| 4HE8HPDBIDCHAINSEQUENCE |
| ID: | 1465599540 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 365 (312) | ||
| Sequences: | 3341 (1459.5) | ||
| Seq/Len: | 10.708 | ||
| Nf(neff/√len): | 82.6 |
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: 10.708).
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 |
| 179_S | 184_D | 3.913 | 1.00 |
| 32_T | 59_P | 3.039 | 1.00 |
| 203_F | 259_I | 3.012 | 1.00 |
| 257_A | 279_M | 2.844 | 1.00 |
| 39_L | 295_A | 2.843 | 1.00 |
| 264_L | 286_F | 2.753 | 1.00 |
| 207_L | 289_F | 2.706 | 1.00 |
| 260_P | 279_M | 2.462 | 1.00 |
| 148_S | 234_T | 2.364 | 1.00 |
| 211_M | 293_I | 2.291 | 1.00 |
| 184_D | 187_N | 2.291 | 1.00 |
| 93_A | 250_I | 2.213 | 1.00 |
| 224_A | 228_L | 2.064 | 1.00 |
| 38_L | 288_F | 2.034 | 1.00 |
| 187_N | 190_K | 1.997 | 1.00 |
| 257_A | 283_I | 1.990 | 1.00 |
| 253_I | 287_L | 1.962 | 1.00 |
| 42_F | 295_A | 1.917 | 1.00 |
| 71_D | 240_K | 1.837 | 1.00 |
| 269_M | 278_W | 1.806 | 1.00 |
| 60_L | 63_A | 1.782 | 1.00 |
| 89_S | 247_A | 1.776 | 1.00 |
| 95_L | 124_Y | 1.773 | 1.00 |
| 202_A | 263_F | 1.764 | 1.00 |
| 207_L | 211_M | 1.729 | 1.00 |
| 93_A | 251_H | 1.726 | 1.00 |
| 175_L | 325_A | 1.662 | 1.00 |
| 140_G | 152_S | 1.658 | 1.00 |
| 81_L | 138_L | 1.639 | 1.00 |
| 194_W | 282_K | 1.622 | 1.00 |
| 188_W | 195_L | 1.611 | 1.00 |
| 90_V | 243_L | 1.605 | 1.00 |
| 206_Y | 259_I | 1.555 | 1.00 |
| 242_A | 246_M | 1.527 | 1.00 |
| 275_P | 278_W | 1.520 | 1.00 |
| 221_L | 305_L | 1.515 | 1.00 |
| 182_L | 258_L | 1.503 | 1.00 |
| 196_F | 264_L | 1.499 | 1.00 |
| 196_F | 203_F | 1.493 | 1.00 |
| 208_I | 313_L | 1.489 | 1.00 |
| 99_L | 124_Y | 1.487 | 1.00 |
| 37_R | 69_K | 1.487 | 1.00 |
| 174_V | 180_L | 1.475 | 1.00 |
| 18_L | 22_V | 1.452 | 1.00 |
| 145_S | 148_S | 1.447 | 1.00 |
| 210_S | 255_A | 1.442 | 1.00 |
| 96_A | 254_T | 1.442 | 1.00 |
| 214_A | 290_F | 1.442 | 1.00 |
| 202_A | 320_W | 1.428 | 1.00 |
| 288_F | 292_W | 1.414 | 1.00 |
| 230_G | 233_H | 1.412 | 1.00 |
| 35_E | 216_R | 1.407 | 0.99 |
| 24_L | 250_I | 1.386 | 0.99 |
| 166_L | 309_G | 1.368 | 0.99 |
| 28_F | 246_M | 1.362 | 0.99 |
| 241_W | 245_Q | 1.347 | 0.99 |
| 169_A | 205_V | 1.332 | 0.99 |
| 256_S | 286_F | 1.316 | 0.99 |
| 124_Y | 128_V | 1.316 | 0.99 |
| 89_S | 135_G | 1.312 | 0.99 |
| 172_A | 321_F | 1.298 | 0.99 |
| 302_Y | 306_L | 1.298 | 0.99 |
| 177_V | 195_L | 1.284 | 0.99 |
| 40_A | 46_M | 1.282 | 0.99 |
| 28_F | 250_I | 1.266 | 0.99 |
| 217_T | 297_W | 1.266 | 0.99 |
| 292_W | 296_T | 1.258 | 0.99 |
| 85_A | 139_S | 1.256 | 0.99 |
| 252_F | 287_L | 1.250 | 0.99 |
| 155_S | 222_P | 1.245 | 0.98 |
| 212_A | 219_F | 1.242 | 0.98 |
| 168_L | 318_L | 1.239 | 0.98 |
| 169_A | 317_A | 1.238 | 0.98 |
| 58_Q | 62_D | 1.235 | 0.98 |
| 199_A | 324_T | 1.234 | 0.98 |
| 66_S | 242_A | 1.233 | 0.98 |
| 98_G | 124_Y | 1.231 | 0.98 |
| 41_R | 46_M | 1.229 | 0.98 |
| 320_W | 324_T | 1.227 | 0.98 |
| 177_V | 185_I | 1.226 | 0.98 |
| 165_G | 209_A | 1.224 | 0.98 |
| 205_V | 208_I | 1.223 | 0.98 |
| 30_F | 59_P | 1.215 | 0.98 |
| 42_F | 292_W | 1.215 | 0.98 |
| 126_F | 167_G | 1.212 | 0.98 |
| 43_Q | 235_E | 1.211 | 0.98 |
| 83_V | 240_K | 1.208 | 0.98 |
| 35_E | 294_R | 1.207 | 0.98 |
| 161_S | 306_L | 1.203 | 0.98 |
| 186_V | 266_G | 1.203 | 0.98 |
| 172_A | 202_A | 1.202 | 0.98 |
| 77_A | 82_F | 1.198 | 0.98 |
| 172_A | 317_A | 1.198 | 0.98 |
| 260_P | 264_L | 1.198 | 0.98 |
| 88_I | 92_F | 1.195 | 0.98 |
| 64_I | 68_F | 1.189 | 0.98 |
| 286_F | 289_F | 1.188 | 0.98 |
| 259_I | 286_F | 1.186 | 0.98 |
| 38_L | 42_F | 1.183 | 0.98 |
| 67_I | 242_A | 1.178 | 0.98 |
| 46_M | 49_N | 1.177 | 0.98 |
| 299_R | 303_D | 1.171 | 0.98 |
| 210_S | 259_I | 1.169 | 0.97 |
| 189_Q | 265_G | 1.151 | 0.97 |
| 34_I | 288_F | 1.150 | 0.97 |
| 34_I | 291_I | 1.146 | 0.97 |
| 138_L | 142_A | 1.131 | 0.97 |
| 179_S | 185_I | 1.131 | 0.97 |
| 65_K | 69_K | 1.128 | 0.97 |
| 158_S | 215_A | 1.125 | 0.97 |
| 265_G | 282_K | 1.124 | 0.97 |
| 97_F | 254_T | 1.123 | 0.97 |
| 257_A | 261_T | 1.119 | 0.96 |
| 74_V | 77_A | 1.117 | 0.96 |
| 214_A | 255_A | 1.112 | 0.96 |
| 165_G | 314_F | 1.111 | 0.96 |
| 27_A | 284_A | 1.110 | 0.96 |
| 26_T | 60_L | 1.108 | 0.96 |
| 27_A | 253_I | 1.105 | 0.96 |
| 222_P | 232_Y | 1.100 | 0.96 |
| 31_M | 287_L | 1.100 | 0.96 |
| 118_L | 124_Y | 1.099 | 0.96 |
| 30_F | 60_L | 1.089 | 0.96 |
| 194_W | 265_G | 1.084 | 0.96 |
| 155_S | 224_A | 1.083 | 0.96 |
| 134_Y | 302_Y | 1.080 | 0.95 |
| 35_E | 291_I | 1.079 | 0.95 |
| 63_A | 246_M | 1.077 | 0.95 |
| 225_E | 229_V | 1.076 | 0.95 |
| 203_F | 263_F | 1.074 | 0.95 |
| 281_L | 285_F | 1.072 | 0.95 |
| 274_V | 277_L | 1.069 | 0.95 |
| 206_Y | 255_A | 1.068 | 0.95 |
| 186_V | 267_W | 1.068 | 0.95 |
| 194_W | 266_G | 1.068 | 0.95 |
| 285_F | 289_F | 1.065 | 0.95 |
| 58_Q | 65_K | 1.064 | 0.95 |
| 264_L | 282_K | 1.063 | 0.95 |
| 36_R | 62_D | 1.059 | 0.95 |
| 261_T | 266_G | 1.048 | 0.94 |
| 158_S | 305_L | 1.046 | 0.94 |
| 215_A | 248_E | 1.044 | 0.94 |
| 233_H | 241_W | 1.043 | 0.94 |
| 139_S | 142_A | 1.040 | 0.94 |
| 90_V | 247_A | 1.040 | 0.94 |
| 43_Q | 48_P | 1.038 | 0.94 |
| 36_R | 45_R | 1.034 | 0.94 |
| 213_E | 216_R | 1.034 | 0.94 |
| 193_G | 197_L | 1.032 | 0.94 |
| 22_V | 25_L | 1.028 | 0.94 |
| 129_S | 132_A | 1.026 | 0.94 |
| 181_N | 184_D | 1.025 | 0.93 |
| 137_F | 156_S | 1.022 | 0.93 |
| 308_F | 313_L | 1.021 | 0.93 |
| 177_V | 188_W | 1.021 | 0.93 |
| 66_S | 252_F | 1.014 | 0.93 |
| 224_A | 232_Y | 1.010 | 0.93 |
| 85_A | 135_G | 1.010 | 0.93 |
| 117_N | 121_G | 1.008 | 0.93 |
| 117_N | 179_S | 1.007 | 0.93 |
| 48_P | 65_K | 1.006 | 0.93 |
| 64_I | 67_I | 1.005 | 0.93 |
| 25_L | 29_A | 1.004 | 0.93 |
| 121_G | 181_N | 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 | |
| 4he8H | 2 | 0.8137 | 100 | 0.121 | Contact Map |
| 2m3eA | 1 | 0.1233 | 7.7 | 0.976 | Contact Map |
| 1jb0I | 1 | 0.1041 | 6.9 | 0.977 | Contact Map |
| 3mp7A | 1 | 0.1562 | 6.6 | 0.977 | Contact Map |
| 4l6vi | 3 | 0.1041 | 6.3 | 0.977 | Contact Map |
| 1jo6A | 1 | 0.1233 | 4.9 | 0.978 | Contact Map |
| 4h25C | 2 | 0.0603 | 4.1 | 0.979 | Contact Map |
| 1q90G | 1 | 0.0822 | 2.5 | 0.981 | Contact Map |
| 2jpkA | 1 | 0.0959 | 2.4 | 0.981 | Contact Map |
| 3pjzA | 2 | 0.2384 | 2.3 | 0.981 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)