| AAC2 chopped |
| ID: | 1487177485 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 295 (289) | ||
| Sequences: | 13366 (7538.3) | ||
| Seq/Len: | 46.249 | ||
| Nf(neff/√len): | 443.4 |
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: 46.249).
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 |
| 253_V | 261_L | 3.548 | 1.00 |
| 158_L | 166_L | 3.425 | 1.00 |
| 55_A | 63_F | 3.021 | 1.00 |
| 247_D | 251_K | 2.972 | 1.00 |
| 252_I | 260_S | 2.884 | 1.00 |
| 152_D | 156_K | 2.815 | 1.00 |
| 52_K | 56_T | 2.753 | 1.00 |
| 155_K | 159_K | 2.729 | 1.00 |
| 250_R | 254_A | 2.711 | 1.00 |
| 251_K | 255_A | 2.650 | 1.00 |
| 156_K | 160_S | 2.545 | 1.00 |
| 49_D | 53_R | 2.523 | 1.00 |
| 157_T | 165_G | 2.494 | 1.00 |
| 249_L | 261_L | 2.416 | 1.00 |
| 148_N | 152_D | 2.395 | 1.00 |
| 228_V | 249_L | 2.256 | 1.00 |
| 88_I | 113_A | 2.249 | 1.00 |
| 53_R | 57_Q | 2.146 | 1.00 |
| 256_E | 260_S | 2.145 | 1.00 |
| 154_Y | 166_L | 2.072 | 1.00 |
| 231_R | 256_E | 2.058 | 1.00 |
| 112_G | 178_V | 1.971 | 1.00 |
| 244_G | 247_D | 1.963 | 1.00 |
| 220_T | 265_C | 1.949 | 1.00 |
| 54_T | 62_S | 1.937 | 1.00 |
| 25_K | 29_Q | 1.929 | 1.00 |
| 147_F | 153_V | 1.800 | 1.00 |
| 242_Y | 248_C | 1.778 | 1.00 |
| 242_Y | 247_D | 1.764 | 1.00 |
| 84_F | 88_I | 1.750 | 1.00 |
| 147_F | 152_D | 1.749 | 1.00 |
| 27_L | 58_E | 1.732 | 1.00 |
| 253_V | 258_V | 1.727 | 1.00 |
| 243_D | 247_D | 1.718 | 1.00 |
| 108_L | 182_G | 1.716 | 1.00 |
| 88_I | 117_L | 1.708 | 1.00 |
| 51_F | 63_F | 1.699 | 1.00 |
| 284_Q | 287_M | 1.696 | 1.00 |
| 161_D | 165_G | 1.691 | 1.00 |
| 131_R | 161_D | 1.691 | 1.00 |
| 195_L | 210_L | 1.685 | 1.00 |
| 19_S | 23_R | 1.675 | 1.00 |
| 149_G | 152_D | 1.652 | 1.00 |
| 22_E | 25_K | 1.650 | 1.00 |
| 281_M | 285_L | 1.630 | 1.00 |
| 30_N | 134_A | 1.609 | 1.00 |
| 44_Y | 50_C | 1.605 | 1.00 |
| 88_I | 110_S | 1.601 | 1.00 |
| 187_M | 217_G | 1.596 | 1.00 |
| 58_E | 65_R | 1.593 | 1.00 |
| 256_E | 263_K | 1.575 | 1.00 |
| 92_F | 110_S | 1.574 | 1.00 |
| 188_Y | 283_D | 1.536 | 1.00 |
| 161_D | 168_R | 1.523 | 1.00 |
| 80_L | 84_F | 1.519 | 1.00 |
| 246_F | 250_R | 1.517 | 1.00 |
| 24_V | 51_F | 1.515 | 1.00 |
| 9_V | 285_L | 1.497 | 1.00 |
| 44_Y | 49_D | 1.489 | 1.00 |
| 229_R | 233_M | 1.488 | 1.00 |
| 86_D | 89_K | 1.471 | 1.00 |
| 152_D | 155_K | 1.470 | 1.00 |
| 158_L | 163_V | 1.460 | 1.00 |
| 49_D | 52_K | 1.456 | 1.00 |
| 127_Y | 131_R | 1.452 | 1.00 |
| 212_W | 273_V | 1.438 | 1.00 |
| 190_S | 194_L | 1.427 | 1.00 |
| 23_R | 27_L | 1.417 | 1.00 |
| 123_Y | 127_Y | 1.411 | 1.00 |
| 190_S | 193_P | 1.403 | 0.99 |
| 45_A | 49_D | 1.370 | 0.99 |
| 202_G | 206_A | 1.368 | 0.99 |
| 246_F | 249_L | 1.367 | 0.99 |
| 87_K | 91_M | 1.356 | 0.99 |
| 89_K | 189_D | 1.344 | 0.99 |
| 92_F | 113_A | 1.341 | 0.99 |
| 7_G | 11_A | 1.337 | 0.99 |
| 191_L | 213_V | 1.334 | 0.99 |
| 191_L | 210_L | 1.333 | 0.99 |
| 153_V | 157_T | 1.314 | 0.99 |
| 180_Y | 218_A | 1.314 | 0.99 |
| 151_I | 155_K | 1.311 | 0.99 |
| 112_G | 182_G | 1.309 | 0.99 |
| 129_R | 133_A | 1.308 | 0.99 |
| 163_V | 167_Y | 1.287 | 0.99 |
| 54_T | 58_E | 1.285 | 0.99 |
| 203_S | 206_A | 1.271 | 0.99 |
| 13_V | 281_M | 1.265 | 0.99 |
| 128_A | 154_Y | 1.264 | 0.99 |
| 156_K | 159_K | 1.253 | 0.99 |
| 170_F | 174_V | 1.250 | 0.99 |
| 183_L | 221_C | 1.250 | 0.99 |
| 58_E | 62_S | 1.244 | 0.98 |
| 30_N | 230_R | 1.243 | 0.98 |
| 116_A | 174_V | 1.235 | 0.98 |
| 9_V | 13_V | 1.230 | 0.98 |
| 67_N | 71_V | 1.220 | 0.98 |
| 105_A | 109_A | 1.209 | 0.98 |
| 162_G | 165_G | 1.202 | 0.98 |
| 253_V | 256_E | 1.189 | 0.98 |
| 111_G | 115_G | 1.177 | 0.98 |
| 247_D | 250_R | 1.175 | 0.98 |
| 242_Y | 251_K | 1.171 | 0.98 |
| 262_F | 265_C | 1.171 | 0.98 |
| 187_M | 191_L | 1.167 | 0.97 |
| 172_P | 245_A | 1.165 | 0.97 |
| 87_K | 90_A | 1.165 | 0.97 |
| 113_A | 117_L | 1.157 | 0.97 |
| 5_L | 8_G | 1.155 | 0.97 |
| 223_Y | 268_N | 1.142 | 0.97 |
| 226_D | 229_R | 1.137 | 0.97 |
| 16_T | 67_N | 1.136 | 0.97 |
| 111_G | 182_G | 1.134 | 0.97 |
| 19_S | 64_W | 1.128 | 0.97 |
| 277_G | 281_M | 1.127 | 0.97 |
| 283_D | 286_Q | 1.117 | 0.96 |
| 120_L | 170_F | 1.115 | 0.96 |
| 48_L | 52_K | 1.112 | 0.96 |
| 8_G | 75_F | 1.112 | 0.96 |
| 183_L | 187_M | 1.109 | 0.96 |
| 77_T | 81_N | 1.103 | 0.96 |
| 209_L | 212_W | 1.096 | 0.96 |
| 84_F | 117_L | 1.092 | 0.96 |
| 109_A | 113_A | 1.088 | 0.96 |
| 223_Y | 227_T | 1.078 | 0.95 |
| 258_V | 262_F | 1.067 | 0.95 |
| 251_K | 254_A | 1.066 | 0.95 |
| 207_S | 211_G | 1.054 | 0.95 |
| 12_A | 71_V | 1.052 | 0.95 |
| 88_I | 92_F | 1.048 | 0.94 |
| 189_D | 192_K | 1.044 | 0.94 |
| 55_A | 60_V | 1.037 | 0.94 |
| 6_M | 285_L | 1.037 | 0.94 |
| 265_C | 269_I | 1.037 | 0.94 |
| 248_C | 252_I | 1.031 | 0.94 |
| 96_K | 106_G | 1.027 | 0.94 |
| 257_G | 260_S | 1.027 | 0.94 |
| 127_Y | 157_T | 1.024 | 0.93 |
| 130_T | 234_M | 1.017 | 0.93 |
| 76_P | 79_A | 1.016 | 0.93 |
| 215_T | 226_D | 1.015 | 0.93 |
| 19_S | 67_N | 1.009 | 0.93 |
| 44_Y | 53_R | 1.008 | 0.93 |
| 213_V | 217_G | 1.006 | 0.93 |
| 281_M | 284_Q | 1.005 | 0.93 |
| 80_L | 121_F | 1.002 | 0.92 |
| 194_L | 197_T | 1.002 | 0.92 |
| 209_L | 213_V | 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 | |
| 4c9gA | 1 | 0.8983 | 100 | 0.044 | Contact Map |
| 1okcA | 1 | 0.9525 | 100 | 0.098 | Contact Map |
| 2lckA | 1 | 0.9729 | 100 | 0.107 | Contact Map |
| 4i5lB | 2 | 0.2136 | 14.7 | 0.951 | Contact Map |
| 1fa2A | 1 | 0.2881 | 4 | 0.962 | Contact Map |
| 2kygA | 2 | 0.1695 | 3.3 | 0.963 | Contact Map |
| 2xfrA | 1 | 0.2712 | 2.6 | 0.965 | Contact Map |
| 2l5rA | 1 | 0.078 | 2.4 | 0.966 | Contact Map |
| 1wdpA | 1 | 0.278 | 2.4 | 0.966 | Contact Map |
| 4jjfA | 2 | 0.2847 | 1.9 | 0.968 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)