| ACT domain low coverage |
| ID: | 1452595546 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 50% gaps before running GREMLIN. |
| Length: | 77 (75) | ||
| Sequences: | 1495 (1112) | ||
| Seq/Len: | 19.933 | ||
| Nf(neff/√len): | 128.4 |
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: 19.933).
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 |
| 12_A | 18_Q | 2.639 | 1.00 |
| 61_S | 73_V | 2.225 | 1.00 |
| 4_R | 48_D | 1.981 | 1.00 |
| 28_G | 56_H | 1.918 | 1.00 |
| 21_T | 25_E | 1.832 | 1.00 |
| 35_M | 45_V | 1.747 | 1.00 |
| 6_H | 74_D | 1.715 | 1.00 |
| 5_L | 61_S | 1.666 | 1.00 |
| 33_L | 47_I | 1.545 | 1.00 |
| 9_I | 15_V | 1.541 | 1.00 |
| 12_A | 15_V | 1.508 | 1.00 |
| 14_G | 20_C | 1.479 | 1.00 |
| 6_H | 46_D | 1.468 | 1.00 |
| 4_R | 46_D | 1.458 | 1.00 |
| 10_G | 71_E | 1.438 | 1.00 |
| 2_L | 50_E | 1.437 | 1.00 |
| 7_A | 64_L | 1.417 | 1.00 |
| 2_L | 31_V | 1.308 | 0.99 |
| 16_L | 29_N | 1.289 | 0.99 |
| 31_V | 50_E | 1.282 | 0.99 |
| 26_A | 63_A | 1.261 | 0.99 |
| 17_G | 24_G | 1.252 | 0.99 |
| 70_V | 75_R | 1.238 | 0.98 |
| 18_Q | 67_C | 1.231 | 0.98 |
| 23_I | 49_V | 1.205 | 0.98 |
| 17_G | 21_T | 1.196 | 0.98 |
| 26_A | 59_N | 1.193 | 0.98 |
| 9_I | 43_F | 1.187 | 0.98 |
| 9_I | 45_V | 1.186 | 0.98 |
| 13_P | 29_N | 1.155 | 0.97 |
| 54_A | 58_T | 1.134 | 0.97 |
| 20_C | 30_I | 1.134 | 0.97 |
| 20_C | 69_T | 1.120 | 0.96 |
| 23_I | 47_I | 1.118 | 0.96 |
| 23_I | 30_I | 1.117 | 0.96 |
| 57_L | 61_S | 1.113 | 0.96 |
| 6_H | 76_T | 1.085 | 0.96 |
| 58_T | 62_A | 1.080 | 0.95 |
| 12_A | 69_T | 1.069 | 0.95 |
| 14_G | 29_N | 1.064 | 0.95 |
| 15_V | 69_T | 1.039 | 0.94 |
| 55_K | 58_T | 1.037 | 0.94 |
| 70_V | 73_V | 1.020 | 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 | |
| 1y7pA | 3 | 0.987 | 99 | 0.258 | Contact Map |
| 2ko1A | 2 | 0.987 | 99 | 0.268 | Contact Map |
| 2fgcA | 1 | 0.987 | 98.6 | 0.352 | Contact Map |
| 2pc6A | 4 | 0.987 | 98.6 | 0.357 | Contact Map |
| 2f1fA | 2 | 0.987 | 98.6 | 0.361 | Contact Map |
| 1zpvA | 3 | 0.987 | 98.4 | 0.386 | Contact Map |
| 2lvwA | 2 | 0.974 | 98.4 | 0.39 | Contact Map |
| 1u8sA | 2 | 0.974 | 97.9 | 0.467 | Contact Map |
| 2jheA | 4 | 0.9221 | 96.8 | 0.562 | Contact Map |
| 2nyiA | 2 | 0.987 | 96.7 | 0.568 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)