| T0833 |
| ID: | 1403812340 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 136 (133) | ||
| Sequences: | 1031 (948.1) | ||
| Seq/Len: | 7.752 | ||
| Nf(neff/√len): | 82.2 |
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: 7.752).
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 |
| 66_N | 70_K | 7.207 | 1.00 |
| 97_D | 101_G | 6.670 | 1.00 |
| 118_S | 122_Q | 4.978 | 1.00 |
| 37_E | 41_K | 4.585 | 1.00 |
| 95_Q | 104_K | 3.131 | 1.00 |
| 64_Q | 73_E | 2.606 | 1.00 |
| 116_N | 125_I | 2.082 | 1.00 |
| 101_G | 121_V | 2.068 | 1.00 |
| 107_Y | 111_D | 1.798 | 1.00 |
| 77_F | 81_R | 1.677 | 1.00 |
| 63_F | 71_V | 1.549 | 1.00 |
| 94_Y | 102_E | 1.498 | 0.99 |
| 65_Y | 71_V | 1.462 | 0.99 |
| 34_D | 42_I | 1.444 | 0.99 |
| 104_K | 114_K | 1.426 | 0.99 |
| 95_Q | 103_I | 1.349 | 0.99 |
| 61_Y | 74_K | 1.337 | 0.99 |
| 122_Q | 129_T | 1.313 | 0.98 |
| 123_N | 126_I | 1.303 | 0.98 |
| 92_I | 108_G | 1.290 | 0.98 |
| 128_S | 131_Y | 1.266 | 0.98 |
| 128_S | 132_E | 1.193 | 0.96 |
| 15_F | 18_M | 1.175 | 0.96 |
| 107_Y | 113_K | 1.153 | 0.95 |
| 9_S | 13_L | 1.144 | 0.95 |
| 13_L | 18_M | 1.120 | 0.94 |
| 5_V | 10_I | 1.118 | 0.94 |
| 94_Y | 105_T | 1.114 | 0.94 |
| 4_S | 8_K | 1.103 | 0.94 |
| 84_D | 87_V | 1.087 | 0.93 |
| 3_T | 13_L | 1.084 | 0.93 |
| 4_S | 13_L | 1.077 | 0.93 |
| 11_L | 18_M | 1.073 | 0.92 |
| 35_T | 44_S | 1.068 | 0.92 |
| 3_T | 8_K | 1.056 | 0.92 |
| 5_V | 9_S | 1.056 | 0.92 |
| 5_V | 11_L | 1.055 | 0.92 |
| 12_A | 15_F | 1.048 | 0.91 |
| 102_E | 105_T | 1.043 | 0.91 |
| 13_L | 17_F | 1.040 | 0.91 |
| 64_Q | 72_S | 1.037 | 0.91 |
| 4_S | 10_I | 1.035 | 0.91 |
| 9_S | 12_A | 1.032 | 0.90 |
| 34_D | 45_K | 1.032 | 0.90 |
| 4_S | 9_S | 1.029 | 0.90 |
| 10_I | 15_F | 1.029 | 0.90 |
| 53_G | 56_N | 1.026 | 0.90 |
| 52_N | 57_K | 1.023 | 0.90 |
| 8_K | 14_V | 1.019 | 0.90 |
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 | |
| 3mswA | 1 | 0.8088 | 98.9 | 0.548 | Contact Map |
| 4iglB | 2 | 0.7868 | 98.6 | 0.594 | Contact Map |
| 4o9xA | 1 | 0.9044 | 98.3 | 0.623 | Contact Map |
| 4iglA | 2 | 0.875 | 96.7 | 0.725 | Contact Map |
| 4ghbA | 2 | 0.8676 | 90 | 0.798 | Contact Map |
| 4a2lA | 6 | 0.7574 | 45.3 | 0.86 | Contact Map |
| 3nokA | 2 | 0.7868 | 19 | 0.885 | Contact Map |
| 3zbiC | 14 | 0.2059 | 14.7 | 0.89 | Contact Map |
| 3vgzA | 4 | 0.7132 | 14.5 | 0.891 | Contact Map |
| 2ecfA | 1 | 0.7721 | 13.4 | 0.892 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)