| 4AGI_A non default parameters |
| ID: | 1482670036 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 50% gaps before running GREMLIN. |
| Length: | 315 (274) | ||
| Sequences: | 821 (664.2) | ||
| Seq/Len: | 2.996 | ||
| Nf(neff/√len): | 40.1 |
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: 2.996).
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 |
| 76_T | 180_F | 2.321 | 1.00 |
| 129_A | 233_F | 2.213 | 1.00 |
| 134_N | 238_N | 2.016 | 1.00 |
| 76_T | 129_A | 1.985 | 1.00 |
| 84_Q | 137_Q | 1.979 | 1.00 |
| 145_G | 250_G | 1.847 | 0.99 |
| 112_I | 215_I | 1.824 | 0.99 |
| 81_N | 185_L | 1.813 | 0.99 |
| 114_A | 125_L | 1.807 | 0.99 |
| 35_I | 136_I | 1.786 | 0.99 |
| 84_Q | 241_W | 1.773 | 0.99 |
| 145_G | 197_G | 1.751 | 0.99 |
| 141_W | 192_Y | 1.727 | 0.99 |
| 29_Q | 130_Q | 1.709 | 0.98 |
| 87_A | 191_A | 1.700 | 0.98 |
| 62_V | 161_I | 1.689 | 0.98 |
| 149_G | 254_K | 1.674 | 0.98 |
| 73_R | 126_R | 1.666 | 0.98 |
| 181_Q | 286_Q | 1.661 | 0.98 |
| 39_L | 244_C | 1.651 | 0.98 |
| 130_Q | 234_V | 1.642 | 0.98 |
| 233_F | 285_F | 1.624 | 0.98 |
| 87_A | 140_M | 1.616 | 0.98 |
| 138_E | 189_Q | 1.614 | 0.97 |
| 130_Q | 181_Q | 1.611 | 0.97 |
| 128_Y | 163_A | 1.596 | 0.97 |
| 75_Y | 284_Y | 1.563 | 0.97 |
| 137_Q | 241_W | 1.549 | 0.97 |
| 140_M | 191_A | 1.519 | 0.96 |
| 136_I | 240_I | 1.519 | 0.96 |
| 25_R | 73_R | 1.514 | 0.96 |
| 140_M | 244_C | 1.510 | 0.96 |
| 77_L | 286_Q | 1.509 | 0.96 |
| 182_T | 188_V | 1.501 | 0.96 |
| 97_G | 201_D | 1.492 | 0.95 |
| 129_A | 180_F | 1.481 | 0.95 |
| 72_I | 176_I | 1.473 | 0.95 |
| 76_T | 233_F | 1.463 | 0.95 |
| 180_F | 233_F | 1.460 | 0.95 |
| 77_L | 130_Q | 1.458 | 0.95 |
| 161_I | 215_I | 1.438 | 0.94 |
| 88_Y | 141_W | 1.436 | 0.94 |
| 78_T | 84_Q | 1.425 | 0.94 |
| 215_I | 266_V | 1.425 | 0.94 |
| 22_N | 123_L | 1.411 | 0.93 |
| 87_A | 244_C | 1.408 | 0.93 |
| 141_W | 245_W | 1.388 | 0.93 |
| 137_Q | 188_V | 1.382 | 0.92 |
| 77_L | 181_Q | 1.376 | 0.92 |
| 39_L | 87_A | 1.372 | 0.92 |
| 86_F | 190_R | 1.363 | 0.92 |
| 148_E | 253_D | 1.358 | 0.92 |
| 133_D | 237_D | 1.356 | 0.91 |
| 62_V | 215_I | 1.346 | 0.91 |
| 192_Y | 245_W | 1.346 | 0.91 |
| 128_Y | 138_E | 1.343 | 0.91 |
| 127_I | 231_I | 1.338 | 0.91 |
| 124_Q | 228_Y | 1.332 | 0.90 |
| 217_A | 229_M | 1.331 | 0.90 |
| 93_G | 145_G | 1.325 | 0.90 |
| 138_E | 242_Q | 1.325 | 0.90 |
| 142_N | 193_D | 1.318 | 0.90 |
| 132_P | 183_D | 1.317 | 0.90 |
| 88_Y | 245_W | 1.317 | 0.90 |
| 240_I | 283_L | 1.310 | 0.90 |
| 189_Q | 242_Q | 1.304 | 0.89 |
| 78_T | 131_K | 1.304 | 0.89 |
| 86_F | 243_V | 1.303 | 0.89 |
| 128_Y | 232_Y | 1.302 | 0.89 |
| 85_E | 189_Q | 1.301 | 0.89 |
| 70_K | 174_P | 1.298 | 0.89 |
| 188_V | 241_W | 1.296 | 0.89 |
| 126_R | 177_R | 1.296 | 0.89 |
| 62_V | 112_I | 1.295 | 0.89 |
| 75_Y | 114_A | 1.288 | 0.88 |
| 37_E | 85_E | 1.282 | 0.88 |
| 25_R | 230_R | 1.275 | 0.88 |
| 74_V | 178_I | 1.270 | 0.87 |
| 37_E | 189_Q | 1.260 | 0.87 |
| 39_L | 140_M | 1.258 | 0.87 |
| 84_Q | 188_V | 1.258 | 0.87 |
| 24_L | 125_L | 1.254 | 0.87 |
| 73_R | 230_R | 1.251 | 0.86 |
| 88_Y | 192_Y | 1.248 | 0.86 |
| 49_E | 151_N | 1.247 | 0.86 |
| 178_I | 283_L | 1.241 | 0.86 |
| 124_Q | 175_S | 1.236 | 0.86 |
| 150_T | 202_L | 1.232 | 0.85 |
| 28_F | 180_F | 1.231 | 0.85 |
| 73_R | 85_E | 1.229 | 0.85 |
| 139_Y | 243_V | 1.218 | 0.84 |
| 85_E | 138_E | 1.216 | 0.84 |
| 38_S | 139_Y | 1.208 | 0.84 |
| 16_A | 162_G | 1.202 | 0.83 |
| 41_E | 142_N | 1.197 | 0.83 |
| 126_R | 230_R | 1.192 | 0.83 |
| 197_G | 304_G | 1.192 | 0.83 |
| 30_D | 36_R | 1.192 | 0.83 |
| 114_A | 217_A | 1.191 | 0.83 |
| 123_L | 174_P | 1.181 | 0.82 |
| 44_W | 94_W | 1.181 | 0.82 |
| 37_E | 138_E | 1.178 | 0.82 |
| 180_F | 285_F | 1.175 | 0.81 |
| 128_Y | 179_W | 1.174 | 0.81 |
| 83_L | 136_I | 1.172 | 0.81 |
| 136_I | 187_L | 1.171 | 0.81 |
| 40_Y | 245_W | 1.170 | 0.81 |
| 179_W | 217_A | 1.166 | 0.81 |
| 45_A | 95_Y | 1.161 | 0.80 |
| 268_I | 281_L | 1.159 | 0.80 |
| 113_A | 162_G | 1.157 | 0.80 |
| 73_R | 177_R | 1.146 | 0.79 |
| 93_G | 197_G | 1.146 | 0.79 |
| 25_R | 126_R | 1.143 | 0.79 |
| 186_K | 239_T | 1.141 | 0.79 |
| 185_L | 238_N | 1.137 | 0.78 |
| 83_L | 187_L | 1.133 | 0.78 |
| 38_S | 243_V | 1.132 | 0.78 |
| 41_E | 89_D | 1.130 | 0.78 |
| 79_E | 183_D | 1.122 | 0.77 |
| 202_L | 255_G | 1.121 | 0.77 |
| 47_G | 149_G | 1.119 | 0.77 |
| 177_R | 230_R | 1.113 | 0.76 |
| 75_Y | 179_W | 1.108 | 0.76 |
| 36_R | 137_Q | 1.107 | 0.76 |
| 93_G | 250_G | 1.107 | 0.76 |
| 37_E | 242_Q | 1.105 | 0.75 |
| 117_L | 220_F | 1.104 | 0.75 |
| 36_R | 241_W | 1.103 | 0.75 |
| 40_Y | 141_W | 1.103 | 0.75 |
| 86_F | 139_Y | 1.094 | 0.74 |
| 184_D | 188_V | 1.086 | 0.74 |
| 71_H | 175_S | 1.086 | 0.74 |
| 234_V | 286_Q | 1.083 | 0.73 |
| 134_N | 185_L | 1.079 | 0.73 |
| 149_G | 201_D | 1.077 | 0.73 |
| 271_W | 282_R | 1.076 | 0.73 |
| 282_R | 296_E | 1.075 | 0.73 |
| 92_T | 196_K | 1.070 | 0.72 |
| 29_Q | 234_V | 1.066 | 0.72 |
| 40_Y | 88_Y | 1.066 | 0.72 |
| 70_K | 123_L | 1.065 | 0.72 |
| 62_V | 266_V | 1.063 | 0.71 |
| 36_R | 188_V | 1.063 | 0.71 |
| 235_N | 241_W | 1.062 | 0.71 |
| 18_V | 115_V | 1.054 | 0.70 |
| 39_L | 191_A | 1.051 | 0.70 |
| 191_A | 244_C | 1.048 | 0.70 |
| 125_L | 229_M | 1.048 | 0.70 |
| 79_E | 132_P | 1.045 | 0.70 |
| 242_Q | 255_G | 1.044 | 0.69 |
| 26_V | 74_V | 1.044 | 0.69 |
| 197_G | 250_G | 1.044 | 0.69 |
| 185_L | 292_S | 1.042 | 0.69 |
| 130_Q | 286_Q | 1.042 | 0.69 |
| 95_Y | 199_Y | 1.040 | 0.69 |
| 109_Y | 212_R | 1.036 | 0.69 |
| 33_G | 134_N | 1.033 | 0.68 |
| 97_G | 149_G | 1.032 | 0.68 |
| 152_L | 257_I | 1.029 | 0.68 |
| 127_I | 283_L | 1.027 | 0.68 |
| 96_N | 253_D | 1.027 | 0.68 |
| 85_E | 242_Q | 1.025 | 0.67 |
| 179_W | 284_Y | 1.023 | 0.67 |
| 20_S | 166_F | 1.016 | 0.66 |
| 177_R | 282_R | 1.016 | 0.66 |
| 115_V | 218_T | 1.015 | 0.66 |
| 181_Q | 234_V | 1.011 | 0.66 |
| 112_I | 161_I | 1.002 | 0.65 |
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 | |
| 4agiA | 4 | 0.9905 | 100 | 0.156 | Contact Map |
| 1ofzA | 2 | 0.927 | 100 | 0.273 | Contact Map |
| 4csdA | 2 | 0.8349 | 100 | 0.403 | Contact Map |
| 2bt9A | 3 | 0.2667 | 98.9 | 0.777 | Contact Map |
| 4irtA | 1 | 0.9175 | 94.9 | 0.885 | Contact Map |
| 4ruqA | 2 | 0.6984 | 93.7 | 0.891 | Contact Map |
| 2xbgA | 1 | 0.8508 | 90.4 | 0.901 | Contact Map |
| 4o9xA | 1 | 0.9397 | 71.2 | 0.921 | Contact Map |
| 4iglA | 2 | 0.8794 | 52.9 | 0.929 | Contact Map |
| 2hesX | 1 | 0.8508 | 49.4 | 0.931 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)