| B8XCH5_TM |
| ID: | 1485956382 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 292 (291) | ||
| Sequences: | 412 (202.7) | ||
| Seq/Len: | 1.416 | ||
| Nf(neff/√len): | 11.9 |
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: 1.416).
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 |
| 93_I | 96_V | 1.989 | 0.98 |
| 123_H | 266_H | 1.986 | 0.98 |
| 89_N | 92_R | 1.924 | 0.97 |
| 126_Y | 256_A | 1.906 | 0.97 |
| 5_I | 98_A | 1.875 | 0.96 |
| 215_A | 219_E | 1.782 | 0.95 |
| 18_P | 53_M | 1.736 | 0.94 |
| 178_D | 193_I | 1.623 | 0.90 |
| 67_P | 71_R | 1.547 | 0.87 |
| 196_R | 215_A | 1.542 | 0.87 |
| 172_V | 207_V | 1.505 | 0.85 |
| 84_R | 199_R | 1.483 | 0.84 |
| 117_V | 124_I | 1.452 | 0.82 |
| 74_L | 264_L | 1.420 | 0.80 |
| 101_V | 105_K | 1.408 | 0.80 |
| 163_D | 200_L | 1.378 | 0.78 |
| 19_D | 49_A | 1.377 | 0.77 |
| 39_G | 42_Q | 1.369 | 0.77 |
| 127_L | 134_D | 1.364 | 0.77 |
| 142_L | 178_D | 1.343 | 0.75 |
| 123_H | 261_F | 1.332 | 0.74 |
| 17_L | 54_V | 1.331 | 0.74 |
| 18_P | 22_A | 1.315 | 0.73 |
| 93_I | 264_L | 1.315 | 0.73 |
| 146_M | 149_V | 1.310 | 0.72 |
| 253_K | 261_F | 1.303 | 0.72 |
| 210_I | 218_G | 1.301 | 0.72 |
| 66_G | 247_L | 1.299 | 0.71 |
| 246_V | 255_V | 1.291 | 0.71 |
| 74_L | 80_A | 1.289 | 0.71 |
| 129_L | 133_P | 1.287 | 0.70 |
| 126_Y | 249_A | 1.286 | 0.70 |
| 139_T | 143_Y | 1.286 | 0.70 |
| 281_F | 284_L | 1.282 | 0.70 |
| 44_D | 120_V | 1.282 | 0.70 |
| 24_Y | 27_P | 1.271 | 0.69 |
| 9_V | 163_D | 1.269 | 0.69 |
| 17_L | 78_S | 1.266 | 0.69 |
| 132_Y | 264_L | 1.262 | 0.68 |
| 268_M | 272_T | 1.259 | 0.68 |
| 183_T | 187_S | 1.258 | 0.68 |
| 28_L | 169_A | 1.252 | 0.67 |
| 96_V | 218_G | 1.249 | 0.67 |
| 52_K | 253_K | 1.244 | 0.67 |
| 15_S | 38_L | 1.241 | 0.66 |
| 51_T | 71_R | 1.241 | 0.66 |
| 261_F | 266_H | 1.237 | 0.66 |
| 53_M | 276_A | 1.230 | 0.65 |
| 20_V | 72_Y | 1.230 | 0.65 |
| 61_A | 252_A | 1.209 | 0.63 |
| 43_Q | 203_L | 1.208 | 0.63 |
| 84_R | 197_Y | 1.204 | 0.63 |
| 127_L | 257_V | 1.201 | 0.63 |
| 118_T | 123_H | 1.196 | 0.62 |
| 188_R | 194_R | 1.193 | 0.62 |
| 196_R | 212_G | 1.192 | 0.62 |
| 196_R | 219_E | 1.190 | 0.62 |
| 221_I | 243_I | 1.189 | 0.61 |
| 17_L | 26_Q | 1.188 | 0.61 |
| 101_V | 144_V | 1.188 | 0.61 |
| 16_L | 81_W | 1.187 | 0.61 |
| 28_L | 42_Q | 1.187 | 0.61 |
| 252_A | 257_V | 1.187 | 0.61 |
| 178_D | 214_F | 1.184 | 0.61 |
| 125_L | 128_V | 1.181 | 0.61 |
| 163_D | 166_L | 1.179 | 0.61 |
| 17_L | 45_A | 1.178 | 0.60 |
| 16_L | 221_I | 1.178 | 0.60 |
| 39_G | 286_S | 1.177 | 0.60 |
| 129_L | 170_E | 1.177 | 0.60 |
| 39_G | 49_A | 1.168 | 0.59 |
| 74_L | 163_D | 1.167 | 0.59 |
| 119_T | 123_H | 1.167 | 0.59 |
| 51_T | 54_V | 1.164 | 0.59 |
| 93_I | 257_V | 1.161 | 0.59 |
| 33_H | 37_P | 1.159 | 0.59 |
| 56_A | 273_M | 1.157 | 0.58 |
| 73_M | 89_N | 1.149 | 0.58 |
| 149_V | 291_L | 1.140 | 0.57 |
| 52_K | 78_S | 1.140 | 0.57 |
| 15_S | 51_T | 1.138 | 0.56 |
| 2_M | 42_Q | 1.132 | 0.56 |
| 197_Y | 201_R | 1.131 | 0.56 |
| 48_G | 255_V | 1.130 | 0.56 |
| 30_P | 37_P | 1.128 | 0.55 |
| 42_Q | 45_A | 1.121 | 0.55 |
| 119_T | 235_L | 1.118 | 0.54 |
| 107_L | 111_R | 1.117 | 0.54 |
| 97_L | 108_D | 1.114 | 0.54 |
| 85_K | 110_I | 1.113 | 0.54 |
| 58_L | 64_P | 1.112 | 0.54 |
| 4_E | 85_K | 1.112 | 0.54 |
| 170_E | 237_I | 1.112 | 0.54 |
| 266_H | 274_P | 1.111 | 0.54 |
| 19_D | 225_V | 1.107 | 0.53 |
| 287_L | 290_R | 1.106 | 0.53 |
| 152_Y | 230_P | 1.105 | 0.53 |
| 110_I | 122_V | 1.104 | 0.53 |
| 39_G | 43_Q | 1.103 | 0.53 |
| 103_L | 238_A | 1.102 | 0.53 |
| 93_I | 288_S | 1.100 | 0.53 |
| 84_R | 200_L | 1.099 | 0.53 |
| 193_I | 261_F | 1.098 | 0.52 |
| 102_G | 107_L | 1.098 | 0.52 |
| 45_A | 51_T | 1.094 | 0.52 |
| 30_P | 34_Y | 1.092 | 0.52 |
| 193_I | 196_R | 1.092 | 0.52 |
| 48_G | 52_K | 1.088 | 0.51 |
| 101_V | 114_R | 1.088 | 0.51 |
| 122_V | 131_W | 1.086 | 0.51 |
| 51_T | 55_A | 1.085 | 0.51 |
| 98_A | 186_S | 1.082 | 0.51 |
| 210_I | 217_Q | 1.082 | 0.51 |
| 93_I | 211_L | 1.080 | 0.51 |
| 35_I | 59_A | 1.075 | 0.50 |
| 38_L | 59_A | 1.074 | 0.50 |
| 41_A | 48_G | 1.069 | 0.49 |
| 6_E | 223_A | 1.068 | 0.49 |
| 17_L | 44_D | 1.067 | 0.49 |
| 1_K | 38_L | 1.065 | 0.49 |
| 267_P | 270_R | 1.064 | 0.49 |
| 71_R | 80_A | 1.064 | 0.49 |
| 11_F | 24_Y | 1.063 | 0.49 |
| 4_E | 10_R | 1.061 | 0.49 |
| 177_L | 181_F | 1.059 | 0.48 |
| 25_G | 44_D | 1.059 | 0.48 |
| 212_G | 215_A | 1.057 | 0.48 |
| 197_Y | 204_A | 1.056 | 0.48 |
| 165_R | 176_E | 1.055 | 0.48 |
| 210_I | 216_A | 1.055 | 0.48 |
| 199_R | 204_A | 1.054 | 0.48 |
| 253_K | 258_A | 1.054 | 0.48 |
| 280_F | 283_R | 1.053 | 0.48 |
| 12_A | 81_W | 1.050 | 0.48 |
| 92_R | 215_A | 1.047 | 0.47 |
| 11_F | 185_P | 1.047 | 0.47 |
| 10_R | 193_I | 1.047 | 0.47 |
| 54_V | 127_L | 1.045 | 0.47 |
| 15_S | 36_R | 1.045 | 0.47 |
| 137_V | 252_A | 1.041 | 0.47 |
| 49_A | 290_R | 1.036 | 0.46 |
| 83_M | 87_K | 1.035 | 0.46 |
| 231_R | 248_Y | 1.035 | 0.46 |
| 59_A | 287_L | 1.032 | 0.46 |
| 228_R | 236_F | 1.028 | 0.45 |
| 217_Q | 282_R | 1.028 | 0.45 |
| 126_Y | 134_D | 1.027 | 0.45 |
| 5_I | 195_A | 1.026 | 0.45 |
| 69_V | 140_A | 1.024 | 0.45 |
| 175_D | 179_E | 1.023 | 0.45 |
| 204_A | 212_G | 1.022 | 0.45 |
| 89_N | 212_G | 1.021 | 0.45 |
| 11_F | 196_R | 1.021 | 0.45 |
| 55_A | 131_W | 1.020 | 0.45 |
| 232_A | 274_P | 1.018 | 0.44 |
| 147_I | 235_L | 1.017 | 0.44 |
| 229_D | 265_R | 1.017 | 0.44 |
| 38_L | 42_Q | 1.016 | 0.44 |
| 94_V | 292_I | 1.013 | 0.44 |
| 74_L | 108_D | 1.012 | 0.44 |
| 238_A | 258_A | 1.011 | 0.44 |
| 197_Y | 200_L | 1.009 | 0.43 |
| 220_R | 280_F | 1.007 | 0.43 |
| 81_W | 243_I | 1.004 | 0.43 |
| 86_S | 227_W | 1.004 | 0.43 |
| 22_A | 38_L | 1.004 | 0.43 |
| 227_W | 231_R | 1.002 | 0.43 |
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 | |
| 3hd7A | 2 | 0.3014 | 12.8 | 0.976 | Contact Map |
| 2xzeQ | 2 | 0.0788 | 10.4 | 0.977 | Contact Map |
| 2kncA | 1 | 0.1781 | 7.1 | 0.979 | Contact Map |
| 4r0cA | 4 | 0 | 5.9 | 0.979 | Contact Map |
| 1q2fA | 1 | 0.1096 | 5.6 | 0.98 | Contact Map |
| 1lypA | 1 | 0.0822 | 5.2 | 0.98 | Contact Map |
| 2kogA | 1 | 0.387 | 5.2 | 0.98 | Contact Map |
| 4aw6A | 4 | 0.5651 | 5.2 | 0.98 | Contact Map |
| 3s4wB | 1 | 0.4212 | 4.7 | 0.98 | Contact Map |
| 1ko6B | 2 | 0.0205 | 4.5 | 0.981 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)