| T0841 |
| ID: | 1404412446 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 253 (231) | ||
| Sequences: | 9853 (7712.6) | ||
| Seq/Len: | 42.654 | ||
| Nf(neff/√len): | 507.5 |
HHblits Results: (2013_03)
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: 42.654).
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 |
| 138_C | 203_C | 6.242 | 1.00 |
| 45_G | 53_I | 3.800 | 1.00 |
| 52_W | 107_L | 3.525 | 1.00 |
| 33_S | 41_H | 3.487 | 1.00 |
| 31_T | 141_A | 3.229 | 1.00 |
| 27_N | 157_V | 3.215 | 1.00 |
| 47_L | 114_V | 3.096 | 1.00 |
| 43_C | 59_C | 3.021 | 1.00 |
| 28_S | 157_V | 2.964 | 1.00 |
| 193_C | 221_C | 2.884 | 1.00 |
| 58_Q | 197_Y | 2.791 | 1.00 |
| 30_W | 124_C | 2.676 | 1.00 |
| 74_L | 114_V | 2.657 | 1.00 |
| 94_A | 109_K | 2.625 | 1.00 |
| 60_F | 106_V | 2.590 | 1.00 |
| 191_G | 228_A | 2.526 | 1.00 |
| 54_L | 211_L | 2.458 | 1.00 |
| 46_S | 211_L | 2.330 | 1.00 |
| 52_W | 109_K | 2.253 | 1.00 |
| 158_A | 190_V | 2.187 | 1.00 |
| 32_V | 45_G | 2.141 | 1.00 |
| 28_S | 141_A | 2.122 | 1.00 |
| 51_Q | 113_S | 2.087 | 1.00 |
| 100_P | 243_V | 2.087 | 1.00 |
| 110_L | 114_V | 2.062 | 1.00 |
| 20_V | 23_G | 2.058 | 1.00 |
| 92_P | 111_E | 2.043 | 1.00 |
| 116_L | 122_L | 1.997 | 1.00 |
| 103_S | 236_F | 1.991 | 1.00 |
| 95_K | 109_K | 1.962 | 1.00 |
| 140_I | 192_A | 1.944 | 1.00 |
| 51_Q | 109_K | 1.929 | 1.00 |
| 91_V | 114_V | 1.921 | 1.00 |
| 32_V | 74_L | 1.918 | 1.00 |
| 179_S | 235_V | 1.892 | 1.00 |
| 93_V | 108_L | 1.875 | 1.00 |
| 105_L | 236_F | 1.871 | 1.00 |
| 140_I | 158_A | 1.856 | 1.00 |
| 46_S | 214_I | 1.851 | 1.00 |
| 46_S | 123_I | 1.849 | 1.00 |
| 141_A | 202_A | 1.810 | 1.00 |
| 181_M | 201_L | 1.756 | 1.00 |
| 123_I | 211_L | 1.746 | 1.00 |
| 97_V | 243_V | 1.743 | 1.00 |
| 168_C | 182_C | 1.713 | 1.00 |
| 138_C | 162_V | 1.704 | 1.00 |
| 49_K | 52_W | 1.673 | 1.00 |
| 217_P | 229_V | 1.667 | 1.00 |
| 237_V | 241_H | 1.664 | 1.00 |
| 231_T | 236_F | 1.629 | 1.00 |
| 73_W | 76_T | 1.626 | 1.00 |
| 55_T | 60_F | 1.595 | 1.00 |
| 50_E | 113_S | 1.594 | 1.00 |
| 73_W | 90_R | 1.584 | 1.00 |
| 123_I | 202_A | 1.555 | 1.00 |
| 192_A | 215_I | 1.534 | 1.00 |
| 191_G | 230_F | 1.516 | 1.00 |
| 164_S | 167_E | 1.508 | 1.00 |
| 165_N | 232_R | 1.489 | 1.00 |
| 32_V | 53_I | 1.477 | 1.00 |
| 148_G | 223_R | 1.476 | 1.00 |
| 72_V | 75_G | 1.469 | 1.00 |
| 35_R | 41_H | 1.416 | 1.00 |
| 94_A | 111_E | 1.397 | 0.99 |
| 30_W | 209_W | 1.397 | 0.99 |
| 31_T | 155_L | 1.395 | 0.99 |
| 91_V | 111_E | 1.393 | 0.99 |
| 152_D | 156_N | 1.375 | 0.99 |
| 180_E | 217_P | 1.364 | 0.99 |
| 232_R | 235_V | 1.356 | 0.99 |
| 47_L | 74_L | 1.355 | 0.99 |
| 161_N | 184_E | 1.325 | 0.99 |
| 26_G | 77_L | 1.321 | 0.99 |
| 140_I | 215_I | 1.321 | 0.99 |
| 179_S | 236_F | 1.308 | 0.99 |
| 140_I | 160_L | 1.292 | 0.99 |
| 105_L | 231_T | 1.275 | 0.99 |
| 138_C | 212_E | 1.274 | 0.99 |
| 203_C | 212_E | 1.258 | 0.99 |
| 134_P | 164_S | 1.249 | 0.99 |
| 26_G | 119_R | 1.247 | 0.99 |
| 201_L | 230_F | 1.234 | 0.98 |
| 138_C | 201_L | 1.224 | 0.98 |
| 215_I | 218_N | 1.221 | 0.98 |
| 28_S | 139_E | 1.218 | 0.98 |
| 47_L | 116_L | 1.201 | 0.98 |
| 31_T | 44_G | 1.201 | 0.98 |
| 74_L | 120_V | 1.199 | 0.98 |
| 191_G | 222_A | 1.183 | 0.98 |
| 124_C | 209_W | 1.164 | 0.97 |
| 34_L | 72_V | 1.161 | 0.97 |
| 52_W | 243_V | 1.157 | 0.97 |
| 177_R | 180_E | 1.151 | 0.97 |
| 139_E | 159_L | 1.150 | 0.97 |
| 98_C | 106_V | 1.147 | 0.97 |
| 183_T | 201_L | 1.138 | 0.97 |
| 30_W | 202_A | 1.123 | 0.97 |
| 163_I | 227_P | 1.117 | 0.96 |
| 160_L | 230_F | 1.112 | 0.96 |
| 53_I | 72_V | 1.101 | 0.96 |
| 55_T | 106_V | 1.084 | 0.96 |
| 125_L | 237_V | 1.084 | 0.96 |
| 137_K | 159_L | 1.073 | 0.95 |
| 99_G | 102_G | 1.062 | 0.95 |
| 76_T | 88_L | 1.049 | 0.94 |
| 47_L | 53_I | 1.049 | 0.94 |
| 31_T | 200_P | 1.044 | 0.94 |
| 161_N | 185_G | 1.036 | 0.94 |
| 58_Q | 104_Q | 1.033 | 0.94 |
| 126_P | 237_V | 1.017 | 0.93 |
| 117_N | 120_V | 1.015 | 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 | |
| 4durA | 2 | 0.9447 | 100 | 0.073 | Contact Map |
| 3nxpA | 1 | 0.9723 | 100 | 0.099 | Contact Map |
| 4nzqA | 1 | 0.9802 | 100 | 0.102 | Contact Map |
| 2f83A | 1 | 0.8458 | 100 | 0.113 | Contact Map |
| 2b9lA | 1 | 0.9763 | 100 | 0.119 | Contact Map |
| 4kkdA | 2 | 0.9526 | 100 | 0.122 | Contact Map |
| 4igdA | 1 | 0.9328 | 100 | 0.123 | Contact Map |
| 2asuB | 1 | 0.8893 | 100 | 0.123 | Contact Map |
| 2xxlA | 2 | 0.9526 | 100 | 0.135 | Contact Map |
| 4f4oC | 4 | 0.8854 | 100 | 0.137 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)