| AAC |
| ID: | 1505232275 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 298 (294) | ||
| Sequences: | 13392 (7618.1) | ||
| Seq/Len: | 45.551 | ||
| Nf(neff/√len): | 444.3 |
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: 45.551).
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 |
| 262_A | 270_F | 3.536 | 1.00 |
| 165_F | 173_L | 3.277 | 1.00 |
| 62_P | 70_F | 3.004 | 1.00 |
| 256_D | 260_K | 2.916 | 1.00 |
| 261_I | 269_A | 2.877 | 1.00 |
| 162_I | 166_K | 2.797 | 1.00 |
| 159_D | 163_K | 2.745 | 1.00 |
| 59_V | 63_K | 2.727 | 1.00 |
| 259_R | 263_K | 2.669 | 1.00 |
| 260_K | 264_D | 2.624 | 1.00 |
| 163_K | 167_S | 2.495 | 1.00 |
| 56_D | 60_R | 2.455 | 1.00 |
| 164_I | 172_G | 2.421 | 1.00 |
| 155_H | 159_D | 2.379 | 1.00 |
| 258_W | 270_F | 2.319 | 1.00 |
| 95_Y | 122_A | 2.300 | 1.00 |
| 265_E | 269_A | 2.222 | 1.00 |
| 234_V | 258_W | 2.163 | 1.00 |
| 60_R | 64_E | 2.104 | 1.00 |
| 237_R | 265_E | 2.095 | 1.00 |
| 161_I | 173_L | 2.083 | 1.00 |
| 33_K | 37_Q | 1.962 | 1.00 |
| 226_L | 274_A | 1.913 | 1.00 |
| 61_I | 69_S | 1.906 | 1.00 |
| 253_G | 256_D | 1.894 | 1.00 |
| 251_Y | 257_C | 1.883 | 1.00 |
| 154_F | 160_C | 1.863 | 1.00 |
| 121_G | 185_I | 1.847 | 1.00 |
| 140_R | 168_D | 1.836 | 1.00 |
| 95_Y | 126_T | 1.819 | 1.00 |
| 91_F | 95_Y | 1.798 | 1.00 |
| 262_A | 267_A | 1.765 | 1.00 |
| 168_D | 172_G | 1.749 | 1.00 |
| 252_T | 256_D | 1.717 | 1.00 |
| 30_E | 33_K | 1.703 | 1.00 |
| 117_L | 189_A | 1.698 | 1.00 |
| 194_V | 223_V | 1.698 | 1.00 |
| 251_Y | 256_D | 1.692 | 1.00 |
| 293_E | 296_K | 1.690 | 1.00 |
| 290_L | 294_I | 1.682 | 1.00 |
| 58_V | 70_F | 1.678 | 1.00 |
| 35_L | 65_Q | 1.663 | 1.00 |
| 38_V | 143_A | 1.656 | 1.00 |
| 99_F | 119_S | 1.650 | 1.00 |
| 286_F | 290_L | 1.643 | 1.00 |
| 27_A | 31_R | 1.634 | 1.00 |
| 17_V | 294_I | 1.616 | 1.00 |
| 235_R | 239_M | 1.605 | 1.00 |
| 65_Q | 72_R | 1.589 | 1.00 |
| 156_G | 159_D | 1.588 | 1.00 |
| 51_Y | 57_C | 1.586 | 1.00 |
| 168_D | 175_Q | 1.575 | 1.00 |
| 265_E | 272_K | 1.568 | 1.00 |
| 93_D | 96_K | 1.563 | 1.00 |
| 202_L | 216_I | 1.560 | 1.00 |
| 159_D | 162_I | 1.556 | 1.00 |
| 255_V | 259_R | 1.550 | 1.00 |
| 197_T | 201_M | 1.542 | 1.00 |
| 195_Y | 292_D | 1.527 | 1.00 |
| 154_F | 159_D | 1.526 | 1.00 |
| 87_L | 91_F | 1.495 | 1.00 |
| 56_D | 59_V | 1.472 | 1.00 |
| 31_R | 35_L | 1.465 | 1.00 |
| 165_F | 170_L | 1.458 | 1.00 |
| 51_Y | 56_D | 1.450 | 1.00 |
| 52_K | 56_D | 1.435 | 1.00 |
| 136_F | 140_R | 1.422 | 1.00 |
| 96_K | 196_D | 1.415 | 1.00 |
| 32_V | 58_V | 1.410 | 1.00 |
| 95_Y | 119_S | 1.403 | 0.99 |
| 132_Y | 136_F | 1.403 | 0.99 |
| 94_K | 98_L | 1.400 | 0.99 |
| 99_F | 122_A | 1.395 | 0.99 |
| 15_G | 19_A | 1.390 | 0.99 |
| 21_V | 290_L | 1.390 | 0.99 |
| 197_T | 200_G | 1.389 | 0.99 |
| 255_V | 258_W | 1.355 | 0.99 |
| 216_I | 220_V | 1.338 | 0.99 |
| 114_A | 118_A | 1.329 | 0.99 |
| 158_G | 162_I | 1.320 | 0.99 |
| 163_K | 166_K | 1.301 | 0.99 |
| 121_G | 189_A | 1.299 | 0.99 |
| 170_L | 174_Y | 1.286 | 0.99 |
| 208_V | 212_V | 1.277 | 0.99 |
| 190_A | 227_V | 1.275 | 0.99 |
| 177_F | 181_V | 1.275 | 0.99 |
| 229_Y | 277_N | 1.275 | 0.99 |
| 198_A | 216_I | 1.271 | 0.99 |
| 61_I | 65_Q | 1.267 | 0.99 |
| 138_R | 142_A | 1.254 | 0.99 |
| 74_N | 78_V | 1.248 | 0.99 |
| 38_V | 236_R | 1.247 | 0.99 |
| 65_Q | 69_S | 1.238 | 0.98 |
| 160_C | 164_I | 1.234 | 0.98 |
| 194_V | 198_A | 1.230 | 0.98 |
| 17_V | 21_V | 1.229 | 0.98 |
| 251_Y | 260_K | 1.210 | 0.98 |
| 217_A | 220_V | 1.210 | 0.98 |
| 27_A | 71_W | 1.209 | 0.98 |
| 13_L | 16_G | 1.205 | 0.98 |
| 198_A | 219_S | 1.200 | 0.98 |
| 169_G | 172_G | 1.199 | 0.98 |
| 120_G | 189_A | 1.191 | 0.98 |
| 179_V | 254_T | 1.190 | 0.98 |
| 84_T | 88_N | 1.188 | 0.98 |
| 137_A | 161_I | 1.185 | 0.98 |
| 94_K | 97_Q | 1.162 | 0.97 |
| 256_D | 259_R | 1.158 | 0.97 |
| 9_L | 13_L | 1.156 | 0.97 |
| 187_Y | 224_A | 1.143 | 0.97 |
| 24_T | 74_N | 1.140 | 0.97 |
| 229_Y | 233_T | 1.134 | 0.97 |
| 190_A | 194_V | 1.133 | 0.97 |
| 55_I | 59_V | 1.127 | 0.97 |
| 122_A | 126_T | 1.126 | 0.97 |
| 262_A | 265_E | 1.121 | 0.97 |
| 292_D | 295_K | 1.116 | 0.96 |
| 232_D | 235_R | 1.113 | 0.96 |
| 91_F | 126_T | 1.102 | 0.96 |
| 20_A | 78_V | 1.101 | 0.96 |
| 267_A | 271_F | 1.097 | 0.96 |
| 260_K | 263_K | 1.096 | 0.96 |
| 221_T | 232_D | 1.094 | 0.96 |
| 266_G | 269_A | 1.090 | 0.96 |
| 95_Y | 99_F | 1.086 | 0.96 |
| 271_F | 274_A | 1.081 | 0.95 |
| 120_G | 124_G | 1.079 | 0.95 |
| 139_T | 240_M | 1.072 | 0.95 |
| 129_C | 177_F | 1.066 | 0.95 |
| 209_H | 212_V | 1.063 | 0.95 |
| 125_A | 181_V | 1.063 | 0.95 |
| 214_W | 217_A | 1.063 | 0.95 |
| 118_A | 122_A | 1.058 | 0.95 |
| 257_C | 260_K | 1.057 | 0.95 |
| 83_P | 86_A | 1.048 | 0.94 |
| 196_D | 199_K | 1.043 | 0.94 |
| 191_Y | 288_L | 1.041 | 0.94 |
| 290_L | 293_E | 1.034 | 0.94 |
| 257_C | 261_I | 1.034 | 0.94 |
| 184_I | 187_Y | 1.033 | 0.94 |
| 234_V | 257_C | 1.032 | 0.94 |
| 215_M | 219_S | 1.027 | 0.94 |
| 291_Y | 295_K | 1.024 | 0.93 |
| 14_A | 18_A | 1.011 | 0.93 |
| 62_P | 67_F | 1.010 | 0.93 |
| 59_V | 62_P | 1.004 | 0.93 |
| 284_G | 287_V | 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
- See coupling matrix (for protein design or mutagenesis)
- 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 | |
| 1okcA | 1 | 0.9799 | 100 | 0.054 | Contact Map |
| 4c9gA | 1 | 0.8859 | 100 | 0.1 | Contact Map |
| 2lckA | 1 | 0.9396 | 100 | 0.123 | Contact Map |
| 4i5lB | 2 | 0.2416 | 17.6 | 0.95 | Contact Map |
| 1fa2A | 1 | 0.2651 | 2.2 | 0.967 | Contact Map |
| 2xfrA | 1 | 0.2483 | 1.6 | 0.97 | Contact Map |
| 3lo3A | 28 | 0.2181 | 1.6 | 0.97 | Contact Map |
| 2kygA | 2 | 0.1544 | 1.5 | 0.97 | Contact Map |
| 4jjfA | 2 | 0.3087 | 1.4 | 0.97 | Contact Map |
| 2l5rA | 1 | 0.0772 | 1.4 | 0.971 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)