| bd |
| ID: | 1478623509 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 50% gaps before running GREMLIN. |
| Length: | 145 (94) | ||
| Sequences: | 45494 (30385) | ||
| Seq/Len: | 483.979 | ||
| Nf(neff/√len): | 3134.0 |
Jackhmmer Results: (2016_04)
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: 483.979).
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 |
| 110_S | 138_E | 4.547 | 1.00 |
| 106_Q | 141_E | 2.554 | 1.00 |
| 93_P | 98_A | 2.456 | 1.00 |
| 114_L | 127_L | 2.410 | 1.00 |
| 107_F | 140_M | 2.271 | 1.00 |
| 103_K | 141_E | 1.977 | 1.00 |
| 85_P | 107_F | 1.888 | 1.00 |
| 87_H | 107_F | 1.850 | 1.00 |
| 120_D | 123_T | 1.791 | 1.00 |
| 125_S | 129_L | 1.743 | 1.00 |
| 94_S | 98_A | 1.726 | 1.00 |
| 109_V | 140_M | 1.674 | 1.00 |
| 91_V | 104_V | 1.598 | 1.00 |
| 110_S | 113_G | 1.545 | 1.00 |
| 102_M | 139_V | 1.490 | 1.00 |
| 112_N | 131_G | 1.461 | 1.00 |
| 96_P | 100_A | 1.451 | 1.00 |
| 140_M | 143_L | 1.448 | 1.00 |
| 119_V | 123_T | 1.441 | 1.00 |
| 102_M | 137_M | 1.434 | 1.00 |
| 127_L | 130_T | 1.410 | 1.00 |
| 131_G | 135_I | 1.392 | 0.99 |
| 86_C | 124_V | 1.391 | 0.99 |
| 111_V | 124_V | 1.342 | 0.99 |
| 111_V | 131_G | 1.313 | 0.99 |
| 116_V | 119_V | 1.289 | 0.99 |
| 109_V | 138_E | 1.283 | 0.99 |
| 81_R | 89_Q | 1.275 | 0.99 |
| 103_K | 106_Q | 1.271 | 0.99 |
| 123_T | 126_N | 1.246 | 0.98 |
| 91_V | 95_G | 1.220 | 0.98 |
| 88_I | 102_M | 1.212 | 0.98 |
| 113_G | 136_V | 1.192 | 0.98 |
| 112_N | 136_V | 1.171 | 0.98 |
| 119_V | 125_S | 1.153 | 0.97 |
| 91_V | 98_A | 1.139 | 0.97 |
| 111_V | 135_I | 1.129 | 0.97 |
| 110_S | 115_N | 1.126 | 0.97 |
| 83_S | 87_H | 1.113 | 0.96 |
| 111_V | 137_M | 1.111 | 0.96 |
| 78_F | 81_R | 1.094 | 0.96 |
| 76_W | 79_V | 1.073 | 0.95 |
| 117_L | 123_T | 1.068 | 0.95 |
| 111_V | 116_V | 1.064 | 0.95 |
| 90_A | 104_V | 1.061 | 0.95 |
| 123_T | 127_L | 1.061 | 0.95 |
| 53_E | 56_L | 1.060 | 0.95 |
| 127_L | 131_G | 1.059 | 0.95 |
| 122_R | 125_S | 1.057 | 0.95 |
| 121_Y | 125_S | 1.040 | 0.94 |
| 65_K | 141_E | 1.037 | 0.94 |
| 122_R | 126_N | 1.035 | 0.94 |
| 116_V | 124_V | 1.024 | 0.93 |
| 112_N | 135_I | 1.017 | 0.93 |
| 82_G | 121_Y | 1.003 | 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 | |
| 2xkxA | 2 | 0.931 | 99.6 | 0.381 | Contact Map |
| 1i16A | 1 | 0.7655 | 99.6 | 0.387 | Contact Map |
| 2dmzA | 1 | 0.669 | 99.5 | 0.403 | Contact Map |
| 2yuyA | 1 | 0.6207 | 99.5 | 0.404 | Contact Map |
| 2bygA | 1 | 0.6 | 99.5 | 0.406 | Contact Map |
| 2fe5A | 1 | 0.5793 | 99.5 | 0.408 | Contact Map |
| 1ueqA | 1 | 0.6966 | 99.5 | 0.41 | Contact Map |
| 2fneA | 3 | 0.6483 | 99.5 | 0.41 | Contact Map |
| 2kpkA | 1 | 0.6897 | 99.5 | 0.411 | Contact Map |
| 1x5qA | 1 | 0.669 | 99.5 | 0.411 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)