| 3j9i_A_native |
| ID: | 1484212162 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 224 (223) | ||
| Sequences: | 6036 (2832.8) | ||
| Seq/Len: | 27.067 | ||
| Nf(neff/√len): | 189.7 |
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: 27.067).
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 |
| 176_P | 179_E | 4.038 | 1.00 |
| 40_I | 184_G | 3.780 | 1.00 |
| 138_R | 150_E | 2.913 | 1.00 |
| 30_G | 39_L | 2.750 | 1.00 |
| 30_G | 139_L | 2.507 | 1.00 |
| 34_A | 174_N | 2.495 | 1.00 |
| 33_F | 180_A | 2.460 | 1.00 |
| 33_F | 36_G | 2.413 | 1.00 |
| 28_A | 68_V | 2.370 | 1.00 |
| 39_L | 130_A | 2.356 | 1.00 |
| 213_R | 219_E | 2.295 | 1.00 |
| 31_M | 184_G | 2.021 | 1.00 |
| 65_V | 103_L | 2.017 | 1.00 |
| 170_E | 186_K | 1.991 | 1.00 |
| 172_K | 179_E | 1.963 | 1.00 |
| 65_V | 100_I | 1.942 | 1.00 |
| 177_E | 207_T | 1.936 | 1.00 |
| 170_E | 183_L | 1.875 | 1.00 |
| 91_K | 97_L | 1.857 | 1.00 |
| 37_V | 130_A | 1.831 | 1.00 |
| 32_K | 150_E | 1.828 | 1.00 |
| 60_L | 63_D | 1.815 | 1.00 |
| 62_D | 91_K | 1.805 | 1.00 |
| 100_I | 131_G | 1.782 | 1.00 |
| 128_I | 154_T | 1.754 | 1.00 |
| 35_N | 208_V | 1.738 | 1.00 |
| 4_T | 12_L | 1.702 | 1.00 |
| 140_F | 150_E | 1.675 | 1.00 |
| 216_D | 219_E | 1.630 | 1.00 |
| 133_D | 136_G | 1.629 | 1.00 |
| 2_A | 5_V | 1.623 | 1.00 |
| 177_E | 181_V | 1.621 | 1.00 |
| 69_T | 76_A | 1.605 | 1.00 |
| 152_K | 173_E | 1.582 | 1.00 |
| 66_A | 212_Y | 1.582 | 1.00 |
| 175_L | 183_L | 1.563 | 1.00 |
| 38_L | 184_G | 1.561 | 1.00 |
| 56_E | 202_E | 1.519 | 1.00 |
| 38_L | 181_V | 1.505 | 1.00 |
| 31_M | 180_A | 1.500 | 1.00 |
| 99_N | 102_N | 1.495 | 1.00 |
| 40_I | 203_I | 1.488 | 1.00 |
| 67_A | 129_F | 1.483 | 1.00 |
| 64_Y | 97_L | 1.470 | 1.00 |
| 11_R | 16_E | 1.460 | 1.00 |
| 87_A | 103_L | 1.446 | 1.00 |
| 67_A | 80_V | 1.427 | 1.00 |
| 86_S | 106_R | 1.415 | 1.00 |
| 36_G | 180_A | 1.405 | 0.99 |
| 172_K | 175_L | 1.401 | 0.99 |
| 33_F | 177_E | 1.393 | 0.99 |
| 61_I | 87_A | 1.382 | 0.99 |
| 166_F | 170_E | 1.362 | 0.99 |
| 217_Q | 220_V | 1.355 | 0.99 |
| 112_Q | 116_Q | 1.354 | 0.99 |
| 181_V | 203_I | 1.319 | 0.99 |
| 181_V | 205_S | 1.306 | 0.99 |
| 36_G | 177_E | 1.304 | 0.99 |
| 207_T | 213_R | 1.301 | 0.99 |
| 58_I | 204_A | 1.292 | 0.99 |
| 86_S | 89_Q | 1.289 | 0.99 |
| 32_K | 152_K | 1.273 | 0.99 |
| 82_F | 86_S | 1.268 | 0.99 |
| 121_R | 124_G | 1.266 | 0.99 |
| 38_L | 205_S | 1.264 | 0.99 |
| 66_A | 204_A | 1.248 | 0.99 |
| 83_A | 107_V | 1.241 | 0.98 |
| 215_Y | 220_V | 1.232 | 0.98 |
| 155_A | 167_L | 1.227 | 0.98 |
| 59_Q | 69_T | 1.219 | 0.98 |
| 62_D | 97_L | 1.199 | 0.98 |
| 89_Q | 93_T | 1.195 | 0.98 |
| 106_R | 110_Q | 1.195 | 0.98 |
| 129_F | 142_C | 1.193 | 0.98 |
| 70_S | 156_I | 1.192 | 0.98 |
| 128_I | 156_I | 1.191 | 0.98 |
| 171_Y | 175_L | 1.180 | 0.98 |
| 82_F | 110_Q | 1.176 | 0.98 |
| 27_T | 159_G | 1.174 | 0.98 |
| 14_Q | 17_Y | 1.169 | 0.97 |
| 39_L | 68_V | 1.164 | 0.97 |
| 153_A | 167_L | 1.159 | 0.97 |
| 12_L | 15_V | 1.158 | 0.97 |
| 218_E | 222_K | 1.142 | 0.97 |
| 166_F | 187_A | 1.137 | 0.97 |
| 62_D | 65_V | 1.136 | 0.97 |
| 40_I | 188_L | 1.132 | 0.97 |
| 182_T | 186_K | 1.129 | 0.97 |
| 7_S | 13_F | 1.125 | 0.97 |
| 66_A | 206_I | 1.124 | 0.97 |
| 218_E | 221_K | 1.122 | 0.97 |
| 171_Y | 174_N | 1.118 | 0.96 |
| 33_F | 207_T | 1.114 | 0.96 |
| 58_I | 68_V | 1.114 | 0.96 |
| 132_I | 208_V | 1.114 | 0.96 |
| 8_P | 13_F | 1.113 | 0.96 |
| 43_K | 202_E | 1.111 | 0.96 |
| 80_V | 84_R | 1.109 | 0.96 |
| 59_Q | 80_V | 1.105 | 0.96 |
| 34_A | 176_P | 1.103 | 0.96 |
| 90_E | 94_Y | 1.094 | 0.96 |
| 10_G | 14_Q | 1.093 | 0.96 |
| 28_A | 41_S | 1.092 | 0.96 |
| 104_V | 148_I | 1.075 | 0.95 |
| 143_D | 147_T | 1.075 | 0.95 |
| 27_T | 163_V | 1.061 | 0.95 |
| 26_S | 42_D | 1.049 | 0.94 |
| 20_E | 23_K | 1.047 | 0.94 |
| 39_L | 66_A | 1.044 | 0.94 |
| 41_S | 58_I | 1.040 | 0.94 |
| 133_D | 138_R | 1.039 | 0.94 |
| 178_K | 182_T | 1.038 | 0.94 |
| 79_L | 125_V | 1.032 | 0.94 |
| 146_G | 157_G | 1.030 | 0.94 |
| 29_L | 184_G | 1.030 | 0.94 |
| 217_Q | 221_K | 1.028 | 0.94 |
| 61_I | 67_A | 1.027 | 0.94 |
| 17_Y | 20_E | 1.025 | 0.93 |
| 141_D | 154_T | 1.021 | 0.93 |
| 85_I | 89_Q | 1.017 | 0.93 |
| 186_K | 189_K | 1.009 | 0.93 |
| 166_F | 183_L | 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
- 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 | |
| 1yarA | 7 | 0.9866 | 100 | 0 | Contact Map |
| 1rypE | 2 | 1 | 100 | 0.009 | Contact Map |
| 1rypB | 2 | 1 | 100 | 0.01 | Contact Map |
| 4r3oB | 2 | 0.9955 | 100 | 0.01 | Contact Map |
| 1rypF | 2 | 0.9911 | 100 | 0.01 | Contact Map |
| 4r3oE | 2 | 1 | 100 | 0.012 | Contact Map |
| 1rypC | 2 | 1 | 100 | 0.014 | Contact Map |
| 3h4pA | 14 | 0.9866 | 100 | 0.018 | Contact Map |
| 4r3oF | 2 | 0.9911 | 100 | 0.019 | Contact Map |
| 1j2pA | 7 | 0.9955 | 100 | 0.02 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)