| gizmo |
| ID: | 1421867367 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 296 (289) | ||
| Sequences: | 12195 (8789.9) | ||
| Seq/Len: | 42.197 | ||
| Nf(neff/√len): | 517.1 |
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: 42.197).
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 |
| 37_T | 276_C | 3.673 | 1.00 |
| 244_E | 292_A | 3.279 | 1.00 |
| 62_A | 101_S | 3.204 | 1.00 |
| 28_A | 59_A | 3.005 | 1.00 |
| 37_T | 41_N | 2.794 | 1.00 |
| 75_W | 105_L | 2.465 | 1.00 |
| 289_R | 292_A | 2.396 | 1.00 |
| 73_L | 102_L | 2.390 | 1.00 |
| 243_T | 292_A | 2.345 | 1.00 |
| 32_R | 63_F | 2.243 | 1.00 |
| 272_P | 276_C | 2.193 | 1.00 |
| 255_D | 293_A | 2.129 | 1.00 |
| 104_Y | 136_R | 2.093 | 1.00 |
| 238_L | 242_L | 2.085 | 1.00 |
| 41_N | 279_I | 2.064 | 1.00 |
| 5_P | 12_A | 2.034 | 1.00 |
| 4_R | 15_A | 2.031 | 1.00 |
| 75_W | 96_A | 2.028 | 1.00 |
| 32_R | 59_A | 2.028 | 1.00 |
| 17_T | 45_S | 2.020 | 1.00 |
| 37_T | 272_P | 1.996 | 1.00 |
| 55_L | 99_G | 1.974 | 1.00 |
| 105_L | 135_L | 1.937 | 1.00 |
| 38_A | 43_V | 1.935 | 1.00 |
| 109_L | 160_S | 1.911 | 1.00 |
| 89_L | 93_K | 1.910 | 1.00 |
| 109_L | 188_E | 1.910 | 1.00 |
| 95_S | 99_G | 1.907 | 1.00 |
| 32_R | 36_F | 1.900 | 1.00 |
| 32_R | 60_G | 1.850 | 1.00 |
| 41_N | 276_C | 1.848 | 1.00 |
| 46_F | 57_K | 1.817 | 1.00 |
| 37_T | 40_E | 1.817 | 1.00 |
| 186_I | 264_A | 1.810 | 1.00 |
| 251_R | 284_F | 1.806 | 1.00 |
| 39_L | 71_L | 1.782 | 1.00 |
| 74_T | 109_L | 1.769 | 1.00 |
| 125_G | 128_D | 1.767 | 1.00 |
| 35_V | 60_G | 1.716 | 1.00 |
| 179_S | 183_F | 1.706 | 1.00 |
| 67_E | 70_L | 1.680 | 1.00 |
| 27_R | 30_D | 1.671 | 1.00 |
| 36_F | 63_F | 1.660 | 1.00 |
| 135_L | 138_L | 1.645 | 1.00 |
| 93_K | 131_K | 1.645 | 1.00 |
| 77_L | 108_L | 1.637 | 1.00 |
| 127_Q | 130_Q | 1.631 | 1.00 |
| 251_R | 255_D | 1.623 | 1.00 |
| 276_C | 280_E | 1.621 | 1.00 |
| 11_V | 137_G | 1.615 | 1.00 |
| 180_Q | 187_G | 1.611 | 1.00 |
| 290_E | 294_R | 1.606 | 1.00 |
| 130_Q | 155_L | 1.584 | 1.00 |
| 236_I | 239_G | 1.578 | 1.00 |
| 149_G | 182_N | 1.574 | 1.00 |
| 30_D | 33_A | 1.573 | 1.00 |
| 36_F | 40_E | 1.559 | 1.00 |
| 175_I | 178_A | 1.549 | 1.00 |
| 128_D | 131_K | 1.528 | 1.00 |
| 20_L | 46_F | 1.516 | 1.00 |
| 28_A | 32_R | 1.514 | 1.00 |
| 144_G | 147_D | 1.510 | 1.00 |
| 3_Y | 12_A | 1.509 | 1.00 |
| 163_Y | 187_G | 1.497 | 1.00 |
| 280_E | 283_R | 1.476 | 1.00 |
| 269_R | 275_V | 1.472 | 1.00 |
| 100_L | 105_L | 1.464 | 1.00 |
| 68_R | 102_L | 1.452 | 1.00 |
| 164_N | 169_W | 1.405 | 0.99 |
| 275_V | 279_I | 1.399 | 0.99 |
| 54_E | 96_A | 1.397 | 0.99 |
| 2_R | 15_A | 1.390 | 0.99 |
| 122_F | 125_G | 1.376 | 0.99 |
| 61_E | 71_L | 1.372 | 0.99 |
| 50_G | 91_A | 1.365 | 0.99 |
| 89_L | 92_L | 1.364 | 0.99 |
| 45_S | 188_E | 1.363 | 0.99 |
| 34_L | 275_V | 1.357 | 0.99 |
| 269_R | 274_G | 1.357 | 0.99 |
| 273_T | 276_C | 1.352 | 0.99 |
| 72_F | 107_L | 1.352 | 0.99 |
| 11_V | 72_F | 1.348 | 0.99 |
| 246_S | 284_F | 1.337 | 0.99 |
| 55_L | 59_A | 1.336 | 0.99 |
| 9_T | 137_G | 1.323 | 0.99 |
| 176_R | 179_S | 1.319 | 0.99 |
| 95_S | 98_E | 1.315 | 0.99 |
| 253_T | 265_A | 1.314 | 0.99 |
| 36_F | 64_A | 1.301 | 0.99 |
| 33_A | 37_T | 1.299 | 0.99 |
| 257_R | 261_E | 1.298 | 0.99 |
| 239_G | 242_L | 1.297 | 0.99 |
| 149_G | 183_F | 1.297 | 0.99 |
| 58_G | 101_S | 1.296 | 0.99 |
| 45_S | 74_T | 1.293 | 0.99 |
| 145_D | 149_G | 1.290 | 0.99 |
| 106_D | 136_R | 1.288 | 0.99 |
| 36_F | 60_G | 1.287 | 0.99 |
| 59_A | 101_S | 1.278 | 0.99 |
| 5_P | 10_G | 1.275 | 0.99 |
| 68_R | 104_Y | 1.267 | 0.99 |
| 247_L | 277_A | 1.253 | 0.99 |
| 55_L | 98_E | 1.253 | 0.99 |
| 89_L | 128_D | 1.249 | 0.99 |
| 77_L | 92_L | 1.247 | 0.99 |
| 235_D | 238_L | 1.243 | 0.98 |
| 254_A | 281_M | 1.232 | 0.98 |
| 44_N | 72_F | 1.230 | 0.98 |
| 113_P | 147_D | 1.225 | 0.98 |
| 20_L | 57_K | 1.224 | 0.98 |
| 29_N | 33_A | 1.224 | 0.98 |
| 240_Y | 244_E | 1.220 | 0.98 |
| 244_E | 289_R | 1.202 | 0.98 |
| 168_G | 234_E | 1.200 | 0.98 |
| 273_T | 277_A | 1.192 | 0.98 |
| 149_G | 179_S | 1.186 | 0.98 |
| 160_S | 188_E | 1.182 | 0.98 |
| 35_V | 46_F | 1.181 | 0.98 |
| 243_T | 295_R | 1.177 | 0.98 |
| 243_T | 289_R | 1.170 | 0.97 |
| 14_S | 43_V | 1.168 | 0.97 |
| 152_A | 183_F | 1.168 | 0.97 |
| 107_L | 160_S | 1.162 | 0.97 |
| 277_A | 280_E | 1.159 | 0.97 |
| 50_G | 95_S | 1.152 | 0.97 |
| 54_E | 99_G | 1.147 | 0.97 |
| 126_L | 138_L | 1.146 | 0.97 |
| 149_G | 153_N | 1.136 | 0.97 |
| 181_N | 258_Q | 1.129 | 0.97 |
| 28_A | 56_L | 1.127 | 0.97 |
| 14_S | 44_N | 1.126 | 0.97 |
| 2_R | 285_S | 1.126 | 0.97 |
| 188_E | 264_A | 1.124 | 0.97 |
| 33_A | 272_P | 1.115 | 0.96 |
| 90_D | 94_R | 1.100 | 0.96 |
| 235_D | 239_G | 1.098 | 0.96 |
| 251_R | 281_M | 1.093 | 0.96 |
| 240_Y | 292_A | 1.087 | 0.96 |
| 93_K | 133_R | 1.080 | 0.95 |
| 142_S | 190_F | 1.065 | 0.95 |
| 97_F | 133_R | 1.063 | 0.95 |
| 274_G | 277_A | 1.061 | 0.95 |
| 93_K | 128_D | 1.060 | 0.95 |
| 246_S | 249_T | 1.058 | 0.95 |
| 124_S | 128_D | 1.039 | 0.94 |
| 9_T | 159_V | 1.035 | 0.94 |
| 258_Q | 262_R | 1.032 | 0.94 |
| 140_V | 148_P | 1.031 | 0.94 |
| 271_L | 274_G | 1.027 | 0.94 |
| 74_T | 107_L | 1.012 | 0.93 |
| 172_R | 187_G | 1.011 | 0.93 |
| 33_A | 36_F | 1.011 | 0.93 |
| 94_R | 133_R | 1.010 | 0.93 |
| 174_R | 178_A | 1.008 | 0.93 |
| 270_D | 274_G | 1.000 | 0.92 |
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
- 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 | |
| 1pyfA | 1 | 0.9426 | 100 | 0.157 | Contact Map |
| 1pz1A | 2 | 0.9493 | 100 | 0.163 | Contact Map |
| 3erpA | 2 | 0.9054 | 100 | 0.163 | Contact Map |
| 3eauA | 1 | 0.9797 | 100 | 0.17 | Contact Map |
| 3lutA | 1 | 0.9696 | 100 | 0.17 | Contact Map |
| 3n6qA | 8 | 0.9054 | 100 | 0.171 | Contact Map |
| 1ur3M | 1 | 0.8885 | 100 | 0.178 | Contact Map |
| 3v0sA | 1 | 0.8412 | 100 | 0.178 | Contact Map |
| 3n2tA | 1 | 0.9392 | 100 | 0.179 | Contact Map |
| 1lqaA | 2 | 0.9561 | 100 | 0.182 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)