| Bilge Ercan |
| ID: | 1501081324 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 260 (256) | ||
| Sequences: | 3269 (1744.9) | ||
| Seq/Len: | 12.770 | ||
| Nf(neff/√len): | 109.1 |
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: 12.770).
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 |
| 212_T | 249_L | 6.085 | 1.00 |
| 216_I | 245_A | 4.711 | 1.00 |
| 48_L | 154_S | 3.672 | 1.00 |
| 44_L | 149_W | 3.627 | 1.00 |
| 224_A | 234_A | 3.288 | 1.00 |
| 151_G | 214_T | 2.940 | 1.00 |
| 44_L | 153_I | 2.799 | 1.00 |
| 30_A | 148_F | 2.678 | 1.00 |
| 60_V | 161_I | 2.546 | 1.00 |
| 98_E | 205_K | 2.447 | 1.00 |
| 63_G | 162_F | 2.299 | 1.00 |
| 106_L | 243_S | 2.137 | 1.00 |
| 120_I | 143_V | 2.135 | 1.00 |
| 98_E | 250_D | 2.112 | 1.00 |
| 95_L | 166_G | 2.018 | 1.00 |
| 208_V | 253_L | 2.017 | 1.00 |
| 49_Y | 54_L | 1.976 | 1.00 |
| 148_F | 211_I | 1.976 | 1.00 |
| 205_K | 250_D | 1.847 | 1.00 |
| 64_V | 169_G | 1.830 | 1.00 |
| 170_G | 185_F | 1.814 | 1.00 |
| 113_G | 217_S | 1.791 | 1.00 |
| 50_N | 54_L | 1.738 | 1.00 |
| 117_T | 238_T | 1.727 | 1.00 |
| 100_G | 163_V | 1.723 | 1.00 |
| 220_N | 241_H | 1.722 | 1.00 |
| 44_L | 48_L | 1.700 | 1.00 |
| 51_V | 116_L | 1.694 | 1.00 |
| 152_V | 211_I | 1.660 | 1.00 |
| 152_V | 210_A | 1.650 | 1.00 |
| 159_T | 163_V | 1.630 | 1.00 |
| 171_S | 182_S | 1.613 | 1.00 |
| 208_V | 249_L | 1.610 | 1.00 |
| 139_P | 222_Y | 1.594 | 1.00 |
| 171_S | 175_V | 1.592 | 1.00 |
| 171_S | 186_W | 1.566 | 1.00 |
| 140_L | 144_I | 1.549 | 1.00 |
| 124_R | 129_L | 1.529 | 1.00 |
| 220_N | 237_R | 1.520 | 1.00 |
| 124_R | 222_Y | 1.519 | 1.00 |
| 55_S | 112_A | 1.510 | 1.00 |
| 70_L | 94_S | 1.508 | 1.00 |
| 160_V | 203_L | 1.467 | 1.00 |
| 159_T | 202_C | 1.463 | 1.00 |
| 56_M | 161_I | 1.449 | 1.00 |
| 229_A | 233_R | 1.448 | 1.00 |
| 60_V | 165_V | 1.446 | 1.00 |
| 61_V | 244_L | 1.418 | 1.00 |
| 74_G | 90_L | 1.406 | 0.99 |
| 224_A | 230_G | 1.399 | 0.99 |
| 26_M | 140_L | 1.392 | 0.99 |
| 227_T | 231_I | 1.381 | 0.99 |
| 96_L | 167_I | 1.376 | 0.99 |
| 25_L | 29_N | 1.369 | 0.99 |
| 65_F | 102_V | 1.362 | 0.99 |
| 108_F | 155_L | 1.349 | 0.99 |
| 7_A | 11_H | 1.331 | 0.99 |
| 124_R | 223_D | 1.320 | 0.99 |
| 27_L | 215_W | 1.313 | 0.99 |
| 43_L | 46_R | 1.313 | 0.99 |
| 212_T | 245_A | 1.301 | 0.99 |
| 128_Q | 243_S | 1.290 | 0.99 |
| 212_T | 216_I | 1.286 | 0.99 |
| 48_L | 153_I | 1.285 | 0.99 |
| 10_G | 14_I | 1.279 | 0.99 |
| 129_L | 143_V | 1.278 | 0.99 |
| 47_Q | 147_R | 1.258 | 0.99 |
| 125_A | 231_I | 1.254 | 0.99 |
| 209_F | 250_D | 1.250 | 0.99 |
| 159_T | 206_S | 1.247 | 0.99 |
| 91_V | 170_G | 1.238 | 0.98 |
| 98_E | 209_F | 1.229 | 0.98 |
| 6_L | 10_G | 1.225 | 0.98 |
| 220_N | 223_D | 1.211 | 0.98 |
| 23_A | 215_W | 1.186 | 0.98 |
| 253_L | 257_M | 1.172 | 0.98 |
| 116_L | 218_L | 1.169 | 0.97 |
| 32_V | 36_E | 1.167 | 0.97 |
| 167_I | 189_M | 1.149 | 0.97 |
| 14_I | 18_R | 1.134 | 0.97 |
| 79_T | 84_E | 1.134 | 0.97 |
| 71_G | 91_V | 1.133 | 0.97 |
| 155_L | 159_T | 1.116 | 0.96 |
| 93_L | 97_R | 1.114 | 0.96 |
| 207_V | 211_I | 1.102 | 0.96 |
| 124_R | 133_E | 1.100 | 0.96 |
| 163_V | 202_C | 1.097 | 0.96 |
| 137_V | 142_R | 1.095 | 0.96 |
| 92_A | 189_M | 1.093 | 0.96 |
| 155_L | 210_A | 1.079 | 0.95 |
| 33_G | 145_S | 1.073 | 0.95 |
| 97_R | 198_D | 1.069 | 0.95 |
| 152_V | 207_V | 1.064 | 0.95 |
| 69_V | 94_S | 1.057 | 0.95 |
| 133_E | 139_P | 1.053 | 0.95 |
| 217_S | 242_S | 1.052 | 0.95 |
| 201_N | 257_M | 1.052 | 0.95 |
| 122_L | 228_S | 1.051 | 0.94 |
| 122_L | 231_I | 1.047 | 0.94 |
| 22_R | 223_D | 1.040 | 0.94 |
| 26_M | 144_I | 1.038 | 0.94 |
| 24_G | 28_F | 1.033 | 0.94 |
| 104_A | 162_F | 1.031 | 0.94 |
| 47_Q | 50_N | 1.025 | 0.93 |
| 138_D | 141_R | 1.020 | 0.93 |
| 145_S | 148_F | 1.020 | 0.93 |
| 219_F | 223_D | 1.018 | 0.93 |
| 57_L | 61_V | 1.006 | 0.93 |
| 200_V | 204_I | 1.006 | 0.93 |
| 46_R | 229_A | 1.005 | 0.93 |
| 205_K | 209_F | 1.003 | 0.93 |
| 112_A | 115_A | 1.002 | 0.92 |
| 111_R | 235_T | 1.002 | 0.92 |
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 | |
| 2zy9A | 2 | 0.5538 | 7.1 | 0.963 | Contact Map |
| 2mgyA | 1 | 0.3923 | 6.7 | 0.964 | Contact Map |
| 1rh5C | 1 | 0.1231 | 3.4 | 0.969 | Contact Map |
| 3ze3A | 6 | 0.2846 | 1.7 | 0.973 | Contact Map |
| 4xp4A | 1 | 0 | 1.6 | 0.973 | Contact Map |
| 2ls2A | 1 | 0.0962 | 1.6 | 0.974 | Contact Map |
| 2a65A | 1 | 0.7538 | 1.5 | 0.974 | Contact Map |
| 4u9nA | 2 | 0.4846 | 1.4 | 0.975 | Contact Map |
| 2nwlA | 3 | 0.3769 | 1.3 | 0.975 | Contact Map |
| 1h2sB | 1 | 0.2154 | 1.3 | 0.975 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)