| LYMPH |
| ID: | 1493434149 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 93 (82) | ||
| Sequences: | 96 (74.6) | ||
| Seq/Len: | 1.171 | ||
| Nf(neff/√len): | 8.2 |
HHblits Results: (2016_02)
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: 1.171).
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 |
| 42_K | 66_K | 1.904 | 0.95 |
| 10_T | 32_G | 1.835 | 0.94 |
| 27_Y | 64_D | 1.759 | 0.92 |
| 25_K | 29_I | 1.754 | 0.92 |
| 29_I | 39_F | 1.611 | 0.87 |
| 3_S | 75_Q | 1.583 | 0.85 |
| 76_T | 82_Q | 1.537 | 0.83 |
| 75_Q | 82_Q | 1.468 | 0.79 |
| 76_T | 79_T | 1.439 | 0.77 |
| 74_I | 77_K | 1.396 | 0.74 |
| 6_S | 58_D | 1.364 | 0.71 |
| 27_Y | 55_W | 1.345 | 0.70 |
| 61_R | 66_K | 1.285 | 0.65 |
| 6_S | 67_S | 1.275 | 0.64 |
| 2_G | 32_G | 1.247 | 0.61 |
| 77_K | 81_T | 1.240 | 0.60 |
| 19_L | 41_T | 1.221 | 0.59 |
| 50_D | 69_T | 1.219 | 0.59 |
| 11_C | 27_Y | 1.212 | 0.58 |
| 38_I | 50_D | 1.204 | 0.57 |
| 78_P | 82_Q | 1.196 | 0.56 |
| 18_R | 35_R | 1.193 | 0.56 |
| 77_K | 80_G | 1.175 | 0.54 |
| 66_K | 77_K | 1.163 | 0.53 |
| 2_G | 34_L | 1.147 | 0.52 |
| 63_M | 68_N | 1.143 | 0.51 |
| 54_T | 58_D | 1.142 | 0.51 |
| 65_R | 71_N | 1.140 | 0.51 |
| 33_S | 41_T | 1.130 | 0.50 |
| 39_F | 56_V | 1.123 | 0.49 |
| 30_T | 33_S | 1.103 | 0.47 |
| 34_L | 57_R | 1.092 | 0.46 |
| 11_C | 55_W | 1.066 | 0.44 |
| 14_L | 33_S | 1.066 | 0.44 |
| 22_S | 37_V | 1.056 | 0.43 |
| 7_D | 33_S | 1.055 | 0.43 |
| 46_K | 75_Q | 1.053 | 0.43 |
| 56_V | 59_V | 1.045 | 0.42 |
| 76_T | 81_T | 1.041 | 0.41 |
| 76_T | 80_G | 1.040 | 0.41 |
| 6_S | 28_T | 1.039 | 0.41 |
| 8_K | 33_S | 1.033 | 0.41 |
| 18_R | 54_T | 1.026 | 0.40 |
| 37_V | 66_K | 1.012 | 0.39 |
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 | |
| 1j8iA | 1 | 1 | 100 | 0.231 | Contact Map |
| 1g91A | 1 | 0.7957 | 99.8 | 0.445 | Contact Map |
| 4oijC | 2 | 0.0108 | 99.8 | 0.457 | Contact Map |
| 1ha6A | 1 | 0.7097 | 99.8 | 0.458 | Contact Map |
| 1m8aA | 2 | 0.6129 | 99.8 | 0.46 | Contact Map |
| 2mp1A | 1 | 0 | 99.8 | 0.461 | Contact Map |
| 1eotA | 1 | 0.7634 | 99.8 | 0.462 | Contact Map |
| 1eigA | 1 | 0.7527 | 99.8 | 0.464 | Contact Map |
| 1esrA | 1 | 0.7742 | 99.8 | 0.465 | Contact Map |
| 2l4nA | 1 | 0.6882 | 99.8 | 0.466 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)