| Btk_all_protein_e20_i8 |
| ID: | 1480603383 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 379 (377) | ||
| Sequences: | 1759 (1165.7) | ||
| Seq/Len: | 4.666 | ||
| Nf(neff/√len): | 60.0 |
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: 4.666).
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 |
| 222_C | 307_M | 3.609 | 1.00 |
| 139_G | 149_I | 3.278 | 1.00 |
| 229_M | 242_L | 3.098 | 1.00 |
| 355_H | 360_E | 2.946 | 1.00 |
| 319_E | 336_L | 2.865 | 1.00 |
| 124_F | 149_I | 2.646 | 1.00 |
| 357_K | 360_E | 2.631 | 1.00 |
| 126_K | 138_Y | 2.553 | 1.00 |
| 241_D | 259_D | 2.452 | 1.00 |
| 229_M | 364_F | 2.383 | 1.00 |
| 228_A | 257_V | 2.345 | 1.00 |
| 284_S | 288_V | 2.141 | 1.00 |
| 241_D | 246_N | 2.135 | 1.00 |
| 222_C | 310_I | 2.074 | 1.00 |
| 264_R | 271_Y | 2.036 | 1.00 |
| 202_L | 206_L | 2.005 | 1.00 |
| 247_C | 255_V | 1.983 | 1.00 |
| 147_V | 150_K | 1.972 | 1.00 |
| 131_G | 136_V | 1.972 | 1.00 |
| 81_Y | 87_A | 1.960 | 1.00 |
| 117_I | 193_I | 1.940 | 1.00 |
| 131_G | 134_G | 1.924 | 1.00 |
| 127_E | 130_T | 1.898 | 1.00 |
| 329_H | 334_L | 1.881 | 1.00 |
| 138_Y | 146_D | 1.880 | 1.00 |
| 220_E | 224_D | 1.875 | 1.00 |
| 233_E | 301_W | 1.849 | 1.00 |
| 364_F | 367_L | 1.846 | 1.00 |
| 349_I | 367_L | 1.843 | 1.00 |
| 172_L | 237_F | 1.813 | 1.00 |
| 129_G | 136_V | 1.806 | 1.00 |
| 173_S | 179_Q | 1.802 | 1.00 |
| 352_S | 370_N | 1.725 | 0.99 |
| 171_N | 235_K | 1.666 | 0.99 |
| 322_T | 325_E | 1.664 | 0.99 |
| 127_E | 135_V | 1.658 | 0.99 |
| 225_V | 306_L | 1.652 | 0.99 |
| 338_R | 347_Y | 1.633 | 0.99 |
| 233_E | 364_F | 1.610 | 0.99 |
| 229_M | 257_V | 1.584 | 0.99 |
| 335_R | 354_W | 1.577 | 0.99 |
| 242_L | 257_V | 1.577 | 0.99 |
| 165_E | 169_M | 1.548 | 0.99 |
| 246_N | 259_D | 1.548 | 0.99 |
| 279_F | 284_S | 1.544 | 0.99 |
| 241_D | 260_F | 1.532 | 0.99 |
| 166_A | 169_M | 1.524 | 0.98 |
| 24_F | 27_R | 1.522 | 0.98 |
| 259_D | 280_P | 1.519 | 0.98 |
| 361_R | 364_F | 1.463 | 0.98 |
| 26_V | 79_I | 1.449 | 0.98 |
| 342_A | 347_Y | 1.449 | 0.98 |
| 295_S | 298_S | 1.445 | 0.98 |
| 321_F | 325_E | 1.438 | 0.98 |
| 294_F | 298_S | 1.431 | 0.97 |
| 8_R | 27_R | 1.429 | 0.97 |
| 334_L | 337_Y | 1.429 | 0.97 |
| 150_K | 165_E | 1.428 | 0.97 |
| 221_M | 249_V | 1.424 | 0.97 |
| 352_S | 366_I | 1.415 | 0.97 |
| 350_M | 354_W | 1.404 | 0.97 |
| 338_R | 344_E | 1.402 | 0.97 |
| 138_Y | 196_Y | 1.401 | 0.97 |
| 229_M | 233_E | 1.386 | 0.97 |
| 349_I | 370_N | 1.372 | 0.96 |
| 245_R | 259_D | 1.369 | 0.96 |
| 307_M | 310_I | 1.366 | 0.96 |
| 28_D | 33_G | 1.363 | 0.96 |
| 305_V | 318_Y | 1.355 | 0.96 |
| 245_R | 280_P | 1.345 | 0.96 |
| 116_E | 185_T | 1.334 | 0.96 |
| 166_A | 183_V | 1.320 | 0.95 |
| 8_R | 29_S | 1.309 | 0.95 |
| 20_K | 23_G | 1.303 | 0.95 |
| 249_V | 255_V | 1.287 | 0.94 |
| 314_G | 317_P | 1.284 | 0.94 |
| 283_W | 287_E | 1.275 | 0.94 |
| 129_G | 133_F | 1.275 | 0.94 |
| 286_P | 343_S | 1.269 | 0.94 |
| 2_Y | 28_D | 1.263 | 0.94 |
| 241_D | 245_R | 1.261 | 0.94 |
| 336_L | 354_W | 1.255 | 0.93 |
| 228_A | 238_L | 1.254 | 0.93 |
| 74_T | 78_L | 1.251 | 0.93 |
| 148_A | 165_E | 1.242 | 0.93 |
| 163_I | 166_A | 1.240 | 0.93 |
| 72_F | 81_Y | 1.236 | 0.93 |
| 283_W | 317_P | 1.231 | 0.93 |
| 136_V | 148_A | 1.231 | 0.93 |
| 248_L | 259_D | 1.230 | 0.93 |
| 326_T | 330_I | 1.225 | 0.92 |
| 243_A | 280_P | 1.225 | 0.92 |
| 258_S | 263_S | 1.219 | 0.92 |
| 228_A | 242_L | 1.217 | 0.92 |
| 228_A | 239_H | 1.217 | 0.92 |
| 297_K | 300_I | 1.212 | 0.92 |
| 125_L | 137_K | 1.209 | 0.92 |
| 60_P | 63_Q | 1.207 | 0.92 |
| 189_P | 192_I | 1.198 | 0.91 |
| 342_A | 350_M | 1.196 | 0.91 |
| 72_F | 82_H | 1.194 | 0.91 |
| 113_G | 116_E | 1.184 | 0.91 |
| 301_W | 364_F | 1.183 | 0.90 |
| 7_T | 11_A | 1.183 | 0.90 |
| 22_G | 27_R | 1.181 | 0.90 |
| 202_L | 205_Y | 1.176 | 0.90 |
| 200_G | 205_Y | 1.173 | 0.90 |
| 358_A | 361_R | 1.171 | 0.90 |
| 246_N | 260_F | 1.171 | 0.90 |
| 218_L | 313_L | 1.163 | 0.89 |
| 73_S | 77_E | 1.163 | 0.89 |
| 240_R | 260_F | 1.159 | 0.89 |
| 300_I | 364_F | 1.157 | 0.89 |
| 231_Y | 239_H | 1.157 | 0.89 |
| 1_W | 8_R | 1.151 | 0.89 |
| 272_T | 276_G | 1.149 | 0.89 |
| 133_F | 136_V | 1.148 | 0.89 |
| 165_E | 241_D | 1.147 | 0.89 |
| 25_I | 28_D | 1.147 | 0.89 |
| 248_L | 261_G | 1.145 | 0.88 |
| 260_F | 263_S | 1.136 | 0.88 |
| 338_R | 350_M | 1.135 | 0.88 |
| 178_V | 197_M | 1.134 | 0.88 |
| 243_A | 271_Y | 1.120 | 0.87 |
| 276_G | 279_F | 1.120 | 0.87 |
| 27_R | 38_S | 1.114 | 0.87 |
| 315_K | 319_E | 1.110 | 0.86 |
| 354_W | 362_P | 1.108 | 0.86 |
| 287_E | 299_D | 1.107 | 0.86 |
| 354_W | 361_R | 1.106 | 0.86 |
| 178_V | 195_E | 1.098 | 0.86 |
| 129_G | 134_G | 1.097 | 0.85 |
| 192_I | 323_N | 1.095 | 0.85 |
| 88_G | 93_L | 1.095 | 0.85 |
| 130_T | 153_K | 1.092 | 0.85 |
| 1_W | 26_V | 1.091 | 0.85 |
| 195_E | 256_K | 1.087 | 0.85 |
| 121_D | 142_R | 1.085 | 0.85 |
| 139_G | 147_V | 1.083 | 0.84 |
| 140_K | 146_D | 1.079 | 0.84 |
| 240_R | 264_R | 1.077 | 0.84 |
| 6_M | 10_Q | 1.076 | 0.84 |
| 230_E | 368_L | 1.074 | 0.84 |
| 29_S | 36_T | 1.067 | 0.83 |
| 335_R | 356_E | 1.066 | 0.83 |
| 131_G | 165_E | 1.061 | 0.83 |
| 38_S | 53_H | 1.060 | 0.83 |
| 246_N | 256_K | 1.059 | 0.83 |
| 115_W | 170_M | 1.059 | 0.83 |
| 178_V | 255_V | 1.053 | 0.82 |
| 366_I | 369_S | 1.051 | 0.82 |
| 301_W | 305_V | 1.049 | 0.82 |
| 200_G | 206_L | 1.047 | 0.82 |
| 305_V | 336_L | 1.047 | 0.82 |
| 241_D | 262_L | 1.046 | 0.82 |
| 121_D | 141_W | 1.046 | 0.82 |
| 63_Q | 73_S | 1.041 | 0.81 |
| 241_D | 261_G | 1.040 | 0.81 |
| 129_G | 245_R | 1.039 | 0.81 |
| 176_K | 227_E | 1.039 | 0.81 |
| 349_I | 371_I | 1.036 | 0.81 |
| 226_C | 368_L | 1.030 | 0.80 |
| 347_Y | 350_M | 1.030 | 0.80 |
| 75_I | 82_H | 1.029 | 0.80 |
| 233_E | 296_S | 1.025 | 0.80 |
| 240_R | 259_D | 1.022 | 0.79 |
| 344_E | 348_T | 1.022 | 0.79 |
| 172_L | 295_S | 1.021 | 0.79 |
| 117_I | 122_L | 1.019 | 0.79 |
| 225_V | 242_L | 1.017 | 0.79 |
| 199_N | 251_D | 1.017 | 0.79 |
| 228_A | 232_L | 1.016 | 0.79 |
| 306_L | 310_I | 1.015 | 0.79 |
| 148_A | 169_M | 1.011 | 0.78 |
| 119_P | 189_P | 1.010 | 0.78 |
| 230_E | 234_S | 1.009 | 0.78 |
| 348_T | 351_Y | 1.007 | 0.78 |
| 256_K | 260_F | 1.007 | 0.78 |
| 239_H | 246_N | 1.004 | 0.78 |
| 201_C | 204_N | 1.000 | 0.77 |
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 | |
| 4xi2A | 1 | 0.934 | 100 | 0.205 | Contact Map |
| 4fl3A | 1 | 0.9261 | 100 | 0.208 | Contact Map |
| 2h8hA | 1 | 0.9868 | 100 | 0.236 | Contact Map |
| 1fmkA | 1 | 0.9499 | 100 | 0.241 | Contact Map |
| 1opkA | 1 | 0.9763 | 100 | 0.243 | Contact Map |
| 1qcfA | 1 | 0.9842 | 100 | 0.244 | Contact Map |
| 2ozoA | 1 | 0.9314 | 100 | 0.247 | Contact Map |
| 1k9aA | 6 | 0.9525 | 100 | 0.254 | Contact Map |
| 3cblA | 1 | 0.8918 | 100 | 0.273 | Contact Map |
| 4rt7A | 1 | 0 | 100 | 0.407 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)