| spdl |
| ID: | 1457370527 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 70 (66) | ||
| Sequences: | 1736 (1514.3) | ||
| Seq/Len: | 26.303 | ||
| Nf(neff/√len): | 186.4 |
Jackhmmer Results: (2015_08)
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: 26.303).
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 |
| 18_E | 29_Q | 2.188 | 1.00 |
| 15_E | 26_Y | 2.031 | 1.00 |
| 29_Q | 46_N | 1.891 | 1.00 |
| 39_N | 50_T | 1.767 | 1.00 |
| 38_Q | 49_M | 1.699 | 1.00 |
| 26_Y | 43_K | 1.652 | 1.00 |
| 16_A | 27_G | 1.644 | 1.00 |
| 22_K | 33_S | 1.603 | 1.00 |
| 13_L | 24_A | 1.521 | 1.00 |
| 34_Q | 38_Q | 1.462 | 1.00 |
| 58_E | 63_Q | 1.411 | 1.00 |
| 46_N | 57_Q | 1.380 | 0.99 |
| 31_V | 41_L | 1.312 | 0.99 |
| 14_K | 25_Q | 1.311 | 0.99 |
| 17_E | 28_L | 1.287 | 0.99 |
| 25_Q | 42_D | 1.283 | 0.99 |
| 22_K | 39_N | 1.257 | 0.99 |
| 19_E | 30_L | 1.203 | 0.98 |
| 18_E | 46_N | 1.188 | 0.98 |
| 15_E | 43_K | 1.181 | 0.98 |
| 15_E | 18_E | 1.171 | 0.98 |
| 5_I | 10_R | 1.127 | 0.97 |
| 6_I | 13_L | 1.101 | 0.96 |
| 46_N | 64_R | 1.091 | 0.96 |
| 43_K | 54_S | 1.085 | 0.96 |
| 23_A | 28_L | 1.084 | 0.96 |
| 61_T | 64_R | 1.080 | 0.95 |
| 4_D | 8_N | 1.078 | 0.95 |
| 41_L | 52_T | 1.078 | 0.95 |
| 36_E | 54_S | 1.066 | 0.95 |
| 50_T | 68_L | 1.059 | 0.95 |
| 52_T | 59_K | 1.056 | 0.95 |
| 11_C | 22_K | 1.053 | 0.95 |
| 11_C | 39_N | 1.048 | 0.94 |
| 28_L | 45_R | 1.030 | 0.94 |
| 26_Y | 36_E | 1.016 | 0.93 |
| 20_R | 31_V | 1.003 | 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 | |
| 3c9iA | 6 | 0.9571 | 93.9 | 0.521 | Contact Map |
| 3qprA | 7 | 0 | 64.2 | 0.668 | Contact Map |
| 4linA | 12 | 1 | 61.2 | 0.675 | Contact Map |
| 3s84A | 2 | 1 | 61 | 0.676 | Contact Map |
| 2l7bA | 1 | 1 | 56.7 | 0.683 | Contact Map |
| 3ghgA | 4 | 0.9571 | 55.2 | 0.687 | Contact Map |
| 1deqA | 4 | 0.9571 | 50.8 | 0.694 | Contact Map |
| 2dfsA | 2 | 1 | 48.1 | 0.7 | Contact Map |
| 2bnxA | 2 | 0.2143 | 41.8 | 0.71 | Contact Map |
| 2a01A | 3 | 1 | 35.8 | 0.721 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)