| Mth_NT_TM_and_loop |
| ID: | 1485866144 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 261 (241) | ||
| Sequences: | 924 (827.6) | ||
| Seq/Len: | 3.834 | ||
| Nf(neff/√len): | 53.3 |
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: 3.834).
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 |
| 164_G | 193_M | 3.231 | 1.00 |
| 103_G | 120_L | 3.003 | 1.00 |
| 234_R | 251_T | 2.778 | 1.00 |
| 169_P | 184_L | 2.666 | 1.00 |
| 19_L | 73_V | 2.478 | 1.00 |
| 256_D | 260_N | 2.250 | 1.00 |
| 178_F | 183_Y | 2.202 | 1.00 |
| 21_R | 186_R | 2.156 | 1.00 |
| 101_L | 164_G | 2.153 | 1.00 |
| 12_A | 69_L | 2.045 | 1.00 |
| 13_Y | 79_I | 2.030 | 1.00 |
| 228_A | 240_A | 2.022 | 1.00 |
| 102_T | 159_V | 1.997 | 1.00 |
| 180_Y | 184_L | 1.942 | 1.00 |
| 15_V | 73_V | 1.929 | 1.00 |
| 238_I | 241_A | 1.862 | 1.00 |
| 8_W | 11_V | 1.756 | 0.99 |
| 119_T | 189_I | 1.754 | 0.99 |
| 183_Y | 187_R | 1.716 | 0.99 |
| 251_T | 254_D | 1.706 | 0.99 |
| 255_S | 259_K | 1.695 | 0.99 |
| 234_R | 254_D | 1.670 | 0.99 |
| 166_L | 191_N | 1.661 | 0.99 |
| 13_Y | 17_L | 1.588 | 0.98 |
| 231_L | 235_Q | 1.578 | 0.98 |
| 102_T | 161_R | 1.576 | 0.98 |
| 224_K | 240_A | 1.569 | 0.98 |
| 103_G | 142_I | 1.551 | 0.98 |
| 106_T | 121_A | 1.509 | 0.97 |
| 166_L | 169_P | 1.505 | 0.97 |
| 12_A | 73_V | 1.472 | 0.97 |
| 174_N | 178_F | 1.471 | 0.97 |
| 180_Y | 183_Y | 1.451 | 0.97 |
| 185_A | 190_Y | 1.430 | 0.96 |
| 219_A | 222_R | 1.430 | 0.96 |
| 238_I | 242_L | 1.424 | 0.96 |
| 175_P | 241_A | 1.421 | 0.96 |
| 234_R | 237_G | 1.390 | 0.95 |
| 252_D | 256_D | 1.359 | 0.95 |
| 103_G | 160_L | 1.323 | 0.93 |
| 158_D | 201_I | 1.317 | 0.93 |
| 184_L | 192_R | 1.310 | 0.93 |
| 119_T | 141_V | 1.303 | 0.93 |
| 169_P | 192_R | 1.295 | 0.92 |
| 104_M | 121_A | 1.283 | 0.92 |
| 102_T | 124_E | 1.266 | 0.91 |
| 21_R | 80_S | 1.257 | 0.91 |
| 233_P | 236_A | 1.235 | 0.90 |
| 41_P | 47_A | 1.229 | 0.90 |
| 154_Y | 160_L | 1.221 | 0.89 |
| 118_Y | 144_R | 1.220 | 0.89 |
| 155_H | 158_D | 1.217 | 0.89 |
| 105_V | 229_A | 1.208 | 0.89 |
| 4_R | 8_W | 1.206 | 0.88 |
| 77_F | 82_W | 1.205 | 0.88 |
| 239_L | 257_T | 1.204 | 0.88 |
| 169_P | 191_N | 1.202 | 0.88 |
| 250_L | 255_S | 1.200 | 0.88 |
| 100_D | 144_R | 1.181 | 0.87 |
| 95_R | 165_Q | 1.173 | 0.87 |
| 41_P | 45_A | 1.170 | 0.86 |
| 152_P | 237_G | 1.166 | 0.86 |
| 157_G | 245_G | 1.161 | 0.86 |
| 120_L | 195_L | 1.156 | 0.85 |
| 67_L | 206_K | 1.153 | 0.85 |
| 42_L | 47_A | 1.149 | 0.85 |
| 5_P | 8_W | 1.143 | 0.85 |
| 227_I | 240_A | 1.141 | 0.84 |
| 105_V | 120_L | 1.134 | 0.84 |
| 117_V | 145_R | 1.131 | 0.84 |
| 79_I | 83_D | 1.122 | 0.83 |
| 184_L | 189_I | 1.121 | 0.83 |
| 156_Y | 217_L | 1.115 | 0.83 |
| 195_L | 220_K | 1.106 | 0.82 |
| 118_Y | 193_M | 1.101 | 0.81 |
| 108_E | 220_K | 1.098 | 0.81 |
| 117_V | 143_Y | 1.093 | 0.81 |
| 157_G | 214_R | 1.088 | 0.80 |
| 93_G | 138_V | 1.088 | 0.80 |
| 235_Q | 243_L | 1.078 | 0.79 |
| 228_A | 247_V | 1.073 | 0.79 |
| 9_V | 72_F | 1.072 | 0.79 |
| 238_I | 250_L | 1.066 | 0.78 |
| 42_L | 88_Q | 1.066 | 0.78 |
| 237_G | 254_D | 1.063 | 0.78 |
| 5_P | 10_T | 1.062 | 0.78 |
| 215_L | 218_A | 1.057 | 0.78 |
| 142_I | 166_L | 1.055 | 0.77 |
| 68_L | 74_A | 1.046 | 0.77 |
| 104_M | 210_N | 1.043 | 0.76 |
| 45_A | 53_Y | 1.043 | 0.76 |
| 155_H | 218_A | 1.041 | 0.76 |
| 78_F | 242_L | 1.040 | 0.76 |
| 61_R | 68_L | 1.038 | 0.76 |
| 123_R | 159_V | 1.038 | 0.76 |
| 171_P | 179_D | 1.033 | 0.75 |
| 162_V | 197_D | 1.027 | 0.75 |
| 182_A | 186_R | 1.026 | 0.75 |
| 174_N | 177_E | 1.017 | 0.74 |
| 44_I | 49_W | 1.014 | 0.73 |
| 153_R | 229_A | 1.012 | 0.73 |
| 4_R | 7_L | 1.008 | 0.73 |
| 172_A | 220_K | 1.006 | 0.73 |
| 240_A | 244_F | 1.004 | 0.72 |
| 13_Y | 20_A | 1.003 | 0.72 |
| 20_A | 81_T | 1.002 | 0.72 |
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 | |
| 3kojA | 2 | 0.3257 | 12.4 | 0.948 | Contact Map |
| 4ev6A | 5 | 0.2222 | 7.2 | 0.953 | Contact Map |
| 4i0uA | 10 | 0.2146 | 6.8 | 0.953 | Contact Map |
| 4damA | 12 | 0.3985 | 4.5 | 0.957 | Contact Map |
| 1jb3A | 1 | 0.4866 | 4.4 | 0.957 | Contact Map |
| 3e0eA | 1 | 0.3295 | 4.1 | 0.958 | Contact Map |
| 2kbnA | 1 | 0.4138 | 4.1 | 0.958 | Contact Map |
| 4gn4B | 1 | 0.3831 | 4 | 0.958 | Contact Map |
| 3ullA | 2 | 0.3755 | 3.5 | 0.959 | Contact Map |
| 3vdyA | 2 | 0.3563 | 3.5 | 0.959 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)