| 3adj |
| ID: | 1512118389 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 76 (72) | ||
| Sequences: | 4887 (3386.1) | ||
| Seq/Len: | 67.875 | ||
| Nf(neff/√len): | 399.1 |
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: 67.875).
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 |
| 26_C | 40_C | 2.700 | 1.00 |
| 7_K | 61_E | 2.646 | 1.00 |
| 29_V | 36_T | 2.622 | 1.00 |
| 25_Q | 43_E | 2.312 | 1.00 |
| 31_T | 34_R | 2.299 | 1.00 |
| 40_C | 60_A | 2.297 | 1.00 |
| 27_Q | 41_T | 2.134 | 1.00 |
| 41_T | 48_K | 2.107 | 1.00 |
| 37_Q | 53_A | 1.929 | 1.00 |
| 6_C | 66_R | 1.906 | 1.00 |
| 39_T | 51_G | 1.842 | 1.00 |
| 41_T | 51_G | 1.831 | 1.00 |
| 39_T | 53_A | 1.706 | 1.00 |
| 11_Q | 24_Y | 1.681 | 1.00 |
| 66_R | 70_L | 1.658 | 1.00 |
| 63_S | 66_R | 1.616 | 1.00 |
| 55_R | 59_D | 1.603 | 1.00 |
| 30_E | 39_T | 1.549 | 1.00 |
| 43_E | 48_K | 1.535 | 1.00 |
| 28_K | 39_T | 1.464 | 1.00 |
| 25_Q | 41_T | 1.432 | 1.00 |
| 13_Y | 17_M | 1.417 | 1.00 |
| 35_V | 55_R | 1.377 | 0.99 |
| 33_G | 36_T | 1.336 | 0.99 |
| 63_S | 67_T | 1.311 | 0.99 |
| 67_T | 71_A | 1.273 | 0.99 |
| 56_T | 59_D | 1.259 | 0.99 |
| 14_A | 22_P | 1.251 | 0.99 |
| 48_K | 51_G | 1.239 | 0.98 |
| 59_D | 63_S | 1.212 | 0.98 |
| 50_T | 68_A | 1.206 | 0.98 |
| 14_A | 44_I | 1.188 | 0.98 |
| 10_L | 42_V | 1.169 | 0.97 |
| 6_C | 62_I | 1.149 | 0.97 |
| 9_L | 69_L | 1.122 | 0.97 |
| 23_L | 43_E | 1.113 | 0.96 |
| 69_L | 73_Q | 1.094 | 0.96 |
| 40_C | 61_E | 1.066 | 0.95 |
| 5_L | 8_N | 1.065 | 0.95 |
| 49_Y | 68_A | 1.059 | 0.95 |
| 6_C | 69_L | 1.021 | 0.93 |
| 30_E | 37_Q | 1.010 | 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 | |
| 2db2A | 1 | 1 | 99.6 | -0.003 | Contact Map |
| 2khxA | 1 | 0.9605 | 99.6 | 0 | Contact Map |
| 3adjA | 1 | 0.9474 | 99.6 | 0.008 | Contact Map |
| 2mdrA | 1 | 0.9868 | 99.6 | 0.019 | Contact Map |
| 1uhzA | 1 | 0.9868 | 99.6 | 0.022 | Contact Map |
| 2cpnA | 1 | 0.9868 | 99.6 | 0.024 | Contact Map |
| 3adlA | 1 | 0.9605 | 99.6 | 0.025 | Contact Map |
| 1whqA | 1 | 0.9737 | 99.6 | 0.025 | Contact Map |
| 2l2nA | 1 | 0.9211 | 99.5 | 0.035 | Contact Map |
| 3adgA | 1 | 0.9342 | 99.5 | 0.036 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)