| CcmC-02 |
| ID: | 1517605241 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 245 (236) | ||
| Sequences: | 1570 (862.1) | ||
| Seq/Len: | 6.653 | ||
| Nf(neff/√len): | 56.1 |
Jackhmmer Results: (2016_04)
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: 6.653).
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 |
| 96_M | 213_S | 2.794 | 1.00 |
| 64_A | 107_A | 2.766 | 1.00 |
| 29_S | 215_T | 2.552 | 1.00 |
| 79_F | 83_V | 2.296 | 1.00 |
| 72_A | 170_L | 2.267 | 1.00 |
| 36_G | 205_S | 2.170 | 1.00 |
| 78_A | 93_V | 2.147 | 1.00 |
| 96_M | 217_T | 2.093 | 1.00 |
| 33_L | 208_G | 2.029 | 1.00 |
| 75_A | 167_V | 2.017 | 1.00 |
| 79_F | 164_L | 1.988 | 1.00 |
| 54_Y | 58_Y | 1.983 | 1.00 |
| 54_Y | 57_I | 1.978 | 1.00 |
| 70_I | 213_S | 1.964 | 1.00 |
| 199_R | 203_R | 1.949 | 1.00 |
| 124_V | 129_L | 1.925 | 1.00 |
| 67_S | 132_E | 1.887 | 1.00 |
| 26_A | 215_T | 1.869 | 1.00 |
| 47_D | 50_Q | 1.868 | 1.00 |
| 105_F | 109_V | 1.836 | 1.00 |
| 90_N | 156_G | 1.817 | 1.00 |
| 149_F | 155_A | 1.817 | 1.00 |
| 212_L | 216_L | 1.779 | 1.00 |
| 32_V | 211_L | 1.774 | 1.00 |
| 91_L | 221_M | 1.771 | 1.00 |
| 35_V | 204_W | 1.770 | 1.00 |
| 38_I | 43_F | 1.768 | 1.00 |
| 121_T | 124_V | 1.761 | 1.00 |
| 132_E | 136_L | 1.760 | 1.00 |
| 127_A | 182_T | 1.733 | 1.00 |
| 52_N | 55_R | 1.698 | 1.00 |
| 174_H | 178_E | 1.697 | 1.00 |
| 65_I | 210_L | 1.687 | 1.00 |
| 85_Q | 157_R | 1.663 | 1.00 |
| 136_L | 140_V | 1.658 | 1.00 |
| 105_F | 136_L | 1.649 | 1.00 |
| 63_A | 106_I | 1.647 | 1.00 |
| 70_I | 96_M | 1.641 | 1.00 |
| 224_L | 227_L | 1.619 | 1.00 |
| 146_W | 159_A | 1.614 | 1.00 |
| 133_L | 137_F | 1.605 | 1.00 |
| 74_M | 163_V | 1.601 | 1.00 |
| 73_S | 96_M | 1.583 | 1.00 |
| 38_I | 42_G | 1.578 | 1.00 |
| 10_I | 13_R | 1.572 | 1.00 |
| 72_A | 167_V | 1.553 | 0.99 |
| 81_G | 90_N | 1.524 | 0.99 |
| 90_N | 146_W | 1.522 | 0.99 |
| 67_S | 107_A | 1.491 | 0.99 |
| 168_V | 172_I | 1.488 | 0.99 |
| 57_I | 202_L | 1.485 | 0.99 |
| 107_A | 132_E | 1.479 | 0.99 |
| 44_A | 54_Y | 1.468 | 0.99 |
| 207_F | 211_L | 1.461 | 0.99 |
| 104_T | 132_E | 1.449 | 0.99 |
| 65_I | 206_I | 1.440 | 0.99 |
| 46_A | 52_N | 1.433 | 0.99 |
| 189_R | 199_R | 1.422 | 0.99 |
| 28_A | 211_L | 1.412 | 0.99 |
| 97_A | 142_V | 1.411 | 0.99 |
| 92_A | 221_M | 1.403 | 0.99 |
| 82_L | 164_L | 1.392 | 0.99 |
| 93_V | 142_V | 1.353 | 0.98 |
| 40_G | 55_R | 1.349 | 0.98 |
| 19_G | 222_R | 1.347 | 0.98 |
| 39_W | 43_F | 1.339 | 0.98 |
| 58_Y | 198_M | 1.328 | 0.98 |
| 5_L | 8_L | 1.324 | 0.98 |
| 9_A | 13_R | 1.324 | 0.98 |
| 138_L | 166_G | 1.323 | 0.98 |
| 32_V | 207_F | 1.320 | 0.98 |
| 142_V | 163_V | 1.311 | 0.98 |
| 91_L | 228_M | 1.283 | 0.97 |
| 29_S | 212_L | 1.273 | 0.97 |
| 46_A | 55_R | 1.272 | 0.97 |
| 24_W | 27_I | 1.269 | 0.97 |
| 43_F | 58_Y | 1.268 | 0.97 |
| 172_I | 179_W | 1.260 | 0.97 |
| 108_L | 133_L | 1.255 | 0.97 |
| 170_L | 173_I | 1.253 | 0.97 |
| 27_I | 31_V | 1.248 | 0.96 |
| 99_I | 217_T | 1.246 | 0.96 |
| 25_L | 211_L | 1.243 | 0.96 |
| 205_S | 208_G | 1.227 | 0.96 |
| 93_V | 163_V | 1.212 | 0.96 |
| 185_Q | 188_T | 1.207 | 0.96 |
| 86_M | 89_A | 1.189 | 0.95 |
| 138_L | 163_V | 1.189 | 0.95 |
| 71_Y | 100_G | 1.188 | 0.95 |
| 74_M | 97_A | 1.186 | 0.95 |
| 116_K | 122_W | 1.183 | 0.95 |
| 75_A | 79_F | 1.175 | 0.95 |
| 16_Q | 20_W | 1.173 | 0.95 |
| 94_A | 224_L | 1.173 | 0.95 |
| 53_S | 118_M | 1.149 | 0.94 |
| 7_Q | 12_P | 1.144 | 0.94 |
| 203_R | 207_F | 1.127 | 0.93 |
| 33_L | 212_L | 1.118 | 0.92 |
| 235_V | 238_L | 1.109 | 0.92 |
| 116_K | 121_T | 1.092 | 0.91 |
| 15_Y | 18_C | 1.086 | 0.91 |
| 12_P | 16_Q | 1.082 | 0.91 |
| 14_L | 221_M | 1.076 | 0.90 |
| 69_G | 210_L | 1.074 | 0.90 |
| 161_I | 164_L | 1.069 | 0.90 |
| 66_W | 210_L | 1.065 | 0.90 |
| 189_R | 192_Q | 1.059 | 0.90 |
| 8_L | 17_I | 1.055 | 0.89 |
| 155_A | 159_A | 1.054 | 0.89 |
| 13_R | 16_Q | 1.046 | 0.89 |
| 103_F | 213_S | 1.032 | 0.88 |
| 25_L | 214_A | 1.031 | 0.88 |
| 26_A | 30_V | 1.029 | 0.88 |
| 94_A | 146_W | 1.023 | 0.87 |
| 7_Q | 13_R | 1.021 | 0.87 |
| 109_V | 112_S | 1.016 | 0.87 |
| 174_H | 177_V | 1.013 | 0.87 |
| 109_V | 113_A | 1.012 | 0.87 |
| 134_V | 147_H | 1.011 | 0.86 |
| 98_P | 220_R | 1.004 | 0.86 |
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 | |
| 4he8J | 2 | 0.5796 | 28.1 | 0.963 | Contact Map |
| 2cfqA | 1 | 0.8408 | 21.1 | 0.966 | Contact Map |
| 4uvmA | 1 | 0.8816 | 16 | 0.967 | Contact Map |
| 4tphA | 2 | 0.7429 | 15 | 0.968 | Contact Map |
| 4ikvA | 1 | 0.849 | 13.8 | 0.968 | Contact Map |
| 2kluA | 1 | 0.2245 | 11.9 | 0.969 | Contact Map |
| 4oh3A | 2 | 0.8898 | 11.3 | 0.969 | Contact Map |
| 4xnjA | 1 | 0 | 10.5 | 0.97 | Contact Map |
| 1vhfA | 1 | 0.3306 | 9.5 | 0.97 | Contact Map |
| 1p1lA | 1 | 0.3306 | 9.4 | 0.97 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)