| querry1 |
| ID: | 1483426533 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 247 (235) | ||
| Sequences: | 3411 (1698.5) | ||
| Seq/Len: | 14.515 | ||
| Nf(neff/√len): | 110.8 |
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: 14.515).
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 |
| 181_S | 184_E | 4.265 | 1.00 |
| 44_A | 189_A | 3.965 | 1.00 |
| 34_G | 43_I | 3.394 | 1.00 |
| 223_Q | 227_V | 3.000 | 1.00 |
| 34_G | 144_L | 2.895 | 1.00 |
| 215_R | 221_E | 2.805 | 1.00 |
| 35_V | 189_A | 2.317 | 1.00 |
| 70_Y | 214_E | 2.296 | 1.00 |
| 43_I | 134_G | 2.281 | 1.00 |
| 37_G | 185_C | 2.277 | 1.00 |
| 8_T | 16_L | 2.218 | 1.00 |
| 41_V | 134_G | 2.114 | 1.00 |
| 143_H | 155_A | 2.068 | 1.00 |
| 69_I | 104_V | 2.032 | 1.00 |
| 38_S | 179_G | 1.994 | 1.00 |
| 32_A | 72_A | 1.972 | 1.00 |
| 218_T | 221_E | 1.921 | 1.00 |
| 104_V | 135_G | 1.877 | 1.00 |
| 6_A | 9_V | 1.867 | 1.00 |
| 187_H | 228_E | 1.849 | 1.00 |
| 37_G | 40_C | 1.839 | 1.00 |
| 3_Y | 12_P | 1.783 | 1.00 |
| 116_Q | 120_Q | 1.769 | 1.00 |
| 175_N | 191_K | 1.766 | 1.00 |
| 231_K | 235_E | 1.754 | 1.00 |
| 15_H | 20_E | 1.735 | 1.00 |
| 41_V | 144_L | 1.629 | 1.00 |
| 65_V | 71_L | 1.611 | 1.00 |
| 137_N | 141_K | 1.598 | 1.00 |
| 68_H | 101_T | 1.579 | 1.00 |
| 132_V | 161_I | 1.563 | 1.00 |
| 219_E | 222_L | 1.554 | 1.00 |
| 177_K | 184_E | 1.548 | 1.00 |
| 86_K | 114_V | 1.463 | 1.00 |
| 66_D | 95_S | 1.462 | 1.00 |
| 18_Q | 21_Y | 1.451 | 1.00 |
| 39_D | 182_R | 1.450 | 1.00 |
| 158_A | 172_M | 1.443 | 1.00 |
| 175_N | 188_F | 1.438 | 1.00 |
| 74_A | 161_I | 1.436 | 1.00 |
| 14_G | 18_Q | 1.422 | 1.00 |
| 145_W | 155_A | 1.422 | 1.00 |
| 16_L | 19_V | 1.405 | 0.99 |
| 224_K | 228_E | 1.404 | 0.99 |
| 24_E | 27_K | 1.396 | 0.99 |
| 190_I | 204_I | 1.396 | 0.99 |
| 186_V | 206_L | 1.380 | 0.99 |
| 22_A | 25_A | 1.372 | 0.99 |
| 227_V | 231_K | 1.368 | 0.99 |
| 44_A | 206_L | 1.367 | 0.99 |
| 42_V | 186_V | 1.365 | 0.99 |
| 171_Y | 188_F | 1.362 | 0.99 |
| 132_V | 159_V | 1.359 | 0.99 |
| 225_F | 228_E | 1.359 | 0.99 |
| 217_L | 222_L | 1.347 | 0.99 |
| 157_R | 178_D | 1.331 | 0.99 |
| 171_Y | 192_S | 1.328 | 0.99 |
| 66_D | 101_T | 1.325 | 0.99 |
| 35_V | 185_C | 1.321 | 0.99 |
| 21_Y | 24_E | 1.320 | 0.99 |
| 116_Q | 119_T | 1.316 | 0.99 |
| 171_Y | 175_N | 1.313 | 0.99 |
| 37_G | 210_Q | 1.313 | 0.99 |
| 11_S | 17_F | 1.308 | 0.99 |
| 64_K | 67_A | 1.308 | 0.99 |
| 102_I | 107_L | 1.292 | 0.99 |
| 12_P | 17_F | 1.292 | 0.99 |
| 125_R | 128_G | 1.286 | 0.99 |
| 229_V | 232_E | 1.286 | 0.99 |
| 90_E | 110_Y | 1.281 | 0.99 |
| 70_Y | 207_L | 1.276 | 0.99 |
| 207_L | 214_E | 1.264 | 0.99 |
| 36_L | 155_A | 1.255 | 0.99 |
| 39_D | 211_Y | 1.254 | 0.99 |
| 186_V | 225_F | 1.250 | 0.99 |
| 86_K | 90_E | 1.242 | 0.98 |
| 40_C | 185_C | 1.234 | 0.98 |
| 182_R | 210_Q | 1.221 | 0.98 |
| 176_Y | 179_G | 1.202 | 0.98 |
| 115_Q | 147_T | 1.199 | 0.98 |
| 95_S | 101_T | 1.196 | 0.98 |
| 10_F | 13_D | 1.193 | 0.98 |
| 11_S | 18_Q | 1.186 | 0.98 |
| 136_F | 211_Y | 1.182 | 0.98 |
| 63_Y | 84_I | 1.177 | 0.98 |
| 40_C | 182_R | 1.168 | 0.97 |
| 132_V | 144_L | 1.161 | 0.97 |
| 210_Q | 215_R | 1.160 | 0.97 |
| 225_F | 229_V | 1.156 | 0.97 |
| 187_H | 232_E | 1.154 | 0.97 |
| 128_G | 149_P | 1.140 | 0.97 |
| 87_A | 111_V | 1.126 | 0.97 |
| 90_E | 93_R | 1.123 | 0.97 |
| 73_F | 80_A | 1.121 | 0.97 |
| 148_D | 152_M | 1.114 | 0.96 |
| 110_Y | 114_V | 1.110 | 0.96 |
| 63_Y | 73_F | 1.108 | 0.96 |
| 160_A | 168_V | 1.105 | 0.96 |
| 230_E | 233_R | 1.097 | 0.96 |
| 65_V | 91_C | 1.092 | 0.96 |
| 69_I | 107_L | 1.083 | 0.96 |
| 30_L | 46_E | 1.082 | 0.96 |
| 71_L | 84_I | 1.082 | 0.96 |
| 34_G | 134_G | 1.078 | 0.95 |
| 3_Y | 11_S | 1.077 | 0.95 |
| 220_E | 224_K | 1.069 | 0.95 |
| 36_L | 157_R | 1.065 | 0.95 |
| 61_K | 74_A | 1.063 | 0.95 |
| 231_K | 234_E | 1.056 | 0.95 |
| 103_D | 106_M | 1.052 | 0.95 |
| 6_A | 10_F | 1.050 | 0.94 |
| 200_G | 203_N | 1.040 | 0.94 |
| 117_K | 121_S | 1.034 | 0.94 |
| 94_F | 100_D | 1.033 | 0.94 |
| 7_I | 16_L | 1.030 | 0.94 |
| 180_M | 184_E | 1.029 | 0.94 |
| 18_Q | 22_A | 1.027 | 0.94 |
| 31_A | 168_V | 1.021 | 0.93 |
| 8_T | 11_S | 1.011 | 0.93 |
| 20_E | 26_V | 1.007 | 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 | |
| 4r3oC | 2 | 0.9717 | 100 | 0.12 | Contact Map |
| 4r3oD | 2 | 0.9717 | 100 | 0.121 | Contact Map |
| 3h4pA | 14 | 0.9271 | 100 | 0.126 | Contact Map |
| 1rypC | 2 | 0.9393 | 100 | 0.136 | Contact Map |
| 1j2pA | 7 | 0.9595 | 100 | 0.138 | Contact Map |
| 4r3oB | 2 | 0.9271 | 100 | 0.138 | Contact Map |
| 1rypD | 2 | 0.9514 | 100 | 0.139 | Contact Map |
| 1rypB | 2 | 0.9271 | 100 | 0.139 | Contact Map |
| 1rypA | 2 | 0.9433 | 100 | 0.142 | Contact Map |
| 1yarA | 7 | 0.8826 | 100 | 0.146 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)