| rotation1grem_ompA |
| ID: | 1422318779 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 346 (338) | ||
| Sequences: | 584 (415.6) | ||
| Seq/Len: | 1.728 | ||
| Nf(neff/√len): | 22.6 |
HHblits Results: (2013_03)
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: 1.728).
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 |
| 271_Q | 275_E | 3.632 | 1.00 |
| 290_I | 294_K | 3.605 | 1.00 |
| 226_N | 269_Y | 3.500 | 1.00 |
| 275_E | 279_Q | 3.429 | 1.00 |
| 260_Y | 304_N | 3.044 | 1.00 |
| 226_N | 276_R | 2.778 | 1.00 |
| 33_K | 59_G | 2.580 | 1.00 |
| 238_L | 284_Y | 2.327 | 1.00 |
| 309_N | 314_V | 2.285 | 1.00 |
| 225_F | 264_I | 2.231 | 0.99 |
| 152_I | 158_T | 2.227 | 0.99 |
| 156_I | 189_Y | 2.227 | 0.99 |
| 29_Y | 63_G | 2.202 | 0.99 |
| 230_L | 284_Y | 2.156 | 0.99 |
| 311_C | 314_V | 2.075 | 0.99 |
| 31_G | 61_F | 2.075 | 0.99 |
| 258_L | 300_M | 2.070 | 0.99 |
| 283_D | 287_S | 2.067 | 0.99 |
| 269_Y | 273_L | 2.025 | 0.99 |
| 307_T | 314_V | 2.013 | 0.99 |
| 224_N | 231_K | 1.999 | 0.99 |
| 115_Y | 147_G | 1.992 | 0.98 |
| 255_V | 295_I | 1.987 | 0.98 |
| 245_L | 294_K | 1.925 | 0.98 |
| 279_Q | 283_D | 1.768 | 0.96 |
| 275_E | 297_A | 1.763 | 0.96 |
| 291_P | 294_K | 1.740 | 0.96 |
| 224_N | 227_K | 1.714 | 0.95 |
| 239_D | 288_K | 1.661 | 0.94 |
| 271_Q | 303_S | 1.635 | 0.93 |
| 272_G | 276_R | 1.622 | 0.93 |
| 162_Y | 181_G | 1.571 | 0.91 |
| 271_Q | 299_G | 1.559 | 0.91 |
| 66_V | 72_F | 1.554 | 0.91 |
| 153_T | 156_I | 1.538 | 0.90 |
| 57_G | 184_S | 1.503 | 0.89 |
| 319_A | 328_R | 1.502 | 0.89 |
| 309_N | 315_K | 1.483 | 0.88 |
| 73_E | 159_R | 1.478 | 0.88 |
| 269_Y | 276_R | 1.445 | 0.86 |
| 257_V | 278_A | 1.445 | 0.86 |
| 318_A | 327_D | 1.429 | 0.85 |
| 308_G | 314_V | 1.426 | 0.85 |
| 320_L | 323_C | 1.422 | 0.85 |
| 112_L | 148_V | 1.419 | 0.85 |
| 274_S | 299_G | 1.412 | 0.84 |
| 245_L | 290_I | 1.406 | 0.84 |
| 239_D | 243_S | 1.391 | 0.83 |
| 269_Y | 302_E | 1.365 | 0.82 |
| 307_T | 311_C | 1.365 | 0.82 |
| 256_V | 298_R | 1.365 | 0.82 |
| 230_L | 238_L | 1.362 | 0.81 |
| 73_E | 103_K | 1.361 | 0.81 |
| 320_L | 328_R | 1.358 | 0.81 |
| 257_V | 295_I | 1.356 | 0.81 |
| 35_G | 57_G | 1.355 | 0.81 |
| 311_C | 323_C | 1.334 | 0.80 |
| 319_A | 329_R | 1.327 | 0.79 |
| 282_V | 297_A | 1.322 | 0.79 |
| 149_E | 163_Q | 1.311 | 0.78 |
| 164_W | 181_G | 1.310 | 0.78 |
| 225_F | 262_D | 1.296 | 0.77 |
| 278_A | 299_G | 1.289 | 0.76 |
| 103_K | 149_E | 1.287 | 0.76 |
| 29_Y | 73_E | 1.279 | 0.75 |
| 30_T | 62_G | 1.259 | 0.74 |
| 239_D | 284_Y | 1.257 | 0.74 |
| 300_M | 304_N | 1.256 | 0.74 |
| 238_L | 244_Q | 1.248 | 0.73 |
| 130_N | 133_G | 1.236 | 0.72 |
| 260_Y | 303_S | 1.233 | 0.72 |
| 262_D | 315_K | 1.229 | 0.71 |
| 320_L | 329_R | 1.225 | 0.71 |
| 70_V | 104_L | 1.215 | 0.70 |
| 66_V | 170_D | 1.215 | 0.70 |
| 76_Y | 149_E | 1.208 | 0.69 |
| 224_N | 261_T | 1.201 | 0.69 |
| 242_Y | 285_L | 1.199 | 0.68 |
| 59_G | 115_Y | 1.198 | 0.68 |
| 14_G | 18_V | 1.192 | 0.68 |
| 320_L | 324_L | 1.187 | 0.67 |
| 318_A | 322_D | 1.181 | 0.67 |
| 318_A | 328_R | 1.171 | 0.66 |
| 311_C | 315_K | 1.170 | 0.66 |
| 223_F | 301_G | 1.167 | 0.65 |
| 323_C | 327_D | 1.165 | 0.65 |
| 73_E | 161_E | 1.162 | 0.65 |
| 279_Q | 297_A | 1.161 | 0.65 |
| 321_I | 324_L | 1.160 | 0.65 |
| 308_G | 311_C | 1.158 | 0.65 |
| 314_V | 327_D | 1.157 | 0.64 |
| 56_L | 66_V | 1.150 | 0.64 |
| 33_K | 163_Q | 1.141 | 0.63 |
| 258_L | 298_R | 1.135 | 0.62 |
| 268_A | 272_G | 1.131 | 0.62 |
| 311_C | 324_L | 1.128 | 0.62 |
| 144_F | 152_I | 1.121 | 0.61 |
| 320_L | 327_D | 1.121 | 0.61 |
| 73_E | 117_R | 1.120 | 0.61 |
| 259_G | 285_L | 1.119 | 0.61 |
| 64_Y | 73_E | 1.119 | 0.61 |
| 8_I | 11_A | 1.117 | 0.60 |
| 65_Q | 116_T | 1.112 | 0.60 |
| 312_D | 316_Q | 1.111 | 0.60 |
| 328_R | 331_E | 1.109 | 0.60 |
| 267_D | 280_S | 1.105 | 0.59 |
| 75_G | 139_G | 1.090 | 0.58 |
| 28_W | 71_G | 1.085 | 0.57 |
| 185_L | 227_K | 1.083 | 0.57 |
| 101_T | 143_V | 1.078 | 0.56 |
| 263_R | 302_E | 1.075 | 0.56 |
| 188_S | 285_L | 1.067 | 0.55 |
| 319_A | 322_D | 1.064 | 0.55 |
| 9_A | 12_L | 1.057 | 0.54 |
| 239_D | 312_D | 1.056 | 0.54 |
| 157_A | 186_G | 1.053 | 0.54 |
| 106_Y | 143_V | 1.051 | 0.53 |
| 222_L | 261_T | 1.049 | 0.53 |
| 198_P | 208_P | 1.047 | 0.53 |
| 282_V | 295_I | 1.045 | 0.53 |
| 61_F | 73_E | 1.045 | 0.53 |
| 243_S | 247_N | 1.044 | 0.53 |
| 199_V | 203_A | 1.041 | 0.52 |
| 111_D | 150_Y | 1.038 | 0.52 |
| 269_Y | 272_G | 1.038 | 0.52 |
| 245_L | 253_G | 1.036 | 0.52 |
| 259_G | 281_V | 1.033 | 0.52 |
| 265_G | 270_N | 1.029 | 0.51 |
| 5_A | 9_A | 1.029 | 0.51 |
| 311_C | 327_D | 1.029 | 0.51 |
| 274_S | 303_S | 1.027 | 0.51 |
| 159_R | 261_T | 1.026 | 0.51 |
| 199_V | 286_I | 1.025 | 0.51 |
| 263_R | 309_N | 1.024 | 0.51 |
| 58_A | 146_G | 1.023 | 0.50 |
| 15_F | 18_V | 1.019 | 0.50 |
| 240_Q | 244_Q | 1.015 | 0.50 |
| 242_Y | 286_I | 1.013 | 0.49 |
| 117_R | 163_Q | 1.013 | 0.49 |
| 203_A | 274_S | 1.013 | 0.49 |
| 117_R | 145_A | 1.010 | 0.49 |
| 3_K | 8_I | 1.010 | 0.49 |
| 112_L | 120_G | 1.009 | 0.49 |
| 230_L | 235_Q | 1.009 | 0.49 |
| 263_R | 311_C | 1.009 | 0.49 |
| 231_K | 234_G | 1.005 | 0.49 |
| 27_T | 64_Y | 1.004 | 0.48 |
| 11_A | 14_G | 1.003 | 0.48 |
| 54_N | 147_G | 1.002 | 0.48 |
| 9_A | 14_G | 1.002 | 0.48 |
| 32_A | 189_Y | 1.001 | 0.48 |
| 103_K | 145_A | 1.000 | 0.48 |
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 | |
| 3nb3A | 3 | 0.396 | 100 | 0.293 | Contact Map |
| 4erhA | 2 | 0.3642 | 100 | 0.654 | Contact Map |
| 1r1mA | 1 | 0.3728 | 100 | 0.665 | Contact Map |
| 2kgwA | 1 | 0.3728 | 100 | 0.678 | Contact Map |
| 4b5cA | 3 | 0.3497 | 100 | 0.68 | Contact Map |
| 4pwtA | 3 | 0.3757 | 100 | 0.689 | Contact Map |
| 2hqsH | 4 | 0.3121 | 100 | 0.691 | Contact Map |
| 3td3A | 8 | 0.3497 | 100 | 0.692 | Contact Map |
| 3ldtA | 1 | 0.4046 | 100 | 0.694 | Contact Map |
| 2k1sA | 1 | 0.4306 | 100 | 0.695 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)