| helicase |
| ID: | 1414521308 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 50% gaps before running GREMLIN. |
| Length: | 451 (279) | ||
| Sequences: | 28524 (16408.4) | ||
| Seq/Len: | 102.237 | ||
| Nf(neff/√len): | 982.3 |
HHblits Results: (2013_03)
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: 102.237).
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 |
| 229_K | 234_D | 3.909 | 1.00 |
| 40_I | 51_T | 3.156 | 1.00 |
| 37_L | 68_L | 3.135 | 1.00 |
| 216_I | 235_W | 2.869 | 1.00 |
| 208_L | 239_V | 2.865 | 1.00 |
| 195_V | 201_G | 2.853 | 1.00 |
| 55_A | 64_M | 2.730 | 1.00 |
| 198_I | 221_K | 2.703 | 1.00 |
| 228_I | 232_T | 2.565 | 1.00 |
| 214_K | 236_D | 2.506 | 1.00 |
| 195_V | 204_I | 2.501 | 1.00 |
| 205_A | 239_V | 2.469 | 1.00 |
| 195_V | 239_V | 2.418 | 1.00 |
| 84_H | 89_I | 2.381 | 1.00 |
| 191_T | 254_R | 2.351 | 1.00 |
| 92_L | 97_T | 2.306 | 1.00 |
| 26_L | 30_A | 2.193 | 1.00 |
| 225_S | 229_K | 2.116 | 1.00 |
| 120_H | 246_M | 2.099 | 1.00 |
| 213_K | 237_F | 2.090 | 1.00 |
| 65_E | 69_R | 2.090 | 1.00 |
| 91_D | 95_H | 2.065 | 1.00 |
| 50_R | 112_N | 2.041 | 1.00 |
| 205_A | 209_R | 2.019 | 1.00 |
| 244_S | 248_A | 1.978 | 1.00 |
| 205_A | 215_V | 1.962 | 1.00 |
| 40_I | 115_I | 1.921 | 1.00 |
| 204_I | 239_V | 1.897 | 1.00 |
| 201_G | 217_Q | 1.883 | 1.00 |
| 19_K | 143_A | 1.859 | 1.00 |
| 216_I | 226_E | 1.857 | 1.00 |
| 120_H | 289_Q | 1.826 | 1.00 |
| 60_V | 63_E | 1.812 | 1.00 |
| 127_I | 131_G | 1.782 | 1.00 |
| 291_R | 304_Q | 1.780 | 1.00 |
| 202_N | 217_Q | 1.770 | 1.00 |
| 24_M | 147_M | 1.764 | 1.00 |
| 36_Y | 147_M | 1.726 | 1.00 |
| 91_D | 94_C | 1.705 | 1.00 |
| 205_A | 217_Q | 1.692 | 1.00 |
| 127_I | 130_R | 1.692 | 1.00 |
| 257_D | 291_R | 1.650 | 1.00 |
| 15_I | 145_I | 1.640 | 1.00 |
| 224_D | 228_I | 1.635 | 1.00 |
| 240_T | 244_S | 1.632 | 1.00 |
| 52_L | 111_Y | 1.624 | 1.00 |
| 230_T | 238_V | 1.597 | 1.00 |
| 60_V | 247_G | 1.591 | 1.00 |
| 280_M | 306_I | 1.582 | 1.00 |
| 216_I | 229_K | 1.580 | 1.00 |
| 200_A | 203_D | 1.577 | 1.00 |
| 226_E | 235_W | 1.571 | 1.00 |
| 293_R | 296_R | 1.570 | 1.00 |
| 201_G | 239_V | 1.550 | 1.00 |
| 114_I | 144_G | 1.538 | 1.00 |
| 207_C | 211_N | 1.511 | 1.00 |
| 292_G | 296_R | 1.472 | 1.00 |
| 257_D | 306_I | 1.451 | 1.00 |
| 55_A | 61_A | 1.444 | 1.00 |
| 34_K | 67_A | 1.436 | 1.00 |
| 193_W | 237_F | 1.419 | 1.00 |
| 197_S | 200_A | 1.416 | 1.00 |
| 33_T | 64_M | 1.411 | 1.00 |
| 201_G | 219_S | 1.385 | 0.99 |
| 62_A | 66_E | 1.379 | 0.99 |
| 62_A | 224_D | 1.368 | 0.99 |
| 88_E | 91_D | 1.366 | 0.99 |
| 229_K | 235_W | 1.358 | 0.99 |
| 200_A | 279_P | 1.357 | 0.99 |
| 95_H | 99_T | 1.351 | 0.99 |
| 52_L | 114_I | 1.348 | 0.99 |
| 108_V | 111_Y | 1.334 | 0.99 |
| 223_F | 227_Y | 1.334 | 0.99 |
| 283_T | 286_S | 1.323 | 0.99 |
| 189_G | 253_E | 1.320 | 0.99 |
| 194_F | 244_S | 1.316 | 0.99 |
| 190_K | 236_D | 1.307 | 0.99 |
| 246_M | 289_Q | 1.299 | 0.99 |
| 76_Q | 79_A | 1.284 | 0.99 |
| 254_R | 305_Y | 1.282 | 0.99 |
| 114_I | 134_S | 1.270 | 0.99 |
| 94_C | 97_T | 1.267 | 0.99 |
| 36_Y | 64_M | 1.261 | 0.99 |
| 225_S | 228_I | 1.257 | 0.99 |
| 245_E | 286_S | 1.252 | 0.99 |
| 13_D | 17_R | 1.248 | 0.99 |
| 51_T | 113_L | 1.243 | 0.98 |
| 35_R | 39_A | 1.232 | 0.98 |
| 258_P | 278_G | 1.228 | 0.98 |
| 85_T | 88_E | 1.223 | 0.98 |
| 219_S | 222_T | 1.211 | 0.98 |
| 233_N | 236_D | 1.195 | 0.98 |
| 191_T | 237_F | 1.182 | 0.98 |
| 50_R | 110_N | 1.182 | 0.98 |
| 53_I | 68_L | 1.161 | 0.97 |
| 90_V | 94_C | 1.153 | 0.97 |
| 150_T | 289_Q | 1.148 | 0.97 |
| 124_P | 127_I | 1.145 | 0.97 |
| 119_A | 146_F | 1.135 | 0.97 |
| 43_E | 113_L | 1.134 | 0.97 |
| 126_S | 130_R | 1.131 | 0.97 |
| 223_F | 226_E | 1.131 | 0.97 |
| 190_K | 253_E | 1.127 | 0.97 |
| 245_E | 290_R | 1.123 | 0.97 |
| 57_T | 246_M | 1.122 | 0.97 |
| 131_G | 161_S | 1.120 | 0.96 |
| 257_D | 290_R | 1.119 | 0.96 |
| 13_D | 16_F | 1.112 | 0.96 |
| 67_A | 249_N | 1.106 | 0.96 |
| 192_V | 240_T | 1.104 | 0.96 |
| 37_L | 40_I | 1.099 | 0.96 |
| 128_A | 131_G | 1.094 | 0.96 |
| 66_E | 69_R | 1.094 | 0.96 |
| 126_S | 129_A | 1.089 | 0.96 |
| 202_N | 219_S | 1.086 | 0.96 |
| 281_P | 287_A | 1.074 | 0.95 |
| 196_P | 200_A | 1.073 | 0.95 |
| 128_A | 132_Y | 1.068 | 0.95 |
| 206_A | 210_K | 1.063 | 0.95 |
| 218_L | 244_S | 1.061 | 0.95 |
| 63_E | 67_A | 1.059 | 0.95 |
| 121_F | 246_M | 1.058 | 0.95 |
| 28_P | 149_A | 1.055 | 0.95 |
| 36_Y | 39_A | 1.052 | 0.95 |
| 226_E | 238_V | 1.051 | 0.94 |
| 129_A | 132_Y | 1.051 | 0.94 |
| 125_A | 129_A | 1.046 | 0.94 |
| 49_L | 112_N | 1.041 | 0.94 |
| 171_E | 174_E | 1.035 | 0.94 |
| 241_T | 295_G | 1.035 | 0.94 |
| 190_K | 252_A | 1.027 | 0.94 |
| 51_T | 115_I | 1.025 | 0.93 |
| 99_T | 102_L | 1.024 | 0.93 |
| 193_W | 239_V | 1.024 | 0.93 |
| 36_Y | 53_I | 1.022 | 0.93 |
| 201_G | 205_A | 1.018 | 0.93 |
| 73_I | 77_T | 1.016 | 0.93 |
| 206_A | 209_R | 1.010 | 0.93 |
| 94_C | 99_T | 1.000 | 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 | |
| 2jlqA | 1 | 1 | 100 | 0.192 | Contact Map |
| 2whxA | 1 | 1 | 100 | 0.198 | Contact Map |
| 2wv9A | 1 | 0.9579 | 100 | 0.202 | Contact Map |
| 1yksA | 1 | 0.9534 | 100 | 0.213 | Contact Map |
| 2z83A | 1 | 0.9446 | 100 | 0.239 | Contact Map |
| 2v6iA | 1 | 0.9335 | 100 | 0.261 | Contact Map |
| 2xauA | 2 | 0.9623 | 100 | 0.57 | Contact Map |
| 4ljyA | 1 | 0.7295 | 100 | 0.57 | Contact Map |
| 2db3A | 4 | 0.6984 | 100 | 0.571 | Contact Map |
| 4d25A | 1 | 0.6984 | 100 | 0.577 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)