| BACT59 after 75 filter |
| ID: | 1449675786 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 61 (57) | ||
| Sequences: | 1918 (1006.4) | ||
| Seq/Len: | 33.649 | ||
| Nf(neff/√len): | 133.3 |
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: 33.649).
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 |
| 42_D | 47_R | 3.611 | 1.00 |
| 10_T | 37_T | 3.025 | 1.00 |
| 15_L | 26_A | 2.982 | 1.00 |
| 51_N | 54_S | 2.825 | 1.00 |
| 20_E | 24_A | 2.486 | 1.00 |
| 22_H | 55_Y | 2.479 | 1.00 |
| 21_S | 52_K | 2.341 | 1.00 |
| 32_R | 36_H | 2.209 | 1.00 |
| 26_A | 53_I | 2.098 | 1.00 |
| 12_V | 58_K | 2.073 | 1.00 |
| 11_L | 26_A | 2.001 | 1.00 |
| 8_R | 39_E | 1.887 | 1.00 |
| 25_C | 49_M | 1.736 | 1.00 |
| 8_R | 60_E | 1.698 | 1.00 |
| 10_T | 58_K | 1.688 | 1.00 |
| 9_V | 40_V | 1.392 | 0.99 |
| 6_K | 39_E | 1.344 | 0.99 |
| 40_V | 46_N | 1.333 | 0.99 |
| 15_L | 27_R | 1.304 | 0.99 |
| 10_T | 60_E | 1.284 | 0.99 |
| 24_A | 28_G | 1.157 | 0.97 |
| 6_K | 41_L | 1.127 | 0.97 |
| 28_G | 49_M | 1.111 | 0.96 |
| 11_L | 15_L | 1.091 | 0.96 |
| 24_A | 27_R | 1.078 | 0.95 |
| 33_R | 36_H | 1.047 | 0.94 |
| 46_N | 49_M | 1.045 | 0.94 |
| 15_L | 23_R | 1.009 | 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 | |
| 1vw4U | 1 | 0.9344 | 99.8 | 0.079 | Contact Map |
| 3j7yZ | 1 | 0.9672 | 99.7 | 0.101 | Contact Map |
| 4tp9Z | 1 | 0.9508 | 99.7 | 0.102 | Contact Map |
| 1bxyA | 2 | 0.9508 | 99.7 | 0.11 | Contact Map |
| 2zjrW | 1 | 0.9016 | 99.7 | 0.133 | Contact Map |
| 3j3vY | 1 | 0.918 | 99.7 | 0.141 | Contact Map |
| 3j21Y | 1 | 0.9508 | 99.6 | 0.198 | Contact Map |
| 1vq8W | 1 | 0.918 | 99.5 | 0.233 | Contact Map |
| 4w20F | 1 | 1 | 99.5 | 0.243 | Contact Map |
| 1vx75 | 1 | 1 | 99.5 | 0.243 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)