| test |
| ID: | 1422784221 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 292 (290) | ||
| Sequences: | 23534 (11454.6) | ||
| Seq/Len: | 81.152 | ||
| Nf(neff/√len): | 672.6 |
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: 81.152).
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 |
| 22_T | 58_S | 4.217 | 1.00 |
| 49_H | 132_Y | 3.746 | 1.00 |
| 199_L | 203_L | 2.977 | 1.00 |
| 122_R | 126_M | 2.563 | 1.00 |
| 49_H | 97_L | 2.548 | 1.00 |
| 100_V | 131_S | 2.453 | 1.00 |
| 79_V | 83_V | 2.343 | 1.00 |
| 231_I | 234_F | 2.299 | 1.00 |
| 111_N | 114_L | 2.223 | 1.00 |
| 100_V | 127_L | 2.147 | 1.00 |
| 150_S | 173_S | 2.142 | 1.00 |
| 106_F | 111_N | 2.133 | 1.00 |
| 39_L | 44_Y | 2.128 | 1.00 |
| 78_F | 82_L | 2.100 | 1.00 |
| 90_T | 136_V | 1.983 | 1.00 |
| 33_I | 48_S | 1.979 | 1.00 |
| 202_V | 206_V | 1.962 | 1.00 |
| 140_L | 144_C | 1.953 | 1.00 |
| 203_L | 206_V | 1.914 | 1.00 |
| 56_C | 91_F | 1.858 | 1.00 |
| 9_I | 13_L | 1.830 | 1.00 |
| 27_I | 31_V | 1.797 | 1.00 |
| 36_N | 283_T | 1.796 | 1.00 |
| 53_V | 94_T | 1.792 | 1.00 |
| 106_F | 203_L | 1.782 | 1.00 |
| 86_F | 90_T | 1.745 | 1.00 |
| 74_R | 77_S | 1.743 | 1.00 |
| 269_N | 273_Y | 1.735 | 1.00 |
| 196_I | 200_S | 1.714 | 1.00 |
| 106_F | 110_R | 1.710 | 1.00 |
| 152_Y | 172_R | 1.707 | 1.00 |
| 120_S | 123_L | 1.688 | 1.00 |
| 30_I | 48_S | 1.653 | 1.00 |
| 104_D | 108_A | 1.636 | 1.00 |
| 107_V | 118_A | 1.626 | 1.00 |
| 81_C | 162_C | 1.619 | 1.00 |
| 127_L | 131_S | 1.589 | 1.00 |
| 126_M | 130_G | 1.571 | 1.00 |
| 234_F | 237_T | 1.569 | 1.00 |
| 217_R | 221_F | 1.551 | 1.00 |
| 201_Y | 204_I | 1.551 | 1.00 |
| 64_K | 68_N | 1.550 | 1.00 |
| 240_F | 244_V | 1.546 | 1.00 |
| 22_T | 267_M | 1.541 | 1.00 |
| 48_S | 52_F | 1.528 | 1.00 |
| 82_L | 147_L | 1.522 | 1.00 |
| 34_R | 48_S | 1.506 | 1.00 |
| 283_T | 286_K | 1.506 | 1.00 |
| 220_A | 223_T | 1.495 | 1.00 |
| 49_H | 128_V | 1.477 | 1.00 |
| 94_T | 135_G | 1.448 | 1.00 |
| 231_I | 237_T | 1.440 | 1.00 |
| 104_D | 119_M | 1.430 | 1.00 |
| 231_I | 235_H | 1.425 | 1.00 |
| 41_I | 44_Y | 1.425 | 1.00 |
| 125_A | 129_L | 1.417 | 1.00 |
| 223_T | 276_R | 1.395 | 0.99 |
| 226_S | 231_I | 1.369 | 0.99 |
| 45_F | 128_V | 1.364 | 0.99 |
| 223_T | 226_S | 1.362 | 0.99 |
| 264_V | 268_L | 1.347 | 0.99 |
| 19_Y | 59_S | 1.344 | 0.99 |
| 77_S | 80_G | 1.337 | 0.99 |
| 50_L | 54_D | 1.330 | 0.99 |
| 203_L | 207_T | 1.317 | 0.99 |
| 86_F | 143_T | 1.300 | 0.99 |
| 162_C | 172_R | 1.298 | 0.99 |
| 97_L | 128_V | 1.297 | 0.99 |
| 10_P | 14_I | 1.294 | 0.99 |
| 237_T | 241_L | 1.273 | 0.99 |
| 235_H | 262_T | 1.271 | 0.99 |
| 205_V | 209_L | 1.263 | 0.99 |
| 33_I | 40_H | 1.251 | 0.99 |
| 98_L | 197_I | 1.251 | 0.99 |
| 25_G | 267_M | 1.244 | 0.98 |
| 198_L | 202_V | 1.241 | 0.98 |
| 29_M | 274_S | 1.241 | 0.98 |
| 2_S | 5_P | 1.239 | 0.98 |
| 264_V | 267_M | 1.236 | 0.98 |
| 232_T | 236_G | 1.234 | 0.98 |
| 23_V | 55_F | 1.231 | 0.98 |
| 95_S | 99_G | 1.231 | 0.98 |
| 79_V | 82_L | 1.226 | 0.98 |
| 52_F | 56_C | 1.224 | 0.98 |
| 106_F | 200_S | 1.223 | 0.98 |
| 238_I | 241_L | 1.218 | 0.98 |
| 28_G | 32_I | 1.217 | 0.98 |
| 235_H | 238_I | 1.214 | 0.98 |
| 31_V | 35_I | 1.196 | 0.98 |
| 23_V | 58_S | 1.195 | 0.98 |
| 122_R | 125_A | 1.195 | 0.98 |
| 108_A | 113_L | 1.194 | 0.98 |
| 110_R | 207_T | 1.173 | 0.98 |
| 114_L | 117_V | 1.171 | 0.98 |
| 224_C | 227_H | 1.166 | 0.97 |
| 236_G | 240_F | 1.166 | 0.97 |
| 114_L | 118_A | 1.162 | 0.97 |
| 225_A | 229_T | 1.155 | 0.97 |
| 46_F | 124_C | 1.154 | 0.97 |
| 99_G | 200_S | 1.153 | 0.97 |
| 230_A | 272_I | 1.148 | 0.97 |
| 3_D | 7_L | 1.147 | 0.97 |
| 27_I | 55_F | 1.142 | 0.97 |
| 24_V | 27_I | 1.140 | 0.97 |
| 29_M | 33_I | 1.134 | 0.97 |
| 206_V | 210_K | 1.130 | 0.97 |
| 239_L | 242_Y | 1.130 | 0.97 |
| 10_P | 13_L | 1.129 | 0.97 |
| 99_G | 196_I | 1.127 | 0.97 |
| 227_H | 231_I | 1.125 | 0.97 |
| 97_L | 132_Y | 1.122 | 0.97 |
| 44_Y | 47_L | 1.118 | 0.96 |
| 21_I | 267_M | 1.117 | 0.96 |
| 108_A | 112_P | 1.115 | 0.96 |
| 51_S | 54_D | 1.114 | 0.96 |
| 115_Y | 119_M | 1.110 | 0.96 |
| 33_I | 39_L | 1.108 | 0.96 |
| 180_L | 184_V | 1.105 | 0.96 |
| 96_F | 134_W | 1.104 | 0.96 |
| 220_A | 224_C | 1.096 | 0.96 |
| 234_F | 238_I | 1.095 | 0.96 |
| 86_F | 136_V | 1.095 | 0.96 |
| 197_I | 201_Y | 1.094 | 0.96 |
| 253_T | 257_A | 1.083 | 0.96 |
| 43_M | 47_L | 1.079 | 0.95 |
| 93_V | 189_N | 1.077 | 0.95 |
| 186_A | 191_I | 1.075 | 0.95 |
| 64_K | 80_G | 1.071 | 0.95 |
| 36_N | 286_K | 1.065 | 0.95 |
| 217_R | 220_A | 1.061 | 0.95 |
| 45_F | 125_A | 1.060 | 0.95 |
| 111_N | 118_A | 1.058 | 0.95 |
| 142_L | 145_S | 1.057 | 0.95 |
| 37_P | 40_H | 1.055 | 0.95 |
| 36_N | 39_L | 1.052 | 0.95 |
| 95_S | 193_T | 1.047 | 0.94 |
| 96_F | 131_S | 1.036 | 0.94 |
| 227_H | 234_F | 1.035 | 0.94 |
| 54_D | 269_N | 1.032 | 0.94 |
| 32_I | 280_V | 1.028 | 0.94 |
| 182_L | 185_F | 1.027 | 0.94 |
| 272_I | 276_R | 1.026 | 0.94 |
| 121_Q | 125_A | 1.025 | 0.93 |
| 1_F | 4_Y | 1.024 | 0.93 |
| 255_K | 260_F | 1.022 | 0.93 |
| 94_T | 97_L | 1.020 | 0.93 |
| 226_S | 237_T | 1.009 | 0.93 |
| 104_D | 115_Y | 1.006 | 0.93 |
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 | |
| 4iarA | 1 | 0.9212 | 100 | 0.19 | Contact Map |
| 2r4rA | 1 | 0.6815 | 100 | 0.212 | Contact Map |
| 4bvnA | 1 | 0.9521 | 100 | 0.218 | Contact Map |
| 3vw7A | 1 | 0.9178 | 100 | 0.22 | Contact Map |
| 4pxzA | 1 | 0.9041 | 100 | 0.222 | Contact Map |
| 4phuA | 1 | 0.8836 | 100 | 0.222 | Contact Map |
| 4buoA | 2 | 0.9692 | 100 | 0.224 | Contact Map |
| 4grvA | 1 | 0.9384 | 100 | 0.225 | Contact Map |
| 2rh1A | 1 | 0.9486 | 100 | 0.226 | Contact Map |
| 1u19A | 2 | 0.9726 | 100 | 0.23 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)