| his2 |
| ID: | 1516928233 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 335 (283) | ||
| Sequences: | 301 (229.7) | ||
| Seq/Len: | 1.064 | ||
| Nf(neff/√len): | 13.7 |
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: 1.064).
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 |
| 25_Q | 29_L | 2.753 | 1.00 |
| 35_C | 124_F | 2.280 | 0.99 |
| 25_Q | 28_N | 2.275 | 0.99 |
| 37_T | 124_F | 2.227 | 0.98 |
| 20_D | 84_Y | 2.174 | 0.98 |
| 176_L | 309_S | 2.134 | 0.98 |
| 167_Y | 227_R | 2.129 | 0.97 |
| 243_T | 290_V | 2.052 | 0.97 |
| 260_C | 271_F | 2.039 | 0.97 |
| 8_S | 19_L | 1.984 | 0.96 |
| 230_Q | 266_H | 1.970 | 0.96 |
| 77_A | 96_I | 1.964 | 0.95 |
| 271_F | 300_L | 1.955 | 0.95 |
| 27_V | 92_T | 1.953 | 0.95 |
| 239_I | 263_V | 1.877 | 0.94 |
| 257_K | 296_D | 1.855 | 0.93 |
| 183_L | 254_Y | 1.850 | 0.93 |
| 6_S | 34_Y | 1.838 | 0.93 |
| 12_S | 15_G | 1.795 | 0.92 |
| 84_Y | 92_T | 1.793 | 0.92 |
| 183_L | 244_S | 1.760 | 0.91 |
| 20_D | 83_R | 1.745 | 0.90 |
| 126_V | 179_G | 1.732 | 0.90 |
| 76_H | 79_E | 1.645 | 0.86 |
| 247_R | 283_V | 1.637 | 0.86 |
| 187_F | 284_G | 1.610 | 0.85 |
| 229_L | 239_I | 1.589 | 0.83 |
| 17_D | 280_V | 1.560 | 0.82 |
| 244_S | 248_K | 1.543 | 0.81 |
| 246_L | 253_P | 1.516 | 0.79 |
| 73_F | 94_F | 1.474 | 0.77 |
| 229_L | 259_L | 1.472 | 0.76 |
| 297_V | 300_L | 1.469 | 0.76 |
| 263_V | 268_G | 1.434 | 0.74 |
| 128_S | 179_G | 1.430 | 0.74 |
| 40_I | 101_E | 1.425 | 0.73 |
| 27_V | 84_Y | 1.417 | 0.73 |
| 164_Q | 230_Q | 1.411 | 0.72 |
| 127_G | 182_D | 1.400 | 0.71 |
| 78_Q | 81_K | 1.397 | 0.71 |
| 138_D | 242_N | 1.358 | 0.68 |
| 229_L | 232_I | 1.354 | 0.68 |
| 102_S | 228_N | 1.346 | 0.67 |
| 129_V | 177_V | 1.328 | 0.65 |
| 244_S | 254_Y | 1.325 | 0.65 |
| 183_L | 186_L | 1.318 | 0.65 |
| 241_I | 273_L | 1.307 | 0.64 |
| 23_V | 92_T | 1.304 | 0.63 |
| 38_E | 177_V | 1.304 | 0.63 |
| 101_E | 185_K | 1.297 | 0.63 |
| 267_C | 270_R | 1.294 | 0.62 |
| 10_D | 15_G | 1.288 | 0.62 |
| 225_V | 259_L | 1.277 | 0.61 |
| 14_H | 41_P | 1.277 | 0.61 |
| 22_V | 98_M | 1.267 | 0.60 |
| 182_D | 240_E | 1.263 | 0.60 |
| 245_A | 254_Y | 1.262 | 0.60 |
| 135_I | 247_R | 1.257 | 0.59 |
| 226_V | 265_K | 1.242 | 0.58 |
| 267_C | 277_A | 1.241 | 0.58 |
| 12_S | 41_P | 1.221 | 0.56 |
| 19_L | 80_I | 1.216 | 0.55 |
| 77_A | 94_F | 1.209 | 0.55 |
| 294_I | 300_L | 1.205 | 0.54 |
| 244_S | 284_G | 1.205 | 0.54 |
| 243_T | 285_V | 1.202 | 0.54 |
| 42_R | 49_Y | 1.195 | 0.53 |
| 264_K | 300_L | 1.190 | 0.53 |
| 14_H | 244_S | 1.180 | 0.52 |
| 33_T | 95_I | 1.172 | 0.51 |
| 76_H | 80_I | 1.168 | 0.51 |
| 26_V | 36_L | 1.167 | 0.51 |
| 170_L | 228_N | 1.157 | 0.50 |
| 241_I | 294_I | 1.151 | 0.49 |
| 286_C | 289_K | 1.147 | 0.49 |
| 10_D | 38_E | 1.145 | 0.49 |
| 95_I | 122_L | 1.145 | 0.49 |
| 262_L | 265_K | 1.145 | 0.49 |
| 22_V | 275_D | 1.144 | 0.49 |
| 27_V | 94_F | 1.138 | 0.48 |
| 258_T | 262_L | 1.135 | 0.48 |
| 136_P | 244_S | 1.132 | 0.47 |
| 185_K | 252_E | 1.130 | 0.47 |
| 42_R | 63_I | 1.127 | 0.47 |
| 170_L | 178_V | 1.126 | 0.47 |
| 14_H | 221_I | 1.125 | 0.47 |
| 183_L | 245_A | 1.116 | 0.46 |
| 41_P | 63_I | 1.116 | 0.46 |
| 80_I | 84_Y | 1.111 | 0.45 |
| 238_A | 272_V | 1.105 | 0.45 |
| 242_N | 274_S | 1.102 | 0.45 |
| 169_M | 178_V | 1.101 | 0.45 |
| 167_Y | 228_N | 1.097 | 0.44 |
| 236_G | 311_S | 1.095 | 0.44 |
| 119_N | 271_F | 1.095 | 0.44 |
| 27_V | 91_R | 1.091 | 0.44 |
| 35_C | 177_V | 1.090 | 0.43 |
| 40_I | 179_G | 1.088 | 0.43 |
| 128_S | 138_D | 1.088 | 0.43 |
| 35_C | 240_E | 1.084 | 0.43 |
| 3_S | 274_S | 1.079 | 0.42 |
| 124_F | 127_G | 1.078 | 0.42 |
| 3_S | 238_A | 1.077 | 0.42 |
| 101_E | 121_I | 1.076 | 0.42 |
| 27_V | 83_R | 1.073 | 0.42 |
| 20_D | 27_V | 1.073 | 0.42 |
| 186_L | 245_A | 1.072 | 0.42 |
| 5_H | 39_H | 1.071 | 0.42 |
| 15_G | 41_P | 1.071 | 0.42 |
| 233_D | 270_R | 1.059 | 0.41 |
| 82_T | 85_A | 1.057 | 0.40 |
| 229_L | 266_H | 1.052 | 0.40 |
| 17_D | 63_I | 1.052 | 0.40 |
| 257_K | 297_V | 1.052 | 0.40 |
| 23_V | 27_V | 1.051 | 0.40 |
| 23_V | 80_I | 1.050 | 0.40 |
| 304_C | 311_S | 1.049 | 0.40 |
| 100_I | 111_A | 1.048 | 0.40 |
| 74_M | 120_D | 1.042 | 0.39 |
| 82_T | 113_R | 1.041 | 0.39 |
| 290_V | 300_L | 1.041 | 0.39 |
| 36_L | 254_Y | 1.041 | 0.39 |
| 31_F | 306_L | 1.041 | 0.39 |
| 123_K | 260_C | 1.038 | 0.39 |
| 171_I | 235_Y | 1.038 | 0.39 |
| 113_R | 292_K | 1.036 | 0.39 |
| 34_Y | 144_W | 1.033 | 0.38 |
| 103_C | 262_L | 1.032 | 0.38 |
| 128_S | 278_H | 1.031 | 0.38 |
| 156_K | 264_K | 1.031 | 0.38 |
| 247_R | 254_Y | 1.029 | 0.38 |
| 102_S | 169_M | 1.028 | 0.38 |
| 3_S | 275_D | 1.025 | 0.38 |
| 14_H | 284_G | 1.025 | 0.38 |
| 46_K | 270_R | 1.019 | 0.37 |
| 43_I | 229_L | 1.018 | 0.37 |
| 129_V | 310_Q | 1.017 | 0.37 |
| 19_L | 40_I | 1.012 | 0.36 |
| 122_L | 287_Y | 1.008 | 0.36 |
| 4_H | 33_T | 1.005 | 0.36 |
| 26_V | 127_G | 1.002 | 0.36 |
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 | |
| 4gc3A | 1 | 0.7701 | 100 | 0.564 | Contact Map |
| 3dcpA | 3 | 0.7851 | 100 | 0.584 | Contact Map |
| 2yxoA | 2 | 0.7881 | 100 | 0.584 | Contact Map |
| 3b0xA | 1 | 0.7045 | 100 | 0.684 | Contact Map |
| 2w9mA | 2 | 0.6836 | 100 | 0.691 | Contact Map |
| 1m65A | 1 | 0.6746 | 100 | 0.694 | Contact Map |
| 3qy7A | 1 | 0.7224 | 100 | 0.696 | Contact Map |
| 2wjeA | 1 | 0.7015 | 100 | 0.702 | Contact Map |
| 2anuA | 6 | 0.609 | 100 | 0.74 | Contact Map |
| 1v77A | 1 | 0.5791 | 99.9 | 0.748 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)