| MC1T 140-460 |
| ID: | 1483610245 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 321 (315) | ||
| Sequences: | 583 (385.7) | ||
| Seq/Len: | 1.851 | ||
| Nf(neff/√len): | 21.7 |
Jackhmmer Results: (2016_04)
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: 1.851).
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 |
| 132_F | 137_S | 2.660 | 1.00 |
| 118_Y | 121_Y | 2.265 | 1.00 |
| 264_W | 268_N | 2.231 | 1.00 |
| 104_L | 107_F | 2.161 | 0.99 |
| 103_V | 107_F | 2.126 | 0.99 |
| 226_R | 230_N | 2.072 | 0.99 |
| 64_F | 68_F | 1.958 | 0.99 |
| 98_A | 101_F | 1.946 | 0.98 |
| 308_F | 311_L | 1.928 | 0.98 |
| 132_F | 138_Y | 1.857 | 0.98 |
| 186_I | 192_A | 1.814 | 0.97 |
| 264_W | 270_M | 1.772 | 0.97 |
| 109_G | 121_Y | 1.692 | 0.95 |
| 139_F | 142_G | 1.681 | 0.95 |
| 216_E | 219_V | 1.670 | 0.95 |
| 150_F | 154_L | 1.660 | 0.95 |
| 158_T | 162_G | 1.660 | 0.95 |
| 229_A | 288_F | 1.654 | 0.95 |
| 92_R | 95_E | 1.629 | 0.94 |
| 98_A | 102_G | 1.628 | 0.94 |
| 102_G | 107_F | 1.602 | 0.93 |
| 215_V | 218_N | 1.579 | 0.93 |
| 230_N | 234_F | 1.572 | 0.92 |
| 205_E | 208_T | 1.557 | 0.92 |
| 244_I | 251_S | 1.553 | 0.92 |
| 226_R | 231_F | 1.550 | 0.92 |
| 60_N | 74_P | 1.546 | 0.92 |
| 97_S | 101_F | 1.539 | 0.91 |
| 309_A | 313_G | 1.531 | 0.91 |
| 208_T | 211_K | 1.516 | 0.91 |
| 215_V | 220_H | 1.513 | 0.90 |
| 226_R | 234_F | 1.512 | 0.90 |
| 153_V | 156_A | 1.495 | 0.90 |
| 43_G | 50_F | 1.490 | 0.90 |
| 226_R | 237_L | 1.479 | 0.89 |
| 31_W | 38_I | 1.473 | 0.89 |
| 215_V | 219_V | 1.464 | 0.88 |
| 97_S | 103_V | 1.448 | 0.88 |
| 149_S | 155_K | 1.441 | 0.87 |
| 91_P | 94_E | 1.425 | 0.87 |
| 231_F | 235_L | 1.402 | 0.85 |
| 187_G | 194_N | 1.397 | 0.85 |
| 192_A | 195_K | 1.385 | 0.84 |
| 186_I | 195_K | 1.383 | 0.84 |
| 282_P | 292_E | 1.375 | 0.84 |
| 53_L | 56_M | 1.369 | 0.83 |
| 103_V | 106_D | 1.361 | 0.83 |
| 161_I | 175_S | 1.361 | 0.83 |
| 226_R | 240_S | 1.361 | 0.83 |
| 102_G | 105_Y | 1.355 | 0.83 |
| 237_L | 240_S | 1.349 | 0.82 |
| 248_V | 251_S | 1.339 | 0.82 |
| 153_V | 158_T | 1.336 | 0.81 |
| 266_E | 270_M | 1.336 | 0.81 |
| 140_L | 145_C | 1.334 | 0.81 |
| 156_A | 160_N | 1.316 | 0.80 |
| 157_M | 162_G | 1.311 | 0.80 |
| 265_W | 268_N | 1.310 | 0.80 |
| 201_M | 204_K | 1.308 | 0.79 |
| 49_Y | 53_L | 1.305 | 0.79 |
| 68_F | 114_S | 1.301 | 0.79 |
| 100_N | 103_V | 1.296 | 0.79 |
| 160_N | 165_G | 1.296 | 0.79 |
| 141_V | 144_M | 1.275 | 0.77 |
| 162_G | 166_G | 1.273 | 0.77 |
| 111_A | 117_F | 1.273 | 0.77 |
| 97_S | 100_N | 1.266 | 0.76 |
| 45_S | 281_C | 1.258 | 0.76 |
| 264_W | 269_E | 1.254 | 0.75 |
| 187_G | 191_T | 1.253 | 0.75 |
| 153_V | 157_M | 1.253 | 0.75 |
| 42_F | 52_F | 1.245 | 0.75 |
| 230_N | 237_L | 1.244 | 0.74 |
| 231_F | 234_F | 1.234 | 0.74 |
| 43_G | 53_L | 1.233 | 0.73 |
| 157_M | 160_N | 1.222 | 0.73 |
| 204_K | 209_E | 1.217 | 0.72 |
| 244_I | 248_V | 1.212 | 0.72 |
| 157_M | 165_G | 1.211 | 0.72 |
| 114_S | 121_Y | 1.201 | 0.71 |
| 195_K | 201_M | 1.197 | 0.70 |
| 43_G | 49_Y | 1.180 | 0.69 |
| 95_E | 101_F | 1.172 | 0.68 |
| 162_G | 165_G | 1.165 | 0.67 |
| 168_D | 172_F | 1.160 | 0.67 |
| 46_V | 116_L | 1.159 | 0.67 |
| 90_V | 93_A | 1.156 | 0.66 |
| 267_K | 270_M | 1.152 | 0.66 |
| 106_D | 111_A | 1.148 | 0.66 |
| 261_T | 264_W | 1.146 | 0.65 |
| 155_K | 160_N | 1.145 | 0.65 |
| 98_A | 103_V | 1.138 | 0.65 |
| 109_G | 118_Y | 1.134 | 0.64 |
| 308_F | 313_G | 1.133 | 0.64 |
| 168_D | 171_T | 1.132 | 0.64 |
| 35_I | 39_E | 1.129 | 0.64 |
| 50_F | 53_L | 1.125 | 0.63 |
| 47_A | 55_W | 1.120 | 0.63 |
| 79_G | 84_S | 1.118 | 0.63 |
| 70_L | 138_Y | 1.117 | 0.63 |
| 305_G | 308_F | 1.114 | 0.62 |
| 160_N | 163_D | 1.107 | 0.62 |
| 308_F | 312_L | 1.106 | 0.61 |
| 133_R | 136_L | 1.102 | 0.61 |
| 177_K | 184_Y | 1.101 | 0.61 |
| 180_T | 203_F | 1.100 | 0.61 |
| 153_V | 162_G | 1.100 | 0.61 |
| 43_G | 74_P | 1.095 | 0.60 |
| 102_G | 106_D | 1.090 | 0.60 |
| 143_I | 146_I | 1.083 | 0.59 |
| 227_F | 230_N | 1.083 | 0.59 |
| 241_G | 247_A | 1.077 | 0.58 |
| 184_Y | 239_G | 1.077 | 0.58 |
| 147_G | 150_F | 1.076 | 0.58 |
| 12_K | 15_A | 1.073 | 0.58 |
| 84_S | 89_T | 1.070 | 0.58 |
| 150_F | 209_E | 1.069 | 0.57 |
| 116_L | 121_Y | 1.066 | 0.57 |
| 47_A | 54_R | 1.059 | 0.56 |
| 237_L | 245_F | 1.058 | 0.56 |
| 114_S | 117_F | 1.058 | 0.56 |
| 292_E | 306_R | 1.057 | 0.56 |
| 278_G | 311_L | 1.054 | 0.56 |
| 35_I | 54_R | 1.054 | 0.56 |
| 307_I | 311_L | 1.046 | 0.55 |
| 169_D | 172_F | 1.045 | 0.55 |
| 70_L | 224_F | 1.043 | 0.55 |
| 107_F | 117_F | 1.042 | 0.55 |
| 188_N | 192_A | 1.042 | 0.55 |
| 137_S | 141_V | 1.041 | 0.54 |
| 134_L | 137_S | 1.038 | 0.54 |
| 50_F | 74_P | 1.037 | 0.54 |
| 50_F | 60_N | 1.036 | 0.54 |
| 141_V | 146_I | 1.036 | 0.54 |
| 205_E | 297_L | 1.035 | 0.54 |
| 83_G | 89_T | 1.035 | 0.54 |
| 246_W | 249_K | 1.029 | 0.53 |
| 156_A | 162_G | 1.027 | 0.53 |
| 43_G | 52_F | 1.027 | 0.53 |
| 10_M | 13_K | 1.026 | 0.53 |
| 187_G | 192_A | 1.026 | 0.53 |
| 308_F | 314_N | 1.025 | 0.53 |
| 227_F | 234_F | 1.025 | 0.53 |
| 241_G | 244_I | 1.023 | 0.53 |
| 244_I | 295_H | 1.020 | 0.52 |
| 240_S | 244_I | 1.020 | 0.52 |
| 43_G | 60_N | 1.019 | 0.52 |
| 99_A | 102_G | 1.019 | 0.52 |
| 223_R | 226_R | 1.017 | 0.52 |
| 72_M | 76_Y | 1.017 | 0.52 |
| 30_P | 40_S | 1.016 | 0.52 |
| 8_M | 11_A | 1.015 | 0.52 |
| 11_A | 15_A | 1.013 | 0.51 |
| 43_G | 46_V | 1.012 | 0.51 |
| 266_E | 269_E | 1.012 | 0.51 |
| 94_E | 97_S | 1.010 | 0.51 |
| 145_C | 149_S | 1.010 | 0.51 |
| 234_F | 237_L | 1.009 | 0.51 |
| 36_K | 39_E | 1.008 | 0.51 |
| 156_A | 161_I | 1.006 | 0.51 |
| 166_G | 169_D | 1.006 | 0.51 |
| 54_R | 117_F | 1.004 | 0.50 |
| 226_R | 233_V | 1.002 | 0.50 |
| 99_A | 103_V | 1.001 | 0.50 |
| 220_H | 231_F | 1.000 | 0.50 |
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 | |
| 4wisA | 2 | 0.7196 | 89 | 0.952 | Contact Map |
| 4x3iA | 1 | 0 | 25.9 | 0.971 | Contact Map |
| 4cbcA | 4 | 0.2866 | 20.3 | 0.972 | Contact Map |
| 3wu2M | 2 | 0.1028 | 13.6 | 0.974 | Contact Map |
| 4ltoA | 4 | 0.405 | 8.3 | 0.976 | Contact Map |
| 3effK | 4 | 0.4299 | 6.4 | 0.978 | Contact Map |
| 3bo0B | 1 | 0.1931 | 5.2 | 0.979 | Contact Map |
| 1yo5C | 1 | 0.1246 | 4.7 | 0.979 | Contact Map |
| 3pjsK | 4 | 0.433 | 4.7 | 0.979 | Contact Map |
| 2igrA | 1 | 0.1028 | 4.2 | 0.979 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)