| hhth |
| ID: | 1508094648 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 323 (316) | ||
| Sequences: | 3843 (2575.7) | ||
| Seq/Len: | 12.161 | ||
| Nf(neff/√len): | 144.9 |
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: 12.161).
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 |
| 146_N | 190_D | 3.738 | 1.00 |
| 146_N | 187_I | 3.707 | 1.00 |
| 179_K | 318_A | 3.666 | 1.00 |
| 223_T | 228_V | 3.533 | 1.00 |
| 281_M | 320_I | 3.474 | 1.00 |
| 139_I | 213_P | 3.369 | 1.00 |
| 13_T | 61_S | 3.316 | 1.00 |
| 285_D | 316_I | 3.031 | 1.00 |
| 56_R | 101_A | 3.026 | 1.00 |
| 58_T | 62_L | 2.973 | 1.00 |
| 259_A | 280_V | 2.951 | 1.00 |
| 268_H | 274_G | 2.915 | 1.00 |
| 98_F | 196_A | 2.892 | 1.00 |
| 187_I | 190_D | 2.810 | 1.00 |
| 109_S | 243_R | 2.802 | 1.00 |
| 224_H | 228_V | 2.644 | 1.00 |
| 241_L | 261_S | 2.484 | 1.00 |
| 140_L | 191_S | 2.433 | 1.00 |
| 221_E | 321_M | 2.394 | 1.00 |
| 33_Y | 273_F | 2.390 | 1.00 |
| 135_R | 197_G | 2.374 | 1.00 |
| 197_G | 201_E | 2.266 | 1.00 |
| 241_L | 257_T | 2.219 | 1.00 |
| 139_I | 193_L | 2.198 | 1.00 |
| 212_V | 236_S | 2.178 | 1.00 |
| 6_P | 67_G | 2.104 | 1.00 |
| 59_S | 95_Y | 2.075 | 1.00 |
| 310_W | 314_Q | 2.062 | 1.00 |
| 235_Q | 239_R | 2.057 | 1.00 |
| 175_A | 318_A | 2.017 | 1.00 |
| 252_W | 256_Q | 2.008 | 1.00 |
| 145_L | 148_A | 1.994 | 1.00 |
| 281_M | 285_D | 1.993 | 1.00 |
| 227_S | 290_S | 1.988 | 1.00 |
| 57_V | 96_L | 1.972 | 1.00 |
| 255_L | 280_V | 1.953 | 1.00 |
| 132_L | 201_E | 1.914 | 1.00 |
| 258_F | 261_S | 1.899 | 1.00 |
| 225_R | 289_H | 1.857 | 1.00 |
| 112_R | 239_R | 1.838 | 1.00 |
| 250_R | 253_P | 1.815 | 1.00 |
| 31_T | 35_L | 1.800 | 1.00 |
| 116_R | 201_E | 1.796 | 1.00 |
| 110_F | 114_Q | 1.767 | 1.00 |
| 132_L | 197_G | 1.761 | 1.00 |
| 62_L | 66_E | 1.759 | 1.00 |
| 189_D | 193_L | 1.727 | 1.00 |
| 91_P | 118_Q | 1.710 | 1.00 |
| 313_T | 317_I | 1.663 | 1.00 |
| 167_C | 170_V | 1.644 | 1.00 |
| 227_S | 289_H | 1.625 | 1.00 |
| 213_P | 216_D | 1.625 | 1.00 |
| 224_H | 309_T | 1.596 | 1.00 |
| 88_K | 91_P | 1.578 | 1.00 |
| 258_F | 286_Y | 1.578 | 1.00 |
| 245_V | 260_F | 1.576 | 1.00 |
| 238_A | 242_R | 1.553 | 1.00 |
| 11_R | 15_C | 1.541 | 1.00 |
| 89_A | 93_F | 1.521 | 1.00 |
| 33_Y | 36_H | 1.519 | 1.00 |
| 176_G | 315_L | 1.511 | 1.00 |
| 29_H | 33_Y | 1.498 | 1.00 |
| 311_A | 315_L | 1.489 | 1.00 |
| 68_K | 111_Q | 1.474 | 1.00 |
| 28_L | 32_E | 1.465 | 1.00 |
| 216_D | 235_Q | 1.458 | 1.00 |
| 255_L | 283_E | 1.449 | 1.00 |
| 263_W | 276_V | 1.441 | 1.00 |
| 251_A | 291_F | 1.403 | 0.99 |
| 113_F | 117_V | 1.402 | 0.99 |
| 226_I | 282_V | 1.397 | 0.99 |
| 317_I | 321_M | 1.378 | 0.99 |
| 226_I | 285_D | 1.367 | 0.99 |
| 14_F | 19_S | 1.340 | 0.99 |
| 247_Q | 250_R | 1.335 | 0.99 |
| 56_R | 108_C | 1.333 | 0.99 |
| 282_V | 317_I | 1.321 | 0.99 |
| 28_L | 31_T | 1.317 | 0.99 |
| 314_Q | 318_A | 1.315 | 0.99 |
| 28_L | 40_S | 1.309 | 0.99 |
| 226_I | 313_T | 1.309 | 0.99 |
| 258_F | 282_V | 1.305 | 0.99 |
| 101_A | 108_C | 1.299 | 0.99 |
| 9_V | 12_W | 1.298 | 0.99 |
| 22_T | 30_Y | 1.286 | 0.99 |
| 246_F | 253_P | 1.285 | 0.99 |
| 249_S | 256_Q | 1.280 | 0.99 |
| 282_V | 320_I | 1.279 | 0.99 |
| 238_A | 254_L | 1.276 | 0.99 |
| 168_I | 172_W | 1.271 | 0.99 |
| 57_V | 92_Y | 1.270 | 0.99 |
| 10_H | 14_F | 1.246 | 0.98 |
| 246_F | 250_R | 1.242 | 0.98 |
| 217_I | 222_R | 1.223 | 0.98 |
| 15_C | 19_S | 1.212 | 0.98 |
| 273_F | 276_V | 1.211 | 0.98 |
| 30_Y | 263_W | 1.210 | 0.98 |
| 23_L | 43_F | 1.203 | 0.98 |
| 8_Q | 11_R | 1.202 | 0.98 |
| 29_H | 267_L | 1.183 | 0.98 |
| 28_L | 42_R | 1.177 | 0.98 |
| 277_C | 280_V | 1.172 | 0.98 |
| 247_Q | 253_P | 1.172 | 0.98 |
| 131_A | 135_R | 1.157 | 0.97 |
| 255_L | 287_L | 1.157 | 0.97 |
| 257_T | 261_S | 1.156 | 0.97 |
| 281_M | 316_I | 1.155 | 0.97 |
| 226_I | 317_I | 1.149 | 0.97 |
| 140_L | 195_A | 1.148 | 0.97 |
| 317_I | 320_I | 1.146 | 0.97 |
| 261_S | 278_W | 1.143 | 0.97 |
| 261_S | 286_Y | 1.140 | 0.97 |
| 112_R | 212_V | 1.139 | 0.97 |
| 18_M | 260_F | 1.136 | 0.97 |
| 133_S | 137_L | 1.127 | 0.97 |
| 175_A | 322_L | 1.121 | 0.97 |
| 66_E | 248_H | 1.114 | 0.96 |
| 18_M | 245_V | 1.114 | 0.96 |
| 92_Y | 96_L | 1.113 | 0.96 |
| 108_C | 212_V | 1.112 | 0.96 |
| 134_W | 138_Q | 1.112 | 0.96 |
| 227_S | 231_R | 1.110 | 0.96 |
| 90_L | 94_S | 1.110 | 0.96 |
| 46_T | 49_S | 1.106 | 0.96 |
| 176_G | 318_A | 1.103 | 0.96 |
| 182_Y | 221_E | 1.091 | 0.96 |
| 169_Y | 173_T | 1.090 | 0.96 |
| 236_S | 239_R | 1.089 | 0.96 |
| 163_Q | 174_T | 1.083 | 0.96 |
| 60_L | 92_Y | 1.066 | 0.95 |
| 60_L | 87_C | 1.059 | 0.95 |
| 254_L | 286_Y | 1.058 | 0.95 |
| 179_K | 221_E | 1.056 | 0.95 |
| 308_L | 312_H | 1.052 | 0.95 |
| 94_S | 113_F | 1.050 | 0.94 |
| 249_S | 253_P | 1.044 | 0.94 |
| 314_Q | 317_I | 1.042 | 0.94 |
| 7_Q | 65_C | 1.042 | 0.94 |
| 250_R | 321_M | 1.036 | 0.94 |
| 136_G | 194_H | 1.035 | 0.94 |
| 292_A | 296_I | 1.032 | 0.94 |
| 18_M | 58_T | 1.031 | 0.94 |
| 229_F | 317_I | 1.029 | 0.94 |
| 288_I | 292_A | 1.027 | 0.94 |
| 78_S | 83_S | 1.023 | 0.93 |
| 158_G | 164_Q | 1.021 | 0.93 |
| 48_S | 103_L | 1.014 | 0.93 |
| 56_R | 196_A | 1.011 | 0.93 |
| 180_L | 314_Q | 1.002 | 0.92 |
| 228_V | 232_K | 1.002 | 0.92 |
| 259_A | 276_V | 1.002 | 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 | |
| 1irqA | 2 | 0.1424 | 2 | 0.974 | Contact Map |
| 3ddlA | 2 | 0.1981 | 1.3 | 0.977 | Contact Map |
| 4ogqE | 1 | 0.096 | 1.1 | 0.977 | Contact Map |
| 2i2jA | 1 | 0.065 | 1.1 | 0.978 | Contact Map |
| 1q90L | 1 | 0.0991 | 1 | 0.978 | Contact Map |
| 1lbjA | 1 | 0.0681 | 0.9 | 0.978 | Contact Map |
| 1ceuA | 1 | 0.1548 | 0.9 | 0.979 | Contact Map |
| 2l0lA | 1 | 0.0836 | 0.9 | 0.979 | Contact Map |
| 4eneA | 2 | 0.2322 | 0.8 | 0.979 | Contact Map |
| 1rmkA | 1 | 0.096 | 0.8 | 0.979 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)