| T0784 |
| ID: | 1400526599 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 155 (86) | ||
| Sequences: | 1066 (521.4) | ||
| Seq/Len: | 12.395 | ||
| Nf(neff/√len): | 56.2 |
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: 12.395).
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 |
| 41_E | 69_E | 2.855 | 1.00 |
| 42_Q | 70_N | 2.421 | 1.00 |
| 57_A | 88_I | 2.364 | 1.00 |
| 42_Q | 101_C | 2.345 | 1.00 |
| 69_E | 100_T | 2.344 | 1.00 |
| 115_K | 119_S | 2.311 | 1.00 |
| 67_Y | 98_M | 2.173 | 1.00 |
| 41_E | 100_T | 2.114 | 1.00 |
| 70_N | 101_C | 1.915 | 1.00 |
| 39_V | 98_M | 1.861 | 1.00 |
| 77_S | 105_V | 1.756 | 1.00 |
| 46_T | 77_S | 1.726 | 1.00 |
| 56_G | 60_T | 1.721 | 1.00 |
| 51_L | 82_K | 1.590 | 1.00 |
| 46_T | 105_V | 1.561 | 1.00 |
| 112_A | 115_K | 1.528 | 1.00 |
| 81_N | 109_S | 1.524 | 1.00 |
| 55_F | 58_A | 1.507 | 1.00 |
| 50_D | 81_N | 1.506 | 1.00 |
| 79_L | 107_S | 1.486 | 1.00 |
| 57_A | 116_L | 1.464 | 1.00 |
| 48_D | 79_L | 1.456 | 1.00 |
| 54_A | 85_E | 1.433 | 1.00 |
| 93_G | 96_G | 1.412 | 1.00 |
| 82_K | 110_E | 1.396 | 0.99 |
| 65_K | 68_N | 1.335 | 0.99 |
| 67_Y | 77_S | 1.324 | 0.99 |
| 39_V | 67_Y | 1.302 | 0.99 |
| 64_A | 95_E | 1.265 | 0.99 |
| 114_K | 117_K | 1.232 | 0.98 |
| 34_G | 37_K | 1.206 | 0.98 |
| 61_G | 65_K | 1.158 | 0.97 |
| 59_N | 90_C | 1.130 | 0.97 |
| 50_D | 54_A | 1.092 | 0.96 |
| 66_L | 97_S | 1.088 | 0.96 |
| 88_I | 116_L | 1.074 | 0.95 |
| 76_D | 104_S | 1.071 | 0.95 |
| 39_V | 46_T | 1.067 | 0.95 |
| 74_L | 78_Y | 1.051 | 0.94 |
| 89_S | 94_K | 1.048 | 0.94 |
| 115_K | 118_I | 1.038 | 0.94 |
| 58_A | 61_G | 1.033 | 0.94 |
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 | |
| 2jp9A | 1 | 0.729 | 99.9 | 0.619 | Contact Map |
| 1ubdC | 1 | 0.6968 | 99.8 | 0.654 | Contact Map |
| 3w5kB | 1 | 0.7032 | 99.8 | 0.655 | Contact Map |
| 2dlqA | 1 | 0.7677 | 99.8 | 0.661 | Contact Map |
| 2i13A | 2 | 0.8774 | 99.8 | 0.662 | Contact Map |
| 2rpcA | 1 | 0.8452 | 99.8 | 0.663 | Contact Map |
| 3zmsC | 1 | 0 | 99.8 | 0.669 | Contact Map |
| 2kmkA | 1 | 0.529 | 99.8 | 0.67 | Contact Map |
| 1tf6A | 2 | 0.7871 | 99.8 | 0.67 | Contact Map |
| 1a1hA | 1 | 0.5355 | 99.8 | 0.67 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)