| Ypq1 |
| ID: | 1494967256 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 308 (296) | ||
| Sequences: | 421 (305.9) | ||
| Seq/Len: | 1.422 | ||
| Nf(neff/√len): | 17.8 |
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: 1.422).
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 |
| 216_G | 278_W | 2.660 | 1.00 |
| 235_F | 238_K | 2.364 | 0.99 |
| 36_N | 90_Q | 2.043 | 0.98 |
| 231_I | 292_I | 1.990 | 0.98 |
| 295_Q | 299_Y | 1.968 | 0.97 |
| 231_I | 291_V | 1.778 | 0.95 |
| 53_W | 57_D | 1.721 | 0.93 |
| 238_K | 299_Y | 1.720 | 0.93 |
| 224_L | 284_G | 1.710 | 0.93 |
| 25_W | 36_N | 1.701 | 0.93 |
| 235_F | 299_Y | 1.693 | 0.93 |
| 41_S | 44_G | 1.667 | 0.92 |
| 57_D | 227_R | 1.665 | 0.92 |
| 228_I | 232_L | 1.622 | 0.90 |
| 66_M | 212_A | 1.600 | 0.90 |
| 49_F | 94_Y | 1.534 | 0.87 |
| 67_Q | 212_A | 1.506 | 0.85 |
| 79_Y | 84_D | 1.474 | 0.84 |
| 29_F | 251_A | 1.472 | 0.84 |
| 216_G | 288_M | 1.466 | 0.83 |
| 219_S | 296_F | 1.442 | 0.82 |
| 223_Y | 227_R | 1.442 | 0.82 |
| 53_W | 223_Y | 1.433 | 0.81 |
| 57_D | 255_N | 1.425 | 0.81 |
| 63_G | 67_Q | 1.420 | 0.80 |
| 57_D | 223_Y | 1.417 | 0.80 |
| 53_W | 227_R | 1.412 | 0.80 |
| 226_S | 251_A | 1.399 | 0.79 |
| 72_T | 278_W | 1.381 | 0.78 |
| 84_D | 281_G | 1.375 | 0.77 |
| 285_T | 293_F | 1.367 | 0.77 |
| 69_L | 237_R | 1.367 | 0.77 |
| 22_I | 45_L | 1.360 | 0.76 |
| 40_K | 44_G | 1.351 | 0.76 |
| 18_G | 31_P | 1.347 | 0.75 |
| 53_W | 255_N | 1.341 | 0.75 |
| 72_T | 216_G | 1.333 | 0.74 |
| 32_Q | 230_Q | 1.325 | 0.74 |
| 223_Y | 255_N | 1.316 | 0.73 |
| 227_R | 255_N | 1.313 | 0.73 |
| 76_L | 285_T | 1.310 | 0.72 |
| 292_I | 295_Q | 1.310 | 0.72 |
| 278_W | 288_M | 1.293 | 0.71 |
| 281_G | 285_T | 1.285 | 0.70 |
| 80_Y | 261_S | 1.266 | 0.69 |
| 66_M | 211_M | 1.265 | 0.69 |
| 57_D | 60_N | 1.261 | 0.68 |
| 22_I | 222_L | 1.255 | 0.68 |
| 73_M | 277_S | 1.245 | 0.67 |
| 219_S | 226_S | 1.241 | 0.67 |
| 69_L | 73_M | 1.237 | 0.66 |
| 36_N | 87_L | 1.235 | 0.66 |
| 228_I | 288_M | 1.233 | 0.66 |
| 15_G | 19_S | 1.229 | 0.65 |
| 53_W | 63_G | 1.223 | 0.65 |
| 123_N | 127_P | 1.220 | 0.65 |
| 32_Q | 234_N | 1.216 | 0.64 |
| 248_F | 255_N | 1.210 | 0.64 |
| 255_N | 258_F | 1.205 | 0.63 |
| 69_L | 212_A | 1.205 | 0.63 |
| 81_T | 220_A | 1.202 | 0.63 |
| 255_N | 261_S | 1.199 | 0.63 |
| 25_W | 251_A | 1.197 | 0.62 |
| 60_N | 255_N | 1.196 | 0.62 |
| 64_A | 74_I | 1.195 | 0.62 |
| 231_I | 240_C | 1.191 | 0.62 |
| 231_I | 279_L | 1.188 | 0.62 |
| 28_V | 73_M | 1.186 | 0.61 |
| 124_E | 129_L | 1.173 | 0.60 |
| 258_F | 284_G | 1.169 | 0.60 |
| 67_Q | 79_Y | 1.169 | 0.60 |
| 49_F | 53_W | 1.162 | 0.59 |
| 21_S | 227_R | 1.156 | 0.58 |
| 230_Q | 295_Q | 1.145 | 0.57 |
| 21_S | 57_D | 1.143 | 0.57 |
| 50_V | 56_G | 1.142 | 0.57 |
| 79_Y | 226_S | 1.142 | 0.57 |
| 29_F | 226_S | 1.142 | 0.57 |
| 18_G | 32_Q | 1.138 | 0.57 |
| 21_S | 223_Y | 1.128 | 0.56 |
| 234_N | 295_Q | 1.128 | 0.56 |
| 17_S | 75_I | 1.126 | 0.55 |
| 50_V | 227_R | 1.120 | 0.55 |
| 56_G | 223_Y | 1.117 | 0.54 |
| 57_D | 90_Q | 1.117 | 0.54 |
| 72_T | 76_L | 1.117 | 0.54 |
| 244_S | 281_G | 1.116 | 0.54 |
| 247_F | 265_I | 1.114 | 0.54 |
| 71_S | 77_A | 1.109 | 0.54 |
| 71_S | 75_I | 1.102 | 0.53 |
| 84_D | 227_R | 1.101 | 0.53 |
| 28_V | 251_A | 1.100 | 0.53 |
| 60_N | 223_Y | 1.097 | 0.52 |
| 25_W | 29_F | 1.091 | 0.52 |
| 131_S | 134_Q | 1.086 | 0.51 |
| 122_F | 139_D | 1.085 | 0.51 |
| 54_L | 88_L | 1.083 | 0.51 |
| 230_Q | 234_N | 1.082 | 0.51 |
| 247_F | 278_W | 1.081 | 0.51 |
| 25_W | 28_V | 1.078 | 0.51 |
| 41_S | 263_I | 1.078 | 0.51 |
| 53_W | 281_G | 1.076 | 0.50 |
| 18_G | 60_N | 1.074 | 0.50 |
| 80_Y | 227_R | 1.074 | 0.50 |
| 223_Y | 258_F | 1.072 | 0.50 |
| 237_R | 240_C | 1.070 | 0.50 |
| 73_M | 212_A | 1.067 | 0.49 |
| 258_F | 261_S | 1.066 | 0.49 |
| 281_G | 284_G | 1.066 | 0.49 |
| 223_Y | 261_S | 1.061 | 0.49 |
| 232_L | 236_K | 1.061 | 0.49 |
| 56_G | 90_Q | 1.058 | 0.48 |
| 35_E | 244_S | 1.056 | 0.48 |
| 60_N | 227_R | 1.055 | 0.48 |
| 45_L | 69_L | 1.053 | 0.48 |
| 31_P | 36_N | 1.049 | 0.48 |
| 28_V | 226_S | 1.049 | 0.48 |
| 227_R | 261_S | 1.047 | 0.47 |
| 226_S | 288_M | 1.047 | 0.47 |
| 29_F | 80_Y | 1.045 | 0.47 |
| 56_G | 261_S | 1.043 | 0.47 |
| 18_G | 56_G | 1.043 | 0.47 |
| 36_N | 60_N | 1.041 | 0.47 |
| 46_S | 87_L | 1.037 | 0.46 |
| 252_C | 286_L | 1.037 | 0.46 |
| 21_S | 258_F | 1.037 | 0.46 |
| 263_I | 280_V | 1.037 | 0.46 |
| 69_L | 219_S | 1.036 | 0.46 |
| 78_A | 260_F | 1.032 | 0.46 |
| 53_W | 80_Y | 1.031 | 0.46 |
| 230_Q | 242_G | 1.030 | 0.46 |
| 76_L | 219_S | 1.029 | 0.46 |
| 64_A | 251_A | 1.028 | 0.45 |
| 223_Y | 251_A | 1.028 | 0.45 |
| 217_Y | 223_Y | 1.027 | 0.45 |
| 53_W | 94_Y | 1.027 | 0.45 |
| 250_F | 259_I | 1.026 | 0.45 |
| 57_D | 261_S | 1.025 | 0.45 |
| 249_L | 292_I | 1.022 | 0.45 |
| 70_L | 262_V | 1.021 | 0.45 |
| 60_N | 251_A | 1.017 | 0.44 |
| 219_S | 251_A | 1.017 | 0.44 |
| 53_W | 60_N | 1.017 | 0.44 |
| 178_G | 182_W | 1.014 | 0.44 |
| 53_W | 258_F | 1.014 | 0.44 |
| 251_A | 255_N | 1.013 | 0.44 |
| 84_D | 226_S | 1.012 | 0.44 |
| 26_I | 84_D | 1.010 | 0.44 |
| 248_F | 281_G | 1.009 | 0.44 |
| 29_F | 247_F | 1.007 | 0.43 |
| 234_N | 242_G | 1.002 | 0.43 |
| 126_Q | 131_S | 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 | |
| 4qncA | 2 | 0.2662 | 99.6 | 0.806 | Contact Map |
| 4x5mA | 3 | 0.2987 | 99.6 | 0.806 | Contact Map |
| 4rngA | 6 | 0.2695 | 99.1 | 0.85 | Contact Map |
| 4qndA | 1 | 0.3084 | 99 | 0.856 | Contact Map |
| 4pypA | 1 | 0.3052 | 26.1 | 0.962 | Contact Map |
| 1v54M | 2 | 0.1169 | 12.5 | 0.967 | Contact Map |
| 2y69M | 2 | 0.1169 | 12.1 | 0.967 | Contact Map |
| 3giaA | 1 | 0.3377 | 9.7 | 0.969 | Contact Map |
| 4djkA | 2 | 0.3474 | 7.5 | 0.97 | Contact Map |
| 3m73A | 1 | 0.2305 | 6.5 | 0.971 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)