0.50 |
| 59_V | 82_R | 1.024 | 0.50 |
| 346_S | 351_S | 1.024 | 0.50 |
| 231_R | 234_G | 1.024 | 0.50 |
| 140_G | 158_V | 1.022 | 0.50 |
| 210_P | 213_P | 1.022 | 0.50 |
| 188_F | 191_V | 1.022 | 0.50 |
| 121_S | 127_Q | 1.020 | 0.50 |
| 27_A | 77_L | 1.020 | 0.50 |
| 89_N | 99_V | 1.017 | 0.49 |
| 29_S | 38_T | 1.017 | 0.49 |
| 61_I | 114_Q | 1.016 | 0.49 |
| 174_E | 179_Y | 1.015 | 0.49 |
| 284_T | 318_K | 1.013 | 0.49 |
| 44_R | 112_W | 1.012 | 0.49 |
| 256_F | 260_D | 1.008 | 0.48 |
| 190_Q | 196_E | 1.006 | 0.48 |
| 229_W | 233_L | 1.005 | 0.48 |
| 218_I | 226_K | 1.004 | 0.48 |
| 94_K | 99_V | 1.004 | 0.48 |
| 90_I | 222_S | 1.003 | 0.48 |
| 244_D | 283_N | 1.002 | 0.48 |
| 30_Q | 77_L | 1.002 | 0.48 |
| 244_D | 257_N | 1.000 | 0.47 |
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 | |
| 1l2mA | 1 | 0.326 | 100 | 0.681 | Contact Map |
| 2hwtA | 1 | 0.2431 | 99.8 | 0.86 | Contact Map |
| 2hw0A | 1 | 0.2928 | 99.7 | 0.876 | Contact Map |
| 1tueA | 6 | 0.4972 | 98.2 | 0.936 | Contact Map |
| 3ec2A | 1 | 0.4061 | 97.9 | 0.94 | Contact Map |
| 2w58A | 2 | 0.4613 | 97.7 | 0.942 | Contact Map |
| 1l8qA | 1 | 0.4613 | 97.4 | 0.946 | Contact Map |
| 4qhsA | 7 | 0.4503 | 97 | 0.949 | Contact Map |
| 1u0jA | 1 | 0.6492 | 97 | 0.949 | Contact Map |
| 2qgzA | 1 | 0.4061 | 96.8 | 0.95 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)