| T0768 |
| ID: | 1399482620 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 170 (166) | ||
| Sequences: | 3085 (2656.4) | ||
| Seq/Len: | 18.584 | ||
| Nf(neff/√len): | 206.2 |
Jackhmmer Results: (2014_04_16)
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: 18.584).
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 |
| 118_L | 122_L | 3.742 | 1.00 |
| 95_V | 99_V | 3.467 | 1.00 |
| 141_I | 145_V | 3.319 | 1.00 |
| 91_T | 114_S | 2.856 | 1.00 |
| 148_M | 151_P | 2.782 | 1.00 |
| 137_K | 159_D | 2.733 | 1.00 |
| 114_S | 137_K | 2.707 | 1.00 |
| 102_I | 106_A | 2.690 | 1.00 |
| 92_G | 115_D | 2.592 | 1.00 |
| 110_C | 133_C | 2.325 | 1.00 |
| 125_I | 129_A | 2.197 | 1.00 |
| 80_I | 106_A | 2.139 | 1.00 |
| 133_C | 155_S | 1.992 | 1.00 |
| 72_G | 75_Y | 1.973 | 1.00 |
| 79_V | 101_S | 1.964 | 1.00 |
| 138_E | 160_T | 1.948 | 1.00 |
| 80_I | 84_A | 1.927 | 1.00 |
| 101_S | 124_Y | 1.897 | 1.00 |
| 100_I | 123_I | 1.826 | 1.00 |
| 98_S | 121_N | 1.826 | 1.00 |
| 115_D | 138_E | 1.814 | 1.00 |
| 111_N | 134_D | 1.739 | 1.00 |
| 123_I | 146_E | 1.731 | 1.00 |
| 112_S | 135_A | 1.661 | 1.00 |
| 135_A | 157_A | 1.630 | 1.00 |
| 125_I | 151_P | 1.573 | 1.00 |
| 93_V | 116_V | 1.524 | 1.00 |
| 124_Y | 147_K | 1.481 | 1.00 |
| 78_T | 100_I | 1.455 | 1.00 |
| 145_V | 148_M | 1.445 | 1.00 |
| 104_R | 126_N | 1.438 | 1.00 |
| 139_I | 161_V | 1.434 | 1.00 |
| 116_V | 139_I | 1.429 | 1.00 |
| 155_S | 158_L | 1.399 | 0.99 |
| 89_N | 112_S | 1.384 | 0.99 |
| 82_E | 103_G | 1.365 | 0.99 |
| 141_I | 163_M | 1.362 | 0.99 |
| 104_R | 127_E | 1.352 | 0.99 |
| 128_L | 131_A | 1.345 | 0.99 |
| 142_P | 145_V | 1.321 | 0.99 |
| 120_E | 143_A | 1.311 | 0.99 |
| 33_V | 36_Y | 1.293 | 0.99 |
| 83_K | 86_E | 1.288 | 0.99 |
| 117_K | 140_T | 1.285 | 0.99 |
| 126_N | 129_A | 1.275 | 0.99 |
| 109_Y | 132_S | 1.273 | 0.99 |
| 130_F | 152_F | 1.268 | 0.99 |
| 119_S | 122_L | 1.231 | 0.98 |
| 106_A | 129_A | 1.216 | 0.98 |
| 95_V | 118_L | 1.202 | 0.98 |
| 60_Y | 92_G | 1.199 | 0.98 |
| 110_C | 155_S | 1.187 | 0.98 |
| 48_L | 53_E | 1.159 | 0.97 |
| 133_C | 136_L | 1.137 | 0.97 |
| 84_A | 106_A | 1.133 | 0.97 |
| 118_L | 141_I | 1.091 | 0.96 |
| 12_L | 15_C | 1.088 | 0.96 |
| 82_E | 104_R | 1.076 | 0.95 |
| 73_Q | 76_P | 1.073 | 0.95 |
| 97_D | 120_E | 1.047 | 0.94 |
| 33_V | 38_F | 1.046 | 0.94 |
| 163_M | 166_M | 1.040 | 0.94 |
| 121_N | 144_S | 1.037 | 0.94 |
| 94_T | 117_K | 1.037 | 0.94 |
| 60_Y | 64_P | 1.036 | 0.94 |
| 83_K | 105_L | 1.033 | 0.94 |
| 97_D | 119_S | 1.032 | 0.94 |
| 102_I | 129_A | 1.026 | 0.94 |
| 132_S | 154_W | 1.020 | 0.93 |
| 110_C | 113_L | 1.019 | 0.93 |
| 134_D | 156_N | 1.017 | 0.93 |
| 129_A | 151_P | 1.016 | 0.93 |
| 71_N | 75_Y | 1.007 | 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 | |
| 4gt6A | 1 | 0.8353 | 99.6 | 0.504 | Contact Map |
| 4fs7A | 1 | 0.8 | 99.4 | 0.552 | Contact Map |
| 2lz0A | 1 | 0.5706 | 99.4 | 0.57 | Contact Map |
| 4fdwA | 1 | 0.9294 | 99.1 | 0.615 | Contact Map |
| 4h09A | 5 | 0.8353 | 99.1 | 0.62 | Contact Map |
| 4kt1A | 1 | 0.8059 | 99 | 0.634 | Contact Map |
| 3t6qA | 2 | 0.7824 | 99 | 0.636 | Contact Map |
| 3sb4A | 2 | 0.9529 | 99 | 0.637 | Contact Map |
| 3zyjA | 2 | 0.8059 | 99 | 0.643 | Contact Map |
| 3zyiA | 1 | 0.8059 | 98.9 | 0.65 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)