| 4CI0_B |
| ID: | 1488369412 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 50% gaps before running GREMLIN. |
| Length: | 275 (218) | ||
| Sequences: | 2166 (922.8) | ||
| Seq/Len: | 9.936 | ||
| Nf(neff/√len): | 62.5 |
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: 9.936).
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 |
| 126_V | 162_I | 3.662 | 1.00 |
| 48_R | 80_D | 2.356 | 1.00 |
| 99_A | 123_A | 2.338 | 1.00 |
| 60_D | 173_P | 2.238 | 1.00 |
| 105_V | 116_L | 2.052 | 1.00 |
| 53_H | 56_G | 2.038 | 1.00 |
| 53_H | 58_T | 2.011 | 1.00 |
| 55_S | 106_C | 1.939 | 1.00 |
| 113_L | 117_K | 1.927 | 1.00 |
| 54_L | 112_S | 1.792 | 1.00 |
| 61_A | 84_G | 1.708 | 1.00 |
| 54_L | 105_V | 1.696 | 1.00 |
| 159_A | 167_A | 1.694 | 1.00 |
| 51_Y | 61_A | 1.679 | 1.00 |
| 99_A | 119_L | 1.594 | 1.00 |
| 49_I | 79_V | 1.591 | 1.00 |
| 97_D | 122_K | 1.580 | 1.00 |
| 50_G | 96_M | 1.569 | 1.00 |
| 173_P | 178_I | 1.554 | 1.00 |
| 101_V | 116_L | 1.518 | 1.00 |
| 73_E | 77_N | 1.514 | 1.00 |
| 61_A | 102_E | 1.484 | 1.00 |
| 97_D | 124_K | 1.476 | 1.00 |
| 236_D | 243_E | 1.468 | 1.00 |
| 53_H | 85_Q | 1.456 | 1.00 |
| 129_F | 178_I | 1.433 | 1.00 |
| 222_G | 237_M | 1.432 | 1.00 |
| 64_L | 71_L | 1.427 | 1.00 |
| 81_I | 87_L | 1.405 | 0.99 |
| 174_S | 177_I | 1.387 | 0.99 |
| 221_I | 261_R | 1.377 | 0.99 |
| 216_N | 219_L | 1.371 | 0.99 |
| 220_C | 230_C | 1.369 | 0.99 |
| 190_M | 194_Q | 1.361 | 0.99 |
| 55_S | 104_S | 1.353 | 0.99 |
| 53_H | 61_A | 1.330 | 0.99 |
| 56_G | 60_D | 1.313 | 0.99 |
| 70_I | 73_E | 1.313 | 0.99 |
| 229_A | 233_R | 1.308 | 0.99 |
| 110_E | 118_E | 1.308 | 0.99 |
| 168_L | 173_P | 1.305 | 0.99 |
| 54_L | 86_T | 1.283 | 0.99 |
| 67_N | 70_I | 1.276 | 0.99 |
| 249_C | 252_C | 1.276 | 0.99 |
| 110_E | 114_H | 1.267 | 0.99 |
| 157_P | 160_D | 1.258 | 0.99 |
| 55_S | 112_S | 1.252 | 0.99 |
| 211_Q | 248_R | 1.243 | 0.98 |
| 222_G | 258_Q | 1.233 | 0.98 |
| 178_I | 182_V | 1.228 | 0.98 |
| 254_I | 257_V | 1.219 | 0.98 |
| 65_T | 87_L | 1.210 | 0.98 |
| 236_D | 239_N | 1.207 | 0.98 |
| 96_M | 124_K | 1.201 | 0.98 |
| 171_C | 261_R | 1.188 | 0.98 |
| 238_T | 258_Q | 1.181 | 0.98 |
| 168_L | 181_T | 1.171 | 0.97 |
| 56_G | 85_Q | 1.166 | 0.97 |
| 254_I | 258_Q | 1.162 | 0.97 |
| 222_G | 261_R | 1.162 | 0.97 |
| 101_V | 162_I | 1.160 | 0.97 |
| 131_S | 135_T | 1.144 | 0.97 |
| 52_I | 96_M | 1.132 | 0.97 |
| 53_H | 86_T | 1.131 | 0.97 |
| 52_I | 58_T | 1.129 | 0.97 |
| 236_D | 244_L | 1.127 | 0.97 |
| 62_M | 66_E | 1.119 | 0.96 |
| 127_C | 181_T | 1.119 | 0.96 |
| 114_H | 118_E | 1.118 | 0.96 |
| 47_P | 98_L | 1.112 | 0.96 |
| 48_R | 82_V | 1.107 | 0.96 |
| 105_V | 113_L | 1.105 | 0.96 |
| 236_D | 245_N | 1.102 | 0.96 |
| 45_A | 48_R | 1.093 | 0.96 |
| 51_Y | 100_L | 1.092 | 0.96 |
| 236_D | 257_V | 1.092 | 0.96 |
| 59_G | 137_C | 1.088 | 0.96 |
| 238_T | 243_E | 1.088 | 0.96 |
| 53_H | 102_E | 1.085 | 0.96 |
| 258_Q | 261_R | 1.074 | 0.95 |
| 77_N | 99_A | 1.072 | 0.95 |
| 116_L | 158_I | 1.070 | 0.95 |
| 133_A | 257_V | 1.067 | 0.95 |
| 202_Y | 209_D | 1.065 | 0.95 |
| 61_A | 86_T | 1.065 | 0.95 |
| 136_G | 170_G | 1.055 | 0.95 |
| 58_T | 85_Q | 1.051 | 0.94 |
| 70_I | 179_A | 1.050 | 0.94 |
| 132_C | 258_Q | 1.046 | 0.94 |
| 110_E | 115_E | 1.044 | 0.94 |
| 56_G | 62_M | 1.040 | 0.94 |
| 64_L | 100_L | 1.038 | 0.94 |
| 71_L | 96_M | 1.037 | 0.94 |
| 240_G | 245_N | 1.034 | 0.94 |
| 117_K | 121_E | 1.033 | 0.94 |
| 226_C | 230_C | 1.031 | 0.94 |
| 132_C | 257_V | 1.023 | 0.93 |
| 227_A | 235_L | 1.018 | 0.93 |
| 156_V | 160_D | 1.017 | 0.93 |
| 64_L | 67_N | 1.016 | 0.93 |
| 208_C | 221_I | 1.014 | 0.93 |
| 235_L | 243_E | 1.009 | 0.93 |
| 133_A | 222_G | 1.006 | 0.93 |
| 49_I | 100_L | 1.005 | 0.93 |
| 127_C | 182_V | 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 | |
| 4omfG | 1 | 0.84 | 100 | 0.343 | Contact Map |
| 4iucS | 1 | 0.7927 | 100 | 0.516 | Contact Map |
| 1h2aS | 1 | 0.7927 | 100 | 0.522 | Contact Map |
| 4uqlA | 2 | 0.7927 | 100 | 0.522 | Contact Map |
| 4ue3S | 2 | 0.7927 | 100 | 0.535 | Contact Map |
| 3ayxB | 2 | 0.8073 | 100 | 0.537 | Contact Map |
| 4u9hS | 1 | 0.7709 | 100 | 0.547 | Contact Map |
| 1yq9A | 2 | 0.7709 | 100 | 0.55 | Contact Map |
| 4kn9S | 2 | 0.7891 | 100 | 0.556 | Contact Map |
| 3myrA | 4 | 0.8036 | 100 | 0.556 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)