| mafft1_gis |
| ID: | 1392158042 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 238 (234) | ||
| Sequences: | 13117 (9914) | ||
| Seq/Len: | 56.056 | ||
| Nf(neff/√len): | 648.1 |
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: 56.056).
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 |
| 115_G | 155_L | 3.924 | 1.00 |
| 9_G | 64_I | 3.660 | 1.00 |
| 5_T | 46_T | 3.524 | 1.00 |
| 40_R | 216_E | 3.180 | 1.00 |
| 85_D | 215_T | 2.579 | 1.00 |
| 140_Y | 149_D | 2.522 | 1.00 |
| 7_R | 46_T | 2.452 | 1.00 |
| 224_D | 228_K | 2.356 | 1.00 |
| 73_I | 78_Q | 2.349 | 1.00 |
| 222_T | 225_K | 2.325 | 1.00 |
| 75_D | 78_Q | 2.298 | 1.00 |
| 5_T | 44_K | 2.279 | 1.00 |
| 73_I | 196_G | 2.243 | 1.00 |
| 38_C | 45_C | 2.233 | 1.00 |
| 207_K | 211_D | 2.209 | 1.00 |
| 58_S | 64_I | 2.112 | 1.00 |
| 7_R | 48_V | 2.074 | 1.00 |
| 36_E | 222_T | 2.069 | 1.00 |
| 36_E | 39_K | 2.060 | 1.00 |
| 123_E | 127_N | 2.031 | 1.00 |
| 104_P | 108_S | 2.022 | 1.00 |
| 142_N | 145_L | 2.019 | 1.00 |
| 81_I | 198_G | 1.989 | 1.00 |
| 21_D | 27_I | 1.984 | 1.00 |
| 85_D | 211_D | 1.981 | 1.00 |
| 215_T | 219_Q | 1.979 | 1.00 |
| 123_E | 139_A | 1.977 | 1.00 |
| 60_K | 80_E | 1.973 | 1.00 |
| 113_H | 138_V | 1.968 | 1.00 |
| 105_T | 108_S | 1.941 | 1.00 |
| 160_Q | 165_A | 1.910 | 1.00 |
| 36_E | 217_L | 1.894 | 1.00 |
| 82_A | 207_K | 1.891 | 1.00 |
| 84_S | 211_D | 1.872 | 1.00 |
| 199_L | 207_K | 1.810 | 1.00 |
| 36_E | 40_R | 1.808 | 1.00 |
| 40_R | 213_A | 1.807 | 1.00 |
| 113_H | 136_D | 1.754 | 1.00 |
| 200_R | 203_D | 1.751 | 1.00 |
| 199_L | 210_F | 1.738 | 1.00 |
| 58_S | 63_K | 1.724 | 1.00 |
| 204_T | 208_A | 1.704 | 1.00 |
| 40_R | 220_D | 1.697 | 1.00 |
| 95_I | 165_A | 1.681 | 1.00 |
| 32_D | 229_K | 1.655 | 1.00 |
| 146_I | 158_A | 1.637 | 1.00 |
| 208_A | 212_K | 1.607 | 1.00 |
| 21_D | 25_E | 1.599 | 1.00 |
| 82_A | 202_D | 1.597 | 1.00 |
| 32_D | 230_Y | 1.595 | 1.00 |
| 8_I | 34_G | 1.535 | 1.00 |
| 68_I | 197_V | 1.500 | 1.00 |
| 112_K | 156_D | 1.499 | 1.00 |
| 35_N | 47_W | 1.490 | 1.00 |
| 149_D | 154_R | 1.488 | 1.00 |
| 114_V | 157_A | 1.482 | 1.00 |
| 118_Q | 141_A | 1.461 | 1.00 |
| 8_I | 66_A | 1.456 | 1.00 |
| 19_S | 27_I | 1.401 | 0.99 |
| 30_D | 87_L | 1.394 | 0.99 |
| 209_A | 212_K | 1.380 | 0.99 |
| 97_A | 153_G | 1.380 | 0.99 |
| 113_H | 156_D | 1.369 | 0.99 |
| 50_S | 58_S | 1.366 | 0.99 |
| 97_A | 100_S | 1.356 | 0.99 |
| 55_L | 67_I | 1.342 | 0.99 |
| 212_K | 216_E | 1.334 | 0.99 |
| 37_M | 213_A | 1.329 | 0.99 |
| 150_L | 155_L | 1.325 | 0.99 |
| 41_M | 213_A | 1.325 | 0.99 |
| 150_L | 158_A | 1.322 | 0.99 |
| 56_I | 81_I | 1.309 | 0.99 |
| 162_E | 166_S | 1.305 | 0.99 |
| 29_F | 226_M | 1.300 | 0.99 |
| 82_A | 204_T | 1.282 | 0.99 |
| 209_A | 213_A | 1.276 | 0.99 |
| 141_A | 145_L | 1.273 | 0.99 |
| 124_A | 128_D | 1.267 | 0.99 |
| 94_L | 157_A | 1.261 | 0.99 |
| 149_D | 155_L | 1.241 | 0.98 |
| 84_S | 210_F | 1.230 | 0.98 |
| 31_I | 35_N | 1.216 | 0.98 |
| 4_Q | 43_V | 1.213 | 0.98 |
| 76_K | 79_Q | 1.213 | 0.98 |
| 99_G | 179_A | 1.210 | 0.98 |
| 62_K | 200_R | 1.197 | 0.98 |
| 213_A | 217_L | 1.189 | 0.98 |
| 216_E | 220_D | 1.181 | 0.98 |
| 213_A | 216_E | 1.178 | 0.98 |
| 222_T | 226_M | 1.169 | 0.97 |
| 125_Y | 129_N | 1.167 | 0.97 |
| 91_D | 162_E | 1.160 | 0.97 |
| 51_D | 54_A | 1.149 | 0.97 |
| 148_S | 152_A | 1.149 | 0.97 |
| 29_F | 227_A | 1.147 | 0.97 |
| 25_E | 35_N | 1.141 | 0.97 |
| 115_G | 146_I | 1.139 | 0.97 |
| 98_K | 177_E | 1.135 | 0.97 |
| 20_K | 49_A | 1.134 | 0.97 |
| 218_R | 223_Y | 1.131 | 0.97 |
| 74_T | 77_R | 1.131 | 0.97 |
| 98_K | 179_A | 1.125 | 0.97 |
| 57_P | 60_K | 1.121 | 0.97 |
| 40_R | 217_L | 1.111 | 0.96 |
| 140_Y | 146_I | 1.109 | 0.96 |
| 43_V | 209_A | 1.107 | 0.96 |
| 67_I | 71_L | 1.100 | 0.96 |
| 96_A | 157_A | 1.094 | 0.96 |
| 92_S | 122_Q | 1.088 | 0.96 |
| 8_I | 45_C | 1.075 | 0.95 |
| 32_D | 35_N | 1.070 | 0.95 |
| 66_A | 210_F | 1.070 | 0.95 |
| 66_A | 199_L | 1.066 | 0.95 |
| 204_T | 207_K | 1.065 | 0.95 |
| 83_F | 198_G | 1.061 | 0.95 |
| 93_R | 162_E | 1.060 | 0.95 |
| 117_L | 120_S | 1.059 | 0.95 |
| 34_G | 47_W | 1.056 | 0.95 |
| 148_S | 151_T | 1.054 | 0.95 |
| 71_L | 198_G | 1.047 | 0.94 |
| 57_P | 61_A | 1.044 | 0.94 |
| 33_L | 223_Y | 1.043 | 0.94 |
| 34_G | 68_I | 1.043 | 0.94 |
| 127_N | 139_A | 1.043 | 0.94 |
| 110_K | 134_G | 1.043 | 0.94 |
| 35_N | 39_K | 1.041 | 0.94 |
| 115_G | 140_Y | 1.041 | 0.94 |
| 107_E | 110_K | 1.033 | 0.94 |
| 54_A | 58_S | 1.025 | 0.93 |
| 40_R | 222_T | 1.025 | 0.93 |
| 29_F | 231_F | 1.024 | 0.93 |
| 34_G | 197_V | 1.020 | 0.93 |
| 116_V | 123_E | 1.016 | 0.93 |
| 17_F | 88_Y | 1.009 | 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
- 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 | |
| 1wdnA | 1 | 0.937 | 100 | 0.11 | Contact Map |
| 4oenA | 2 | 0.9286 | 100 | 0.122 | Contact Map |
| 1lstA | 1 | 0.9958 | 100 | 0.149 | Contact Map |
| 2ylnA | 1 | 0.9538 | 100 | 0.158 | Contact Map |
| 3vv5A | 2 | 0.9538 | 100 | 0.168 | Contact Map |
| 4g4pA | 1 | 0.9412 | 100 | 0.175 | Contact Map |
| 3hv1A | 2 | 0.9664 | 100 | 0.179 | Contact Map |
| 3i6vA | 1 | 0.916 | 100 | 0.184 | Contact Map |
| 3kbrA | 1 | 0.9286 | 100 | 0.185 | Contact Map |
| 1pb7A | 1 | 0.9244 | 100 | 0.185 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)