| 3 |
| ID: | 1458129675 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 91 (90) | ||
| Sequences: | 261 (202.3) | ||
| Seq/Len: | 2.900 | ||
| Nf(neff/√len): | 21.3 |
HHblits Results: (2015_06)
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: 2.900).
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 |
| 13_E | 22_K | 3.293 | 1.00 |
| 21_K | 48_D | 2.922 | 1.00 |
| 21_K | 51_D | 2.763 | 1.00 |
| 6_D | 26_K | 1.975 | 1.00 |
| 78_L | 81_L | 1.857 | 0.99 |
| 9_L | 44_L | 1.845 | 0.99 |
| 82_A | 85_L | 1.806 | 0.99 |
| 47_M | 55_K | 1.634 | 0.98 |
| 21_K | 45_L | 1.516 | 0.96 |
| 44_L | 60_Y | 1.452 | 0.94 |
| 24_K | 55_K | 1.436 | 0.94 |
| 25_M | 54_D | 1.428 | 0.94 |
| 68_L | 85_L | 1.425 | 0.93 |
| 11_A | 14_N | 1.386 | 0.92 |
| 20_L | 24_K | 1.373 | 0.92 |
| 47_M | 65_G | 1.339 | 0.90 |
| 66_L | 73_L | 1.321 | 0.89 |
| 12_L | 15_L | 1.312 | 0.89 |
| 39_I | 44_L | 1.302 | 0.89 |
| 80_E | 84_Q | 1.245 | 0.85 |
| 57_V | 75_D | 1.241 | 0.85 |
| 18_D | 22_K | 1.195 | 0.82 |
| 36_Y | 64_Y | 1.180 | 0.81 |
| 7_A | 80_E | 1.137 | 0.77 |
| 61_L | 79_Q | 1.115 | 0.76 |
| 39_I | 69_T | 1.098 | 0.74 |
| 13_E | 16_S | 1.093 | 0.73 |
| 16_S | 28_L | 1.082 | 0.72 |
| 24_K | 52_L | 1.053 | 0.69 |
| 8_I | 12_L | 1.043 | 0.68 |
| 8_I | 66_L | 1.039 | 0.68 |
| 66_L | 87_T | 1.039 | 0.68 |
| 63_S | 82_A | 1.030 | 0.67 |
| 38_R | 70_M | 1.017 | 0.66 |
| 47_M | 69_T | 1.014 | 0.65 |
| 29_T | 57_V | 1.008 | 0.65 |
| 52_L | 86_Q | 1.000 | 0.64 |
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 | |
| 1pn5A | 1 | 1 | 99.9 | 0.088 | Contact Map |
| 2kn6A | 1 | 1 | 99.9 | 0.099 | Contact Map |
| 1ucpA | 1 | 1 | 99.9 | 0.107 | Contact Map |
| 3qf2A | 2 | 0.978 | 99.9 | 0.111 | Contact Map |
| 2l6aA | 1 | 0.989 | 99.9 | 0.113 | Contact Map |
| 2m5vA | 1 | 1 | 99.9 | 0.121 | Contact Map |
| 2hm2Q | 1 | 0.978 | 99.9 | 0.123 | Contact Map |
| 2mpcA | 1 | 0.978 | 99.9 | 0.123 | Contact Map |
| 4ewiA | 2 | 0.978 | 99.9 | 0.128 | Contact Map |
| 2km6A | 1 | 1 | 99.9 | 0.134 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)