| 4x5m |
| ID: | 1489269836 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 100 (91) | ||
| Sequences: | 7278 (4928.7) | ||
| Seq/Len: | 79.978 | ||
| Nf(neff/√len): | 516.7 |
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: 79.978).
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 |
| 24_I | 28_R | 3.139 | 1.00 |
| 78_V | 82_I | 2.348 | 1.00 |
| 25_K | 29_T | 2.047 | 1.00 |
| 15_T | 19_F | 2.038 | 1.00 |
| 15_T | 18_A | 1.908 | 1.00 |
| 31_N | 34_G | 1.807 | 1.00 |
| 26_T | 32_T | 1.776 | 1.00 |
| 26_T | 79_I | 1.769 | 1.00 |
| 48_I | 70_L | 1.731 | 1.00 |
| 32_T | 80_T | 1.690 | 1.00 |
| 51_I | 67_I | 1.567 | 1.00 |
| 27_I | 79_I | 1.533 | 1.00 |
| 16_T | 19_F | 1.517 | 1.00 |
| 79_I | 83_N | 1.482 | 1.00 |
| 24_I | 27_I | 1.444 | 1.00 |
| 43_F | 47_V | 1.437 | 1.00 |
| 62_V | 66_N | 1.436 | 1.00 |
| 44_L | 70_L | 1.433 | 1.00 |
| 5_L | 9_L | 1.420 | 1.00 |
| 82_I | 86_K | 1.343 | 0.99 |
| 9_L | 13_F | 1.310 | 0.99 |
| 21_P | 24_I | 1.285 | 0.99 |
| 20_A | 24_I | 1.258 | 0.99 |
| 30_R | 83_N | 1.258 | 0.99 |
| 6_L | 10_F | 1.212 | 0.98 |
| 23_S | 75_P | 1.194 | 0.98 |
| 35_I | 40_Y | 1.191 | 0.98 |
| 63_L | 66_N | 1.177 | 0.98 |
| 11_A | 14_F | 1.172 | 0.98 |
| 75_P | 79_I | 1.161 | 0.97 |
| 62_V | 65_A | 1.161 | 0.97 |
| 89_V | 92_S | 1.159 | 0.97 |
| 47_V | 69_T | 1.154 | 0.97 |
| 38_V | 42_M | 1.153 | 0.97 |
| 50_W | 54_G | 1.141 | 0.97 |
| 8_G | 12_A | 1.108 | 0.96 |
| 40_Y | 76_V | 1.072 | 0.95 |
| 22_Q | 34_G | 1.067 | 0.95 |
| 11_A | 16_T | 1.041 | 0.94 |
| 65_A | 69_T | 1.034 | 0.94 |
| 80_T | 84_R | 1.032 | 0.94 |
| 60_F | 64_I | 1.031 | 0.94 |
| 87_K | 90_L | 1.028 | 0.94 |
| 51_I | 55_I | 1.021 | 0.93 |
| 71_F | 75_P | 1.015 | 0.93 |
| 50_W | 53_Y | 1.014 | 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 | |
| 4x5mA | 3 | 0.94 | 99.8 | 0.09 | Contact Map |
| 4rngA | 6 | 0.81 | 99.6 | 0.251 | Contact Map |
| 4qncA | 2 | 0.82 | 99.6 | 0.259 | Contact Map |
| 4qndA | 1 | 0.88 | 99.5 | 0.292 | Contact Map |
| 4u4vA | 1 | 0 | 32.3 | 0.85 | Contact Map |
| 4ikvA | 1 | 0.86 | 23 | 0.86 | Contact Map |
| 2m20A | 2 | 0.42 | 19.1 | 0.865 | Contact Map |
| 3l1lA | 1 | 0.91 | 19 | 0.865 | Contact Map |
| 3wvfA | 2 | 0.56 | 18.2 | 0.866 | Contact Map |
| 3giaA | 1 | 0.91 | 14.6 | 0.872 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)