| LYR |
| ID: | 1430841055 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 94 (88) | ||
| Sequences: | 370 (285.9) | ||
| Seq/Len: | 4.205 | ||
| Nf(neff/√len): | 30.5 |
Jackhmmer Results: (2015_01_07)
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: 4.205).
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 |
| 38_K | 42_T | 2.516 | 1.00 |
| 49_Q | 58_L | 2.345 | 1.00 |
| 49_Q | 54_V | 2.172 | 1.00 |
| 46_N | 49_Q | 2.034 | 1.00 |
| 19_F | 39_T | 1.919 | 1.00 |
| 9_R | 13_L | 1.846 | 1.00 |
| 19_F | 62_A | 1.663 | 0.99 |
| 44_R | 47_M | 1.642 | 0.99 |
| 75_I | 78_M | 1.590 | 0.99 |
| 11_Q | 14_S | 1.543 | 0.98 |
| 31_F | 76_S | 1.523 | 0.98 |
| 74_V | 79_Y | 1.417 | 0.97 |
| 18_E | 77_Q | 1.376 | 0.96 |
| 64_N | 67_G | 1.367 | 0.96 |
| 70_K | 74_V | 1.360 | 0.95 |
| 65_D | 68_V | 1.354 | 0.95 |
| 23_A | 69_L | 1.349 | 0.95 |
| 56_M | 60_K | 1.342 | 0.95 |
| 84_L | 87_E | 1.339 | 0.95 |
| 29_Y | 32_R | 1.309 | 0.94 |
| 71_R | 75_I | 1.308 | 0.94 |
| 30_N | 34_Y | 1.304 | 0.94 |
| 27_N | 76_S | 1.282 | 0.93 |
| 60_K | 63_K | 1.246 | 0.92 |
| 9_R | 23_A | 1.238 | 0.91 |
| 28_N | 44_R | 1.233 | 0.91 |
| 19_F | 65_D | 1.233 | 0.91 |
| 61_E | 64_N | 1.228 | 0.91 |
| 23_A | 28_N | 1.201 | 0.90 |
| 20_I | 44_R | 1.186 | 0.89 |
| 77_Q | 80_T | 1.176 | 0.88 |
| 51_D | 55_L | 1.174 | 0.88 |
| 57_N | 60_K | 1.173 | 0.88 |
| 28_N | 81_F | 1.165 | 0.88 |
| 52_P | 79_Y | 1.114 | 0.84 |
| 69_L | 76_S | 1.101 | 0.84 |
| 22_N | 25_Q | 1.098 | 0.83 |
| 57_N | 63_K | 1.079 | 0.82 |
| 35_F | 41_T | 1.065 | 0.81 |
| 78_M | 89_L | 1.061 | 0.80 |
| 61_E | 65_D | 1.035 | 0.78 |
| 16_Y | 40_R | 1.035 | 0.78 |
| 7_P | 12_V | 1.025 | 0.77 |
| 75_I | 80_T | 1.023 | 0.77 |
| 42_T | 69_L | 1.022 | 0.77 |
| 38_K | 83_R | 1.017 | 0.76 |
| 53_K | 56_M | 1.010 | 0.76 |
| 59_F | 63_K | 1.009 | 0.75 |
| 29_Y | 37_S | 1.007 | 0.75 |
| 29_Y | 38_K | 1.002 | 0.75 |
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 | |
| 1s94A | 2 | 0.4468 | 40.1 | 0.893 | Contact Map |
| 4jg4A | 1 | 0.9149 | 13.2 | 0.915 | Contact Map |
| 2w84A | 1 | 0.5957 | 6.6 | 0.926 | Contact Map |
| 1dd9A | 1 | 0.5532 | 5.9 | 0.928 | Contact Map |
| 2jucA | 1 | 0.5851 | 4.8 | 0.93 | Contact Map |
| 2h9zA | 1 | 0.3085 | 4.8 | 0.931 | Contact Map |
| 2z0qA | 1 | 0.3511 | 4.7 | 0.931 | Contact Map |
| 2kygC | 1 | 0.4043 | 4 | 0.933 | Contact Map |
| 3zqsA | 2 | 0.4043 | 3.7 | 0.934 | Contact Map |
| 3dmcA | 2 | 0.9574 | 3.7 | 0.934 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)