| T0798 |
| ID: | 1401386785 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 198 (167) | ||
| Sequences: | 18491 (11088.3) | ||
| Seq/Len: | 110.725 | ||
| Nf(neff/√len): | 858.0 |
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: 110.725).
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 |
| 23_R | 151_S | 3.215 | 1.00 |
| 12_D | 94_N | 3.137 | 1.00 |
| 115_V | 157_A | 2.845 | 1.00 |
| 20_L | 83_V | 2.711 | 1.00 |
| 144_I | 160_N | 2.646 | 1.00 |
| 83_V | 117_N | 2.505 | 1.00 |
| 160_N | 163_T | 2.438 | 1.00 |
| 81_L | 115_V | 2.403 | 1.00 |
| 86_I | 116_G | 2.370 | 1.00 |
| 142_S | 160_N | 2.300 | 1.00 |
| 89_H | 131_E | 2.275 | 1.00 |
| 117_N | 148_A | 2.171 | 1.00 |
| 133_R | 137_E | 2.164 | 1.00 |
| 84_Y | 143_F | 2.136 | 1.00 |
| 129_T | 133_R | 2.029 | 1.00 |
| 153_N | 156_E | 1.972 | 1.00 |
| 79_G | 161_I | 1.944 | 1.00 |
| 20_L | 154_V | 1.926 | 1.00 |
| 9_L | 21_L | 1.924 | 1.00 |
| 86_I | 119_S | 1.911 | 1.00 |
| 132_A | 136_A | 1.801 | 1.00 |
| 8_V | 77_A | 1.786 | 1.00 |
| 55_A | 162_L | 1.776 | 1.00 |
| 116_G | 145_E | 1.773 | 1.00 |
| 146_T | 157_A | 1.740 | 1.00 |
| 119_S | 145_E | 1.721 | 1.00 |
| 119_S | 152_T | 1.704 | 1.00 |
| 160_N | 164_E | 1.672 | 1.00 |
| 99_L | 112_I | 1.649 | 1.00 |
| 113_M | 144_I | 1.619 | 1.00 |
| 96_E | 138_K | 1.611 | 1.00 |
| 88_K | 91_T | 1.611 | 1.00 |
| 20_L | 157_A | 1.553 | 1.00 |
| 19_N | 148_A | 1.524 | 1.00 |
| 81_L | 161_I | 1.519 | 1.00 |
| 9_L | 81_L | 1.480 | 1.00 |
| 135_F | 139_N | 1.478 | 1.00 |
| 134_A | 138_K | 1.464 | 1.00 |
| 85_D | 118_K | 1.464 | 1.00 |
| 85_D | 88_K | 1.392 | 0.99 |
| 113_M | 160_N | 1.367 | 0.99 |
| 115_V | 146_T | 1.341 | 0.99 |
| 7_V | 79_G | 1.309 | 0.99 |
| 132_A | 143_F | 1.308 | 0.99 |
| 5_F | 165_I | 1.304 | 0.99 |
| 82_L | 95_V | 1.292 | 0.99 |
| 100_K | 103_R | 1.287 | 0.99 |
| 164_E | 167_R | 1.278 | 0.99 |
| 156_E | 159_K | 1.255 | 0.99 |
| 82_L | 99_L | 1.240 | 0.98 |
| 115_V | 144_I | 1.236 | 0.98 |
| 87_A | 121_L | 1.233 | 0.98 |
| 81_L | 157_A | 1.207 | 0.98 |
| 47_Q | 52_T | 1.203 | 0.98 |
| 125_R | 145_E | 1.196 | 0.98 |
| 36_T | 62_G | 1.193 | 0.98 |
| 118_K | 121_L | 1.188 | 0.98 |
| 155_E | 159_K | 1.179 | 0.98 |
| 22_S | 30_N | 1.177 | 0.98 |
| 133_R | 136_A | 1.159 | 0.97 |
| 20_L | 24_F | 1.149 | 0.97 |
| 128_P | 131_E | 1.132 | 0.97 |
| 131_E | 134_A | 1.125 | 0.97 |
| 99_L | 103_R | 1.121 | 0.97 |
| 47_Q | 50_G | 1.116 | 0.96 |
| 53_I | 162_L | 1.098 | 0.96 |
| 114_L | 141_L | 1.092 | 0.96 |
| 100_K | 104_D | 1.083 | 0.96 |
| 130_D | 134_A | 1.081 | 0.95 |
| 156_E | 160_N | 1.080 | 0.95 |
| 23_R | 27_N | 1.076 | 0.95 |
| 84_Y | 132_A | 1.073 | 0.95 |
| 116_G | 132_A | 1.072 | 0.95 |
| 20_L | 148_A | 1.063 | 0.95 |
| 12_D | 15_V | 1.059 | 0.95 |
| 79_G | 165_I | 1.052 | 0.95 |
| 23_R | 154_V | 1.043 | 0.94 |
| 34_K | 37_I | 1.042 | 0.94 |
| 96_E | 135_F | 1.032 | 0.94 |
| 116_G | 143_F | 1.029 | 0.94 |
| 22_S | 26_R | 1.007 | 0.93 |
| 61_A | 64_E | 1.005 | 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 | |
| 3cpjB | 1 | 0.8283 | 100 | 0.332 | Contact Map |
| 4lhwA | 5 | 0.8687 | 100 | 0.335 | Contact Map |
| 3dz8A | 1 | 0.8535 | 100 | 0.336 | Contact Map |
| 2a5jA | 1 | 0.8535 | 100 | 0.341 | Contact Map |
| 2f7sA | 2 | 0.8788 | 100 | 0.348 | Contact Map |
| 2yc2C | 2 | 0.702 | 100 | 0.348 | Contact Map |
| 1zbdA | 1 | 0.8788 | 100 | 0.35 | Contact Map |
| 2ew1A | 1 | 0.8586 | 100 | 0.351 | Contact Map |
| 2gf9A | 1 | 0.8636 | 100 | 0.351 | Contact Map |
| 4dkxA | 2 | 0.7879 | 100 | 0.352 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)