| spdl |
| ID: | 1457419197 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 70 (69) | ||
| Sequences: | 98 (54) | ||
| Seq/Len: | 1.420 | ||
| Nf(neff/√len): | 6.5 |
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: 1.420).
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 |
| 64_R | 67_E | 1.738 | 0.94 |
| 59_K | 62_L | 1.710 | 0.93 |
| 52_T | 55_Y | 1.664 | 0.92 |
| 20_R | 32_E | 1.555 | 0.88 |
| 59_K | 63_Q | 1.522 | 0.86 |
| 57_Q | 62_L | 1.370 | 0.77 |
| 31_V | 45_R | 1.337 | 0.75 |
| 6_I | 12_R | 1.333 | 0.74 |
| 26_Y | 64_R | 1.326 | 0.74 |
| 48_M | 51_M | 1.318 | 0.73 |
| 17_E | 67_E | 1.296 | 0.71 |
| 8_N | 22_K | 1.286 | 0.70 |
| 21_L | 32_E | 1.285 | 0.70 |
| 32_E | 40_Q | 1.281 | 0.70 |
| 50_T | 54_S | 1.273 | 0.69 |
| 56_E | 59_K | 1.269 | 0.69 |
| 33_S | 36_E | 1.215 | 0.64 |
| 27_G | 30_L | 1.207 | 0.63 |
| 49_M | 62_L | 1.203 | 0.63 |
| 18_E | 21_L | 1.182 | 0.61 |
| 32_E | 35_N | 1.181 | 0.61 |
| 39_N | 47_E | 1.173 | 0.60 |
| 27_G | 36_E | 1.171 | 0.60 |
| 10_R | 14_K | 1.171 | 0.60 |
| 23_A | 30_L | 1.153 | 0.58 |
| 36_E | 42_D | 1.127 | 0.55 |
| 60_Y | 63_Q | 1.100 | 0.53 |
| 6_I | 11_C | 1.092 | 0.52 |
| 27_G | 32_E | 1.072 | 0.50 |
| 28_L | 34_Q | 1.072 | 0.50 |
| 59_K | 68_L | 1.040 | 0.47 |
| 63_Q | 67_E | 1.033 | 0.46 |
| 53_E | 62_L | 1.026 | 0.45 |
| 27_G | 57_Q | 1.026 | 0.45 |
| 23_A | 27_G | 1.024 | 0.45 |
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 | |
| 2qagB | 1 | 0 | 45.8 | 0.843 | Contact Map |
| 2bnxA | 2 | 0.2143 | 43.6 | 0.846 | Contact Map |
| 2dfsA | 2 | 1 | 32 | 0.857 | Contact Map |
| 4q4gX | 1 | 0 | 19.9 | 0.87 | Contact Map |
| 4y66B | 3 | 0.9714 | 19.8 | 0.871 | Contact Map |
| 3qprA | 7 | 0 | 19.7 | 0.871 | Contact Map |
| 3ghgA | 4 | 0.9143 | 19.2 | 0.871 | Contact Map |
| 1m1jA | 2 | 1 | 18.2 | 0.872 | Contact Map |
| 4kv9A | 2 | 0 | 17.6 | 0.873 | Contact Map |
| 1deqA | 4 | 0.9714 | 14.7 | 0.877 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)